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 $100

Win-IR Pro System

Reference Manual

091-0834H

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 Important Notice

Bio-Rad Laboratories, Inc., has prepared this manual for use by its personnel, licensees,
and customers. The information contained herein is owned or licensed by Bio-Rad
Laboratories, Inc., and constitutes proprietary information. Distribution of this
information is made to Bio-Rad personnel and customers in strict confidence for the
sole purpose of assisting in the use, understanding, and maintenance of Bio-Rad
equipment and software. Data including dimensions, tolerances, and descriptions
contained herein, do not constitute purchase specifications which are established only
by quotation. This information may not be reproduced, copied, disclosed to others, or
used as a basis for manufacture or sale of apparatus without prior written approval from
Bio-Rad.

Users are cautioned that Bio-Rad reserves the right to make changes without notice in
the specifications and materials contained herein. Bio-Rad shall not be responsible for
damage (including consequential) caused by reliance on the materials presented,
including, but not limited to typographical or arithmetic errors.

FTS, Win-IR, Win-IR Pro, EasyIR, EasyCheck, EasyQuant and Tracer are trademarks
of Bio-Rad Laboratories, Inc.

All other brand and product names mentioned herein appear for identification purposes
only and may be trademarks or registered trademarks of their respective holders.

Copyright © 1983-1997, Bio-Rad Laboratories, Inc. All rights reserved.

If you find an error, omission, or problem of any sort in these documents, or if you have
suggestions for their improvement if reissued, please let us know. Write to:

Technical Publications
Bio-Rad Laboratories, Inc.
237 Putnam Avenue
Cambridge, MA 02139
U. S. A.

email: [email protected]

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 Contents

PREFACE XIX

About the Documentation xix

Typographic conventions xx

What You Should Already Know xx

Installation xxi

Customer Support xxii

Training xxii

1 BASIC CONCEPTS AND OPERATIONS 1

Basic Concepts 1

Trace 7
X-Axis 11
Vertical Lines 16
Position Labels 18

Regions 22

Properties 26
Adding Comments 27
Adding Custom Properties 28

Annotations 32
Create Annotation 32
Format the Annotation Text 33
Resize the Label Box 35
Move the Label Box 36
Delete the Label Box 36
Move the Attachment Point 37

Printing the Screen Image 39

2 PEAKS 41

Definition 41

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Peak Display 42
Peak Direction 42
Defining peaks 43
Peak edges 44
Baseline edges 46
Center Point of Peak (location) 54

Display Properties 56
Moving Peak Labels 58

Multiple Peak Selection 58

Removing Peaks 59

Reference Peaks 62
Differences between Peaks and Reference Peaks 63

Peak Templates 65
Peak Templates and the Document 67
Differences between Peaks and Peak Templates 68

Predefined Peaks 68

Global Peak Preferences 70

3 MAIN SCREEN AND DOCUMENT TYPES 71

Overview 71
Documents 71
Views 74

Common Features 75
Title Bar 76
Menu Bar 76
Status Bar 76
Radar Box 77
Buttons 77
Autoscaling Buttons 78
Scan 78
File Buttons 78
Raman Laser Button 79
Spectrum Buttons 79

Multi-Spectral Document Window 80

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Locking/Unlocking a Spectrum into Display 81

Trace Display 81
Spreadsheet 82
General Layout of Transforms Programs 83

Search Library Document Window 84

Saving the Library 89

Quantitation Calibration Document Window 91

Kinetics Document Window 96

Kinetics Document Control Panel—Edit page 99
Copying Extracted Spectra to the Clipboard 110
Exporting Extracted Spectra to a .SPC File 111
Auto-Pick Peaks 112
Kinetics Document Control Panel—Batch Process page 113
Other Kinetics Document Features 114
Printing Chromatograms 116

Image Document Window 117

Frequency Slices 119
Extracting a Spectrum 120
Custom Value Programs 126
Transforms 128
Exporting SPC Files 129
Exporting DXF Files 129
Three-dimensional View 130

4 INTRODUCTION TO THE SPREADSHEET 135

Navigating the Spreadsheet 137

Modifying the Spreadsheet 138

Viewing the Spreadsheet 138
Resizing Rows and Columns 139
Typing in the Name Field 140
Editing Spreadsheet Cells 141
Adding Columns 143
Removing Columns 145
Re-ordering Columns in the Spreadsheet 146
Copying Rows in the Spreadsheet 146
Re-ordering Rows in the Spreadsheet 147
Deleting Rows in the Spreadsheet 148

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Spectrum Operations 149

Spectrum Selection using the Spreadsheet 149
Trace Display Order in the Window 150
Copying Spectra between Documents 150
Copying Column Information 153
Core Spectrum Information 154

Saving Spreadsheet Format 155

5 HISTORY, REPROCESS, METHOD 157

History 157

Reprocess 161
Displaying the Interferogram 167

Method 168

6 FILE MENU 169

New... 170

Open... 171

Close 177

Close All 178

Save 178

Save As... 178

AIA Data Exchange File (.cdf) 181

Run 185

Print... 186

Print Preview 188

Print Setup... 188

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Print Composition 189

New 189
Open 189

Most Recently Opened Documents 189

Exit 189

7 EDIT MENU 191

Undo... 192

Cut 192

Copy 192

Paste 196

Peak List... 198

Changing Peak Parameters 199
Placing Peak Parameters in the Spreadsheet 205

AIA Properties... 208

Select All Visible 210

8 VIEW MENU 211

Status Bar 212

Event Log 212

Floating the Event Log Box 213
Resizing the Event Log Box 215
Docking the Event Log Box 215
Overlap with Control Panel Sidebars 215

Trace Control Bar 217

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Property Browse Bar 222

Tree Structure of the Property Lists 223
Property Values 224
Adding Property Columns to the Spreadsheet 226
Hiding the Property Browse Bar 227
Showing the Property Browse Bar 227
Moving the Property Browse Bar 227

Shadow Tools 229

Autoscaled 229

Entire Spectrum 229

Zoom In 229

Zoom Out 230

Display Limits... 230

Document Default... 230
Selected Spectrum... 232

X Axis Units 234

History 235

Hit List 240

3D... 241
Exporting 3D Data 256

Lock Selected 257

Unlock Selected 257

Locking/Unlocking a Spectrum into Display 257
Locking/Unlocking a Property for Printing 258

Go To... 259

Remove Columns 260

Load Plot Template 262

Save Plot Template 262

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Kinetics Document Entries 266

Kinetics Edit Bar 267
Spreadsheet 268
Chromatogram Edit Window 269

Hide Gram-Schmidt Chromatogram 270

Show Peaks 271

Show Labels 272

9 COLLECT MENU 273

Rapid Scan... 274

Raman Scan... 274

Step-Scan... 274

Step-Scan Multi-channel... 275

Step-Scan TRS... 275

Step-Scan Fast TRS 275

Step-Scan DSP... 275

Step-Scan DSP(2)... 275

Kinetics... 276

Stingray... 276

Shadow… 276

Define a Scan... 276

Co-add More 276

Reset Spectrometer 276

Raman Laser 276

Temperature Controller 277

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10 TRANSFORMS MENU 279

General Considerations 280

Absorbance 282

%Transmittance 283

Compute 284

Ratio 292

Zap 297

UltraZap 300

Truncate 303

Smooth 306
Boxcar Smoothing 306
Savitsky-Golay Smoothing 306
Fourier Smoothing 308
Smoothing Example 309

Differentiate 312

Deconvolve 315

Advanced 321
Apodize... 321
Filter... 324

Define Reference... 331

Spectral Subtract... 332

Baseline Correct... 338

Baseline Correction Procedure 341

Auto Subtract 341

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More Transforms 342

Kramers-Krönig [nk]... 342
ATRCorrect... 346
BlackBody... 349
Wavenumbers 351
Microns 352
Nanometers 353

11 OPERATIONS MENU 355

New 356
Peak 356
Reference Peak 358
Peak Template 358
Position Label 359
Annotation 359
Comment 360
Chemical Structure 360
Custom Property 360
Custom Value 361

Drag Regions 362

Quantitative Analysis 363

Simple 364

Search... 375
Search Considerations 375
Searching 376
Spectral Search 378
Name Search 380
Peaks Search 380
Structures Search (Optional) 382
Common Search Features 382
Example of Spectral Search 394
Example of Name Search 395
Example of Peaks Search 396
Interpreting the Hit Quality Index (HQI) 396
Subtracting Known Components 397
Batch Search 398

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2D-IR 402
From In Phase/Quadrature Spectra... 402
Exporting 3D Data 411
From Series of Spectra... 412

Reprocess 416

Peak Pick 416

Create Empty Spectrum 419

Copy Spectrum 420

Spectral Arithmetic 421

Unary... 421
Scalar... 423
Binary... 424
3-D Interpolation 426
Exporting PAS Interpolation 3D Data 441
Raman Convert 442

Change ZPD Location... 443

PAS Linearize... 447

IR Mentor 451

12 OPTIONS MENU 453

Edit Color 454

Configuration... 459
Load Recent File on Startup 459
Plot Title 460
Predefined Peaks 461
Named Collects 461
Auto-Save After Collect 461
Force Calibration After Startup 461

Search 462

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13 WINDOW MENU 463

New Window 465

Cascade 465

Tile 467

Arrange Icons 469

Close All 469

Maximize traces 470

Maximize spreadsheet 471

Open Windows 471

14 HELP MENU 473

Index 474

Using Help 475

About Win-IR Pro... 476

About Win-IR Pro Security... 476

15 PRINT COMPOSITION 477

Overview 477
Template Window 478
Objects 484
Spectrum and Interferogram Objects 486
Right Mouse Button 488
Creating a Template 489
Printing with a Template 492

Batch Mode 494

Creating a Batch Mode Template 494
Using a Batch Mode Template 497

File Menu 499

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New 499
Open 499
Close 499
Save 499
Save As 499
Print 499
Print Preview 499
Print Setup 503
most recent files opened 504
Exit 504

Edit Menu 504

Cut 504
Copy 504
Paste 504
Delete 505
Font 505
Background Color 505
Grid 506
Object 507
Orientation 511

View 511
Status Bar 511
Palette Bar 511
Spectrum Label 511
Grid 511
Show Peak 512
Show Labels 512
Batch 512
Trace Control Bar 512

Window 512
New Window 512
Cascade 513
Tile 513
Arrange Icons 513
Split 513
open windows 513

Help 514
Index 514
Using Help 514
About Win-IR Pro 514

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16 FREQUENTLY ASKED QUESTIONS 515

Computer Operations 515

Display-Related Questions 522

Document-Related Questions 533

Baseline-Related Questions 534

Others 534

A ADDING NEW USER ACCOUNTS 543

Why Have Different Accounts? 543

Security 544

Passwords 544

Adding a New User Account 545

User Copy 552

B DEFAULT COLOR SETTINGS 555

Pen 555

Brush 556

Text 556

C IMPORTING SPECTRA 557

Win-IR and GRAMS/386 Spectra 557

Bio-Rad 3200 Series Spectra 560

Importing 3200 Series Spectra to the PC 560
Converting 3200 Format Spectra to Win-IR Pro Format Spectra 563

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D ALGORITHMS AND FUNCTIONS 567

Search Algorithms 567

Apodization Functions 569

Boxcar 569
Norton-Beer 570
Trapezoid 570
Happ-Genzel (Hamming) 571
Triangle 571

Phase Correction 572

E HARDWARE CONFIGURATION 575

F 3200 SERIES SPECTROMETER PARAMETERS 583

G WIN-IR PRO FILE EXTENSIONS 585

H WIN-IR PRO FILES 589

I QUANTITATIVE ANALYSIS 593

General Considerations 594

Calibration Standards Considerations 595

Summary of Important Issues for Calibration Standards 597

Error Sources 598

Solvents 598
Gases 599
Polymers 600
Films 600
Liquids 602
Internal Reflectance Spectroscopy 603
Diffuse Reflectance Spectroscopy 603
Powdered/Ground Samples 604

Data Collection 605

Spectrometer Performance 606

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Spectral Manipulations 607

Smoothing 608
Fringe Removal 608
Fourier Self-Deconvolution 608
Derivative 608
Interpolation 609
Spectral Subtraction 609
Baseline Correction 609

Quantitative Analysis Flow Chart 611

J DECONVOLUTION 613

General Considerations 613

Simulated Spectral Examples 614

K DIAGNOSTICS AND SERVICE ACCESS 625

Gain Ranging Multiplication 625

Autoalign Locations 627

L ACCELERATOR KEYS 631

M LIBRARY CONVERSION 633

Overview 633
Restrictions and Considerations 634

Using the Search Library Converter 634

Library File Extensions 640

N CUSTOM VALUE PROGRAMS 641

Overview 641

Visual Basic 642

Visual Basic Example 647

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INDEX 649

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 Preface

ABOUT THE DOCUMENTATION

This book, the Win-IR Pro System Reference Manual (Bio-Rad part # 091-0834),
explains:
• the basic concepts of the Win-IR Pro system, including the screens,
document types, spreadsheets, etc.
• how to use the menus and menu entries to process data that you have
collected or have imported into the Win-IR Pro system

It also covers adding new accounts to your PC, importing data collected on other
systems, and other relevant tasks.

The README.RTF file contains updates made since this book was printed. It is
installed in C:/Program Files/Win-IR_Pro. Use WordPad (supplied with Windows NT
4.0) to open and read this. Print a copy of this file and store it with this manual for
future reference.

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 xx

The Win-IR Pro Installation and Configuration Manual (091-0837) tells about the PC
that is used to control the spectrometer and the printers that are supported by the
software.

Each spectrometer supported by Win-IR Pro has its own manual covering hardware, site
requirements (power, purge gas, cooling), maintenance, data collection, and similar
topics. This manual is supplied with the spectrometer.

Typographic conventions
Text in this font indicates a

• a box label
• a choice from a menu
• an item to be typed in

Context and specific instructions tell you which it is.

Text in small caps are keyboard keys; for example, NUMLOCK.

Key combinations, written as CTRL+A means press and hold the CTRL key, and then press
the A key. Release them at the same time.

Note
Unless it is otherwise specified, you may use either
upper-case or lower-case letters.

WHAT YOU SHOULD ALREADY KNOW

This book assumes that you are familiar with the basic features and operations of
Microsoft Windows NT on your PC. In particular, you should know :

• how to start Windows NT on your PC

• choosing
• clicking
• double-clicking
• dragging

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 xxi

• formatting disks
• copying files
• Task bar
• Windows NT Explorer

If you are not familiar with these concepts, review the Windows NT documentation that
you received with your Windows NT software.

INSTALLATION
The Windows NT and Win-IR Pro software are installed at the factory by Bio-Rad. If
you need to re-install Windows NT, follow the instructions that came with the
Windows NT disks. You should reboot your PC after installing, or re-installing, Win-
IR Pro.
The Win-IR Pro software is in the Win-IR_Pro sub-directory of the Program Files
directory as shown below.

bin contains the executable files and other files necessary to run Win-IR Pro
Load history contains records of the installation process. They are mostly of use to
Bio-Rad Customer Service.
Sample data contains a number of spectra that you can copy and use to practice
working with Win-IR Pro. They are identified in the Appendix H.
Scripting contains software and files necessary for the execution of the scripting
library language.
Scripting contains a number of examples of scripts that you can copy and use for
samples development of your own scripts.
Spectrometer contains software and files defining the hardware configuration of the
Configuration spectrometer.

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Use the Folder subentry in the New entry in the File menu in the Windows NT Explorer to
create your own directories to store the data that you collect. Do not store your files in
the Win-IR Pro directory or in its sub-directories; the contents of these directories can
be altered by Win-IR Pro software installations.

If you need to re-install Win-IR Pro, follow the instructions in the Win-IR Pro
Installation and Configuration Manual (091-0837).

CUSTOMER SUPPORT
If you have a problem concerning Win-IR Pro that is not addressed in the
accompanying documentation, please call or fax us at:
Tel: 1-800-333-4246 (U. S. only)
1-617-234-7086
Fax: 1-617-234-7188
or write to us at:
Technical Publications
Bio-Rad Digilab Division
237 Putnam Avenue
Cambridge, Massachusetts 02139, U. S. A.
email: [email protected]

Training
Training courses are available at the Bio-Rad Digilab Division headquarters in
Cambridge, Massachusetts, on a periodic basis. These courses are most valuable after
you have working experience with your instrument. Upon completing the course you
will be able to operate the instrument at an advanced level.

Bio-Rad maintains an application laboratory to conduct a continuing effort in methods

development. The laboratory can help as users as they explore new techniques with
which they are unfamiliar. Application Laboratory personnel also provide information
regarding technical advances in the FT-IR field. Bio-Rad encourages users to feel free
to communicate with this group, as your input can be valuable to us in determining how
we can best serve you.

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There is a Users’ Group to further technical exchanges. Bio-Rad holds the National
Users’ Group Conference every summer at Cambridge, Massachusetts, headquarters of
Digilab Division. On a more irregular basis, Regional Users’ Group conferences are
also held. Information pertaining to these conferences are mailed to all customers well
in advance of the conference date.

For details on any of the above topics, contact your local Bio-Rad office or call Bio-Rad
Digilab Division Headquarters in Cambridge, Massachusetts:

1-617 234-7086 (telephone)

1-800 225-1248 (toll-free inside U. S. A.)
1-617 234-7188 (Fax)

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 1
Basic Concepts and
Operations

BASIC CONCEPTS
In this chapter we define and discuss the basic concepts of Win-IR Pro.

Win-IR Pro: Bio-Rad’s software package that allows you to collect spectra, to
manipulate them, to perform quantitative analyses, to search libraries for spectral
identification, and to print these spectra, reports, etc. To start Win-IR Pro, from the
Taskbar, select Start / Programs / Win-IR-Pro (Common) / Win-IR_Pro. Win-IR Pro follows
the Windows NT standards for both local and network use. Networking is integrated
into Win-IR Pro.

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 2 Chapter 1 Basic Concepts and Operations

Windows NT allows multiple copies of Win-IR Pro to be memory-resident at the same

time. Because Win-IR Pro controls the spectrometer, it is not desirable to have more
than one copy resident in memory. To see how many copies are memory resident, look
at the Taskbar to see if there is duplication.

If there is more than one copy, put the cursor on the one to be closed and click the right
mouse button to get this menu.

Select Close to stop that copy of Win-IR Pro. See your Windows NT documentation
for more details, if required.

Screen: the sum of all text and graphical information visually presented to the user on
the computer monitor. It may also refer to the physical part of the monitor on which
this information is presented.

Cursor: The cursor (sometimes called a pointer) is a visual indication of what you are
pointing to. It moves as you move your mouse. The appearance of the cursor changes
depending upon where in the document you are pointing, what document you are into,
what options you have selected, etc. These changes are described in the sections which
discuss the Win-IR Pro functions they are associated with.

CAUTION
The Windows NT cursor must be set to Windows
Default for the Win-IR Pro cursor to assume the
proper shapes. If your cursor does not behave as
described in this manual, it is likely that the Windows
NT cursor has been changed. See Chapter 16 for
details of restoring the Windows NT cursor to its
default setting.

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 Chapter 1 Basic Concepts and Operations 3

Document: The document is the basic building block of the Win-IR Pro system.
Documents can contain one or many spectra. When a document is opened the
information contained within it can be presented as traces on a display window, a
spreadsheet, or both. Each spectrum has a trace, a spreadsheet row, and associated
properties and history. For example,

trace

window shade
spreadsheet

Note
See Chapter 3 for a complete description of this screen
and its components.

There is a multiple document interface; that is, more than one document can be open at
one time. This makes it possible to easily transfer data between documents.

Because Win-IR Pro adheres to Windows NT standards, the document windows can be
moved and resized in the normal manner. Document windows can also be tiled
horizontally

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 4 Chapter 1 Basic Concepts and Operations

or cascaded using the Window menu (see Chapter 13 for details).

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 Chapter 1 Basic Concepts and Operations 5

File: The portion of the computer disk memory in which the document is stored. Files
are accessed by name. Each file is a document. Existing files are opened by selecting
Open from the File menu. New files are created by selecting New from the File menu.
See Chapter 4 for details. Windows NT allows you to have filenames longer than eight
characters; see your Windows NT documentation for details on filenames, restricted
characters, etc.

Note
Do not use the character [ or the character ] in file names.
Win-IR Pro uses these square brackets internally to
indicate subfiles.

Do not use file names with embedded periods, for

example, liquid.37.bsp.

Directory: A directory may be thought of as a special kind of file which contains other
files and/or directories (often called sub-directories).

Note
Do not use the character ( or the character ) in directory
names. Although Windows NT supports the use of these
characters, Win-IR Pro does not. Using parentheses in
directory names will make some transforms inoperative.

Create directories to store your files. Do not store them in

the Win-IR Pro directory or its sub-directories; their
contents are subject to change by Bio-Rad.

Spectrum: A set of number pairs representing the wavenumber and intensity at that
wavenumber. Less rigorously, spectrum may be used for any set of data pairs with even
X-axis spacing, such as interferograms. Trace (see below) is a somewhat more general
term.

Properties: The data items of a spectrum, including the spectrum data set itself, the
spectrum history, and derived and user input. Collect conditions are properties primarily
for data imported from the 3200-series; otherwise, they would be sub-properties of
history. You can see these properties by selecting Property Browse Bar from the View

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 6 Chapter 1 Basic Concepts and Operations

menu (Chapter 8). You can add properties to the spectrum using the right mouse button
as described later in this chapter.

History: A record of the conditions under which the spectrum was collected and of any
subsequent manipulations or modifications of the spectrum. You can see the history by
selecting History from the View menu (Chapter 8), or by double-clicking in a history cell
in the spreadsheet.

Tab Pages: Sometimes there is more information, choices, or entries than can be clearly
and conveniently presented in one dialog box. In this case, closely related items are
grouped together in a special kind of dialog box called a tab page. You can rapidly go
from one page to another by clicking the tab with the desired page label. You can think
of these tabs as the tabs on file folders or index cards; they serve the same purpose.

An example— the Rapid Scan dialog box— is shown below. The tabs are Electronics,
Optics, Advanced, Background, and Computations. Each tab is attached to the
corresponding page. Clicking a tab brings its page to the front; you can then view
and/or alter entries as required.

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 Chapter 1 Basic Concepts and Operations 7

Spreadsheet: Presents information about each trace in the document in a two-

dimensional array. Each row in the array represents information for a particular trace.
Each column presents a particular piece of information about that trace, that is a
property or sub-property. The left-most column is the ID column or Spectrum ID.

The spreadsheet is discussed in detail in Chapter 4.

TRACE
Trace: The trace is the display of the spectrum on the monitor screen. Colloquially, this
may also be spoken of as the spectrum.

Zoom: Zooming is the magnification of a portion of a trace. You can select portions of
the spectrum to view in the main window, or with the Radar Box, described below.

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 8 Chapter 1 Basic Concepts and Operations

Normally, when the cursor is not on the trace it looks like ; use the cursor to alter the
position and the portion of the trace that appears in the trace display.
Note
If the cursor is placed on the trace, the magnifying glass
disappears; the cursor is then used to scale the trace, not
zoom it.
Place the cursor at the corner of a rectangle that outlines the portion of the spectrum
you want to display. Hold down the left mouse button and draw the rectangle.

Release the mouse button. The display immediately changes.

Note
If you want to abort the zoom, draw the rectangle so that
it is smaller than about 5 mm on a side. When you release
the mouse button zooming will not take place.

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 Chapter 1 Basic Concepts and Operations 9

The radar box (lower left) also reflects the change in the display.

Radar Box: The radar box is at the lower left of the window. It displays the entire
spectrum, independent of what portion of the spectrum is displayed in the main trace
window. The main trace display rectangle shows the portion of the spectrum shown in
the main display. If you change the main display by zooming, autoscaling, altering X
(and/or Y) limits, this rectangle will change to reflect what is visible in the main display.

Main trace display rectangle

Note
If more than one spectrum is selected, the radar box will
display the last one that was selected.

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Zooming with the radar box: Place the cursor on the edge of the main trace display
rectangle in the radar box. The cursor will change to at the vertical edges, at the
horizontal edges, and or at the corners. Hold down the left mouse button and
drag the edge of the rectangle; the main display changes as you modify this rectangle.
Release the mouse button to stop altering the display. In the example below, the main
trace display rectangle in the radar box was altered; the main trace display shows this
change.

Scrolling with the radar box: Place the cursor inside the main trace display rectangle in
the radar box. The cursor will change to . Hold down the left mouse button and
drag the rectangle; the main display changes as you drag this rectangle. Release the
mouse button to stop altering the display. In the example below, the main trace display
rectangle in the radar box was dragged; the main trace display shows this change.

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Note
You can move the main trace display box so that none of
the spectrum is visible in the main display. The easiest
way to recover from this is to click the button.

X-Axis
X-axis Scroll: Scrolling is the movement of the trace with respect to the window (it can
also be considered as moving a window about the trace to view portions of the trace).
Place the cursor in the middle third of the X-axis ruler; the cursor changes shape to .
Hold down the left mouse button and move the cursor along the X-axis ruler. The trace
and the X-axis ruler will move with the cursor. Release the mouse button when you are
satisfied with the new position of the trace. In the example below, the trace has been
shifted to the left.

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Note
In three-dimensional views, the cursor also changes as
described above. However, its use there is not
recommended, use the other methods described for that
particular view.

X-axis Expanding/Compressing: In this procedure, the trace is anchored at one end of

the display and it can be stretched out or compressed to see more details, or to see more
of the spectrum. Place the cursor in the left (or right) third of the X-axis scale; the
cursor changes shape to (or ). Hold down the left mouse button and move the
cursor along the X-axis ruler. When you move the cursor to the left (right), the trace
expands; when you move the cursor to the right (left) the trace compresses. The X-axis
ruler changes to correspond with the new trace display. Release the mouse button when
you are satisfied with the new position of the trace. In the example below, the cursor
was put in the left third, and the trace compressed.

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Note
In three-dimensional views, the cursor also changes as
described above. However, its use there is not
recommended, use the other methods described for that
particular view.

X-axis Units: The default unit for the X axis is wavenumber (cm-1). In some
applications, it is useful to have the X-axis units be microns (or nanometers). You can
change the X-axis units by selecting Wavenumbers, Microns, or Nanometers from the
Transforms / More Transforms submenu. See Chapter 10 for details.

Y-axis Rescale: You can interactively change the Y-axis scaling of the trace. Place the
cursor on the trace; the magnifying glass in the cursor disappears . Hold down the left
mouse button; the cursor changes to a double-headed arrow . Holding down the left
mouse button you can drag the trace, changing the Y-axis scale. Release the mouse
button and the new values appear on the Y axis.

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Y-axis Relabel: You can change the Y-axis trace label. Place the cursor on the trace
(but not in a region of the trace where a peak has been defined, see Chapter 2) or in the in
the Spectrum column of the trace you want to relabel. Click the right mouse button.
This menu appears:

Select Properties. The Core Spectrum Information dialog box appears

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 Chapter 1 Basic Concepts and Operations 15

Type in the new Y-axis label, and click OK.

Alternatively, in the spreadsheet, place the cursor in the Spectrum column of the trace
you want to relabel, and double-click. The Core Spectrum Information dialog box
appears. Type in the new Y-axis label, and click OK. For more details, see Chapter 4.

Notes
This changes the label of the Y-axis, not its units.

Peak Direction is discussed in Chapter 2.

Y-axis Scroll: Scrolling is the movement of the trace with respect to the window (it can
also be considered as moving a window about the trace to view portions of the trace).
Place the cursor in the middle third of the Y-axis ruler; the cursor changes shape to .
Hold down the left mouse button and move the cursor along the Y-axis ruler. The trace
and the Y-axis ruler will move with the cursor. Release the mouse button when you are
satisfied with the new position of the trace. In the example below, the trace has been
shifted to the left.

Y-axis Expanding/Compressing: In this procedure, the trace is anchored at one end of

the display and it can be stretched out or compressed to see more details, or to see more
of the spectrum. Place the cursor in the upper (or lower) third of the Y-axis scale; the
cursor changes shape to (or ). Hold down the left mouse button and move the
cursor along the Y-axis ruler. When you move the cursor up (down), the trace expands;

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 16 Chapter 1 Basic Concepts and Operations

when you move the cursor down (up) the trace compresses. When you release the
mouse button, the Y-axis ruler changes to correspond with the new trace display.

Vertical Lines
Often it is useful to have a vertical line drawn on the screen. This allows you to examine
a number of traces to see if there is a shift in the position of the peaks. To draw a
vertical line, place the cursor at the desired x-value location in the x-axis scale or the
regions ruler and click the right mouse button. This menu appears:

Click New and select Vertical Line.

A vertical line is drawn through the x-value position of the cursor.

Note
If the regions ruler is not visible, it will automatically be
selected when the vertical line is chosen.

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Vertical line

ruler

If you want to know the exact position of the vertical line, place the cursor on the line in
the regions ruler and click the right mouse button. The following menu appears.

Select Properties; the Edit Property dialog box appears.

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Either Left Edge or Right Edge gives the exact position of the line.

Moving the line: place the cursor over the extension of the line into the ruler. Hold
down the left mouse button and drag the line to the desired position. Release the mouse
button.

Deleting the line: place the cursor on the line in the regions ruler and click the right
mouse button. The following menu appears.

Select Delete. This deletes the selected line.

Alternatively, place the cursor over the extension of the line into the ruler. Click the left
mouse button to select the line. Press the DELETE key on the keyboard.

If you select more than one vertical line, only the last one selected is displayed.
Previously selected lines are indicated by short lines in the ruler; if you place the cursor
over one of these and click the left mouse button, this vertical line will be displayed,
replacing the existing line.

New vertical line

Position of previous vertical line

Position Labels
You can label the x- and y-coordinates of a point on a trace. First, select the trace. To
label a point, place the cursor in the window at the desired x-value location at any y-

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 Chapter 1 Basic Concepts and Operations 19

value point (except in a defined peak) and click the right mouse button. This menu
appears:

Click New and select Position Label.

The point is labeled with its x- and y-coordinates.

x-coordinate

y-coordinate

Editing Position Labels: place the cursor on the x-coordinate, y-coordinate, or the line
joining them to the trace. The cursor changes to . Click the right mouse button; this
menu appears:

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Select Properties. The Edit Label Property dialog box appears.

On the Display tab page.

Label Content: determines what is in the position label.

Visible: select Center to have the x-coordinate shown; select Value to have the y-
coordinate shown. The default is to have both shown.

Decimal Precision: how many numbers (0 - 8) are displayed after the decimal
point. The default is 3.

Label Direction: orientation of the label; either Vertical or Horizontal (default).

If you want to find out the exact attachment point or change it, click the Center tab.

Note
You can also change the attachment point by putting the
cursor on it, holding down the left mouse button,
dragging it to the desired location, and releasing the
mouse button.

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Method: how the attachment point is determined.

At Point: attachment point is at value entered in Center Point.

Extreme in Region: attachment point is the extreme (maximum for absorbance

spectra, minimum for transmittance spectra) in the region defined by the values
entered in Left Limit and Right Limit.

Average in Region: the attachment point is at the arithmetic mean of the Left Limit
and Right Limit of the region.

Center of Gravity: the attachment point is determined by the average of the

x-values in the region defined by the values entered in Left Limit and Right Limit
weighted by the spectrum height at each x-value.

∑ xy i i
peak _ location = i

∑ y i i

where yi is the height of the spectrum at wavenumber xi; all xi are inside the
defined region.

OK: return to main screen and implement values set in the dialog box.

Cancel: return to main screen; do not implement any changes made since last clicking the
Apply button.

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Apply: immediately implement changes entered in dialog box. This button is enabled
only if changes are entered in the dialog box. Changes made through the Apply button
cannot be reversed by using the Cancel button.

Help: enter the on-line Help system.

Moving Position Labels: you may want to move the position label, especially if labels
overlap or interfere with each other. Place the cursor on the x-coordinate or the y-
coordinate of the position label. The cursor changes to . Hold down the left mouse
button and drag the position label as desired. Release the mouse button.

Deleting Position Labels: place the cursor on the attachment point, the line, or one of
the coordinates and click the right mouse button. The following menu appears.

Select Delete. This deletes the selected position label.

Alternatively, place the cursor on the x-coordinate, y-coordinate, or the line joining them
to the trace. The cursor changes to Click the left mouse button to select the position
label. Press the DELETE key on the keyboard.
REGIONS
In some instances, you want to perform an operation on a part (or parts) of the trace, for
example, deconvolution. There are two ways to define a region— by using the right
mouse button, or by selecting Operations / Drag Region.

Defining a region with the right mouse button: To define a region:

1. In the regions ruler, place the cursor at the x-coordinate that will be the
center of the region in the x-axis scale or the regions ruler.

2. Click the right mouse button. This menu appears:

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3. Select New / Region.

This creates a region centered at the x-coordinate of the cursor and

extending 10% of the displayed x-axis in either direction from the center. .
The region is defined by the vertical dashed lines. The white bar at the
bottom of the region means that this region is active and selected.

Note
If the regions ruler is not visible, it will automatically be
selected when the vertical line is chosen.

You can determine the exact limits of the region by placing the cursor in the
white area of the regions ruler and clicking the right mouse button. Select
Properties from the menu that appears.

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The Edit Properties dialog box appears with the desired information.

4. The limits of this region can be modified. See “Modifying a Region,” below.

5. You can create additional regions, as desired.

Defining a region with the ruler:

1. If the ruler is not present, select Drag Region from the Operations menu. A
check mark (√) appears in front of Drag Regions if it is selected. Or, press
the toggle button at the bottom of the screen; the button remains
depressed until it is clicked again. Drag Regions (region selection) is now
enabled. A blank rectangle (the ruler) appears at the bottom of the trace
display, just above the x-axis scale.

2. Put the cursor into the ruler at one end of the region to be selected. The
cursor changes to .

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 Chapter 1 Basic Concepts and Operations 25

ruler

3. Hold down the left mouse button and drag the cursor to the other end of the
region being defined. Release the button. The region is defined by the
vertical dashed lines. The white bar at the bottom of the region means that
this region is active and selected.

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4. Repeat this procedure to define additional regions, if desired.

Modifying a region:

1. Select the region to be modified by putting the cursor on the ruler inside that
region and clicking the left mouse button.

2. Place the cursor at the edge of the region to be moved. The cursor changes
to .

3. Hold down the left mouse button and drag the edge of the region to the new
desired position. Release the mouse button.

Deleting a region:

1. Select the region to be deleted by putting the cursor on the ruler inside that
region and clicking the left mouse button.

2. Place the cursor in the white area of the regions ruler and click the right
mouse button. The following menu appears.

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Select Delete. This deletes the selected region.

OR

After selecting the region, press the DELETE key on the keyboard or the DEL key
on the numeric keypad (NUM LOCK off).
PROPERTIES
You can add properties and their values to any spectrum in a document using the right
mouse button. Consider, for example, this spectrum:

Adding Comments
1. Place the cursor in the trace window. Click the right mouse button; from the
New submenu, select Comment.

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 28 Chapter 1 Basic Concepts and Operations

The Add Comment to Spectrum dialog box appears.

2. Put the cursor in the scroll box and type in whatever comment is desired.
Any text, including comment text from a previous session may be altered
and/or deleted.

3. Click the OK button to save the new comment text. A column headed
Comment is added to the spreadsheet and the value for this spectrum is the
text of the comment. You may have to resize the spreadsheet cell (see
Chapter 4 for details) to view all the text). If you do not want this column in
the spreadsheet, remove it with View / Remove Columns (see Chapter 8 for
details).

Click Cancel to leave the text, if any, as it was before this session.

Click Help to enter the on-line help system.

Adding Custom Properties

1. Place the cursor in the trace window. Click the right mouse button; from the
New submenu, select Custom Property… .

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The Add Custom Property to Spectrum dialog box appears. The default
selection (Property Source) is to create a new property.

2. To add a new property, select the parameters as follows:

Name: the name of the property to be added.

Type: the type of property;select the appropriate type from the pull-down
menu. The types are:

Text: a character string.

Number: a numerical value (double-precision)
Time: the time and date at which this property was created.
Chemical Structure: a graphical display of the molecule.

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Value: once Name and Type are entered, this box becomes active. Enter the
value of the property. The type of Value must match Type.

Property Source: where the property to be added to the spectrum comes from.
Select From Saved List: pick a property from the existing list (see
section below).
Create New: create a new property with a value.
Add to Saved List: if selected, the new property is added to the
list of properties which can be added to a spectrum.

Add to Spreadsheet Column: select this option if a column for this property is
to be added to the spreadsheet when the property creation process is
completed.

Click OK to add the new property to the spectrum and (if selected) to the
saved list and to the spreadsheet.

Click Cancel to leave the text, if any, as it was before this session.

Click Help to enter the on-line help system.

3. To add a property to the spectrum from the saved list, first select the Select
From Saved List option from the Property Source choice. The dialog box then
becomes:

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Name: use the pull-down menu to select the name of the property to be
added to the spectrum

.
Type: the property type for the selected property automatically appears in
this box. The types are:
Text: a character string.
Number: a numerical value (double-precision)
Time: the time and date at which this property was created.
Chemical Structure: a graphical display of the molecule.

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Value: once Name is selected, this box becomes active. Enter the value of the
property. The type of Value must match Type.

Property Source: where the property to be added to the spectrum comes from.
Select From Saved List: pick a property from the existing list; this
option should be selected,
Create New: create a new property with a value (see above section).
Add to Saved List: this is disabled for items already in the
saved list.

Add to Spreadsheet Column: select this option if a column for this property is
to be added to the spreadsheet when the property creation process is
completed. .

Click OK to add the saved property to the spectrum and (if selected) to the
spreadsheet.

Click Cancel to leave the text, if any, as it was before this session.

Click Help to enter the on-line help system.

3. Edit Saved List: click this button to bring up the list of existing saved
properties for the purpose of deleting one or more of them from the list. The
Edit Saved List dialog box appears

Highlight all properties to be removed from the saved list using the standard
ctrl+left-mouse-click procedure.

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Click OK to remove the selected properties from the saved list and return to
the Add Custom Property to Spectrum dialog box.

Click Cancel to leave the saved list as it was and return to the Add Custom
Property to Spectrum dialog box.

Click Help to enter the on-line help system.

ANNOTATIONS
You can place text annotations on the display ; each annotation can be connected to a
point on the spectrum— for example, a peak, a group of peaks, or some interesting
feature of the spectrum.

Create Annotation
1. Place the cursor near the feature to be annotated. Click the right mouse
button. From the New entry, select Annotation.

An annotation box containing the text New Label appears. This box is
connected to the spectral trace by a line. The point at which this line touches
the trace is called the attachment point.

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2. Place the cursor in the label box and double click the left mouse button; the
cursor changes to a vertical insertion bar. You can now replace the text New
Label by highlighting it and typing in new text. Enter and edit text as you
would in a word processor such as Word.

Format the Annotation Text

1. Place the cursor in the label box; double-click the left mouse button.

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2. Highlight the selected text.

3. Place the cursor in the label box and click the right mouse button. The
formatting menu appears.

4. Select the format to be performed.

Note
Although they are not shown, the usual shortcut control
key combinations are implemented in this menu.

Copy copy the highlighted item to the clipboard.

Cut copy the highlighted item to the clipboard, then delete the
highlighted item.
Paste paste the clipboard into the label box at the vertical insertion
mark

Bold make the highlighted text boldface.

Italic make the highlighted text italic.
Underline underline the highlighted text.

Font causes the Font dialog box to appear.

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You can select the Font, Font style, Size, Effects and Color for the
highlighted text. The appearance of the text with these selections is
shown in the Sample box. Script is normally Western.

Insert Object allows insertion of an ActiveX object such as a graphic, Excel

spreadsheet, etc.

Resize the Label Box

1. Make sure the box is selected; it will be a rectangle whose edges are short
diagonal segments with a small square at each of the corners and in the
center of each side of the rectangle.

Resize vertically
Resize both dimensions Resize both dimensions
Resize horizontally Resize horizontally
Resize both dimensions Resize both dimensions
Resize vertically

2. Place the cursor on one of the small squares and hold down the left mouse
button. The cursor changes to a double-headed arrow showing in what
direction the box can be resized.

3. Drag the box to the desired size; release the left mouse button.

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Move the Label Box

1. Place the cursor inside the box. Hold down the left mouse button; the cursor
will change to a four-headed arrow.

2. Holding down the left mouse button, drag the box to the desired position.
Release the left mouse button. The attachment point does not change.

Delete the Label Box

1. Make sure the box is selected; it will be a rectangle whose edges are short
diagonal segments with a small square at each of the corners and in the
center of each side of the rectangle.

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2. Place the cursor in the label box and click the right mouse button. The
following menu appears.

Select Delete. This deletes the selected annotation.

Move the Attachment Point

1. Click on the label box area or on the attachment line. The attachment point
is now displayed.
Attachment point

2, If you want to know the exact position of the attachment, place the cursor on
the attachment point, the line, or in the label box and click the right mouse
button. The following menu appears.

3. Select Properties; the Edit Label Properties dialog box appears.

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Method: how the attachment point is determined.

At Point: attachment point is at value entered in Center Point.

Extreme in Region: attachment point is the extreme (maximum for absorbance

spectra, minimum for transmittance spectra) in the region defined by the values
entered in Left Limit and Right Limit.

Average in Region: the attachment point is at the arithmetic mean of the Left Limit
and Right Limit of the region.

Center of Gravity: the attachment point is determined by the average of the

x-values in the region defined by the values entered in Left Limit and Right Limit
weighted by the spectrum height at each x-value.

∑ xy i i
peak _ location = i

∑ y i i

where yi is the height of the spectrum at wavenumber xi; all xi are inside the
defined region.

You can also change the attachment point by putting the cursor on it, holding down the
left mouse button, dragging it to the desired location, and releasing the mouse button.

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PRINTING THE SCREEN IMAGE

At times, you will want to capture the image on the screen in order to print it. This
includes documents with multiple trace displays, contour and perspective displays, etc.
The word processor WordPad and the graphic editor Paint are included with Windows
NT. However, you can use most word processors and graphic editors to perform the
same functions.

Note
Some keyboards and/or computers require you to press
the SHIRT + PRINT SCRN keys, rather than just the PRINT SCRN key.
Consult the documentation that came with your computer.

To print the screen image using WordPad:

1. Set the Win-IR Pro display as desired. Press the PRINT SCRN key on the
keyboard. This copies the screen image to the Windows NT clipboard.

2. From the Taskbar select Start / Programs / Accessories / WordPad. The

WordPad application starts.

3. Select Paste from the Edit menu.

4. If necessary, size the screen image so it fits on the page. The details of sizing
an image in Write are given in its Help menu.

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5. If you want to have the maximum size of the screen image, select Print Setup
from the File menu. Then, set Orientation to Landscape. Click the OK
button.
6. Select Print from the File menu. Click the OK button.

To print the screen image using Paint:

1. Set the Win-IR Pro display as desired. Press the PRINT SCRN key on the
keyboard. This copies the screen image to the Windows NT clipboard.
2. From the Taskbar select Start / Programs / Accessories / Paint. The Paint
application starts.
3. Select Paste from the Edit menu.
4. You can use the tools in Paint to edit the screen image, crop it, add text, etc.
The details of using Paint are given in its Help menu.
7. If you want to have the maximum size of the screen image, select Print Setup
from the File menu. Then, set Orientation to Landscape. Click the OK
button.

8. Select Print from the File menu. If you have not cropped the screen image,
click the Properties button; then select the Advanced tab page. If the Graphic
icon is not expanded, click the Graphic icon; then highlight Scaling. Set
Scaling to 60% (Portrait) or 77% (Landscape) to get the printed image on a
single page. These values will be different if you cropped the screen image.
Experiment to find the best scaling factor. Click the OK button, to return to
the Print dialog box, then click OK to start printing.

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 2
Peaks

DEFINITION
A peak is a local maximum in a spectrum indicating that there is absorbance in the
sample at that wavenumber. Some, but not all, of the peaks in the example below are
indicated.

peaks

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 42 Chapter 2 Peaks

PEAK DISPLAY
A defined peak can be displayed in three ways: area (default), height, or center. Which
one you choose depends upon which properties of the peak you are working with.

Area (default) Height Center

Note
Only one number is displayed for center because the
numbers would identical. However, see Reference
Position for Center Value, later in this chapter.

Reference Peaks and Peak Templates are discussed later in this chapter.

Peak Direction
In absorbance and absorbance-like spectra, peaks point upwards, in transmission
spectra peaks point downwards, in some spectra—for example single-beam—they may
point in both directions. To make sure that you can define peaks properly for the
spectrum you are using, place the cursor on the spectra where no peak has been defined.
Click the right mouse button and select Properties. The Properties dialog box appears.

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 Chapter 2 Peaks 43

Select the Peak Direction desired and click the OK button. You can now define peaks as
appropriate for this spectrum.

Defining peaks
1. Place the cursor on the peak to be defined and click the right mouse button.
This menu appears:

2. Select New / Peak.

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 44 Chapter 2 Peaks

The peak is selected.

Area label
center of
Peak location
peak
label

area of peak
above
left edge of
baseline
peak
right edge of
left
peak
baseline of
peak
right baseline
of peak

This display is the peak area. The center of the peak is at the maximum; the baseline
edges are at the minima between the selected peak and the adjacent peaks (whether
selected or not); each peak edge is halfway between the corresponding baseline edge
and the centerline along the x axis.

You can manually adjust the peak edges and the baseline edges (but not the center of
the peak) in area mode.

Peak edges
Place the cursor on the peak edge box whose position you wish to change. There are
two methods of moving this box.

Interactive: hold down the left mouse button and drag this box to the desired position;
then, release the mouse button.

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 Chapter 2 Peaks 45

Menu: put the cursor on the peak right edge box and click the
right mouse button; this menu appears.

Select Properties. The Edit Right Edge Point of Peak dialog box appears.

Type the desired value in the Center Point box. The method for peak
edges is At Point.

OK: implement new values and return to main screen.

Cancel: ignore all changes made to values since last clicking the Apply button
and return to main screen.

Apply: implement new values; remain in Edit Right Edge Point of Peak dialog box.
These changes cannot be undone with the Cancel button.

Help: enter the on-line Help system.

Note
This is the dialog box for the Right Edge Point; there is a
similar dialog box for the Left Edge Point.

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 46 Chapter 2 Peaks

You can also put the cursor on the peak label, click the right mouse button, and select
Properties. Then, click on the Right Edge (or Left Edge) tab. The same tab page as above
appears.

In the example below, both peak edges have been changed to make the peak narrower.
The area has decreased and the new value is displayed.

Baseline edges
The box showing the location of the baseline edge can be split (into a left and right
box) to define a region; the baseline edge is the point of extreme value (minimum for
absorbance spectra, maximum for transmittance spectra) in that region. To define each
baseline region, place the cursor on the baseline edge box (or split) whose position you
wish to change. There are two methods of moving this box.

Interactive: hold down the left mouse button and drag this box to the desired position;
then, release the mouse button.

Note
The split box cannot be dragged over its corresponding
other half.

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 Chapter 2 Peaks 47

Menu: click the right mouse button; this menu appears.

Select Properties. The Edit Right Baseline Point of Peak dialog box appears.

Method
At Point: the right baseline is defined by a single point.

Extreme in Region:if the baseline box is split, the right baseline is defined
by the extreme value of the spectrum in that region (minimum for
absorbance spectra, maximum for transmittance spectra).

Average in Region: if the baseline box is split, the x-position of the right
baseline point (x) is the arithmetic mean of the x-positions of the left and
right limits of the baseline region. The y-position of the right baseline
point (y) is the average of the y-position values in the region. The (x,y)
point is not necessarily on the spectrum. This technique reduces the
effect of noise within the baseline region.

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 48 Chapter 2 Peaks

Values
Type the desired value(s) in the Left Limit and/or Right Limit box(es).

Notes
These are the left and right limits of the region in which
the baseline point will be located; they are not the left and
right baseline points.

The same dialog box appears whether you put the cursor
on the left or right half of the baseline edge box.

OK: implement new values and return to main screen.

Cancel: ignore all changes made to values since last clicking the Apply button
and return to main screen.

Apply:implement new values; remain in Edit Property dialog box. These changes
cannot be undone with the Cancel button.

Help: enter the on-line Help system.

Note
This is the dialog box for the Edit Right Baseline Point of
Peak; there is a similar dialog box for the Left Baseline
Point of Peak.

You can also put the cursor on the peak label, click the right mouse button, and select
Properties. Then, click on the Right Baseline (or Left Baseline) tab. The same tab page as
above appears.

In the example below, both baseline edges have been changed. The baseline has
changed and so has the area of the peak above the baseline.

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 Chapter 2 Peaks 49

Height display:allows you to move the peak from the maximum point between the edges
(for example, the peak might be shifted because two peaks are convolved). You can
also adjust the baseline, but not the peak edges in height mode.

To access height mode, put the cursor under the peak or on the
label and click the right mouse button; this menu appears.

Select Properties. The Edit Peak Properties dialog box appears. Click on the
General tab.

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 50 Chapter 2 Peaks

Name: the name labeling the peak. The default is of the form Peakn, where n is
the order in which the peak was defined. You can give the peak any name you
want. If you select Name on the Display tab page (see below), then the peak
name is displayed as part of the label to the left of the parentheses holding the
location and value.

Value: select display mode for peak.

Height
Area
Center

Baseline Definition:
select both left and right—the baseline is a straight line connecting the
two baseline points
select none—the baseline is the x-axis
select only left or right—the baseline is a horizontal line through the
selected baseline point.

Use Left Point: baseline is a horizontal line through the left baseline point.
Use Right Point: baseline is a horizontal line through the right baseline
point.

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 Chapter 2 Peaks 51

Auto Center: moves the right half box of the left baseline point to the x-
position of the center of the peak; moves the left half box of the right
baseline point to the x-position of the center of the peak. These half
boxes move if the center of the peak moves. If the baseline boxes have
not been split, then selecting Auto Center splits the boxes and moves
them as above. This option is most useful in kinetics documents (see
Chapter 3 for details).

In the example below, height mode is selected, and both baseline points are used. The
second peak label now displays height; see below for details on modifying the labels.

peak location

left baseline edge

right baseline edge

Reference Peak: reference peaks are those whose areas and/or heights will be
used as a standard against which other peaks will be ratioed. Reference peaks
are discussed later in this chapter.

Ratio Against Reference Peak: if selected, the Value part of the peak label
will be the ratio of the area (height) of this peak to the area (height) of
the reference peak selected from the pull-down menu. Which ratio
appears depends upon whether Area or Height is selected in the Value part
of this dialog box; no ratio is calculated if Center is selected. It does not
matter which Value of the reference peak has been selected.

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 52 Chapter 2 Peaks

In the example below, a reference peak was inserted at 3026.412 wavenumbers;

the height of the selected peak was ratioed to the height of the reference peak.

Ratio of heights

Reference peak

Selected peak

Reference Position For Center Value: this displays the wavenumber of the peak
relative to a value that you select. This is of most use in image files, but is
displayed here to show the format. Value must be set to Center for this feature to
be enabled.

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 Chapter 2 Peaks 53

In this example, the reference has been set to 3000 cm-1. Both the absolute
wavenumber and the relative wavenumber of the center of the peak are
displayed.

Apply style to all existing peaks: if this is selected, then when Apply or OK is
clicked, all existing peaks, in any trace in this document, will use the style
defined for this peak. Style includes such parameters as Value, Baseline
Definition, Label Content, Label Direction, etc.

Use this peak style when creating new peaks : if this is selected, then when Apply or
OK is clicked, all subsequently created peaks, in any trace in this type of
document (multi-spectral, kinetics, etc.), will use the style defined for this peak.
Style includes such parameters as Value, Baseline Definition, Label Content, Label
Direction, etc.

OK: implement new values and return to main screen.

Cancel: ignore all changes made to values since last clicking the Apply button
and return to main screen.

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 54 Chapter 2 Peaks

Apply: implement new values; remain in Edit Peak Properties dialog box. These
changes cannot be undone with the Cancel button.

Help: enter the on-line Help system.

Center Point of Peak (location)

Place the cursor on the peak center box . There are two methods of moving this box.

Interactive: hold down the left mouse button and drag this box to the desired position;
then, release the mouse button.

Menu: put the cursor on the peak center box and click the
right mouse button; this menu appears.

Select Properties. The Edit Center Point of Peak dialog box appears.

Method: how the peak location is determined.

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 Chapter 2 Peaks 55

At Point: peak location is at value entered in Center Point.

Extreme in Region:peak location is the extreme (maximum for

absorbance spectra, minimum for transmittance spectra) in the region
defined by the values entered in Left Limit and Right Limit.

Average in Region: the peak location is at the arithmetic mean of the Left
Limit and Right Limit of the region.

Center of Gravity:the peak location is determined by the average of the

x-values in the region defined by the values entered in Left Limit and Right
Limit weighted by the spectrum height at each x-value.

∑xy i i
peak _ location =
i

∑y i i

where yi is the height of the spectrum at wavenumber xi; all xi are inside
the defined region.

OK: implement new value and return to main screen.

Cancel: ignore all changes made to values since last clicking the Apply button
and return to main screen.

Apply:implement new values; remain in Edit Center Point of Peak dialog box.
These changes cannot be undone with the Cancel button.

Help: enter the on-line Help system.

You can also put the cursor on the peak label, click the right mouse button, and select
Properties. Then, click on the Center tab. The same tab page as above appears.

In the example below, the peak has been shifted slightly to the left (higher
wavenumber).

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 56 Chapter 2 Peaks

Baseline edges: are adjusted exactly the same as when the area is displayed; see above
for details.
DISPLAY PROPERTIES
A number of the properties of the peak labels can be changed. This can be done
regardless of what value is displayed.

To modify the peak labels, put the cursor under the peak or on
the label and click the right mouse button; this menu appears.

Select Properties. The Edit Peak Properties dialog box appears. Click on the
Display tab.

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 Chapter 2 Peaks 57

Label Content: select the material to be displayed for each label.

Visible: if selected (default), this label is displayed, otherwise the label is
not displayed. If Center is not displayed, Value will be displayed in the its
position.
Center: the position of the center of the peak.
Value: the area, height, or center of the peak as selected on the
General tab page.
Name: the name of the peak as entered on the General tab page
(default is Peakn—Peak1, Peak2, etc.).

Decimal Precision: how many decimal places are displayed; the default is
3. If a value less than 3 is selected, the number is rounded (not truncated.
Content: select what is to be displayed. The first label is Wavenumber;
the second is Height, Area, or Center depending upon what Value has been
selected on the General tab page.

Label Direction: select the orientation of the label.

Vertical: from bottom to top
Horizontal: from left to right (default)

OK: implement new value and return to main screen.

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 58 Chapter 2 Peaks

Cancel: ignore all changes made to values since last clicking the Apply button
and return to main screen.

Apply: implement new values; remain in Edit Peak Properties dialog box. These
changes cannot be undone with the Cancel button.

Help: enter the on-line Help system.

In the example below, Wavenumber and Height are displayed horizontally to 2 decimal
places; Name is also visible.

Moving Peak Labels

You may want to move the peak label, especially if labels overlap or interfere with each
other. Place the cursor on the peak label. The cursor changes to . Hold down the left
mouse button and drag the peak label as desired. Release the mouse button.
MULTIPLE PEAK SELECTION
You can select as many peaks as desired by this process. The mode and display for
each peak is independent of the others.

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 Chapter 2 Peaks 59

To modify peak parameters, make the peak active by putting the cursor on its label and
clicking the left mouse button.

Note
If you click the cursor on an already defined peak, it will
highlight the existing peak, not define a new one.

After peaks have been picked, they and/or their parameters can be added to the
spreadsheet using Edit / Peak List. See Chapter 7 for details.
REMOVING PEAKS
Individual peak can be removed from the peak table (deselected). . methods of deleting

1. Place the cursor in the area under the peak and click the left mouse button to
make this peak active.

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 60 Chapter 2 Peaks

2. There are two methods of deleting a selected position label:

Click the right mouse button; this menu appears

Select Delete.

OR

Press the DELETE key on the keyboard.

The peak is no longer labeled and is removed from the peak table.

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 Chapter 2 Peaks 61

See View / Property Browse Bar (Chapter 8) and Edit / Peak List (Chapter 7) for details of
the peak table.

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 62 Chapter 2 Peaks

REFERENCE PEAKS
A reference peak is defined in a spectrum so that the area (height) of other peaks in the
spectrum can be normalized to the area (height) of the reference peak. To define a
reference peak:

1. Place the cursor on the peak to be defined as a reference peak and click the
right mouse button. This menu appears:

2. Select New / Reference Peak.

The reference peak will be selected. In this example, we have edited the
reference peak’s properties to make Name visible. The default name for
reference peaks is RefPeakn—RefPeak1, RefPeak2, etc.

Note
Because Reference Peaks look like Peaks in the display,
we recommend that you always select Name for your
Reference peaks to help distinguish them from the regular
peaks of the spectrum.

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 Chapter 2 Peaks 63

Reference peaks are manipulated exactly the same as peaks. You can alter the center,
edges, and baselines. You can choose to display area, height, or center. You can
specify what and how will be in the label.

Differences between Peaks and Reference Peaks

Some features in Win-IR Pro do not treat reference peaks in the same way as they treat
peaks. Some major examples are shown below.

Edit / Peak List:

reference peaks do not appear in the peak list (see Chapter 7). The peak
list for the example above looks like.

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 64 Chapter 2 Peaks

The peak is shown, but the reference peak is not.

Operations / Search:
in Peaks search, the reference peaks are neither displayed nor
considered (see Chapter 11).

File / Print Composition:

Reference peaks are not included in either peak lists or in the
display of the spectrum (see Chapter 15).

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 Chapter 2 Peaks 65

PEAK TEMPLATES
A peak template defines a peak for all spectra in the document. One use of this could be
to observe what happens to a set of peaks in a time-varying system; this would typically
be used with kinetics. Another possible use is to look at peaks in a number of different
samples to observe what effects the sampling conditions had on this peak. To define a
peak template:

1. Place the cursor on the peak to be defined as a peak template and click the
right mouse button. This menu appears:

2. Select New / Peak Template.

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 66 Chapter 2 Peaks

The peak template will be selected. In this example, we have edited the
reference peak’s properties to make Name visible. The default name for
peak templates is TmpltPkn—TmpltPk1, TmpltPk2, etc.

Peak templates are manipulated exactly the same as peaks. You can alter the center,
edges, and baselines. You can choose to display area, height, or center. You can
specify what and how will be in the label.

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 Chapter 2 Peaks 67

Peak Templates and the Document

Peak templates are a property of the document. As shown above, their Value appears in
a column in the spreadsheet. The column heading is the Name of the peak template. An
entry for each peak template is created in the property browse bar. However, the
property browse bar is not automatically selected when a peak template is defined; to
see the property browse bar, select View / Property Browse Bar.

If a peak template is modified (for example, baselines, edges, center, etc. are changed),
the same modification is automatically made for all spectra in the document.

When a new spectrum is added to the document, the peak template is automatically
added to this spectrum’s trace. The Value of the peak template is put into the
corresponding spreadsheet cell.

If you delete a peak template, the corresponding column in the spreadsheet is also
automatically deleted; the peak template entry is deleted from the property browse bar.
Peak template numbers not reset. If you define a new peak template, its number will be
the next in sequence after the highest numbered previous peak template.

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 68 Chapter 2 Peaks

Differences between Peaks and Peak Templates

Some features in Win-IR Pro do not treat peak templates in the same way as they treat
peaks. As with reference peaks,

Edit / Peak List: peak templates do not appear in the peak list (see Chapter 7

Operations / Search:
in Peaks search, the peak templates are neither displayed nor
considered (see Chapter 11).

File / Print Composition:

peak templates are not included in either peak lists or in the
display of the spectrum (see Chapter 15).
PREDEFINED PEAKS
Predefined peaks allow you to save the parameters of a peak, peak template, or
reference peak and then use those parameters to define a peak, peak template, or
reference peak in the same or another document. The peak parameters are saved in a
file; the default file is C:\USERS\DEFAULT\Win-IR_Pro\Peaks.Def. You can change the
file in which the predefined peaks are stored by selecting Options / Configuration (see
Chapter 12 for details). If you change the file name after predefining some peaks, then
those peaks will not be found; you must move the old file to the new location.

Note
It does not matter whether the original is a peak, peak
template, or reference peak; it can be used to define any
(or all) of these.

To save a peak as predefined,

1. You must already have defined a peak (peak template, reference peak). If
you want the peak saved under a name other than its existing default name,
use the General tab page of the Edit Peak Properties dialog box to change the
name.

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 Chapter 2 Peaks 69

2. Put the cursor on the peak label and click the right mouse button.

3. Select Save As Predefined. The peak will be saved under its existing name. If
the peak has no name (for example, if you deleted the name), then the Save
Peak Name dialog box appears.

Enter a meaningful value for Name.

4. If the name of the peak already exists in the predefined peak file, this
message appears.

Yes: replace the existing predefined peak with the new one.
No: return to the Set Peak Name dialog box.
Cancel: return to the main screen without predefining a peak.

You can predefine as many peaks (peak templates, reference peaks) as desired.

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 70 Chapter 2 Peaks

GLOBAL PEAK PREFERENCES

You can globally set the style of the peak labels—that is, are the labels to be horizontal
or vertical, what values are to be displayed, how many decimal points should be shown,
what mode is the peak to be (height, area, center), etc. After you have selected a peak
with the desired style.

1. Select the peak that is to be used as your standard. Put the cursor on the
peak label and click the right mouse button. This menu appears.

2. If you select Save as Template, then all subsequently created peaks, in any
trace in this type of document (multi-spectral, kinetics, etc.), will use the
style defined for this peak. Style includes such parameters as Value, Baseline
Definition, Label Content, Label Direction, etc.

3. If you select Apply to All, then all existing peaks, in any trace in this
document, will use the style defined for this peak. Style includes such
parameters as Value, Baseline Definition, Label Content, Label Direction, etc.

Note
You can select both options, if desired.

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 3
Main Screen and
Document Types

OVERVIEW
Documents are used to collect and manipulate spectra. Each document can contain
more than one spectrum; any number of documents can be open at any one time.

Documents
There are three basic formats for Win-IR Pro documents—multi-spectra, kinetics, and
image.

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 72 Chapter 3 Main Screen

When spectra are collected into a Multi-Spectral Document, the latest spectrum is put at
the top of the spreadsheet. As spectra are collected into a Kinetics Document, the latest
one collected is put at the bottom of the spreadsheet.
Multi-Spectral Documents: this type of document may contain a number of spectra.
They do not necessarily have to have any systematic relationship to each other.
Therefore, these spectra are accessed either through their location in the document (View
/ Go To, discussed in Chapter 8), or, more commonly, by selecting a spectrum in the
spreadsheet which displays a row of information for each spectrum in the document.
The spreadsheet is discussed briefly in this chapter and, in much more detail, in Chapter
4. Multi-Spectral Documents can contain interferograms, single-beam spectra, ratioed
spectra, and chromatograms. These may have been collected under Win-IR Pro or
imported from the 3200 series data systems or from Win-IR or GRAMS. A typical
Multi-Spectral Document is shown below.

