Feat: Implement a visualisation feature to NiTransforms #212
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Can you post screenshots? |
Creation of new directory vim containing scripts for plotting
…to plotting feature
…tion descriptions
…draft) interactive slider feature to switch between slices.
… plot. Implemented function descriptors.
…n up straneous comments and code; implement NotImplemented errors for sliders
Overview (3x3 plot grid): Distorted grid lines superimposed over deformed brain density map: Quiver plot of the deltas field: Hopefully this sets a good (or useful) base for the implementation of a visualisation module to nitransforms, or at least can act as a good starting point to spring new ideas. |
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Additional details and impacted files@@ Coverage Diff @@
## master #212 +/- ##
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+ Coverage 94.39% 94.71% +0.31%
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Files 15 16 +1
Lines 1713 2004 +291
Branches 323 374 +51
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+ Hits 1617 1898 +281
- Misses 79 83 +4
- Partials 17 23 +6
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@effigies this is now ready for review! Latest plots can be accessed through the CircleCi workflow, under build_pytest > Artifacts. These shouldn't be too different (if at all) to the links posted above. |
…e or more spatial dimensions (see someones_displacement_field.nii.gz). Fixed.
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I'd be more comfortable with some of the numeric code if it came with tests; e.g., comparing the construction of the Jacobian determinant image with that generated by ANTs' CreateJacobianDeterminantImage. Given that this is visualization, there is less concern that we have an error (that will presumably show up in a visualization) and no other numeric code depends on this.
I would be okay merging as-is, but I left some small comments.
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The final cell seems to have failed:
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I've worked more on the notebook and fixed this since the last commit, it simply requires a 3x3 subplot (I carelessly copy pasted a 1x3 figure)
Edit: committed to fix, should work now 👍
| try: | ||
| """if field provided by path""" | ||
| self._voxel_size = nb.load(transform).header.get_zooms()[:3] | ||
| assert len(self._voxel_size) == 3 | ||
| except TypeError: | ||
| """if field provided by numpy array (eg tests)""" | ||
| deltas = [] | ||
| for i in range(self._xfm.ndim): | ||
| deltas.append((np.max(self._xfm._field[i]) - np.min(self._xfm._field[i])) | ||
| / len(self._xfm._field[i])) | ||
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| assert np.all(deltas == deltas[0]) | ||
| assert len(deltas) == 3 | ||
| self._voxel_size = deltas |
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It would be better not to rely on different code paths for tests and public API, if at all possible.
Can the test be rewritten to save a NIfTI image into tmp_path and pass that to PlotDenseField()?
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Addition of new file vis.py. Calls nitransform's nonlinear DenseFieldTransform class to illustrate corresponding transform objects through:
which can be illustrated all together (3x3 grid of plots, showing axial, coronal and sagittal projections for each graph) or individually.