Custom colors in VolumeRGB

[candytaco]

Added things to VolumeRGB to allow data channels to be mapped to custom base colors instead of just red, green, and blue. Also added an option to have all three data channels to use the same vmin and vmax. Backwards compatible as the default behavior is to bypass all the new features and map data channels directly to RGB.

Also added a Colors class to keep track of colors to use.

Specify custom colors:
volume = cortex.VolumeRGB(visual, progression, integration, subject, transform, channel1color = cortex.Colors.RoseRed, channel2color = cortex.Colors.LimeGreen, channel3color = cortex.Colors.DodgerBlue)

Force shared ranges:
volume = cortex.VolumeRGB(visual, progression, integration, subject, transform, shared_range = True)

Also have a minor thing to specify an overlays file in quickflat.make_svg

[codecov]

Codecov Report

Merging #366 into master will decrease coverage by 0.09%.
The diff coverage is 30.35%.

@@            Coverage Diff             @@
##           master     #366      +/-   ##
==========================================
- Coverage   28.81%   28.71%   -0.10%     
==========================================
  Files          60       60              
  Lines        8521     8612      +91     
==========================================
+ Hits         2455     2473      +18     
- Misses       6066     6139      +73     

Impacted Files	Coverage Δ
cortex/quickflat/view.py	35.67% <0.00%> (ø)
cortex/utils.py	15.31% <0.00%> (ø)
cortex/dataset/viewRGB.py	56.07% <29.24%> (-20.15%)	⬇️
cortex/__init__.py	61.11% <100.00%> (ø)
cortex/dataset/__init__.py	100.00% <100.00%> (ø)
cortex/dataset/views.py	72.33% <100.00%> (ø)

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 69903bf...b2f51f7. Read the comment docs.

[mvdoc]

added comments on some minor issues that would be nice to be fixed before merging

[mvdoc]

extra spaces can be removed

[mvdoc]

"Invalid error for channel2 without the last channel?

[mvdoc]

same as comment before

[mvdoc]

space in kwargs ;-)

[mvdoc]

spaces in kwargs :-)

[mvdoc]

this docstring also needs to be fixed (red/green/blue component)

[mvdoc]

it looks like some changes to VolumeRGB are not backward compatible, because a test fails

=================================== FAILURES ===================================

______________________________ test_dataset_save _______________________________

    def test_dataset_save():

        tf = tempfile.NamedTemporaryFile(suffix=".hdf")

        mrand = np.random.randn(2, *volshape)

        rand = np.random.randn(*volshape)

        ds = cortex.Dataset(test=(mrand, subj, xfmname))

        ds.append(twod=cortex.Volume2D(rand, rand, subj, xfmname))

        ds.append(rgb =cortex.VolumeRGB(rand, rand, rand, subj, xfmname))

        ds.append(vert=cortex.Vertex.random(subj))

        ds.save(tf.name)

    

        ds = cortex.load(tf.name)

        assert isinstance(ds.test, cortex.Volume)

        assert ds.test.data.shape == mrand.shape

        assert isinstance(ds.twod, cortex.Volume2D)

        assert ds.twod.dim1.data.shape == rand.shape

        assert ds.twod.dim2.data.shape == rand.shape

>       assert ds.rgb.volume.shape == tuple([1] + list(volshape) + [4])

cortex/tests/test_dataset.py:99: 

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <Dataset with views [vert, test, twod]>, attr = 'rgb'

    def __getattr__(self, attr):

        if attr in self.__dict__:

            return self.__dict__[attr]

        elif attr in self.views:

            return self.views[attr]

    

>       raise AttributeError

E       AttributeError

cortex/dataset/dataset.py:48: AttributeError

[candytaco]

OOH right. I had written the color mapping function to assume a 1D array of voxel values, so it couldn't handle 3D or 4D volumes. Will fix that soon.

[mvdoc]

cool, thanks!