This document contains two spectra; Spectrum 1 has been selected.

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 Chapter 3 Main Screen 73

The following documents may be thought of as special types of Multi-Spectral

documents.

Background Documents: contain a background single-beam spectrum collected for use

in ratioing the sample single-beam spectrum to obtain a transmittance, absorbance, etc.
spectrum. Background spectra for either Multi-Spectral Documents (*.bkg) or Kinetics
Documents (*.kbg) are stored in this way.

Note
When you archive documents, it is a good idea to also
archive their background spectra to allow for future
reprocessing (see Chapters 5 and 11 for details about
reprocessing spectra).

Calibration Documents: contain spectra either collected directly into them or copied
into them from other documents. They also contain the concentrations of the
components for each spectrum as well as a least-squares calibration of the
concentrations to the spectra (see Chapter 11 for details).

Library Documents: may be thought of as a collection of chemically related spectra

collected under standard conditions. Bio-Rad supplied libraries are read-only and are
accessed through Operations / Search. You can browse a library by using File / Open, but
you cannot search it that way.

Kinetics Documents: the spectra in this type of document are all explicitly related to
each other. They are the spectra of a system or process as it evolves in time. Some
examples of this include gas chromatography (GC), thermogravimetric analysis (TGA),
and kinetics spectra. Individual spectral in this type of document are accessed through
the spreadsheet (the default is for the spreadsheet to be hidden) or through the
chromatogram (seen in the lower part in the example below). Details of the kinetics
document are discussed later in this chapter.

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 74 Chapter 3 Main Screen

Views
Some data presentations appear to be documents, but are actually views of the data.
They are presented in document format to allow consistent use of the viewing and
manipulation features of Win-IR Pro.

Search Hit List: presents the sample spectrum above the row of column labels in the
spreadsheet. The hits are listed below, one spectrum per row, in decreasing goodness of
fit, that is, the best hit is at the top of the list. Search hit lists are discussed in Chapter
11.

Three-dimensional views: are generated from sets of kinetics spectra (View / 3D; see
Chapter 8), from in-phase/quadrature spectra or series of spectra (Operations / 2D-IR, see
Chapter 11) or from PAS spectra (Operations / Spectral Arithmetic / 3D Interpolation, see
Chapter 11). These views allow for a two-dimensional presentation (by contours,
colors, and isometrics) of the three-dimensional data.

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 Chapter 3 Main Screen 75

COMMON FEATURES
There are many features, such as buttons, menus, etc. that are common to all types of
documents.
Before any documents are opened, the screen looks like this.

title bar
menu
bar

buttons

radar
box

status
bar

There are two major actions you can take now.

Collect data which will automatically open a document of the proper type depending
upon your choice from the Collect menu. This operation is discussed in the manual that
came with your spectrometer.
Open (File / Open) an existing document for collection, manipulation, printing.
Notes
Multiple documents of one or more types can be open
simultaneously.
Multiple views of one document can also be open
simultaneously.

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 76 Chapter 3 Main Screen

Once any document is opened (using File / Open, for example), the full menu bar is
displayed.

Title Bar
The title bar controls the usual Windows operations. If the document window is
maximized, the name of the active document is displayed in the title bar.
Title Resize button

Control menu Active document Minimize button Close button

Menu Bar

Each menu in the menu bar (File, Edit, etc.) is described in detail in its own chapter later
in the book. The contents of the menus can change depending upon the type of the
active document.

If no document is open, then only the menu subset below is displayed:

Status Bar
The text in the left side of the status bar gives a brief description of the results of
clicking the button that the cursor is on. For example,

If the cursor is in the spectrum display window (and has been clicked), the X and Y
coordinates of the cursor are shown in the right side of the status bar. For example,

The status bar also shows the progress of an action—such as collecting data, errors, and
other information as appropriate. It may be hidden using the View menu. This toggles of
the √ beside its name in the menu.

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 Chapter 3 Main Screen 77

Radar Box
The radar box is at the lower left of the window. It displays the entire spectrum
independent of what portion of the spectrum is displayed in the main trace window.
The main trace display rectangle shows the portion of the spectrum shown in the main
display. If you change the main display by zooming, autoscaling, altering X (and/or Y)
limits, this rectangle will change to reflect what is visible in the main display.

Main trace display rectangle

The main trace display rectangle can be moved and resized by placing the cursor on it,
holding down the left mouse button and dragging it. The main display changes as you
modify this rectangle. Release the mouse button to stop altering the display. An
example of this is shown in Chapter 1.

If you want to display a portion of the spectrum outside the current display, put the
cursor in the radar box, hold down the left mouse button, draw a box around the portion
to be displayed, and release the button.

Note
If a number of spectra are visible in the main display, the
last one selected is shown in the radar box.

Buttons
The buttons at the bottom of the screen are used as shortcuts for commonly performed
operations. Some are equivalent to a selection of an item from a menu. The details are
discussed in the chapter for that menu.

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 78 Chapter 3 Main Screen

Autoscaling Buttons
Autoscales the trace in the Y direction. This is the same as selecting Autoscaled
from the View menu.

Autoscales the trace in both the X and Y directions. This is the same as
selecting Entire Spectrum from the View menu.

Scan
Collect data using rapid scan according to the named collect selected
from the pull-down menu. If no scan is defined, the parameters of the
current spectrum are used. Data collection and processing proceed as far
as is specified by the Computation tab page of the collect.
Collect a background using rapid scan according to the named collect
selected from the pull-down menu. If no scan is defined, the parameters
of the current spectrum are used.

This is the Named Collects pull-down menu. Select the collect desired
for scanning and, optionally, further manipulation. The creation and
editing of named collects are discussed in your spectrometer manual.

File Buttons
Opens a new document of the type currently active. This is similar to selecting
New from the File menu, except that with the menu you have a choice of
document type.

Opens an existing document. This is the same as selecting Open from the File
menu.

Saves the currently active document. This is the same as selecting Save from
the File menu.

Prints the currenlty active document. Equivalent to selecting Print from the File
menu.

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 Chapter 3 Main Screen 79

Raman Laser Button

Turns the Raman laser power on and off. To set the power level, you must select
Raman Laser from the Collect menu.

Spectrum Buttons
Allows you to use the cursor to interactively define spectrum regions for future
operations. Same as selecting Drag Region from the Operations menu.

Shortcut: Defines the currently selected spectrum as the reference spectrum for
spectral subtraction. (Select Define Reference from the Transforms menu to
choose any spectrum to be the reference spectrum.)

Shortcut: Allows you to perform interactive spectral subtraction using the

currently defined reference spectrum. (Select Spectral Subtraction from the
Transforms menu to choose any spectrum to be the reference spectrum.)

Allows you to perform interactive baseline subtraction to the active spectrum.

Same as selecting Baseline Correct... from the Transforms menu.

Allows you to perform simple quantitative analysis on the active spectrum.

Same as selecting Quantitative Analysis / Simple from the Operations menu.

Allows you to begin searching libraries for a match to the active spectrum.
Same as selecting Search from the Operations menu.

Approximately doubles the height of the y-axis of the trace. Same as selecting
Zoom In from the View menu.

Approximately halves the height of the y-axis of the trace. Same as selecting
Zoom Out from the View menu.

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 80 Chapter 3 Main Screen

MULTI-SPECTRAL DOCUMENT WINDOW

Traces are displayed in

this part of the window

This window
can be resized,
minimized, or
moved using
standard
Windows
techniques

The windowshade
can be dragged up
or down to control
the display of the
traces relative to
the spreadsheet, or
to completely hide
either the traces or
the spreadsheet

Radar box Status bar Buttons The spreadsheet is displayed

in this part of the window

The multi-spectral document window can contain multiple spectra. It has a trace
display and a spreadsheet display. The spreadsheet can be hidden by selecting Maximize
traces from the Window menu (or press F11 on the keyboard). The traces can be hidden
by selecting Maximize spreadsheet from the Window menu (or press F12 on the keyboard).

You can adjust the division of the document window by placing the cursor on the bar
between the trace display and the spreadsheet. The cursor changes to . Hold down
the left mouse button and drag the bar up to increase the spreadsheet display area or
down to increase the trace display area. When the partition is satisfactory, release the
mouse button.

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 Chapter 3 Main Screen 81

Certain operations (for example, by selecting Trace Control Bar from the View menu),
cause a dialog box to appear on the right-hand side of the window. In this case, the
trace display is automatically resized. However, the spreadsheet display is not resized;
if the columns are full, a horizontal scroll bar appears at the bottom of the spreadsheet
display.

Spectra within a document can be selected either through the trace display or through
the spreadsheet; see below for details. A spectrum selected through the spreadsheet is
always both visible and selected for operations. Spectra in the trace display can be
made visible but not selected for operations; this is true even if the spectra were
originally selected through the spreadsheet.

Locking/Unlocking a Spectrum into Display

Spectra can be locked into the main display (or unlocked) using Lock Selected (or Unlock
Selected) from the View menu (see Chapter 6).

Trace Display

The trace(s) is displayed in the upper part of the window. The label in the upper left
(polystyrene in this example) is the text in the Name column of the spreadsheet.

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 82 Chapter 3 Main Screen

Spectrum Selection using the Trace Display

A spectrum (or set of spectra) selected for operations are displayed in green; unselected
traces are displayed in other colors.

• Single spectrum selection: place the cursor on the trace and click the left
mouse button. If you click on another trace, that spectrum becomes selected
and the first spectrum is deselected. This does not affect their visibility.
• Multiple spectra selection: place the cursor on the trace and click the left
mouse button; the spectrum is selected. Place the cursor on the trace of any
other spectrum, hold down the CTRL key and click the left mouse button; this
second spectrum is also selected. This process can be repeated as desired.
Using control-click, any spectrum can be toggled between selected and
deselected without affecting the status of any of the other spectra.

Spreadsheet

The spreadsheet presents information about each trace in the document, one row per
trace. It provides direct access to each trace in a multi-spectral document. If there are
too many spectra in the document to fit in the spreadsheet box, a vertical scroll bar
automatically appears to allow access to all spectra. Details of the spreadsheet are
given in the chapter “Introduction to the Spreadsheet.”

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 Chapter 3 Main Screen 83

General Layout of Transforms Programs

When invoked, many of the transforms (see Chapter 8) present a common appearance.
They split the screen and place a control panel sidebar on the right side of the window.
Below, Baseline Correct is used as an example.

original
data control
panel

resulting window
data shade

The original trace is in the upper half of the split screen; the modified trace is in the
lower half of the split screen. (Since nothing has been done yet, the two traces are
currently identical.) After completing the transform, you can replace the original trace
with the transformed one (click Replace), add the transformed trace to the document
along with whatever traces were originally there (click Add), or cancel the entire
procedure (click Cancel). All three choices return you to the main screen. Details of
each transform are in Chapter 8.
Note
Zooming, scrolling, and the radar box are still active in
these programs.

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 84 Chapter 3 Main Screen

SEARCH LIBRARY DOCUMENT WINDOW

You can create and edit your own search libraries; you cannot edit the search libraries
supplied by Bio-Rad. Before you can create a Search Library document, you must
define the parameters of the library. Select New from the File menu; the New dialog box
appears.

Note
In order to create a search library, you must have at least
9 Megabytes free on your hard disk for temporary files,
etc. Most of this memory is released when the library is
made read-only and/or closed.

You need an additional 3 Megabytes each if you include

peaks and structures (see below).

Now select Search Library and click OK. The Create a New Search Library dialog box
appears.

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 Chapter 3 Main Screen 85

Name: the filename under which the Search Library will be stored. This name
must conform to all Windows NT file names convention. Do not use the name
of an existing library. If you enter the name of an existing library, the OK button
will be disabled and the message Library Already Exists will appear above it.

Delete this Name entry and the OK button is re-enabled; the message disappears.

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 86 Chapter 3 Main Screen

Resolution: the resolution (data point spacing, in cm-1) of the spectra in the
library. If a spectrum was collected at a lower resolution, points will be
interpolated. If a spectrum was collected at a different resolution, it will be
resampled and it will either be smoothed or have points interpolated. Normally,
there is no reason to have the library at a higher resolution than that of the
spectra. Setting a higher resolution increases the space needed for the library
and also increases the search time. We recommend that the resolution be set at
4 cm-1.
Note
Digital resolution is the spacing between points in the
data file (typically, a library). Interpolating values
between existing points increases the digital resolution.

Optical resolution of a spectrum a function of the

collecting instrument and the collection parameters.
Once a spectrum is collected, its resolution is fixed and
cannot be improved.

Range: the upper and lower limits (in cm-1) of the library spectra. If you add a
spectrum to the library whose range exceeds those limits, it is truncated. If you
add a spectrum to the library whose range falls inside those limits, it is extended
with zeros to the limits. The default range is 4000 to 700 cm-1.

Include peaks:if checked, any peak tables in the spectra being copied will also be
copied into the Search Library.

Include structures:
if checked, any [molecular] structures in the spectra being
copied will also be copied into the Search Library.

Caution
If you create a library without structures or peaks
they cannot be added later.

If you later want to add structures or peaks, you must create a new library—
including those features—and copy the spectra into that library. You can then
enter structures or peaks into the newly created libraries.

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 Chapter 3 Main Screen 87

Y-resolution:the number of bytes (8 bits/byte) that will be used for the Y-axis
scale. The default is 1; this value is recommended for library searches.
Increasing the Y-resolution increases the size of the Search Library document.
Y-resolution Y-axis range
1 byte/point 0-255
2 bytes/point 0-511
4 bytes/point 0-1023
Title:a text string describing the contents of the Search Library. This will appear
in the description when this library is highlighted in the Search Library Selection
dialog box (see Chapter 11).
Location: the directory in which the search library will be stored. Click on the
pull-down menu arrow and select a directory pathname. The default value is
c:\Search libraries. Additional pathnames can be added to this list through the
Search Library Path dialog box (see Search, Chapter 11 for details).

Copyright: a text string which will appear for each entry in the library. This will
be the contents of the copyright column in the hit list after a search.
After the values are entered, click the OK button. An empty Search Library document is
opened.

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 88 Chapter 3 Main Screen

The empty Search Library document looks like a Multi-spectral document except that
the Collect menu is absent. You cannot collect into a Search Library document.
Spectra must be collected elsewhere and copied into the Search Library document.

When a Search Library document is created, it can be both read from and written to;
you can add spectra, delete them, etc.. If you want to make it read-only, deselect Edit
User Library from the Edit menu.

Notes
Writeable libraries are significantly larger than the read-
only form. The library size decreases when the library is
made read only again. If there is not enough room to
make a library writeable, switch to File Manager, delete
files, compress files, or move them to another disk, and
try again.

When you make a library writeable, it cannot be accessed

from any other copy of Win-IR Pro that is running. Any
attempt to do so will result in a message saying that the
library is not accessible. When the library is made read-
only or closed, it can then be read by any number of
copies of Win-IR Pro.

The library is read-only. The library is writeable.

The library can be searched. The library can be searched.

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 Chapter 3 Main Screen 89

Once the library is writeable, you can add spectra and edit their rows in the spreadsheet.
Spectra can be copied using the Edit / Copy and Edit / Paste commands, or they can be
dragged from a spreadsheet in another document into the Search Library document’s
spreadsheet (see Chapter 4 for details).

After a spectrum is copied into the Search Library document, its row in the spreadsheet
can be edited. The usual columns in a search library document are: Name, Spectrum (a
small plot of the spectrum), Copyright, and Chem Structure.

Caution
If you delete a spectrum from the library, it is marked
as deleted and the spectrum is set to 0 (zero) over the
entire range; the slot originally used by this spectrum
is still assigned—it is not automatically removed or
overwritten by another entry. When this library is
searched, this entry is skipped. However, if you edit
the name of a spectrum marked as deleted (for
example, double-clicking in the name cell of this
entry), the spectrum will no longer be considered as
deleted but as a zero-value spectrum; it will be
searched. The methods of the comparison algorithms
will often give a high hit quality index for a zero-
valued spectrum and it will appear high in the hit list.

Once you have deleted a spectrum, adding a new

spectrum to the library should fill the slot marked as
deleted.

When you have completed added spectra to the Search Library document and
(optionally) editing their spreadsheet rows, make the Search Library document read-
only by selecting √ Edit User Library from the Edit menu.

Saving the Library

Unlike the rest of Win-IR Pro, libraries are edited as if they were a data base program—
all changes are saved immediately to the file whose name you specified in the Create a
New Search Library dialog box. Therefore, the File / Save entry is disabled (grayed out).

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 90 Chapter 3 Main Screen

When you are finished the current session of editing the library, close it by selecting
Close from the File menu. This will make the library read-only, make any final saves
necessary, and close the library. You can now use this library in searches; see Chapter
11 for details.

Note
If you create a library and save it, you can open it at a
later time and add additional spectra using the procedure
above. You can also delete spectra from your library by
selecting that spectrum and pressing the Delete key. See
Chapter 4 for details of the spreadsheet operations.

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 Chapter 3 Main Screen 91

QUANTITATION CALIBRATION DOCUMENT WINDOW

When a new quantitation document is opened, it looks like this:

Spreadsheet of the Standards spectra will Calibration curve will be

standards spectra will be be displayed here displayed here
displayed here

windowshades—move horizontal windowshade to view/hide spreadsheet; move vertical

windowshade to partition screen between standards spectra and calibration curve

The Quantitation Calibration Document window has the same structure as the Multi-
Spectral Document window with the addition of a calibration curve window on the
right. An example of the creation of the calibration curve is given in the “Quantitative
Analysis” section of Chapter 11. The following is a brief overview of quantitative
analysis calibration. A more complete discussion of the theory and practice is given in
Appendix I.

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 92 Chapter 3 Main Screen

1. Create standard samples using known concentrations of compounds. These

compounds are those expected to be in samples to be analyzed, and whose
concentrations in those samples is to be determined.

2. Collect the spectra of these standard samples either directly into document,
or copy previously collected standards spectra into it, using Win-IR Pro’s
Edit / Copy and Edit / Paste menu entries..

3. Select a feature of the spectrum—usually a peak—that changes when the

concentrations change.

4. Enter the concentrations of each component each spectrum into the

document.

5. Do a least squares fit between the concentrations and the spectral features
you have selected; this is normally linear, following Beer’s Law that
absorption is a linear function of concentration. Sometimes, the chemistry
or physics of the situation may cause a deviation from linearity, especially at
higher concentrations; in that case, the data are fitted to a quadratic curve
(see Appendix I).

Note
Normally, the calibration equation should be
overdetermined. That is, there should be more standards
spectra than are required for a mathematical fit to the
calibration curve (exact fits are provided by 2 standards
for a linear, and 3 for a quadratic calibration curve). This
allows statistical and random noise to be averaged out.

6. Use this calibration curve to determine the component concentrations of the

unknown samples (see Chapter 11)

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 Chapter 3 Main Screen 93

After the document contains standards spectra, it looks like this.

Note
The horizontal windowshade has been raised slightly to
view the entire spreadsheet.
In this example, this is the region
of the spectra that changes with
the changes in concentration

By default, all spectra are initially included in calculating the calibration curve.
Double-click in the cell to exclude any spectrum. The contents change to No

Use the right mouse button menu to define a Component. Once this is done, you can use
all the peak editing tools available to define the peak parameters—select Properties from
the right mouse button menu. You can adjust the center, edges, and/or baselines of the
component. These edits are done exactly the same as for any peak. You can also decide
whether the calibration will be based upon peak area, peak height, ratio of peak areas,

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 94 Chapter 3 Main Screen

or ratio of peak heights. Use the General tab page of the Edit Peak Properties dialog box
to define whether area or height is to be used.

Note
If a ratio of height or area is to be used, first define the
reference peak against which the component is to be
ratioed; then use the General tab page of the Edit Peak
Properties dialog box.

Calibration Curve Window: to control the details of the calibration curve.

1. Put the cursor in the right hand side of the screen and click the right mouse
button.

2. Select Properties from the menu. The Edit Property dialog box appears.

Component: identifies the component of the spectra being used to establish

the correlation curve.

Curve Specifications: select the equation for the curve that is to be fitted to the
data points. The Apply button is enabled; click the Apply button for a new
calibration curve. The coefficients of the equation will change and be

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 Chapter 3 Main Screen 95

displayed in a, b, c.

If you want to fit data to a predetermined curve, select the type of equation
and enter the values of the coefficients.

Regress When Changed: if selected, the equation coefficients will change if

the curve type is changed and Apply is clicked. The Correlation Coefficient will
be displayed with the calibration curve.

Calculate Predictions Now: when selected, his creates a new column in the
spreadsheet; CompSugar (Predicted) in this example shown below. These are
the concentration values calculated from the calibration curve for the
absorbance values in the standards spectra. Note that, as expected, they are
close to the nominal values.

Correlation Coefficient: displays the calculated correlation coefficient.

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 96 Chapter 3 Main Screen

KINETICS DOCUMENT WINDOW

This document is used to collect kinetics data and step-scan TRS data.

A new kinetics document looks like this.

Collect data into this document following the instructions in the spectrometer manual
supplied with your particular spectrometer.

Note
A kinetics background is collected into a separate kinetics
background document. It may be collected either before
or after collecting the kinetics data. It must exist before
you ratio the kinetics data.

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 Chapter 3 Main Screen 97

When kinetics data collection is complete, the display appears as below.

Control
Panel
Sidebar
Batch Process
tab page
extracted
spectrum Edit tab page
Extracted
Spectra
controls
Copy spectra
to Grams file
chromatogram Copy spectra
to clipboard
Kinetics Functional
tab Groups
buttons controls
Gram-Schmidt
calculation
Auto-Pick
Peaks

Trace Display: The last spectrum collected is displayed in the upper part of the
document window. The Gram-Schmidt chromatogram is displayed in the lower part of
the document window.

Tab Buttons: These buttons control the activation of the ruler bars in the trace
windows. They also control the type of spectrum or Gram-Schmidt basis vectors
selected from a region.

Peaks: activates the ruler bar in the lower window. When you define a region
by dragging the cursor, an extracted spectrum is created by co-adding the
individual spectra in this region.

Background: activates the ruler bar in the lower window. When you define a
region by dragging the cursor, a background spectrum is created by co-adding

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 98 Chapter 3 Main Screen

the individual spectra in this region. This background can be used as the
background for any extracted spectrum in the document. .

Gram-Schmidt: activates the ruler bar in the lower window. When you define a
region by dragging the cursor, it defines the interferograms from which the
Gram-Schmidt basis vectors are calculated. If you define more than one region,
information from all the interferograms in all the regions are used to calculate
the Gram-Schmidt basis vectors. .

Export Regions: activates the ruler bar in both the upper and lower windows. In
the lower window, define a region to define the spectra to be copied when you
select Edit / Copy. You can then Edit / Paste the spectra into a .bsp document.
You can also paste the defined spectra into a Grams file. In both the lower and
upper windows, the spectra and wavenumber range of those spectra in the
defined region can be used to display the information in 3D or to perform the
generalized 2D algorithm calculation.

Control Panel: The lower part of the control panel (Functional Groups) initially selects
the Gram-Schmidt chromatogram which is based upon the entire spectrum.

The upper part of the control panel (Extracted Spectra) initially selects the last spectrum
collected. It is labeled Extraction 0. The Extraction Template is chosen to be Extract at time,
and the time of the end of the data collection is displayed in the Time box.

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 Chapter 3 Main Screen 99

Kinetics Document Control Panel—Edit page

Both functional groups and extracted spectra can be defined on the edit page.

Functional Groups: there are two mechanisms to define and label functional groups

• use the right mouse button in the extracted spectra part of the window
• use the Functional Groups part of the control panel.

The functional groups defined are displayed in the lower part of the document window.

To create a functional group using the right mouse button:

1. Zoom in on the area of interest in the upper part of the document window.

2. Put the cursor on the peak that specifies the functional group. Click the
right mouse button and select Functional Group from the submenu. The
functional group so defined appears in the lower part of the document
window. Its name, Functional Group 1, appears in the control panel sidebar.

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 100 Chapter 3 Main Screen

Note
The other choices—Peak, Reference Peak, Region, Vertical
Line, and Position Label function exactly the same as for
multi-spectral documents. See Chapter 2 for details.

To create a functional group using the control panel sidebar:

1. Press the Create button; the Create Functional Group dialog box appears.

In this example, a predefined peak exists. If you want to use another

predefined peak, select it from the pull-down menu. You can accept the
existing name of the predefined peak or enter a different one in the Name:
window. Then, click the OK button to create a functional group.

2. If you do not want to use a predefined peak to create the functional group,
select Create New and click the Edit Parameters button. The Edit Peak
Properties dialog box appears.

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 Chapter 3 Main Screen 101

3. You can accept the default name or enter your choice for the functional
group.

4. In the dialog box, use the tab pages to enter values to define the peak, or the
region about the peak, for which the functional group chromatogram will be
displayed in the lower part of the document. These are described in detail in
Chapter 2. Some special items

Center
At Point: the chromatogram is calculated for the specific chosen point of the
spectrum. Win-IR Pro will find the actual value on the x-axis (in wavenumbers)
for that peak and replace the approximate value you have entered.

At Extreme in Region: the more common method is to define a region about a

peak; then, Win-IR Pro will find the x-value of the maximum excursion from
zero in that region and use that value.

Note
If kinetics or TRS bands go negative, use Extreme in
Region to track the absorbance at a single point. Unlike
Win-IR Pro at Release 2.3 and earlier, the extreme in

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 102 Chapter 3 Main Screen

region is the maximum excursion from zero, whether this

excursion is positive or negative.

Edges
Left Edge: upper value for functional group chromatogram region.
Right Edge: lower value for functional group chromatogram region.

Baselines
Baseline Left: value defining the baseline at wavenumbers higher than the region.
Baseline Right: value defining the baseline at wavenumbers less than the region.

Note
In some cases, as in this example, the structure of the
spectrum does not allow for reasonable left and right
baselines to be defined. In this case, Win-IR Pro will
choose to set both baseline values equal to the one that is
reasonable.

OK: return to the Create Functional Group dialog box with the new values selected
for the parameters.

Cancel: returns to the Create Functional Group dialog box with the values in effect
since the last use of the Apply button.

Apply:when this button is clicked, the existing set of values is saved. The Cancel
button does not return the parameters to their original values.

Help: enters the on-line help system.

5. Click the OK button to define the functional group. Click the Cancel button
to return to the Kinetics document without creating a new functional group.
The example here has been named FG #12.

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 Chapter 3 Main Screen 103

Modifying Functional Groups: There are three methods to modify the definition of a
functional group, or to change the label and/or the parameters displayed. See Chapter 2
for details of each method.

1. Select the peak in the extracted spectrum that defines the functional group.
Use the cursor to interactively change the center, edges, and/or baselines as
desired.

2. Select the peak in the extracted spectrum that defines the functional group.
Put the cursor on the label or in the active area under the peak and click the
right mouse button. Select Properties from the sub-menu. The Edit Peak
Properties dialog box appears. Use the tab pages to alter the properties.

3. In the control panel sidebar, highlight the name of the functional group to be
edited. Click the Edit button. The Edit Peak Properties dialog box appears.
Use the tab pages to alter the properties.

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 104 Chapter 3 Main Screen

Removing Functional Groups: There are two methods for removing a functional
group.

1. Select the peak in the extracted spectrum that defines the functional group.
Put the cursor on the label or in the active area under the peak and click the
right mouse button. Select Delete from the sub-menu.

2. In the control panel sidebar, highlight the name of the functional group to be
removed. Click the Remove button.

The functional group is removed from the list and its chromatogram is no longer
displayed in the lower part of the window.

Notes
You cannot remove the Gram-Schmidt chromatogram. If
you do not wish it to be displayed, select Hide Gram-
Schmidt Chromatogram from the View menu. The Gram-
Schmidt label disappears from the list and the
chromatogram is no longer displayed.

To redisplay the label and the Gram-Schmidt

chromatogram, select Show Gram-Schmidt Chromatogram
from the View menu.

The Hide/Show Gram-Schmidt Chromatogram menu entry is

available only in an opened kinetics document.

Global Functional Groups: you can save the parameters of the functional group so
that this functional group can be used for all kinetics documents (global functional
group). To define a global functional group:

1. Create a functional group using one of the methods described above.

2. Select the peak in the extracted spectrum that defines the functional group.
Put the cursor on the label or in the active area under the peak and click the
right mouse button. Select Save as Predefined from the sub-menu. The
predefined peak will be saved using the existing name of the peak.

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If there is an already existing predefined peak with this name, the Bio Rad
Win IR Pro dialog box appears.

3. Yes: replaces the existing predefined peak with the newly defined one.

No: The Set Peak Name dialog box appears.

4. Give the global functional group a meaningful name and click the OK
button.

If you decide not to create a global functional group, click the Cancel button.

Extracted Spectra:the upper part of the control panel allows you to define and label
extracted spectra. The spectra defined here are displayed in the upper part of the
document window.

Note
Before extracting spectra, you usually want to extract a
background or backgrounds. Click the Background tab
button and use the cursor in the lower window ruler to
define the background extractions.

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Creating an extracted spectrum: if you wish to type in values, you must create a
label. Press the Create button; the Edit Property dialog box appears.

You can use the extraction number or enter a name for the extracted spectrum.

Extraction Mode: definesthe point, or region, of the chromatogram from which a

spectrum will be extracted and which will be displayed in the upper part of the
document.
Extract At Time: extract the spectrum at the specific defined time. Enter the Left
Edge (time for which you want the spectra extracted).

Flat Coaddition:extract the average spectrum in the defined region, co-adding the
spectra in the region with equal weight.
Weighted Coaddition: extract the weighted average spectrum in the defined
region. Each spectrum in the region is multiplied by the value of the
chromatogram for that spectrum. The result is normalized.
If one of the coaddition methods is selected, you can define the region by
entering the edges.

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 Chapter 3 Main Screen 107

Name: the name by which the extracted spectrum will be labeled.

Left Edge: lower time value for extracted spectrum region.
Right Edge: upper time value for extracted spectrum region.

Use background: select the background to be used for the extracted spectrum.

None: no background is used.

Nearest: use the background that is closest to the selected extract time or, if there
is more than one background within a coaddition region, use the earliest
background (the leftmost one) within the region.

Previous: use the closest background earlier than the selected extract time or the
left edge of the coaddition region. If there is no background defined to the left of
the selected time or region, no background is used (same as selecting None).

User-Defined: select a background from the pull-down menu.

Press the OK button. Wait until the spectrum is extracted and displayed before
proceeding. In the example below, extraction is for a specific time; for clarity of
presentation, only the extracted spectrum and the Gram-Schmidt chromatogram are
shown.

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Alternatively, an extracted spectrum can be created by placing the cursor in the

ruler of the lower display. Click the Peaks tab button. Hold down the left mouse
button and drag to create a region, or click to extract an individual scan-set. In
the example below, we zoomed in on a region of interest.

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You can now name the extracted spectrum as discussed above by using the Edit
button.

Removing an extracted spectrum: put the cursor on the label of the spectrum to be
removed and click the left mouse button; this highlights the label. Press the Remove
button. The extracted spectrum is removed from the list and its trace is no longer
displayed in the upper part of the window.

Relabeling an extracted spectrum: extracted spectra, when created via the ruler, are
labeled as Extraction 1, etc. To relabel an extracted spectrum, highlight the spectrum
label, then press the Edit button. The Edit Extraction dialog box appears.

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 110 Chapter 3 Main Screen

Type in the new name for the spectrum. Then click OK.
Cancel returns you to the main screen without relabeling the functional group.

Help enters the on-line Help system.

Copying Extracted Spectra to the Clipboard

You can copy the extracted spectra into a multi-spectral document using the following
procedure.

1. Click the Export Regions tab button.

2. In the lower part of the kinetics document window, define one or more
extract regions. Select all regions from which spectra are to be copied using
the ctrl-click combination.

3. Click the Copy to Clipboard button on the control panel sidebar.

4. Select New from the File menu. The New dialog box appears.

5. Select Multi-Spectral Document. Click OK.

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6. Select Paste from the Edit menu. The selected spectra are pasted into this
new document.

Notes
The time at which each spectrum was collected
(extracted) is also copied into the new document.

None of the spectra pasted into this new document are

named. We recommend that you name them, so that they
are identified meaningfully.

Exporting Extracted Spectra to a .SPC File

You can copy the extracted spectra into a .spc file using the following procedure.

1. Click the Export Regions tab button.

2. In the lower part of the kinetics document window, define one or more
extract regions. Select all regions from which spectra are to be exported
using the ctrl-click combination.

3. Click the SPC File Export button on the control panel sidebar. The Save As
dialog box appears.

4. Use standard Windows NT procedures to navigate to a directory and enter a

file name. The name must have a .spc extension.

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Notes
The time at which each spectrum was collected
(extracted) is also copied into the new document.

None of the spectra pasted into this new document are

named. We recommend that you name them, so that they
are identified meaningfully.

Auto-Pick Peaks
When the Pick button is pressed, all the peaks meeting the sensitivity criterion in the
spectra associated with the selected (highlighted) functional groups are picked. This
means that each peak label appears in the Extracted Spectra scroll box, for example,
Peak 4 of Functional Group 5. These peaks can be accessed through the scroll box and
through the spreadsheet (discussed later in this section). The peaks can be de-selected
from either the scroll box or the spreadsheet. Enter the sensitivity in the Sensitivity text
box; the higher the number, the more peaks that are picked.

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Kinetics Document Control Panel—Batch Process page

Click on the Batch Process tab in the sidebar control panel. The screen now shows

The text on this tab page reads:

Select an entry from the Transforms menu; entries

that cannot work on the kinetics spectra are disabled.

Set the parameters; the same parameters will be used

for all the spectra in the file.

Select Replace or Add; this will be done for all the

spectra in the file.

After the transforms are completed, the new spectra will replace the original ones, or be
added to the spreadsheet, as you selected.

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Other Kinetics Document Features

There are a number of menu entries in the View menu specific to Kinetics documents.

Kinetics Edit Bar: displays the control panel sidebar. If this is de-selected, the kinetics
document looks like:

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 Chapter 3 Main Screen 115

Spreadsheet: select this to view the spreadsheet. The spreadsheet allows direct access to
the extracted spectra (see Chapter 4 for details of the spreadsheet). The kinetics
document looks like:

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 116 Chapter 3 Main Screen

Chromatogram Edit Window: if selected, shows the lower traces (chromatograms); if de-
selected, this display is hidden and the kinetics document looks like:

Hide Gram-Schmidt Chromatogram : hides the Gram-Schmidt chromatogram display.

When this is selected, the entry changes to Show Gram-Schmidt Chromatogram.

Show Peaks: ifpeaks are labeled (see Chapter 11), selecting this option hides the label
display. When this is selected, the entry changes to Show Peaks.

Printing Chromatograms
It is possible to print chromatograms by copying them into a Multi-spectral document.
Details of this process are given in Chapter 16 , “Frequently Asked Questions.”

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 Chapter 3 Main Screen 117

IMAGE DOCUMENT WINDOW

This document allows you to manipulate data collected with an image array detector.

When an image file (.dat) is opened, the screen initially looks like this.

Array detector intensity at windowshade extracted spectra

a specific frequency will be displayed here
(wavenumber)

3D and color
display control
panel (see text
for details)

set parameters
to step through
and display
frequency
slices
Select array
start auto
point to
frequency
extract
stepping
spectrum

Select Access custom value programs.

frequency slice Label extracted peaks.
to display

Note
It is possible to open the raw image data collect files
(.seq) if required. For details on how to do this, see Open
in Chapter 6.

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 118 Chapter 3 Main Screen

After the file is opened, Frequency Slice displays the lowest wavenumber at which
collection was made (here, 1975.103 cm-1). To the right of that, Range displays the
frequency range (in wavenumbers) for which data was collected. On the right. In
Animate Slice Show, Step shows the difference (in wavenumbers, here 7.715) between
frequency slices; this is roughly the same as the resolution of the data collection.

You can use zooming in the left-hand part of the Image document. We recommend that
you do not use the expansion/compression feature in this part of the document.

The radar box works as described earlier in this chapter.

Note
The Extract Spectrum at boxes show values of -1 indicating
that no spectrum has been extracted.

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 Chapter 3 Main Screen 119

Frequency Slices
The view in the left-hand side uses the x- and y-axes for detector column and rows.
The z-axis, represent by color, is the intensity of the spectrum at a particular frequency.
This frequency is shown in the Frequency Slice box. You can display a different slice by
clicking on the button (one step lower) or the button (one step higher). You can
also change the frequency slice by typing a number in the box, followed by the ENTER key
on the keyboard. The intensity for that frequency slice will then be displayed.
Note
Win-IR Pro will round your entry down to the next lower
valid frequency.

You can observe the system automatically step through a range of values using the
Animate Slice Show controls.

Start: enter the lowest value of frequency you wish to observe.

Stop: enter the highest value of frequency that you wish to observe.
Step: this is the difference between frequencies. Normally, it would be left at
the default; if you want to move through the frequency slices faster, you
could set it at a multiple of the default value.

Play: click this button to observe the frequency slices in the left-hand side of the
document. The frequency of the slice being viewed in given in the
Frequency Slice box. After the animation is finished, you are viewing the
highest slice. If you want to stop the animation before it has completed,
press any key on the keyboard.

The example below shows the end of an animation. Start was set to 2900; Stop to 2960;
Step to 7.715 (the default). The first slice was actually at 2893.217, (2900 rounded
down to the nearest valid frequency); the last slice shown was at 2954.935 (the last
valid frequency below 2960).

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 120 Chapter 3 Main Screen

Extracting a Spectrum
Spectra can be extracted by one of three methods.

1. Put the cursor on the desired point in the array and click the left mouse
button. The spectrum is extracted for that point and displayed in the right
hand box.

2. Put the cursor on the x-axis at the desired point and click the left mouse
button. Then, put the cursor on the y-axis at the desired point and click the
left mouse button. The intersection of the lines defines the point at which
the spectrum is to be extracted.

3. In the Extract Spectrum at area of the lower control bar, enter the row and
column that defines the point at which the spectrum is to extracted. These
values can either be typed in or entered using the spin arrows to the right of
the Row: and Col: boxes.

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 Chapter 3 Main Screen 121

Notes
The extraction point can be changed by putting the cursor
on the line in the ruler (either x or y), holding down the
left mouse button, and dragging the line to the new
position.
The example below shows a spectrum extracted at the selected point. The selection
process used was:
1. Step through the frequency slices (either manually or automatically) until a
structure of interest is seen. In this case, it was at approximately 2932 cm-1.

2; Zoom in on an area of interest to make it easier to select the point at which

extraction is to be done.

3. Put the cursor on the point on interest and click the left mouse button.

The display now looks like:

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 122 Chapter 3 Main Screen

Note
You can use all the normal zoom, scroll, etc. features
discussed earlier in Chapters 1 and 3, in the extracted
spectrum part of the document.

Zoom in on the extracted spectrum and, using the right mouse button menu New / Image
Peak entry, define an image peak at ~2932 cm-1. The default name TmpltPk1 is
displayed in the Peak: box. You can edit this image peak and re-label this peak with any
name using the Properties entry on the right mouse menu (see Chapter 2 for details of
peak editing). In this example, we will change the image peak name to P2932.

Note
Changing the name of the peak cannot be done using the
Feature box; you must use the standard peak editing
procedures.

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 Chapter 3 Main Screen 123

Note
This image peak is defined for all extracted spectra. If
there were predefined image spectra, they could be used
to define an image peak using Operations / New / Image
Peak (see Chapter 11 for details).

The array on the left hand side of the screen currently shows the total spectral intensity
for each detector. To see the area under the 2932 cm-1 peak at each detector in the
array:

1. Put the cursor in the peak area, or on the peak label, and click the right
mouse button.

2. Select Properties from the right mouse button menu. The Edit Peak Properties
dialog box appears.

3. Click the General tab.

4. Select Area. Click the OK button.
5. Select Feature Image.

6. Click the Apply button.

Calculating Feature Image is displayed in the status bar during this process. The display is
shown below. After the redisplay, the Apply button is disabled.

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 124 Chapter 3 Main Screen

To view peak height in the array, instead of peak area:

1. Put the cursor in the peak area, or on the peak label, and click the right
mouse button.

2. Select Properties from the right mouse button menu. The Edit Peak Properties
dialog box appears.

3. Click the General tab.

4. Select Height. Click the OK button.
5. Select Feature Image.
The display now looks like this; the Apply button is enabled once again.

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 Chapter 3 Main Screen 125

Click the Apply button; when calculations are completed, the peak height at each array
detector is displayed in the left hand side of the screen.

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 126 Chapter 3 Main Screen

Printing: to print the extracted spectrum

1. Put the cursor on the extracted spectrum and click the left mouse button.

2. Select File / Print or click the button on the main screen.

Copying the Extracted spectrum: to copy the extracted spectrum

1. Put the cursor on the extracted spectrum and click the left mouse button.

2. Select Edit / Copy.

3. Access a multi-spectral document either through File / Open, File / New, or the
Window menu.

4. Select Paste from the Edit menu to put the spectrum into this document. It
can now be treated like any other spectrum.

Custom Value Programs

A custom value program operates on the spectrum for each detector in the array and
calculates a single value for that spectrum. The area and height of an image peak
(described above) can be thought of as special “built-in” custom value programs. You
can write your own custom value programs and execute them in the image document
window as follows.

1. Create a custom value program according to the procedure specified in

Appendix N.

2. Start Win-IR Pro; open an Image document.

3. Select Operations / New / Custom Value. The Enter a Custom Value’s Program
ID dialog box appears.

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 Chapter 3 Main Screen 127

4. Enter the program ID. In this example, it is Transform.Value; this program

displays the height of the largest peak in each spectrum. If required by your
program, enter the Optional Argument. Click the Add button. The program ID
now appears in the Feature pull-down menu. The Apply button is enabled.

5. Select Feature Image.

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 128 Chapter 3 Main Screen

6. Select the ID of the custom value program from the menu and click the Apply
button to execute it.

The results of the custom value program are displayed in the left side of the screen.

Transforms
A subset of the transforms operates on the array data. For details on the use of any
particular transform and on its parameters, see Chapter 10. When you select a
transform, the transform operates on the spectra at all points in the array and replaces
the original spectra with the transformed ones. If you want to preserve the original data,
make a copy of the image file before performing the transform.

Certain transforms require that you define a region of the spectrum before invoking the
transform. Extract a spectrum at any point in the array and define the region. This
region will be used by the transform for all points in the array.

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 Chapter 3 Main Screen 129

Exporting SPC Files

The spectra for all points in the array can be exported to a Win-IR or GRAMS multifile.
Export begins at the array element in the lower left hand corner and proceeds to the
lower right corner; it continues at the leftmost element of the next row from the bottom.
The process ends when the upper right array element is reached. The multifile is about
16 Mbytes in size—slightly larger than the original image file (.dat). To export the file:

1. Select File / Export SPC. The Save As dialog box appears.

2. Choose a directory and a file name (with the .dxf extension) for the exported
data. Click the Save button.

This .spc file can be opened by Win-IR, GRAMS, or Win-IR Pro (see File / Open in
Chapter 6 for details)

Exporting DXF Files

The graphic in the left hand side of the screen (a frequency slice, output of a custom
value program, etc.) can be exported as a .dxf file; these files can be imported into a
number of graphical editors and CAD-CAM applications. To export the file:

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 130 Chapter 3 Main Screen

1. Select Operations / Export DXF. The Save As dialog box appears.

2. Choose a directory and a file name (with the .dxf extension) for the exported
data. Click the Save button.

Three-dimensional View
The left-hand view can be moved, rotated, and presented in a number of formats. The
control panel sidebar on the right hand of the screen controls the presentation of the
data. The portion of the window used by the different graphics can be altered by
moving the horizontal and vertical window shades. In all the examples below, the
vertical window shade has been moved to the right to better show the three-dimensional
graphics The first example shows a 3D view of the frequency slice at 2932 cm-1.

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 Chapter 3 Main Screen 131

The next is a three-dimensional view of the peak area at each array detector.

Finally, a three-dimensional view of the peak height at each array detector.

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Three Dimensional Controls

Draw Mode: how the three-dimensional aspect will be represented in two dimensions.

Wireframe: the points of the calculated three-dimensional plot are connected

with straight lines. Lines that are hidden by the shape of the display are not
shown. This draw mode disables both Colors and Palette.

Solid:the lines and the frames they define are filled in with different shades of a
single color to give a better idea of the shape of the surface of the contour plot.

Color Bleed:
uses multiple colors for the surface. These colors change gradually
and smoothly as the height of the plot varies above the base plane. (Default)

Contours:shows contour lines on the surface at constant heights about the base
plane. The contour intervals are pre-set and cannot be changed.

Colors: sets the rangeof colors used to represent the extreme z-values of the plot.

Always Autoscale: if this is selected, then whenever you zoom in on a portion of

the plot, the color will be scaled so that the full color range is used for that
portion. This is useful if you zoom in on weak features that may be displayed in
very similar colors in the full plot.

If you are not autoscaling the colors, then you can set the values to be used in
the display. If you use the arrows to the right of the intensity boxes to set
values, they will be implemented immediately. If you type in values, they will
not be implemented until you press the Enter key on the keyboard.

Upper Intensity: enter the color value to be used at the maximum z-value
of the plot.
Lower Intensity: enter the color value to be used at the minimum z-value
of the plot.

Palette: the draw modes may be observed with three different color schemes.

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 Chapter 3 Main Screen 133

Note
In wireframe mode, Palette is disabled.
Monochrome: gray scale.
Color 1: shades from red to white to blue.
Color 2: shades from red through orange, yellow, and green to blue. (default)

Background: select the color for the background. A white background may be better if
you are capturing screens for insertion in a publication with a monochrome printer.

Black:background is black. the plot is shown against a black background

(default).

White: the plot is shown against a white background. This may be more
desireable for formats other than wireframe

Zoom: makes the plot appear closer (increases size) or farther away (decreases size).
Use the slide bar to change the value.

Y Scale: makes the height of the peaks taller or shorter. Use the slide bar to change the
value.

Rotation: these controls move the three-dimensional plot about two axes. Regardless of
the rotation, the axes remain in the foreground of the display. Rotation of large arrays
may be slow. Press the ESC key to stop the rotation.
Flat View:
if selected, displays a projection of the isometric view. If de-selected,
the isometric view (3D) is shown.

Default Angle:press this button to return the plot to its default position
(Pitch = 18°, Yaw = 1°).

Pitch: rotates the plot about a horizontal axis parallel to the monitor screen.
Click on the upper part to rotate the plot to show its Bottom; click on the lower
part of the bar to rotate the plot to show its Top. Each time you click the end of
the slide bar, the plot rotates 9°.

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 134 Chapter 3 Main Screen

Yaw: rotates the plots about a vertical axis. The plot can be rotated either to the
Right or to the Left. Each time you click the end of the slide bar, the plot rotates
18°.

For both Pitch and Yaw, you can enter the value of the angle. If you change the
angle with the arrows to the right of the text box, the values are implemented
immediately. If you type in values, the values are not implemented until you
press the Enter key on the keyboard.

Subsets of menus are also available. Their entries operate the same as they do in the
main Win-IR Pro document window.

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 4
Introduction to the
Spreadsheet

Documents can contain multiple spectra (traces). These spectra do not have to be
related to each other, do not have to have the same resolution, range, etc. The
spreadsheet presents information about each trace in the document in a two-
dimensional array. Each row in the array presents information for a particular trace.
Each column contains a particular piece of information about the traces. Each cell
contains a particular piece of information about that trace. In this default example, the
columns are Spectrum ID (not named), Name, and Spectrum.

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 136 Chapter 4 Introduction to the Spreadsheet

column cell

row

Notes
The name of the individual spectrum is not necessarily
the same as that of the document. The document name is
used by the Windows NT file system. The spectrum
name is internal to the document and is used only by
Win-IR Pro.

When spectra are collected into a Multi-Spectral

Document, the latest spectrum is put at the top of the
spreadsheet. As spectra are collected into a Kinetics
Document, the latest one collected is put at the bottom of
the spreadsheet.

Whenever a trace is deleted, its corresponding spreadsheet row is deleted. When a trace
is added to the document, a new row is added to the spreadsheet. If any of the columns
is not meaningful for a particular trace, or if that information is not available for that
trace, then the spreadsheet cell is left blank. In the example below, the spectrum
luther2(3) has been added to the document; it appears as the Spectrum 2 line in the
spreadsheet.

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 Chapter 4 Introduction to the Spreadsheet 137

If there are too many spectra in the document (as in the example below), or too many
columns for the traces, to fit in the spreadsheet box, scroll bars automatically appear to
allow access to all parts of the spreadsheet.

All changes made to the spreadsheet are retained if the document is saved (for example
with Save or Save As... from the File menu) before it is closed.

Any changes made to the structure of the spreadsheet, such as resizing cells, adding or
removing columns is saved when the document is saved. This new structure is used
when you open any document of the same type (multi-spectral, kinetics, etc.) and
remains in effect until you alter the spreadsheet and save the document.

If spectra in the spreadsheet were collected with different ranges then, when one is
selected by clicking in the spectrum ID cell, the display will autoscale the X- and Y-
axes for that spectrum. Any other spectra visible in the display will be shown with
those autoscaled limits.

NAVIGATING THE SPREADSHEET

You can navigate through the spreadsheet either by placing the cursor in the desired cell
and clicking the left mouse button or by using the keyboard.

↑ or PAGE UP move up one row in the spreadsheet

↓ or PAGE DOWN move down one row in the spreadsheet
← or HOME move left one column in the spreadsheet
→ or END move right one column in the spreadsheet

Notes

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Movement in the spreadsheet does not wrap. That is,

moving right from the rightmost column does not go to
the leftmost column, etc.

You cannot access the ID column using the arrows or

page keys; you must use the cursor.

If you double click in a text cell, then the arrow keys

become local editing keys for movement within that cell.

MODIFYING THE SPREADSHEET

Columns with other properties can be added to the spreadsheet. All columns (except
the Spectrum ID) can be deleted from the spreadsheet. The rows and columns can be
resized; the entry in the Name column can be retyped.

Note
When you delete a column from the spreadsheet, you are
deciding to not display information about the spectrum.
That information still exists in the document; you can
choose to display it again later.

Viewing the Spreadsheet

You can adjust the proportion of the window devoted to the spreadsheet by

• Placing the cursor on the windowshade, holding down the left mouse button
and dragging the windowshade up (to increase spreadsheet portion) or down
(to decrease spreadsheet portion). Dragging windowshades is discussed in
detail in the chapter on the main screen and document types.

• Selecting Maximize traces from the Window menu (or pressing the F11 key) to
have the traces fill the entire window of the document.

• Selecting Maximize spreadsheet from the Window menu (or pressing the F12
key) to have the spreadsheet fill the entire window of the document.

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Resizing Rows and Columns

At times, the entry in a spreadsheet cell is too large for the default size; cells are not
automatically resized to accomodate their contents. Text in a spreadsheet cell may
appear to be complete even though it is actually truncated. This is especially true for hit
lists. Resize the cell (by changing the row and/or column size) to make certain that you
are not overlooking any text. For example, consider this spreadsheet listing library
search hits,

The long chemical names and the copyright dates have been truncated; some of the
chemical structures are also hard to see. To change the column width:

1. Place the cursor on the right hand boundary of the column whose size is to
be changed. The cursor must also be in the gray label row.

2. When the cursor changes to , hold down the left mouse button.

3. Drag the right side of the column to the desired position and release the
button.
Here, we have increased the width of three of the columns to better display the
information in them.

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You can also resize rows in a similar manner.

1. Place the cursor on the lower boundary of the row whose size is to be
changed. The cursor must also be in the gray spectrum ID column.

2. When the cursor changes to , hold down the left mouse button.

3. Drag the lower edge of the row to the desired position and release the
button.

Typing in the Name Field

When you modify the spectrum (for example, by a transform) and add the modified
spectrum to the document, it shows up in the spreadsheet with a blank in the name
column. In the example below, the spectrum polyr.bsp was subtracted from the
spectrum polys.bsp; the difference spectrum was then added to the document; it appears
at the top of the spreadsheet as Spectrum1 with a the same name as the original
spectrum.

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To add a name (or to replace whatever name is already in that cell), place the cursor in
the Name cell to be changed and click the left mouse button. Then, type whatever text
you want in that cell. In the example below, the new name is polys-polyr. Because it
does not fit, the column was widened to accommodate it.

Editing Spreadsheet Cells

The contents of individual cells of the spreadsheet can be copied to the clipboard; in
some cases, it is also possible to modify the contents of these cells.

Non-editable (read-only) cells: the cells in some columns cannot be altered; these
columns contain the values of properties which cannot be set by the user—for example,
time of creation of the spectrum, scan parameters, etc. If you put the cursor in such a
cell and click the right mouse button, this menu appears

You can copy the contents of this cell to the clipboard and paste them elsewhere (an
editable cell, a word processor, an external spreadsheet, etc.).

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Editable (read/write) cells: the cells in some columns can be altered. Place the cursor
in the select cell and click the right mouse button. This menu appear.

The menu entries have their usual meanings:

Undo: if possible, undo the last operation performed in this cell.

Cut: copy the contents of the cell to the clipboard and delete the contents of the
cell.
Copy: copy the contents of the cell to the clipboard.
Paste: paste the contents of the clipboard into the cell, replacing any highlighted
portions of the cell.
Delete: delete the contents of the cell.
Select All: highlight the contents of the cell.

Depending upon the specific history of the operations in this cell, dofferent
combinations of enries are enabled or disabled.
Text Editing: When you first enter a cell using the directional arrows, you are put into
simple (replace) edit mode. In this mode, whatever you type replaces the former
contents of the cell. If you double click the left mouse button, you will be in full
(modify) edit mode. You can now modify the existing contents by deleting text,
inserting, etc.
If, after typing in the spreadsheet cell, you decide that you do not want to make this
change, immediately select Edit / Undo or press the ESC key on the keyboard. The cell
will revert to its previous contents.

Adding Columns
The default spreadsheet has three columns: spectrum ID, name, and a small plot of the
spectrum. For example, consider this document:

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If it is not already present, select Property Browse Bar from the View menu.

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 144 Chapter 4 Introduction to the Spreadsheet

A view of the property tree is shown at the left. The tree

has been opened to display the properties. We will add
History to the spreadsheet.

Highlight the property to be added to the spreadsheet.

Click the right mouse button. Select Add Column from the
menu. A new column is created labeled by the name in the
property list. Use History in this example,

The History column was resized for a better display. The value of the property is
displayed for all the spectra in the spreadsheet.
If there are multiple spectra in the document, and if these spectra have a value for that
property, then those values will also appear in that column of the spreadsheet.

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Select View / Property Browse Bar to remove the property browse bar.
See Property Browse Bar in the View menu chapter for more details.

Removing Columns
There are two ways to remove columns from the spreadsheet—using the right mouse
menu or using View / Remove Columns. In either case, you must first select the columns
to be deleted.

Select a column by clicking in its label; this highlights the column label.
To select a range of columns for removal: click the left mouse button in the label of the
left (or right) most column to be removed; put the cursor in the label of the right (or
left) most column to be removed; hold down the SHIFT key and click the left mouse
button.
To select a non-contiguous set of columns for removal: place the cursor in the label of
one of the columns to be removed and click the left mouse button; this column is
selected. Place the cursor in the label of any other column to be removed, hold down
the CTRL key and click the left mouse button; this second column is also selected. Repeat
this process as desired. Using control-click in its label, any column can be toggled
between selected and deselected for removal without affecting the status of any of the
other columns.

Either, place the cursor in a selected label, click the right mouse button, and select
Delete. OR Select Remove Columns from the View menu.

The selected columns are removed from the spreadsheet.

Note
You cannot Undo a column removal. To restore the
column to the spreadsheet, use Property Browse Bar from
the View menu as described above.

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Caution
Do not remove the name and spectrum columns of the
spreadsheet. If you remove the spectrum, use the
Property Browse Bar to add Spectrum to the
spreadsheet. If you remove the name, use the Property
Browse Bar to add SpectName to the spreadsheet

Re-ordering Columns in the Spreadsheet

To move a column (property) in the spreadsheet

1. Place the cursor in the header cell of the column to be moved.

column to be moved

2. Hold down the left mouse button until a small rectangle appear at the base of
the cursor arrow.

3. Move the modified cursor to the header of the column that you wish to be
immediately to the right of the selected column when the spreadsheet is
reordered. That is, the moved column will replace this column and push it,
and all rows to its right, one column over to the right.

4. Release the mouse button. Wait for the spreadsheet to be redrawn.

new position of column

Copying Rows in the Spreadsheet

To copy a row within a spreadsheet:

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 Chapter 4 Introduction to the Spreadsheet 147

1. Click the cursor in the leftmost column of the row to be copied; this
highlights the cell.

2. Click the right mouse button; this menu appears.

If nothing is currently in the clipboard, then the Paste entry

may be disabled (grayed out).

3. Select Copy. Click the cursor in the leftmost column of the row that you wish
to be immediately below the row pasted in. That is, the pasted row will
replace this row and push it, and all rows below it, down.

4. Click the right mouse button; this menu appears.

5. Select Paste.

Re-ordering Rows in the Spreadsheet

There are two ways to move a row (spectrum) in the spreadsheet—using the right
mouse menu or dragging the row.

1. Click the cursor in the leftmost column of the row to be moved; this
highlights the cell.

2. Click the right mouse button; this menu appears.

If nothing is currently in the clipboard, then the Paste entry

may be disabled (grayed out).

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 148 Chapter 4 Introduction to the Spreadsheet

3. Select Cut. Click the cursor in the leftmost column of the row that you wish
to be immediately below the moved row. That is, the moved row will
replace this row and push it, and all rows below it, down.

4. Click the right mouse button; this menu appears.

5. Select Paste.

Alternatively:

1. Place the cursor in the leftmost column of the row to be moved.

2. Hold down the left mouse button until a small rectangle appears at the base
of the cursor arrow.

3. Move the modified cursor to the leftmost column of the row that you wish to
be immediately below the selected row when the spreadsheet is reordered.
That is, the moved row will replace this row and push it, and all rows below
it, down.

4. Release the mouse button. Wait for the spreadsheet to be redrawn.

Deleting Rows in the Spreadsheet

To delete a row within a spreadsheet:

1. Click the cursor in the leftmost column of the row to be deleted; this
highlights the cell.

2. Click the right mouse button; this menu appears.

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 Chapter 4 Introduction to the Spreadsheet 149

If nothing is currently in the clipboard, then the Paste entry

may be disabled (grayed out).

3. Select Delete.
SPECTRUM OPERATIONS
The spreadsheet is the major tool for direct access to a spectrum in multi-spectral files.
It is also used to select spectra for display, copying, etc.

Spectrum Selection using the Spreadsheet

Once a spectrum (or set of spectra) is selected, it is visible (indicated by the bold font in
the leftmost column–the ID column) and it is selected for operations (indicated by a
colored box outlining the selected cell in the spreadsheet; the column heading is shown
in reverse video). Visible means that the trace (or traces) appears in the trace window.
Spectra selected for operation are shown in green. Any selection operation in the
speadsheet clears both the visibility and selection for operation status of any previously
selected unlocked spectra. (See Chapter 8 for details of locking and unlocking rows
and columns of the spreadsheet.)

• Single spectrum selection: place the cursor in the ID column and click the
left mouse button. If you click on another row, that spectrum becomes
selected and the first spectrum is deselected.
• Range of spectra selection: place the cursor in the ID column are the start (or
end) of the range of spectra and click the left mouse button. Place the cursor
in the ID column of the end (or start) of the range of spectra; hold down the
SHIFT key and click the left mouse button. Any previously selected spectra

outside this range are deselected.

• Non-consecutive spectra selection: place the cursor in the ID column and
click the left mouse button; the spectrum is selected. Place the cursor in the
ID column of any other spectrum, hold down the CTRL key and click the left
mouse button; this second spectrum is also selected. This process can be
repeated as desired. Using control-click, any spectrum can be toggled
between selected and deselected without affecting the status of any of the
other spectra. For example,

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Trace Display Order in the Window

When you use the spreadsheet to select spectra, the spectra traces are displayed in the
window in the order selected. That is, the first spectrum selected is the uppermost trace
in the window, the second spectrum selected is just below the first, etc.

If you select spectra one at a time using CTRL-CLICK, the display order of the traces in the
window is the same as the selection order of the spectra in the spreadsheet.

If you select a contiguous set of spectra, the upper trace corresponds to the first
spectrum selected using CLICK; the lowest trace corresponds to the spectrum selected
using SHIFT-CLICK. Intermediate spectra and their traces are ordered sequentially from first
to last.

Copying Spectra between Documents

In addition to using the Cut/Copy and Paste entries of the right mouse button menu,
described previously in this chapter, spectra can be copied by dragging them from one

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 Chapter 4 Introduction to the Spreadsheet 151

document to another. In this example, we will copy some spectra from a multi-spectral
document into a new and empty multi-spectral document. (Spectra can also be copied
into documents that already have spectra in them.). First, create a new document by
selecting New from the File menu; the New dialog box appears.

Select Multi-Spectral Document and click the OK button. This creates a new, empty multi-
spectral document.

If it is not already open, open the document from which the spectra will be copied.
Select Tile from the Window menu. The screen displays both documents.

To copy the spectra:

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 152 Chapter 4 Introduction to the Spreadsheet

1. Select the spectra to be transferred, using the techniques described in the

previous section. You may find it convenient to select Maximize spreadsheet
from the Windows menu (or press the F12 button on the keyboard).

2. Place the cursor in the Spectrum ID column of one of the spectra to be

transferred.

3. Hold down the left mouse button and drag the cursor into the trace portion
of the target document. The cursor will change to a circle with a diagonal in
it (the sign for forbidden) until it reaches the trace area; there it will change
to an arrow with small rectangle and a + sign.

4. Release the mouse button. The selected spectra will be copied into the
target document.

This is an example of copying using the drag-and-drop technique. You can also copy
between documents using Edit / Copy and Edit / Paste. This technique is discussed in
Chapter 7.

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 Chapter 4 Introduction to the Spreadsheet 153

Copying Column Information

There are two ways of copying (non-graphical) columns from the Win-IR Pro
spreadsheet to external spreadsheets and word processor documenting —using the right
mouse menu or using View / Remove Columns. In either case, you must first select the
columns to be copied.

Select a column by clicking in its label; this highlights the column label.
To select a range of columns for removal: click the left mouse button in the label of the
left (or right) most column to be removed; put the cursor in the label of the right (or
left) most column to be removed; hold down the SHIFT key and click the left mouse
button.
To select a non-contiguous set of columns for removal: place the cursor in the label of
one of the columns to be removed and click the left mouse button; this column is
selected. Place the cursor in the label of any other column to be removed, hold down
the CTRL key and click the left mouse button; this second column is also selected. Repeat
this process as desired. Using control-click in its label, any column can be toggled
between selected and deselected for removal without affecting the status of any of the
other columns.

