Compare tractograms (TODI, TDI, ACC) #767

frheault · 2023-10-23T13:16:00Z

Quick description

Scripts to compute differences between tractograms (or bundles)
2 big tractograms can be multi processed (2x2GB = 2h at 20 CPU)

It computes TODI+ACC, Correlation of TDI, voxel-wise distances of streamlines (using FSS)

4 outputs
out_acc.nii.gz: How does local orientations compare?
out_correlation.nii.gz How does the density of streamlines agrees?
out_diff.nii.gz How different is the shape of the streamlines?
out_heatmap.nii.gz Power means of 3 others?

Type of change

Check the relevant options.

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

Checklist

My code follows the style guidelines of this project (run autopep8)
I added relevant citations to scripts, modules and functions docstrings and descriptions
I have performed a self-review of my code
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation
My changes generate no new warnings
I moved all functions from the script file (except the argparser and main) to scilpy modules
I have added tests that prove my fix is effective or that my feature works
New and existing unit tests pass locally with my changes

pep8speaks · 2023-10-23T13:16:06Z

Hello @frheault, Thank you for updating !

In the file scilpy/tractanalysis/reproducibility_measures.py:

Line 648:80: E501 line too long (80 > 79 characters)

In the file scilpy/tractanalysis/tests/test_reproducibility_measures.py:

Line 11:80: E501 line too long (88 > 79 characters)

In the file scripts/scil_tractogram_pairwise_comparison.py:

Line 41:80: E501 line too long (88 > 79 characters)
Line 92:80: E501 line too long (85 > 79 characters)
Line 98:80: E501 line too long (82 > 79 characters)

In the file scripts/tests/test_tractogram_pairwise_comparison.py:

Line 29:9: E128 continuation line under-indented for visual indent
Line 30:9: E128 continuation line under-indented for visual indent
Line 33:1: E302 expected 2 blank lines, found 1
Line 40:9: E128 continuation line under-indented for visual indent
Line 41:9: E128 continuation line under-indented for visual indent
Line 42:23: W292 no newline at end of file

Comment last updated at 2024-03-20 17:08:21 UTC

arnaudbore · 2023-10-23T13:53:14Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-10-23T14:02:12Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-11-02T16:31:06Z

Build passed ! Good Job 🍻 !

arnaudbore · 2023-11-03T15:39:36Z

Build passed ! Good Job 🍻 !

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arnaudbore · 2023-12-14T16:32:38Z

Build passed ! Good Job 🍻 !

…nto compare_tractogram_big

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arnaudbore · 2023-12-18T20:44:38Z

Build passed ! Good Job 🍻 !

arnaudbore · 2024-01-12T21:07:18Z

Build passed ! Good Job 🍻 !

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arnaudbore · 2024-01-15T14:49:16Z

Build passed ! Good Job 🍻 !

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arnaudbore · 2024-01-29T19:28:41Z

Build passed ! Good Job 🍻 !

arnaudbore · 2024-02-02T18:19:34Z

Build passed ! Good Job 🍻 !

scripts/scil_tractogram_pairwise_comparison.py

arnaudbore · 2024-02-02T19:40:42Z

Build passed ! Good Job 🍻 !

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arnaudbore

A couple of things to fix but otherwise GTG - fix pep8

scilpy/image/volume_operations.py

arnaudbore · 2024-02-21T19:38:45Z

scilpy/tractograms/streamline_operations.py

@@ -388,3 +389,34 @@ def smooth_line_spline(streamline, smoothing_parameter, nb_ctrl_points):
    smoothed_streamline[-1] = streamline[-1]

    return smoothed_streamline
+
+
+def generate_matched_points(sft):


arnaudbore · 2024-02-21T19:42:03Z

scripts/scil_tractogram_pairwise_comparison.py

+                             is_header_compatible_multiple_files,
+                             load_tractogram_with_reference,
+                             validate_nbr_processes)
+from scilpy.tractograms.tractogram_operations import tractogram_pairwise_comparison


I like scilpy.tractanalysis.reproducibility_measures it seems to fit our needs here. We'll see in the future if we need to create scilpy.tractograms.reproducibility_measures or scilpy.bundles.reproducibility_measures

scripts/scil_tractogram_pairwise_comparison.py

arnaudbore · 2024-02-21T19:48:39Z

scripts/scil_tractogram_pairwise_comparison.py

+                   help='Optional input mask.')
+    p.add_argument('--skip_streamlines_distance', action='store_true',
+                   help='Skip computation of the spatial distance between '
+                        'streamlines.')


