WIP: New labels maps and simplification of tractometry profile scripts #554

frheault · 2022-03-03T16:50:03Z

Adding new functionalities to scil_compute_bundle_voxel_label_map.py

Support multiples (co-registered) input to improve longitudinal tractometry and add the new (yet undertested) labeling approach based on bundle-shape (instead of simple euclidian distance to a single centroid).

Also, remove the need for NPZ file in tractometry and rely simply on NIFTI file instead (simpler to follow). Fix a problem with double weighting using density (can explain if needed)

Finally, use a memmap for distance to centroids instead of pure RAM. So big bundle can have their labels map computed with >> 20 points!

This PR requires an update to the Tractometry-Flow pipeline.

pep8speaks · 2022-03-03T16:50:09Z

Hello @frheault, Thank you for updating !

In the file scilpy/tractanalysis/distance_to_centroid.py:

Line 59:80: E501 line too long (80 > 79 characters)
Line 61:80: E501 line too long (82 > 79 characters)

In the file scilpy/utils/metrics_tools.py:

Line 232:80: E501 line too long (81 > 79 characters)

In the file scilpy/utils/streamlines.py:

Line 10:80: E501 line too long (80 > 79 characters)
Line 155:80: E501 line too long (83 > 79 characters)
Line 157:80: E501 line too long (87 > 79 characters)
Line 167:80: E501 line too long (88 > 79 characters)

In the file scripts/scil_compute_bundle_mean_std.py:

Line 46:80: E501 line too long (80 > 79 characters)

In the file scripts/scil_compute_bundle_mean_std_per_point.py:

Line 33:80: E501 line too long (81 > 79 characters)
Line 45:80: E501 line too long (80 > 79 characters)

In the file scripts/scil_compute_bundle_voxel_label_map.py:

Line 91:80: E501 line too long (80 > 79 characters)
Line 225:80: E501 line too long (82 > 79 characters)

In the file scripts/scil_uniformize_streamlines_endpoints.py:

Line 40:80: E501 line too long (82 > 79 characters)

Comment last updated at 2022-07-27 18:26:08 UTC

scil-admin · 2022-03-03T17:28:03Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-554/1/

…bels_map

scil-admin · 2022-04-19T18:27:29Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-554/2/

scil-admin · 2022-04-19T23:32:43Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-554/3/

scil-admin · 2022-04-29T00:01:58Z

Build passed ! Good Job 🍻 !

…bels_map

scil-admin · 2022-05-12T18:57:07Z

Build passed ! Good Job 🍻 !

arnaudbore

I think I covered everything but will do a second round once you fixed everything.

scilpy/utils/metrics_tools.py

scilpy/utils/streamlines.py

arnaudbore · 2022-05-19T14:39:26Z

scilpy/utils/streamlines.py

+                centroid = get_streamlines_centroid(ref_bundle.streamlines,
+                                                    20)[0]
+            else:
+                centroid = get_streamlines_centroid(sft.streamlines, 20)[0]


Why 20 points has never been an arg and is hardcoded ?

This is simply because I have to convert streamlines to an array with an equal number of pts, it could be 10, 20, 50, but in the end, it changes virtually nothing.

scripts/scil_compute_bundle_mean_std.py

scripts/scil_compute_bundle_mean_std_per_point.py

scripts/scil_compute_bundle_voxel_label_map.py

Co-authored-by: arnaudbore <arnaud.bore@gmail.com>

scil-admin · 2022-05-19T20:58:51Z

Build passed ! Good Job 🍻 !

…nto new_labels_map

scil-admin · 2022-05-20T16:23:57Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-554/7/

…bels_map

frheault · 2022-05-20T18:10:01Z

@arnaudbore The import inside the function is a circular dependency, everything crash if I put it at the top.

scil-admin · 2022-05-20T18:46:18Z

Build passed ! Good Job 🍻 !

scil-admin · 2022-06-16T19:18:35Z

Build passed ! Good Job 🍻 !

…bels_map

scil-admin · 2022-07-27T19:02:49Z

Build passed ! Good Job 🍻 !

arnaudbore · 2022-09-16T18:34:08Z

Build Failed 💥
https://jenkins.scil.usherbrooke.ca/job/scilpy/job/PR-554/11/

…bels_map

arnaudbore · 2022-09-23T15:05:34Z

Build passed ! Good Job 🍻 !

arnaudbore

Help is missing - no npz saved anymore.

scripts/scil_compute_bundle_voxel_label_map.py

…bels_map

…w_labels_map

arnaudbore · 2022-10-05T16:01:44Z

Build passed ! Good Job 🍻 !

…bels_map

arnaudbore · 2022-10-05T20:22:57Z

Build passed ! Good Job 🍻 !

frheault added 13 commits March 10, 2021 15:45

Robustness check

fc650ce

tmp

964670d

update

bd16ed3

merged

35ae0dc

New ref for uniformize

5412f9d

flake8 + test

d95658a

new memory friendly

61ee157

Fix correlation

66a63bc

reformating everything

959cc0a

switch to nii instead of npz

14ddff4

add older script

e329ff6

add older script

a016230

Update with master

ae88ea8

frheault mentioned this pull request Mar 3, 2022

New labels map update scilus/tractometry_flow#13

Merged

scil-admin requested a review from arnaudbore March 3, 2022 17:27

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

03ab865

…bels_map

use right labels_map

143eb5c

Fix test

0f0dcb0

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

ff9faea

…bels_map

arnaudbore reviewed May 19, 2022

View reviewed changes

Update scilpy/utils/metrics_tools.py

fadde20

Co-authored-by: arnaudbore <arnaud.bore@gmail.com>

scil-admin requested a review from arnaudbore May 19, 2022 20:58

Update for Arnaud comments

99e8c16

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

5e0c0a6

…nto new_labels_map

frheault added 2 commits May 20, 2022 13:01

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

ff10ae6

…bels_map

Fix circular dependencies

e408970

Increased min test to 1e16

11139d4

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

5878c81

…bels_map

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

39991e6

…bels_map

mdesco approved these changes Oct 3, 2022

View reviewed changes

arnaudbore reviewed Oct 4, 2022

View reviewed changes

scripts/scil_compute_bundle_voxel_label_map.py Outdated Show resolved Hide resolved

frheault added 5 commits October 5, 2022 10:16

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

ba88ccf

…bels_map

Added help and datatype for labels

6356fdc

Fix conflict after merge

c5b8b5d

Fix conflict

5c26060

Merge branch 'new_assign_color' of github.com:frheault/scilpy into ne…

f272e35

…w_labels_map

arnaudbore self-requested a review October 5, 2022 16:01

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

0c3ac9a

…bels_map

arnaudbore merged commit 0911369 into scilus:master Nov 2, 2022

frheault deleted the new_labels_map branch February 28, 2024 21:08

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WIP: New labels maps and simplification of tractometry profile scripts #554

WIP: New labels maps and simplification of tractometry profile scripts #554

frheault commented Mar 3, 2022

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WIP: New labels maps and simplification of tractometry profile scripts #554

WIP: New labels maps and simplification of tractometry profile scripts #554

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