1. Place the cursor in a selected label.

2. Click the right mouse button; this menu appears.

If nothing is currently in the clipboard, then the Paste entry

may be disabled (grayed out).

3. Select Copy.

4. Open the desired application (Excel, Word, etc.)

5. Paste the information into the application following the rules and procedures
of that application.

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 154 Chapter 4 Introduction to the Spreadsheet

You can also copy non-graphical information with Edit / Copy. The details of this
process are discussed in Chapter 7, in the Copy section.

Core Spectrum Information

Displays fundamental information about the spectrum. The Core Spectrum Information
status box is displayed if you double click on the Spectrum in the spreadsheet, on the
Ydata spectrum in the spreadsheet, or on Ydata in the History list. This status box shows
the x-axis point separation, starting point, ending point; the y-axis units, and peak
direction. For example,

Double-click here to get Core

Spectrum Information about this
spectrum

Double-click here to get Core

Spectrum Information about this
spectrum

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 Chapter 4 Introduction to the Spreadsheet 155

You can change the label of the y-axis to one that more exactly describes the particular
spectrum. Type the desired text in the box and clicking OK. This does not change the
y-axis numbers.
SAVING SPREADSHEET FORMAT
The spreadsheet formats are saved on a per-document type (Multi-Spectrum, Kinetics,
etc.) basis. The following applies to each type of document.

Whenever a document is closed, its format (column contents and order) is saved in
memory. If another document of that type is opened—whether existing or new—it will
have that format. For an existing document, this means that the spreadsheet format may
not be the same as the one you previously had.

This does not affect documents that are already opened.

When you exit Win-IR Pro, whatever spreadsheet format is in memory for that
document type, will be saved and used when you restart Win-IR Pro and open a
document of that type.

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 5
History, Reprocess,
Method

HISTORY
Every spectrum collected under Win-IR Pro has a history associated with it. This
history is a list of the operations that were performed to collect the interferogram and,
optionally, to transform it by such processes as Compute (to get a single-beam
spectrum), Ratio (to get an Absorbance spectrum), Transmittance, Differentiation,
Deconvolution, etc.

All parameters are saved, whether they appear to be relevant or not. These parameters
can be examined by selecting View / History and then double-clicking Scan in the History
Browser dialog box. Note that the Background file name is not found under Scan, but
rather under Ratio, because it is a ratio parameter.

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 158 Chapter 5 History, Reprocess, Method

You can see the history of a spectrum by selecting History from the View menu. The
History Browser dialog box appears. (If the spectrum has no history, the History entry will
be disabled–grayed out.)

Note
When a spectrum is imported, it arrives with no history.
Its history begins if it is manipulated subsequent to its
import. Spectra that do not have Collect as their first
operation (see below) were not collected using Win-IR
Pro.

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 Chapter 5 History, Reprocess, Method 159

To see the details of an operation, place the cursor on the + box to the left of the row,
and click the left mouse button. If there are details, the operation expands to show
them.

This may be done for any or all of the operations.

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 160 Chapter 5 History, Reprocess, Method

Time-Date Stamp: At release 2.1 of Win-IR Pro, the time and date of the operation are
automatically added to the operation. An example of this is shown above for Peak Pick.
Operations that were performed before release 2.1 have a blank for the time-date stamp,
as shown above for Truncate.

User Stamp: At release 2.5 of Win-IR Pro, the user login name of the person
performing the operation is automatically added to the operation. An example of this is
shown above for Peak Pick. Operations that were performed before release 2.5 have a
blank for the user stamp, as shown above for Truncate.

To collapse the details of the operation, place the cursor on the left-hand box and click
the left mouse button once. If you exit the History Browser dialog box without collapsing
the details of the operations, they will automatically be collapsed for you.

Return to the main menu by clicking either the OK or Cancel button. More details about
the history browser are in the View menu chapter under History and Property Browse Bar.

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 Chapter 5 History, Reprocess, Method 161

REPROCESS
Because the interferogram is always saved as part of the document in which the
spectrum was collected, you can always start from the interferogram and reprocess it as
desired.

Note
Certain operations require additional spectra to be present
to perform the operation. For example, Ratio requires that
the background spectrum exists; Spectral Subtract requires
that the reference spectrum exists to be subtracted from
the original spectrum. If a required spectrum is not found
where expected, Win-IR Pro informs you of this, and
allows you to locate this spectrum or to select another one
in its stead.

Using the spreadsheet, select the spectra to be reprocessed.

Then select Reprocess... from the Operations menu. The trace display is split in two:

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 162 Chapter 5 History, Reprocess, Method

The first spectrum selected, polystyrene, is displayed. The original spectrum is in the
upper part of the window; the corrected spectrum is in the lower part of the window.
Since nothing has yet been done, the two spectra are identical. The sidebar control
panel appears at the right side of the window. These controls allow reprocessing.

Collect does not appear in the list of Transform operations in the control panel because
Reprocess... uses the collected and saved interferogram; Reprocess... does not collect
data, it recalculates using data in the previously collected interferogram.

If you want to view and/or change the parameters used in an transform, highlight that
transform (for example, Ratio). The Ratio dialog box appears.

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 Chapter 5 History, Reprocess, Method 163

Make whatever changes you desire. You must have a background single-beam
spectrum available to perform the ratio. If the original background was not found, you
must load an appropriate background file to be ratioed against. You can use the Network
button to connect network disks to your local system.

Note
Changing some parameters here may require subsequent
operations to be modified or deleted. For example, if the
spectral type (To) were changed from Absorbance to
Kubelka Munk, deconvolution with the original parameters
may no longer give meaningful results.

In all the dialog boxes, Cancel returns you to the main window with no changes made;
OK returns you to the main window and changes the parameters.

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 164 Chapter 5 History, Reprocess, Method

If you edit a procedure, you can have the changes apply immediately after you have
pressed OK in the procedure dialog box, or you can choose to apply these changes (and,
perhaps, changes in other procedures) manually.

Select the Auto Apply box to have edit changes applied to the spectrum immediately after
exiting from the dialog box. In this example, select the Truncate operation. The
existing right hand limit is 400; change it to 600.

Click OK. The Corrected spectrum is now truncated at 600 cm-1.

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 Chapter 5 History, Reprocess, Method 165

If you unselect Auto Apply; then chnages made when editing are not applied after you
click the OK button in the transform dialog box. However, the Apply button is enabled.
You can edit this and other transforms, as desired. When the Apply button is clicked,
then all the transform modifications are processed.

Use the STOP label to halt the reprocessing at the stage you want to view. To do this

1. Place the cursor over the STOP label and hold down the left mouse button.

2. Drag the STOP label on top of the transform after the last transform
operation you want to occur and release the mouse button.

For example, to view the single-beam trace, place the STOP label just after Compute (on
top of Ratio) and release the mouse button.

It does not matter whether the Auto Apply box is checked or not; the Corrected trace will
show the spectrum at the desired stage of operations.

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 166 Chapter 5 History, Reprocess, Method

Although it appears as if you are “rolling back” the Transform operations, what is
actually happening is that the original interferogram is reprocessed, using the original or
modified parameters, to the result of the operation that you wish to view.

After you are satisfied with the changes, select one of the buttons to determine what is
to be done with the Corrected spectrum.

Replace: replace the existing original spectrum with the corrected spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

Add: add the corrected spectrum to the document that contains the original spectrum.
Both spectra are now in the main menu display. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Cancel:return to the main menu display without acting upon the current spectrum or
any subsequent spectra. Spectra previously replaced or added are not altered by this.

Do All:if this is selected, then Use Current Method is enabled. Click either Add or Replace.
This spectrum and all subsequent spectra are processed and all the corrected spectra are
either added to the spreadsheet (Add)or replace the original spectra (Replace). Spectra
previously replaced or added are not altered by this. The procedures (and their
parameters) used to reprocess the spectra depend upon whether Use Current Method is
selected.
Note
This is different from the Do All procedure in the
transformations (see Chapter 10).
Use Current Method: this is only enabled if Do All is selected. If this is selected, then the
procedures and parameters selected for this spectrum are applied to this spectrum and to
all subsequent spectra; if it is not selected, then this spectrum and all subsequent spectra
are reprocessed according to their own existing procedures.

Help: enter the on-line Help system.

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 Chapter 5 History, Reprocess, Method 167

Displaying the Interferogram

To display the interferogram in the spreadsheet, for the previous example:

1. Select the polystyrene spectra in the spreadsheet.

2. Select Reprocess from the Operations menu.

3. Drag STOP back on top of Compute; release the mouse button. The
interferogram is displayed in the lower part of the window.

4. Press the Add button.

5. Select the interferogram, relabel it (see Chapter 4), and zoom in on the
centerburst. The inteferogram is shown in the picture below.

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 168 Chapter 5 History, Reprocess, Method

METHOD
Method allows you to process subsequent samples in exactly the same manner and with
the same parameters as a previous sample. The first sample (usually) proceeds through
Collect, Compute, and Ratio. After that, other transforms may be applied. To create a
method

1. Use Reprocess until the sequence of transforms is exactly what you want.

2. Select the spectrum that is to be the basis for the method; it will display
green (default color).

3. Select Define a Scan... from the Collect menu. The Rapid Scan tab pages
appear. If you click OK immediately, the existing parameters will be used to
define the Scan.

You can change any number of parameters (but they must be meaningful for
the scan), and then click OK. The next data collect will use these
parameters. See your spectrometer manual for a detailed discussion of the
collection parameters.

Future data collection and processing will be done according to this method, unless you
explicitly change data collection parameters.

Notes
Method works only for Rapid Scan.

Data collection parameters cannot be changed by

Reprocess following a scan.

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 6
File Menu

These commands control which documents are opened for data collection and
manipulation, including the printing of traces, spreadsheets, etc. See Chapter 3 for an
explanation of the document types and what they are used for.

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NEW...
If selected, the New dialog box appears. Select the type of document to be created.

Multi-Spectral Document: This is the default document; it is used to collect data (other
than kinetics data) with a spectrometer, and to manipulate and save that data later. It
can be used to hold any type of spectrum. When saved, the file has a .bsp extension.

Search Library: allows you to create and edit your own search libraries. When saved,
these libraries have a .bri extension.

Quantitation Calibration Document:The document used to contain the calibration spectra,

the concentrations, and the calibration computations. Spectra can be collected directly
into this document or previously collected spectra can be copied into it from other
documents.

Kinetics/TRS Document:Used to collect sets of related spectra such as kinetics, gas

chromatography (GC), thermogravimentric analysis (TGA) and time-resolved
spectrscopy. When saved, the file has a .kin extension.

Note
The background for a kinetics experiment is saved in a
separate file with a .kbg extension.

Print Composition: Used to create a page of spectral information to be printed. See

Chapter 15 for details on how to place objects on this page. When saved, the file has a
.bpt extension.

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 Chapter 6 File Menu 171

Image Document: Used to collect data from an array detector. This feature is not
currently supported.

OK:create a new document of the selected type and return to the main menu with the
empty document displayed.

Cancel: return to the main menu without creating a document.

Help: access the on-line Help facility.

CAUTION
Until the new document is written to the disk using
Save or Save As... from the File menu, it only has a
temporary name (Spectra1, Search1, etc.). If you want
to retain the document, you must save it. This follows
standard Windows and Windows NT protocol. See
Close later in this chapter for details.

OPEN...
Opens an existing document. When this is selected, the Open dialog box appears.

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 172 Chapter 6 File Menu

Select a file name from the File Name list. Change directories (and drives), if desired,
using standard Windows techniques in the Directories list. Select the type of file from
the List Files of Type list; the default is Bio-Rad Spectra (*.bsp). The types of files
available are:

Bio-Rad Spectra (*.bsp): spectral data collected from a spectrometer using the Win-IR Pro
software, or other data converted and saved as the Bio-Rad Spectra format.

spectral data collected from a spectrometer using the

3200 Format Spectra (*.dt, *.sb, *.ig):
Bio-Rad 3200 series software (DDS).
*.dt spectrum
*.sb single-beam
*.ig interferogram
*.ch chromatogram

GRAMS/386 Spectra, Win-IR (*.spc): spectral

data collected from a spectrometer using
Win-IR or GRAMS/386, or converted from other formats to GRAMS format.
Comments in .spc files are imported into Win-IR Pro.

Comma Separated Value (*.csv): spectral files that are in spreadsheet format (do not
confuse this generic spreadsheet with the one in the lower half of the Win-IR Pro
windows). A typical line of data in these files is

X-axis value
, (a comma)
Y-axis value
newline character

If this is a multifile, then the additional Y-axis values are on the same line, separated
from the first Y-axis value by commas. A header defines file type, axes labels, etc.

Comma-separated value files are easily exported to most commercially available

spreadsheets.

Phase Array Data (*.phs): this is the file into which the phase correction, calculated in
Compute, is stored.

Kinetics Background (*.kbg): a background spectrum used for kinetics data collection.

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 Chapter 6 File Menu 173

AIA Data Exchange (*.cdf): anew standard developed by the Analytical Instruments
Association. It is designed to allow easy interchange of data between different vendors’
equipment.

Sadtler SearchMaster (*.irf): a file in

Sadtler format, usually collected using Sadtler
SearchMaster, containing one spectrum.

Search Library (*.isl or *.bri): vendor-supplied

libraries of spectra against which unknown
spectra will be compared to obtain matches.

Note
File / Open will show all installed libraries. If you try to
open a library that you do not have permission to access,
you will see a message saying Can’t open filename for
reading.

Quant (*.bsq): the calibration document used for simple quantitative analysis.

Kinetics/TRS Data (*.kin): the set of related spectra (and optional analysis) obtained from
kinetics data collection or from TRS data collection.
Bio-Rad Microscope Mapping Spectra (*.bsm): data collected using Bio-Rad’s Shadow Pro.
Raw Image Data (.seq): thisis the data prior to its being processed to Image Data (.dat)
files. The capability of opening these files may, at times, be very useful, because of the
way Image data is collected. There are three cases:
• No processed image file (.dat) exists. The . seq file will be processed to
create a .dat file. The .dat file will then be opened. Before this occurs, there
is a dialog box allowing you to cancel this action.
• A processed image file (.dat) exists, but is not open. You are asked if the
.seq file is to be reprocessed; if it is the existing .dat file is overwritten.
• A processed image file (.dat) exists and is open. A message box informs
you that the .seq file cannot be opened.

Image Data: (*.dat): data collected from array detectors.

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 174 Chapter 6 File Menu

All Files (*.*): display all files in the directory regardless of their extension.

Open a file by selecting it and clicking OK, or by double clicking the name.

Drives:a pull-down menu appears with a list of all connected drives. Select the drive on
which the desired file is stored. If the drive is not connected, click the Network button to
connect that drive to your computer.

Preview: if checked, the trace for the selected file will be displayed in the box on the
right. You can rapidly scan through the files with the ↑ and ↓ keys. This is possible for
files on network drives, as well as on your local drive.

Note
Image files (.dat) do not show a preview, even if the
Preview box is selected.

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 Chapter 6 File Menu 175

If a document that contains more than one spectrum is selected, it is possible to preview
any of the spectra in that document. In the next two dialog boxes below, the first and
eleventh spectra in the document are previewed.

Note
Only numbers are displayed in this box; there are no
spectrum names even if you have named the spectra in
the spreadsheet.

This is done by clicking the number in the preview box. If there are more than four
spectra in the document, a scroll bar appears.

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 176 Chapter 6 File Menu

Note
Preview works for any of these files regardless on the
disk on which it resides; it does not matter whether the
disk is on your local system or connected to your system
via the network.

OK: open the selected document and return to the main menu with the document
displayed.

Cancel: return to the main menu without opening a document.

Network: click to bring up the Connect Network Drive dialog box. With this, you can
connect to any drive on the network to access files. If you need more information, see
the Windows NT documentation you received with your system.
Note
In order to connect a drive to your system, the network
administrator must have given you the appropriate access
rights.

Help: access the on-line Help facility.

If you have the Explorer window active, you can highlight a document and drag it into
the Win-IR Pro window to open it. This is an example of drag-and-drop.

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 Chapter 6 File Menu 177

CLOSE
Closes the currently active document. If any changes have been made to the document
since the last time it was saved, you will be asked if you want to save those changes.

Yes: save changes made since last save and close document.

No: close document without saving changes made since the last save.

Cancel: do not close document; return to main menu.

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 178 Chapter 6 File Menu

CLOSE ALL
Closes all open documents, For each document, if any changes were made to that
document since the last time it was saved, you will be asked if you want to save those
changes.

Yes: save changes made since last save and close document.

No: close document without saving changes made since the last save.

Cancel: do not close document; return to main menu.

SAVE
Saves the currently active document to the disk under its existing name. File / Save
automatically converts all export trace files (.dt, .spc, etc.), to Bio-Rad Spectrum format
(.bsp), but does not overwrite the original file.

Caution
Do not save files in the Win-IR Pro directory or its
sub-directories; create your own directories for saving
these files.

SAVE AS...
Saves the currently active document to the disk with a newly specified name and/or
directory and/or file type. When this is selected, the Save As dialog box appears.

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 Chapter 6 File Menu 179

Enter the desired name for the document in the File Name box. Use standard Windows
procedures to change the directory, if desired. Click OK when you are ready to save the
document. Windows NT supports the use of long file names.

Caution
Do not save files in the Win-IR Pro directory or its
sub-directories; create your own directories for saving
these files.

With Save As, you can create Bio-Rad spectra (*.bsp), GRAMS/386 and Win-IR spectra
(*.spc), comma-separated value spectra (*.csv), Phase Array Data files (*.phs), AIA Data
exchange (*.cdf) and Sadtler SearchMaster (*.irf) document types. These types are
described under Open.

If the spectra in the spreadsheet of your .bsp file have the identical format, then when
you save as an .spc file, they will all be saved to a GRAMS multifile.

If the spectra in the spreadsheet of your .kin file come from a kinetics or a TRS
experiment, then when you save as an .spc file, the time information will be preserved
as well as the exported spectra being saved in a multifile.

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 180 Chapter 6 File Menu

Notes
If the target is a Sadtler SearchMaster (*.irf) file, then the
file you are saving can contain only one spectrum. If it
contains more than one spectrum, you will get an error
message and no Sadtler SearchMaster file will be created.

Kinetics/TRS documents can be saved as .spc multifiles.

Comments are saved when saving in the .spc format.

OK: save the document under the selected name and return to the main menu with the
document still displayed.

Cancel: return to the main menu without saving the document.

Help: access the on-line Help facility.

Network: click to bring up the Connect Network Drive dialog box. With this, you can
connect to any drive on the network to access files.

Note
This assumes that the network administrator has given
you the appropriate access rights. If not, you will either
be unable to connect to a network drive or, if you can
connect, you will get a message such as

Follow the instructions in this message.

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 Chapter 6 File Menu 181

AIA Data Exchange File (.cdf)

There are additional features if you save a file as an AIA Data Exchange File. This is a
standard format promulgated by the Analytical Instrument Association. You have the
option to add information that is not normally stored in Win-IR Pro documents. For
example, consider the file abspoly.bsp:

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 182 Chapter 6 File Menu

1. Select Save As... from the File menu. The Save As dialog box appears.

2. Use the List Files of Type: pull-down menu to select

AIA Data Exchange (*.cdf).

3. Click OK to save the document as an AIA Data Exchange file (the other
buttons have their usual functions, as described above). The AIA FTIR Data
Exchange Information dialog box appears.

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 Chapter 6 File Menu 183

4. To change (or insert) a value for the specification, highlight the

specification. The value appears in the Value box on the right side. Use the
cursor and standard word-processing techniques to type in a new value.

Note
If the specification cannot be changed (read-only), then
its value will be in gray rather than black, and you will
not be able to alter it.

5. If you want to add additional specifications, click the Add More Items...
button. The Add AIA Item dialog box appears.

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 184 Chapter 6 File Menu

6. Highlight the specifications to be added. Contiguous specifications can be

selected using the standard Windows shift-click selection technique.
Individual specifications can be toggled on and off using the standard
Windows ctrl-click technique. When all specifications have been selected,
click the OK button (if you decide not to add any specifications, click the
Cancel button, instead).

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7. The new specifications are added to the AIA FTIR Specifications box.

8. Set the values for these added specifications, following the procedure in
Step 4, above.

9. Click the OK button to save the file as an AIA Data Exchange file.

Note
Any .cdf file can be opened directly, using File / Open.
See the details in the Open section earlier in this chapter.
RUN
Allows you to run programs, including executable Win-IR Pro scripts from Win-IR Pro.
You do not need to have a document open in Win-IR Pro to access this entry. When
selected, the Open dialog box appears. The default file type is executable (*.exe).

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 186 Chapter 6 File Menu

Use standard Windows NT techniques to access the file to be executed; then, click OK
to start the application.
PRINT...
Prints the screen view of the currently selected spectrum on the printer specified as part
of the Windows Control Panel or by the File / Print Setup menu selection. See the Win-
IR Pro Installation and Configuration Manual for details on how to select printers and
install printer drivers.
In addition to the spectrum in the main window, you can print any text column in the
spreadsheet as part of this page.
1. Use the cursor and left mouse button to highlight the spreadsheet column to
be printed.
2. Choose Lock Selected from the View menu.
3. Repeat this process for all desired columns. If you decide not to print a
column, then highlight it and choose Unlock Selected from the View menu.
Note
Alternatively, use the CTRL key with the mouse button to
toggle on and off the columns to be printed. This use is
detailed in Chapter 4.

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 Chapter 6 File Menu 187

4. Select the spectrum to be printed by highlighting its ID in the leftmost

column.

5. Select Print from the File menu. The Print dialog box appears.

Note
Because the output of Win-IR Pro does not span multiple
pages, only the All button in Print Range is available and is
automatically chosen. This will print all selected items.

6. Use the printer in Landscape mode. To make sure of this, click the Setup
button. The Print Setup dialog box appears.

7. Be sure that Orientation is Landscape. Click the OK button to return to the

Print dialog box.

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 188 Chapter 6 File Menu

8. Click the OK button to begin printing.

The number of traces that can be printed is determined by how many can fit on the page
(a function of page size and orientation). The types of lines used for printing and
identifying the traces are in groups of 5. That is, the same type of line is used for trace
1, trace 6, trace 11, etc.

If you select more columns in the spreadsheet than can fit on the printed page, only
those columns that completely fit on the page will be printed. The rest will not be
printed.

Note
If you are using a color printer, the default colors for
some of the traces may not have sufficient contrast—for
example, yellow—to show clearly on the page. Use
Options / Edit Color to change the appropriate traces until
the printed copy is as desired. Be sure to record these
color value settings.

PRINT PREVIEW
This feature is not currently implemented. Check the README.WRI file for the latest
information.
PRINT SETUP...
Selects the output device and allows you to set its parameters. Normally, this is the
printer and it has already been set up as part of the system installation. The dialog
boxes and the specific values of the printer parameters depend upon the printer attached
to the system. See the Win-IR Pro Installation and Configuration Manual for details on
how to select printers and install printer drivers.

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 Chapter 6 File Menu 189

PRINT COMPOSITION

Open existing or create new print composition templates. You can select information
associated with spectra in a document (text or graphics), arrange the information on a
page (or pages), add comments, and print this information. Templates can be saved for
future use with similiar spectra. There are two submenu entries.

New
Create a new print composition template.

Open
Open an existing print composition template.

Print composition is discussed in detail in Chapter 15.

MOST RECENTLY OPENED DOCUMENTS

The most recently (up to four) opened files are displayed here. You can reopen any of
these files by clicking its name.

EXIT
Save all open documents to disk, close the documents, close Win-IR Pro and return to
Windows NT.

When you re-start Win-IR Pro, it will automatically open the last document that was
opened prior to selecting Exit. This document is in position 1 in the most recently
opened documents section of the File menu (immediately above Exit)

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 7
Edit Menu

These commands copy and paste data and graphics using the system clipboard. They
also allow modification of the spreadsheet.

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 192 Chapter 7 Edit Menu

UNDO...
If possible, undo the last operation. Undo will be followed by a brief description of the
process to be undone. For example, following a smoothing operation, this entry will be
Undo Smooth. If the operation cannot be undone, then the entry will say Can’t Undo and
it will be greyed out (disabled).

CUT
Copy the spectral data to the clipboard and delete it from the document.

When you Cut or Copy from Win-IR Pro, the spectral data (including history and other
properties), not its graphic representation, is copied to the clipboard. If it is pasted into
a Win-IR document, then all information is transferred and the spectral data are
represented graphically.

If the clipboard is pasted into a spreadsheet, then only the spectral information is
transferred and it appears as two columns of numbers (the X- and Y-values). The
clipboard cannot be pasted into all applications; for example, if you try to paste it into
Word, nothing will happen.

Note
If you want to copy the graphic representation into other
applications, use one of the commercially available screen
capture applications. These actually save the image and
allow it to be pasted into other applications, such as word
processors.

COPY
The same as Cut, except that the spectrum and spreadsheet in the document are not
deleted. This is more commonly used than Cut.

Consider the spectrum below.

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 Chapter 7 Edit Menu 193

1. Place the cursor in the document window, and click the left mouse button.

2. Select Copy from the Edit menu.

3. Start a spreadsheet application, such as Excel.

4. Place the cursor where you want the first data point to be written.

5. Select Paste from the Edit menu. A typical result is seen below.

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 194 Chapter 7 Edit Menu

Edit / Copy canalso copy the non-graphical data from columns of the Win-IR Pro
spreadsheet into an external spreadsheet such as Excel. Consider the example below,

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 Chapter 7 Edit Menu 195

1. Highlight the columns to be copied; in this example, we select Name, History,

and Created (see Chapter 4 for details on how to select columns).

2. Select Copy from the Edit menu.

3. Access the external spreadsheet; in this example, Excel is used.

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 196 Chapter 7 Edit Menu

4. Select Paste from the Edit menu.

Notes

Data from the Win-IR Pro spreadsheet columns can also

be pasted into word processor documents.

Graphic data (such as Spectrum or Y-Data) cannot be

copied. If these columns are selected, the corresponding
external spreadsheet cells, or word processor columns,
will be empty.

You cannot take data from spreadsheets or word

processor documents and paste them into Win-IR Pro
spreadsheets.

PASTE
Paste the contents of the Win-IR Pro clipboard into the Win-IR Pro document. This is
often used to copy spectra between documents. You can also copy spectra within the
same document, if desired.

When you paste a spectrum into a document, its row is placed just above the lowest
numbered selected row; the rows below the new spectrum are renumbered. This allows
to to control where in the spreadsheet a spectrum is placed.

You can also modify a spectrum using an external spreadsheet and then replace the
original spectrum.

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Note
You must Paste data copied from an external spreadsheet
into a selected spectrum in an opened document. (This
should be the same spectrum that you originally copied
the data from.) The data from the external spreadsheet
replaces the spectral data in Win-IR Pro. The rest of the
spectral information (resolution, interferogram, etc.)
remain the same.

The process is:

1. Select a spectrum in Win-IR Pro and Copy it to the clipboard.

2. Switch to... an external spreadsheet.

3. Paste the x,y data into this spreadsheet.

4. Modify the data as desired.

5. Copy all the data to the clipboard.

6. Switch to... Win-IR Pro.

7. Make sure that the proper spectrum is selected. If not, select it.

8. Paste the data into that spectrum.

Note
The History property is not affected by this external
processing of the spectrum.

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 198 Chapter 7 Edit Menu

PEAK LIST...
You must select peaks before this entry is enabled. Select peaks with Operations / Peak
Pick to automatically pick peaks (Chapter 11), or select them manually as described in
Chapter 2. In this example, 8 peaks have been labeled using Peak Pick.

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 Chapter 7 Edit Menu 199

Changing Peak Parameters

When you select Peak List..., the Edit Peaks dialog box appears.

Peaks are numbered sequentially from the lowest wavenumber to the highest
wavenumber of their centers. The following information is shown for each peak:

Height
Center (cm-1)
Area
Left Edge (cm-1)
Right Edge (cm-1)
Left Baseline (cm-1)
Right Baseline (cm-1)

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 200 Chapter 7 Edit Menu

The area and height are calculated from the other parameters. You cannot enter or alter
the peak area or peak height directly; they can be altered indirectly by changing the
values for the center, edges, and baselines of the selected peak.

To alter the values of the peak parameters. First select the desired peak from the Select
Peak list; then, click the Edit button. The Edit Property dialog box appears. Each tab page
allows you to change specific peak parameters. The details of all these tab pages and
the peak parameters are discussed in Chapter 2.

The tab pages are shown below. The Display tab page is not accessible through Edit /
Peak List; use the procedures discussed in Chapter 2.

General

Value: select Height, Area, or Center.

Baseline Definition:
select both left and right—the baseline is a straight line connecting the
two baseline points
select none—the baseline is the x-axis

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 Chapter 7 Edit Menu 201

select only left or right—the baseline is a horizontal line through the

selected baseline point.

Use Left Point: baseline is a horizontal line through the left baseline point.
Use Right Point: baseline is a horizontal line through the right baseline
point. .
Auto Center: moves the right half box of the left baseline point to the x-
position of the center of the peak; moves the left half box of the right
baseline point to the x-position of the center of the peak. These half
boxes move if the center of the peak moves. If the baseline boxes have
not been split, then selecting Auto Center splits the boxes and moves
them as above. This option is most useful in kinetics documents (see
Chapter 3 for details).

Center

Method: how the center of the peak is to be determined.

At Point: the center of the peak is at value entered in Center Edge.
Extreme in Region: the center of the peak is at the extreme (maximum for
absorbance spectra, minimum for transmission spectra) value of
the spectrum in the region defined by the values in Left Limit and
Right Limit.

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Average in Region: the x-position of the center of the peak is at the

arithmetic mean of the value of the Left Limit and Right Limit.
Center of Gravity: the center of the peak is where the vertical line dividing
the peak area (in the region defined by the values in Left Edge and
Right Edge) in half intersects the spectrum. See Chapter 2 for
details of this equation.

Right Baseline

Method: how the right baseline is to be determined.

At Point: the right baseline point is at value entered in Center Edge.
Extreme in Region: the right baseline point is at the extreme (maximum
for absorbance spectra, minimum for transmission spectra) value
of the spectrum in the region defined by the values in Left Limit
and Right Limit.
Average in Region: if the baseline box is split, the x-position of the right
baseline point (x) is the arithmetic mean of the x-positions of the
left and right limits of the baseline region. The y-position of the
right baseline point (y) is the average of the y-position values in
the region. The (x,y) point is not necessarily on the spectrum.
This technique reduces the effect of noise within the baseline
region

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 Chapter 7 Edit Menu 203

Left Baseline

Method: how the left baseline is to be determined.

At Point: the left baseline point is at value entered in Center Edge.
Extreme in Region: the left baseline point is at the extreme (maximum for
absorbance spectra, minimum for transmission spectra) value of
the spectrum in the region defined by the values in Left Edge and
Right Edge.
Average in Region: if the baseline box is split, the x-position of the left
baseline point (x) is the arithmetic mean of the x-positions of the
left and right limits of the baseline region. The y-position of the
left baseline point (y) is the average of the y-position values in
the region. The (x,y) point is not necessarily on the spectrum.
This technique reduces the effect of noise within the baseline
region

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 204 Chapter 7 Edit Menu

Right Edge

Enter the value desired for the Right Edge.

Left Edge

Enter the value desired for the Left Edge.

In general, type the new information in the appropriate box. If any of the values and/or
methods are changed, the Apply button is enabled.

OK: implement values on tab page and return to the Edit Peaks dialog box.

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 Chapter 7 Edit Menu 205

Cancel: do not implement any changes to values made since the Apply button was last
clicked; return to the Edit Peaks dialog box.

Apply: immediately change the peak values; this also causes the Area and Height to be
recalculated and displayed. Changes made this way cannot be reversed with the Cancel
button.

Help: enter the on-line Help system.

Placing Peak Parameters in the Spreadsheet

Each of the items of information for each peak can be placed into the spreadsheet. To
do this:

1. Select the peak

2. Click in the box to the left of the peak item to be entered.

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 206 Chapter 7 Edit Menu

This item will be placed into the spreadsheet. There is no global selection; that is, you
cannot, with one command, specify that all Centers or all Areas will be in the
spreadsheet. All items must be selected individually.

In the example below, the spreadsheet shows the values for the centers of peaks 1 and 7,
the height of peak 4, and the area under peak 3. The column is labeled with both the
property and the peak. For example,

Peak 03 Area

Peak 01
Center

Peak 07
Center

Peak 04
Height

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 Chapter 7 Edit Menu 207

The buttons other than Edit in the Edit Peaks dialog box are:

OK: make all changes the peak table and to the spreadsheet; return to the main menu.

Cancel: return to the main menu without making any changes to either the peak table or
to the spreadsheet.

Help: enter the on-line Help system.

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 208 Chapter 7 Edit Menu

AIA PROPERTIES...
This menu entry allows you to add and alter the AIA FTIR specifications. These
specifications are part of the AIA file format and are normally saved in the .cdf files.
When selected, the AIA FTIR Data Exchange Information dialog box appears.

1. To change (or insert) a value for the specification, highlight the

specification. The value appears in the Value box on the right side. Use the
cursor and standard word-processing techniques to type in a new value.

Note
If the specification cannot be changed (read-only), then its
value will be in gray rather than black, and you will not
be able to alter it.

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 Chapter 7 Edit Menu 209

2. If you want to add additional specifications, click the Add More Items...
button. The Add AIA Item dialog box appears.

3. Highlight the specifications to be added. Contiguous specifications can be

selected using the standard Windows shift-click selection technique.
Individual specifications can be toggled on and off using the standard
Windows ctrl-click technique. When all specifications have been selected,
click the OK button (if you decide not to add any specifications, click the
Cancel button, instead).

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 210 Chapter 7 Edit Menu

4. The new specifications are added to the AIA FTIR Specifications box.

5. Set the values for these added specifications, following the procedure in
Step 1, above.

6. Click the OK button to save the specifications in the active document for the
selected spectrum..
SELECT ALL VISIBLE
Selects all spectra that are currently displayed on the screen. This is useful in the
following situation (among others).

1. Open a document (.bsp) with multiple spectra.

2. Select a group of the spectra; for example 1 to 10.

3. Use the cursor vertical expansion capability (see Chapter 1) to adjust the y-
axis scaling of one of the spectra. This is now the only selected spectrum.

4. To reselect all the displayed spectra, select Edit / Select All Visible. All the
visible spectra are now selected in the spreadsheet.

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 8
View Menu

MULTI-SPECTRAL DOCUMENTS KINETICS DOCUMENTS

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 212 Chapter 8 View Menu

STATUS BAR
If selected (default), the status bar is displayed at the bottom of the screen. A √ mark
shows that the status bar is selected. Unselecting this entry hides the status bar; the √
mark is no longer on the menu.

The text in the left side status bar gives a brief description of the results of clicking the
button that the cursor is on. For
example,

If the cursor is in the spectrum display window, the X and Y coordinates of the cursor
are shown in the right side of the status bar. For example,

The status bar also shows the progress of an actions—such as collecting data, errors,

EVENT LOG
Once activated, the event log displays all messages generated by Win-IR Pro, including
error messages. The event log can be activated either

• automatically, when an error or some other event occurs during setup or data
collection, OR

• manually, by selecting Event Log from the View menu.

The event log can be turned off by either

• manually, by selecting √ Event Log from the View menu OR

• when it is floating, by clicking the Close button on the extreme right of the
event log title bar.

When it is initially activated by manual selection, the event log box look like this.

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 Chapter 8 View Menu 213

Alternate docking
positions for event
log box

Event log box drag

border (all 4 sides)

Event messages
appear in here

Event log box in

docked position

The event log box can either be docked or floating. It is docked when it is above the
Bio-Rad bar at the bottom of the screen. It can also be in any of the other three
positions shown in the figure above, if you find one of them to be more convenient.

Floating the Event Log Box

When the event log box is undocked, it can be resized. You can float the box by

• putting the cursor in the drag border and double-clicking the left mouse
button OR

• putting the cursor in the drag border, holding down the left mouse button,
and dragging the event log box away from its docked position until its
outline changes size; then release the mouse button.

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 214 Chapter 8 View Menu

Outline of event log

box after undocking
but before release of
mouse button

Event log box close

button

Event log box after

release of mouse
button

Note
If the Event Log box is sized too large, it cannot be
undocked by dragging. However, it can be undocked by
double-clicking in the drag border.

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 Chapter 8 View Menu 215

Resizing the Event Log Box

The box must be floating if it is to be resized. To resize the Event Log box, put the
cursor in the drag border; the cursor changes to a double-head arrow. Hold down the
left mouse button, and move the cursor in the direction of either of the arrowheads to
increase or decrease the size of the box; release the left mouse button when you are
done. You can move the box by putting the cursor in the Event Log box title bar,
holding down the left mouse button, and then moving the entire box. Release the
mouse button when you are done.

Docking the Event Log Box

You can dock the box by

• putting the cursor in the drag border and double-clicking the left mouse
button OR

• putting the cursor in the drag border, holding down the left mouse button,
and dragging the error log box towards its docked position until its outline
changes size (extends across the Win-IR Pro screen horizontally); then
release the mouse button.

When you dock the Event Log box, its size along the edge changes to the extent of the
Win-IR Pro screen; its other dimension remains at what it was before it docked.

Overlap with Control Panel Sidebars

In some cases, the event log may overlap the control panel sidebar, as is shown below.

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 216 Chapter 8 View Menu

To fix this, undock the event box, resize it, and redock it as described in the sections
above. In the example below, the event box has been reduced in height and no longer
obscures the operational part of the control panel sidebar.

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 Chapter 8 View Menu 217

You can also move the event box to the left side of the screen or hide it by selecting
View / Event Log.

TRACE CONTROL BAR

This entry controls the positioning and separation of multiple traces displayed in one
document. If selected, the trace control bar appears on the right-hand side of the screen.
The trace box is redrawn so that the displayed traces are not truncated on the right.

Status Bar Trace Control Bar

Note
More than one control panel sidebar can be active at one
time.

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 218 Chapter 8 View Menu

Scaling: allows the size of the trace(s) along the Y-axis to be varied . The Y-axis scale
changes after the traces are rescaled. If the baseline is moved, the Y-axis zero-point
moves along with it.

Independent: each trace can be scaled individually using the cursor. Place the
cursor on the trace; the magnifying glass in the cursor disappears . Hold
down the left mouse button; the cursor changes to a double-headed arrow
Hold down the left mouse button and drag the trace to the desired Y-axis scale.
Release the mouse button and the new values appear on the Y axis.

Note
The button affects only the selected (green) trace(s).

The button scales all traces along the X-axis but

scales only the selected (green) trace(s) along the Y-axis.

Constant: all
traces are scaled by the same factor. Use the cursor to rescale any
one trace and the other traces will also be rescaled.

Proportional: first use Independent Scaling to match up peaks in two (or more)
traces to the same value. Select Proportional. If one trace is rescaled, the others
will also be rescaled. However, they will each be rescaled by a different factor.
This factor will keep the matched peaks in the different traces at the same value.

Positioning: this
allows you to offset, and control the Y-axis offset, of a number of
spectra being displayed simultaneously.

Independent: the traces can be moved up or down, and the scale can be
compressed or expanded. To move the traces up or down, place the cursor in
the middle third of the Y-axis ruler; the cursor changes shape to . Hold down
the left mouse button and move the cursor along the Y-axis ruler. The trace
and the Y-axis ruler will move with the cursor. Release the mouse button
when you are satisfied with the new position of the traces.
To expand or compress the trace Y-axis, place the cursor in the upper (or
lower) third of the Y-axis scale; the cursor changes shape to (or ). Hold
down the left mouse button and move the cursor along the Y-axis ruler. When

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 Chapter 8 View Menu 219

you move the cursor up (down), the Y-axis scale expands; when you move the
cursor down (up) the Y-axis scale compresses. . The trace and the Y-axis ruler
will move with the cursor. Release the mouse button when you are satisfied
with the new position of the traces.. The radar box also reflects the change in
the display.

Baseline: the left hand Y-axis intersections of the traces are spread out according
to the %Y Separation values.

Constant: zero values of the traces are spread out according to the %Y Separation
values.

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 220 Chapter 8 View Menu

%Y Separation: the percentage of the full-scale Y-axis in the display used to set the
position of the traces. These boxes are not active if Independent Positioning is chosen.

Trace: sets the distance (in percent of full-scale Y-axis) between the baselines of
the traces.

Baseline: sets the location of the baseline of the active (green) trace above the
lower edge of the trace display.

If you use the arrows (see above) to set the values, then they are applied immediately.
You can also type percentages in these boxes. If you type in values, the Apply button is

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 Chapter 8 View Menu 221

enabled. Press the Apply button to tell Win-IR Pro that you have completed typing
values and that these values should be applied to the display.

OK: close the control bar and return to the main menu with the settings on the control
bar implemented.

Help: access the on-line Help facility.

Note
Make sure the requested separation range does not exceed
100%. Specifically,

(number of spectra X trace separation) + baseline < 100%

For example, if you have selected 32 spectra, with a

baseline at 3%, then the trace separation can be 0, 1, 2, or
3 only.

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 222 Chapter 8 View Menu

PROPERTY BROWSE BAR

When Win-IR Pro is started, the property browse bar is displayed. It is normally at the
left side of the screen; however, you may choose to move it, as described below. The
property browse bar shows information about all open documents. In the example
below, four documents have been opened.

Use the Window menu to access each of the open

documents

Open documents, one line per document

Property browse bar

Place cursor here and drag side of property browse

bar to change its width

Notes
When you highlight a document or any of its properties,
that document is automatically made the active document.

Change the width of the property browse bar by placing

the cursor on the property browse bar boundary; hold
down the left mouse button and drag the boundary to the
desired position; release the mouse button.

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 Chapter 8 View Menu 223

Tree Structure of the Property Lists

The property list follows the standard Windows NT tree structure such as that sued in
the Windows NT Explorer. If there is a + to the left of the icon, it indicates that
additional structure exists at the next level down. For example, clicking on the + to the
left of abspolys.bsp displays a line for exact spectrum in that document.

Document

Spectra in
document

Note
Once an icon is opened, a – is displayed to its left;
clicking the – closes that icon.

You can continue to open the icons until individual properties are reached.

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 224 Chapter 8 View Menu

Properties

Property Values
To see the value of a property, place the cursor over the name of that property in the
property browse bar. The value is displayed in a small box. If there is no value for this
property (for example, user stamp in spectra collected prior to Release 2.5), no value
box is shown.

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 Chapter 8 View Menu 225

Cursor pointing here

Value displayed here

If you wish to turn off this feature, place the cursor in the property browse bar, click the
right mouse button and select Show Data Tips from the menu.

The values will not longer be displayed. To re-activate this display, place the cursor in
the property browse bar, click the right mouse button and select Show Data Tips from the
menu.

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 226 Chapter 8 View Menu

Adding Property Columns to the Spreadsheet

To add a property column to the spreadsheet, first select (by highlighting) this property
for any spectrum in the document.

Once the property has been selected, you can put it into the spreadsheet as a column by
one of two methods.

• Put the cursor on the highlighted property, hold down the left mouse button
and drag the cursor to the spreadsheet. Release the mouse button.

• Put the cursor in the property browse bar, click the right mouse button and
select Add Column from the menu.

Either method creates a new column to the immediate right of the rightmost existing
column. Any spectrum which does not have this property (for example, a spectrum that
was not searched for would have 0 in a HitList property column) will show a 0, a blank,
or other appropriate entry indicating this.

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 Chapter 8 View Menu 227

Note
Columns in the spreadsheet can be rearranged but
dragging. See “Re-ordering Columns in the Spreadsheet”
in Chapter 4 for complete details.

Hiding the Property Browse Bar

There are three ways to hide the property browse bar when it is displayed.

• Select Property Browse Bar from the View menu.

• Place the cursor in the property browse bar, click the right mouse button and
select Hide from the menu.

• Click the close button at the upper right of the property browse bar.

Showing the Property Browse Bar

When the property browse bar is not displayed, select Property Browse Bar from the View
menu to display it.

Moving the Property Browse Bar

The property browse bar is normally on the left side of the screen; it can be moved to
the right side.

Note
The property browse bar can also be placed on the top or
bottom of the screen or floated. However, the vertical
nature of the property tree is best displayed with the
property browse bar on the left or right side.

To move the property browse bar:

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 228 Chapter 8 View Menu

1. Put the cursor in the property browse bar, click the right mouse button and
select Float. The property browse bar changes to a small window and is no
longer connected to the side of the screen.

Title bar

Property browse
bar (floating)

2. Put the cursor on the title bar of the property browse bar, hold down the left
mouse button and drag the property browse bar to the desired position on the
right hand side of the screen.

3. Put the cursor in the property browse bar, click the right mouse button and
select Dock. The property browse bar is now on the right side of the screen.

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 Chapter 8 View Menu 229

SHADOW TOOLS
This entry is not enabled unless a Shadow Pro document is open. If selected, it causes
the Shadow Pro tool palette to appear. These tools are used to manipulate the view in
the Shadow Pro document. For details see, Shadow Pro User’s Manual (091-0991).
AUTOSCALED
Causes autoscaling along the Y axis only. The X axis is not changed. Equivalent to the
button.

ENTIRE SPECTRUM
Causes autoscaling along both the X- and Y-axes so that the entire spectrum is
displayed in the trace box. Equivalent to the button.

ZOOM IN
Zooms in on the spectrum in the Y-direction only; the new Y-axis labels are
immediately displayed. Equivalent to the button.

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 230 Chapter 8 View Menu

ZOOM OUT
Zooms out from the spectrum in the Y-direction only; the new Y-axis labels are
immediately displayed. Equivalent to the button.

DISPLAY LIMITS...

Document Default...
Causes the Document Display Limits dialog box to appear. Use this dialog box to set
limits for the currently active document. These display limits apply only to this
document. Other documents can have different display limits.

Spectrum Type: highlight the type of spectrum for which you want to set limits.
These limits will apply to all spectra of that type within this document. When a
spectrum type is selected, the values of its axes units are displayed after the X-

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 Chapter 8 View Menu 231

Limits and Y-Limits. For example, in the dialog box above, the x-axis units are
Wavenumbers; the y-axis units are Absorbance. The Typical Range for the X-Limits
and for the Y-Limits is displayed below the entry boxes. Any particular
document may not contain all the listed spectrum types.

X-Limits: enter a value for the Start and End limits in wavenumbers. These will
be the new end points of the display. Values can be entered by typing,or by
clicking the arrows to the right of the entry box.

Notes
If the Start value is less than the End value, then the trace
will be reversed. Entering Auto or pressing Reset does not
restore the original orientation; you must enter numerical
values to do this.
If you enter Auto, then the actual value (start and/or end)
from data collection will be used. Auto is not case-
sensitive.

Reset: sets the X-Limits to Auto.

Y-Limits: enter a value for the Minimum and Maximum limits in whatever the
current Y-axis units are. These will be the new scaling values for the display in
the Y-direction. Values can be entered by typing, or by clicking the arrows to
the right of the entry box.
If the Maximum value is less than the Minimum value, the trace is
displayed as if the values were entered correctly.
If you enter Auto, then trace will be autoscaled along the Y-axis.
Reset: sets the Y-Limits to Auto.

Reset All: sets the X-Limits and Y-Limits to Auto.

OK: return to the main menu display and implement the new X- and Y-limits.
Cancel: return to the main menu display without changing any of the X- or Y-limits.
Help: enter the on-line Help system.

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 232 Chapter 8 View Menu

Note
When you enter numerical values into the Display Limits
dialog box, those limit values then apply to all windows.
It is good practice to reset all values to Auto once the
requirement for specific values has passed.

Selected Spectrum...
Causes the Display Limits dialog box to appear. Use this dialog box to set specific limits
for the selected sprectum only.

X-Limits: enter a value for the Start and End limits in wavenumbers. These will
be the new end points of the display.

Notes
If the Start value is less than the End value, then the trace
will be reversed. Entering Auto or pressing Reset does not
restore the original orientation; you must enter numerical
values to do this.

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 Chapter 8 View Menu 233

If you enter Auto, then the actual value (start and/or end)
from data collection will be used. Auto is not case-
sensitive.

Reset: sets the X-Limits to Auto.

Y-Limits:enter a value for the Minimum and Maximum limits in whatever the
current Y-axis units are. These will be the new scaling values for the display in
the Y-direction.

If the Maximum value is less than the Minimum value, the trace is
displayed as if the values were entered correctly.

If you enter Auto, then trace will be autoscaled along the Y-axis.

Reset: sets the Y-Limits to Auto.

Reset All: sets the X-Limits and Y-Limits to Auto.

OK: return to the main menu display and implement the new X- and Y-limits.

Cancel: return to the main menu display without changing any of the X- or Y-limits.

Help: enter the on-line Help system.

Note
When you enter numerical values into the Display Limits
dialog box, those limit values then apply to all windows.
It is good practice to reset all values to Auto once the
requirement for specific values has passed.

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 234 Chapter 8 View Menu

X AXIS UNITS
Controls the units along the X axis.

SSP isan acronym for “standard spectral plot.” This is one in which the X axis has
been expanded in the region below 2000 cm-1 by a given factor. This expansion is both
shown in the display and printed.

No SSP: no expansion (factor of 1) takes place in the X axis (default).

X2 SSP: the X axis below 2000 cm-1 is expanded by a factor of 2.

X4 SSP: the X axis below 2000 cm-1 is expanded by a factor of 4.

If you want to convert the x-axis units to microns or nanometers, see Transforms / More
Transforms in Chapter 10.

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 Chapter 8 View Menu 235

Note
Standard spectral plot is implemented only for
Wavenumbers; it is not implemented for Microns or
Nanometers.

HISTORY
Displays the history of the collection of the spectrum and any changes made after data
collection in the History Browser status box. Such changes can include computing the
single-beam spectrum, ratioing against a reference spectrum, and a number of actions
available from the Transforms menu, such as smoothing, differentiation, zapping,
deconvolution, etc. This entry is disabled (greyed-out) if no history exists for the
spectrum. This is often the case for imported spectra collected under systems other than
Win-IR Pro.

Note
If the spectrum was collected under Win-IR Pro, then the
data collection information will be included in the history
(Scan).

History at release 2.1 and later will have a time-date

stamp for each operation; operations prior to release 2.1
will have a blank in the time-date stamp data.

History at release 2.5 and later will have a user stamp for
each operation; operations prior to release 2.5 will have a
blank in the user stamp data.

In this example, the polystyrene spectrum stored in abspolys.bsp is used.

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 236 Chapter 8 View Menu

Since there is a history, the History entry is enabled. Select History from the View menu..
The History Browser dialog box appears.

Put the cursor over the box to the far left of the operation name and click the left mouse
button. It is expanded to give details. For example, if expand Compute

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 Chapter 8 View Menu 237

More than one operation can be expanded at a time. For example, highlight Ratio also,

Any one operation (or any one item in the expanded operation) can be highlighted by
placing the cursor on it and clicking the left mouse button. If you then select the Add
column to Spreadsheet box, the select item is marked with a red check mark. This means
it will be added to the spreadsheet when you exit the dialog box.

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 238 Chapter 8 View Menu

Remove an item from this list by highlighting it and deselecting the Add column to
Spreadsheet box; the check mark will vanish. In the example below, three items have
been flagged to be added to the spreadsheet.

OK: return to the main menu display and modify the spreadsheet, if so specified.
Cancel: return to the main menu display without modifying the spreadsheet.
Help: enter the on-line Help system.
The example below shows the three flagged items added to the spreadsheet. Columns
can be removed from the spreadsheet using Remove Columns from the View menu. This
is discussed later in this chapter.

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 Chapter 8 View Menu 239

If you select an operation, such as Scan, Compute, Ratio, Truncate, etc. and add it as a
column to the spreadsheet, the column header will be the name of that operation (Scan,
etc.). The contents of the cell will be Done (or a blank, if that operation was not
performed for another row in the spreadsheet).

If you double click an operation to display its parameters and select parameters to be
added to the spreadsheet, the parameter column heading will be Operation Parameter (for
example, Truncate Region) and the cell will have the value of that parameter. Whether
Operation is to the left of Parameter or above it depends upon the width of the column.

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 240 Chapter 8 View Menu

HIT LIST
This entry is enabled after a successful search; otherwise it is disabled (greyed-out).
Selecting this entry displays a new document window with the selected sample
spectrum and its search hits.

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 Chapter 8 View Menu 241

3D...
Presents a three-dimensional view of the spectra in a Kinetics Document, with time,
wavenumber, and absorbance as the axes. This entry is disabled unless the active
document is a Kinetics Document.

In this example, we will use kinetics.kin.

Click the Export Regions button.

To select the region of interest for wavenumber: click the right mouse button, select
New / Region; then use the cursor in the extracted spectra ruler to adjust the size of the
region. In this example, set it to 3150 to 2000 cm-1.

Use the cursor to select the regions of interest for time. In this example, we will be
looking at 3 to 6 minutes.

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 242 Chapter 8 View Menu

When 3D... is selected, the Select Edge Values dialog box appears.

The limits selected using the cursor are shown here. New values can be entered by
typing.

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 Chapter 8 View Menu 243

Spectral Range: the region of each spectra to be used in creating the 3D view.

Left Edge: the lower limit (in cm-1) of the spectra.

Right Edge: the upper limit (in cm-1) of the spectra.

Time Range: defines the time interval in which the spectra used to create the 3D view
appear.

Start Time: the beginning of the time range (minutes).

Stop Time: the end of the time range (minutes).

OK: creates the 3D view and displays it (see below).

Cancel: return to the main window without generating a 3D view.

Help: enter the on-line Help system.

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 244 Chapter 8 View Menu

The initial 3D view is shown below:

use this ruler to absorbance vs. wavenumber (spectrum) control panel
select time for that time is displayed here

windowshade

3D view, from above, of the use this ruler to select absorbance vs. time, for that
selected spectra—colors wavenumber wavenumber, is displayed here
indicate magnitudes

Two-dimensional cross-sections: To select a spectrum for a given time, place the

cursor in the vertical ruler and click the left mouse button. The spectrum is displayed in
the upper middle of the window.

To select a plot of absorbance vs. time for any wavenumber, place the cursor in the
horizontal ruler and click the left mouse button. The absorbance-vs.-time plot is
displayed in the lower middle of the window.

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 Chapter 8 View Menu 245

Once you have selected a trace you can adjust its display. In this example, the upper
trace has been selected. Choose View / Display Limits / Selected Spectrum. The Display
Limits dialog box appears.

See the section on Display Limits in this chapter for details of how to use this dialog
box. If you select the lower trace, and choose View / Display Limits / Selected Spectrum,
the dialog box appears with the limits for that trace.

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 246 Chapter 8 View Menu

Note
Under certain conditions and color selections, the
extracted line may vanish. To cause it to reappear:
1. Select Options / Edit Color...
2. Click the + next to Pen.
3. Select Region Line.
4. Click on the black box (lower left of the rectangle
of Basic Colors).
5. Click the OK button.

Select a trace, in either the upper or lower display, by clicking on it. You can now use
the normal zoom and scaling operations in that display.

In the example below, both a time and a wavenumber have been selected.

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 Chapter 8 View Menu 247

The portion of the window taken up by each of the three displays can be altered by
dragging the windowshades to the desired location (see Chapter 1 for details of moving
windowshades).

Printing a cross section: Select a trace, in either the upper or lower display, by clicking
on it. Select Print from the File menu, or click the button. The Print dialog box
appears. Press OK if the settings are as desired; otherwise, see Print in Chapter 6 for
details of the settings.

Three-dimensional view: This view can be moved, rotated, and presented in a number
of formats. The control panel sidebar on the right hand of the screen controls the
presentation of the data. The portion of the window used by the different graphics can
be altered by moving the horizontal and vertical window shades. In all the examples
below, the vertical window shade has been moved all the way to the right to better show
the three-dimensional graphics.

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Draw Mode: how the three-dimensional aspect will be represented in two dimensions.

Wireframe: the points of the calculated three-dimensional plot are connected

with straight lines. Lines that are hidden by the shape of the display are not
shown. This draw mode disables both Colors and Palette.

Solid:the lines and the frames they define are filled in with different shades of a
single color to give a better idea of the shape of the surface of the contour plot.

Color Bleed:
uses multiple colors for the surface. These colors change gradually
and smoothly as the height of the plot varies above the base plane. (Default)

Contours:shows contour lines on the surface at constant heights about the base
plane. The contour intervals are pre-set and cannot be changed.

Colors: sets the rangeof colors used to represent the extreme z-values of the plot.

Note
In wireframe mode, Colors is disabled.

Always Autoscale: if this is selected, then whenever you zoom in on a portion of

the plot, the color will be scaled so that the full color range is used for that
portion. This is useful if you zoom in on weak features that may be displayed in
very similar colors in the full plot.

If you are not autoscaling the colors, then you can set the values to be used in
the display. If you use the arrows to the right of the intensity boxes to set
values, they will be implemented immediately. If you type in values, they will
not be implemented until you press the Enter key on the keyboard.

Upper Intensity: enter the color value to be used at the maximum z-value
of the plot.
Lower Intensity: enter the color value to be used at the minimum z-value
of the plot.

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Palette: the draw modes may be observed with three different color schemes.
Note
In wireframe mode, Palette is disabled.
Monochrome: gray scale.
Color 1: shades from red to white to blue.
Color 2: shades from red through orange, yellow, and green to blue. (default)

Background: select the color for the background. A white background may be better if
you are capturing screens for insertion in a publication with a monochrome printer.

Black:background is black. the plot is shown against a black background

(default).

White: the plot is shown against a white background. This may be more
desireable for formats other than wireframe

Zoom: makes the plot appear closer (increases size) or farther away (decreases size).
Use the slide bar to change the value.

Y Scale: makes the height of the peaks taller or shorter. Use the slide bar to change the
value.

Rotation: these controls move the three-dimensional plot about two axes. Regardless of
the rotation, the axes remain in the foreground of the display. Rotation of large arrays
may be slow. Press the ESC key to stop the rotation.
Flat View:
if selected, displays a projection of the isometric view. If de-selected,
the isometric view (3D) is shown.
Default Angle:press this button to return the plot to its default position
(Pitch = 18°, Yaw = 1°).

Pitch: rotates the plot about a horizontal axis parallel to the monitor screen.
Click on the upper part to rotate the plot to show its Bottom; click on the lower
part of the bar to rotate the plot to show its Top. Each time you click the end of
the slide bar, the plot rotates 9°.

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 250 Chapter 8 View Menu

Yaw: rotates the plots about a vertical axis. The plot can be rotated either to the
Right or to the Left. Each time you click the end of the slide bar, the plot rotates
18°.

For both Pitch and Yaw, you can enter the value of the angle. If you change the
angle with the arrows to the right of the text box, the values are implemented
immediately. If you type in values, the values are not implemented until you
press the Enter key on the keyboard.

Subsets of all menus except Transforms are also available. Their entries operate the
same as they do in the main Win-IR Pro document window.

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Examples:

In this example, Draw Mode has been set to Wireframe, Color Palette to Monochrome, and
Background to White. Flat View has been de-selected and the image has been rotated by
30° about each axis.

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Zoom nearer gives this view.

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 Chapter 8 View Menu 253

Zoom farther, and make Y Scale taller gives this view.

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In the example below, Flat View has been selected; Draw Mode is set to Contours.

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 Chapter 8 View Menu 255

As is the case in all the 3D plots, you can use the cursor to draw a rectangle about the
area of interest to zoom in on it.

Printing the 3D View:.To print the three-dimensional (left-hand side) part of the
screen, select File / Print or click the button at the buttom of the screen. In the
example below, the following parameters have been changed from their defaults:

Draw Mode Wire Frame

Palette Monochrome
Background White
Flat view de-selected

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 256 Chapter 8 View Menu

The full screen is on the left; the printed image is on the right.

The printed image is exactly what is in the three-dimensional portion.

If you want to print the entire screen image use either WordPad or Paint. These two
applications are supplied as part of Windows NT. The procedure is described in
Chapter 1.

Exporting 3D Data
The data triads (x, y, z) can be exported by selecting Operations / Export DXF. The file
created has a .dxf extension and can be opened and manipulated by applications such as
Autocad.

Notes
This menu entry is only accessible in a 3D graphics view.

These .dxf files cannot be inserted into word processors

using the usual .dxf filter.

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 Chapter 8 View Menu 257

LOCK SELECTED
Select a row (spectrum) or a column (property) in the spreadsheet and select Lock
Selected.

If a spectrum is selected, this spectrum continues to be displayed even if other spectra

are selected in the spreadsheet. If a spectrum is locked, its Spectrum # is displayed in
italics. This is useful for comparing one spectrum against a series of others.

If a property is selected, this property will be printed out as part of the plot when File /
Print is chosen. If a property is locked, its label is displayed in italics.

UNLOCK SELECTED
Select a row (spectrum) or a column (property) in the spreadsheet and select Unlock
Selected.

This spectrum is no longer locked into the view and will disappear when another
spectrum is selected from the spreadsheet.

The property will no longer appear on the plot when File / Print is chosen.

Locking/Unlocking a Spectrum into Display

When a spectrum (set of spectra) is (are) selected for operation, it (they) can be locked
into the main display by selecting Lock Selected from the View menu. They will remain
locked and in the trace display until explicitly unlocked by selecting Unlock Selected
from the View menu. This is useful if you want to compare one spectrum against a
succession of others.

Note
Selecting a spectrum does not automatically lock it;
locking must be done explicitly

Locked spectra are indicated by italics in the leftmost column (called the ID column) of
the spreadsheet. In the example below, Spectrum 1 is locked.

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 258 Chapter 8 View Menu

Locking/Unlocking a Property for Printing

When a property (set of properties) is (are) selected for operation, it (they) can be
locked into the main display by selecting Lock Selected from the View menu. They will
remain locked and in the trace display until explicitly unlocked by selecting Unlock
Selected from the View menu.

Locked properties are indicated by italics in the top row (label row) of the spreadsheet.
In the example below, HitList and History are locked.

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 Chapter 8 View Menu 259

GO TO...
Allows you to select any spectrum in the document without having to choose through
the spreadsheet. This is useful for documents with large number of spectra. The Go To
dialog box appears

Enter the number of the desired spectrum and click OK. That spectrum appears in the
trace. The corresponding entry in the spreadsheet is highlighted. If you enter too low a
number, Spectrum 1 (the first spectrum) is selected. If you enter a number larger than
the last spectrum in the spreadsheet, the last spectrum is selected.

Note
If you have a large number of spectra in a document, you
can easily access the end by selecting Go To... and
entering a very large number (such as 999).

Cancel: return to the main menu without changing the spectrum (or spectra) current
active.

Help: access the on-line Help facility.

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 260 Chapter 8 View Menu

REMOVE COLUMNS
Select the column (or columns) to be removed by placing the cursor in the column label
box and clicking the left mouse button. Multiple columns can be selected in the usual
manner (see “Introduction to the Spreadsheet” Chapter 4, for details).