@frheault a quick sentence here please.

arnaudbore · 2024-02-21T19:50:26Z

scripts/scil_tractogram_pairwise_comparison.py

+    if args.out_prefix and args.out_prefix[-1] == '_':
+        args.out_prefix = args.out_prefix[:-1]
+    out_corr_filename = os.path.join(args.out_dir,
+                                     '{}_correlation.nii.gz'.format(args.out_prefix))


Good enough

arnaudbore · 2024-02-21T19:51:39Z

scilpy/tractograms/tractogram_operations.py

+        List of the computed differences in the same order as the input voxel.
+    """
+    global sft_1, sft_2, matched_points_1, matched_points_2, tree_1, tree_2, \
+        sh_data_1, sh_data_2


We keep it as it is.

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arnaudbore

A quick comment and a pep8 fix then LGTM @EmmaRenauld or @karanphil if you have some time I would need a second review of this code. Thank you in advance

scilpy/tractograms/tests/test_tractogram_operations.py

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EmmaRenauld

Thanks!

EmmaRenauld · 2024-03-06T15:15:03Z

scilpy/image/volume_operations.py

+
+def normalize_metric(metric, reverse=False):
+    """
+    Normalize a metric array to a range between 0 and 1,


This could actually work with an array of any dimension. It does not have to be a volume. Ex, it is probably useful everytime we want to change the range of a colormap. Should we put it in utils? @arnaudbore

scilpy/tractanalysis/reproducibility_measures.py

scilpy/tractograms/streamline_operations.py

Transfer script

8a200c4

frheault changed the title ~~Compare tractograms (TODI, TDI, ACC)~~ WIP - Compare tractograms (TODI, TDI, ACC) Oct 23, 2023

Pep8 and docstring

abf57c3

arnaudbore self-requested a review October 23, 2023 13:53

frheault added the enhancement label Oct 23, 2023

arnaudbore changed the title ~~WIP - Compare tractograms (TODI, TDI, ACC)~~ [WIP - Compare tractograms (TODI, TDI, ACC) Nov 2, 2023

arnaudbore changed the title ~~[WIP - Compare tractograms (TODI, TDI, ACC)~~ [WIP] Compare tractograms (TODI, TDI, ACC) Nov 2, 2023

arnaudbore added the WIP Work In Progress label Nov 2, 2023

Skip

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frheault and others added 4 commits November 27, 2023 15:55

Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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rename script

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frheault added 2 commits December 18, 2023 15:01

Merge branch 'compare_tractogram_big' of github.com:frheault/scilpy i…

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Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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frheault changed the title ~~[WIP] Compare tractograms (TODI, TDI, ACC)~~ Compare tractograms (TODI, TDI, ACC) Dec 18, 2023

Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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frheault added 3 commits January 29, 2024 11:55

Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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Converting the main to a wrapper function

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Add _ to wrapper

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First pass emmanuel comments

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EmmaRenauld reviewed Feb 2, 2024

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Fix typo/errors

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frheault added 6 commits February 12, 2024 10:21

test start

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Added test

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Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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arnaudbore requested changes Feb 21, 2024

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frheault added 6 commits February 21, 2024 16:12

Reorganize functions and tests

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Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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Fix conflcit

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Fix kdtree type error

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arnaudbore approved these changes Mar 1, 2024

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frheault and others added 4 commits March 1, 2024 12:59

Merge branch 'master' of github.com:scilus/scilpy into compare_tracto…

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Remove data from moved test

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EmmaRenauld reviewed Mar 6, 2024

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frheault and others added 3 commits March 17, 2024 21:39

Fix Conflict

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Passing test

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Missing import

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EmmaRenauld approved these changes Mar 19, 2024

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Fix conflicts

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arnaudbore merged commit 234b88c into scilus:master Mar 20, 2024
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Compare tractograms (TODI, TDI, ACC) #767

Compare tractograms (TODI, TDI, ACC) #767

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Compare tractograms (TODI, TDI, ACC) #767

Compare tractograms (TODI, TDI, ACC) #767

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frheault commented Oct 23, 2023 • edited Loading

Quick description

Type of change

Provide data, screenshots, command line to test (if relevant)

Checklist

pep8speaks commented Oct 23, 2023 • edited Loading

Comment last updated at 2024-03-20 17:08:21 UTC

arnaudbore commented Oct 23, 2023

arnaudbore commented Oct 23, 2023

arnaudbore commented Nov 2, 2023

arnaudbore commented Nov 3, 2023

arnaudbore commented Dec 14, 2023

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