Note
The display of information is removed. The actual
information is still in the file and can be redisplayed, if
desired, at a later time.

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 Chapter 8 View Menu 261

Select Remove Columns from the View menu. The selected columns are removed from
the spreadsheet.

Note
If no columns are selected, then the Remove Columns
entry is disabled (greyed-out).

Caution
Do not remove the name and spectrum columns of the
spreadsheet. If you remove the spectrum, use the
Property Browse Bar to add Spectrum to the
spreadsheet. If you remove the name, use the Property
Browse Bar to add SpectName to the spreadsheet.

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 262 Chapter 8 View Menu

LOAD PLOT TEMPLATE

The plot composition template describes how the printed page will appear. In
particular, it defines which columns in the spreadsheet will be printed; this information
was saved using Save Plot Template (see below). These templates are saved in files
(with a .pct extension). Select this entry to load the desired existing template. The Load
Plot Composition Template dialog box appears.

Use the standard procedures to select a file. This template file may be local or
accessible over the network (use the Network button). Click OK to load the file. Cancel
closes the dialog box without loading a new template. Help accesses the on-line Help
system.

SAVE PLOT TEMPLATE

After you have chosen the spreadsheet columns to be printed by selecting and locking
them, you can save this list of columns with Save Plot Template. This list of columns
can be used for any other document by using Load Plot Template (see above). Select Save
Plot Template and the Save Plot Composition Template dialog box appears.

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 Chapter 8 View Menu 263

Choose a name for the plot template and save it in the appropriate directory.

The example below shows how to have data acquisition parameters printed out with the
spectrum.

1. Select View / Property Browse Bar.

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 264 Chapter 8 View Menu

2. Open the property tree until you see the History entry; select History by
highlighting it. Click the right mouse button and select Add Column from the
menu. This puts a History column into the spreadsheet. Hide the Property
Browse Bar if it is no longer required.

History entry in property tree

History column

3. Double-click the History entry in the spreadsheet. The History Browser dialog
box appears.

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 Chapter 8 View Menu 265

4. Click the + to the left of Scan to expand the scan parameters. Highlight a
parameter you want printed with the spectrum but clicking on it. Click in
the Add column to spreadsheet box so that it is selected. Repeat this process
for all the parameters you want printed. When these have been selected,
press the OK button. You are returned to the main screen.

5. Shift-click to select the columns in the spreadsheet that are to appear in the
plot. The column headings are shown darker than unselected column
headings.

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 266 Chapter 8 View Menu

6. Select View / Lock Selected. The selected column header labels are now
shown in italics.

7 Select View / Save Plot Template; save this as a .pct file.

8. Whenever you want to print a spectrum with these collection parameters,

bring up the template using View / Load Plot Template.
KINETICS DOCUMENT ENTRIES
The entries Kinetics Edit Bar, Spreadsheet, and Chromatogram Edit Window appear only
when a kinetics document is active. These entries are independent and the choice of
one does not imply nor preclude the choice of any of the others.

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 Chapter 8 View Menu 267

Kinetics Edit Bar

If you select the View / √ Kinetics Entry Bar entry, the sidebar control panel will no longer
be displayed, the document screen will be redrawn, and the √ mark will also disappear.
Select this entry again, to make the kinetics edit bar and the √ mark reappear.

√ Kinetics Edit Bar

Kinetics Edit Bar

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 268 Chapter 8 View Menu

Spreadsheet
If you select the View / Spreadsheet entry, the spreadsheet for the extracted spectra will
be displayed, the document screen will be redrawn, and the √ mark will also appear.
Select this entry again, to make the spreadsheet and the √ mark disappear.

√ Spreadsheet

Spreadsheet

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 Chapter 8 View Menu 269

Chromatogram Edit Window

If you select the View / √ Chromatogram Edit Window entry, the chromatogram edit
window will no longer be displayed, the document screen will be redrawn, and the √
mark will also disappear. Select this entry again, to make the chromatogram edit
window and the √ mark reappear.

√ Chromatogram Edit Window

Chromatogram Edit Window

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 270 Chapter 8 View Menu

HIDE GRAM-SCHMIDT CHROMATOGRAM

This menu entry appears only when a kinetics document is active.

If you select the View / Hide Gram-Schmidt Chromatogram entry, the Gram-Schmidt
chromatogram will no longer be displayed, the Gram-Schmidt entry will be removed
from the Functional Groups list in the control panel sidebar, and the menu entry will
change to Show Gram-Schmidt Chromatogram. Select Show Gram-Schmidt Chromatogram
to restore the display and menu to their previous conditions.

Notes
Hide(and Show) Gram-Schmidt Chromatogram is normally
used only when the chromatogram edit window is shown.

You can hide the Gram-Schmidt chromatogram even if

no other functional groups have been created.

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 Chapter 8 View Menu 271

SHOW PEAKS
Peaks can be picked and labeled, either with the right mouse button menu or Operations
/ Peak Pick. If this is done, the View / Show Peaks entry has a √ mark to the left of it,
indicating that peak labels are shown. If you select the View / √ Show Peaks entry, the
peak labels will no longer be displayed, and the √ mark will also disappear. Select this
entry again, to make the peak labels, annotations, and the √ mark reappear.

√ Show Peaks

Show Peaks

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 272 Chapter 8 View Menu

SHOW LABELS
If position labels or annotations are added to the spectrum display, then View / Show
Labels entry has a √ mark to the left of it, indicating that these labels and annotations are
shown. If you select the View / √ Show Labels entry, the labels and annotations will no
longer be displayed, and the √ mark will also disappear. Select this entry again, to
make the labels, annotations, and the √ mark reappear.

√ Show Labels

Show Labels

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 9
Collect Menu

The commands in this menu allow you to set up your spectrometer and to collect
backgrounds and data. The specific entry to be chosen and the parameters to be set for
collection depend upon what Bio-Rad spectrometer you are using and the specific

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 274 Chapter 9 Collect Menu

software installed for data collection. The details of data collection are covered in the
spectrometer manual that you received with your system.

Notes
If you have the “workstation version” of the software,
then the entire Collect menu may be disabled (grayed-out).

The step-scan choices will be absent if your spectrometer

does not support step-scan.

If you have a document open, and if it is a compatible document type, scan puts the
newly collected spectrum into that document, adding it to the existing spectra.

If no document is open, scan opens a new document for you.

Below is a brief description of the types of scanning. For details, see the documentation
that was shipped with your spectrometer.
RAPID SCAN...
Used to collect data for samples that do not vary with time.

RAMAN SCAN...
Used to collect a Raman spectrum. This is disabled unless the Raman software has
been installed.
STEP-SCAN...
Used to collect data from samples which are changed cyclically with time, or where the
entire spectrum must be modulated at the same frequency. These include photoacoustic
and multiple modulation experiments.

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STEP-SCAN MULTI-CHANNEL...
Used to collect data from more than one input source (channel) during one scan. These
channels can be inputs from different detectors, or from one detector, processed in
several different ways. At each retardation position, the spectrometer polls the inputs
and sends the signals to the data processing hardware and software. A common use of
multi-channel spectroscopy is the simultaneous acquisition of both in-phase and
quadrature signals in phase-modulated step-scanning experiments
STEP-SCAN TRS...
Time-resolved spectroscopy (TRS) is the study of fast repetitive events by FT-IR, using
a variety of techniques to alter the sample, typically photolysis or some other dynamic
change. Typically, sets of data are collected at each retardation step. This creates a
two-dimensional array of data. Interferograms can be constructed “across” the spectra
for constant time delays within each step. These interferograms are transformed to
yield time-resolved spectra.
STEP-SCAN FAST TRS
Rapid TRS allows collection at much higher speeds (time resolution). This requires
additional optional electronics to be installed in the PC. Conceptually, it is the same as
step-scan TRS.
STEP-SCAN DSP...
During step scan the spectrometer is not in a continuous scan, but quickly steps to a
requested point, collects data at that point, and steps to the next point. The signal of
interest during Step Scan DSP arises from the cyclical change in optical retardation.
This change and the signal arising from it is called phase modulation. Step Scan DSP is
used to recover (demodlate) the signal of interest from the side bands around the phase
modulation frequency. In Win-IR Pro, Step Scan DSP is implemented primarily for
photoacoustic spectroscopic depth profiling. For details, see your spectrometer manual.
STEP-SCAN DSP(2)...
Used in experiments where, in addition to phase modulation, there is also a low-
frequency modulation of the sample. One example of this is polymer stretching where
it is desired to have spectra for different amounts of stretching.

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 276 Chapter 9 Collect Menu

KINETICS...
Used to collect data from samples that vary with time, but not in a cyclical manner.
Examples are curing, polymerization, drying, etc.
STINGRAY...
Used to collect data with an array detector. This generates image (.dat) files.
SHADOW…
Used to collect data with microscope mapping; this is an optional product. See the
Shadow Pro User’s Manual (091-0991) for details.
DEFINE A SCAN...
Defines a method for collecting a spectrum (and manipulating it) in exactly the same
manner as a previously collected (and manipulated) spectrum. All collection
parameters, the background spectrum, and manipulation parameters are the same.

Note
When this entry is selected, the method is defined.
However, there is no system response nor message
generated to the user. No data collection is done.
Collection is done by one of the selections above.

CO-ADD MORE
Allows you to continue to collect more data and to add it to the existing spectrum. This
is often used when initial investigation of the spectrum reveals insufficent statistics or
signal-to-nose ratio in the intially collected spectrum.
RESET SPECTROMETER
Resets the spectrometer. The specific actions that occur depend upon which
spectrometer it is. See your spectrometer manual for details of Reset.
RAMAN LASER
Allows you to turn the Raman laser on, set a power level, and/or turn the laser off.

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 Chapter 9 Collect Menu 277

TEMPERATURE CONTROLLER
Allows you to set the temperature for GC-IR (gas chromatography-infrared)
experiments. You can monitor the gas cell and transfer line temperatures any selected
interval between 1 and 10 seconds. This interface also allows selection of the
communications port to be used between the PC and the temperature controller.

Note
If there is no temperature controller, or if the
communications line is not properly configured, you will
get this error message.

You can still access the Temperature Controller dialog box,

but you cannot exchange information unless a properly
configured controller is connected.

The Temperature Controller dialog box has two tab pages—Monitor and Settings.

Monitor

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 278 Chapter 9 Collect Menu

Gas Cell Temp: the temperature in the gas cell.

Transfer Line Temp.: the temperature in the transfer line.

Current Set Point: enter the desired equilibrium temperature.

Settings:

Current Port: select the communications port used.

Monitor Update Interval:

how often should the temperature controller send the gas cell and
transfer line temperature measurements to the PC where they can be displayed on the
Monitor page.

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 10
Transforms Menu

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 280 Chapter 10 Transforms Menu

GENERAL CONSIDERATIONS
If you have selected a number of spectra, and then select a transform (for example,
Transmittance), then that transformation will be applied to all the selected spectra.

We recommend that you maximize the document window to fill the space available
when working with these transforms. Use the toolbar maximize button or double-
click in the document window. When you get one of the transform displays, the
spreadsheet is minimized and is not visible, so you do not need to select Maximize
Traces or press the F11 key.

1. In some transforms the sidebar control panel on the right hand side takes up
most of the length of the screen. Maximizing the document window makes
for a full, legible display.

2. In some transforms (such as Baseline Correct) you interact with the trace.
The larger it is, the easier it is to manipulate it.

To maximize traces, either select Maximize Traces from the Window menu or press the
F11 key.

To define a region of the spectrum (this is only required for a few of the transforms)

1. Select Drag Regions from the Operations menu. A check mark (√) appears in
front of Drag Regions if it is selected. Alternatively, press the toggle
button at the bottom of the screen. Region selection is now enabled. A
blank rectangle (the ruler) appears at the bottom of the trace display, just
above the X-axis scale.

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 Chapter 10 Transforms Menu 281

ruler

2. Put the cursor into the ruler at one end of the region to be selected. The
cursor changes to .

3. Hold down the left mouse button and drag the cursor to the other end of the
region being defined. Release the button. The region is defined by the
vertical dashed lines. The white bar at the bottom of the region means that
this region is active and selected.

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4. Repeat this procedure to define additional regions, if desired.

For more details, see Drag Regions in Chapter 11.

ABSORBANCE
Absorbance spectra can be converted from %Transmittance spectra by selecting
Absorbance from the Transforms menu.

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%TRANSMITTANCE
Transmittance is an alternative way of viewing the spectrum. Absorbance spectra can be
converted to %Transmittance spectra by selecting %Transmittance from the Transforms
menu.

Notes
The two traces are related by this formula:
100
Absorbance = log = – log Transmittance
%Transmittance

If the spectrum is an absorbance spectrum, then Absorbance is disabled

(greyed-out); if the spectrum is a % transmittance spectrum, then
%Transmittance is disabled (grayed-out).

Sample file
%Transmittance = x 100
Background file

%Transmittance ranges from 100 (total transmittance) to 0 (no transmittance).

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COMPUTE
Computes a single beam spectrum from an interferogram, performing a series of
functions including a Fourier transform, apodization, and phase correction. Once a
single-beam spectrum is computed, you can ratio it against a background spectrum to
obtain a number of different types of spectra (see Ratio, later in this chapter for details)

Note
When the single-beam computation is performed, it
replaces the interferogram in the display. However, the
interferogram is saved in the document and may be
recalled by using Reprocess... from the Operations menu.

For example consider the interferogram collected for a polystyrene sample.

Select Compute; the Compute dialog box appears.

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General Page
Selecting the Compute operation normally displays the General page of the Compute
dialog box:

If the Compute Advanced page is displayed, press the General tab to return to the General
page.

Apodization Function: Indata collection, the interferogram is sampled over a finite

distance. Information that would be present at a larger distance (greater
retardation) from the centerburst is lost. This causes a distortion in the shape of
narrow lines because the information for these lines was truncated at the limit of
resolution. This is usually only noticeable for gas spectra.

The band shape distortion shows up as negative side lobes at the base of an
absorption peak in the transformed spectrum. These lobes are more pronounced
for peaks with a half bandwidth close to the resolution used in collecting the
spectrum.

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Apodization is a method to control the line shapes; it does cause some decrease
in resolution. When comparing or ratioing spectra, the same apodization must
be used.

Select the type of apodization function to apply to the interferogram. Details are
given in the Algorithms and Functions appendix. The choices are:

Boxcar
Triangle
Happ-Genzel (also called Hamming)
Trapezoid
NB Weak (Norton-Beer weak)
NBMedium (Norton-Beer medium)
NBStrong (Norton-Beer strong)

For normal analytical spectroscopy, NBMedium is the recommended apodization.

Trapezoidal Breakpoint:enter breakpoint if Trapezoid apodization is selected. Trapezoid is

a generalized form of the Boxcar + Triangle apodizations; its breakpoint is illustrated in
the following figure:

0
0 0.5 1

breakpoint

If the breakpoint = 0, the function is triangular; if the breakpoint =1, it is a boxcar.

Zero Filling Factor:

causes the interferogram to be extended with zeros before
computing. It has the effect of interpolating points in the spectrum. Auto is the
recommended operating setting (see below for details).

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Compute requires 2k points in a data array, where k is an integer, to compute the

single-beam from the input interferogram. If necessary, the input data array is
extended with zeros.

Nt the total number of points in the interferogram

Nb the basis number of points in the interferogram; that is, the points in the
centerburst and those after it.
zff is the zero filling factor.

1. If the basis number is not a power of 2, then a value Nd is calculated where

Nd = zff * 2k - Nb (2k is the next power of 2 above Nb).

2. The number of points in the data array is then extended with zeros, so that
there are zff * 2k data points in it. That is, we add

zff * 2k - Nt = Nd + Nb - Nt zeros to the data array.

3. If this number is negative, a message is displayed, requesting that you

increase the zero filling factor (zff)

The effective numerical values for zff are 1, 2, 4, 8, . . . 2k; other values will be
rounded up to one of these, but the software will not report this to you. In cases
where the basis number of points is close to a power of 2, small changes in data
can result in large changes to the final output. For example, if basis number of
points=2047, zff =2 gives 4096 points, while for basis number of points=2049,
zff =2 gives 8192 points. For most purposes, set zff to Auto., which uses 0.8 * Nb
instead of Nb as the basis for the calculation, and computes a zff =2 value from
that number. This means one data point is interpolated between each actually
collected sata point. For example, for a 2 cm-1 spectrum, there will be a data
point displayed at each 1 cm-1 spacing.

Advanced Page

Press the Advanced tab to display the Compute Advanced page:

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Use Standard Processing:

if checked, all parameters are set to the default values and
cannot be changed. To change one or more parameters, de-select Use Standard
Processing.

Output Type: select one or more types of desired output spectra. Each selection is saved
as a separate spectrum in the document. The Fourier Transform produces a complex
result, which has a real and an imaginary part.

Real: if checked, generates and saves the real part of the computed spectrum.
This is the default output type.

Imaginary: if checked, generates and saves the imaginary part of the computed
spectrum.

Magnitude: if checked, generates the magnitude spectrum, which is sometimes

used in multiple modulation experiments.

Magnitude spectrum = (real spectrum) 2 + (imaginary spectrum) 2

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To obtain a phase spectrum, use Operations - Spectral Arithmetic - Binary after

collecting the data.

Phase Parameters: the software automatically corrects for any small phase shifts in the
interferogram, introduced by the spectrometer, by calculating the Fourier transform of a
small portion of the interferogram around the centerburst. This produces a very low
resolution spectrum that represents the instrument phase. Then, this small spectrum is
used to correct the phase of the spectrum. See Appendix D for more information on
phase correction.

Size (Points): enter the total number of points around the centerburst that are
used to calculate the phase correction. Auto, which is the recommended value,
calculates the number of points to be used as follows (the total number of points
is limited to 512, i.e., 29):

Symmetric interferogram: takes 10% of the specified number of points after

the interferogram centerburst and rounds this number up to the next power
of 2. For example, for an symmetric interferogram with 2048 points on
either side of the centerburst, 204.8 of those points (10%) are selected and
rounded up to the next power of 2, which is 256.

Asymmetric interferogram: takes the specified number of points before the

interferogram centerburst; uses the greatest power of 2 that is rounded down
from that number. For example, for an asymmetric interferogram with 550
points before and 2048 points after the centerburst, 550 points before the
interferogram are selected and rounded down to 512.

Apodization: select the apodization function used in calculating the phase

correction. Auto means to use the same apodization function as selected in the
Processing Parameters - Apodization Function.

Phase Correction: select the type of phase correction to be used.

Auto: use standard phase correction, which extracts data symmetrically

around the interferogram peak and computes a phase correction array. This
is the recommended value.

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Store Phase: if checked, generate an Auto phase correction and store the
phase correction array in the file specified by Filename below. This file will
have a .phs extension and can be opened with File Open.

None: do not perform any phase correction. This might be used if you plan
to calculate a power spectrum.

Use Stored: do not compute a phase correction array. Instead, read the phase
correction data from the file specified by Filename below. This might be
used if you collect data that does not have a centerburst, such as in double
modulation experiments.

Filename: the name of either the file into which the phase correction data
is to be stored (Store Phase), or the file from which the phase correction
data will be read (Use Stored).

Browse: this button is enabled if the cursor is clicked in the Filename

box. When Browse is pressed, the standard Windows NT file selection
dialog box appears. Use this to select the appropriate file, either on a
local or a network drive.

Included Frequency: when undersampling is used, the frequency bandwidth is decreased

(frequency aliasing). In some cases this may cause the spectral region of interest to lie
outside the base band (starting at 0). If a number is entered here, the software sets the
lower limit of the bandwidth so that the desired frequency is included in the bandwidth.
Auto selects the base band.

For example, a UDR of 1 gives a free-scanning spectral range of 15,800 cm-1 and is
normally used for the 0-15,800 cm-1 region. With appropriate equipment (source,
beamsplitter, filter, detector, etc.), however, it could be used for the 15,800-31,600 cm-1
region. In this case, Included Frequency would be set to a value such as 20,000 cm-1, so
that the software calculates the x-axis correctly.

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 292 Chapter 10 Transforms Menu

RATIO
Calculates the ratio of two single beam spectra–usually the ratio of a sample spectrum
to a background spectrum.

Note
When the ratioed spectrum is computed, it replaces the
single-beam spectrum in the display. However, the
interferogram is saved in the document and the single-
beam spectrum may be recalculated by using Reprocess...
from the Operations menu..

Consider, for example, the single-beam spectrum below.

When selected the Ratio dialog box appears.

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% Noise Level Ratio: in cases where the background spectrum values are zero, or close to
zero, the result of performing a ratio may have little meaning. To prevent this,
background reference spectrum points whose values are less than the specified value are
not used in the calculation. The most recently calculated value, or 0, is output instead.
The level is specified as a percentage of the maximum height of the background
spectrum. If the default Auto is chosen, the % Noise Level Ratio is taken to be 5%.
To: select the type of spectrum to be calculated; the choices are:
Absorbance: this is the default spectrum calculation. It is equal to
log10 (reference/sample)

Reflectance: this calculation is only meaningful if you are performing a

reflectance experiment.
R = (sample spectrum/reference spectrum)

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% Reflectance: (expressed as a percentage)

100*R

PAS (Photoacoustic spectrum): the calculations are equivalent to the

transmittance function, but the spectrum resembles an absorbance spectrum, in
that the peaks point upwards.
Kubelka Munk: calculated from a reflectance spectrum used in diffuse reflectance
spectroscopy. If R is the reflectance, then the Kubelka-Munk function is
(1.0-R)2/2R

Log 1/Reflectance

log10(1/R)

Raman Relative Intensity: calculates by ratioing against the instrument response.

The x-axis is Raman shifted relative to the excitation wavenumber.

Note
Transmittance is not shown because it is considered to be a
change in the display of Absorbance rather than a
transformation of the spectrum.

Background: use the standard Windows selection technique to pick the background
reference file (spectrum). This file may be located on another disk. If that disk is not
yet connected to your computer, use the Network key to connect it to your computer.
When selected, the background file is shown in the preview window.

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Note
If the document contains multiple spectra, you can scroll
through them to find the background you want.

Current: if selected, this allows you to use a spectrum in the currently selected
document.

OK: calculate the ratio and compute the spectrum type selected above. Replace the
single beam spectrum with this newly calculated ratio.

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Cancel:return to the main menu without calculating a ratio or replacing the single beam
spectrum.

Help: enter the on-line help system.

Network: allows you to connect a remote disk on the network to your computer in order
to access a background spectrum.

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ZAP
Interpolates a straight line within a selected region (or regions) of the spectrum (“zaps”
a spectrum). Zap can be used for a number of reasons including:

• remove spikes in the interferogram from thin films that produce fringing,
• eliminate bands where the background or reference spectrum is totally
absorbing because of detector cutoff or bands in the reference spectrum,
• “remove” strong, interfering bands during spectral subtraction and spectral
search,
• “remove” carbon dioxide and water vapor bands from a spectrum.

First, select Drag Regions from the Operations menu (or press the button). Define
the region(s) to be zapped.

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 298 Chapter 10 Transforms Menu

Select Zap from the Transforms menu; the Zap dialog box appears.

Regions (in Wavenumbers): displays the region(s) of the spectrum that will be zapped.

Region: If you want to alter a region to be zapped, highlight that region in the Regions (in
Wavenumbers) window by clicking on the corresponding line of text; then, type in the
edge values for Left and Right.
Left: left edge of the region to be zapped.
Right: right edge of the region to be zapped.

Then, click the Apply button. The highlighted values will changed to those just entered.

Note
Although you can alter the edge values after the region(s)
been defined interactively, you cannot invoke Zap unless
a region has been defined. Entering new values in Left
and Right does not change the display in the upper
window. If you click on the text line in the upper
window, the original values are restored.

Replace: replace the existing spectrum with the transformed spectrum.

Add: add the transformed spectrum to the document that contains the original spectrum.

Cancel: return to the main menu display without acting upon the original spectrum.

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Help: enter the on-line Help system.

The result is shown below (in this example the transformed spectrum was added to the
document).

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ULTRAZAP
Allows the change of individual data points in the spectrum or interferogram. It is
typically used in interferograms to remove spikes caused by fringing in a sample or to
add spikes for reference in emission or modulation experiments lacking a centerburst.
Before selecting UltraZap, use the spreadsheet to select those traces that you want to
manipulate. When UltraZap is selected, a control panel appears on the right side of this
display. The name of the trace is displayed in the upper left of the screen; if you have
selected a number of traces, this identifies which one you are working on.

We have usd the zoom function to expand the portion of the interferogram to be
manipulated.

Move the cursor to the data point to be changed. When the cursor is on the trace, it
changes to . Hold down the left mouse button. The cursor changes to . Move the

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 Chapter 10 Transforms Menu 301

cursor up or down to drag the data point to its desired new location. Any number of
data points can be moved as often as desired.

Point Value: change a point in the spectrum by entering its new coordinates.

X: enter the horizontal-axis coordinate of the new point.

Y: enter the vertical-axis coordinate of the new point.

Set button: click the button to change the selected point in the spectrum and
display it in the trace.

Clear All Zap Points: return all altered points to their original values.

Replace: replace the existing original spectrum with the altered spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

Add: add the altered spectrum to the document that contains the original spectrum. Both
spectra are now in the main menu display. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

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Note
The interferograms are zoomed to show the region of
interest.

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.

Do All:if selected, then the UltraZap parameters selected for this spectrum are applied to
this spectrum and to all subsequent spectra; they are all either Replaced or Added.
Spectra previously replaced or added are not altered by this.

Help: enter the on-line Help system.

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 Chapter 10 Transforms Menu 303

TRUNCATE
Truncation is generally used to eliminate noisy edges of a spectrum, containing little or
no useful spectral information.

First, select Drag Regions from the Operations menu (or press the button). Define
the region to be retained, not the region to be discarded.

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 304 Chapter 10 Transforms Menu

Select Truncate from the Transforms menu; the Truncate dialog box appears

Region to Be Saved: defines the region of the spectrum that will be retained. If you want
to redefine or refine the region to be retained, type in the edge values for Left and Right.
Left: left edge of the region to be retained.
Right: right edge of the region to be retained.

Note
Although you can alter the edge values after the region
been defined interactively, you cannot invoke Truncate
unless this region has been defined.

Replace: replace the existing spectrum with the truncated spectrum.

Add: add the truncated spectrum to the document that contains the original spectrum.

Cancel: return to the main menu display without acting upon the original spectrum.

Help: enter the on-line Help system.

The result is (in this example, Replace was used):

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 306 Chapter 10 Transforms Menu

SMOOTH
Smoothes the current trace. Spectral smoothing is used to reduce high-frequency noise
and improve the signal-to-noise ratio. There is some decrease in resolution
accompanying this process. The different smoothing functions allow some tradeoffs
between noise reduction and resolution; the optimum choice depends upon the details
of the spectrum itself. The Smooth dialog box appears.

Smoothing Function: select among Boxcar, SG (Savitsky-Golay), and Fourier smoothing

functions.

Boxcar Smoothing
Boxcar: uses the boxcar function; this function is equal to 1 for Number of points about
the point being smoothed and 0 elsewhere. It is a moving average. Boxcar smoothing
gives equal weight to all points within the convolution region defined by Number of
points. Boxcar smoothing has the greatest smoothing and, consequently, the greatest
loss of resolution.

Savitsky-Golay Smoothing
Savitsky-Golay smoothing is a convolution method using a least squares fit of a
polynomial to a moving convolution region of data points1. It then calculates a new
central value in the region based upon the polynomial. Smoothing is controlled by the
degree of the polynomial and the number of smoothing points parameters.

1
Abraham Savitsky and Marcel J. E. Golay, Analytical Chemistry, 36, 1627-1639, 1964.

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 Chapter 10 Transforms Menu 307

Note
The nature of the convolution gives the identical fit for
quadratic and cubic, as well as for quartic and quintic
polynomials.

S-G quad-cubic:requires a minimum of 5 points. Retains more resolution, but

does not smooth the data as much as the quart-quintic.

S-G quart-quintic:
requires a minimum of 7 points; it can cause resolution
degradation for very sharp peaks that are less than 7 points wide.

Number of Points: The boxcar and Savitsky-Golay smoothing processes, at any point use
that point and the same number of points on the X-axis to the right and left of it in the
calculations. Therefore, only an odd number of points can be entered; if an even value
is entered, it is incremented by 1 and that new odd value used. The valid ranges and
meanings are:

Boxcar 3 - 255 boxcar width

Savitsky-Golay quad/cubic
Savitsky-Golay quart/quintic
5-25
7-25
} number of points in the convolution
function

Because the convolution region for N=2k+1 points requires that there be k points on
either side of the center, you will lose k points at the lower and upper end of the
spectrum as an intrinsic feature of the smoothing process. For example, if N=7, then 3
points will be lost at either end of the spectrum.

The larger the number of points used, the more smoothing that will occur and the
greater the loss of resolution. In general, try to fit the number of points in the
convolution region to the spectral data. Do not include more than one inflection point
of the observed data in the convolution region. In practice, this is usually obtained by
setting the number of points in the region equal to the width of the peak at half-height
(and rounding up, if necessary, to the next odd number).

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Fourier Smoothing
2
Fourier: the Fourier smoothing is a multi-step process.

1. Perform a Fourier transform of the spectrum.

2. Apply a truncation filter function to the transformed spectrum. The range is

from 0 (which gives no spectrum) to 1 (which gives the original spectrum).
The default value is 0.2 which gives a good smoothing without significant
loss of resolution. This value is set by the Strength parameter (see below).

3. Perform an inverse Fourier transform.

Strength: the fraction of the transformed spectrum (starting from 0) to be used in the
inverse transform. If this is not equal to 1, then the high frequency noise is reduced.

Note
Fourier smoothing is equivalent to using a smoothing
function whose transform is a boxcar.

Because the real data are discrete, Fourier processing can

sometimes introduce artifacts into the data. These are
usually seen as high-frequency periodic signals imposed
on the smoothed data. Savitsky-Golay smoothing does
not suffer these effects.

The buttons in the dialog box are:

Replace:
smooth trace according to selected method and return to main menu. The
smoothed trace replaces the original trace.

Add: smooth trace according to selected method and return to main menu. The
smoothed trace is added to the document; the original trace is not overwritten.

2
Jyrki K. Kauppinen, Douglas J. Moffatt, Henry H. Mantsch, and David G. Cameron, “Smoothing of
spectral data in the Fourier domain”, Applied Optics, 21, 1866-1872, 1982.

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 Chapter 10 Transforms Menu 309

Cancel: return to the main menu without smoothing the trace.

Help: access the on-line Help facility.

Smoothing Example
Consider the noisy spectrum P0000880.bsp

Zoom in on part of the spectrum to determine the width of the peaks at half height.

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At half height the peak is about 40 cm-1 wide. Because the resolution is 4 cm-1, there
are about 10 points in the peak. Use 9 or 11 as the parameter to smooth the curve. An
alternate method of determining the width is to zoom in on the spectrum and count the
places where the curve breaks.

Using the Savitsky-Golay quart/quintic method with 11 points, the spectrum is smoothed
to look like the plot below.

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DIFFERENTIATE
Differentiates the current trace. The trace must be in absorbance format.

Note
Differentiation can help you distinguish overlapping
bands. Both differentiation and deconvolution can be
used to determine peak positions in complex spectra.
Both techniques generate sidelobes, but their
displacement from the main peak is different for each
method. A useful check on whether a small is a real peak
or a sidelobe is to perform both differentiation and
deconvolution and compare the peak maxima postions.

After selecting this entry, the Differentiate dialog box appears.

Type: the derivative can be approximated by two techniques.

Difference: calculates the nth derivative using the difference method, that is, the
new point at x is (yx+1 - yx-1). The value of n is specified by Derivative Order.

Note
This does not shift the spectrum. The end points are
extended at each order of differentiation by setting y-1 =
y0 and ymax+1 = ymax, and then taking the difference.

Fourier: the steps of the process are

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 Chapter 10 Transforms Menu 313

1. Fourier cosine transform of the spectrum

2. Multiply by 2πxn (n is the derivative order)
3. Apodize with sinc2 function (sinc x = [sin x]/x)
4. Inverse Fourier transform back to a spectrum
The symmetry properties of the cosine transform mean that only even values of
n give correct derivatives; odd values of n do not correspond mathematically to a
derivative spectrum.
Because differentiation amplifies high frequency spectral noise, the apodization
function is used to smooth the spectrum. The amount of smoothing is
controlled by the Pass Band Edge parameter. A value of 1.0 retains the entire
interferogram.

Derivative Order: order of the derivative to be generated (integer). The Fourier algorithm
used requires even integers only for meaningful results. If you need an odd derivative
order, use the Difference method or a combination of Difference and Fourier.

Pass Band Edge: (Fourier only) a smoothing parameter. It determines the fraction of the
cosine transform to be retained. This portion is multiplied by the apodization function
and the other points are set to 0 (range 0.0 to 1.0). The minimum value should be
UDR * Res
ZFF * ν1/2

UDR undersampling ratio

Res resolution
ZFF zero-filling factor
ν1/2 half-height bandwidth of the narrowest spectral line

Replace: differentiate trace according to selected method and return to main menu. The
differentiated trace replaces the original trace.
Add: differentiate trace according to selected method and return to main menu. The
differentiated trace is added to the document; the original trace is not overwritten.
Cancel: return to the main menu without differentiating the trace.
Help: access the on-line Help facility.

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 314 Chapter 10 Transforms Menu

An example of a second order Difference spectrum (we have zoomed into the smaller
region 3200-2900 cm-1 and autoscaled in the Y direction):

The second order derivative of the same spectrum, using Fourier techniques and a Pass
Band Edge of0.5.

The derivative spectra are roughly the same, independent of the method.

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 Chapter 10 Transforms Menu 315

DECONVOLVE
Deconvolution is the enhancement of the apparent resolution of overlapping peaks
where the limiting resolution is the natural width of the bands, not the resolution with
which the spectrum was collected.3 This aids in identifying the principal bands that
comprise a more complex band with overlapping features. This can be useful for more
accurate determination of the number of peaks in a region, the band positions, and areas
under peaks. Individual peaks are assumed to have Lorentzian line shapes. A broad
peak may be described as the convolution of a very sharp peak (a delta function) with a
Lorentzian line shape function. Peak position and area are unchanged, but peak height
is changed. For reliable results, the following conditions should be satisfied.

1. Signal-to-noise ratio should be as high as possible; 100:1 is possible, but

1000:1 is desirable.
2. The spectral limits used to define the spectral region for deconvolution
should include a portion of the baseline so that noise level can be monitored.
The first few data points should not show any curvature.
3. The spectrum must be in the absorbance format. Maximum absorbance
must be one or less.
4. The deconvolution region should be chosen so that the widths of the bands
are all approximately the same.
5. The Bessel function is recommended for apodization; it minimizes the
amount of noise introduced by the deconvolution process.

3
David G. Cameron and Douglas J. Moffatt, “Deconvolution, Derivation, and Smoothing of Spectra
Using Fourier Transforms”, Journal of Testing and Evaluation, 12, No. 2, 78-85, March 1984.
Wang-Jih Yang and Peter R. Griffiths, “Optimization of Parameters for Fourier Self-deconvolution”,
Computer Enhanced Spectroscopy, 1, No. 3, 157-165, 1983.
Jyrki K. Kauppinen, Douglas J. Moffatt, Henry H. Mantsch, and David G. Cameron, “Fourier Self-
Deconvolution: A Method for Resolving Intrinsically Overlapped Bands”, Applied Spectroscopy, 35, No.
3, 271-276, May/June 1981.
Jyrki K. Kauppinen, Douglas J. Moffatt, David G. Cameron, and Henry H. Mantsch, “Noise in Fourier
self-deconvolution”, Applied Optics, 20, No. 10, 1866-1879, May 1981.
Jyrki K. Kauppinen, Douglas J. Moffatt, Henry H. Mantsch, and David G. Cameron, “Fourier
Transforms in the Computation of Self-Deconvoluted and First-Order Derivative Spectra of Overlapped
Band Contours”, Analytical Chemistry, 53, 1454-1457, 1981.

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 316 Chapter 10 Transforms Menu

Note
The maximum effective resolution after deconvolution
cannot be higher than the instrument resolution used to
record the data.

A more detailed discussion of deconvolution is given in Appendix J.

In the document below, we have selected polys.bsp (polystyrene spectrum) and a

smoothed version of polys.bsp with the region between about 1300 and 1100 cm-1
selected using the cursor.

Select Deconvolve from the Transforms menu.

If no region was defined, then the Deconvolution dialog box appears.

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 Chapter 10 Transforms Menu 317

Click Yes to deconvolve the entire spectrum. This does not usually yield optimum
results.

Click No to return to the main menu without performing any transform.

Notes
You will obtain the best results where the linewidths are
similar, and where a small region is selected, as in the
example below.

If you have selected more than one spectrum, the same

region will be used for all these spectra.

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 318 Chapter 10 Transforms Menu

In this example, we have zoomed in on the region of interest. The original spectrum is
in the upper half of the display; the deconvolved spectrum is in the lower half. The
spectrum currently being processed is identified by its name; in this example, it is
Original - polys(10 smooth.

The deconvolution parameters are:

K factor:
the peak width narrowing factor. It determines the width of the
function (0 means zero the spectrum).

Half Width:the width at half-height of the peak shape function. Values range
from 1.0 to 100.0 cm-1.

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 Chapter 10 Transforms Menu 319

HW Increment: the value by which the half-width is changed when the spin box
arrows are used.

Apply button: If you use the spin-box arrows to set the values, then they are
applied immediately to the deconvolved trace. You can also type in the K factor
and Half Width boxes. If you type in values, they are not applied until the Apply
button is pressed. Press the Apply button to tell Win-IR Pro that you have
completed typing values and that these values should be applied to the trace.

Derivative: displays the second derivative spectrum in the upper window.

Apodization:reduces the side lobes appearing around the deconvolved peaks. Bessel is
preferred. See the Algorithms and Function appendix for addition details about the
apodization functions. The choices are:

None
Bessel: minimizes the amount of noise introduced by the deconvolution process.
Sinc2
Triangle2

Replace: replace the existing original spectrum with the altered spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

Add: add the altered spectrum to the document that contains the original spectrum. Both
spectra are now in the main menu display. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

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 320 Chapter 10 Transforms Menu

In this example, the deconvolved spectrum has been added to the spreadsheet. The next
trace (Original - polys(1)) is now displayed in the upper half; the lower half shows the
new deconvolved spectrum, using the existing parameters.
Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.
Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.
Do All:if selected, then the Deconvolution parameters selected for this spectrum are
applied to this spectrum and to all subsequent spectra; they are all either Replaced or
Added. Spectra previously replaced or added are not altered by this.
Help: enter the on-line Help system.

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 Chapter 10 Transforms Menu 321

ADVANCED

Apodize...
This process is not the same as is used to apodize interferograms during computation of
single-beam spectra. It is an alternate method of smoothing spectra. The process is:
1. The original spectrum (shown in the top part of window) is Fourier
transformed to an interferogram (not shown).
2. The interferogram is multiplied by the apodization function (not shown).
3. The apodized interferogram is Fourier transformed to a new, apodized
spectrum (shown in the bottom part of the window).

First select the spectra to be apodized using the spreadsheet; then select Transforms /
Advanced / Apodize. When this entry is selected, the trace display is split in two and a
dialog box appears on the right of the traces.

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 322 Chapter 10 Transforms Menu

The Original trace is in the upper part; the Apodized (or to be apodized) trace is in the
lower part. Set the values in the dialog box.

K factor:
the peak width narrowing factor. It determines the width of the apodized
function (0 means zero the spectrum).

Half Width: the width at half-height of the peak shape function. Values range from 1.0 to
100.0 cm-1.

HW Increment: the value by which the half-width is changed when the spin box arrows
are used.

Apodization: select
the apodization function to be used. The function used depends upon
the actual experiment. Triangle is recommended for general use. If either high
resolution or good quantitative accuracy is necessary, use the NB Weak (Norton-Beer)
function. Use stronger apodization if the spectra have a large spread in the intensity of
the bands, especially if the peak widths are of the order of instrument resolution. The
available functions are:

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 Chapter 10 Transforms Menu 323

Bessel
NB Weak
NB Medium
NB Strong
Happ-Genzel: (sometimes called Hamming)
Triangle

See the Algorithms and Functions appendix for details of the apodization functions.

Selecting a new apodization function immediately applies it with the previously chosen
parameters.

Apply: click this button to apply a newly selected K factor, Half Width, and/or HW
Increment to the spectrum. The result is displayed in the Apodized trace box

Note
Selecting a new apodization function automatically clicks
the Apply button.

At this point, no changes have been made to the original spectrum. Therefore, other
apodizations may be performed until the desired result is obtained.

Replace: replace the existing original spectrum with the altered spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

Add: add the altered spectrum to the document that contains the original spectrum. Both
spectra are now in the main menu display. Go the the next trace spectrum from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.

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 324 Chapter 10 Transforms Menu

Do All:if selected, then the Apodization parameters selected for this spectrum are
applied to this spectrum and to all subsequent spectra; they are all either Replaced or
Added. Spectra previously replaced or added are not altered by this.

Help: enter the on-line Help system.

Filter...
Filtering selectively zeros certain parts of the interferogram before it is transformed into
a spectrum, leaving other parts untouched. With a trapezoidal filter, the sloping parts
can give more realistic band shapes in the filtered spectrum.. Filtering provides
smoothing, fringe removal, and baseline correction. The process is:
1 Compute the cosine transform of an absorbance spectrum. This yields an
interferogram (sometimes called a cepstrum).
2 Multiply the interferogram by a trapezoidal apodization function (the filter–
see below).
3. Compute the cosine transform of the result.
The interferogram is normalized, with a range from 0 to 1. The bandedge (Edge) values
are decimal fractions specifying where the zeroing of the interferogram begins and
ends. The transition bandwidth (TBW) controls the slope for the trapezoidal
apodization.

Very sharp cutoff filters (TBW=0) may cause sidelobes in the filtered spectrum. These
sidelobes are prominent if the bandedge corresponds to a region of the interferogram
with a large amplitude. If the interferogram region has a small amplitude in that region,
then a sharp cutoff has little effect on sidelobes. Widening the transition bandwidth
minimizes the effect of sidelobe occurrence.

The edge(s) and bandwidth values are determined empirically by viewing the
interferogram. Select the region(s) of the interferogram to be zeroed (edge) and how
rapidly the data is to decrease to zero (transition bandwidth).

The filters are shown below.

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 Chapter 10 Transforms Menu 325

Lowpass Filter Edge 2

for spectral smoothing
(removes high-frequency features,
that is, noise)
0 TBW 1

Highpass Filter Edge 1

for baseline correction
(removes low-frequency features,
that is, slopes)
0 TBW 1

Bandpass Filter Edge 1 Edge 2

for spectral smoothing
and baseline correction

0 TBW TBW 1

Notch Filter Edge 1 Edge 2

for fringe removal
(removes spikes)

0 TBW TBW 1

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 326 Chapter 10 Transforms Menu

Consider a spectrum with many fringes, spike.bsp:

First, form the spreadsheet, select all the spectra to be filtered. Then select Transforms /
Advanced / Filter. When Filter is selected, the trace display is split in two and a dialog box
appears on the right of the traces.

Note
This is clearly not the ideal combination of filter type and
parameters for this spectrum.

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 Chapter 10 Transforms Menu 327

The Fast Cosine Transform of Original x Filter interferogram trace is in the upper part; the
Filtered spectrum is in the lower part. Set the values in the dialog box.

Edge 1: the low band edge for Bandpass and Notch filters; the band edge for the Highpass
filter. The default is 0.200.

Edge 2: the high band edge for Bandpass and Notch filters; the band edge for the Lowpass
filter. The default is 0.800.

Transition BW: the bandwidth determining the slope of the side of the trapezoid. Values
range from 0 to 1 (in increments of 0.001); the default is 0.05.

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 328 Chapter 10 Transforms Menu

select the filter type to be used. These filters, and their applications, are
Filter Type:
described above. The available filters are:

Lowpass
Highpass
Bandpass
Notch

Selecting a new filter immediately applies it to the interferogram with the previously
chosen parameters.

Apply: click this button to apply a newly selected parameter to the interferogram.. The
result is displayed in the Filtered trace box

Note
Selecting a new filter automatically clicks the Apply
button.

In this example, select Notch filter, and set the values to zero out the spikes in the
cepstrum.

Edge 1: 0.200

Edge 2: 0.800

Transition BW : 0.050

Click the Apply button; the resulting spectrum is shown below.

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 Chapter 10 Transforms Menu 329

At this point, no changes have been made to the original spectrum. Therefore, other
filters may be selected until the desired result is obtained.

Replace: replace the existing original spectrum with the filered spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

Add: add the filtered spectrum to the document that contains the original spectrum. Both
spectra are now in the main menu display. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

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 330 Chapter 10 Transforms Menu

Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.

Do All:if selected, then the Filter parameters selected for this spectrum are applied to
this spectrum and to all subsequent spectra; they are all either Replaced or Added.
Spectra previously replaced or added are not altered by this.

Help: enter the on-line Help system.

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 Chapter 10 Transforms Menu 331

DEFINE REFERENCE...
Defines the reference spectrum that will be subtracted in spectral subtraction. The
Define Reference dialog box appears.

File Name: type in or use the standard Windows NT procedure to select the pathname of
the file to be used as the reference spectrum. If appropriate, use the preview box on the
right to select the subfile.
OK: load the selected reference and return to main menu
Use Current: choose the currently selected spectrum to be the reference spectrum.
Cancel: return to the main menu without selecting a new reference.
Network: connect to a network disk.
Help: access the on-line Help facility.

Note
Pressing the button makes the currently active
spectrum the reference spectrum.

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 332 Chapter 10 Transforms Menu

SPECTRAL SUBTRACT...
Subtracts the reference spectrum (subtrahend) from the selected spectrum. In this
example, first, open the mixture spectrum, polys.bsp. Spectral subtraction should only
be performed on data in an absorbance-type format.

Select Spectral Subtract... from the Transforms menu, the Spectral Subtract dialog box
appears.

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 Chapter 10 Transforms Menu 333

Reference: the spectrum that is to be subtracted, the subtrahend.

File Name:if the reference file has already been selected, its name appears here.
Otherwise, type in or use the standard Windows NT procedure to select the
pathname of the file to be used as the reference spectrum. If appropriate, use the
preview box on the right to select the subfile. The reference file may have been
previously selected using Transforms / Define Reference... or by using the
button.

Use Current:if selected, the currently active spectrum will be chosen as the
reference spectrum.
Subtraction Factor:the reference spectrum will be multiplied by this number
when it is subtracted from the sample spectrum. The initial default value is
1.000.

OK: load the selected reference, perform the initial subtraction, and go to a split screen
with the subtraction control panel sidebar.
Note
If you click the button, it performs the subtraction
using a Subtraction Factor of 1.000.

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 334 Chapter 10 Transforms Menu

Cancel: return to the main menu without performing a subtraction..

Network: connect to a network disk.

Help: access the on-line Help facility.

In this example, the following screen appears,

Note
You can zoom, scroll, etc., the Y-axis in the display. You
can autoscale windows and traces separately.

Subtraction Factor: the number by which the reference spectrum is multiplied

before it is subtracted from the original spectrum. It initially displays the value
set in the Spectral Subtract dialog box.

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 Chapter 10 Transforms Menu 335

Increment: the amount by which the Subtraction Factor is changed when one of the
arrows to the right of its box is clicked.
Apply button: if you type new values into Subtraction Factor or Increment, click
this button to have them applied to the difference spectrum.
Reset Factor: resets the Subtraction Factor to the original value and the Increment
to 0.100.
Autosubtract:attempts to optimize the subtraction. After it is complete, the
subtraction factor used is displayed in the Subtraction Factor box.
You can use the mouse to drag regions of the Subtraction Result spectrum to the
baseline. These are regions where the spectra are known to be nearly identical in both
the original and reference spectra. First, zoom in on the region between 2000 and 1000
cm-1.

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 336 Chapter 10 Transforms Menu

In the lower window (Subtraction Result), put the cursor on the peak near 1450 cm-1.
Hold down the left mouse button. The cursor changes to –. Drag the peak down to
the baseline. The Subtraction Factor will change as you do this. After dragging and
autoscaling, the spectrum now looks like this.

When you are finished with subtraction, use the control buttons on the control panel
sidebar.

Replace: replace the existing original spectrum with the difference spectrum. Go the the
next trace selected from the spreadsheet; if you were working on the last spectrum,
return to the main menu display.

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 Chapter 10 Transforms Menu 337

Add: add the difference spectrum to the document that contains the original spectrum.
Both spectra are now in the main menu display. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.

Do All: if selected, then the Subtraction parameters selected for this spectrum are applied
to this spectrum and to all subsequent spectra; they are all either Replaced or Added.
Spectra previously replaced or added are not altered by this.

Help: enter the on-line Help system.

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 338 Chapter 10 Transforms Menu

BASELINE CORRECT...
Generates a baseline-corrected spectrum from the selected spectrum. When selected,
the trace display is split in two and the control panel sidebar appears on the right of the
traces. In this example, we have used the difference spectrum polys-polyr (see the
previous section for details).

Note
Use this transform only with absorbance or absorbance-
like (PAS, etc.) spectra for correct operation.

The Original trace is in the upper part; the Corrected (or to be corrected) trace is in the
lower part.

You can zoom in on a part of the spectrum by placing the cursor in the Corrected
spectrum trace area and using the normal zooming procedure. Points are usually added
in flat (feature-free) regions of the spectrum. You can zoom out and autoscale (that is,

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 Chapter 10 Transforms Menu 339

use and ) without affecting the baseline points you have added. After zooming,
press the button to return to baseline correction mode.

Put the cursor in the original spectrum portion of the window; the cursor changes to .
Place the tip of the arrow at the desired location on the Original spectrum and click the
left mouse button. A small white square (shown in black in the picture below) marks
this location. You can move this baseline point by placing the cursor on it, holding
down the left mouse button, and dragging it, and then releasing the mouse button. The
Corrected spectrum is changed and displayed in real time. As you add more points, the
Corrected spectrum changes to reflect them.

Type: select how the selected baseline points are to be connected. This defines the new
baseline.

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 340 Chapter 10 Transforms Menu

Linear:as baseline points are added, they are connected to the adjacent existing
baseline points by straight lines. If no adjacent point exist, a horizontal line is
drawn through the selected baseline point.

Spline:a cubic spline (a smooth curve) is calculated to connect the baseline

points. There must be at least four points in order to fit a cubic curve. If you
choose fewer than four points the Information dialog box appears.

Define at least four points and then choose Spline, if you wish to use that type of
connection.

Force points onto data:if you click the Force button, all existing baseline points will be
moved vertically to the actual value of the Original spectrum. However, additional
points will not be forced to the data unless you click the Force button after defining
them, or if you subsequntly move them.

Delete Point: removes the last point you added.

Delete All Points: removes all points, returning the corrected spectrum to its original
state.

Replace: replace the existing original spectrum with the baseline-corrected spectrum.
Go the the next trace selected from the spreadsheet; if you were working on the last
spectrum, return to the main menu display.

Add: add the baseline-corrected spectrum to the document that contains the original
spectrum. Both spectra are now in the main menu display. Go the the next trace selected
from the spreadsheet; if you were working on the last spectrum, return to the main
menu display.

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 Chapter 10 Transforms Menu 341

Skip:Do not alter the current spectrum. Go the the next trace selected from the
spreadsheet; if you were working on the last spectrum, return to the main menu display.

Cancel:return to the main menu display without acting upon the current spectrum or any
subsequent spectra. Spectra previously replaced or added are not altered by this.

Do All:if selected, then the Deconvolution parameters selected for this spectrum are
applied to this spectrum and to all subsequent spectra; they are all either Replaced or
Added. Spectra previously replaced or added are not altered by this.

Help: enter the on-line Help system.

Baseline Correction Procedure

The usual procedure for correcting a baseline is:

1. Add points with Type=Linear.

2. Click Force points onto data.

3. Set Type=Spline. If the spline correction generates odd behavior of the

baseline, then

4. Add more points, or move existing points.

5. Click Force points onto data.

If the baseline is satisfactory, click the Add button; if not, then continue adding or
moving points.
AUTO SUBTRACT
Automatically calculates an optimized subtraction factor, multiplies the reference
spectrum by this factor, and subtracts it from the active spectrum. This is equivalent to
selecting the Autosubtract button in Spectral Subtract. It also replaces the original
spectrum with the difference spectrum. Before selecting this entry, you can define a
region, or regions, of the spectrum to be used in calculating the optimized subtraction
factor. If no region is selected, the entire spectrum is used for calculation. Selection of
regions are usually based upon visual inspection of the sample and reference spectra.

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 342 Chapter 10 Transforms Menu

The subtraction factor is calculated to minimize the sum of the mean-square differences
between the mean-centered sample spectrum and the mean-centered reference spectrum
in the selected region(s).
MORE TRANSFORMS

Kramers-Krönig [nk]...
Computes the complex index of refraction from a reflectance spectrum, allowing
specular reflectance spectra obtained from dielectric materials to be transformed into
absorbance-like spectra.4

4
George W. Chantry, “The Kramers-Kronig dispersion relations,” pp. 214-230 and Appendix 1, pp. 399-
401, in Long-wave Optics, Volume 1 Principles, Orlando, FL: Academic Press, Inc., 1984. See also the
discussion on Fresnel equations, pp. 230-235, and Appendix 2, pp. 402-405.
R. T. Graf, J. L. Koenig, and H. Ishida, Applied Spectroscopy, 39, 405, 1985.
K. Ohta and H. Ishida, Applied Spectroscopy, 42, 952, 1988.
L. D. Tickanen, M. Tejedor-tejedot, and M. A. Sanderson, Applied Spectroscopy, 46, 1848, 1992.
V. Hopfe, E. H. Korte, P. Klobes, and W. Grahlert, Applied Spectroscopy, 47, 423, 1993.

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 Chapter 10 Transforms Menu 343

Note
The Y-axis of the spectrum should be either in
Reflectance or %Reflectance units to get a meaningful
transformation. If another type of spectrum is used, this
error box appears

Click the OK button to continue.

When selected, the Kramers-Krönig Transform dialog box appears. Choose to calculate
either an n (real part) spectrum or k (imaginary part) spectrum, or both, by selecting the
appropriate box.

k: the spectrum of the imaginary part of the complex index of refraction. This
is a good approximation to the absorbance spectrum of the material.
n: the spectrum of the real part of the complex index of refraction. It is not
usually needed.
OK: the index of refraction spectrum (or spectra) is calculated and added to the
document along with the current trace. During calculation, the Reporting Progress...
status box appears. You can stop the process by pressing the Cancel button.

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 344 Chapter 10 Transforms Menu

Cancel: return to the main menu without performing any calculation.

Help: enter the on-line help facility.
Consider the reflectance spectrum, shiny.bsp,

Create both the n and the k spectra. The k spectrum will be spectrum 1 (labeled as K),
the n spectrum will be spectrum 2 (labeled as N), and the original spectrum will be
spectrum 3. You may want to edit the spreadsheet to more completely identify the
newly created spectra.

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 Chapter 10 Transforms Menu 345

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 346 Chapter 10 Transforms Menu

ATRCorrect...
This transform corrects the relative intensities of a mid-range infrared spectrum
collected using the Attenuated Total Reflectance (ATR) method.5 In an ATR spectrum
the light penetrates into the sample to a depth proportional to wavelength (as well as the
reflection angle, the refractive index of sample, and the refractive index of the ATR
element). Longer wavelengths pass through more of the material and, therefore, are
absorbed more. An ATR spectrum differs from an absorbance spectrum in that
absorbances at low frequencies are proportionally greater than those at higher
frequencies. While other effects exist, in a typical spectrum the largest spectral
pertubation is from the wavelength-dependent variation of the penetration depth. It can
be corrected using this transformation
Acorrected = (Aatr)* (frequency)n
where the correction exponent, n can be any reasonable positive. Typical values range
from 0.5 to 5.0 value (the default is 1.0). The value of n which best corrects real spectra
need not be 1.0; it must be determined empirically. It is usually between 0.5 and 1.5.

Note
An exponent of 1 is always appropriate for ATR; the
depth of penetration is a linear function of wavelength.
Other values of the exponent might be used for spectra
obtained using other techniques, for example, PAS.

Two correction algorithms are available. The first is normally used for qualitative
experiments. The second is used when you are running the same sample with different
crystals and want to compare the results.

When selected, the ATR Correct dialog box appears.

5
Peter R. Griffith and James A. de Haseth, Fourier Transform Infrared Spectrometry, equation 5.2, page
194, John Wiley & Sons, 1986.

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 Chapter 10 Transforms Menu 347

Algorithm 1: used for qualitative experiments.

Correction Exponent: enter the selected value.
Algorithm 2: used for quantitative and comparison measurements.
Crystal Angle of Incidence (degrees): enter the angle being used in your experiment.
Crystal Name: use the pull-down menu to select the crystal.

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 348 Chapter 10 Transforms Menu

If you are using a crystal other than one of those listed, select Special. The dialog box
then allows you to enter its refractive index.

Crystal Refractive Index: this is displayed automatically for the selected type of crystal,
except for Special (see above).

Sample Refractive Index: enter the value for the sample.

For either algorithm:

Replace: the current trace is replaced by the ATR-corrected spectrum.

Add: the ATR-corrected spectrum is added to the document; the current trace is not
overwritten.
Cancel: return to the main menu without performing an ATR correction.
Help: enter the on-line help facility.

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 Chapter 10 Transforms Menu 349

BlackBody...
It is sometimes useful to ratio a spectrum (especially an emission spectrum) against the
theoretical emission spectrum of a blackbody at the same temperature. In order to
guarantee that you can perform arithmetic operations with the original spectrum, it is
used as a template to compute a blackbody spectrum in the same format (resolution,
wavenumber range, etc.). The transform can compute the blackbody spectrum for any
temperature. When selected, the Blackbody dialog box appears.

Temperature (Kelvin): enter the temperature of the sample (in K). Room temperature is
approximately 300 K.

K = °C + 273.15; °C = (°F - 32) * (5/9)

Planck Equation Output: select

the output display. It can either be in units of
Energy/Wavelength (microns) or in units of Energy/Wavelength (cm-1). The discussion
below explains the difference between the two displays.

OK: the new trace is displayed in addition to the original trace.

The Planck blackbody equation for energy per unit wavenumber as a function of
wavenumber and temperature is3

8πhc 2 w 3
E (w, T ) dw = hcw dw
e kT
−1

3
George W. Chantry, “Mathematical theory of black-body radiation,” pp.85-98, in Long-wave Optics,
Volume 1 Principles, Orlando, FL: Academic Press, Inc., 1984.

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 350 Chapter 10 Transforms Menu

h is Planck’s constant (6.6256 x 10-27 erg-seconds)

k is Boltzmann’s constant (1.38054 x 10-16 erg/K)
c is the speed of light (2.997925 x 1010 cm/second)
T is temperature (K)
w is the wavenumber (cm-1)

The equivalent equation for energy per unit wavelength, λ (cm) and temperature is

( ) dλ
5
8πhc 2 1λ
E (λ , T ) dλ = hc
e λkT
−1

multiply the wavelength in cm by 104 to get the wavelength in microns.

E(w,T) and E(λ,T) have their maxima in different parts of the spectrum. The maximum
in E(λ,T) is found by differentiating the core function and setting the derivative to 0.
This yields Wien’s displacement law

λmaxT = 2.8978 x 10-1 cm-K or 2.8978 x 103 microns-K

The wavenumber in the E(λ,T) curve corresponding to λmax is

wmax (cm-1) = 3.451 T

Cancel: return to the main menu without creating a blackbody spectrum.

Help: enter the on-line help facility.

Note
If the spectrum X-axis units are wavenumbers (cm-1),
then the blackbody spectrum will be energy/cm-1. If you
want to display the blackbody spectrum as energy/micron
(or energy/nanometer), select View / X Axis Units / Microns
(or Nanometers).

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 Chapter 10 Transforms Menu 351

Wavenumbers
Display the spectrum using wavenumbers (cm-1) as the unit of the X axis (default). The
spectrum below has wavenumbers for its x-axis unit.

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Microns
Display the spectrum using microns (10-6 meters, more properly micrometers) as the
units of the X axis.

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 Chapter 10 Transforms Menu 353

Nanometers
Display the spectrum using nanometers (10-9 meters) as the units of the X axis.

Notes
The transform is disabled for the existing x-axis units; for
example, if a spectrum is displayed in wavenumbers, the
Transforms / More Transforms / Wavenumbers entry is
disabled.

When spectra are transformed, the mathematical

interpolation causes a small loss of information.
Therefore, transforming a spectrum, and transforming it
back to its original x-axis units does not yield a spectrum
identical to the original one. You can restore the original

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 354 Chapter 10 Transforms Menu

spectrum by using Operations / Reprocess. You can also

save the original spectrum using Operations / Copy
Spectrum (see Chapter 11).

Wavenumbers are inverse lengths, therefore, the spectrum

will not appear the same if Microns or Nanometers are
chosen instead of Wavenumbers. For example, the same
spectrum is displayed below with wavenumbers (left) and
microns (right) as the X-axis units.

The number of points is the same in the transformed and original function. This means
that points tend to cluster around low-values of the wavenumber. If you want to
transform a single-beam spectrum to microns (or nanometers), it is best to truncate it,
removing the points near 0 wavenumbers.

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 11
Operations Menu

In general, operations take spectral data and use them to create, find, or analyze, in
distinction to transforms which actually change the spectrum itself.

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 356 Chapter 11 Operations Menu

NEW
Allows you to define a variety of peaks, of trace labels, and to register custom value
programs.

Peak
When selected, the Create Peak dialog box appears. In this example, a peak called
Abspoly-A was predefined in another document.

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To create a peak with the same parameters as Abspoly-A, select Select Predefined and
click the OK button. This creates a peak with the parameter of Abspoly-A. If you want the
peak to have a different name, enter this in the Name window of the dialog box.

Notes
If more than one peak is predefined, selected the desired
predefined peak from the pull-down menu.

It does not matter whether the predefined peak was a

peak, reference peak, or peak template; it will be defined
as a peak.

If you want to make any modifications to the predefined

peak parameters before creating the peak, click the Edit
Parameters button. This brings up the standard peak
editing dialog box.

You can edit this peak— including changing its name— using the procedures described in
Chapter 2.

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 358 Chapter 11 Operations Menu

Alternatively, you can create a peak that was not predefined. The procedure is:

1. Select Create New.

2. Click the Edit Parameters button. The Edit Peak Properties dialog box
appears.

3. Edit the peak parameters using the tab pages; see Chapter 2 for details. You
will probably want to change the name of the peak also.
Note
The default peak parameters defines a peak in the center
of the spectrum with edges at ~±6.7% and baselines at
~±10% of the total spectrum from the center. These
values are for the full spectrum and are independent of the
portion of the spectrum being displayed.
4. Click the OK button. This returns you to the Create Peak dialog box.
5. Click the OK button. The peak is now defined and can be edited using
standard techniques.

Reference Peak
The operation is exactly the same as for Peak, except that a reference peak is defined. .

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 Chapter 11 Operations Menu 359

Peak Template
The operation is exactly the same as for Peak, except that a peak template is defined.
Note
If the active document is Kinetics, then this entry is called
Functional Group; if the active document is quantitation
calibration, then this entry is called Component; if the
active document is Image, then this entry is called Image
Peak.

Position Label
Inserts a position label (with x- and y-coordinates) at the selected position of the trace.
When selected, the Edit Label Properties dialog box appears.

Set the parameters as discussed in the “Position Label” section of Chapter 1.

Annotation
You can place text annotations on the display ; each annotation can be connected to a
point on the spectrum— for example, a peak, a group of peaks, or some interesting
feature of the spectrum. When selected, the Edit Label Properties dialog box appears.

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 360 Chapter 11 Operations Menu

Set the parameters as discussed in the “Annotation” section of Chapter 1

Comment
You can add comments to the spectrum. When selected the Add Comment to Spectrum
dialog box appears.

Place the cursor in the box and click the left mouse button. You can now type in a
comment. For details see the “Adding Comments” section of Chapter 1.

Chemical Structure
Chemical structure is not implemented at the current release.

Custom Property
You can add custom properties to the trace and spreadsheet. When selected, the Add
Custom Property to Spectrum dialog box appears.

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 Chapter 11 Operations Menu 361

Follow the procedures in the “Adding Custom Properties” section of Chapter 1 to create
new custom properties or to use existing custom properties previously defined.

Custom Value
This entry registers custom value programs so that they can be executed within Win-IR
Pro on an opened image (.dat) document. The program calculates a value for each
spectrum in the array— such as spectrum area, highest peak, etc. This output can be
displayed on the screen. See Appendix N for details of constructing such programs and
assigning them a Program ID (ProgID).
When selected, the Enter a Custom Value’s Program ID dialog box appears.

Enter the Program ID that was defined in creating the program; click the Add button.
This program is added to the list that appears in the Feature pull-down menu on the
image document main window (see “Image Document Window” in Chapter 3 for more
details).

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Note
The Program ID is defined within the program; it is
entered into the registry when the DLL is created. It is
not the program file name.

Optional Argument: you may have written your program to use an optional argument (or
arguments). If this is the case, enter those arguments here. This entry will be passed to
the program as a character string. Your program must be written to analyze this string
and make use of the information (see Appendix N for more information).

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 Chapter 11 Operations Menu 363

DRAG REGIONS
Toggles the regions ruler on and off. Use this region to interactively select regions of the
trace. Some of the selections in the Transforms menu work on a region of the spectrum,
rather than the whole spectrum. When this entry is selected, a blank rectangle (the ruler)
appears at the bottom of the trace display, just above the X-axis scale.

ruler

Multiple regions can be defined for any spectrum. To define a region by dragging:
1. Put the cursor into the ruler at one end of the region to be selected. The
cursor changes to .

2. Hold down the left mouse button and drag the cursor to the other end of the
region being defined. Release the button. The region is defined by the
vertical dashed lines. The white bar at the bottom of the region means that
this region is active and selected.

See the “Regions” section in Chapter 1 for details of modifying and deleting regions.

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 364 Chapter 11 Operations Menu

QUANTITATIVE ANALYSIS
Perform a quantitative analysis on the spectrum.

Simple quantitative analysis is available as a standard part of Win-IR Pro.

In order to perform quantitative analysis on a spectrum, you must already have

generated a Quantitation Calibration Document. This document contains spectra of
components of known concentrations, the concentrations, and a least-squares fit of the
concentrations to the spectral data. The procedure following in this chapter assumes
that such a calibration document exists. See Chapter 3 for an explanation of the
Quantitation Calibration Document. A detailed discussion of the theory and practice of
quantitative analysis is in Appendix I.

Note
Before performing quantitative analysis, select View /
Display Limits, and set all entries to Auto. Autoscaling can
be enabled by putting the cursor in the radar box and
clicking the left mouse button.

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 Chapter 11 Operations Menu 365

Simple
First, open the calibration document.

Then, before performing a quantitative analysis, make sure that the calibration document
is ready.

1. Select Open from the File menu.

2. Set List Files of Type to Quant (*.bsq). This lists all files with a .bsq extension.

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 366 Chapter 11 Operations Menu

3. For this example, select Sugar2.bsq and open it.

4. The Include in Quant Analysis column is in the spreadsheet; its cell values are
set to Yes. If you do not want to use a spectrum for the quantitative analysis,
double-click in its Include in Quant Analysis cell. This will change the value
from Yes to No. Double-click a No entry, if you wish to change it to Yes.

Note
If you delete the Include in Quant Analysis column (for
example, by using View / Remove Column), you can
redisplay it using View / Property Browse Bar.

5. Select all the spectra in the document. Zoom in on the region where the
spectra differ (in this example, about 1500-850 cm-1).

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6. Place the cursor on the component to be used for the calibration and click
the right mouse button. Select New / Component. The Component Name
dialog box appears.

7. In this example, highlight the entry, and type CompSugar to replace

Component1. Click the OK button.

Notes

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 368 Chapter 11 Operations Menu

Alternatively, select Operations / New /Component to use a

predefined component. See Chapter 11 for details.

You can edit and/or save any component in your

quantitation calibration document for use in other
documents, with the right mouse button’s menu entry
Save As Predefined. See Chapter 2 for for details.

When a component is selected using the right mouse

button, the calibration will be based upon the default
setting, that is, upon the area of the selected component.
Other data that can be used to perform the calibration area
peak height, ratio of peak areas, or ratio of peak heights.
In the case of the latter two, you must also define a
reference peak against which the ratios can be performed.

A new column CompSugar has been added to the spreadsheet. The

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 Chapter 11 Operations Menu 369

calibration curve (right half of screen) is flat because there is no

concentration entered in the cells (this is equivalent to a value of 0).

9. Enter the known values of the sugar concentration. In this example, they are
15, 10, 5, and 0. The calibration curve changes as shown below.

The default calibration curve is linear with a non-zero intercept (ax + b). The
correlation coefficient (R2) is shown in the upper left corner of the calibration
curve window.
10. Select Save from the File menu.
The Quant Calibration document is now ready. Before you begin analysis, you should
examine the calibration curve to see if any of the values vary significantly from the
curve. If you want to use a calibration curve other than the default or view the
coefficients of the calibration curve, follow this procedure.
1. Place the cursor in the calibration (right hand) side of the window.

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 370 Chapter 11 Operations Menu

2. Click the right mouse button and select Properties from the menu. The Edit
Property dialog box appears.

Curve Specifications: select the equation for the curve that is to be fitted to
the data points. The Apply button is enabled; click the Apply button for a new
calibration curve. The coefficients of the equation will change and be
displayed in a, b, c.

Regress When Changed: if selected, the equation coefficients will change if

the curve type is changed and Apply is clicked. The Correlation Coefficient will
be displayed with the calibration curve.

Calculate Predictions Now: when selected, his creates a new column in the
spreadsheet; CompSugar (Predicted) in this example shown below. These are
the concentration values calculated from the calibration curve for the
absorbance values in the standards spectra. Note that, as expected, they are
close to the nominal values.

Correlation Coefficient: displays the calculated correlation coefficient.

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 Chapter 11 Operations Menu 371

New column with predicted values

Notes
If you remove the column with concentrations, it does not
affect the calibration for that component; the spreadsheet
is displaying (or not displaying) the concentration
information. Use View / Property Browse Bar to re-display
the concentrations column.

After you have created a calibration curve, you can print it. The title of the plot, the
equation used, the value of the coefficients, and the correlation coefficient are printed in
the upper left corner of the plot.

1. Put the cursor in the Quant Validation Plot portion of the window and click the
left mouse button.

2. Click the button or select Print from the File menu and click OK.

3. Close the file by selecting File / Close.

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 372 Chapter 11 Operations Menu

Quantitative Analysis: You can now begin analysis.

1. Select Open from the File menu and select the spectra to be analyzed. In this
example, use drinks.bsp.

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 Chapter 11 Operations Menu 373

Note
For illustrative purposes, History has been added to the
spreadsheet. See Property Browse Bar in Chapter 8, if you
wish to do this.

2. Select the spectra to be analyzed. In this case, select both spectra.

3. Select Quantitative Analysis / Simple from the Operations menu. The

Quantitative Analysis dialog box appears.

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 374 Chapter 11 Operations Menu

4. Select the desired Quant Calibration document using the standard Windows
NT procedures. Use sugar2.bsq for this example. This performs the analysis.
The results are entered into the spreadsheet.

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 Chapter 11 Operations Menu 375

The history of both of the analyzed spectra has been incremented by 1. Select one
spectrum; then select History from the View menu.

This tells you what calibration document was used to analyze the spectrum.

If you wish to save the document under its current name

4. Select Save from the File menu.

5. Select Close from the File menu.

You can save the document with a new name by selecting Save As... from the File menu.

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 376 Chapter 11 Operations Menu

SEARCH...
Searches the libraries to try to find a match for the selected spectrum. After the search
is completed a hit list is displayed showing libraries entries with the best matches.

Normally, only absorbance (or absorbance-like) spectra are searched for in the libraries,
because most commercial libraries have their entries in that format. If you select a
spectrum of a type other than an absorbance the Operations / Search entry is disabled.
However, if you need to search libraries for a non-absorbance spectrum, this entry can
be enabled using Options / Search (see Chapter 12 for details).

Note
If you manually terminate a search before its conclusion
(by pressing the Cancel button), a hit list will be displayed
showing the matches already found. However, this list is
incomplete and using it to identify the sample spectrum
may lead to errors and misassignments.

Search Considerations
There are several types of searches: spectral, names, peaks, and-if you have loaded
advanced search-structures. Each type of search compares a feature, or features, of the
unknown spectrum, to the corresponding feature of the spectra in the selected library, or
libraries. In some searches (spectral, peaks), a “goodness-of-fit” parameter (the Hit
Quality Index, or HQI) is calculated showing how closely the unknown matches the
library spectrum. A specified number of the best matches are retained. In other
searches (name, structures), the test is pass/fail; either the library spectrum entry
contains the specified name (or structure) or it doesn’t. Because HQI is always 0.0 for a
successful pass/fail search, the matches are not listed in any particular order.

When a spectral or peaks search is performed, the HQI must be calculated for each
spectrum in the library. This current HQI is compared to the worst HQI in the list; if the
current spectrum’s HQI is as good as, or better than, the worst HQI in the list, the
current spectrum is added to the hit list in the proper place. This comparison and
insertion takes time. The hit list is kept in memory in a format similar to a .bsp file. A
large hit list can consume considerable memory and can possibly cause the computer to
run out of memory. Typically, you need to keep only 30-40 hits for a spectral or peaks
search hit list.

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 Chapter 11 Operations Menu 377

You can speed searching by pre-searching the libraries with names or structures
searches, followed by a re-search (discussed later in this section). These pre-searches
make use of additional information you have about the unknown. For example, if you
know that the unknown contains chlorine, there is no need to spend time calculating
HQIs for spectra that are known not to contain chlorine. If you know a particular
molecular structure exists in your unknown, you want to perform a spectral or peaks
search only on those spectra containing that structure. You normally keep all hits in a
pre-search because they all have the same HQI.
Note
All libraries supplied by Bio-Rad contain names; not all
contain structures. The Search Library Selection box (see
below) contains a list of what type of information is stored
in each library.
After a pre-search hit list is created, you can re-search this list, as if it were a library.
This is normally done using a spectral or peaks search. Details of these procedures are
discussed later in this section.

Searching
When Operations / Search is selected, the search control sidebar appears.

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 378 Chapter 11 Operations Menu

Details of the control sidebar are shown below.

select type of Note
search to be The Structures search tab
performed page will not appear unless
you have purchased the
Advanced Search product
and run the enabling floppy
the remainder of
the tab page for
each search
allows you to set
parameters
specific to that
type of search

these features are

common to all searches

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 Chapter 11 Operations Menu 379

Spectral Search
A spectral search compares the spectrum to spectra in the selected libraries. A
goodness-of-fit is calculated for each spectrum in the libraries and the best hits are
displayed in a hit list.

Algorithm: the method by which the library entries are compared to the sample spectrum.
The recommended algorithm is Euclidean with baseline correction selected. The
correlation and two derivative algorithms effectively do a baseline correction and might
be useful if there is a slowly varying, non-linear baseline. Mathematical details of the
algorithms are shown in Appendix D.

Baseline correct?: if selected, a two-point baseline correction is performed on the

unknown spectrum before the libraries are searched. It should be selected if you are
using the Euclidean algorithm.

Search mask: Search masks remove interferences from sample spectra by ignoring
certain spectral regions during the search. Some of these interferences arise from
materials commonly used to prepare the sample (for example, nujol mull). Other
interferences may come from small amounts of water vapor or carbon dioxide which are
present in many spectra unless care is taken to desiccate and/or purge the spectrometer.

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 380 Chapter 11 Operations Menu

You can define any region, or number of regions, to be masked in the spectrum. Draw in
the regions to be masked (see “Defining a Region” in Chapter 1). A number of standard
masks, corresponding to common sources of interference, may also be selected from the
Search mask pop up menu; these are listed in the table below. Masks are additive

MASK NAME SPECTRAL REGIONS IGNORED (CM-1)

Water vapor 3900-3500 and 2000-1280
Carbon dioxide 2450-2250 and 700-650
Nujol mull 3100-2700, 1500-1420, 1390-1360, and 740-710
Fluorolube 1350-0
Carbon tetrachloride 820-720
Carbon disulfide 1650-1420

You can delete any defined region in the usual manner (see Drag Regions, earlier in this
chapter for details).

Clear mask: deletes all masks defined for this spectrum.

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 Chapter 11 Operations Menu 381

Name Search
Among other uses, name searches can locate spectra in a library for use as a reference
spectrum. All libraries have Names in the Includes list (see below).

Enter a single text string. If there are spaces in the string, the string should be enclosed
in either single (') or double (") quotes. If one type of quote appears in the text string,
use the other type as a delimiter.

The test is a pass/fail one. If there is a match, the library entry is returned with a Hit
Quality Index of 0.00, otherwise it is not returned. Because every entry in the hit list
from a names search is a perfect match. there is no ranking of the matches.

Peaks Search
Searches for the peaks you have selected in the unknown spectrum. You must have
selected at least one peak for this search to be performed. The libraries to be searched
must have Peaks in the Includes list (see below); otherwise, the Search and Re-search
buttons will be disabled. A goodness-of-fit is calculated for each spectrum in the libraries
and the best hits are displayed in a hit list.

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 382 Chapter 11 Operations Menu

If the peaks have not already been selected, you may select them by clicking the Pick
Peaks button. This is equivalent to selecting Operations / Peak Pick, described later in this
chapter. You could also pick individual peaks using the right mouse button, as described
in Chapter 2.

Before comparing the unknown (sample) spectrum to the library spectrum, each
spectrum is independently normalized so that its largest peak has a y-value of 1.
Maximum error in position: this value is in wavenumbers. If the position of the peak in the
library spectrum differs by more than this value from the position of the peak in the
sample spectrum, this peak is rejected. If the two peaks are closer together than this
value, this peak is accepted.
Maximum error in height: If the normalized height of the peak in the library spectrum
differs by more than this value from the normalized height of the peak in the sample
spectrum, this peak is rejected. If the two peaks are closer together than this value, this
peak is accepted.
A hit quality index (HQI)is calculated for each picked peak in the sample spectrum. The
closer the sample peak is to the library peak in wavenumber and normalized height, the
better the HQI will be. After each peak is compared, an overall HQI is calculated for
the match between the sample spectrum and the library spectrum.

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Structures Search (Optional)

Allows you to build partial molecular structures and search libraries for matches. The
libraries to be searched must have Structures in the Includes list (see below); otherwise,
the Search and Re-search buttons will be disabled. You cannot perform a structures re-
search on a hit list created by any of the searches.

In this case (the most common), the sample spectrum has no structure associated with it
in the document, so the message No structure is displayed. If you have installed
Advanced Search, you can click the Create search structure button and build a structure.
Details of building a molecular structure are in the Win-IR Pro Advanced Search
Manual(091-0985). After you create the structure and return to Win-IR Pro, this
structure is displayed, replacing the message No structure.

Common Search Features

This describes the lower half of the search control sidebar. These features are common
to all searches.

Hits to keep: when the unknown spectrum is compared to a library entry, a “goodness of
fit” called the Hit Quality Index is calculated measuring how much the sample spectrum
varies from the library entry. A perfect match is 0.0, indicating that if the spectra were

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subtracted there would be no residual. Search saves the best hits up to the number
entered in this box. Typically, in a spectral search, only 30-40 hits are required. In a
pre-search, such as a names search, where the test is pass/fail, the search process
terminates when the specified number of hits is achieved. If this number is too small,
there is the possibility of erroneously excluding possible spectra that would be found
later in the pre-search.

Keep all: if checked, all hits will be saved. If you are using Name Search, once Number of
hits to keep has been reached, no further hits will be saved. It is advisable to check Keep
all in this case. However, if you are not using Name Search, it is not advisable to check
Keep all, especially if you are searching a library with many entries. It will take a very
long time and occupy a significant amount of disk space.

Libraries to search: a list of the libraries that are to be searched. Libraries can be added to
or removed from this list by clicking Edit List. The line below the box entries will be
searched displays the number of library entries that will be checked for the type of search
you have selected. In the example below, the polymers libraries have structures, but the
Canadian forensics library does not. If a spectral search is selected, 5647 entries from
the three libraries will be searched. However, if a structures search is selected, only the
first two libraries will be search (2349 entries). If 0 entries are indicated, the libraries
you have selected cannot be used for the type of search you want to use.

Spectral Search Structures Search

Note
All libraries have Spectra and Names; not all libraries have
Peaks and Structures. See Edit list below to see what
information is stored in each library.

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Edit list: clicking this button makes the Search Library Selection dialog box appear.

Note
The list above is an illustrative example. Your library list
may differ depending upon what libraries you have
purchased or built.

Each line is a library that can be searched. Highlight (click once) a library to get
information about it. For example, Bio-Rad demo lib

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Sadtler collection
code (if an SRL
library)

Information
stored with each
library entry:
Names
Peaks
Spectra
Structures

Amount of
storage allocated
for each y value
of the library;
usually 1 byte is
sufficient
Copyright notice Library encrypted or
not encrypted
Pathname of library
Resolution at which library entries are stored
Overall library contents
Library owner:
Library format: Bio-Rad/Galactic User
Bio-Rad
Other Commercial
Spectral range of library entries

Number of spectra in the library

Library name
This information can help you to decide whether or not you want to search this
library.

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if this is selected, the

Mark inaccessible libraries with ‘NA’and include them in the list:
libraries which have been loaded but cannot be accessed are displayed in the list.
These libraries cannot be accessed either because the setup program on the
enabling floppy has not been executed, or because the enabling floppy was not
configured for your system’s dongle. Win-IR Pro Accessibility is not changed by
selecting this check box; selecting this check box only displays non-accessible
libraries.

Note
The only way to change “not accessible” libraries to
“accessible” libraries is to obtain the appropriate enabling
floppy from Bio-Rad.

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You can highlight (single-click) an inaccessible library to view information about

it, but you cannot select it for search (double-click).

To select a library for search, double click the line. An X appears to the left of
the library name. You can toggle libraries on and off as often as you want.

Two libraries have been selected in this example. When you select a library in the
Search Library Selection dialog box, it immediately appears in the Libraries to
search: window on the control panel sidebar. When you de-select a library in the
Search Library Selection dialog box, it immediately disappears from the Libraries to
search: window on the control panel sidebar.

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Libraries selected here

Appear immediately here

Select All: selects all libraries listed to be searched.

Deselect All: resets the list so that no libraries are selected to be searched.

Library Path: when clicked the Search Library Path dialog box appears. This
allows you to select those library directories whose contents will appear
in the list of Search libraries. You can also use this dialog box to define
existing directories to be library search directories, that is, directories in
which libraries are stored, and which can be accessed through the Search
Library Selection dialog box.

There are two classes of library— some are common to all users, while
some are specific to an individual user. The differences are not intrinsic
to the library, but are based upon the licenses purchased.

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The libraries listed in the Search Library Selection dialog box are located
in C:\Search libraries, as shown above; this is the default directory for
libraries. If you want to designate an additional directory as a search
library directory (A directory where libraries are, or will be, stored),
click in the dialog box and type in its full pathname. You must include
the drive; no blanks are permitted in the pathname. You can also use
Browse (see below) to look through the file system to add library
pathnames.

Browse: allows you to add the directories from which libraries will be
presented in the Search Library Selection dialog box. That is, you will be
able to search these libraries. If Browse is clicked, it brings up a
standard Windows NT file search dialog box called Open. Use standard
Windows NT techniques to select those search library directory paths to
be added to the search list. To select a directory, you must select one of
the libraries in the directory. It does not matter which library is chosen.
The buttons have their usual meanings.

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Any library file

name must
appear here.
This causes the
directory to be
selected

In this example, we have used the Network button to connect to another

system on the network to access more libraries.

Open: return to the Search Library Selection dialog box with the additional
set of library paths to be searched. The names of all libraries in the
selected directory are placed in the Search Library Selection dialog box.

Cancel: return to the Search Library Selection dialog box without changing
the set of search libraries, if any.

The path of the new set of libraries is displayed. Click OK to return to

the Search Library Selection dialog box.

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Note
To remove a set of libraries from the Search Library
Selection dialog box, go to the Search Library Path dialog
box (above), highlight the library path, and press DELETE.

In this example, you did not have rights to the libraries in the selected
directory. You cannot select any of these libraries to be searched. If you
try to select one of these libraries you get this message:

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Click OK to return to the Search Library Selection dialog box.

Done: return to the search control sidebar with the newly selected list of libraries
to be searched.

Help: enter the on-line Help system.

Search: begins the specified type of search, using the selected libraries in the Libraries to
search box.

You can always search the libraries using an absorbance spectrum. If you want to search
using other types of spectra, use Options / Search (see Chapter 12) to choose which ones
can be used. If you attempt to search using a type of spectrum that is neither absorbance
nor one selected with Options / Search, the following dialog box appears.

Click Yes to allow a search to be performed Click No to

cancel the search.

When the search is completed, a hit list is displayed. The sample is at the top of the
spreadsheet, separated from the possible matches, which are arranged with best matches
at the top.

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Re-search: A search must be performed before performing a re-search. If re-search is

selected, then another search is performed using the existing hit list as the search library.
Usually, you would first perform a name search or a peaks search using a number of
libraries, followed by a spectral search.

Note
Normally, you first perform a names (or structures)
search, followed by a spectral or peaks search.

The procedure is:

1. Perform a name search, for example, using Keep All. Select all the libraries
that might have the spectrum you are looking for. This will produce a hit
list. This procedure may take a long time, because a large hit list could be
generated.

2. Select the Spectral search tab page and set the parameters. Change Hits to
keep to a reasonable number, typically in the range of 10 to 30.

3. Click the Re-search button. The spectral search will now use the existing hit
list as its search library. The new hit list, a subset of the name search hit list is
displayed.

Done: close the search control sidebar without performing any more searches.

Help: enters the on-line help system.

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Example of Spectral Search

The spectrum antifreeze.bsp is used for this example. Two libraries: Bio-Rad demo lib and
Bio-Rad tutorial lib will be searched. After the search is completed, the Search Hits view
screen appears. (The spreadsheet cells have been resized manually to shown their
contents clearly.)

The original spectrum is displayed at the top of the spreadsheet. It is separated from the
library entries by the column labels. This trace is always displayed. If a library entry is
displayed also (see below), the unknown will be in a color other than green.
The library entries are ordered best hit first. The left most column shows the HQI, the
library name, and the library entry number. The name of the library entry, its spectrum,
copyright date, chemical structure, and whatever other properties you have chosen for
the columns (if these properties are stored in the library) are displayed. If you add a
column, that property will automatically be added for all the library entries (if that

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property was stored in the library). Select a library entry by clicking in its row; its
spectrum will be shown in green in the trace display above. All standard spreadsheet
selection procedures (see Chapter 4) work in the hit list view.

Example of Name Search

We will search the Bio-Rad tutorial library to see if it contains the spectrum of octane.
After the name search is completed, the Search Hits view appears. (The spreadsheet
cells have been resized manually to show their contents clearly.)

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Example of Peaks Search

We will search the Bio-Rad basic polymers libraries (volumes 1 and 2). After the search
is completed, the Search Hits view appears. (The spreadsheet cells have been manually
resized to show their contents clearly.)

Interpreting the Hit Quality Index (HQI)

The HQI is a measure of the similarity between an unknown spectrum and a library
spectrum. A HQI of 0.0 means the two spectra are identical; a higher HQI indicates an
increasing amount of difference, that is, less of a match.
Typically, a HQI below 0.30 indicates an acceptable match between the unknown and the
library entry. A HQI below 0.15 indicates nearly identical spectra. Since the largest
possible HQI is 2.00, a HQI on the order of 1.00 indicates a bad match. A HQI above 0.60
suggests the search was unsuccessful.

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Another indicator of a reliable identification is the size of the gap between the first and
second hits. If that gap is small and the first and second hits are different substances,
then the identification is likely to be questionable. Spectral search generally cannot
unambiguously identify noisy spectra, spectra of mixtures, and spectra of higher
members of homologous series (such as the n-alkanes).
The pattern among the lowest several HQIs is more signficant than the value of the single
lowest HQI. When looking at the HQIs of the best several hits in the search, a good
search is typified by one of two patterns.
The first pattern has the HQI of the best hit around 0.30 or lower and a gap of perhaps
0.20 between it and the next best hit. The second hit and worse hits are clustered
together. For example, a pattern of 0.23; 0.41; 0.43; 0.44 indicates a strong likelihood of
a good identification. This pattern also indicates a likelihood of success if the HQI values
are higher. For example, best hits HQIs of 0.53; 0.75; 0.77; 0.78 might indicate a good
search if an examination of the unknown spectrum shows that it is noisy.
The second pattern has all the best hits clustered together, with very low HQIs. For
example, the best hits HQI's are: 0.11; 0.12; 0.12; 0.14; 0.15. This is a typical pattern for
a library containing a large number of very similar spectra such as long-chain
hydrocarbons. For example, the IR spectra between 3-methyl nonane and 3-methyl
decane are so nearly identical that no significant distinction exists between the HQIs
resulting from a search. Such a search would fail to produce unambiguous results. This
sort of pattern provides a very good indication of the class of compounds and, usually,
of the range of chain lengths, but other techniques (such as chromatography) must be
used to identify the specific compound.
In any event, you should always display and plot the spectra. Visual inspection and
comparison of the search results with the unknown spectrum is always an important
identification measure. Use ZOOM to examine in detail parts of the comparison spectra
for the harder to identify compounds. For example, a very noisy spectrum will have a
substantially raised HQI, but may still provide useful identification.

Subtracting Known Components

Very few samples will be purely one component, although, in some cases, one
component will dominate. Once this component is identified, it can be subtracted from
the sample spectrum and the remainder searched for additional components. The
procedure is outlined below.

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1. Perform search on the sample spectrum.

2. Select (highlight) the library spectrum in the Hit List that is to be subtracted.

3. Press the button. This defines the library spectrum to be the reference
spectrum.
4. Close the Search Hit List. This returns you to the original document with
the sample spectrum.

5. Press the button. This subtracts the reference spectrum from the sample
spectrum. Follow the procedures under Spectral Subtraction in Chapter 10.
6. After the subtraction is satisfactory, press the Add button on the control
panel sidebar; do not press Replace— that will delete your original sample
spectrum.
7. Perform search on the difference spectrum.
8. You can repeat this process as long as you get meaningful results.

Batch Search
You can search more than one spectrum at a time against the selected libraries. One
after another, the selected spectra are compared against the entries in the libraries. Each
search is of the same type (spectral, name, peaks, or structures) and the same libraries
are searched. After all searches are completed, a Hit List column is added to the
spreadsheet. It contains the number of hits retained by the search; spectra that were not
searched for show 0 for the number of hits. The view the hit list for a spectrum, put the
cursor in the Hit List cell of that spectrum and double click. The hit list appears.

In the following example, we use the spectrum kinetics.kin. The spreadsheet is made
visible by selecting View / Spreadsheet. Spectrum1, Spectrum3, and Spectrum5 have been
selected to be searched for, as seen below.

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1. Select the spectra to be searched for. Here, Spectrum1, Spectrum3, and

Spectrum5 have been selected.

2. Select Operations / Search. The Search control panel sidebar appears.

3. Select the type of search, parameters and the libraries to be searched exactly
the same as if you were searching for one spectrum. This is discussed earlier
in the Search section of this chapter.

4. Click the Search button. The libraries will be searched for all selected
spectra.

5. After the searches are completed, a Hit List column will automatically be
added to the spreadsheet. The cell contents will indicate how many hits were

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 Chapter 11 Operations Menu 401

retained for that spectrum. This value is 0 for spectra that were not selected
to be searched for.

6. Click Done to remove the Search control panel sidebar.

7. To view the hit list for a spectrum, double-click on its cell in the Hit List
column. The hit list for that spectrum appears.

Note
If you double-click in a cell with 0 hits, nothing will
happen.

8. For example, double-click in the Hit List cell for Spectrum3

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The spreadsheet cell sizes have been manually adjusted (see Chapter 4 for
details) to better show their contents.

9. Select File / Close to close the hit list. Use the Window menu to return to the
main view if you do not want to close the hit list.

10. Spectral subtractions, etc. can be performed exactly as if only one spectrum
was searched for.

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 Chapter 11 Operations Menu 403

2D-IR

From In Phase/Quadrature Spectra...

The theory and some examples of the 2D-IR technique have been described in the
literature1. Briefly, external perturbations induce a fluctuation of the IR spectrum. Two

1
Isao Noda, “Two-Dimensional Infrared Spectroscopy”, Journal of the American Chemical Society,
111, 8116-8118, 1989.
Isao Noda, “Two-Dimensional Infrared (2D IR) Spectroscopy: Theory and Applications”, Applied
Spectroscopy, 44, No.4, 550-561, 1990.
Richard A. Palmer, Christopher J. Manning, James L. Chao, Isao Noda, Anthony E. Dowrey, and
Curtis Marcott, “Application of Step-Scan Interferometry to Two-Dimensional Fourier Transform
Infrared (2D FT-IR) Correlation Spectroscopy”, Applied Spectroscopy, 45, No. 1, 12-17, 1991.
I. Noda, A. E. Dowrey, and C. Marcott, “Recent Developments in Two-Dimensional Infrared (2D IR)
Correlation Spectroscopy”, Applied Spectroscopy, 47, No. 9, 1317-1323, 1993.
I. Noda, “Generalized Two-Dimensional Correlation Method Applicable to Infrared, Raman, and
Other Types of Spectroscopy”, Applied Spectroscopy, 47, No. 9, 1329-1336, 1993.
Boiana O. Budevska, Christopher J. Manning, and Peter R. Griffiths, “Comparison of Two-
Dimensional Power and Phase Spectra generated from Sample Modulation Step-Scan FT-IR
Experiments, Appl. Spec. 48, 1556-1558 (1994).

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independent spectra are correlated to produce a 2D spectrum. These 2D spectra are

particularly useful in studying the interactions between functional groups.2
Before this is chosen, an in-phase spectrum and a quadrature spectrum should be
selected; this example uses the stretch.bsp multi-spectrum document. The Create 2D-IR
Spectrum dialog box appears.

In this case, the In-Phase Spectrum is Spectrum1; select it from the pull-down menu.
Quadrature Spectrum then automatically changes to Spectrum2. The Absorbance
Spectrum is Spectrum3; it will be used as a reference along the edges of the 2D-IR plot.
Do not select Spectrum3 when Spectrum1 and Spectrum2 are chosen.

Region Data: the region of the two spectra to be used in creating the 2D-IR view.

Sanong Ekgasit and Hatsuo Ishida, “Quantitative Two-Dimensional Infrared (2D IR) Spectroscopy:
Theoretical Development for General and Specific Cases,” Appl. Spec. 49, 1243-1253 (1995).
2
See reference 1, above.

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Left Edge: the upper limit (in cm-1) of the spectrum.

Right Edge: the lower limit (in cm-1) of the spectrum.

Spectrum Type: both spectra are used to calculate the synchronous and the
asynchronous— they are different types of cross correlations.
Synchronous: correlate changes that happen together.
Asynchronous: correlate changes that are out of phase.

OK: creates the 2D-IR view and displays it (see below).

Cancel: return to the main window without generating any 2D-IR spectrum.

Help: enter the on-line Help system.

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In general, better performance is obtained if small regions (for example, up to 500 cm-1)
are chosen. The time to display a large range (for example 4000-400 cm-1 at 4 cm-1) 2D
display can be several minutes, and considerable storage space (>20MB) can be
required.

This entry creates 2D-IR displays from in-phase and quadrature spectra. The displays
can be moved, rotated, and presented in a number of formats. The control panel sidebar
on the right hand of the screen controls the presentation of the data.

Draw Mode: how the three-dimensional aspect will be represented in two dimensions.

Wireframe: the points of the calculated three-dimensional plot are connected with
straight lines. Lines that are hidden by the shape of the display are not shown.
This draw mode disables both Colors and Palette.

Solid: the lines and the frames they define are filled in with different shades of a
single color to give a better idea of the shape of the surface of the contour plot.

Color Bleed: uses multiple colors for the surface. These colors change gradually
and smoothly as the height of the plot varies above the base plane. (Default)

Contours: shows contour lines on the surface at constant heights about the base
plane. The contour intervals are pre-set and cannot be changed.

Colors: sets the range of colors used to represent the extreme z-values of the plot.

Note
In wireframe mode, Colors is disabled.

Always Autoscale: if this is selected, then whenever you zoom in on a portion of

the plot, the color will be scaled so that the full color range is used for that
portion. This is useful if you zoom in on weak features that may be displayed in
very similar colors in the full plot.

If you are not autoscaling the colors, then you can set the values to be used in
the display. If you use the arrows to the right of the intensity boxes to set

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values, they will be implemented immediately. If you type in values, they will not
be implemented until you press the Enter key on the keyboard.

Upper Intensity: enter the color value to be used at the maximum z-value
of the plot.
Lower Intensity: enter the color value to be used at the minimum z-value
of the plot.

Palette: the draw modes may be observed with three different color schemes.

Note
In wireframe mode, Palette is disabled.

Monochrome: gray scale.

Color 1: shades from red to white to blue.
Color 2: shades from red through orange, yellow, and green to blue. (default)

Background: select the color for the background. A white background may be better if
you are capturing screens for insertion in a publication with a monochrome printer.

Black: background is black. the plot is shown against a black background

(default).

White: the plot is shown against a white background. This may be more
desireable for formats other than wireframe

Zoom: makes the plot appear closer (increases size) or farther away (decreases size).
Use the slide bar to change the value.

Y Scale: makes the height of the peaks taller or shorter. Use the slide bar to change the
value.

Rotation: these controls move the three-dimensional plot about two axes. Regardless of
the rotation, the axes remain in the foreground of the display. Rotation of large arrays
may be slow. Press the ESC key to stop the rotation.

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Flat View: if selected, displays a projection of the isometric view. If de-selected,

the isometric view (3D) is shown.

Default Angle: press this button to return the plot to its default position
(Pitch = 18°, Yaw = 1°).

Pitch: rotates the plot about a horizontal axis parallel to the monitor screen. Click
on the upper part to rotate the plot to show its Bottom; click on the lower part of
the bar to rotate the plot to show its Top. Each time you click the end of the slide
bar, the plot rotates 9°.

Yaw: rotates the plots about a vertical axis. The plot can be rotated either to the
Right or to the Left. Each time you click the end of the slide bar, the plot rotates
18°.

For both Pitch and Yaw, you can enter the value of the angle. If you change the
angle with the arrows to the right of the text box, the values are implemented
immediately. If you type in values, the values are not implemented until you
press the Enter key on the keyboard.

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A zoom is shown in the example below.

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A flat view with monochrome contours is shown below.

Subsets of the menus are also available. Their entries operate the same as they do in the
main Win-IR Pro document window.

In particular, you can adjust the display limits. Choose View / Display Limits / Selected
Spectrum. The Display Limits dialog box appears.

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See the section on Display Limits in Chapter 8 for details of how to use this dialog box.

In addition, the box zoom is still active and works in the same way. You can zoom in
the off-diagonal areas to see the results of correlating different regions, that is, you will
have different ranges on the x- and y-axes.

You can use the button and the radar box in the same way in the same way as
before.

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The printed image is exactly what is in the three-dimensional portion.

If you want to print the entire screen image use either WordPad or Paint. These two
applications are supplied as part of Windows NT. The procedure is described in Chapter
1.

Exporting 3D Data
The data triads (x, y, z) can be exported by selecting Operations / Export DXF. The file
created has a .dxf extension and can be opened and manipulated by applications such as
Autocad.

Notes
This menu entry is only accessible in a 3D graphics view.

These .dxf files cannot be inserted into word processors

using the usual .dxf filter.

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 Chapter 11 Operations Menu 413

From Series of Spectra...

Uses the generalized algorithm3 to create a display from any array (or subset) of spectra.
This 2D-IR view is used to detect correlations between the spectral changes at different
frequencies during measurements. The dialog boxes are different for non-kinetics and
kinetics documents.

Non-kinetics documents: Use the spreadsheet to select at least two spectra in the
document. This example uses the luther.bsp multispectrum document with spectra 10
through 20 selected. When From Series of Spectra is selected, the Create 2D-IR Spectrum
From Spectrum Array dialog box appears.

A typical correlation would be done using about 10 spectra over about 1000 cm-1 at
8 cm-1 resolution.

Region Data: the region of the spectra to be used in creating the 2D-IR view.

Left Edge: the lower limit (in cm-1) of the spectrum.

Right Edge: the upper limit (in cm-1) of the spectrum.

Spectrum Type: the spectra are used to calculate the synchronous and the
asynchronous— they are different types of cross correlations.
Synchronous: correlate changes that happen together.

3
I. Noda, “Generalized Two-Dimensional Correlation Method Applicable to Infrared, Raman, and
Other Types of Spectroscopy”, Applied Spectroscopy, 47, No. 9, 1329-1336, 1993.

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 414 Chapter 11 Operations Menu

Asynchronous: correlate changes that are out of phase.

OK: creates the 2D-IR view and displays it (see below).

Cancel: return to the main window without generating any 2D-IR spectrum.

Help: enter the on-line Help system.

Notes
In this case there is no “static” spectrum, so no spectra are
displayed along the edges.

We have used the zoom box to select an area of interest.

This is shown in the radar box.

The controls and operations, including those for printing and exporitng data, are
identical to those of the From In-phase/Quadrature Spectra, described earlier in this
chapter.

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 Chapter 11 Operations Menu 415

Kinetics documents: First click the Export Regions button on the kinetics document
window. Spectra are selected using the dialog box. When From Series of Spectra is
selected, the Select Edges Values dialog box appears. (This example uses the kinetics
document kinetics.kin.)

Spectral Range: the region of the spectra to be used in creating the 2D-IR view.
Left Edge: the lower limit (in cm-1) of the spectrum.
Right Edge: the upper limit (in cm-1) of the spectrum.

Time Range: defines the spectra that are to be included in creating the 2D-IR view.
Start Time: exclude all spectra collected before this time.
End time: exclude all spectra collected after this time.

In a kinetics document where the time resolution is 1 second, a typical example would
be creating a 2D-IR view over a period of one minute and a few hundred wavenumbers.

Spectrum Type: the spectra are used to calculate the synchronous and the
asynchronous— they are different types of cross correlations.
Synchronous: correlate changes that happen together.

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 416 Chapter 11 Operations Menu

Asynchronous: correlate changes that are out of phase.

OK: creates the 2D-IR view and displays it (see below).

Cancel: return to the main window without generating any 2D-IR spectrum.

Help: enter the on-line Help system.

The controls and operations, including those for printing and exporting data, are
identical to those of the From In-phase/Quadrature Spectra, described earlier in this
chapter.

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 Chapter 11 Operations Menu 417

REPROCESS
In addition to saving the operations performed upon a spectrum, Win-IR Pro saves the
intermediate stages. Therefore, you can view any stage of the spectrum’s development.
Select Reprocess; the Reprocess dialog box appears.

To recover the spectrum at any intermediate point

1 Place the cursor on the red STOP at the end of the list of operations and hold
down the left mouse button. Another STOP appears.

2 Drag the new STOP to the place on the list where you want processing to stop.
Release the mouse button. The spectrum will be reprocessed to that point.

Note
The interferogram is saved in the document, although it is
not visible. You can start again with the interferogram
and step through all the processing.

See Chapter 5 for complete details of Reprocess and History.

PEAK PICK
Performs automatic picking of peaks based upon height, area, and other properties of
the spectrum. When selected the Peak Pick dialog box appears.

There are eight levels of Sensitivity with 1 being the least sensitive (fewest peaks) and 8
being the most sensitive (most peaks). Examples of peak pick with sensitivities of 1 and
3 are shown below.
Sensitivity = 1

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 418 Chapter 11 Operations Menu

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 Chapter 11 Operations Menu 419

Sensitivity = 3

After peaks have been picked, they may be modified; see the discussion in Chapter 2 for
details. Peaks may be investigated and their parameters added to the spreadsheet using
Edit / Peak List (see Chapter 7 for details).

Individual peaks can be removed:

1. Place the cursor on the peak label and click the left mouse button.
2. Press the Delete key on the keyboard.
Note
Peak picking takes place over the entire spectrum even if
only a portion of it is displayed at the time the peaks are
picked.

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 420 Chapter 11 Operations Menu

CREATE EMPTY SPECTRUM

Creates an empty (all Y-axis values are 0) spectrum in the same document as the
selected spectrum. The empty spectrum has the same collection parameters as the
original selected spectrum.

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 Chapter 11 Operations Menu 421

COPY SPECTRUM
Creates an exact duplicate of the selected spectrum in the same document. The
duplicate spectrum has the same collection parameters as the original selected spectrum.

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 422 Chapter 11 Operations Menu

SPECTRAL ARITHMETIC
Allows arithmetic operations to be performed upon a spectrum (that is, its points) or on
a pair of spectra The modified spectrum can be added to the document or it can replace
the existing spectrum in the document..

Unary...
Allows unary operations to be performed upon the spectrum. Unary operations work
upon the spectrum itself with no external qualifiers such as multipliers, etc. The Spectral
Arithmetic: Unary Operations dialog box appears.

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 Chapter 11 Operations Menu 423

Negate: create a new spectrum whose values are the negative of the original
spectrum.
1/y: create a new spectrum whose values are the reciprocal of the values of the
original spectrum.
10^y: create a new spectrum whose values are 10 raised to the power of the
Y-axis values of the original spectrum.
log(y): create a new spectrum whose values are the logarithm (base 10) of the
values of the original spectrum.
ln(y): create a new spectrum whose values are the natural logarithm (base e) of
the values of the original spectrum.
exp(y): create a new spectrum whose values are the exponential (e raised to the
power of the Y-axis values) of the original spectrum.
FFT: create a new spectrum that is a fast Fourier transform of the original
spectrum. The FFT algorithm used us that of Cooley and Tukey.4
Note
The Fast Fourier transform is not reversible. That is,
performing a second FFT on the transformed spectrum
does not yield the original spectrum. To save the original
spectrum, use the Add button.
Replace: make the desired calculation, replace the existing spectrum and return to the
main menu.

Add: make the desired calculation, add the new spectrum to the spreadsheet, and return
to the main menu.

Cancel: return to the main menu without making any changes to the selected spectrum.

Help: enter the on-line Help system.

4
Cooley, J. W. and Tukey, J. W., “An Algorithm forthe Machine Computation of Complex Fourier
Series,” Mathematics of Computing, 19, 297-301 (April 1965).

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 424 Chapter 11 Operations Menu

Scalar...
Allows you to perform scalar operations to the selected spectrum. The Spectral
Arithmetic: Scalar Operations dialog box appears.

Value: enter the number to be used in the calculation. This number may be
negative, as well as positive or 0.

(+) Add Value: add the number entered above to the Y-axis value of each point
of the spectrum.

(-) Subtract Value: subtract the number entered above from the Y-axis value of
each point of the spectrum.

You can subtract a spectrum from a number by first selecting Negate in the
Unary operations, then adding the negated spectrum.

(*) Multiply by Value: multiply the Y-axis value of each point of the spectrum by
the number entered above.

(/) Divide by Value: divide the Y-axis value of each point of the spectrum by the
number entered above.

You can divide a number by a spectrum by first selecting 1/y in the Unary
operations, then multiplying the reciprocal spectrum.

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 Chapter 11 Operations Menu 425

(^) Power Value: raise the Y-axis value of each point of the spectrum to the
power (number) entered above.

Replace: make the desired calculation, replace the existing spectrum and return to the
main menu.

Add: make the desired calculation, add the new spectrum to the spreadsheet, and return
to the main menu.

Cancel: return to the main menu without making any changes to the selected spectrum.

Help: enter the on-line Help system.

Binary...
Allows you to perform arithmetic operations on the selected spectrum and a reference
spectrum. The Spectral Arithmetic: Binary Operations dialog box appears.

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 426 Chapter 11 Operations Menu

If the reference spectrum has not been selected, use standard Windows NT procedures
to select it. If the spectrum is on a drive not currently connected to your system, click
the Network button to connect it.

Use Current: if selected, the current spectrum is used as the reference spectrum.

Note
The reference spectrum must have been collected with the
same parameters as the original spectrum.

(+) Add Reference: to each point of the original spectrum, add the value of the
corresponding point in the reference spectrum. Replace the original spectrum
with the new spectrum.

(-) Subtract Reference: from each point of the original spectrum, subtract the
value of the corresponding point in the reference spectrum. Replace the original
spectrum with the new spectrum.

(*) Multiply by Reference: multiply each point of the original spectrum by the value
of the corresponding point in the reference spectrum. Replace the original
spectrum with the new spectrum.

(/) Divide by Reference: divide each point of the original spectrum by the value of
the corresponding point in the reference spectrum. Replace the original
spectrum with the new spectrum.

Phase Angle: arctan(Sample/Reference): divide each point of the original spectrum

by the value of the corresponding point in the reference spectrum. Calculate the
arctangent of this ratio. Replace the original spectrum with the new spectrum.

Replace: make the desired calculation, replace the existing spectrum and return to the
main menu.

Add: make the desired calculation, add the new spectrum to the spreadsheet, and return
to the main menu.

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 Chapter 11 Operations Menu 427

Cancel: return to the main menu without making any changes to the selected spectrum.

Help: enter the on-line Help system.

3-D Interpolation
Creates PAS (Photoacoustic spectroscopy) Interpolated Spectra from an in-phase and a
quadrature spectrum5. This would be created in a step-scan MCS experiment. By
performing a geometric interpolation:

Sθ = Sin-phase cos θ + Squadrature sin θ

intermediate spectra can be created. The phase angle is related to the samnpling depth,
so that

Sθ ∝ Sdepth

This interpolation operation produces a spectral surface where the axes are frequency
(x), phase angle (y), and intensity (z).

In this example, we will use pas2.bsp which contains an in-phase and quadrature
spectrum of mylar.

5
Noble, Deborah, “FT-IR PAS steps up to depth profiling,”, Anal. Chem. 66, 757A-760A (1994).
Palmer, Richard A. and Dittmar, Rebecca M., “Step-scan FT-IR photothermal spectral depth profiling
of
polymer films,” Thin Solid Films, 223, 31-38 (1993).
Bajic, Stanley J., Luo, Siquan, Jones, Roger W., and McClelland, John F., “Analysis of Underground
Storage Tank Waste Simulants by Fourier Transform Infrared Photoacoustic Spectroscopy,” Appl.
Spec.
49, 1000-1005 (1995).

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 428 Chapter 11 Operations Menu

Both these spectra must be selected for this entry to be enabled. Choose 3D Interpolation
from the Spectral Arithmetic submenu of the Operations menu; the Create PAS Interpolated
Spectra dialog box appears.

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 Chapter 11 Operations Menu 429

Spectra

In-Phase Spectrum: select the in-phase spectrum using its spreadsheet position.
Quadrature Spectrum: select the quadrature spectrum using its spreadsheet
position.
Actual In-Phase Angle: the default angle is taken to be 0. If you know what the
actual angle is, enter it here. Changing this angle has the effect of
moving the 3D display along the angle axis.

Region Data: the region of the two spectra to be used in creating the PAS view.

Left Edge: the lower limit (in cm-1) of the spectrum.

Right Edge: the upper limit (in cm-1) of the spectrum.

Interpolation: define the range on which the interpolation is to take place.

Range (°): interpolate between these limits (in degrees).

Angle Increment (°): the size of the increment for interpolation (in degrees).

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 430 Chapter 11 Operations Menu

OK: creates the PAS view and displays it (see below).

Cancel: return to the main window without generating any PAS spectrum.

Help: enter the on-line Help system.

The initial view of the 3D interpolated spectrum is shown below.

use this ruler to absorbance vs. wavenumber (spectrum) control panel

select angle for that angle is displayed here

windowshades

3D view, from above, of use this ruler to select absorbance vs. angle, for that
interpolated spectrum— colors wavenumber wavenumber, is displayed here
indicate magnitudes

Two-dimensional cross-sections of the interpolated spectrum: To select a spectrum

at any angle, place the cursor in the vertical ruler and click the left mouse button. The
spectrum is displayed in the upper middle of the window.

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 Chapter 11 Operations Menu 431

To select a plot of absorbance vs. angle for any wavenumber, place the cursor in the
horizontal ruler and click the left mouse button. The absorbance-vs.-angle plot is
displayed in the lower middle of the window.

Once you have selected a trace you can adjust its display. In this example, the upper
trace has been selected. Choose View / Display Limits / Selected Spectrum. The Display
Limits dialog box appears.

See the section on Display Limits in Chapter 8 for details of how to use this dialog box.
If you select the lower trace, and choose View / Display Limits / Selected Spectrum, the
dialog box appears with the limits for that trace.

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 432 Chapter 11 Operations Menu

Note
Under certain conditions and color selections, the
extracted line may vanish. To cause it to reappear:
1. Select Options / Edit Color...
2. Open the Pen icon.
3. Select Region Line
4. Click on the color in the lower left of the Basic
Color block (black).

5. Click the OK button.

In the example below, both an angle and a wavenumber have been selected.

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 Chapter 11 Operations Menu 433

Select a trace, in either the upper or lower display, by clicking on it. You can now use
the normal zoom and scaling operations in that display.

Printing a cross section: Select a trace, in either the upper or lower display, by clicking
on it. Select Print from the File menu, or click the button. The Print dialog box
appears. Press OK if the settings are as desired; otherwise, see Print in Chapter 6 for
details of the settings.

The portion of the window taken up by each of the three displays can be altered by
dragging the windowshades to the desired location (see Chapter 1 for details of moving
windowshades).

Three-dimensional interpolated spectrum: This spectrum can be moved, rotated, and

presented in a number of formats. The control panel sidebar on the right hand of the
screen controls the presentation of the data. The portion of the window used by the
different graphics can be altered by moving the horizontal and vertical window shades.
In all the examples below, the vertical window shade has been moved all the way to the
right to better show the three-dimensional graphics.

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 434 Chapter 11 Operations Menu

Draw Mode: how the three-dimensional aspect will be represented in two dimensions.

Wireframe: the points of the calculated three-dimensional plot are connected with
straight lines. Lines that are hidden by the shape of the display are not shown.
This draw mode disables both Colors and Palette.

Solid: the lines and the frames they define are filled in with different shades of a
single color to give a better idea of the shape of the surface of the contour plot.

Color Bleed: uses multiple colors for the surface. These colors change gradually
and smoothly as the height of the plot varies above the base plane. (Default)

Contours: shows contour lines on the surface at constant heights about the base
plane. The contour intervals are pre-set and cannot be changed.

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 Chapter 11 Operations Menu 435

Colors: sets the range of colors used to represent the extreme z-values of the plot.

Note
In wireframe mode, Colors is disabled.

Always Autoscale: if this is selected, then whenever you zoom in on a portion of

the plot, the color will be scaled so that the full color range is used for that
portion. This is useful if you zoom in on weak features that may be displayed in
very similar colors in the full plot.

If you are not autoscaling the colors, then you can set the values to be used in
the display. If you use the arrows to the right of the intensity boxes to set
values, they will be implemented immediately. If you type in values, they will not
be implemented until you press the Enter key on the keyboard.

Upper Intensity: enter the color value to be used at the maximum z-value
of the plot.
Lower Intensity: enter the color value to be used at the minimum z-value
of the plot.

Palette: the draw modes may be observed with three different color schemes.

Note
In wireframe mode, Palette is disabled.

Monochrome: gray scale.

Color 1: shades from red to white to blue.
Color 2: shades from red through orange, yellow, and green to blue. (default)

Background: select the color for the background. A white background may be better if
you are capturing screens for insertion in a publication with a monochrome printer.

Black: background is black. the plot is shown against a black background

(default).

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 436 Chapter 11 Operations Menu

White: the plot is shown against a white background. This may be more
desireable for formats other than wireframe

Zoom: makes the plot appear closer (increases size) or farther away (decreases size).
Use the slide bar to change the value.

Y Scale: makes the height of the peaks taller or shorter. Use the slide bar to change the
value.

Rotation: these controls move the three-dimensional plot about two axes. Regardless of
the rotation, the axes remain in the foreground of the display. Rotation of large arrays
may be slow. Press the ESC key to stop the rotation.

Flat View: if selected, displays a projection of the isometric view. If de-selected,

the isometric view (3D) is shown.
Default Angle: press this button to return the plot to its default position
(Pitch = 18°, Yaw = 1°).
Pitch: rotates the plot about a horizontal axis parallel to the monitor screen. Click
on the upper part to rotate the plot to show its Bottom; click on the lower part of
the bar to rotate the plot to show its Top. Each time you click the end of the slide
bar, the plot rotates 9°.

Yaw: rotates the plots about a vertical axis. The plot can be rotated either to the
Right or to the Left. Each time you click the end of the slide bar, the plot rotates
18°.

For both Pitch and Yaw, you can enter the value of the angle. If you change the
angle with the arrows to the right of the text box, the values are implemented
immediately. If you type in values, the values are not implemented until you
press the Enter key on the keyboard.

Subsets of the File, Edit, Options, Window, and Help menus are also available. Their
entries operate the same as they do in the main Win-IR Pro document window.

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 Chapter 11 Operations Menu 437

Examples:

In this example, Draw Mode has been set to Wireframe and Background to White. Flat
View has been de-selected and the image has been rotated (Yaw).

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 438 Chapter 11 Operations Menu

Zooming in gives this view.

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 Chapter 11 Operations Menu 439

Zooming out and increasing Y Scale gives this view.

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 440 Chapter 11 Operations Menu

In the example below, Flat View has been selected; Draw Mode is set to Contours.

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 Chapter 11 Operations Menu 441

You can use the cursor to draw a rectangle about the area of interest to zoom in on it.

Printing the 3D View:.To print the three-dimensional (left-hand side) part of the
screen, select File / Print or click the button at the buttom of the screen. In the
example below, the following parameters have been changed from their defaults:

Draw Mode Wire Frame

Palette Monochrome
Background White
Flat view de-selected

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 442 Chapter 11 Operations Menu

The full screen is on the left; the printed image is on the right.

The printed image is exactly what is in the three-dimensional portion.

If you want to print the entire screen image use either WordPad or Paint. These two
applications are supplied as part of Windows NT. The procedure is described in Chapter
1.

Exporting PAS Interpolation 3D Data

The data triads (x, y, z) can be exported by selecting Operations / Export DXF. The file
created has a .dxf extension and can be opened and manipulated by applications such as
Autocad.

Notes
This menu entry is only accessible in a 3D graphics view.

These .dxf files cannot be inserted into word processors

using the usual .dxf filter.

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 Chapter 11 Operations Menu 443

Raman Convert
When selected, the Raman Convert dialog box appears.

Raman Laser Wavenumber: the value to be used to convert the absolute wavenumber
spectrum to a Raman-shifted spectrum. This value is a physical property of the
excitation laser. Once it is known and set for the hardware, there is usually no reason to
change it.

OK: set the Raman laser wavenumber to the value entered; return to the main screen.

Cancel: return to the main screen without altering the value.

Help: enter the on-line Help system.

Note
The Raman Laser Wavenumber value can also be altered
through the Laser or Computations tab pages of Collect /
Raman-Scan...

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 444 Chapter 11 Operations Menu

CHANGE ZPD LOCATION...

Under certain conditions it may be necessary to manually change the Zero Path
Difference (ZPD) which is normally determined automatically during setup.

For example, multiple modulation experiments, such as vibrational circular dichroism,

polymer stretching, these give interferograms which are essentially “difference”
interferograms: the differential absorbance between two states of the sample, or of the
polarization of the incident light. The spectra are flat lines centered at zero with small
positive and negative excursions, and these interferograms therefore have no
centerburst, and just weak (symmetrical) sidebursts. [The normal centerburst arises from
the large positive single-beam curve.]

Additionally, in some MCS experiments, data collection is performed at different speeds

and using different electronic filters than setup. This causes the centerburst to “shift.”

The ZPD is the zero point used by the Fourier transform to calculate the single-beam
spectrum from the interferogram.

The document below contains a number of interferograms; consider the third one, which
does not have as well-defined a centerburst as the others.

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 Chapter 11 Operations Menu 445

To move the ZPD,

1. Select Operations / Change ZPD Location....The Change ZPD Location dialog

box appears, offering 4 choices:

Default from Collect: use whatever ZPD location was determined during
setup.

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 446 Chapter 11 Operations Menu

Most Negative Value: set the ZPD at the largest negative value of the
interferogram.

The ZPD has been shifted to the left by about 0.001 cm.

Shift ZPD to X = : set the ZPD to the location typed into the box to the left of
this line. Location is in optical retardation (cm). For example, enter 0.002

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 Chapter 11 Operations Menu 447

The ZPD in the interferogram above is now where 0.002 cm was in the
original interferogram.

Copy Selected to All Igrams: use the current location of the ZPD, as defined
for this interferogram, for all the interferograms contained in this document.

For example, in a multiple modulation experiment, the ZPD might be

transferred from an interferogram with a well-defined centerburst to one
without, after shifting the well-defined centerburst to zero retardation.

2. Click the OK button to implement the selection.

Cancel returns to the main menu without making any changes to the ZPD
location.

Help enters the on-line Help system.

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 448 Chapter 11 Operations Menu

PAS LINEARIZE...
This method allows you to compute linear photoacoustic FT-IR spectra using one
sample and one reference interferogram. This method produces spectra similiar to
transmission spectra through the reduction of saturation that is normally a factor in
amplitude computation.

You must have an interferogram selected to enable the PAS Linearize... entry.

Note
This spectrum replaces the interferogram. The
interferogram cannot be recovered by the Operations /
Reprocess procedure. Use Operations / Copy Spectrum
before PAS Linearize... if you want to save the
interferogram.

When you select PAS Linearize... the PAS Linearize dialog box appears.

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 Chapter 11 Operations Menu 449

Region Data: defines the region to be displayed for the linearized PAS spectrum (in
wavenumbers).
Low: the lower edge of the region.
High: the upper edge of the region.

Reference: defines the interferogram to be used as the reference in calulating the phase
array.
File Name: the name of the file containing the interferogram to be used as the
reference interferogram.

Use Current: if checked, the currently selected interferogram in this document is

used as the reference interferogram.

Drives: select the drive on which the file resides.

List Types of Files: this will normally be Bio-Rad Spectra or 3200 Format Spectra.

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 450 Chapter 11 Operations Menu

Compute: set the parameters for the calculation. When this button is clicked the
Compute dialog box appears

General tab page

Apodization Function: normally Triangle is selected.

Zero Filling Factor: normally Auto is selected.

Advanced tab page

Use Standard Processing: this is normally checked; it disables the rest of

the parameter settings on this page. Unless you have a specific reason to
do otherwise, use the default settings.

Output Type: this is ignored by the PAS linearization process.

Phase Parameters

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 Chapter 11 Operations Menu 451

Size (Points): set to Auto.

Apodization: set to Auto.
Phase Correction: set to Auto by the calculation
Store Phase: ignored
File Name: ignored

Included Frequency: set to Auto.

OK: return to the PAS Linearize dialog box with the new parameter
settings.

Cancel: return to the PAS Linearize dialog box with the previous
parameter settings.

Help: enter the on-line Help system.

OK: calculate the PAS linearized spectrum and display it.

Cancel: return to the main window without calculating the PAS linearized spectrum.

Help: enter the on-line Help system.

Network: connect to other disks on the network to access non-local files.

When OK is clicked, two computations are done. First, the reference interferogram is
computed using auto phase correction generating a phase array which is stored. This
stored phase array is used in the calculation of the spectrum from the sample
interferogram.

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 452 Chapter 11 Operations Menu

IR MENTOR
Invokes the IR Mentor, if this product has been loaded on the system; if it has not been
loaded, this menu entry is disabled (grayed-out). IR Mentor is an on-line data base of
characteristic group frequency ranges and approximate band intensities, with associated
bar charts, to assist in the interpretation of infrared spectra. It is a tool for instruction
and for interpreting complex spectra.

Every time your select Operations / IR Mentor, a new copy of the application is opened.
It is not automatically closed when you return to Win-IR Pro. You may want to
manually close IR Mentor when you have finishing a session.

See the IR Mentor Pro Manual (091-1017) for details.

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 12
Options Menu

These menu entries allow you to change certain Win-IR Pro default settings.

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 454 Chapter 12 Options Menu

EDIT COLOR
This allows you to change the colors of objects, backgrounds, spectra, etc. from the
default. Selecting this entry brings up the Edit Color Dialog box. There are three types
of objects that can be colored: Pen, Brush, and Text.

Pen: objects that are lines. These include spectra, points, boxes, etc.

Brush: objects that are areas. These include backgrounds, regions, etc.

Text: objects that are printing characters. These include labels, etc.

First, expand the list for the type of object to be edited. You can do this by single
clicking the box with the + in it, by double clicking the object type symbol, or by
double clicking the object type name.

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 Chapter 12 Options Menu 455

A list of objects of that type is displayed in the List: box. Select the object to be color
edited by highlighting it; its current color is shown on the right by a heavy black
rectangle surround its color box.

Selected object Color of object

To change a color:

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 456 Chapter 12 Options Menu

1. Select the type of object–Pen, Brush, or Text.

2. In List, highlight the specific object to be changed. The color of that object
is indicated by a heavy black rectangle surrounding the color box of the
object..

3. Click on the box containing the desired new color for the object.

Note
Be careful that you do not select Pen or Text colors that
are too close to that of the Brush areas on which they will
appear. In that case, some lines or text may seem to
vanish.

4. If you want to create a color other than one of the 48 Basic Colors—first,
click on the custom color to be edited (white boxes are the same as the other
boxes), then click the Define Custom Colors... button. The Color dialog box
expands.

Note
On some monitors, the expanded Color dialog box goes
off the right side of the screen. Drag the dialog box to the
left to correct this.

An expanded view of the right half of the dialog box is shown below.

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 Chapter 12 Options Menu 457

place the cursor in

this area and click grab the triangle
on the desired color with the cursor
and slide it up and
down to change
hue, saturation,
luminosity, etc.

displays current
values for these color
parameters; you can
displays the also type in values by
chosen color putting the cursor in
the appropriate box

press button to add

color to left hand
side of dialog box
5. Use the controls to select the desired custom color. Then, press the Add to
Custom Color button; this will put the new custom color in one of the boxes
in the lower half of the left side of the dialog box. Once a custom color has
been added, it may be used the same as a basic color. You may want to
record the values of the 6 parameters (hue, saturation, luminosity, red, green,
blue) for future reference.
The location of the marker in the square color box controls hue (x-axis) and
saturation (y-axis). The position of the marker in the narrow (right hand
box) controls luminosity: top=white, bottom=black (default). You need a
position away from the two extremes to get a non-white or non-black color.
Notes
If you have not selected a custom color box, then the new
custom color is put in the first box in the Custom Colors
part of the dialog box; the next color goes in the box
directly below it, etc. Every time you reopen the dialog
box, the placement of the custom colors is the same. The
new custom color is not put into the first empty box.

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 458 Chapter 12 Options Menu

If you change a color, it does not change the color of the

objects that are currently the original color. If you want
to change the color of an object, you must explicitly
select it and then select the color to be assigned to it. If
this is not done, the color assigned to this object is
unpredictable.

At this time, if you do not want to add a custom color, just return to working
in the left side of the dialog box. Pressing Cancel will close the dialog box
and return to the main screen will all changes canceled.

6. If you wish to change the color of any other object, repeat steps 1 to 5.

7. When you are done editing object colors, press one of the buttons at the
bottom of the dialog box to affect the action described below.

OK: return to the main menu and implement all the changes made through
the Edit Color dialog box.

Defaults: returns the colors for all objects to the Bio-Rad facotry-supplied
colors.

Cancel:return to the main menu without implementing any changes made

through the Edit Color dialog box.

Help: enter the on-line Help system.

Note
A list of the factory-installed default RGB color settings
in given in Appendix B.

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 Chapter 12 Options Menu 459

CONFIGURATION...
Selecting this entry brings up the Configurations Options dialog box.

Load Recent File on Startup

If Load Recent File on Startup is selected, then after Win-IR Pro starts, it automatically
opens the file that was in memory when you exited Win-IR Pro. This is the default.

If Load Recent File on Startup is not selected, then Win-IR Pro starts with a blank screen.

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 460 Chapter 12 Options Menu

Use File / Open or File / New to bring spectra into memory.

Note
Win-IR Pro remembers what the most recent file was,
even if you do not load it on startup. Thus, if you select
Load Recent File on Startup after it was de-selected,
Win-IR Pro will load the most recent file, even though
this spectrum did not appear on the screen.

Plot Title
The plot title is printed in the upper left corner of the spectrum plot. Use File / Print or
the button to plot a spectrum. The default text is Bio-Rad Win-IR Pro. To change
this label, type a new label in this box, and click OK.

Note
Once you have clicked OK, the text change is permanent.
If you want to alter the value again, repeat the selection
procedure.

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 Chapter 12 Options Menu 461

Predefined Peaks
Specifies the file in which the predefined peaks parameters are saved. The default file
is C:\Program Files\Win-IR Pro\Peaks.Def. You can change this file by typing a new
pathname into the entry window.

Click the Browse button to bring up the standard Open dialog box. You can select a file
for saving the predefined files using standard Windows NT procedures.

See “Peaks” in Chapter 2 and New in Chapter 11 for details of the use of predefined
peaks.

Named Collects
Specifies the directory in which the named collect files are saved. The default directory
is C:\Program Files\Win-IR Pro\MyExperiments. You can change this directory by typing a
new directory pathname into the entry window.
Click the Browse button to bring up the standard Open dialog box. You can select a
directory for saving the named collects using standard Windows NT procedures. You
can select any file within the directory to select the directory.
See your spectrometer manual for details on the use of named collects.

Auto-Save After Collect

If Auto-Save After Collect is selected, then the document is written to the disk file
immediately after a data collection is completed. This is the default.

Note
If no file name has been selected, Win-IR Pro will display
a dialog box requesting that you enter one.

If Auto-Save After Collect is not selected, then the document is not written to the disk file
immediately after a data collection is completed.

Force Calibration After Startup

If Force Calibration After Startup is selected (this is the default), then the spectrometer
automatically performs a calibration whenever it is powered up. After the calibration,
you can collect data.

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 462 Chapter 12 Options Menu

SEARCH
Normally, only absorbance (or absorbance-like) spectra are searched for in the libraries,
because most commercial libraries have their entries in that format. If you select a
spectrum of a type other than an absorbance the Operations / Search entry is disabled.
However, if you need to search libraries for a non-absorbance spectrum, this entry can
be enabled.

1. Select Search from the Options menu. The Search Options dialog box appears.

2. Select the type(s) of spectrum you want to search by clicking in the box to
the right of the spectrum type. You can select more than one type using the
ctrl-click combination.

Select all: search will be enabled for all types of spectra.

Deselect all: search will be enabled only for absorbance-like spectra.

OK: return to the main menu with changes made.

Cancel: return to the main menu with no changes made.

Help: enter the on-line Help system.

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 13
Window Menu

In all the examples in this chapter the original screen is:

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 464 Chapter 13 Window Menu

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 Chapter 13 Window Menu 465

NEW WINDOW
Creates another window (document) identical to the original one. The original window
has :1 appended to it; the new window is identified by :2. This makes it possible to
manipulate the traces, spreadsheets, etc. while still saving the original document.

Caution
If you Save the modified document, it will overwrite
the original one. Use Save As... instead to preserve the
original document.

CASCADE

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 466 Chapter 13 Window Menu

Arranges all opened document windows one behind the other as:

To make any document window active, place the cursor on that window and click the
left mouse button.

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 Chapter 13 Window Menu 467

TILE
Arranges all opened document windows vertically, that is, one above the other.

There is no vertical scroll bar for the spreadsheets. Normally, this would be used to
compare traces and, if implemented, the spreadsheets would be hidden. To hide all the
spreadsheets, you must choose each window, in turn, to be active and select Maximize
Traces. With spreadsheets hidden, the same documents look like this.

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 468 Chapter 13 Window Menu

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 Chapter 13 Window Menu 469

ARRANGE ICONS
Arranges the icons for minimized document windows.

CLOSE ALL
Closes all open windows. If unsaved changes have been made to any window, Win-IR
Pro will ask you if you want to save those changes before closing the window.

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 470 Chapter 13 Window Menu

MAXIMIZE TRACES
Moves the window shade in the document window to eliminate the spreadsheet display.

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 Chapter 13 Window Menu 471

MAXIMIZE SPREADSHEET
Moves the window shade in the document window to eliminate the trace display.

OPEN WINDOWS
Lists the open document windows in Win-IR Pro. To make a document window the
active window, select it from this list. When a window is opened, it is added to this list;
when a window is closed, it is removed from this list.

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 14
Help Menu

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 474 Chapter 14 Help Menu

INDEX
Causes the top-level Win-IR Pro Help window to appear. To understand how to use the
on-line help, select Using Help from the Help menu (see below).

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 Chapter 14 Help Menu 475

USING HELP
Cause the Help Topics: Windows Help window to appear. This on-line help is standard
throughout all windows NT products. It is written by Microsoft to be self-explanatory.

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 476 Chapter 14 Help Menu

ABOUT WIN-IR PRO...

Causes the Win-IR Pro product identification box to appear. This is particularly useful
because it displays the Release (version) number of the product.

ABOUT WIN-IR PRO SECURITY...

Displays a text file containing information about the licenses and permissions installed
on your system. The file can be printed out. The information is useful to Bio-Rad’s
Customer Service.

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 15
Print Composition

The print composition template is a page on which you can place information from
spectra in a document, arrange it to your needs, add titles and comments, and print it.
Because the template, when saved, does not contain the data itself, but rather records of
what data is to go where on the page, the template can be used with any document you
choose.
OVERVIEW
The print composition template is associated with a document. To use the template,
you must first open a Win-IR Pro document, select the spectra whose information is to
be printed, and then create a template (or open an existing template). Any saved
template can be opened, and then edited or modified in the same manner as a new
template.

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 478 Chapter 15 Print Composition

After you have opened a Win-IR Pro document and selected the spectra to be printed,
• select File / Print Composition / Open to open an existing print composition
template, OR

• select File / Print Composition / New to create a new print composition

template.
Note
If more than one Win-IR Pro document is opened, the
currently active document is the one that will be used for
print composition.

This chapter will step you through building and using some example templates. The
latter part of the chapter is a reference to all the features available in print composition.

Template Window
A new template window looks like this.

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 Chapter 15 Print Composition 479

palette bar

grid
spectra
right-hand edge of page
(scroll right to view)

windowshade

bottom of page
(scroll down to view)
status bar

Spectra: spectra are on the left-hand side of the plot composition template. Initially,
they are condensed—the spectra and spectrum properties are not displayed. There are
three ways to display the spectrum properties:

• Double-click the spectrum identification (Print Composition1, etc.).

• Double-click the small spectrum icon.

• Click the left-hand box (it contains a +).

Repeat this procedure for the desired spectrum name (Spect1, etc.). The spectrum
properties are now displayed.

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 480 Chapter 15 Print Composition

spectrum

spectrum properties

Notes
All the spectrum properties are displayed and available,
even if they were not in a column in the document
spreadsheet.

Items that exist as part of the Win-IR Pro document, but

which are not displayed there (for example, peak labels),
are displayed when the Spectrum object is placed on the
print composition page.

Properties are copied to the print composition template by dragging and dropping.
Place the cursor on the desired property; hold down the left mouse button; move the
cursor across the windowshade to the desired location; release the mouse button. In the
example below, Spectrum has been placed in the print composition template. Text

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 Chapter 15 Print Composition 481

objects (this excludes Spectrum, Interferogram, ChemStructure, etc.) are treated as

COMMENT Control objects for the purposes of being edited and modified.

Note
Spectrum Labels identify which spectrum on the left-hand
side supplied the information; they are not printed with
the rest of the information.

Spectrum Spectrum
Label

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 482 Chapter 15 Print Composition

If more than one spectrum is selected for the print composition template, the spectra are
listed on the left-hand side in the order in which they were chosen from the spreadsheet.
This order procedure is the same as that for displaying traces in the Win-IR Pro
window. See “Trace Display Order in the Window” in Chapter 4 for details.

Therefore, the number used in the spectrum identification on the left-hand side (Spect1,
Spect2, etc.) is not the same number indicating position in the spreadsheet ( Spectrum1,
Spectrum2, etc.). Spreadsheet position or spectrum name can be determined by placing
the cursor over ID or SpectName and reading the value (see the “Property Browse Bar”
section of Chapter 8 for details), or by dragging ID or SpectName into the print
composition template.

Spreadsheet position Spectrum name

(spectrum ID)

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 Chapter 15 Print Composition 483

Palette bar: contains tools that are used to add objects to the print composition page;
these objects are not properties that are contained in the spectrum. When the cursor is
placed on each tool, a brief description of it is shown in the Status Bar. To add a field,
place the cursor on the tool, hold down the left mouse button, drag the cursor to the
desired place on the print composition page, and release the mouse button.

Tool Function
Add a title field

Add a comment field

Title:contains a one-line text string, normally used to label a page and/or the
entire print composition.

Comments: contains a multi-line text string. It can be used to specify any

desired information that is not normally contained in the spectrum.

Comparison of Title and Comments objects

FEATURE TITLE COMMENT

Text Location Centered in the box Starts at upper left hand
corner of box

Text Quantity One line Multiple lines

Text Editing Use Edit / TITLE Control Object Use Edit / COMMENT Control
/ Properties to access TITLE Object / Edit to put cursor in
Control Properties dialog box. comment box. Use standard
Use this to change title. insertion and deletion
techniques.

Grid: assists you in aligning the printing objects. Grid size can be changed by selecting
Edit / Grid (see the reference section, below).

Windowshade: divides the template window into the spectral part (left) and the print
composition part (right). It can be moved by placing the cursor on the window shade,
holding down the left mouse button, dragging the window shade, and release the mouse

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 484 Chapter 15 Print Composition

button. Alternately, select Window / Split to move the windowshade (see the reference
section, below). Place it in a position that is convenient for you.

Status Bar: gives a brief description of the results of using the tools in the palette bar.
If you decide you do not need this, it may be hidden by de-selecting View / Status Bar
(see the reference section, below).

Right-hand side of page: is indicated by a vertical, dashed blue line. Any item to the
right of this line will not be printed. Additional space can be obtained by scrolling
down. Any number of pages can be used in the template.

Bottom of page: scroll down to see the horizontal, dashed blue line that indicates the
bottom of the page. Existing pages will also have a vertical, dashed blue line. If you
want to create additional pages, just drag an object into the portion of the print
composition screen below the horizontal, dashed blue line. This automatically creates a
new page immediately following the last existing one.

Note
The horizontal and vertical edge lines for the new page
may not be visible until you have performed another
operation that refreshes the screen.

Objects
All items placed on the print composition page are objects that can be manipulated
independently of the other objects. Objects can be placed over one another and both
will print. If you place an object over a Spectrum or Interferogram object, the object will
appear to vanish; however, it is on the print composition page and will print. You can
see its location by selecting File / Print Preview.

Objects can be graphical (such as Spectrum, Interferogram, or ChemStructure) or non-

graphical. Of the non-graphical objects, ID and SpectName are Comment Control
objects; all other non-graphical objects are Title Control objects.

Notes
Avoid overlapping page boundaries. If an object overlaps
a page boundary, parts will be printed on each page.

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An object can be in one of three states-unselected, selected, and edit. You can tell what
state an object is in by its border.

State Border
Unselected

Selected

Edit

To go from
• Unselected to Selected: put the cursor in the object and single-click.
• Unselected to Edit: put the cursor in the object and double click.
• Selected to Edit: put the cursor in the object and double click.
• Selected to Unselected: put the cursor outside the object and single click.
• Edit to Unselected: put the cursor outside the object and single click.
• Edit to Selected: first, go to Unselected; then put the cursor in the object and
single click.
Unselected State: you can observe the object on the page; you can do nothing to it.
Objects that are unselected are not affected by non-global changes. They are affected
by Edit / Font and Edit / Background Color.
Selected State: in this state, you can perform operations on the object itself. You can
• move the object on the page; put the cursor in the object, hold down the left
button and drag the object ot the desired position, release the button.
• resize the object; put the cursor on one of the eight small black squares on
the border, when the cursor changes to a single double-headed arrow, hold
down the left button, drag the object to the desired size, release the button.

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 486 Chapter 15 Print Composition

• delete the object by pressing the Delete key, by selecting Edit / Delete, or by
selecting Edit / Cut; the last procedure also copies the object to the print
composition clipboard.

Edit State: in this state, you can perform operations on the contents of the object. You
can:

• edit the text that appears in any non-graphic object.

• delete the object by selecting Edit / Cut; this procedure also copies the object
to the print composition clipboard

Spectrum and Interferogram Objects

The Spectrum and Interferogram objects differ from the other objects placed on the print
composition page.

• Traces from more than one spectrum can be displayed in a single Spectrum
or Interferogram object. First, drag and drop Spectrum or Interferogram from
one spectrum. Then, drag Spectrum or Interferogram from the same or
another spectrum, and drop it on top of the existing object. Any number of
spectra can be placed in one display.

The Spectrum Label changes from identifying a single spectrum to Spect....

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 Chapter 15 Print Composition 487

Note
The traces can be offset with respect to each with the
Trace Control Bar. This is described in the reference
section, later in this chapter, and in Chapter 8.

• When the Spectrum or Interferogram object is first placed on the page the full
spectrum is shown, regardless of what limits were chosen for the display in
the main window. The zoom box, radar box, and autoscale buttons work the
same as in the main window. You can use the zoom box in the Spectrum or
Interferogram object to look at any portion of the spectrum; the portion
selected is shown in the radar box. In the example below, we have zoomed
in on a region of interest (3300-2700 cm-1). The radar box shows what part
of the spectrum is displayed. Because the Spectrum object is selected, the
XY-autoscale and Y-autoscale buttons are enabled.

Spectrum: zoom
box has been used
to select a region
of interest.

Radar box: shows

the location of the
region of interest
within the
spectrum

Autoscale buttons
are enabled

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 488 Chapter 15 Print Composition

Note
When you save the template, the spectrum limits are also
saved. In this example, if we opened this template for
another document, the Spectrum object would initially be
displayed for the region 3300-2700 cm-1.

• If the original spectrum is displayed with the X2 SPP or X4 SPP view, then
the Spectrum object is also displayed in the SSP view.

• The Spectrum or Interferogram object is active; both the x-axis and the y-axis
can be compressed or expanded as if it were a Win-IR Pro document (See
Chapter 1). The y-axis label displayed on the left-hand side is that of the
most recently selected trace.

• There are items associated with the display in the Win-IR Pro document that
can be hidden, for example, peak labels, position labels, or annotations.
When the Spectrum or Interferogram object of such a spectrum is placed on
the print composition page, these items are visible. These items are
considered part of the spectrum’s information; hiding them is only a display
option in the main Win-IR Pro document. They can be displayed or hidden
in print composition by using View / Show Peaks and View / Show Labels.

Right Mouse Button

If you place the cursor in an object and click the right mouse button, the object is placed
into edit state, and a menu appears.

Note
Right mouse button operations are not supported for
graphic objects such as Spectrum, Interferogram, or
ChemStructure.

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 Chapter 15 Print Composition 489

Select the desired item and click the left mouse button. Only those items that are
appropriate for that particular object are enabled.

Properties: allows you to change certain properties of the object. It is identical to

selecting Edit / OBJECT_TYPE Control Object / Properties. This feature is described
below in the reference section.

Size to Content: resizes the object box based upon its contents.

Note
Some boxes may not appear to be resized. In actuality,
they are, but room has been left for possible editing.
Boxes can be manually resized by dragging corners or
line centers.

Clear: removes all text from a Comments object. The cursor is left in the object box to
allow new text to be entered.

If the right mouse button is clicked on the composition page, but not on an object, a
menu appears that lets you change global conditions:

These have the same effects as selecting the corresponding entry from the View or Edit
menu.

Creating a Template

1. Open a document with the type of spectra that you are going to use.
Normally, this is the document containing spectra that you wish to print.

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 490 Chapter 15 Print Composition

2. In the spreadsheet, select the spectra to be used in creating the print

composition template.

3. Select File / Print Composition / New from the Win-IR Pro menu bar.
4. Create the print composition. Test it and modify it until you are satisfied.

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Note
Template files can be opened and further modified later,
if so desired.

5. Save the print composition as a Print Template (.bpt) file.

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Printing with a Template

1. Open the document containing the spectra to be printed.

2. In the spreadsheet, select the spectra to be printed.

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3. Select File / Print Composition / Open from the Win-IR Pro menu bar.

4. Open the desired Print Template (.bpt) file. The data from the document
appears in the appropriate locations in the template.

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5. Select File / Print.

Notes
If the number of spectra selected from the document are
more than are expected by the template, data from the
excess spectra will not be placed in the template.
If the number of spectra selected from the document are
fewer than are expected by the template, those locations
on the template will be empty.

The print composition template is associated with the document that was active when
the template was created or opened. If you want to use this template with another
document, you must
1. Close the print composition template; save it if appropriate.
2. Make the other document active.
3. Open the print composition template.
BATCH MODE
Batch mode allows you to create a template that will process groups of spectra. In
batch mode, if your template expects three spectra and you have selected six, then they
will be processed in two groups of three. If you were not in batch mode, the template
would ignore the fourth, fifth, and sixth spectra.

Creating a Batch Mode Template

The procedure to create a batch mode template is:

1. Open a document similar in type to that whose spectra are to be processed.

In this example select three spectra.

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2. Select File / Print Composition / New. The print composition screen appears.
Expand the property browse bar until the spectra are listed individually.

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3. Create a print template.

4. Select File / Save. Save this as BatchTest1.BPT.

5. Select File / Close. The template is ready for use.

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Using a Batch Mode Template

1. Open the document with the spectra to be processed. Select the spectra to be
processed.

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2. Select File / Print Composition / Open. Select BatchTest1.BPT. The spectra are
grouped into batches. Click on a Page button at the bottom the template to
view a batch of spectra. The values associated with those spectra will appear
in the print template. In this example, Page 3 has been selected.

Note
Select View / Batch from the menu bar to see the template
with only the first set of data selected. You can then
modify the template, and select View / Batch again to see
all the data.

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REFERENCE
FILE MENU
Most of the File menu entries work the same as their counterparts in the main Win-IR
Pro screen. See Chapter 6 for details.

New
Allows you to create any type of Win-IR Pro document.

Open
Allows you to open any existing Win-IR Pro document.

Close
Closes the active Print Composition template. If there are more than one Print
Composition template open, then these other templates remain open.

Save
Saves the currently active Print Composition template to disk unders its existing name.

Save As
Saves the currently active Print Composition template to disk with a newly specified
name, as a print composition file.

Print
Prints the currently active Print Composition template.

Note
Spectrum Labels are not printed.

Print Preview
Allows you to view the page(s) as a whole prior to printing them. Any number of pages
can be constructed. The next page is immediately below the current page. Any items
beyond the right-hand edge of the page (shown as a dashed line in the Print
Composition view) are not printed. You cannot modify the pages, only view them;
changes can be made by returning to the Print Composition view (click the Close
button).

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Notes
Items that overlap pages will not print properly. You
must make sure that you have not placed any fields or
objects so that they are on two pages.

Different printers have slightly different margins; what

you get on the paper printout may not be exactly what you
see on the screen. Do not place objects directly abutting
the edges of the paper.

The buttons at the top of the view have the following functions.
Print:
print the print composition file. Use Print Range in the Print dialog box if
you want to print other than all pages.

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Win-IR Pro returns you to the plot composition view.

Next Page: display the next page in the print composition file. If you are
displaying two pages, then each pages number is incremented by 1; that is, if
you were looking at pages 1 and 2, you will now be looking at pages 2 and 3. If
you are viewing the last page, this button is disabled.

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Prev Page: display the previous page in the print composition file. If you are
displaying two pages, then each pages number is decremented by 1; that is, if
you were looking at pages 2 and 3, you will now be looking at pages 1 and 2. If
you are viewing the first page, this button is disabled.

Two Pages: show two pages side by side on the screen. Two pages can only be
seen at the lowest level of magnification. When two pages are displayed, the
button label changes to One Page.

One Page: change the display from two pages side by side to one page. When
one page is displayed, the button label changes to Two Pages.

Zoom In: zoom in and magnify the view, viewing less of the page. There are
three levels of magnification; the default is the least. Two pages can only be
viewed as the lowest level of magnification. If you place the cursor in a page, it
changes to a magnifying glass. Click the left mouse button to increase
magnification; this is equivalent to clicking the Zoom In button.

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Zoom Out: zoom out and make the items smaller, viewing more of the page.
There are three levels of magnification; the default is the least.

Close: close the Print Preview view and return to the Print Composition view.

Print Setup
Selects the output device and allows you to set its parameters. Normally, this is the
printer and it has already been set up as part of the system installation. The dialog
boxes and the specific values of the printer parameters depend upon the printer attached
to the system. See the Win-IR Pro Installation and Configuration Manual for details on
how to select printers and install printer drivers. A typical example is shown below.

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most recent files opened

The most recently (up to four) opened files are displayed here. You can reopen any of
these files by clicking its name.

Exit
Saves all open documents to disk, closes all documents, closes Win-IR Pro (not just
Print Composition), and returns to Windows NT.
EDIT MENU

Cut
Copies an object in the selected or edit state to the clipboard and deletes it from the
print composition page.

Copy
Copies an object in the selected or edit state to the clipboard but does not delete it from
the print composition page. .

Paste
Places the contents of the print composition clipboard on the print composition page. .

Delete
Removes an object in the selected (but not the edit) state from the print composition
page.

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Font
Globally changes the text properties in all objects, except the Spectrum object. When
selected, the Font dialog box appears. This is a standard Windows NT dialog box.

Select the Font, Font Style, Size, and Color from the pull-down menus (the default is
Arial, Regular, 9 point, Black). You can also choose to have the text with Strikeout and/or
Underline. An example of what the text looks like with the selected properites is shown
in the Sample window. Click OK to implement the selected text properties, click Cancel
to return without changing the text properties; click Help to enter the on-line help
system.

Text properties in individual objects can be changed by making the object active, and
selecting Edit / Object / Properties. Click on the Fonts tab page. Changes made here
affect the highlighted object only.

Background Color
Globally changes the background color of all objects, except the Spectrum object. When
selected, the Color dialog box appears. This is a standard Windows NT dialog box.

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Select the color by clicking it (the default is white, in the lower left-hand corner). Click
OK to implement the selected color, click Cancel to return without changing the
background color; click Help to enter the on-line help system.

Colors in individual objects can be changed by making the object active, and selecting
Edit / COMMENT Control Object / Properties. Click on the Colors tab page. Changes made
here affect the highlighted object only.

Note
Custom Colors is not implemented.

Grid
Changes the distance between grid lines. The grid width can be any number between 10
and 70 pixels (inclusive); the default is 30 pixels. The incised squares in the lower part
of the dialog box show the cell size for 10 and 70 pixels.

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Object
Allows editing of certain properties of objects. The entry name changes to
OBJECT_TYPE Control Object when an object is in the selected or edit state.. There are
two actions that can be taken; both do not apply to all objects.

Edit: puts the object into the edit state. For Comments and comments-like objects,
places the cursor in the object so that the text can be edited.

Properties: each object has specific properties that can be modified. Selecting this
brings up the OBJECT_TYPE Control Properties dialog box. These dialog boxes have a
number of tab pages. Some of the tab pages are specific to the type of object; Colors
and Fonts are common properties of all objects.

Colors: click the Colors tab. This is a standard Windows NT color control dialog
box that is used in many applications.

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Property Name:allows you to change the colors that apply to the specific print
composition object selected. Choose the property name from the pull down
menu and click the color you want it to be.

System Color: allows you to change the colors of system objects, such as Title
Bars, Highlighted Text, etc. Choose the property name from the pull down menu
and click the color you want it to be. Normally, these system-level choices are
made from Control Panel / Color in the Program Manager.

Note
Many combinations of colors that are acceptable on a
color monitor will not have such clarity when printed in
grayscale. You must experiment to find the combination
that meets your needs. The default colors provide such a
combination.

Fonts: click the Fonts tab. This is a standard Windows NT font control dialog
box that is used in many applications.

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Property Name: select the text whose font is to be modified.

Font: the font to be used. In general, avoid display fonts except for large-size
titles. Times New Roman is a good serif font; Arial is a good sans serif font.

Font Style: Regular, Bold, Italic, or Bold Italic.

Size: measured in points (72 to the inch).

Effects: special effects can be selected.

Strikeout: if selected, a horizontal line is drawn through the character

(this feature is sometimes called strikethrough). This sentence has had
strikeout applied.

Underline: if
selected, the text is underlined. This sentence has had
underline applied.

Sample: This area displays the font selected so that you can see how it appears.

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Title Control Object: the Title can be entered or altered; the Border Style of the
title box itself can be chosen.

Comment Control Object: the Border of the comment box can be chosen.

OK: exit the Control Properties dialog box and implement all selections.

Cancel: exit the Control Properties dialog box without implementing any selections.

Apply:implement all selections made; do not exit the Control Properties dialog box. This
button is not enabled unless a selection is made that differs from the current value.

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Orientation
Selects the orientation of the page. There are two options

Portrait Landscape

Note
If you change the orientation of the print template, check
that none of the existing objects overlap a page boundary.
VIEW
Allows certain controls and information items on the screen to be hidden or visible as
you choose. If the menu entry has a √ to its left, then the item is visible, otherwise it is
hidden. The picture at the beginning of this chapter shows the location of the Status
Bar, Palette Bar, and Grid. Spectrum Labels are attached to the lower right corner of
each object placed upon the page.

Status Bar
Hides or shows the status bar.

Palette Bar
Hides or shows the palette bar.

Spectrum Label
Hides or shows the annotation labels attached to each object on the page.

Grid
Hides or shows the grid. To change grid spacing, use the Edit / Grid entry, described
above.

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Show Peak
If checked (√) all peaks defined in the main window are displayed (default), even if they
were subsequently hidden in the main display. Select this entry to remove the √ mark.
In this case, no peaks are displayed in print composition. Showing or not showing
peaks applies to all Spectrum and Interferogram objects on the page.

Show Labels
If checked (√) all position labels and annotations defined in the main window are
displayed (default), even if they were subsequently hidden in the main display. Select
this entry to remove the √ mark. In this case, no position labels or annotations are
displayed in print composition. Showing or not showing position labels and
annotations applies to all Spectrum and Interferogram objects on the page.

Batch
If selected, puts print composition into batch mode.

Trace Control Bar

Before this is enabled, you must first drag either a Spectrum or an Interferogram object to
the print composition page. Make this object Unselected; then make it Selected. The
Trace Control Bar is now enabled. Choosing it brings up the right hand side bar control
panel. These controls allow you to position the traces in a Spectrum or Interferogram
object with more than one trace. See “Trace Control Bar” in Chapter 8 for details on its
use.
WINDOW
Except for Split, these menu entries behave the same as they do in the main Win-IR Pro
document. See Chapter 13 for details.

New Window
Creates another print composition document identical to the original one. The original
window as :1 appended to it; the new window is identified by :2. This allows you to
create part of a print composition document, make additions, save this (use Save As, not
Save), and return to the original unaltered print composition document.

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Cascade
Arranges all opened document windows (not just print composition documents) one
behind the other, offset both horizontally and vertically, so that all title bars are visible.

Tile
Arranges all opened document windows (not just print composition documents)
vertically, that is, one above the other.

Arrange Icons
Arranges the icons for minimized document windows.

Split
If selected, the cursor changes to a two-headed horizontal arrow, split in the center by
two parallel vertical lines. It is positioned in the middle of the windowshade. If you
move the cursor to the left or right the windowshade follows it (moving the cursor up or
down has no effect on the screen). When the windowshade is where you want it to be,
click the left mouse button to return to normal operation. This entry is equivalent to
placing the cursor on the windowshade, holding down the left mouse button, dragging
the windowshade, and releasing the left mouse button.

open windows
Lists all open document windows in Win-IR Pro. To make a document window the
active window, select it from this list. When a window is opened, it is added to this list;
when a window is closed, it is removed from this list.

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HELP
This is a subset of the Win-IR Pro Help menu. See Chapter 14 for details.

Index
Causes the top-level Win-IR Pro Help window to appear.

Using Help
Causes the Help Topics: Window Help window to appear. This on-line help is standard
throughout all Windows NT products. It is written by Microsoft to be self-explanatory.

About Win-IR Pro

Causes the Win-IR Pro product identification box to appear.

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 16
Frequently Asked
Questions

COMPUTER OPERATIONS
Q. My dongle no longer seems to function; why is this?

A. We have had reports of dongle failure when an Iomega zip drive was plugged into
the parallel port while powered up. When you install zip drives, make sure you
follow the vendor’s instructions and have the drive powered down before
connecting it to the parallel port.

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Q. Why do I have to reboot the computer twice in the process of installing Win-IR
Pro?
A. You do not normally need to reboot the system more than once when installing
Win-IR Pro. However, at some releases of Win-IR Pro, you must first upgrade the
operating system. After you install this newer version of the operating system (or a
debug patch to the operating system), you must reboot the computer for this
upgrade to take effect. When you install Win-IR Pro (this installation program is
called SetUp.exe), you must reboot the computer to have the new Win-IR Pro
drivers, etc. take effect.

Q. My system will not start. How do I fix this?

A. One possible problem is an IRQ conflict. The spectrometer card is set to IRQ 10.
The network card should be set to IRQ 5 or 11. However, many network cards are,
by default, set to IRQ 10. To resolve this:

1. Remove the spectrometer card and attempt to boot your system.

2. If it starts, follow the manufacturer’s instructions for changing the IRQ
setting.
3. Shut down the system and insert the spectrometer card.

4. Restart the system.

Q. My system is running slowly and the disk light is on most of the time. How do I
correct this?

A. There are a number of possibilities; they are all concerned with the way Windows
NT handles memory.

1. You may be running out of space on your disk. In this case, archive data
that you want to retain. Look at the c:\temp directory and delete unneeded
files there.

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Note
Windows NT will not let you delete files that are required
for the applications that are running, or that Windows NT
thinks are required (see under Shutdown below).
2. If you are running out of virtual memory, you may want to increase the size
of the Paging File. To do this, you must first be logged in as an
administrator; then:
From the Task bar, select Start / Settings/ Control Panel.

Double-click the System icon

Select the Performance tab page.

Under Virtual Memory, click the Change button.

Type in a larger size for the Paging File. Space used by the Paging File is
not available for storage.

Click the Set button. Click the OK buttons until you return to the Control
Panel.

Close the Control Panel.

3. From the Task bar, select Start / Shut Down. When the system is restarted,
the unneeded temporary files will have been deleted.

Q. To increase storage, I added another hard drive to my system. The Win-IR Pro
software is installed on drive c:, but I want the default drive to be d:. How do I do
this?
A. In order to do this, you must have put a Win-IR Pro shortcut in the Profiles directory
and/or on your desktop.

Put the cursor on the shortcut icon and click the right mouse button; a menu
appears; select Properties from the menu. The Win-IR_Pro Properties dialog box
appears. Click the Shortcut tab.

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Type the desired working directory in the Start in box. Click OK.

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Q. On a long data collection, the software sometimes seems to “hang.”

A. Turn off your screen saver, if it is running—from the Task bar, select Start / Settings /
Control Panel.

Double click the Display icon. The Display Properties dialog box appears.

Click the Screen Saver tab.

Use the pull-down menu to change Screen Saver to (None) and click the OK button.

Screen savers are not designed to work with programs that write data to the
screen—like Collect—and may cause unpredictable behavior.

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Q. During data collection, the computer system crashed.

A. This can occur if you do not have sufficient disk space available at the start of the
data collect. You need at least 10 MB for regular data collection, and at least 64
MB for DSP data collection. Check the TEMP and TMP directories for files which
can be deleted. You may also want to archive inactive files.

Q. When I was configuring the hardware using the spectrometer applet, the rear
detector entry had a blank. When I selected this, the system crashed.

A. This is no longer a problem. In some older versions of the software, this occurred if
the registry was corrupted. From the Task bar, select Programs / Administrative Tools /
RegEdit 32. Select the key HKEY_LOCAL_MACHINE\SOFTWARE\Bio-Rad\Win-IR
Pro\Spectrometer Configuration and delete it. This will solve the problem.

Q. There are two spectrometer applet icons when I open the Control Panel. How do I
remove one?

A. In Explorer, go to the directory WINNT35/SYSTEM32. Look for the file(s)

Spectrometer.cpl. There will be two files with this name. Delete the older file.

Q. Sometimes I get an error message on start-up that says: OLE Initialization has failed.
Win-IR Pro will not start.

A. The computer system is shipped with networking turned on, because most of the
systems running Win-IR Pro are connected to networks. The above error occurs
when networking is turned on, but the system is not connected to a network. To
turn networking off:

1. From the Task bar, select Start / Settings / Control Panel.

2. Double-click the Network icon. The Network dialog box appears. Click the
Services tab.

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3. Select an entry in the Network Services scroll list and click the Remove
button. The following dialog box appears.

Answer Yes.

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4. Continue until all network software has been removed.

5. Click OK to implement the software removal.

6. Close the Control Panel.

7. Log off, shutdown the system, and reboot it for the changes to take effect.

Note
Because some of the software must be removed in a
specific order, you may have to repeat this process until
all the software is removed.

DISPLAY-RELATED QUESTIONS
Q. Sometimes it seems that no trace appears even though a trace was selected. This
sometimes happens when extracting a trace from the image file. What can be done
about this?

A. The standard way to solve this problem is to select Option / Edit Colors from the
menu bar and then to change the background and/or the trace (spectrum) colors so
there will be contrast. However, there is another way in which this situation can
occur unexpectedly. The default Win-IR Pro background color is obtained from
Windows NT; the other Win-IR Pro default colors are coded into the program. To
find out what the default background color is:

1. Select Start / Setting / Control Panel from the taskbar.

2. Double click the Display icon.

3. Click the Appearance tab.

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4. Select Desktop from the Item pulldown list.

Select Desktop here

Background color shown here

The color shown is used for the Windows NT background and for the
default Win-IR Pro background. If this color is changed, it will be used in
Win-IR Pro as the default background color the next time the file current.pv
is created.

A typical color mismatch scenario is:

1. User changes Windows NT color scheme (desktop color changed).

2. User deletes current.pv file for some reason.

3. User starts Win-IR Pro and some of the inactive traces may be difficult or
impossible to see.

To fix this, change the desktop color back to its default value, delete current.pv; restart
Win-IR Pro.

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Q. When I use Options/ Edit Color to change the zoom box color, I do not get the exact
color I picked. If I pick black for the zoom box with a white background, the zoom
box does not show up on the display (however, the zoom box function still works).
How do I fix this?

A. In order for the zoom box to be drawn it must be in the XOR mode. This means the
color selected for the zoom box is XORed with the background color. Experiment
to find your desired zoom box color. For example, with a white background,
choosing light blue (column 5, row 2 in the color chart) for the zoom box yields a
red zoom box; choosing yellow (column 2, row 1 in the color chart) for the zoom
box yields a dark blue zoom box.

Q. The Windows NT Taskbar covers up part of the display of the control side bars for
kinetics, 3D, quantitative analysis, etc.; how do I eliminate this?

A. There are two options. The simplest is to move the taskbar to another edge of the
screen.

1. Put the cursor on part of the taskbar which does not have an application.

2. Hold down the left mouse button, drag the taskbar to the desired edge of the
screen, and release the mouse button.

Alternatively, you can have the task bar autohide. To do this:

1. Put the cursor on a part of the taskbar which does not have an application;
click the right mouse button. A menu appears.

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2. Click on Properties with the left mouse button. The Taskbar Properties dialog
box appears.

3. Select Auto hide. Click OK. The taskbar will now hide itself when an
application is running.

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Q. My cursors do not behave as described in the manual.

A. Win-IR Pro requires that the Windows NT cursors to set to their default values.
Someone has probably changed these. To restore the default values.

1. From the Task bar, select Start / Settings / Control Panel.

2. Double-click the Mouse icon. The Mouse Properties dialog box appears.
Click the Pointers tab. In this example, someone has changed the cursors to
Hands 2.

3. Put down the Scheme menu and select Windows Default.

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4. Click OK to implement the default cursors.

5. Close the Control Panel.

Q. Some of the dialog boxes overlap and cover up edit boxes and/or buttons; how do I
fix this?

A. You have the screen fonts set to Large Fonts; it should be set to Small Fonts. To fix
this:

1. From the Task bar, select Start / Settings / Control Panel.

2. Double-click the Display icon. The Display Properties dialog box appears.
Click the Settings tab.

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3. Pull down the Font Size menu and select Small Fonts.

4. Click OK to save the new settings.

5. Close the Control Panel.

Note
You must exit and restart Windows NT for the changes to
take effect.

Q. Why do the colors in my display appear “muddy?”

A. Your display is set for 256 colors; it should be set for 65536 (64K) colors. To reset
the colors:

1. From the Task bar, select Start / Settings / Control Panel.

2. Double-click the Display icon. The Display Properties dialog box appears.
Click the Settings tab.

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3. Pull down the Color Palette menu and select 65536 Colors.

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The dialog box should now look like this.

4. Click OK to save the new settings.

5. Close the Control Panel.

Note
You must exit and restart Windows NT for the changes to
take effect.

Q. I do not see the X and Y coordinates of the cursor in the right hand side of the
status bar.

A. Select the trace by clicking on it. The X and Y coordinates will now be seen.

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Q. In a number of the control panels (for example, the Trace Control Bar) the Apply
button seems to always be disabled (grayed out).

A. If you change parameters by selecting them from a pull-down menu, the new value
is automatically applied upon selection. If you type in a new value, this enables the
Apply button. Press the Apply button to apply the newly typed value. When you
select from the menu, the Win-IR Pro knows what value to use. When you type in a
value, pressing the Apply button tells Win-IR Pro that you have completed entering
that value.

Q. When I work in the radar box, I often cannot resize the rectangle indicating what
part of the spectrum is displayed. Instead, a new rectangle is created and I have to
use autoscale to redisplay the main spectrum. In other cases, when I try to double-
click, an event occurs between the first and second click.
A. Your mouse is too sensitive; to decrease the mouse sensitivity:
1. From the Task bar, select Start / Settings / Control Panel.
2. Double-click the Mouse icon. The Mouse Properties dialog box appears.
Click the Motion tab.

3. In the Pointer speed bar, drag the indicator toward Slow. Then click OK.

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4. Try the new mouse setting. If it still is a problem, repeat the process. If
necessary, decrease the speed again.
5. To adjust the double click speed, access the Mouse Properties dialog box, but
click the Buttons tab.

6. In the Double-click speed bar, drag the indicator toward Slow. Adjust the
Double Click Speed so that it is appropriate for your reaction times. Then
click OK.
7. Close the Control Panel.
Q. I don’t want the splash screen to be displayed every time I start win-IR Pro. How
can I turn off the splash screen?
A. In the directory c:\Program Files\Win-IR Pro\bin there is a file called Splash.dll. If you
rename this file or move it to another directory the splash screen will no longer
appear upon startup or when you select Help / About Win-IR Pro from the menu bar. If
you want to restore the splash screen either give the file its original name or move it
back to this directory. You can also eliminate the splash screen by deleting
Splash.dll but then, in order to restore the splash screen, you would have to copy the
file from the installation CD-ROM.

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DOCUMENT-RELATED QUESTIONS
Q. When I collect a spectrum, it is stored in the same document as the background.
How do I avoid this?

A. When you collect data, that data is collected into the currently active (highlighted)
document. If you previously collected a background, and that background
document is active, the sample data will be collected into the background document.
Close the background document if you want your sample data to be collected into a
separate document.

Q. When I open a new document, it doesn’t ask for a name. Why is this?

A. This is in accordance with Windows and Windows NT procedure which does not
ask for a filename until the first time a document is saved. If you want to assign a
filename before you collect data, open the document using File / New, and then use
File / Save As to assign it a name. If that document is active when you start a scan,
data will be collected into that document. You must then use File / Save to save the
data.

Q. When I minimize a document and then open a new document, it is opened in an

iconized (minimized) state; is this supposed to happen?

A. Yes. A new document is opened in the same style as the last document.

Q. If you are in the middle of a transform—or a similar procedure—and you click the
close box ( ), the document is closed, but you are not asked if you want to save any
changes. Why is this?

A. You are only asked if you want to save changes if you have made a change to the
document. When you select , it is equivalent to clicking the Cancel button,
followed by File / Close. If you did not make a change to the spectrum, you will not
be prompted because of this action. If previous procedures have changed the
document, then you will be prompted.

BASELINE-RELATED QUESTIONS
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Q. How do you perform a quantitative analysis without baseline correction?

A. To remove the baseline correction of the components in the calibration document,

first select the component by clicking its label. Then, use the right mouse button
menu to select Properties. When the Edit Peak Properties dialog box appears, select
the General tab page. In the Baseline Definition portion of this page you will normally
find Use Left Point and Use Right Point selected; de-select them. Click the OK button.
Baseline correction is now removed from all calibration curves for this component.

Q. After I performed a zoom in baseline correction, the cursor did not change back to
the baseline correction cursor. How do I make this happen?

A. You can toggle between the zoom and baseline correction modes by clicking the
zoom and baseline correction buttons at the bottom of the main window.

Q. When I use Zap to zero the spectrum at either end, the last point is not set to 0. How
do I make this point 0?

A. Zap does a linear interpolation between points; it cannot modify the end points. If
you want to zero the end points use the Truncate or Ultrazap transform instead.
OTHERS
Q. I want to de-select a peak (that is, remove its label), but when I click on the peak it
does not allow me to do this.

A. To de-select a labeled peak, put the cursor on the peak and press the left mouse
button; then, press the Delete key on the keyboard. The peak is now deselected. This
is a change from releases 2.2 and previous.

Avoid putting the cursor on the trace and clicking; this will select the trace and, if
you press the Delete key, the trace will be deleted. If you do this, immediately select
Undo from the Edit menu and the trace will reappear.

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click on peak
label for peak
de-selection

do not click on
trace for peak
de-selection

Q. In a Kinetics document, sequential spectra are displayed from top to bottom; in a

Multi-spectral Document, the spectra are displayed from bottom to top.

A. The order of the spectra in the display window has no particular significance in
Win-IR Pro; they may appear in different order in different circumstances.

Q. How do I select non-contiguous spectra (or columns) in the spreadsheet or in the

search hit list view?

A. Win-IR Pro follows standard Windows NT convention in this matter.

To select non-contiguous spectra: select one spectrum by putting the cursor in its
Spectrum ID cell and clicking the left mouse button. Put the cursor in the Spectrum
ID cell of the second spectrum you want to select; hold down the Ctrl key on the
keyboard and click the left mouse button. Both spectra are now selected; continue
as desired. You can toggle any spectrum between selected and non-selected by
putting the cursor in its Spectrum ID cell, holding down the Ctrl key, and clicking
the left mouse button.

To select contiguous spectra: select the first spectrum by putting the cursor in its
Spectrum ID cell and clicking the left mouse button. Put the cursor in the Spectrum
ID cell of the last spectrum in the group you want to select; hold down the Shift key

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on the keyboard and click the left mouse button. All spectra in the group are now
selected. You can toggle any spectrum between selected and non-selected by
putting the cursor in its Spectrum ID cell, holding down the Ctrl key, and clicking
the left mouse button.

Use the same procedure to select columns in the spreadsheet. To select columns,
put the cursor in the column header cell and click the left mouse button.

More details on selection and other aspects of the spreadsheet are given in Chapter
4.

Q. I have a spreadsheet with many spectra in it. I want to display a group of them and

• see which trace corresponds to which row

• page though the other rows in the document to compare their traces to the
displayed group.

A. First, select the rows whose traces you want to display (see above for selection of
non-contiguous rows). Then, select View / Lock Selected from the main menu. The
IDs of the locked rows will be displayed in italic type. Use the ↑ and ↓ keys to
scroll through the rows of the spreadsheet. In the example below, spectra 2 through
5 have been selected and locked; spectrum 7 is also displayed (it is the uppermost
trace).

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Q. When I select View / History, I cannot find any information about the background
(other than number of background scans) under Scan in the History Browser.
A. Background is not a Scan, but a Ratio parameter. Double-click Ratio in the History
Browser dialog box to get information about the background file name.

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To get information about the background collection parameters:

1. Open the document containing the background file, in this example background.bsp.

2. If there is more than one trace in the document, select the background trace.

3. Select View / History.

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4. Double-click Scan.

5. Scroll, if necessary, to see all the parameters.

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Q Can I print a chromatogram?

A. A chromatogram can be printed by the following method:

1. Select the chromatogram to be printed.

2. Choose Edit / Copy.

3. Choose File / New. Highlight Multi-Spectral Document and click OK.

4. Choose Edit / Paste. This will paste the chromatograms into the new
document as if they were spectra.

5. If you want to add the wavenumber range information to the spreadsheet so

that it can be printed out, first choose View / History.

6. In the History Browser dialog box, highlight Functional Group Analysis to

display its parameters.

7. Highlight Peak Region; click the *Add Columns button; click the OK button.
Peak region information has been added to the spreadsheet.

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8. You can now print these chromatograms as if they were spectra.

Caution
You cannot manipulate these chromatograms and
then paste them back into the original document.
Win-IR Pro no longer recognizes them as
chromatograms. This does not affect the
chromatograms in the original document.

Q. If kinetics or TRS bands go negative, what is the best way to track them using a
FGC?

A. When you create the functional group, select New and click the Edit Parameters
button. When the Edit Peak Parameters dialog box appears, click on the Center tab
page. In the Method portion of the page, select Extreme in Region. This will select the
center to be either the maximum positive or the maximum negative excursion from
zero.

Q. Although my reference single-beam spectrum is good, it is considerably smaller

than the sample so the Noise Level Ratio parameter in the Ratio transform causes
the entire ratioed spectrum to be zero. This is not infrequent in multiple modulation
experiments. How do I overcome this?

A. If you know that the reference spectrum is acceptable, use the following procedure:

1. Use Operations / Spectral Arithmetic / Scalar to multiply the reference spectrum by

a scalar.

2. Perform the ratio.

3. Use Operations / Spectral Arithmetic / Scalar to divide the result by the same scalar,
if required.

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 A
Adding New User
Accounts

WHY HAVE DIFFERENT ACCOUNTS?

In a typical laboratory situation, a Win-IR Pro workstation may be used by a number of
experimenters or by one experimenter performing different experiments. Data
collection parameters are saved for each user account. Therefore each account can be
customized by the individual (or group) experimenter. This means that you can change
parameters without interfering with other users. In addition, using multiple accounts
allows you to easily and automatically separate the data for different experiments into
their own directories.

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SECURITY
Physical security can vary from a single-user non-networked console in a controlled-
access environment to a multiple user console connected to a multi-purpose network in
a non-access-controlled environment. As physical security decreases, use the software
security supplied by Windows NT to compensate for it. The major tools are separate
accounts, user groups, and passwords. In general,

SITUATION SUGGESTION(S)
single user probably do not need passwords

single-purpose passwords on each account

network

multipurpose see your network administrator

network

Proper password creation and use is only part of running a secure system. This is a
large topic covered in the Windows NT documentation and in commercially available
books.

PASSWORDS
Passwords minimize accidental or deliberate attempts to access or alter data. If you use
passwords and your organization does not have a password policy, the following
guidelines may be helpful. Normally, passwords should be at least 6 characters (more
is better); passwords are case-sensitive; blanks (spaces) are not allowed in passwords.
Passwords should have no obvious connection with the user. Do not use telephone
extensions, nicknames, birthdays, anniversaries, etc. Phrases (multiple words run
together) are harder to decipher than single words. A numeral or other non-alphabetic
character also increases security. Do not write down passwords and leave them in desk
drawers, in instrument log books, or attach them to the computer monitor.

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 Appendix A Adding a New User Account 545

ADDING A NEW USER ACCOUNT

Notes
For complete details on adding new users, see your
Windows NT documentation.

Some of the procedures below are designed to allow you

to write scripts to create new user accounts—for example,
setting up accounts with default passwords and forcing
users to change them upon first logon, defining home
directories in terms of user names, etc. See the Windows
NT documentation for details.

In order to create a new user account you must be logged on as a member of the
Administrators group. Windows NT provides a default account for this. The User name
is Administrator with no password as a default. In Windows NT there are a number of
system management functions, including proper loading of software, that can only be
done when logged on as a member of the Administrators group. We recommend that you
change the default (that is, no password) to your own password.

Caution
Do not forget or lose track of this password. There is
no way to retrieve it.

From the Task bar, select Start / Programs / Administrative Tools (Common) / User Manager.

The User Manager dialog box appears.

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Select New User... from the User menu. The New User dialog box appears.

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Username: This is the name the user will log on under. It can be as many as
20 characters (upper or lower case). It cannot include " / \ [ ] : ; |
= > + * ? < >. Username is case-insensitive.

Full Name: The complete name of the user or the user account; it may be any
length and include any character (optional).

Description: A description of the user or the user account; it may be any

length and include any character (optional).

Password: A string of up to 14 characters. Password is case-sensitive. When

the password is typed, it is not echoed on the screen; a string of
the character * is displayed, one for every character in the
password.

Confirm Re-enter the password to make sure that it was entered correctly
Password: the first time. When the password is typed, it is not echoed on
the screen; a string of the character * is displayed, one for every
character in the password.

User Must Change Password at Next Logon: typically, this is used in systems where the
Administrator sets up the accounts but the policy is that the Administrator should not
know the user passwords.

User Cannot Change Password: do not check this; it is not normally needed given the user
pattern for this type of computer.

Password Never Expires: clear this (unselected) if you want to force the a user to change
passwords regularly. This generally increases security for that account.

Account Disabled: do not check this. This is normally used to lock out a user prior to a
possible deletion of the account.

In this example, the New Users dialog box looks like this:

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 548 Appendix A Adding a New User Account

Click the Groups button. The Group Memberships dialog box appears.

All accounts are members of the Users group. Add Power Users group by

1. Highlight Power Users in the Not member of: box.

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 Appendix A Adding a New User Account 549

2. Click the <-Add button.

Power Users is now moved to the Member of: box. Sites may define their own user
groups with abilities to share certain files, etc. If the new user is to be a member of any
of these groups they can be added now in the same way as Power Users.

When all groups have been added, click OK. You are returned to the New User dialog
box. Click the Profile button. The User Environment Profile dialog box appears.

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 550 Appendix A Adding a New User Account

User Profile Path:

an optional network pathname. This allows the administrator to
establish a mandatory user profile on a server. See the Windows NT documentation for
details.

Logon Script Name: the name of a batch file (.CMD or .BAT) or an executable file (.EXE)
that is to be run when the user logs on. These files are normally stored in the directory
c:\winnt\system32\repl\import\scripts. More than one user can have the same logon script.

Note
User Manager does not check to see if the logon script
actually exists. If the specified logon script does not exist
at logon, the log on process will continue. No message
will be sent to the user.

Home Directory:creates the user’s default directory. This directory is the default for File
Open, Save As, and for other applications where the directory is not otherwise
specified. More than one user can have the same home directory. If you use the
variable %username% as the final directory in the home directory pathname, it will have
the same name as the user’s name. In the example above, that would be kinnison. We
recommend that you use c:\users\%username% as a default.

Notes
User Manager does not check to see if the home directory
actually exists. If the specified home directory does not
exist at log on, Windows NT will create this directory.

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If no home directory was specified, the user is assigned

users\default as the home directory. This directory is on
the same device as Windows NT.

Click OK; this returns you to the New User dialog box. Click the Dialin button. The
Dialin Information dialog box appears.

Grant dialin permission to user: select if you want to permit this user to dial in to the
system.

Call Back: specify type of system callback.

No Call Back: disable callback.
Set By Caller: system prompts user for callback telephone number.
Preset To: system calls back only to telephone number entered in this box. This
is recommended for highest security.

Click OK: this returns you to the New User dialog box.
Click OK to create the new user account.
If the passwords do not match you will get this status box.

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 552 Appendix A Adding a New User Account

Re-enter the password and the confirmation. Then click OK again. This returns you to
the User Manager dialog box. You can add more user accounts or close the dialog box.

USER COPY
If you want to add a number of users with the same Groups and Profiles, highlight the
user who is to be copied for example, kinnison).

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Select Copy... from the User menu. The Copy of kinnison dialog box appears.

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 554 Appendix A Adding a New User Account

This prepares a template for a new user with the same Groups, Profile, and Description as
the original user (kinnison).

Enter the desired Username and Full Name. Enter and confirm the Password; select the
password options as described above. If desired, you can change the Groups, Profile, and
Description. For example,

Click OK to create this user account and return to the User Manager dialog box. You can
continue to create new user accounts or close this dialog box.

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 B
Default Color Settings

Colors for most of the objects that appear on the Win-IR Pro screen can be set using
Edit Color from the Options menu. The default factory settings are listed in this appendix.
At release 2.3, unused objects in Pens (Global Graph, Peak Region, and Background)
and Brushes (Region) were removed from Edit Color.

PEN
OBJECT USE RED GREEN BLUE
Crosshair Points for unselected spectra on 255 255 0
quantitation calibration curves
Drop Points Unselected points on a correction 255 255 0
baseline
Baseline Correction baseline 0 0 255
Peak Exact location of trace peaks 240 86 43
ZoomBox In the radar box: the outline of the area 255 0 0
being selected to fill the trace display

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 556 Appendix B Default Color Settings

Spectrum 5 Spectrum displayed, but not selected 170 0 70

Spectrum 4 Spectrum displayed, but not selected 255 200 255
Spectrum 3 Spectrum displayed, but not selected 255 255 0
Spectrum 2 Spectrum displayed, but not selected 0 0 255
Spectrum 1 Spectrum displayed, but not selected 255 0 0
Active Spectrum Selected spectrum 32 255 64
Non-Editable Quantitation plot 255 255 255
Selected
Region Line Dashed vertical lines showing extent of 0 0 0
region
Ticks On x- and y-axes 255 0 0
Aperture Microscope mapping 255 255 255

BRUSH
OBJECT USE RED GREEN BLUE
Background Background for trace and quantitation 0 128 128
plots
Control Point Selected point on a correction baseline 255 255 255
Peak Area under dropped peaks 32 255 64
Stage Tracker Microscope mapping 255 255 255
Collected Point Microscope mapping 0 255 0
Target Collection Microscope mapping 255 0 0
Point
Aperture Handles Microscope mapping 255 255 255

TEXT
OBJECT USE RED GREEN BLUE
Peak Label Wavenumber of dropped/picked peaks 255 255 255
Trace Label Name/type of data displayed 255 255 255

Objects in italic are specific to microscope mapping.

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 C
Importing Spectra

WIN-IR AND GRAMS/386 SPECTRA

Win-IR and GRAMS/386 spectra are identified by their .spc extension. These spectra
were collected on spectrometers controlled by the Win-IR or GRAMS/386 software
running on a PC. The files containing these spectra can be copied via disk, tape, over a
network, etc. to your PC and placed in a directory. To open these spectra, select Open
from the File menu. The Open dialog box appears.

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 558 Appendix C Importing Spectra

Select Grams Spectrum, WinIR (*.spc) from the List Files of Type pull down menu. A list
of files of these types appear. You can change drives to access these files or use the
Network button to connect to other drives on your network.

Select the desired spectrum and open it by clicking the OK button.

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 Appendix C Importing Spectra 559

Convert the spectrum to Win-IR Pro format by selecting Save As... from the File menu.
The Save As dialog box appears.

1. Make sure the Save File as Type is set to Bio-Rad Spectra (*.bsp).
2. Select the desired directory.
3. Type an appropriate name for the spectrum in the File Name box.

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 560 Appendix C Importing Spectra

4. Click the OK button. The spectrum is converted to Win-IR Pro format and
saved on the disk.

Note
Multifiles (*.spc containing multiple spectra) are
imported in the same manner as files with a single trace.
Subfiles can also be previewed, locally or over the
network.

BIO-RAD 3200 SERIES SPECTRA

The Idris_Import application allows you to convert data directly from 3.5-inch 3200
series data disks. You do not need to use a 3200 series computer. It imports all the
contents of a 3200 disk; it is not possible to preview the disk contents, or to select
individual files to import. However, after importing the files, you can choose to delete
those that are not of interest.

Importing 3200 Series Spectra to the PC

1. Insert the 3.5-inch 3200 series data disk in your disk drive.
2. From the Task bar, select Start / Programs / Win-IR_Pro (Common) /
Idris_Import. The Idris_Import Windows Application window appears.

3. Select Import... from the Import menu. The Import Dialog box appears.

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 Appendix C Importing Spectra 561

4. Set the values in this dialog box.

Source Drive: select either A or B depending upon which drive holds the 3200
series data disk.

Destination Drive:use the standard Windows techniques to select a

destination drive and directory in which all the spectra on the source disk
will be stored. Use the Network button, if necessary, to connect to a network
disk.

Create Directory: if a new directory is desired in which to store the converted

files, click this button. The Create Directory dialog box appears.

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 562 Appendix C Importing Spectra

Type the pathname of the desired new directory and click the OK button.

5. Click the OK button to convert all the data files on the 3200 series data disk,
store the converted files in the Destination Drive directory with a .dt extension,
and return to the Idris_Import Windows Application window.

If you click Cancel:, you return to the Idris_Import Windows Application

window without converting the 3200 series data files.

If you click Help:, you enter the on-line Help system.

First, Idris_Import reads the files from the floppy disk into memory. It reports
its progress in the Disk Read status box.

Then, it writes the converted files in the Destination Drive directory with a .dt
extension. . It reports its progress in the Disk Write status box.

6. Repeat as desired for other 3200 series data disks.

7. Select Exit from the Import menu to leave the application.

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 Appendix C Importing Spectra 563

Converting 3200 Format Spectra to Win-IR Pro Format Spectra

Select Open from the File menu. The Open dialog box appears.

Select 3200 Format Spectra (*.dt,*.sb,*.ig) from the List Files of Type pull down menu. A
list of files of these types appear. You can change drives to access these files or use the
Network button to connect to other drives on your network.

Select the desired spectrum and open it by clicking the OK button.

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 564 Appendix C Importing Spectra

Convert the spectrum to Win-IR Pro format by selecting Save As... from the File menu.
The Save As dialog box appears.

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 Appendix C Importing Spectra 565

1. Make sure the Save File as Type is set to Bio-Rad Spectra (*.bsp).
2. Select the desired directory.
3. Type an appropriate name for the spectrum in the File Name box.
4. Click the OK button. The spectrum is converted to Win-IR Pro format.

Note
Multifiles (.dt) and chromatograms (.ch) are imported in
the same manner as files with a single trace; GC
measurements are a typical example of this. Subfiles can
also be previewed, locally or over the network.

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 D
Algorithms and
Functions

SEARCH ALGORITHMS
The equations used to calculate the hit quality index (HQI) are shown below, where:

HQIi hit quality index for library entry i

Uw value of the unknown spectrum at wavenumber w
|Uw| absolute value of Uw
dUw first difference of the value of the unknown spectrum at wavenumber w
|dUw| absolute value of dUw
Liw value of library entry i at wavenumber w
|Liw| absolute value of Liw
dLiw first difference of the value of library entry i at wavenumber w
|dLiw| absolute value of dLiw
|U|2 Σw (Uw)2
|Li|2 Σw (Liw)2

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 568 Appendix D Algorithms and Functions

Euclidean: this is the fastest algorithm; if it is used, then Baseline correct should
be selected.

∑(
2
Uw Liw
(HQI)i2 =
w
|U| |Li| )
Absolute value:

(HQI)i2 = ∑(w
|Uw|
|U|
|Liw|
|Li| )
Derivative:

∑(
dLiw 2
dUw
(HQI)i2 =
w
|U| |Li| )
Abs. Value Deriv.:

(HQI)i2 = ∑(w
|dUw|
|U|
–
|dLiw|
|Li| )
Correlation: similar
to the Euclidean algorithm except that both the unknown
spectrum and the library entry values are measured from their respective means.
This should remove any constant bias from either the unknown or the library
entry. Masking is applied before the means are calculated to prevent any
contributions from masked points to the final HQI.

∑(
2
Liw
(HQI)i2 =
w
Uw
|U| |Li| )

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 Appendix D Algorithms and Functions 569

where

n number of points in the unknown/library entry

Uw Uw - Σw (Uw)/n

Liw Liw - Σw (Liw)/n

|U|2 Σw (Uw)2

|Li|2 Σw (Liw)2

APODIZATION FUNCTIONS
In data collection the interferogram is sampled over a finite distance. Information that
would be present at a larger distance (greater retardation) from the centerburst is lost.
This causes a distortion in the shape of the narrow lines because the information for
these lines was truncated at the limit of resolution. This is usually noticeable only for
gas spectra. Apodization is a method to control the line shapes; this causes some
decrease in resolution. Apodization is also a part of transforms such as deconvolution,
filtering, etc.

Boxcar
The boxcar apodization function is of the form:

1 for − ∆ ≥ δ ≥ ∆
0 for δ > ∆

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 570 Appendix D Algorithms and Functions

It gives the narrowest peaks (FWHH-full width at half height) of any of the functions.
However, it also introduces more sidelobes than other apodization functions. This can
cause problems as the sidelobes can overlap bands in gas phase spectra.

Norton-Beer
The Norton-Beer apodization functions are of the form:

i
n  δ 2
∑ Ci 1 −   
i =0   ∆ 

Normally, n = 3. The coefficients for the three preferred functions are:

C0 C1 C2 C3
Norton-Beer weak 0.348093 -0.087577 0.703484 0
Norton-Beer medium 0.152442 -0.136176 0.983734 0
Norton-Beer strong 0.045335 0 0.554883 0.399782

Trapezoid
The trapezoidal apodization function combines the boxcar with the triangular. If D(δ)
is the boxcar function (see above) and k∆ is the point at which the triangular portion of
the function begins, then the trapezoidal function takes the form:

 1   δ   k  δ  δ 
  D(δ )1 −  −   D  1 −
1− k   ∆   1 − k   k   k∆ 

0 k∆ ∆
Usually k is taken to be 0.5; in this case, the equation reduces to:

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 Appendix D Algorithms and Functions 571

 δ  2δ 
2 D(δ )1 −  − D(2δ )1 − 
 ∆  ∆

Happ-Genzel (Hamming)
The apodization function is of the form:
 πδ 
0.54 + 0.46 cos  
 ∆

The FWHH and ILS functions given by this apodization are similar to those given by
the triangular function. The Happ-Genzel apodization gives a larger first side lobe than
the triangular function; however, the second and subsequent side lobes are smaller than
for the triangular function.

Triangle
The apodization function is of the form:

δ
1− for − ∆ ≤ δ ≥ ∆
∆
0 for δ > ∆

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 572 Appendix D Algorithms and Functions

PHASE CORRECTION
The phase correction is used in calculated the single-beam spectrum from the
interferogram. In the phase-correction method of L. Mertz, the instrument phase is
calculated by computing a low-resolution array of points selected symmetrically about
the centerburst, generating an array of complex values. Each of these complex values
has a unique phase angle in the range 0 to 2π.

A symmetric array is used so that the apodization function is even, and has zero phase.

The phase angle itself is not calculated. Calculating the phase angle directly

θ = arctan (R/I)

can lead to ambiguity as to which quadrant the angle is in. For example, the equal
ratios

+R/+I + = -R/-I could be in the first or third quadrants and

-R/+I + = +R/-I could be in the second or fourth quadrants

where R and I are the real and imaginary parts.

Instead the unit vectors (Rp’ and Ip’) are calculated and saved for later stored phase
calculations

Rp’ = Rp/√(Rp2 + Ip2)

Ip’ = Ip/√(Rp2 + Ip2)

R = real part; I = imaginary part; p = phase.

Phase correction can now be considered to be a vector rotation (subtraction of the phase
angle) in Cartesian space.

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 Appendix D Algorithms and Functions 573

The results of the full resolution spectrum Fast-Fourier Transform (FFT)—Rs and Is—
are rotated to give the final phase-corrected results (Rf and If), that is,

Rf = RsRp’ + IsIp’

This implementation allows phase correction to be performed on complex data entirely

in the Cartesian co-ordinate domain, without time-consuming operations like
computing transcendental functions such as arctan(x), which have singularlities and are
single-valued only for ±π/2.

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 E
Hardware Configuration

Before you are able to collect data, you must configure the hardware. This tells
Win-IR Pro what hardware is installed on the optical bench.

1. If Win-IR Pro is running, Exit from it.

2. Select Start / Settings / Control Panel from the Task bar.

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 576 Appendix E Hardware Configuration

3. Double click the Spectrometer icon. The Spectrometer’s Optical Bench

Configuration dialog box appears.

4. Select the spectrometer that you are using from the pull-down menu.

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 Appendix E Hardware Configuration 577

Note
The Interface feature is designed for use by Bio-Rad
Customer Service; do not change the default settings
unless directed to do so. It is possible to change the IRQ
of the spectrometer controller card to any value from 10
to 15 if there is an IRQ conflict with another card. If you
change the jumper settings on the spectrometer control
card (for I/O Port and/or Memory Address), you must
also change these values using the pull-down menus on
the dialog box. In general, you should not change these
values.

The example below uses the FTS 6000. The configuration tab pages may be
somewhat different for other spectrometers.

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 578 Appendix E Hardware Configuration

5. Click the Detectors tab to see the Detectors tab page.

status
line

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 Appendix E Hardware Configuration 579

6. Use the pull-down menus to select the Type of detector at each location.
When you select a detector type, additional information about that detector
appears in the status line.

Note
Not all spectrometers have provision for detectors at all
locations.

7. In the right-hand (Name) box, type a brief, meaningful description of the

detector; for example, GC, microscope, etc. This description will then
appear in the Optics tab page when you select one of the scan entries from
the Collect menu.

8. Click the Sources tab to see the Sources tab page.

9. Use the pull-down menus to select the Type of source at each location.
When you select a source type, additional information about that detector
appears in the status line.
Note
Not all spectrometers have provision for dual sources.

status line

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 580 Appendix E Hardware Configuration

10. In the right-hand (Name) box, type a brief, meaningful description of the
source; for example, Ceramic, far-IR, etc. This description will then appear
in the Optics tab page when you select one of the scan entries from the Collect
menu.

11. Click the Aperture tab to see the Aperture tab page.

12. Use the Source Aperture pull-down menu to select the aperture that is
installed in your spectrometer. If you have a Raman or Emission experiment
aperture, select it from the Raman/Emission Aperture pull-down menu. . This
information will then appear in the Optics tab page when you select one of
the scan entries from the Collect menu.
13. Click the External Switches tab to see the External Switches tab page.

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 Appendix E Hardware Configuration 581

14. Enter the appropriate information in the boxes if you have external switches
installed.

15. Click OK to register these values and return to the Control Panel program
group. Cancel returns to the Control Panel program group without registering
any change to the values.

If you have made any changes the Optical Bench Configured message box
appears.

16. Close the Control Panel program group.

17. Select Start / Shut Down from the Task bar.
18. Reboot the system. You can now run Win-IR Pro.

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 F
3200 Series
Spectrometer
Parameters

If you import spectra collected from the Bio-Rad 3200 series spectrometers, the header
elements will be available through View / Property Browse Bar. The meaning of these is
given in the table below.

A_SYM The type of interferogram originally collected—either

symmetrical double-sided) or asymmetrical (single-sided)

apt Aperture value (in cm-1) or NI (not installed).

beam Beam destination.

created Date of creation of the file whose trace is displayed.

det Detector.

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 584 Appendix F 3200 Series Spectrometer Parameters

ELWN Wavenumber of the He-Ne alignment laser (in cm-1).

FSTAT File status is either GOOD or BAD. BAD means the function
executed incompletely or failed.

grr The gain ranging radius in points around the centerburst.

ID Win-IR Pro identification of this spectrum within this

document. This is the entry in the left-hand column.

PKLOC Position, in points, of the centerburst of the interferogram.

RES Scanning resolution (in cm-1).

SCANS Number of co-added data collection scans.

sen Amplifier gain.

SpectName Name of the spectrum; this is the same as the entry in the
default Name column. The entry in this cell is displayed as
the label for the active trace.

speed Scanning velocity (in KHz).

TYPE Type of spectrum: absorbance, transmittance, etc.

UDR Undersampling ratio.

xlabel Label for the X axis; the default is wavenumber.

YData Display of the spectrum.

zff Zerofilling factor.

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 G
Win-IR Pro File
Extensions

The file extensions used in the Win-IR Pro software are listed in the table below..

.bpt Bio-Rad print composition template files, used to organize spectral

information on a page for printing.

.brc Bio-Rad-supplied library structure files.

.bri Bio-Rad-supplied library index of spectra

.brp Bio-Rad-supplied library peaks files.

.brn Bio-Rad-supplied library name files.

.brs Bio-Rad-supplied library spectra files. against which unknown spectra

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 586 Appendix G Win-IR Pro File Extensions

will be compared looking for matches. There are several different files
that make up a library.

.bsm Bio-Rad Microscope Mapping spectra generated by Shadow Pro.

.bsp Spectral data collected from a spectrometer using the Win-IR Pro
software, or other data converted and saved as the Bio-Rad Spectra
format.

.bsq Calibration document used for simple quantitative analysis.

.cdf AIA data exchange files.

.clm Collect Method files that store scan parameters. The default storage
directory is c:\Program Files\Win-IR Pro\MyExperiments.

.csv Spectral files that are in spreadsheet format (do not confuse this generic
spreadsheet with the one in the lower half of the Win-IR Pro windows).

.dat Array image files.

.dat Sadtler library chemical structure files. These should not be opened using
File / Open. [Not used within Win-IR Pro]

.dt Spectrum collected from a spectrometer using the Bio-Rad 3200 series
software (DDS).

.dxf Data triads exported from three-dimensional views. These files can be
opened by Autocad and compatible applications.

.idx Library index files—used by both Sadtler and Galactic libraries.

.ig Interferogram collected from a spectrometer using the Bio-Rad 3200

series software (DDS).

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 Appendix H Win-IR Pro File Extensions 587

.inf Sadtler library properties files. These are not converted and are not used in
Win-IR Pro.

.ipk Sadtler library IR Peaks files.

.ipl Galactic library peaks files. These are not converted and are not used in
Win-IR Pro.

.irf Sadtler SearchMaster files.

.isl Galactic library spectra files.

.ism Sadtler library IR spectra files

.itl Galactic library name files.

.kbg Background spectrum used for kinetics data collection.

.kin Set of related spectra (and optional analysis) obtained from kinetics data
collection.

.lib Galactic library special files. These are not converted and are not used in
Win-IR Pro.

.na Digilab 3200 library names files.

.nam Sadtler library names files.

.ni Digilab 3200 library names index files.

.pct The print template files that contain information about how a page should
be formatted with information to be printed out.

.phs Phase array storage files.

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 588 Appendix G Win-IR Pro File Extensions

.pls Calibration document used for PLS analysis. PLS is a separately

purchased product.

.pv Stores the values of the parameters used by Win-IR Pro when you log on
to the computer.

.s1 Digilab 3200 library dual-resolution first spectra files.

.s2 Digilab 3200 library dual-resolution second spectra files.

.sb Single-beam collected from a spectrometer using the Bio-Rad 3200 series
software (DDS).

.seq Raw data files (array image date).

.sl Digilab 3200 library ordinary (single) resolution spectra files.

.spc Spectral data collected from a spectrometer using Win-IR or

GRAMS/386, or converted from other formats to GRAMS format
.txt Sadtler library text files. These are not converted and are not used in Win-
IR Pro.

.vpk Sadtler library vapor phase peaks files. These are not converted and are
not used in Win-IR Pro.

.vps Sadtler library vapor phase spectra files. These are not converted and are
not used in Win-IR Pro.

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 H
Win-IR Pro Files

Win-IR Pro files are normally installed on disk C in C:\Program Files\Win-IR Pro. The
following directories are under C:\Program Files\Win-IR Pro.

Caution
The contents of these directories are altered by
installations. Do not store your files in the Win-IR
Pro directory or any of its subdirectories. Create your
own directories for data storage.

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 590 Appendix H Win-IR Pro Files

bin: contains the executable files and other files necessary to run Win-IR Pro.

Executable file for importing spectra collected on 3200

series-controlled spectrometer

Advanced search (requires enabling floppy)

Executable file for Win-IR Pro

Win-IR Pro help file

Load history:
contains records of the installation process. They are mostly of use to
Bio-Rad Customer Service.

MyExperiments: contains the named collect method files.

Sample data: contains a number of spectra that you can copy and use to practice working
with Win-IR Pro. Check the README.TXT file for late additions that are not included in
the list below.

40BLNKNM.IG Interferogram of sample for PAS linearization

40BLNKSY.IG Interferogram of shifted sample
40GCREF.IG Interferogram of reference for PAS linearization
8-IN.BSP In-phase spectrum
8-QU.BSP Quadrature spectrum
ABSPOLYS.BSP Absorbance spectrum of polystyrene
ASTM-5.SPC Polypropylene/Polyethylene film spectrum

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 Appendix H Win-IR Pro Files 591

BENZENE.BSP UV-Visible spectrum

BETH.BSP
BKG.BSP Background single-beam spectrum
DEFAULT.PV default parameter values
DICHLORO.BSP Gas phase spectrum
DRINKS.BSP Spectra of two soft drinks containing sugar
ETGLYCOL.SPC Ethylene glycol
HGNO3.DT Raman spectrum of HgNO3; .dt format
ITPP.BSP Isotactic polypropylene
ITPP.CSV Isotactic polypropylene
ITPP.SPC Isotactic polypropylene
KINBACK.KBG Kinetics background spectrum
KINETICS.IG Kinetics interferogram
KINETICS.KIN Kinetics spectra
KINETICS.SP Kinetics spectra
KNO3.DT Raman spectrum of KNO3; .dt format
LUTHER2.BSP Series of spectra of a time-varying event
P0000880.BSP “noisy” GC/IR spectrum
P0000880.SPC “noisy” GC/IR spectrum
pas2.bsp Photoacoustical spectrum
POLYR.BSP Spectrum of polystyrene
POLYS.BSP Spectrum of polystyrene/polycarbonate resin
RAMAN.BSP Raman spectrum of KNO3 and HgNO3; .bsp format
SHINY.BSP A reflection spectrum
SMOOTH.SPC
SPIKE.BSP A spectrum with many high-frequency spikes
STRETCH.BSP Spectra from polymer stretching experiment
SUGAR.DT
SUGAR2.BSP Original sugar/water spectra
SUGAR2.BSQ Sugar solution calibration document

Scripting library: contains software and files necessary for the execution of the scripting
language.

Note

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 592 Appendix H Win-IR Pro Files

Scripting can only be used if you have purchased the

optional scripting language (Bio-Rad part number 099-
1856).

Scripting samples: contains

a number of examples of scripts that you can copy and use
for development of your own scripts.

ATRCorrect Starts Win-IR Pro, opens a file and selects the first spectrum in
that file. It then gets a copy of the data points in the spectrum
using DataArray property. This array is transformed using an
ATR Correction algorithm and passed back to Win-IR Pro.
HundredPercentLine Collects two scans, ratios them, and presents the hundred percent
line
Normalize Starts Win-IR Pro, opens a file and selects the first spectrum in
that file. It then gets s copy of the data points in the spectrum
using DataArray property. This array is transformed by
normalizing it between 0 and 1 and passed back to Win-IR Pro.
PeakAreaIntoExcel Starts Win-IR Pro, opens a file and selects the first spectrum in
that file. It then drops a peak and calculates its area. The area is
pasted into a spread sheet cell after starting Excel, adding a
workbook, and getting the first sheet.
ScanIntoOneFile Starts Win-IR Pro, opens a file, collects a background and saves it.
You can then collect a number of spectra (up to 5); they are
ratioed against this background and all are saved in this file.
ScanIntoSeveralFiles Starts Win-IR Pro, opens a file, collects a background and saves it.
You can then collect a spectrum; it are ratioed against this
background and are saved in this file. You can then collect
another spectrum; it is saved in another file along with the
previously collected background. The default in the script is to
collect up to 5 spectra.
Transform Starts Win-IR Pro, opens a file and selects the first spectrum in
that file. It then performs the apodization transform on that
spectrum. This template can be modified for other transforms.

Spectrometer Configuration: contains the files generated by, and required for,
spectrometer configuration.

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 I
Quantitative Analysis

For a good overview of the quantitative analysis process, including dealing with solid
and gaseous samples, see Compton, Senja V. and Compton, David A. C., “Quantitative
Analysis—Avoiding Common Pitfalls,” Practical Sampling Techniques for Infrared
Analysis, edited by Patricia B. Coleman, Boca Raton, FL: CRC Press, 1993.

Quantitative analysis methods cover, but are not limited to, spectral subraction,
transmittance measurements of optical filters, library search comparisons, pathlength
determinations, discriminate analysis, and the more traditional concentration reports
based on direct or indirect application of the Beer-Lambert Law. In this appendix, the
issues affecting this last form of quantitative analysis are addressed, although many of
the topics discussed are applicable to the other methods1.

1
See “Practical Sampling Techniques for Infrared Analysis,” edited by P. B. Coleman, CRC Press, Boca
Raton, FL, 1993, for a more in-depth discussion.

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 594 Appendix I Quantitative Analysis

GENERAL CONSIDERATIONS
Several important criteria need to be met prior to the numerical calculations needed for
the reporting of quantitative results. First, the analyst must adequately define the
quantitative problem under consideration. Some of the issues to be addressed are (but
not limited to):

• How quickly do the results need to be reported?

• Who is to perform the analysis and what is his/her skill level?
• Where is the analysis to take place (environmental conditions)?
• How frequently does the analysis need to be performed?
• What is to be measured, in what units, and how precisely and accurately?
• What is (are) the expected concentration range(s)?
• Are there multiple suppliers for the components?
• Are there multiple production methods/facilities?
• Are any materials substituted for one another or added occasionally to adjust
selected properties, such as pH?
• Does the material change with time?
• What consumables are to be used?

From the answers to these questions, a rough idea of the actual analysis requirements
and procedure can be made—IR techniques eliminated due to lengthy analysis time,
lack of operator skill level, or cost of equipment/consumables; suppliers from whom to
get components; and the required range to be covered by the analysis.
Additionally, the analyst must become familiar with all the species present in the
samples to be analyzed and their compatibilities with the materials/equipment that they
come in contact with during analysis. Nothing can replace good laboratory practices
nor the knowledge of general chemistry principles when analyzing samples. Such
things as halide compound reactivity, water incompatibility, sample drying in inert
spectrometer atmosphere, and chelating reactions to form metal complexes in
accessories cannot be overlooked.

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 Appendix I Quantitative Analysis 595

CALIBRATION STANDARDS CONSIDERATIONS

The second step of a quantitative analysis problem is to “make-up” the standards to be
used for the calibration of the quantitative analysis method. Ideally, the standards
should come directly from the production facility so that they reflect the actual
processing conditions. However, in most instances this is not feasible and they must be
synthesized in the analytical laboratory. In all cases, the selection of samples to be used
for a calibration must adequately cover the expected range variation(s). This means that
the expected extreme concentrations (minimum and maximum) for each component
must be included as extrapolation outside the calibrated concentration range is
questionable. This does not mean that the entire range of possible concentrations (0-
100% for each component) needs to be covered, unless that situation is expected to
arise. Additionally, if the accuracy at the extremes of a range is important, the
concentrations covered by the calibration samples must span a larger range than the
expected concentration for that component. For example, if c is the expected
concentration of a component. The range for the concentration can be expressed as c+d
to c-d. For accuracy at the extremes of this range, the concentration range covered by
the calibrations standards should be c+1.5d to c-1.5d.

The standards must be composed of linearly independent concentration data. Linear

dependence exists in simple dilutions (multiples) of a single standard, where the
components are in constant relative proportions to one another throughout the series, or
in instances when the concentration of two or more components adds to a constant. In
the first case, unless each component has an isolated unique infrared absorption band
exhibiting no overlap with any other component, no interactions occur among the
chemical species, and the samples are examined with a reproducible, known pathlength,
the standards would be useless in the calibration of a working quantitative method as
they would not describe the expected compositions of the sample to be analyzed. The
second situation provides a case in which a plane is defined in space, that is, the sum of
the concentration(s) is a constant. If this constant changes to a new value (for example,
from 12% to 10% in a batch production) the analysis is not defined and extrapolation of
the method to obtain a quantitative value is invalid.

When selecting samples to be used for calibration standards in a system composed of

multiple species, at least two components should be at differing levels in each blend.
Typically, this eliminates linearly dependent data sets. All component concentrations
should be represented the same number of times in the calibration standards. This
prevents a single component from dominating the spectral features used for quantitative

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 596 Appendix I Quantitative Analysis

measurements. Additionally, the standards should be composed of evenly separated

concentration levels across the expected range to permit interpolation between data
points in the calibration.

The system under study for quantitative analysis should be overdetermined. This is
accomplished by recording the spectra of more standard mixtures than there are
components in the system. The use of more data than is necessary reduces the effect of
random errors. As a rule of thumb, two times the minimum number of standards is
adequate. An additional advantage of this oversampling is that back-calculations can be
performed which provide:

• an indication of the quality of the calibration (average error)

• a detection of perturbation in a system by determining one component less

accurately

• a means of discovery for deviation from Beer’s law at high concentrations

• an identification of a bad standard or poor measurement in the calibration set

• evidence for inappropriate selection of spectral regions for measurements.

In an exactly determined case where only the minimum number of standards have been
used, a “perfect-fit” of the data with no insight into the “goodness” of the quantitative
method exists.

The precision of the standard mixture compositions is generally better than the
precision of the analytical system under development. The importance of significant
figures cannot be stressed strongly enough. If the standards are prepared with
concentrations good to only two significant figures, the values reported for each of the
components in the final analytical report are good to only two significant figures.
Information cannot be obtained where no real data exists. Additionally, if other
analytical techniques are used to provide concentrations values for the standard
samples, then the errors reflected in those measurements are incorporated into the
infrared analysis.

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 Appendix I Quantitative Analysis 597

In a multicomponent analysis, the mutual interference of the spectra, not the number of
components, is what is being measured. The components cannot be determined
individually, but all must be determined together. Therefore it is extremely important
to use the actual materials used in the formulation of the final product rather than
ultrapure grades of the components. This also means that standards including
alternative supplier sources of components must be prepared. The “impurities” in the
components have specific infrared absorbances which contribute to the overall
composite spectrum of a standard. If their contributions are not included in the
calibration step, their absorbances cannot be compensated for in the measurements used
to calculate concentrations.

Finally, the analysis should be tested frequently as part of a normal operating procedure
to verify its validity. Reanalyze samples previously reported (assumes product stability)
or analyze synthesized blinds (consisting of both in- and out-of-specification products).

Summary of Important Issues for Calibration Standards

• Actual production starting materials must be used in fomulation of standards

• Full expected ranges for each component must be incorporated
• Dilutions are not valid standards
• No constant concentrations for components or sums of components are
allowed
• Even spacing of concentration levels across expected range is advised
• Variation of levels for at least two components in each standard minimizes
linear dependence of data
• Same number of concentration variations for each component in standards
prevents dominance by a single material
• Overdetermination (more standards than minimally required) reduces the
effect of random errors
• Significant figures determine final reported analytical values
• Errors reflected in methods for concentration determination are incorporated
into IR method

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 598 Appendix I Quantitative Analysis

ERROR SOURCES
Some of the most common sources of errors in preparing samples for examination,
either calibration reference or quantitative analysis, are discussed below. The detection
of a potential problem can often be made quickly and easily when every reference and
each sample is examined in duplicate (two complete separate samplings) and then
compared. This procedure minimizes random errors and verifies reproducibility in
measurements. Additionally, multiple examinations verify the homogeneity of the
material, insuring that the tiny portion used for the analysis is representative of the bulk.

Solvents
The use of solvents in preparation of a sample may introduce numerous problems.

First, it may cause a reaction to take place—intermolecular (for example, hydrogen

bonding, aggregation, preferential conformation, or unfolding) or chemical (formation
of a new species). This behavior can be detected by direct comparison (through overlay
plots, spectral subtraction, etc.) of two or more reference standard spectra and observing
any shifts in band frequencies or the appearance of new absorption bands. Another test
is to place a sample in the spectrometer and acquire spectra at time intervals. Direct
comparison of these spectra will reveal the presence of any species created by chemical
reactions over time.

Second, dilution of a sample by a solvent may cause the presence of micelles,

emulsions, suspensions or precipitates to be formed in the resultant solution. All these
behaviors result in irreproducible data collection and preclude useful quantitative
measurements.

Third, when a solution is examined, the sample vessel must be adequately sealed to
eliminate evaporation of volatile species which would affect the overall reported
concentration levels.

Fourth, it is important to verify that the solution does not have any entrapped gases
(bubbles) as the pathlength of the sample would change in addition to the concentration
of components (two variables).

Fifth, solvents typically contain a number of “impurities” which are purposely added for
stability (for example, buffers). Variations in the concentrations of these species will

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 Appendix I Quantitative Analysis 599

contribute to the overall spectrum used for calibration or analysis. Additionally, the
“impurities” may chemically react with the system under investigation by serving as a
catalyst, binding as a complexing agent, reacting with creation of new chemical species,
or binding to active sites.

Sixth, the use of volatile solvents for cleaning purposes (for example, washing internal
reflection elements, liquid cells, spatulas, mortar and pestle, etc.) may leave residue
following evaporation. One easy test to check for solvent volatility is to place some of
the solvent onto an infrared transparent window and allow it to evaporate under the
corresponding experimental conditions used for the analysis. A transmission spectrum
collected through this window would record the spectral features of any interfering
residue species.

Seventh, the use of solvent evaporation for sample preparation may cause residual
solvent to be retained in the sample through incomplete evaporation (entrapment,
adsorption to active sites, complex formation, etc.).

Eighth, water (atmospheric moisture) may be introduced into a sample by the cooling
process resulting from the rapid evaporation of a solvent with a low boiling point (for
example, ether, acetone, methylene chloride). The strong spectral features due to water
cause significant interferences when making quantitative measurements. Additionally,
chemical reactions may occur in moisture-sensitive samples.

Gases
It is extremely important to carefully control both the temperature and pressure when
performing quantitative measurements upon vapor species. Absorption band
intensities, widths (pressure broadening), and areas are dependent upon both of these
conditions. The extinction coefficient of a species in terms of its partial pressure may
be a function of the total pressure of the sample. It is highly recommended that samples
be pressurized to 760 Torr with an inert gas (such as nitrogen) to minimize the effects
of pressure broadening and be allowed to achieve thermal equilibrium following filling
of the gas cell prior to any spectral measurments.

One problem encountered in trace-component analysis when using long-path gas cells is
due to selective adsorption or desorption of materials from the cell walls. The cell
should be evacuated and filled (or flushed with an inert gas) several times before a
spectrum is recorded to erase the cell “memory”.

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 600 Appendix I Quantitative Analysis

Compatibility of vapor species with the materials composing the gas cell should be
known. Hydrogen fluoride and tungsten hexafluoride gases are extremely corrosive and
require the use of specially designed cells as they attack most glass and halide salt
surfaces. Many organics will attack the polymer O-rings used to seal some gas cells,
resulting in leaks or the creation of new species from chemical reations. The use of
grease for ground glass joints in manifold connections and stopcocks should be
minimized, with selection of only heavy grease with low volatility. This is because it
may selectively absorb some gaseous species (subsequently providing memory effects)
or may appear in the recorded sample’s spectrum as it volatile.

Polymers
Standard reference samples for polymers are typically difficult to obtain, due, in part, to
slight variations in their formulations which may be attributed to the method used in
their manufacture. Thus, a polymer generated from a copolymerization process will not
exhibit identical features to that corresponding to a block polymer nor to one comprised
of individual homopolymers, due to different bond formations (for example,
crosslinking) and functional group environments (that is, with associations such as
hydrogen bonding).

A polymer’s crystallinity and stereochemistry is dictated by the reaction mechanism

causing crosslinking a specific sites. Since catalysts (both organic and inorganic) are
oftentimes used to control the reaction pathway to generate a specific molecular
structure in the polymer, they contribute unique spectral features (including light
scattering particles) to the composite spectrum of the sample. Thus, polymers prepared
from different catalysts cannot be realistically analyzed by the same calibration method.

An additional issue concerning polymer formulations is the presence of trace additives

such as UV inhibitors, antioxidants, flame reatardants, plasticizers, and antiozonants,
which all exhibit spectral absorbances. Their variable concentration levels must be
taken into account when recording the spectra used for calibration.

Films
One of the most difficult problems in making standard transmission measurements of a
film is that in uniformity, both in sample thickness and homogeneity. Free-standing
films should have their thickness reported as an average based upon several
measurements taken across the film by a micrometer. Several spectra for each film

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 Appendix I Quantitative Analysis 601

sample should be recorded at different rotations in the beampath, with the quantitative
results reported as an average from the measurements, in order to minimize the effects
of nonuniformity in the sample pathlength.

Pressed films, prepared between the platens of a hydraulic press may require heat to
allow for the deformation of the sample into a thin sheet. The temperature, length of
exposure, and pressure must be carefully controlled to insure that the same physical and
chemical state of the sample is achieved each time. Spacers can be used to insure that
all the films are produced with the same thickness. In all instances, films should be taut
and flat during examination, free of crevices and holes, and mounted without stretching,
which would alter film thickness and introduce possible stress orientation.

Films cast from volatile solvents may contain additives (such as BHT, butylated
hydroxtoluene) or other low volatility impurities. Spectral absorbances due the
interloping species will adversely affect the development of any method or the analysis
of samples. A spectrum for a “blank” of the residue remaining (if present) after solvent
evaporation should be recorded to discover if any infrared active species is present. A
variety of other problems may also arise when casting films from solvents - incomplete
volatilization (retention) of the solvent, condensation of atmospheric moisture from
rapid cooling during solvent evaporation, occurrence of polymorphism and formation of
aggregated domains based upon evaporation rate, degradation (for example, oxidative
decomposition) when applying heat to accelerate solvent evaporation, inclusion of
entrapped bubbles (air or other gaseous species), or chemical reaction with the solvent
used for dissolution.

The use of rolling to produce films offers several disadvantages—carryover

contamination from previous samples due to incomplete cleaning, difficult
reproducibility in temperature and pressure parameters, possible evaporation of volatile
materials, and irreproducible orientation effects may be introduced into the final film.
If a method is developed based upon production-rolled film, all samples should be
marked with the roll direction. The analysis then must involve positioning the film in
the spectrometer in the same direction for each examination.

There are two additional problems which may be encountered when performing
quantitative analysis on films by transmission - opacity and particulates. The first
means that typically the energy will be low, resulting in poor signal-to-noise ratio, or
that the sample will possess regions of total infrared absorbance, useless for quantitative

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 602 Appendix I Quantitative Analysis

analysis. The second condition results in the scattering of the infrared radiation as it
passes through the film. As the scattering is based upon particle size, it results in
various nonlinear anomalies in the spectra. Usually these particulates are not uniformly
distributed throughout a film, residing as aggregated domains, which makes quantitative
analysis difficult, if not impossible.

Liquids
The standard liquid cell is normally filled using a syringe which attached to its Luer
Lok fitting. Most plastic disposable syringes are internally coated with a silicone
lubricant which can be easily extracted into organic solvents. Additionally, the
plasticizers present in some rubber plunger tips can be selectively extracted by organic
solvents. Therefore, the use of glass syringes or pipettes is highly recommended to
prevent contamination.

Typically, the liquid sample is introduced into the liquid cell from the bottom fitting so
that the air is forced upwards through the top opening in the cell to prevent entrapped
bubbles. For the filling of extremely thin cells (<0.1 mm), a second, empty syringe is
attached to the upper port and the plunger withdrawn to create a vacuum in the cell,
causing the sample to flow into the space.

Variable-temperature liquid cells require that the analyst allow sufficient time prior to
collecting a spectrum so that thermal equilibrium is reached, eliminating any spectral
artifacts related to changing temperature.

The best quantitative measurements are made if the liquid cell is not moved after the
introduction of the first sample by using a flow-through design. This is because
sample-cell positioning is difficult to reproduce accurately. If this is not possible, the
cell should always be inserted into its holder in the same direction each time and fit
snugly into its holder to guard against any motion.

It is advisable to periodically measure the liquid cell thickness as many window

materials slowly dissolve with use. A method for determining or verifying the
pathlength of a cell (or thin film) is to use the interference fringes superimposed on the
baseline of its spectrum. This is done by recording the spectrum of the empty cell
ratioed against the empty beam of the instrument. The distance can be calculated by:

Pathlength = [10 x n]/2[f1 -f2]

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 Appendix I Quantitative Analysis 603

where pathlength is cell thickness in millimeters, f1 and f2 are frequencies (cm-1) of two
maxima from the interference fringes observed in the empty cell spectrum, and n is the
number of maxima occurring between f1 and f2.

Many liquid cells are equipped with halide salt windows which are hygroscopic.
Therefore, the analyst must keep in mind that the presence of water in any amount will
degrade the performance (subsequently the quantitative measurement) of the cell
through fogging, etching, and pitting of the window. This moisture may be present as a
component in the sample under analysis or may result from exposure to a damp
environment or use of a poor cleaning technique which permits condensation of
atmospheric water vapor.

Internal Reflectance Spectroscopy

Carefully designed IRS experiments can permit quantitative measurements to be made.
However, data collection must be reproducible. One of the major design considerations
is the repeatable contact of the sample against the internal reflection element (IRE),
inclusive of total IRE coverage and quality of contact (same pressure, no air pockets).
Band-ratioing techniques may be used to perform quantitative measurements, as they
are somewhat pressure independent as long as the bands are in the same general spectral
region (typically no more than 100-200 cm-1 apart).

Diffuse Reflectance Spectroscopy

Typically a mixture consisting of between 1-10% by weight of finely powdered sample
in an inert diluent is used for analysis. The physical mixing of the powders should
insure uniform distribution throughout the mixture without introducing pressure effects
or moisture inclusion. Neat samples should only be used when measurements are to
made on weakly absorbing spectral regions. The diffuse reflectance cup (sample
holder) requires reproducible loading, with pressure being applied to uniformly pack the
powder and create a flat surface. A background spectrum of the diluent material is used
for obtaining a ratioed spectrum and should be acquired from the same batch (lot and
grinding session) of the material used to dilute the sample.

Reflection does not occur at exactly the same frequency as absorption for strong bands,
which causes band shifts and distortions (Reststrahlen). The reflection contribution,
comparable to stray light, can be somewhat reduced for a sample by decreasing the
particle size or more tightly packing the material into the sampling cup. Some studies

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 604 Appendix I Quantitative Analysis

have shown that the off-axis accessory design exhibits linear absorbance response over
a wider range of usable sample concentrations than the straight through design.

Powdered/Ground Samples
When sample morphology dictates that it acquire the form of a fine powder for
examination (for example, pressed halide disks, diffuse reflectance, nujol mulls) usually
a ball mill or mortar and pestle are used. However, it must be remembered that the
pressure and heat generated in the grinding process may cause changes to the sample
including polymerization, degration, oxidation, loss of symmetry, and alteration of
crystallinity. Minimization of structural damage can sometimes be achieved by
performing a “moist” grind (with isopropyl alcohol for inorganics) or using ultrasonic
radiation.

Grinding the sample in the presence of a halide salt is not advisable. Rather, the two
powders (as in diffuse reflectance and pressed pellets) are physically mixed following
their separate grindings. The first reason is that the differences in hardness between the
sample and the diluent will cause nonuniformity of particle size between the two
materials, with the “softer” material simply deforming or being ground finer. However,
more importantly, are that ion exchange (for example., organic acid becoming an acid
salt) and isomorphous substitution of cations in a latticework may occur causing the
“wrong” material to be analyzed.

The greatest obstacle for the analysis of powdered solids, is making the particle size
small, uniform and reproducible. The size should be small, less than the wavelength of
radiation used for its examination as light-scattering takes over from absorption with
increasing particle size and may become the predominant effect in the recording of its
infrared spectrum. Reproducibility in particle size is improved when grinding the same
sample size for the same time period. Using wire mesh sieves for the isolation of a
particle size fraction for analysis can be useful, however, caution must be used so that
the fraction examined is truly representative of the whole sample and does not
selectively favor/exclude a particular component.

Halide salts (powders, windows) are hygroscopic, and should be stored in desiccators or
warm ovens. The materials should have their spectra recorded versus an open beam for
detection of any impurities. They should not be stored near organic materials that have
substantial vapor pressure as surface adsorption of the volatile species will occur.

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 Appendix I Quantitative Analysis 605

Calcination, in air, can eliminate the presence of most organic impurities without
adversely affecting crystallinity.

DATA COLLECTION
All spectra to be used for quantitative measurements need to be made in a format where
the ordinate axis is linear with sample concentration. The most commonly used format
for the ordinate axis is Absorbance (others are Kubelka-Munk and PAS). Do not use
the %T format not be used, since this is a logarithmic scale with respect to
concentration.

Spectral regions possessing bands between 0.2-0.7 Absorbance units are recommended
for quantitative analysis. This does not mean that bands falling outside this range
cannot be used, but rather, that adherence to Beer’s Law is more likely with data
meeting these criteria.

Strictly speaking. the number of calibration samples required for a quantitative analysis
is equal to the number of components in the system. However, this does not permit
overdetermination. Therefore, it is recommended that the number of calibration
samples be equal to twice the number of components in the system. In that way,
overdetermination is possible to yield a “goodness” of fit, in addition to generating
“blinds” to verify that the method does work.

For every reference standard and each sample analyzed, a minimum of two complete
samplings should be made (run in duplicate). Additionally, when collecting the spectra
for the calibration standards, the references should be examined in random sequence.
This means that the second examination (duplicate) of a sample should not be made
directly after its first data collection and that the standards should not be examined in
increasing or decreasing concentration order. Such practice makes it easily to verify
sampling reproducibility by comparison of duplicate samples and to eliminate possible
errors from buildup/carryover relating to selective retention of a component.

The single beam background for computing a ratioed spectrum should be collected
through the accessory or holder used for examining the sample. This is to insure that
the IR beam is attenuated in the same manner as when the sample spectrum is recorded,
any spectral features characteristic of the accessory will be ratioed out in the

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 606 Appendix I Quantitative Analysis

computation of an absorbance spectrum, and that the infrared beampath will be

identical between the reference and sample examinations.

The whole beam area at the sample position, with no holes in the sample, should be
completely filled otherwise the spectrum will exhibit distortions caused by the
intensities of the absorption peaks being artifically depressed.

A method that solely relies upon a single holder, crystal or cell should never be
developed. This refers to an analysis based upon a single, particular pair of windows,
bottle of halide powder, diffuse reflectance cup, IRE, syringe, etc. This should not be
confused with using a fixed pathlength cell where the sample thickness is of
importance. The rigors demanded of a good analytical procedure precludes it from
dependence upon the accidental destruction of such “lucky” equipment.

SPECTROMETER PERFORMANCE
Good quality data required for high analytical precision and accuracy can only be
obtained if the spectrometer is performing properly. Several practices can be followed
for the monitoring of instrument performance to insure good quantitative analysis.

First, the regular collection of a 100% Transmittance line under predefined conditions
(that is., co-addition time, resolution, apodization, aperture size, etc.) should be made.
This consists of two sequentially collected single-beam spectra ratioed to obtain a %T
spectrum. The spectrum should be flat, featureless, and positioned at 100% T. A flat
spectrum showing an offset from 100% T is typical of temperature instability (for
example, source, thermally cooled detector, surrounding environment). Sloping
baslines are usually due to misalignment of the spectrometer optics or accessory. The
100% T line should be collected prior to the introduction of an accessory or sample as it
reflects the instrument’s performance. The sources for any spectral artifacts should be
isolated and removed (for example., electrical spikes and vibrations). Additionally, the
noise level (RMS and/or peak-to-peak) should be measured in a predefined region,
typically between 2200 - 2000 cm-1 as there exists little spectral interference in this
region and the mid-infrared detector response is greatest here. A rise in noise level will
indicate spectrometer performance problems, which may be due to misalignment or
degradation of source or detector.

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 Appendix I Quantitative Analysis 607

Next, one of the above collected single-beam black body curve spectra should be
examined and compared to previously collected single-beam curves. The maximum of
the spectrum should remain constant as it is based upon the temperature of the source.
If it should drop suddenly, it is indicative of the spectrometer’s source “burning out”
and requires its replacement. “Icing” of a liquid nitrogen cooled detector (MCT), due to
loss of vacuum can be observed by an increase in the intensity of a triangular-shaped
band near 3250 cm-1. This requires that the dewar be reevacuated, typically by shipment
back to the vendor. Finally, the region of the single-beam spectrum characteristic to
low frequency detector/optics cutoff should be examined. This region reflects detector
nonlinearity from saturation and should be flat at zero, recording no infrared energy
being detected. In cases of nonlinearity, the cutoff may never reach zero (seeing energy
when none is present), descend below zero (recording negative energy), or stray back
and forth about zero. This behavior may require that the infrared beam be attenuated
with metal mesh screens, optical filters or apertures to obtain a linear response. All
attenuating items should be handled as optical elements, carefully shielded from dust,
and never touched, so as to prevent contamination that would contribute spurious
infrared absorbances in collected spectra.

These same measurements should be made following the introduction of the accessory
used for sample examination has been made into the spectrometer. If any problems
exist, then alignment of the accessory must be performed. If attenuation of the beam
with filters, screens, or apertures is necessary for linearity, both the background and
sample spectra must be collected with them in identical position to duplicate a
reproducible beampath.

SPECTRAL MANIPULATIONS
It is not necessary for the analyst to make the infrared spectra “look nice” prior to
performing quantitative measurements. In fact, most data treatments to improve the
visual appearance of the data adversely alter the information so as to make it useless for
quantitation through the application of irreproducible operator bias.

However, if application of data manipulation is necessary, there are three criteria that
should be followed:

1. insure that all spectra are in a linear format (that is, absorbance type)

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 608 Appendix I Quantitative Analysis

2. use only data treatment that is absolutely necessary to make the required
quantitative measurements
3. insure that any manipulations are performed identically on all spectra—
calibration, reference, and unknowns

Smoothing
Smoothing degrades spectral resolution and is an extremely poor analytical practice. In
fact, the use of a moving smoothing function (for example, Savitzky-Golay) will affect
band shape and peak position. Therefore, if a spectrum is too “noisy” for good
measurements it should either be collected at a lower resolution or the data co-added for
a longer period of time. If smoothing is a necessity, a Fourier-space smoothing function
(high-pass filter) is preferable, as it affects band shapes less than a moving smooth
function.

Fringe Removal
Multiple internal reflection inside a cell or film may result in the presence of spectral
fringes. Although the fringes do allow for thickness calculations, they can be a major
problem when implementing a quantitative method.

If the fringe is a high frequency wave, then the interferogram can be inspected for the
presence of a secondary (and tertiary) centerburst. Software removal of this extraneous
centerburst(s) will eliminate the wave from the computed spectrum. If the fringe is a
low frequency wave, then it may be better to treat this as a baseline correction problem
and use a Fourier high-pass fileter for removal.

Fourier Self-Deconvolution
Fourier self-deconvolution reduces spectral band widths, but maintains band areas.
Therefore, band intensity increases. However, spectral noise increases rapidly with the
degree of band narrowing which requires that only spectra with high SNR can be used.
It is advised that only a conservative level of resolution enhancement should be applied
to data for quantitative analysis.

Derivative
Derivation is not recommended in conjuction with quantitation of FT-IR data. This is
because the intensity of a derivative peak depends on the width and data point spacing
of the original band. Any minor changes in band width leads to large alterations of
derivative intensity, which can be very marked on the narrow mid-IR bands. Next, the

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 Appendix I Quantitative Analysis 609

second derivative exhibits side lobes that point in the same direction as the main
derivative peak, resulting in a very complex spectrum for measurements. Last,
derivation greatly increases spectral noise usually necessitating the application of
additional smoothing functions (another source of bias).

Interpolation
The resolution of a spectrum can be artificially enhanced to provide better band shapes
for manipulations through interpolation. The easiest method fits a polynomial to known
points. However, the preferred method is to add zeros to the end of an interferogram
prior to computing the Fourier transform.

Spectral Subtraction
Spectral subtraction may prove useful for quantitative analysis in two ways. First, it can
be used as a preparative step for spectra where a sample requires removal of interfering
absorbance bands due to solvent, water vapor, or substrate. Spectral subtraction is not
valid however, if the sovent or substrate interacts with the sample as it would result in
residual spectral features characteristic of the interaction.

Secondly, under carefully controlled conditions, spectral subtraction can be used as a

quantitative tool. In general, the pathlength of the the sample must remain constant. In
this application, the spectral subtraction factor recorded for complete removal of a
“pure” component from a mixture can be used to calculate the concentration of that
component.

Baseline Correction
It is highly advised that baseline correction never be directly applied to spectral data.
Rather, absorbance band measurements should be made relative to baseline definitions
within a quantitative analysis package. In some isolated cases, where the baseline is
simply elevated or tilted, a simple one- or two-point tilt baseline correction may be
applied without adversely affecting spectral data for quantitative measurements
provided all spectral files (standards and unknowns) are treated identically.

Some of the issues directly affected by baseline correction follow. First, an elevated
baseline may push strongly absorbing spectral bands into a nonlinear range and cause
peak maxima to have a high level of noise. Second, spectral information may be
present in the baseline which correlates to the concentration of a component (for
example, carbon black) and can be used by sophisticated software packages. Third, a

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 610 Appendix I Quantitative Analysis

baseline exhibiting severe curvature probably means that the experimental conditions
are ill defined. Last, baseline corrections should never be performed on a spectrum in a
%T format as nonlinear factors are introduced by the logarithmic function.

If it is necessary to remove a curved baseline, the use of a high-pass filter in Fourier-

space is preferred to a manual baseline correction as it has less analyst bias. A Fourier-
space filter treats all spectra in a similar fashion, avoiding irreproducibility.

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 Appendix I Quantitative Analysis 611

QUANTITATIVE ANALYSIS FLOW CHART

Set down criteria for analysis

Create rough draft of analysis method

Review chemistry of system under investigation

No
Make sure the spectrometer is working properly
Service Instrument

Generate calibration standards

Check for linear relationships and validity
Ideally create 2 times number of components

Collect spectra of calibration standards

Run in duplicate and compare
Run in random sequence

Calibrate quantitative method

Verify method works on blinds No

Run samples

Yes Periodically check that method still works

Use retains previously analyzed
No
Generate blinds (in- and out-of spec)

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 J
Deconvolution

GENERAL CONSIDERATIONS
Deconvolution attempts to enhance the apparent resolution of overlapping peaks where
the limiting resolution is the natural width of the bands, not the resolution with which
the spectrum was collected. The individual peaks are assumed to have Lorentzian line
shapes. A broad peak may be described as the convolution of a very sharp peak (a delta
function) with a Lorentzian line shape function. Integrated bands areas are retained
following deconvolution, in addition to peak positions, which means that quantitative
information can still be extracted from the spectra. However, peak amplitude
(intensity) is changed due to the narrowing of the band from removal of the Lorentzian
line shape.
In order to obtain reliable results when using deconvolution to enhance the apparent
resolution of overlapping band contours, a number of conditions must be met:

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 614 Appendix J Deconvolution

• The spectral data should be recorded with as high a signal-to-noise (SNR) as

possible. It is possible to work with noise levels of 1% (100:1), but a SNR
of at least 1000:1 is desirable.

• The maximum achievable effective resolution after deconvolution cannot be

higher than the instrumental resolution used to record the data.

• The spectral region to be used in deconvolution should be in an absorbance

format.

• The maximum absorbance in the spectral region to be deconvolved should

be less than 1.

• The region for deconvolution should be limited to the area in which the band
widths are all approximately the same.

• The spectral limits used to define the spectral region for deconvolution
should include a portion of the baseline so that the noise level can be
monitored. Additionally, the first few data points should not show any
curvature because this will give a truncation effect.

Additionally, in regions where water vapor absorbs, major problems with deconvolution
may occur. This is because even trace ripples on the original spectrum will
automatically be overdeconvolved since the water lines are as sharp as the instrument
resolution.

SIMULATED SPECTRAL EXAMPLES

The synthetic spectrum shown has a single peak with a width at half height of 30 cm-1,
peak intensity of 0.5 absorbance and location of 1600 cm-1. After cosine transformation
of the 2000 - 1450 cm-1 region, this peak may be described as the product of a cosine
wave (the frequency of the wave corresponds to the location of the sharp peak in the
spectrum) with an exponential decay function.

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 Appendix J Deconvolution 615

The cosine transform of a Lorentzian line shape with width at half height W is an
π
exponential function e-2 Wx.

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 616 Appendix J Deconvolution

When the cosine transform of a Lorentzian peak is multiplied by the appropriate

exponential function (representing the cosine transform of a Lorentzian peak of the
identical width), a pure cosine function results.

When this interferogram is subjected to another cosine transform, this deconvolved

peak appears as a sinc function having a much sharper main peak than the original
Lorentzian peak. This peak is at the same location in the spectrum as the original
Lorentzian peak.

Since the prominent sidelobes of the sinc function may complicate the interpretation of
spectra containing more than one peak, the interferogram should be apodized before
performing the final cosine transform. The effect of apodization is to broaden the very
narrow peak resulting from transformation of the cosine function and to reduce its
sidelobes. This apodization is controlled by the K factor parameter, which governs an
exponential weighting function operating on the interferogram. The value of the K
factor corresponds to the desired amount of narrowing in the original peak. For
example, a K factor of two results in a final peak width of one half the width of the
original peak.

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 Appendix J Deconvolution 617

Four apodization functions may be applied to the interferogram: boxcar, Bessel, sinc2
and triangle2. The previous example shows the result of boxcar apodization with a K
value of two. The next figure shows the result of Bessel apodization of the
interferogram with a K value of two.

The deconvolved spectrum results from applying a cosine transform to the Bessel
apodized interferogram. The reduction in magnitude of the sidelobes is evident, and the
peak is half as wide as the original Lorentzian peak. Note the change in the Y-axis
scale (intensity). However, the peak area remains the same.

The satisfactory results of the above example depended upon choosing the correct width
at the half-height of the Lorentzian peak shape function to be deconvolved. When the
chosen half-width is too large, the peak is over-deconvolved, and large sidelobes are
present. For example, the figure below shows two peaks one at 1600 cm-1 (same as
above) and another narrower peak with a width of 20 cm-1 located at 1400 cm-1.

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 618 Appendix J Deconvolution

When deconvolved by a Lorentzian function with a half-width of 30 cm-1, the peak at

1600cm-1 is correctly deconvolved, but the peak at 1400 cm-1 is overdeconvolved,
producing large negative sidelobes.

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 Appendix J Deconvolution 619

In general, selecting an optimum value for the half-width parameter is not possible
where overlapping peaks have quite different half-widths.

In this example, the C-H stretching region of a polystyrene based polymer, between
3200 and 2700 cm-1 is selected for the illustration of the deconvolution process. The
spectrum used is polys.bsp. The flat baseline area, outside of the overlapping band
region is included for reasons which will become evident.

Before selecting Deconvolve, define the region (3200-2700 cm-1) to be deconvolved

using the cursor.

By examination, a value for the half bandwidth (HBW ) of the narrowest band is made.
For example, a value of 16 cm-1 will be the initial estimate (3033 - 3017 cm-1). A
K factor of 2 is input, as initially a resolution enhancement of 2 will be sought. Type
these values into the appropriate entry boxes, and press Apply. It is advisable to begin
with a small value for the K factor so that the bandwidth parameter can be optimized
without artifacts occurring from the simultaneous variance of two parameters. Bessel

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 620 Appendix J Deconvolution

apodization is suggested as it minimizes the amount of noise introduced by the

deconvolution process.

It is obvious from the presence of the negative sidelobes that the half-bandwidth used
was too wide. It is difficult to discern which bands are real from the artifacts created by
the sidelobe maxima.

To remove the negative sidelobes, a smaller HBW value is used. The only parameter
requiring change at this time is the half bandwidth. The HBW value of 8 cm-1 is entered
and Apply is pressed. The deconvolved spectrum with an HBW of 8 cm-1 is displayed.

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 Appendix J Deconvolution 621

The noise level is quite low in the regions of retained baseline and no sidelobes exist.
However, the bands are not resolved to the baseline. Therefore, a wider half bandwidth
will be used to better define this region.

Change the HBW parameter to 11.5 cm-1 and press Apply.

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 622 Appendix J Deconvolution

The noise level in the spectrum is low and the majority of the bands have been resolved
to the baseline. The band at 3001 cm-1 shows the presence of negative sidelobes. This
is because its HBW is significantly different from the other overlapping bands in the C-
H stretching region. It is a good example for illustrating the reason for only
deconvolving small spectral regions where bands have the same HBW .

Now that a deconvolved spectrum without significant negative sidelobes has been
obtained, the K factor (that is., resolution enhancement factor) can be adjusted. Enter a
value of 3 for the K value and press Apply (HBW remains at 11.5).

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 Appendix J Deconvolution 623

The excessive noise in the baseline region indicates over-deconvolution. The noise is
different from normal spectral noise as it appears as non-random bursts on the baseline.
The figure below shows the final deconvolved result, with a HBW of 11.5 cm-1 and K
factor of 2.1. The noise level is at an acceptable low level and there exists minimal
negative sidelobe intervention.

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 624 Appendix J Deconvolution

Referring back to conditions to be met for proper deconvolution to occur, the maximum
achievable resolution after deconvolution cannot be higher than the instrumental
resolution used to record the data. Since the HBW s in the spectrum were found to be
approximately 11.5 cm-1, or nearly twice the resolution used to collect the data (4 cm-1),
it would be considered prudent to record the spectrum at improved resolution in order
to check the results. This is because the effective resolution has been imporved by a
factor of 2.1 (K factor), with distinguishable band definitions defined by 11.5
(HBW )/2.1 (K factor), or 5.5 cm-1 separation. The values of 4 cm -1 (collection
resolution) versus 5.5 cm-1 (effective resolution) closely approximate one another,
therefore, recollecting the spectrum at 2 cm-1 would assure that no artifacts were
introduced by approaching the instrumental resolution with the effective resolution used
for deconvolution. Additionally, the data point spacing will be changed from 2 cm-1 to
1 cm-1 giving the final deconvolved result a better defined line shape.

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 K
Diagnostics and Service
Access

GAIN RANGING MULTIPLICATION

The gain ranging factors (add and multiply) are updated evey time you select Calibrate in
Setup. There is eeldom a need to access this. The factors are stored in the registry. To
access this value:

1. From the Task bar, select Start / Programs / Administrative Tools / RegEdit 32.
A number of windows open.

2. Select the HKEY_LOCAL_MACHINE on Local Machine window.

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 626 Appendix K Diagnostics and Service Access

3. Double click HKEY_LOCAL MACHINE. The subentries under this entry

appear.

4. Continue clicking to navigate through the chain of entries:

System
Current ControlSet
Services
brd-obe2
Calibration

5. The item Add Factor: REG_SZ: gives the addition factor. In this example, it is
80.7.

The item Mult Factor: REG_SZ: gives the multiplication factor. In this
example, it is 14.1.

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 Appendix K Diagnostics and Service Access 627

6. Select Exit from the Registry menu to close RegEdit 32.

AUTOALIGN LOCATIONS
Each time an autoalignment is run, the autoalignment locations are stored in the file
C:\win32app\Win-IR_Pro\bin\autoalign.txt. This file can be opened and read by any text
editor. The file is created anew every time the spectrometer is autoaligned. Do not
modify this file. A typical autoalign.txt file is shown below.

x= -37, y = -75, gain = 4, measurement = 3013

x= -37, y = -75, gain = 4, measurement = 3002
x= -12, y = -75, gain = 4, measurement = 3011
x= 12, y = -75, gain = 4, measurement = 3018
x= 37, y = -75, gain = 4, measurement = 5669
x= 50, y = -50, gain = 4, measurement = 7436
x= 25, y = -50, gain = 4, measurement = 8716
x= 25, y = -50, gain = 3, measurement = 5529
x= 0, y = -50, gain = 3, measurement = 3506
x= -25, y = -50, gain = 3, measurement = 3080
x= -50, y = -50, gain = 3, measurement = 2821
x= -62, y = -25, gain = 3, measurement = 2729
x= -37, y = -25, gain = 3, measurement = 3548
x= -12, y = -25, gain = 3, measurement = 4876

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 628 Appendix K Diagnostics and Service Access

x= 12, y = -25, gain = 3, measurement = 4232

x= 37, y = -25, gain = 3, measurement = 5632
x= 62, y = -25, gain = 3, measurement = 4673
x= 75, y = 0, gain = 3, measurement = 4491
x= 50, y = 0, gain = 3, measurement = 4600
x= 0, y = 0, gain = 3, measurement = 8356
x= 0, y = 0, gain = 2, measurement = 5372
x= -25, y = 0, gain = 2, measurement = 3142
x= -50, y = 0, gain = 2, measurement = 3172
x= -75, y = 0, gain = 2, measurement = 2654
x= -62, y = 25, gain = 2, measurement = 2467
x= -37, y = 25, gain = 2, measurement = 4563
x= -12, y = 25, gain = 2, measurement = 2381
x= 12, y = 25, gain = 2, measurement = 8815
x= 12, y = 25, gain = 1, measurement = 5138
x= 37, y = 25, gain = 1, measurement = 4344
x= 62, y = 25, gain = 1, measurement = 2429
x= 50, y = 50, gain = 1, measurement = 4507
x= 25, y = 50, gain = 1, measurement = 7097
x= 0, y = 50, gain = 1, measurement = 4431
x= -25, y = 50, gain = 1, measurement = 2774
x= -50, y = 50, gain = 1, measurement = 2447
x= -37, y = 75, gain = 1, measurement = 2285
x= -12, y = 75, gain = 1, measurement = 2816
x= 12, y = 75, gain = 1, measurement = 2399
x= 37, y = 75, gain = 1, measurement = 7097
x= 25, y = 50, gain = 1, measurement = 7097
x= 25, y = 51, gain = 1, measurement = 7193
x= 25, y = 61, gain = 1, measurement = 7525
x= 25, y = 71, gain = 1, measurement = 7292
x= 25, y = 61, gain = 1, measurement = 7499
x= 26, y = 61, gain = 1, measurement = 7582
x= 36, y = 61, gain = 1, measurement = 7964
x= 46, y = 61, gain = 1, measurement = 7540
x= 36, y = 61, gain = 1, measurement = 7989
x= 36, y = 66, gain = 1, measurement = 8168
x= 36, y = 66, gain = 0, measurement = 5460

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 Appendix K Diagnostics and Service Access 629

x= 36, y= 71, gain = 0, measurement = 5501

x= 36, y= 76, gain = 0, measurement = 5479
x= 36, y= 74, gain = 0, measurement = 5497
x= 36, y= 72, gain = 0, measurement = 5490
x= 36, y= 74, gain = 0, measurement = 5485
x= 41, y= 74, gain = 0, measurement = 5608
x= 46, y= 74, gain = 0, measurement = 5622
x= 51, y= 74, gain = 0, measurement = 5486
x= 49, y= 74, gain = 0, measurement = 5566
x= 47, y= 74, gain = 0, measurement = 5601
x= 45, y= 74, gain = 0, measurement = 5646
x= 43, y= 74, gain = 0, measurement = 5639
x= 45, y= 74, gain = 0, measurement = 5649
x= 45, y= 75, gain = 0, measurement = 5649
x= 45, y= 74, gain = 0, measurement = 5630
x= 45, y= 74, gain = 0, measurement = 5635
x= 46, y= 74, gain = 0, measurement = 5630
x= 45, y= 74, gain = 0, measurement = 5629
x= 45, y= 74, gain = 0, measurement = 5661
x= 45, y= 75, gain = 0, measurement = 5675
x= 45, y= 76, gain = 0, measurement = 5691
x= 45, y= 77, gain = 0, measurement = 5700
x= 45, y= 78, gain = 0, measurement = 5709
x= 45, y= 79, gain = 0, measurement = 5725
x= 45, y= 80, gain = 0, measurement = 5721
x= 45, y= 79, gain = 0, measurement = 5718
x= 46, y= 79, gain = 0, measurement = 5731
x= 47, y= 79, gain = 0, measurement = 5727
x= 46, y= 79, gain = 0, measurement = 5729

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 L
Accelerator Keys

Keys Menu entry selection

CTRL + A View / Autoscale
CTRL + C Edit / Copy
CTRL + E View / Entire Spectrum
CTRL + L View / Lock Selected
CTRL + N File / New...
CTRL + O File / Open...
CTRL + P File / Print...
CTRL + S File / Save
CTRL + U View / Unlock Selected
CTRL + V Edit / Paste
CTRL + X Edit / Cut
CTRL + Z Edit / Undo...
F1 Help / Index
F2 Edit / Select All Visible
F11 Window / Maximize Traces
F12 Window / Maximize Spreadsheet

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 M
Library Conversion

OVERVIEW
The Bio-Rad Search Library Converter program converts libraries in the Bio-Rad 3200
library, Sadtler user library, or Galactic user library format into a library in the Sadtler
user library, Galactic user library, or Win-IR Pro library format. Once all your libraries
are converted, there is no need for further use of this program. In fact, most Win-IR Pro
users will never have occasion to run this program.

The resolution, range, and number of bytes per point are the same in the converted
output library as they are in the input library. Any spectra marked as deleted in the input
library are not copied into the output library. Thus, if the input library had 200 spectra
of which 20 were marked as deleted, the output library would have 180 spectra.

The input library is not modified. The output library is created in the input library
directory. The output library can be moved afterwards. See the “Search” section in the
Operations chapter for details on library pathnames and search paths.

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 634 Appendix M Library Conversion

Note
A library consists of a number of files. They have the
same filename but different extensions. The extensions
are listed at the end of this appendix. When you move the
library, be sure to move all its files.

Restrictions and Considerations

3200: There are two types of 3200 libraries— single (ordinary) resolution (file extension
.sl) and dual resolution (file extensions .s1 and .s2). There are no special considerations
for single-resolution libraries.

A dual resolution library has two spectrum files. One, usually the .s1 file, has a lower
resolution (for example, 16 cm-1). The other, usually .s2 file, has a higher resolution (for
example, 4 cm-1). The lower resolution file would be the one actually searched; the
spectra displayed would be the corresponding ones in the higher resolution file. This
scheme was meaningful when computers were slower; it is no longer necessary. When
converting dual resolution libraries, select the higher resolution file, normally the file
with the .s2 extension. However, you should always check both files to be certain which
one has the higher resolution. This information is presented in the Library to be converted
dialog box (see step 5 in the example below).
Sadtler: You cannot convert Sadtler-proprietary libraries, only Sadtler user libraries.
Libraries converted to Sadtler user libraries should be opened with the Sadtler User
Library Manager. There will be a message about normalization; select OK, and re-
normalize the library. This takes a few seconds for a modestly-sized (few hundred
entries) library.
Galactic: You can convert only Galactic spectral libraries. You cannot convert Galactic
encrypted libraries. You cannot convert Galactic structures, peaks, or properties. If you
attempt to convert Galactic libraries with structures or peaks, a warning message will be
displayed.
USING THE SEARCH LIBRARY CONVERTER
The BioRadSearchLibraryConverter program is supplied on the Win-IR Pro CD-ROM in
the Library converter directory. However, it is not installed by the Setup.exe program. If
you want to use this program, you can start it from the CD-ROM or copy it to your hard

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 Appendix M Library Conversion 635

disk (we recommend putting it in c:/Program Files/Win-IR Pro/bin) and running it from
there.

The example below shows the conversion of a Bio-Rad 3200 format library to a Bio-Rad
Win-IR Pro format library. Assume the library is stored in c:/3200 Libraries.

1. Start the converter program by clicking on its icon in the Windows Explorer.
The Bio-Rad Search Library Converter dialog box appears.

2. Select Convert what kind of library? 3200 library.

Select To what kind of library? Win-IR Pro library.

Note
If you choose Sadtler user library as the input library, then
Sadtler user library will be disabled (grayed-out) as the
type of output library; if you choose Galactic library as the
input library, then Galactic library will be disabled
(grayed-out) as the type of output library

3. Click the Convert button. The Open dialog box appears.

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 636 Appendix M Library Conversion

4. Use the standard Windows NT procedures to access the directory in which

you have stored the 3200 libraries, in this example c:/3200 Libraries.

5. Select the library to be converted by highlighting it. Click the Open button.

Note
Only one library can be converted at a time. Repeat the
procedure to convert more libraries.

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 Appendix M Library Conversion 637

The dialog box Library to be converted appears.

.
This dialog box displays the properties of the library and its contents.

Resolution is of particular interest if you are converting 3200 dual resolution

libraries; check both spectral files and convert only the higher resolution file.
This is discussed in the “Restrictions and Considerations” section, above.

Library is unlocked: you can convert this library. If the message says Library is
locked (for example, if the library is a Galactic encrypted library or a Sadler-
supplied library), then the OK button is disabled (grayed out) and you cannot
convert this library. In this case, press the Cancel button to terminate the
procedure.

Contains: displays what information is in the library; see “Search” in the

Operations chapter for detailed explanations. All libraries contain Names and
Spectra. If the input library is Galactic containing Peaks or Structures, this
data will not be converted. If you attempt to do so, you will get a warning
message.

You can click Cancel to stop the conversion process.

6. Click OK to continue the conversion process. The dialog box Define the
output library appears.

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 638 Appendix M Library Conversion

7. Type in the appropriate information.

Collection code: if your output library format is Sadtler or Galactic, enter a

code to identify the library. This code should not conflict with any Sadtler or
Galactic libraries you have installed. Typically, Sadtler and Galactic libraries
use 2-letter codes; use 3-letter or 4-letter codes to avoid conflicts The
Collection code is not meaningful for Win-IR Pro libraries.

Library title: text descriptive of the library.

Copyright notice: leave this as is, or modify it as desired.

Library output file name: enter the name you want to use for the name of the
new library file; the converter will append the appropriate extension. The
default is to use the same name as the input library. The converted file is
created in the same directory as the input file; you cannot use a pathname.

Caution
We strongly recommend that you rename the library
if you are converting from a Sadtler user library to a
Galactic library, or vice versa, because these library
files use the same extensions. Failure to rename the
library will render one of the libraries unuseable.

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 Appendix M Library Conversion 639

8. Click the OK button. The library will be converted and the converter
program will terminate. Repeat steps 1 to 8 to convert additional libraries.

9. If desired, copy the new libraries into the directory used for your search
libraries; the default is c:/Search libraries.

Note
In this case, the library produced consists of three files; be
sure to move all of them or Win-IR Pro Search will not
work properly. In general, there will be more than one file
for each library.

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 640 Appendix M Library Conversion

LIBRARY FILE EXTENSIONS

LIBRARY EXTENSION FILE USE

3200 .na names

.ni names index
.s1 first spectrum file with dual resolution library
.s2 second spectrum file with dual resolution library
.sl spectrum file for ordinary (single) resolution library
— either .sl or .s1 and .s2 will be present

Sadtler .dat chemical structure (optional)

.idx index
.inf properties (not converted)
.ipk IR Peaks (optional)
.ism IR spectrum
.nam name
.txt not converted
.vpk vapor phase peaks (not converted)
.vps vapor phase spectra (not converted)

Galactic .idx index

.isl spectrum
.ipl peaks (not converted)
.itl name
.lib special file (not converted)

Bio-Rad .brc structure (optional)

Win-IR Pro .bri index
.brn name
.brp peaks (optional)
.brs spectrum

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 N
Custom Value Programs

OVERVIEW
This interface allows you to write programs that can access the raw data collected by an
array detector and perform customized transforms upon this data. The program
operates upon each spectrum to calculate one value of data type double. This could be
the location of the largest peak in the spectrum, the area of a particular peak, the ratio of
heights between two peaks, etc. This feature is specifically designed for use with image
(.dat) files; see “Custom Value”, Chapter 11 and “Image Document Window”, Chapter
3, for details of registration and execution.

Programs can be written either in any language that supports ActiveX, for example, in
Visual Basic (including Bio-Rad’s scripting language extensions to Visual Basic) or in
Visual C++. In this appendix, we will discuss the use of Visual Basic to write custom
value programs.

After a program is complete, it is registered for execution in Win-IR Pro using the
Operations / New / Custom Value menu entry.

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 642 Appendix N Custom Value Programs

VISUAL BASIC
To create a server with the Program ID of Transform.Value:

1. Start Visual Basic

2. Select File / New Project to create a new Visual Basic project

3. Select Tools / Options; the Options dialog box appears. Click on the Project tab
page. Set the options as follows:

Startup Form Sub Main

Project Name This name is the first part of the Program ID. In this
example, set it to Transform.
Start Mode OLE Server

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 Appendix N Custom Value Programs 643

Click the OK button.

4. Select Insert / Module to add a Standard Module to the project.

5. To create a Sub Main for the Standard Module, select Insert / Procedure; the
Insert Procedure dialog box appears.

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 644 Appendix N Custom Value Programs

Set the following parameters:

Name Main (type in)

Type Sub
Scope Public

6. Click the OK button. The Standard Module now contains the Sub Main code.

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 Appendix N Custom Value Programs 645

7. Select Insert / Class Module to add a Class Module.

8. Put the cursor inside the Class Module and click the right mouse button.
Select Properties from the menu; the Properties palette appears.

9. Set the properties to the values in the list below:

Instancing Creatable MultiUse

Name enter the name you have chosen for this class; it is the
second part of the Program ID. In this example, the name
is Value.
Public True

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 646 Appendix N Custom Value Programs

10. Add a Public Procedure called Result to this class as shown below.

11. Select Run / Start With Full Compile to test the server.

12. Select File / Make OLE DLL File to generate the dll. The Make OLE DLL File
dialog box appears.

13. Enter a name for the server program (with a .dll extension). The name need
not be the same as the Program ID. Click the OK button.

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 Appendix N Custom Value Programs 647

14. Select Run / Save Project. This will step you through a number of standard
Save dialog boxes. Save the project, file, form, module, etc. in the desired
directory with the desired names.

15. Exit Visual Basic.

In order to run this program from the Image Document Window, you must first register
it with Win-IR Pro.

1. Start Win-IR Pro.

2. Select Operations / New / Custom Value. The Custom Value dialog box appears.

3. Enter the Program ID. Click Add.

You are now ready to run this program from the Image Document Window.

Visual Basic Example

’===================================================================
’ These steps were followed to create this server with ProgID,
’ Transform.Value:
’ 1) Start a new VB project, and set the project options in
’ Tools/Options... as follows:
’ I) Startup Form = Sub Main,
’ II) Project Name = Transform, and
’ III) Start Mode = OLE Server.
’ 2) Add a Standard Module to the project and create a Sub Main
’ for it.
’ 3) Add a Class Module and set its properties as follows:
’ I) Instancing = Creatable MultiUse,
’ II) Name = Value, and (choose another name for another
class)
’ III) Public = True.
’ 4) Add a Public Procedure called "Result" to this class whose
’ signature is shown below:
’ Public Sub Result(spect As Object, retVal As Double)
’ ’ Your code goes here.
’ End Sub
’ 5) Add a Public Procedure called "Initialize" to this class whose
’ signature is shown below:
’ Public Sub Initialize(OptionalData As String)
’ ’ Your code goes here.
’ End Sub
’ The OptionalData argument can be used to set data members for

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 648 Appendix N Custom Value Programs

’ this class.
’ 6) For testing the server do a Start with Full Compile.
’ 7) From File Menu run Make OLE Dll File... to genrate the dll.
’===================================================================

Option Explicit

Dim m_Factor As Double

’ This sample finds the max value in the spectrum.

Public Sub Result(spect As Object, retVal As Double)
Dim ydataObj As Object
Dim ydata As Variant
Dim lowPtNum, highPtNum, n As Long
Dim theMax As Double

’ Get the ydata array form the spectrum:

Set ydataObj = spect.Spectrum
ydata = ydataObj.DataArray()

’ Get the bounds of passed in ydata array:

lowPtNum = LBound(ydata)
highPtNum = UBound(ydata)

’ Itearate through the elements of ydata to find its max value:

theMax = ydata(lowPtNum)
For n = lowPtNum To highPtNum
If (theMax < ydata(n)) Then theMax = ydata(n)
Next

’Retrun the reault in retVal.

retVal = theMax * m_Factor
End Sub

Public Sub Initialize(OptionalData As String)

m_Factor = CDbl(OptionalData)
End Sub

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 Index

% .
% Noise level ratio, 293 .bkg file, 73
.brc file, 640
.bri file, 173, 640
( .brn file, 640
( .brp file, 640
do not use in directory names, 5 .brs file, 640
.bsm file, 173
.bsq file, 173
) .cdf file, 173, 181
) .ch file, 172
do not use in directory names, 5 .csv file, 172
.dat file, 174, 640
.dt file, 172
.dt format spectra, 562

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 650 Index

.dxf files, 129 2

.idx file, 640
.ig file, 172 2D-IR
.inf file, 640 display, 402
.ipk file, 640 display kinetics spectra, 414
.ipl file, 640 display series of spectra, 412
.irf file, 173 flat view, 409
.isl file, 173, 640 from in-phase/quadrature spectra, 403
.ism file, 640 isometric, 409
.itl file, 640 menus, 409
.kbg file, 73, 173 view, 405
.kin file, 173 views, 74
.lib file, 640 zoom, 408
.na file, 640
.nam file, 640
.ni file, 640
3
.phs file, 173 3200 format spectra, 172
.pls file, 173 3200 header parameters, 583
.s1 file, 640 3200 libraries
.s2 file, 640 change format, 633
.sb file, 172 dual resolution, 634
.seq file, 173 single resolution, 634
.sl file, 640 3200 series spectra, 560
.spc file, 129, 172 convert, 563
.spc format spectra, 557 3D
.spc multifile, 180 background color, 133, 249, 406, 434
.txt file, 640 color palette, 132, 249, 406, 434
.vpk file, 640 draw mode, 132, 248, 405, 433
.vps file, 640 exporting data, 256, 411
flat view, 254, 439
[ isometric, 254, 439
menus, 134, 250, 435
[ palette, 132, 249, 406, 434
do not use in filenames, 5 pitch plot, 133, 250, 407, 435
rotation, 133, 249, 406, 435
select regions, 241
] spectral range, 243
] time range, 243
do not use in filenames, 5 Y scale, 133, 249, 406, 435
yaw plot, 134, 250, 407, 435
zoom, 252, 436
3D Interpolation, 426, 427
change line colors, 431
3D view
2-D cross sections, 244
change line colors, 246
kinetics, 241
print, 255
print cross section of, 247, 432

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 Index 651

A Annotations, 32, 359

create, 32
Abort delete, 36
search, 375 enter text, 33
zoom, 8 format text, 33
About Win-IR Pro, 476 hide, 272
Absolute value move, 36
derivative search algorithm, 568 resize, 35
search algorithm, 568 show, 272
Absorbance Apertures
format for deconvolution, 614 emission, 580
peaks, 41 Raman, 580
spectra, 282 source, 580
Access spectrum, 259 type, 580
Accounts. See User accounts Apodization, 569
Action boxcar function, 569
status, 76 deconvolution, 616
Activate for phase correction, 289
event log, 212 for smoothing, 321
ActiveX. See also OLE function, 322
Adding functions, 569
user accounts, 543 Happ-Genzel function, 571
Addition factor Norton-Beer functions, 570
gain ranging, 625 rapid scan parameter, 286
AIA rapid scan phase parameter, 289
add FTIR Specifications, 184, 209 trapezoid function, 570
Data Exchange file, 181 trapezoidal breakpoint, 286
FTIR specifications, 183, 208 triangle function, 571
properties, 208 Applets
standards, 173 duplication of spectrometer, 520
Algorithms spectrometer, 520
absolute value derivative search, 568 Apply
absolute value search, 568 button, 221, 319
correlation search, 568 button disabled, 531
derivative search, 568 Area
Euclidean search, 568 peaks, 200
optimize subtraction factor, 342 value, 200
search, 378 Area mode
Analysis peaks, 44
brief overview, 91 Arithmetic
quantative, 363 binary, 424
simple, 364 scalar, 423
Analytical Instruments Association. See AIA spectral, 421
Angle unary, 421
default, 133, 249, 407, 435 Arrange icons, 469
Animate slice show, 119 Array
data, 7, 174
extract spectrum, 120
stored phase, 450
Array detector. See also Stingray

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 652 Index

collection, 276 Baseline correction

Asymmetry, 289 quantitative analysis without, 534
ATR correction, 346 zoom, 534
Attachment points, 32 Baselines
move, 37 auto center, 51, 201
Attenuated Total Reflectance. See ATR calibration correction, 609
Auto center correction, 338, 378
baselines, 51, 201 deconvolution, 614
Autoalign.txt file, 627 defining, 47
Autoalignment locations, 627 definition, 79, 201
Autohide edges, 46
taskbar, 524 how drawn, 50, 200
Automatic subtraction, 341 kinetics, 102
Auto-pick peaks, 112 left, 203
Auto-Save linear correction, 340
after data collection, 461 methods, 47
Autoscale positioning, 219
buttons, 78 right, 202
colors, 132, 248, 405, 434 separation, 220
enable, 363 spline correction, 340
print composition, 487 Batch
X-axis and Y-axis, 229 search, 398
Autosubtract, 335, 341 Batch mode
regions for optimization, 341 create template, 494
Axis print composition, 512
compress, 15 print template, 494
expand, 15 use template, 497
expansion, 78 Batch processing
trace, 15 kinetics transforms, 113
Batch templates
create, 494
B use, 497
Back calculations, 596 Beer’s Law, 92
Background Bessel apodization
change colors in Print Composition, 505 deconvolution, 620
color, 522 bin
color in 3D, 133, 249, 406, 434 directory, xxi
current document, 295 Binary arithmetic, 424
document, 73 Bio-Rad spectra, 172
information in History Browser, 537 bkg file, 73
kinetics, 96 Black body
kinetics tab button, 98 calibration curve, 606
spectrum, 73, 294 spectrum, 349
Background scan Blinds, 596
buttons, 78 Borders
Bandpass filter, 325 edit in objects, 510
Bands
negative, 101, 541
Bandwidth
deconvolution, 614

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 Index 653

Boxcar window, 94
apodization, 569 Calibration standards
smoothing, 306 components, 596
brc file, 640 errors, 598
bri file, 173, 640 general considerations, 595
brn file, 640 linear independence, 595
brp file, 640 multiple species, 595
brs file, 640 overdetermination, 596
Brush problems, 598
default colors, 556 summary, 597
bsm file, 173 using actual materials, 597
bsq file, 173 Call back, 551
Buttons, 77 Card
Apply, 221, 319 network, 516
Apply disabled, 531 spectrometer, 516
autoscaling, 78 spectrometer interface, 577
background scan, 78 Cartesian space, 572
file, 78 Cascade windows, 4, 466
kinetics tab, 97 cdf file, 173, 181
laser, 79 Cells
Raman laser, 79 editable, 142
sample scan, 78 non-editable, 141
scan, 78 text editing of, 142
spectrum, 79 Center
peak, 201
Center of gravity
C center point, 55
Calculations peak, 201
predict, 95, 369 Center point
Calibration center of gravity, 55
baseline correction, 609 location method, 20, 38, 54
black body curve, 606 peak, 54
component, 366 Center value
curve, 91, 368 reference position, 52
curve specifications, 95, 369 Centerburst
derivative, 609 missing from interferogram, 443
document, 73, 364 Cepstrum, 324
documents, 73, 170 ch file, 172
Fourier self-deconvolution, 608
fringe removal, 608
interpolation, 609
measurement procedures, 605
print curve, 370
smoothing, 608
spectral manipulation, 607
spectral ranges, 605
spectral subtraction, 609
spectrometer performance, 606
standards, 595, 596
Calibration curve

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 654 Index

Change Sadtler, 638

background color in print composition, 505 Collects
display colors, 529 Auto-Save after, 461
display font size, 528 data, 274
fonts in print composition, 505 named, 78, 461
grid size, 483 Color
grid size in print composition, 506 background, 522
I/O port, 577 desktop, 522
IRQ, 577 zoom box, 524
library format, 633 Colors
memory address, 577 3D palette, 132, 249, 406, 434
name field, 141 autoscale, 132, 248, 405, 434
object state, 485 change, 456, 529
peak parameters, 199 change in Print Composition, 505
regions, 25 default, 555
working directory, 517 edit, 454, 456
X-axis units, 13 edit in objects, 507
Characters intensity, 132, 248, 405, 434
in filenames, 5 muddy, 528
Chemical structure, 360 revert to default values, 458
Chromatogram Edit Window, 269 Columns
Chromatograms add to spreadsheet via property browse bar, 226
edit window, 116 adding to spreadsheet, 143
import, 565 copy to external documents, 154
print, 540 copying into spreadsheets, 194
Circular reasoning. See Proof by assumption copying into word processor documents, 194
Class module do not remove Name, 261
custom value program, 645 hit list, 399
Clear ID, 7
object contents in print composition, 489 remove, 260
Clipboard reordering, 146
Win-IR Pro, 192 re-ordering in spreadsheets, 227
Close resizing, 139
all documents, 178 Comma separated value, 172
all windows, 469 Comments, 360
display in Print Preview, 503 add to spectrum, 27
documents, 177 delete, 27
print composition template, 499 edit, 27
Close all print composition, 483
documents, 178 Components
Close box add to quant analysis, 365
documents, 533 calibration, 366
Co-add edit, 367
more, 276 quantitation calibration, 93
Co-addition extraction, 106 remove from quant analysis, 365
Code subtracting major, 398
Sadtler collection, 638 Composition
Coefficient print, 189
correlation, 95, 369 Compress, 12
Collection code axis, 15

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 Index 655

spectrum, 79 Corrections
Compress trace, 12, 15, 219 ATR, 346
definition, 12, 15 phase, 572
Compute, 284 Correlation
Compute operation coefficient, 95, 369
rapid scan parameter, 285, 287 Correlation search algorithm, 568
Computers Cosine transform
reboot after installation, 516 deconvolution, 614
Concentrations, 593, 595 Create
column in spreadsheet, 370 annotation, 32
Conditions functional groups, 99
record, 6 peaks, 356, 358
Configure peaks using predefined peaks, 357
hardware, 575 print composition template, 489
Constant reference peaks, 358
positioning, 219 search library, 85
scaling, 218 user libraries, 85
Control panel, 575 Cross sections
kinetics, 98 print, 247, 432
sidebar, 83, 280 CRT, 2
Control panel sidebar csv file, 172
overlap with event box, 215 Current, 295
Controllers current.pv
temperature, 278 file, 522
Conventions Cursors, 2
typographic, xx default, 2, 526
Conversion definition, 2
disallowed between library formats, 635 problems, 2
search library example, 635 Custom properties, 360
Convert add to spectrum, 28
3200 series spectra, 560, 563 Custom value, 361
library, 633 class module, 645
Raman, 442 program, 126, 641
spectra, 559 program example, 127
Coordinates public procedure, 646
X,Y, 530 standard module, 643
Copy Visual Basic, 642
columns into spreadsheets, 194 Visual Basic example, 647
columns into word processor documents, 194 Customer support, xxii
columns to external documents, 154 Cut
extracted spectra, 110, 126 object, 192
object, 192 to clipboard in Print Composition, 504
rows, 146
spectrum, 420
to an external spreadsheet, 193
to clipboard in Print Composition, 504
users, 552
Copyright
search library, 87
Core spectrum information, 14, 154

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 656 Index

D rows, 148
selected objects in print composition, 505
dat file, 174, 640 spectra from libraries, 89
Data splash screen, 532
array, 174 temporary files, 516
change points, 300 vertical lines, 17
exchange, 173 Derivatives
phase array, 173 calibration, 609
view, 74 search algorithm, 568
Data collection, 274 Deselect
calibration, 605 regions, 25
disk space required, 520 Desktop
spectral format, 605 color, 522
Date Detectors
stamp, 160, 235 array, 276
Deactivate rear is blank, 520
event log, 212 status line, 578
Decimal precision, 20 Stingray, 276
Deconvolution, 315 type, 579
absorbance format, 614 Dial in, 551
apodization, 616 Dialog box, 6, 81
bandwidth, 614 Difference differentiation, 312
baseline, 614 Differentiation
Bessel apodization, 620 difference method, 312
conditions, 613 Fourier method, 312
cosine transform, 614 spectrum, 312
examples, 614 Diffuse Reflectance Spectroscopy
K factor, 617 errors, 603
remove negative sidelobes, 620 Digilab 3200 libraries
sidelobes, 616 importing, 633
signal-to-noise ratio, 614 Digital resolution, 86
sinc transform, 616 Digital Signal Processing. See DSP
water vapor contamination, 614 Direction
Default peak, 42
angle, 133, 249, 407, 435 Directories, 5
colors, 458, 555 bin, xxi
cursors, 2, 526 change working, 517
Define definition, 5
baseline, 201 Load history, xxi
regions, 22, 280 name, 5
step scan, 274 named collects, 461
terms, 1 restricted characters in names, 5
Delete Sample data, xxi
annotations, 36 structure, xxi
comments, 27 Win-IR Pro, 589
functional groups, 104
label box, 36
objects, 486
position labels, 22, 60
regions, 25

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 Index 657

Disk space most recently opened, 189

insufficient, 520 multiple, 3
required for data collection, 520 multi-spectral, 71, 72, 80, 170
required for DSP collection, 520 naming, 533
Disks new, 170
light on, 516 open, 75, 171
Display, 2 open by drag-and-drop, 176
change colors, 529 opened by Scan, 274
change font size, 528 print composition, 170
library properties, 637 Quantitation calibration, 170
limits, 245, 409, 430 quantitation new, 91
multiple, 3 quantitative analysis, 91
multiple spectra, 536 save, 178
one page in print composition, 502 save as..., 178
peak properties, 56 search, 170
radar box, 9, 77 search library, 84, 85
search library properties, 637 spreadsheet, 82
set limits for Lower trace, 245, 431 TRS, 170
set limits for upper trace, 245, 430 window, 80
spectrum, 81 window division, 80
trace, 81 Dongle, 387
two pages in print composition, 502 failure, 515
Display Document Limits Drag
reset, 232 regions, 362
Display Limits subtraction, 335
reset, 233 Drag and drop, 176
DLL print composition, 480
OLE, 646 Draw mode
Docking 3D, 132, 248, 405, 433
event log box, 215 Drop peaks, 42
property browse bar, 227 DSP
Document display limits, 230 step scan, 275
Documentation DSP data collection
Win-IR books, xix disk space required, 520
Documents, 3, 5 DSP(2). See digital signal processing
activate in window, 466 step scan, 275
active, 533 dt file, 172
background, 73 Dual resolution
calibration, 73, 364 3200 library, 634
close, 177 Duplicate
close all, 178 spectrometer applets, 520
closing with the close box, 533 spectrum, 420
collecting into, 533 dxf files, 129
current, 295
definition, 3
iconized, 533
image, 117, 171
kinetics, 71, 73, 96, 97, 170
library, 73
minimized, 533

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 658 Index

E calibration standards, 598

diffuse reflectance spectroscopy, 603
Edge points films, 601
Edges gas adsorption, 599
baseline, 46 gas desorption, 599
functional groups, 102 gas reactions, 600
peaks, 44 gases, 599
right, 204 internal reflectance spectroscopy, 603
Edit liquids, 602
borders in objects, 510 OLE Initialization, 520
color, 454 polymers, 600
colors in objects, 507 powdered/ground samples, 604
comments, 27 quantitative analysis, 597
components, 367 residual solvent, 599
fonts in objects, 508 solvent entrapment, 598
functional groups, 103 solvent evaporation, 598
objects in print composition, 507 solvent impurities, 599
peaks, 199 solvent reaction, 598
properties in print composition, 489 solvent residues, 599
registry, 625 solvent silution, 598
title, 510 solvents, 598
Edit list water in solvents, 599
no reference peaks, 64 Esc key
Edit menu for undo, 142
print composition, 504 Euclidean search algorithm, 568
Edit object, 485 Event box
properties, 486 overlap with control panel sidebar, 215
Editing Event log
cells, 142 activate, 212
position labels, 19 deactivate, 212
spreadsheet cells, 141 Event log box
Eliminate cannot undock, 214
splash screen, 532 docking, 215
Embedded periods floating, 213
do not use in filenames, 5 moving, 215
Emission resizing, 215
aperture, 580 too large, 214
Empty spectrum, 419 undocking, 213
Enable
trace control bar, 512
Enabling floppy, 387
Encrypted libraries
Galactic, 634
End points
zero with Truncate, 534
Entries
to be searched, 383
Error messages
Library Already Exists, 85
Errors

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 Index 659

Examples Extraction
custom value program, 127 co-addition, 106
name search, 395 template, 106
peaks search, 396
plot template, 263
print composition template creation, 489
F
print composition template printing, 492 Failure
scripts, 592 dongle, 515
search library conversion, 635 Fast Fourier Transform, 572
smoothing, 309 Fast TRS
spectral search, 394 step scan, 275
Visual Basic custom value program, 647 File buttons, 78
Exchange File menu
data, 173 print composition, 499
Exit, 189 Filenames, 5
Win-IR Pro, 504 restricted characters, 5
Expand, 12 restriction on embedded periods, 5
axis, 15 Files, 5
spectrum, 7 .bkg, 73
trace, 7 .brc, 640
X axis, 234 .bri, 173, 640
Expand trace, 12, 15, 219 .brn, 640
definition, 12, 15 .brp, 640
Expansion .brs, 640
axes, 78 .bsm, 173
spectrum, 79 .bsq, 173
y axis, 78 .cdf, 173, 181
Explorer, 1 .ch, 172
Export .csv, 172
3D data, 256, 411 .dat, 174, 640
DXF files, 129 .dt, 172
extracted spectra to .spc file, 111 .dxf, 129, 256, 411, 441
PAS 3D data, 441 .idx, 640
spc files, 129 .ig, 172
spectra, 180 .inf, 640
Export regions .ipk, 640
kinetics tab button, 98 .ipl, 640
Extensions .irf, 173
files, 585 .isl, 173, 640
library files, 640 .ism, 640
External .itl, 640
switches, 581 .kbg, 73, 173
Extracted spectra, 106 .kin, 173
copy, 110 .lib, 640
copying, 126 .na, 640
export to .spc file, 111 .nam, 640
name, 106 .ni, 640
print, 126 .phs, 173
relabel, 109 .pls, 173
removing, 109 .s1, 640

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 660 Index

.s2, 640 event log box, 213

.sb, 172 property browse bar, 227
.seq, 173 Floppies
.sl, 640 enabling, 387
.spc, 129, 172 Fonts
.txt, 640 change in Print Composition, 505
.vpk, 640 change size, 528
.vps, 640 edit in objects, 508
3D data, 256, 411 too large, 527
AIA Data Exchange, 181 Formats
autoalign.txt, 627 change 3200 library, 633
background, 73 change Galactic library, 633
calibration, 73 change in spreadsheet, 155
current.pv, 522 change library, 633
definition, 5 change Sadtler library, 633
delete temporary, 516 disallowed library conversion, 635
export DXF, 129 kinetics, 71
export SPC, 129 multi-spectral, 71
extensions, 585 retain inspreadsheet, 155
extensions for libraries, 640 spreadsheet, 155
kinetics, 73 Fourier
library, 73, 634 differentiation, 312
load recent on startup, 459 self-deconvolution calibration, 608
multi-spectral, 72, 73 smoothing, 308
open, 75 Frequency
Paging, 517 included, 290
PAS 3D data, 441 slice, 119
predefined peaks, 461 Frequently asked questions, 515
preview, 174 Fringe removal
quantitative analysis, 91 calibration, 608
search library, 84 Full name, 547
spectrometer.cpl, 520 Functional groups
Win-IR Pro, 589 create, 99
Films edges, 102
cast, 601 edit, 103
errors, 601 global, 104
opacity, 602 modify, 103
particulates, 602 name, 100
pressed, 601 predefined peaks, 100
rolled, 601 remove, 104
Filters Functions
bandpass, 325 apodization, 322
highpass, 325
interferogram, 324
lowpass, 325
notch, 325
types, 324
Flat view, 133, 249, 407, 435
2D-IR, 409
Floating

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 Index 661

G Height mode
peaks, 49
Gain ranging Help
addition factor, 625 how to use, 475
multiplication factor, 625 Index, 474
Galactic. See GRAMS Help menu
Galactic libraries print composition, 514
change format, 633 Hidden lines, 132, 248, 405, 433
encrypted, 634 Hide
importing, 633 annotations in print composition, 512
proprietary, 634 Gram-Schmidt chromatogram, 104, 116, 270
Gases grid in print composition, 511
adsorption errors, 599 palette bar in print composition, 511
desorption errors, 599 peaks, 116
errors, 599 peaks in print composition, 512
reactions with measurement cell, 600 position labels in print composition, 512
GC-IR, 278 property browse bar, 227
Global functional groups, 104 spectrum label in print composition, 511
Global preferences status bar in print composition, 511
peaks, 53, 70 taskbar, 524
GRAMS multifiles trace control bar in print composition, 512
export to, 179 Highpass filter, 325
from kinetics or TRS, 179 History, 6
GRAMS spectra, 172 add to spreadsheet, 238
Gram-Schmidt definition, 6
kinetics tab button, 98 expand, 236
Gram-Schmidt chromatogram spectra lacking, 158
hide, 116, 270 spectral, 157, 235
hide/show, 104 viewing, 158
show, 116, 270 viewing operations, 159
Graphic editor, 40 History Browser
Graphical objects, 484 background information, 537
Grid Hit list, 240
change size in Print Composition, 506 column, 399
print composition, 483 re-search, 393
Ground samples search against, 393
calibration errors, 604 Hit Quality Index. See HQI
Groups, 547 Hits
Power Users, 547 keep all, 383
number of to keep, 383
HQI, 567
H
Hamming. See Happ-Genzel
Happ-Genzel function
apodization, 571
Hardware
configure, 575
Height
peaks, 200
value, 200

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 662 Index

I Input
library, 635
I/O Port Installation, xxi
change, 577 reboot computer after, 516
Iconized Interface
document, 533 multiple document, 3
Icons spectrometer controller card, 577
arrange, 469 Interferograms
spectrometer, 576 filter, 324
ID, 7 object in print composition, 486
column, 7 phase correction size, 289
program, 361 remove spikes, 300
spectrum, 7 saved, 161
ID column, 7 without centerburst, 443
Idris_Import Internal Reflectance Spectroscopy
application program, 560 errors, 603
idx file, 640 Interpolated spectra
ig file, 172 2-D cross sections, 429
Image 3-D, 432
document, 117, 171 Interpolation, 297
print, 40 3-D, 426, 427
window, 117 Calibration, 609
Image array PAS, 426
peaks, 123 Iomega
transform spectra, 128 zip drive, 515
Image Data, 174 ipk file, 640
Image documents ipl file, 640
execute custom value programs, 126 IR Mentor, 451
Imaginary spectrum, 288 irf file, 173
Import IRQ
3200 series spectra, 560 change, 577
chromatograms, 565 conflict, 516
multifiles, 560, 565 isl file, 173, 640
search libraries, 633 ism file, 640
spectra, 557 Isometric
spectra have no history, 158 2D-IR, 409
Inaccessible libraries, 387 itl file, 640
Included frequency
rapid scan parameter, 290
Independent
K
positioning, 219 K factor
scaling, 218 deconvolution, 617
Index kbg file, 173
Help, 474 Keep All Hits, 383
of refraction, 342 Keys
inf file, 640 Esc for undo, 142
Initial columns kin file, 173
spreadsheet, 136
In-phase/quadrature spectra
2D-IR display, 403

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 Index 663

Kinetics, 276 Raman, 276

2D-IR display, 414 Raman wavenumber, 442
3D view, 241 Left
background, 96 baseline, 203
background tab button, 98 edge, 204
baselines, 102 lib file, 640
batch processing, 113 Libraries
control panel, 98 3200 dual resolution, 634
data, 173 3200 single resolution, 634
document, 71, 73, 97 adding spectra, 90
edit bar, 114, 267 change 3200 format, 633
export regions tab button, 98 change format, 633
Gram-Schmidt tab button, 98 change Galactic format, 633
negative bands, 101, 541 change Sadtler format, 633
peaks tab button, 97 conversion example, 635
print cross section of 3D view, 247 converter, 633
spreadsheet, 73 create user, 85
tab button, 97 creation, 85
to multifiles, 179 deleted spectrum, 633
trace display, 97 deleting spectra, 89, 90
Kinetics documents, 170 disallowed conversions, 635
chromatogram edit window, 116 display properties, 637
spreadsheet, 115, 268 document, 73
view entries, 114 edit, 89
View menu entries, 266 entries to be searched, 383
window, 96 file extensions, 640
Kramers-Krönig transform, 342 files, 634
Galactic encrypted, 634
Galactic proprietary, 634
L move, 639
Label box moving, 634
delete, 36 not accessible, 387
enter text, 33 parameters, 85
format text, 33 path, 388
move, 36 renaming, 638
resize, 35 Sadtler proprietary, 634
Labels Sadtler user, 634
coordinates, 18 search, 79, 173, 375
deleting, 22, 60 select for searching, 385
displayed in print composition, 480 user, 84
editing, 19 vendor-supplied, 173
hide, 271 window, 84
moving, 21, 58 writeable not shared, 88
orientation, 57 Library Already Exists
peaks, 57 error message, 85
position, 18, 359 Library conversion
show, 271 select input, 635
y-axis, 155 select output, 635
Laser Licenses
button on toolbar, 79 information, 476

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 664 Index

Limits Main screen, 80

display, 245, 409, 430 Main trace display rectangle, 9
document displayl, 230 Make
reset to Auto, 363 library, 85
set for lower trace display, 245, 431 Mapping
set for upper trace display, 245, 430 microscope, 276
spectral, 232 Masks
Line colors search, 378
change in 3D Interpolation, 431 Maximize
change in 3D view, 246 spreadsheet, 471
Linear traces, 280, 470
baseline correction, 340 MCS. See Multi-channel step scan
independence calibration standards, 595 Memory
interpolation, 297 virtual, 517
PAS spectra, 447 Memory Address
Linearly independent data, 595 change, 577
Lines Mentor
deleting, 17 IR, 451
hidden, 132, 248, 405, 433 Menu bar, 76
moving, 17 Menus
multiple, 18 2D-IR, 409
vertical, 16 3D, 134, 250, 435
Liquids buttons, 77
calibration errors, 602 Edit in print composition, 504
cell pathlength, 602 File in print composition, 499
Load history Help in print composition, 514
directory, xxi named collects, 78
Load Plot Template, 262 right mouse button, 488
Load Recent File on Startup, 459 View in print composition, 511
Location Window in print composition, 512
autoalignment, 627 Methods, 168
peaks, 54 compute operation, 285, 287
search library, 87 selecting, 168
Lock using, 168
display, 81 Microimaging. See Shadow Pro
spectrum, 81 Microns, 13
Lock selected, 257 convert single beam to, 354
Locking X-axis units, 352
properties, 258 Microscope mapping, 173, 276
spectra, 257 Minimize
Log in. See Logon spreadsheet, 139
Logon script, 550 Minimized
Lower trace document, 533
display limits, 245, 431
Lowpass filter, 325

M
Magnification, 7
Magnitude spectrum, 288

Win-IR Pro System Reference Manual

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 Index 665

Modify N
functional groups, 103
regions, 25 na file, 640
Module nam file, 640
class, 645 Name search
standard, 643 example, 395
Monitors, 2 Named collects
More directory location, 461
co-add, 276 menu, 78
Most recently opened documents, 189 Names
Mouse change field field, 141
right button, 488 directory, 5
sensitivity, 531 documents, 533
Move file, 5
annotations, 36 for extracted spectra, 106
attachment point, 37 functional groups, 100
event log box, 215 peak, 57
label box, 36 reference peaks, 62
libraries, 639 search, 380
peak labels, 58 Nanometers, 13
position labels, 21 convert single beam to, 354
property browse bar, 227 X-axis units, 353
search libraries, 634, 639 Navigating through spreadsheets, 138
vertical lines, 17 Negative bands
Muddy colors, 528 kinetics or TRS, 101, 541
Multi-channel step scan, 275 Network
Multicomponent analysis, 596 card, 516
Multifiles New
export to, 179 document, 170
from idenitcally formatted spectra, 179 file, 5
from kinetics or TRS, 179 peak, 356
import, 560, 565 window, 465
save Kinetics/TRS as, 180 Next Page
Multiple Print Preview, 501
copies, 2 ni file, 640
copies of Win-IR Pro, 2 nk transform, 342
display, 3 Noise level ratio, 293
programs, 2 overriding in some experiments, 541
windows, 3 use with small reference spectra, 541
Multiple document interface, 3 Non-absorbance spectra
Multiple modulation search, 392
small reference spectrum, 541 Non-contiguous spectra, 535
Multiple peaks, 59 Non-graphical objects, 484
Multiple species Norton-Beer functions
calibration standards, 595 apodization, 570
Multiplication factor Notch filter, 325
gain ranging, 625 Number of hits, 383
Multi-spectra
preview, 175
Multi-spectral documents, 72, 80, 170

Win-IR Pro System Reference Manual

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 666 Index

O Overlaps
event box and control panel sidebar, 215
Objects on screen, 527
changing state, 485 Overlay
clear contents in print composition, 489 plots, 217
delete in print composition, 505 Oversampling, 596
deleting, 486
edit, 485
edit in print composition, 507
P
graphical, 484 Page boundaries
interferogram, 486 print composition, 484
non-graphical, 484 Page orientation
overlapping, 484 Print Composition, 511
print composition, 484 Pages
resize in print composition, 489 access, 6
selected, 485 definition, 6
spectrum, 486 label, 6
states, 485 tab, 6
unselected, 485 Paging File, 517
OLE. See also ActiveX Paint
OLE DLL, 646 print using, 40
OLE Initialization Error, 520 Palette bar
One page print composition, 483
Print Preview, 502 Parameters
Opacity 3200 file headers, 583
films, 602 alter peaks, 200
Open change, 162
document, 75 changing peaks, 199
documents, 171 library, 85
file, 5, 75 peaks, 68
windows, 471 peaks into spreadsheets, 206
Operations print with spectrum, 263
details, 159 view, 162
regions, 22 Particulates
viewing history, 159 films, 602
Optical resolution, 86 PAS
Options export data, 441
custom value program, 642 interpolated spectra, 428
Order of display interpolation, 426
traces, 150 linear spectra, 447
Orientation print 3D view, 440
peak labels, 57 print cross section of 3D view, 432
Print Composition, 511 views, 74
Output Passwords, 544
library, 635 Paste
Overdeconvolution, 618 from clipboard in Print Composition, 504
Overdetermination, 596 object, 196
advantages, 596
quantitative analysis, 92
Overlapping objects, 484

Win-IR Pro System Reference Manual

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 Index 667

Path pick peak list, 59

library, 388 picking sensitivity, 416
Pathlengths predefined, 68, 461
liquid cell, 602 ratio against reference, 51
Peak labels redefine region, 44
moving, 58 reference, 51, 62
Peaks, 41 reference and normal, 63
alter parameters, 200 reference not in edit list, 64
and peak templates, 68 reference not in peaks search, 64
area, 200 reference not in print composition, 64
area in array, 123 relative wavenumber, 52
area mode, 44 remove, 534
array height, 125 removing from peaks table, 59
automatic picking, 416 right baseline, 202
auto-pick, 112 right edge, 204
baseline definition, 201 search on, 380
center, 201 show, 116
center of gravity, 201 show labels, 271
center point, 54 storing parameters, 68
center point method, 20, 38, 54 template, 65
changing parameters, 199 templates and documents, 67
create, 356, 358 value, 200
create using predefined peaks, 357 Peaks search, 380
deconvolve, 315 example, 396
define, 42 no reference peaks, 64
definition, 41 Pen
direction, 42 default colors, 555
display properties, 56 Periods
edges, 44 do not use in filenames, 5
edit, 199 Permissions
existing preferences, 70 information, 476
future preferences, 70 Phase
global preferences, 53, 70 angle, 425
height, 200 apodization, 289
height in array, 125 correction, 289
height mode, 49 correction, 572
hide, 116 correction size, 289
hide labels, 271 parameters, 289
in image array, 123 Phase Array
kinetics tab button, 97 stored, 450
label, 42, 57 Phase Array Data, 173
left baseline, 203 phs file, 173
left edge, 204 Physical security, 544
list, 198 Pitch, 133, 250, 407, 435
location, 54 Planck equation output, 349
multiple, 59 Plot templates
name, 57 example, 263
New, 356
parameters into spreadsheets, 206
peak pick list, 418

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 668 Index

Plots calibration curve, 370

load template, 262 chromatograms, 540
overlay, 217 cross section, 247, 432
save template, 262 extracted spectrum, 126
stacked, 217 PAS 3D view, 440
title, 460 print composition template, 492, 499
pls file, 173 Print Preview, 500
Pointer. See Cursor screen, 40
Pointers, 2 screen image, 39
Points setup, 188, 503
attachment, 32 spreadsheet entries, 186
Polymers using Paint, 40
catalyst contamination, 600 using WordPad, 39
errors, 600 Print composition
trace additives, 600 autoscale, 487
Position labels, 18, 359 batch mode, 512
deleting, 22, 60 change background color, 505
editing, 19 change fonts, 505
hide, 272 change grid size, 506
moving, 21 clear object contents, 489
show, 272 close template, 499
Positioning comments, 483
baseline, 219 control windowshade position, 513
constant, 219 copy to clipboard, 504
independent, 219 cut to clipboard, 504
traces, 218 delete objects, 505
Powdered samples document, 170
calibration errors, 604 drag and drop, 480
Power Users, 547 Edit menu, 504
Precision, 596 edit object borders, 510
decimal, 20 edit object colors, 507
quantitative analysis, 596 edit object fontss, 508
Predefined peaks, 68 edit objects, 507
create peaks with, 357 edit title object, 510
file location, 461 File menu, 499
functional groups, 100 grid, 483
Predictions Help menu, 514
calculate, 95, 369 hidden labels, 480
Preferences no reference peaks, 64
apply to existing peaks, 70 objects, 484
apply to future peaks, 70 order of spectra, 482
peaks, 53, 70 page boundaries, 484
Pre-search, 376 page orientation, 511
Preview palette bar, 483
file, 174 paste from clipboard, 504
multi-spectra, 175 print template, 499
Previous page radar box, 487
Print Preview, 502 resize objects, 489
Print, 186 save template, 499
3D view, 255 save template under another name, 499

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 Index 669

show/hide annotation label, 511 add to spreadsheet, 29, 31

show/hide annotations, 512 AIA, 208
show/hide grid, 511 custom, 360
show/hide palette bar, 511 definition, 5
show/hide peaks, 512 edit in print composition, 489
show/hide position labels, 512 edit object, 486
show/hide status bar, 511 library, 637
show/hide trace control bar, 512 locking, 258
spectral properties, 479 locking for printing, 258
spectrum labels, 481 remove from saved list, 31
split window, 513 saved list, 29
SSP, 488 search library, 637
status bar, 484 selected object, 485
template, 189, 477 source, 29, 31
template creation, 489 types, 28, 30
template printing, 492 unlocking, 258
title, 483 unselected object, 485
View menu, 511 value, 29, 31
view page layout before printing, 499 Property browse bar, 222
Window menu, 512 add column to spreadsheet, 226
windowshade, 484 docking, 227
zoom box, 487 floating, 227
Print Preview hide, 227
close preview, 503 moving, 227
Next Page, 501 property values, 224
one page, 502 resize, 222
previous page, 502 show, 227
print, 500 tree structure, 223
print composition template, 499 Property values
two pages, 502 Property browse bar, 224
zoom in, 503 Proportional scaling, 218
zoom out, 503 Proprietary libraries
Procedure Galactic, 634
public, 646 Public procedure
Profiles, 549 custom value program, 646
User Environment, 549
user path, 550
Program ID, 361
Q
Programs Quant, 173
custom value, 126, 641 search, 173
custom value options, 642 Quantitation
execute from image documents, 126 calibration documents, 170
execute from inside Win-IR Pro, 185 document, 91
register custom value, 361 Quantitation calibration
Proof by assumption. See Circular reasoning component, 93
Properties, 5
3200 file headers, 583
add new to spectrum, 28
add saved to spectrum, 29
add to spectrum, 26

Win-IR Pro System Reference Manual

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 670 Index

Quantitative analysis, 79, 363 search library, 86

add component, 365 Rapid scan, 274
back calculation, 596 apodization, 289
brief overview, 91 apodization, 286
calibration, 595 compute operation, 285, 287
calibration standards, 595, 596, 597 imaginary spectrum, 288
considerations, 594 included frequency, 290
control panel, 91 magnitude spectrum, 288
deviations, 596 phase correction, 289
display concentrations column, 370 phase parameters, 289
document, 91 real spectrum, 288
errors, 597, 598 trapezoidal breakpoint, 286
example, 371 Ratio, 292
general background requirements, 594 against reference peak, 51
hide concentrations column, 370 spectral type, 293
impurities, 597 Raw Image Data, 173
issues, 594 Read-only
method development, 596 search library, 88
methods, 593 Real spectrum, 288
overdetermination, 596 Reboot, 517
oversampling, 596 computer after installation, 516
overview, 593 Records
perturbation, 596 condition, 6
precision, 596 Reference
procedure, 594 peak, 51, 62
remove component, 365 peaks compared to normal, 63
reproducibility, 598 Reference Peak
significant figures, 596 create, 358
standards, 91, 595 Reference position
verification, 597 for center value, 52
windows, 91 Reference spectra, 79, 331, 425
without baseline correction, 534 need for, 161
Questions Reflectance spectra, 342
frequently asked, 515 Regions
change, 25
define, 362
R defining, 22, 280
Radar box, 9, 77 definition, 79
image, 118 delete, 25
print composition, 487 deselect, 25
scroll, 10 in autosubtract, 341
zoom, 10 Kinetics tab button, 98
Raman modify, 25
aperture, 580 select, 22, 25
convert, 442 select for 3D view, 241
laser, 276 use ruler to select, 24, 280
laser button on toolbar, 79 use ruler to select, 362
laser wavenumber, 442
scan, 274
Range

Win-IR Pro System Reference Manual

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 Index 671

Register in directory names, 5

custom value programs, 361 in filenames, 5
Registry edit, 625 Restrictions
Regression, 95, 369 on trace separation, 221
Re-install Right
Windows NT, xxii baseline, 202
Win-IR Pro, xxii edge, 204
Relabel Right mouse button, 488
Y-axis, 14 Rotation
Relative wavenumber 3D, 133, 249, 406, 435
for peaks, 52 Rows
Remove copying, 146
columns, 145, 260 deleting, 148
functional groups, 104 reordering, 147
peaks, 534 resizing, 139
peaks from peak table, 59 traces of contiguous, 150
properties from savedlist, 31 Ruler, 24, 280, 362
splash screen, 532 Run, 185
Rename
library, 638
search library, 638
S
Reorder s1 file, 640
columns, 146 s2 file, 640
rows, 147 Sadtler
Reprocess, 161, 416 collection code, 638
STOP label, 165 SearchMaster, 173
Rescale Sadtler libraries
Y-axis, 13, 230 change format, 633
Re-search, 393 proprietary, 634
Reset user, 634
Display Document Limits, 232 Sadtler user libraries
Display Limits, 233 importing, 633
spectrometer, 276 Sample data
Resize directory, xxi
annotations, 35 Sample scan
columns, 139 buttons, 78
event log box, 215 Save
label box, 35 automatically after data collection, 461
objects in print composition, 489 documents, 178
property browse bar, 222 print composition template, 499
rows, 139 Save As
Resolution document types, 180
digital, 86 documents, 178
dual in 3200 library, 634 print composition template, 499
optical, 86 Save as Predefined, 69
search library, 86 Save Plot Template, 262
single in 3200 library, 634
Re-start
Win-IR Pro, 189
Restricted characters

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 672 Index

Saved list manual termination, 375

properties, 29 mask, 378
remove properties from, 31 names, 380
Savitsky-Golay smoothing, 306 non-absorbance spectra, 392
sb file, 172 peaks, 380
Scalar arithmetic, 423 pre-search, 376
Scaling spectral, 378
constant, 218 structures, 382
independent, 218 Search Library
proportional, 218 conversion example, 635
traces, 217 convert, 633
Scan, 274 creation, 85
buttons, 78 disallowed conversions, 635
co-add more, 276 display properties, 637
from active spectrum, 276 document, 84
kinetics, 276 edit, 89
Raman, 274 file extensions, 640
rapid, 274 move, 639
Screen image name, 85
print, 39 parameters, 85
Screen saver read-only, 88
disable, 519 renaming, 638
Screens, 2 window, 84, 85
definition, 2 writeable, 88
display, 81 SearchMaster
no documents open, 75 Sadtler, 173
print, 40 Security, 476, 544
quantitative analysis, 91 physical, 544
split, 83 software, 544
Scripts Select
examples, 592 regions, 22, 25
execute from inside Win-IR Pro, 185 Select all visible, 210
logon, 550 Select spectra
Scroll via spreadsheet, 149
definition, 11, 15 via trace display, 82
radar box, 10 Selected objects, 485
spreadsheet, 137 properties, 485
trace, 9, 11, 15, 218 Sensitivity
Search auto-pick peaks, 112
after subtraction, 398 mouse, 531
algorithm, 378 peak picking, 416
batch, 398 Separating
considerations, 375 baselines, 220
documents, 170 traces, 220
enable for non-absorbance spectra, 375, 462 seq file, 173
example, 394, 395, 396 Setup
features common to all searches, 382 print, 188, 503
incomplete, 375 Shadow, 276
libraries, 375 Shadow Pro
library, 79, 173 tools, 229

Win-IR Pro System Reference Manual

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 Index 673

Show installation, xxi

annotations, 272 security, 544
annotations in print composition, 512 workstation version, 274
Gram-Schmidt chromatogram, 104, 116, 270 Solvents
grid in print composition, 511 calibration errors, 598
labels, 272 dilution, 598
palette bar in print composition, 511 entrapment, 598
peak labels, 271 evaporation, 598
peaks, 116, 271 impurities, 599
peaks in print composition, 512 residual solvent, 599
position labels in print composition, 512 residues, 599
property browse bar, 227 water contamination, 599
spectrum label in print composition, 511 Sources
status bar in print composition, 511 aperture, 580
trace control bar in print composition, 512 property, 29, 31
Shutdown and restart, 517 Spash screen
Sidebar, 280 remove, 532
control panel, 83 spc
Sidelobes multifile, 180
deconvolution, 616 spc file, 129, 172
remove negative in deconvolution, 620 Specifications
Signal-to-noise ratio add, 184, 209
deconvolution, 614 AIA FTIR, 183, 208
Significant figures, 596 Spectra, 3, 5
Simple analysis, 364 .spc format, 557
Sinc transform 2-D cross sections, 244, 429
deconvolution, 616 2D-IR display, 412
Single resolution 3200 format, 172
3200 library, 634 3200 series, 560
Single-beam, 292 3-D, 432
convert to microns, 354 absorbance, 282
convert to nanometers, 354 access directly, 259
Size add comments, 27
effect of interferogram symmetry on, 289 add custom properties, 28
Size to Content add new properties, 28
in print composition, 489 add points to, 301
sl file, 640 add properties, 26
Slices add saved properties, 29
animate show, 119 adding to libraries, 90
frequency, 119 arithmetic operations, 421
Slow system, 516 background, 73, 294
Smoothing baseline corrected, 338
boxcar, 306 binary operations upon, 424
by apodization, 321 Bio-Rad, 172
calibration, 608 blackbody, 349
example, 309 compare, 536
Fourier, 308 compress, 12
Savitsky-Golay, 306 convert, 559
spectrum, 306 convert 3200 series, 563
Software convert single beam to microns, 354

Win-IR Pro System Reference Manual

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 674 Index

convert single beam to nanometers, 354 real, 288

copy, 420 reference, 331, 425
copy extracted, 110 reference small in some experiments, 541
copy into Win-IR Pro, 197 reflectance, 342
copying between spreadsheets, 151 replace, 197
copying extracted, 126 reprocess development, 416
core information, 154 scalar operations upon, 423
define scan from, 276 scan to, 293
define subtraction reference, 332 scroll, 11
definition, 5 search non-absorbance, 375, 462
deleted from library, 633 search on non-absorbance, 392
deleting from libraries, 89, 90 select all displayed, 210
differentiate, 312 select non-contiguous, 535
display, 82 select via spreadsheet, 149
duplicate, 420 select via trace display, 82
effect of deleting on spreadsheet, 136 selection, 81
empty, 419 single beam, 73
expand, 12 smooth, 306
export, 180 subtrahend, 333
export extracted, 111 transform image array, 128
extract from array, 120 transmittance, 283
extracted, 106 truncate, 303
format, 562 unary operations upon, 421
format, 71 unlocking, 257
GRAMS, 172 view, 74
GRAMS/386, 557 window, 80
history, 157, 235 Win-IR, 557
hit list, 240 with no history, 158
identical to multifiles, 179 zoom, 79
IDs, 7 Spectral limits, 232
imaginary, 288 Spectral manipulation
import, 557 calibration, 607
import 3200 series, 560 Spectral properties
imported, 158 print composition, 479
in print composition, 479 Spectral ranges
invisible, 522 3D, 243
lock/unlock, 81 calibration, 605
locking, 257 Spectral search, 378
magnitude, 288 example, 394
multiple display, 536 Spectral subtraction, 332
need for reference, 161 calibration, 609
order in print composition, 482 Spectrometer.cpl file, 520
order of display, 535
PAS interpolated, 428
PAS linear, 447
phase, 425
phase parameters, 289
print extracted, 126
print parameters with, 263
process outside Win-IR Pro, 197

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 Index 675

Spectrometers print entries, 186

applet, 520 remove columns, 260
controller card interface, 577 removing columns, 145
duplicate applets, 520 re-ordering columns, 227
icon, 576 reordering columns, 146
network card, 516 reordering rows, 147
performance for calibration, 606 resizing with windowshade, 138
reset, 276 retain format, 155
Spectrum scroll bars, 137
object, 486 trace display, 150
Spectrum buttons, 79 undo editing, 142
Spectrum ID, 7 SSP. See Standard Spectral Plot
Spectrum Labels print composition, 488
print composition, 481 Stacked
Splash screen plots, 217
Win-IR Pro, 476 Stamp
Spline baseline correction, 340 time-date, 160, 235
Split user, 160, 235
windows in Print Composition, 513 Standard module
Split screens, 83 custom value program, 643
Spreadsheets, 3, 82, 135 Standard Spectral Plot, 234
add column via property browse bar, 226 print composition, 488
add history to, 238 Standards, 595
add property, 29, 31 AIA, 173
adding columns, 143 quantitative analysis, 91
contiguous rows, 150 Startup
copy data to, 193 load recent file, 459
copying columns, 153 Status bar, 76, 212
copying data between, 151 print composition, 484
copying rows, 146 Status line
core spectrum information, 154 detectors, 578
definition, 7, 135 Step scan, 274
deleted spectra, 136 DPS, 275
deleting rows, 148 DPS(2), 275
display of traces, 150 fast TRS, 275
editable cells, 142 multi-channel, 275
editing cells, 141 TRS, 275
format, 155 Stingray
format change, 155 array data collection, 276
hit list, 399 STOP label
initial columns, 136 in reprocess, 165
kinetics, 73, 115, 268 Store
maximize, 471 in directories, 5
minimize, 139 Stored phase array, 450
modifying, 138 Structures
multi-spectral, 72 chemical, 360
navigating through, 138 search on, 382
non-editable cells, 141 Subdirectories, 5
non-wrap in navigation, 138 Subtract
peak parameters into, 206 auto, 341

Win-IR Pro System Reference Manual

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 676 Index

by dragging, 335 windows, 3

spectrum, 332 Time
using the mouse, 335 range in 3D, 243
Subtraction stamp, 160, 235
factor, 342 Title
spectrum, 79 edit, 510
Subtrahend, 333 plot, 460
Support print composition, 483
customer, xxii search library, 87
Switches Title bar, 76
external, 581 Tools
Symmetry, 289 Shadow Pro, 229
System Trace control bar, 81, 217
running slowly, 516 enable in print composition, 512
Traces, 3, 5
axis, 15
T compress, 12, 15, 219
Tabs pages definition, 7
definition, 6 display, 80, 81, 82
Taskbar expand, 12, 15, 219
autohide, 524 invisible, 522
Telephones kinetics, 97
call back, 551 lock/unlock, 81
dial in, 551 maximize, 280, 470
Temperature order of display, 150
controller, 278 positioning, 218
Templates scaling, 217
and documents, 67 scroll, 9, 11, 15, 218
and peaks, 68 separating, 220
batch mode, 494 separation restriction, 221
create batch, 494 window, 80
creating, 489 zoom, 8
example, 263 Training, xxii
extraction, 106 Transforms, 83
load, 262 batch processing, 113
peak, 65 change parameters, 162
print composition, 189, 477 image array spectra, 128
printing, 492 Kramers-Krönig, 342
save, 262 nk, 342
use batch, 497 view parameters, 162
window, 478 Transmittance spectrum, 283
Text Trapezoid function
default colors, 556 apodization, 570
enter in annotation, 33 Trapezoidal breakpoint
enter in label box, 33 rapid scan parameter, 286
format in annotation, 33
format in label box, 33
Tile
windows, 467
Tiled

Win-IR Pro System Reference Manual

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 Index 677

Tree structure writeable, 88

property browse bar, 223 User Manager, 545
Triangle function User profile path, 550
apodization, 571 Username, 547
TRS. See Time-resolved spectroscopy Users
data, 173 adding accounts for, 543
negative bands, 101, 541 Power, 547
step scan, 275 stamp, 160, 235
to multifiles, 179 Users Copy, 552
TRS documents, 170 Using
Truncate Help, 475
spectrum, 303
use instead of Zap, 534
Turn off
V
event log, 212 Values
Two pages area, 200
Print Preview, 502 comma separated, 172
txt file, 640 custom, 361
Types height, 200
properties, 28, 30 peak, 200
Typographic conventions, xx property, 29, 31
Property browse bar, 224
U Vertical lines, 16
deleting, 17
UltraZap spectrum, 300 moving, 17
Unary arithmetic, 421 multiple, 18
Undo View menu
in spreadsheet, 142 kinetics document entries, 114, 266
last operation, 192 print composition, 511
Undocking Views, 2, 74
event log box, 213 2D-IR, 74
Units 3-D, 130, 247
X-axis, 13 3D kinetics, 74
Unlock flat, 133, 249, 407, 435
display, 81 PAS, 74
properties, 258 search hit list, 74
spectra, 257 three-dimensional, 74
spectrum, 81 Virtual memory, 517
Unlock selected, 257 Visual Basic
Unselected objects, 485 custom value program, 642
properties, 485 vpk file, 640
Upper trace vps file, 640
display limits, 245, 430
User Environment Profiles, 549
User libraries, 84
adding spectra, 90
create, 85
deleting spectra, 89
not shared, 88
read-only, 88

Win-IR Pro System Reference Manual

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 678 Index

W software, 274
Writeable
Water vapor libraries not shared, 88
deconvolution, 614 search library, 88
Wavenumbers, 13
Raman laser, 442
relative, 52
X
X-axis units, 351 X, Y coordinates, 530
Window menu X-axis
print composition, 512 change units, 13, 234
Windows compress, 12
activate, 466 expand, 12, 234
calibration curve, 94 microns, 352
cascade, 466 nanometers, 353
cascaded, 4 scroll, 11
close all, 469 units, 13
definitions, 80 wavenumbers, 351
division, 80 X-axis and Y-axis autoscaling, 229
image, 117 X-coordinate
kinetics document, 96 labels, 18
manipulations, 80 XOR mode
multiple, 3 zoom box, 524
new, 465
open, 471
quantitative analysis, 91 Y
radar, 9 Y scale
template, 478 3D, 133, 249, 406, 435
tile, 467 Yaw, 134, 250, 407, 435
tiled, 3 Y-axis, 230
Windows NT contract, 13
re-install, xxii expand, 15
Windowshade expansion, 78
control position in Print Composition, 513 label, 155
print composition, 484 relabel, 14
resizing spreadsheet, 138 rescale, 13, 230
Win-IR Pro, 1 Y-coordinate
closing multiple copies, 2 labels, 18
definition, 2 Y-resolution
exit, 189, 504 search library, 87
file extensions, 585
files, 589
multiple copies, 2 Z
re-install, xxii
Zap
re-start, 189
limitations at end points, 534
splash screen, 476
spectra, 297
WordPad
Zero end points
print using, 39
Truncate, 534
Working directory
Zero Path Difference. See ZPD
change, 517
Zero-filling factor, 286
Workstation version
Zero-valued spectrum, 419

Win-IR Pro System Reference Manual

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 Index 679

Zip drive, 515 trace, 8

Zoom, 7, 118, 436 Zoom box
2D-IR, 408 color, 524
3D, 252 print composition, 487
abort, 8 XOR mode, 524
baseline correction, 534 ZPD
definition, 7 change, 443
out, 230 explanation, 443
Print Preview, 503
radar box, 10

Win-IR Pro System Reference Manual

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 Bio-Rad Offices
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 Bio-Rad Offices
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 Bio-Rad Patents

This product may be covered by one or more of the following patents:

U.S. Patents: 3,286,582 3,841,920 4,086,652 4,138,727 4,413,908 4,420,690 4,646,329

4,828,367 4,935,633 4,958,308 5,166,749 5,262,635 5,265,039 5,295,017
5,579,462 5,612,784 5,633,997, 5,760,785 & Corresponding Foreign Patents &
Patent Applications
British Patent 972,265
Other Patents Applied For

Current as of March 2, 1998

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