Alter tractogram (trim, cut, replace, subsample, transform) #992

frheault · 2024-05-16T19:41:21Z

Quick description

New script to simulate alteration of tractogram (should be used for bundle, so maybe I will rename)
The operation are describe in the docstring of the script:

This script is used to alter a bundle to reach specific minimum dice
coefficient from the original bundle. The script will subsample, trim, cut,
replace or transform the streamlines until the minimum dice is reached.
(cannot be combined in one run, use the script multiple times if needed)

All operation use a dichotomic search to find the parameter that gets as close
as possible to the specified minimum dice coefficient (with an epsilon for
convergence).

The subsample operation will remove streamlines until the minimum dice is
reached. This affect the whole bundle.

The trim operation will used the lowest density voxels (starting at 1) to
remove points from the streamlines until the minimum dice is reached.
This typically affect the edge of the bundle.

The cut operation will remove points from the start (or end) streamlines until
the minimum dice is reached. This affect one end of the bundle.

The replace operation will upsample the tractogram (generate new streamlines
with noise) and then subsample the tractogram. This effectively replace
streamlines with similar ones until the minimum dice is reached.
This affect the whole bundle.

The transform operation will apply random transformations to the streamlines
until the minimum dice is reached. This affect the whole bundle.

...

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 · 2024-05-16T19:41:29Z

Hello @frheault, Thank you for updating !

In the file scilpy/tractograms/tractogram_operations.py:

Line 990:80: E501 line too long (80 > 79 characters)
Line 1003:80: E501 line too long (81 > 79 characters)
Line 1038:80: E501 line too long (80 > 79 characters)
Line 1060:80: E501 line too long (80 > 79 characters)
Line 1142:80: E501 line too long (80 > 79 characters)
Line 1237:80: E501 line too long (80 > 79 characters)
Line 1249:80: E501 line too long (80 > 79 characters)

In the file scripts/scil_tractogram_alter.py:

Line 49:80: E501 line too long (83 > 79 characters)
Line 50:80: E501 line too long (81 > 79 characters)
Line 51:80: E501 line too long (83 > 79 characters)

Comment last updated at 2024-06-18 14:03:36 UTC

codecov · 2024-05-16T20:27:59Z

Codecov Report

Attention: Patch coverage is 17.05426% with 214 lines in your changes missing coverage. Please review.

Project coverage is 67.63%. Comparing base (3191a0b) to head (9eb4594).
Report is 25 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #992      +/-   ##
==========================================
- Coverage   68.14%   67.63%   -0.51%     
==========================================
  Files         419      420       +1     
  Lines       21369    21662     +293     
  Branches     3216     3243      +27     
==========================================
+ Hits        14561    14651      +90     
- Misses       5533     5746     +213     
+ Partials     1275     1265      -10

Components	Coverage Δ
Scripts	`69.15% <71.98%> (+0.01%)`	⬆️
Library	`65.48% <43.57%> (-1.19%)`	⬇️

EmmaRenauld

Round 1 of comments. I didn't really read the code yet, only the descriptions.

Pep8 also needs to be addressed.

EmmaRenauld · 2024-06-24T18:17:55Z

scilpy/tractograms/tractogram_operations.py

+        input tractogram.
+    """
+    # Import in function to avoid circular import error
+    from scilpy.tractanalysis.reproducibility_measures import compute_dice_voxel


This means that our management is not perfect yet.

tractanalysis.reproducibility_measures.compute_dice_voxel seems to be usable with any map. So it is not necessarily a tractanalysis method. Maybe it could go in image.volume_operations (or in volume_math if we also want to offer this option in scil_volume_math). Or in stats.something but I don't like it as much.

EmmaRenauld · 2024-06-24T18:25:29Z

scripts/scil_tractogram_alter.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+


I would indeed rename. But not just bundle: the goal of this script is not simply to alter. I would imagine that a scil_tractogram_alter.py would ask user how to alter. Here it decides alone (if no option is provided). Can we put a longer, but more significative name? scil_bundle_alter_to_dice?

Also, I see that in your new methods (ex, subsample_streamlines_alter), you have an option baseline_sft=None that is never used in your script. Can you add an option --reference_bundle in your script?

I am not sure what you mean by "Here it decides alone (if no option is provided)."

I agree that the name scil_bundle_alter.py does not mean much
Here are a few more suggestions:

scil_bundle_alter_preserve_overlap.py

scil_bundle_alter_optimize_overlap.py

scil_bundle_alter_to_target_dice.py

(alter could be replaced by adjust, vary, adapt, modify, but I like alter because of the definition: change or cause to change in character or composition, typically in a comparatively small but significant way)

baseline_sft: It is used in another function (replace)

EmmaRenauld · 2024-06-24T18:34:06Z

scripts/scil_tractogram_alter.py

+
+"""
+This script is used to alter a bundle to reach specific minimum dice
+coefficient from the original bundle. The script will subsample, trim, cut,


It took me a little while to understand the goal of the script. Maybe something like this for the first sentence?

This script is used to alter a bundle while keeping it similar enough to the original version (keeping the dice coefficient above a given threshold).

EmmaRenauld · 2024-06-24T18:34:26Z

scripts/scil_tractogram_alter.py

+This script is used to alter a bundle to reach specific minimum dice
+coefficient from the original bundle. The script will subsample, trim, cut,
+replace or transform the streamlines until the minimum dice is reached.
+(cannot be combined in one run, use the script multiple times if needed)


This is not clear for me. What cannot be combined? Do you mean Cannot be used on multiple bundles in one run? Or the various operations choices cannot be combined?

various operations choices cannot be combined

EmmaRenauld · 2024-06-24T18:35:23Z

scripts/scil_tractogram_alter.py

+replace or transform the streamlines until the minimum dice is reached.
+(cannot be combined in one run, use the script multiple times if needed)
+
+All operation use a dichotomic search to find the parameter that gets as close


operations.

EmmaRenauld · 2024-06-24T18:45:50Z

scilpy/tractograms/tractogram_operations.py

+    """
+    Shuffle the orientation of the streamlines. The streamlines are not
+    reversed, only the orientation of the points within the streamlines is
+    shuffled.


I am not sure I understand the difference.

Yes its unclear, it is not a blanket reverse all streamlines, it is a shuffle head/tail of random streamlines

EmmaRenauld · 2024-06-24T18:46:50Z

scilpy/tractograms/tractogram_operations.py

+def replace_streamlines_alter(sft, min_dice=0.90, epsilon=0.01):
+    """
+    Replace streamlines based on a dice similarity metric.
+    The function will upsamples the streamlines (with parallel transport),


EmmaRenauld · 2024-06-24T18:47:12Z

scilpy/tractograms/tractogram_operations.py

+
+
+def trim_streamlines_alter(sft, min_dice=0.90, epsilon=0.01):
+    # Import in function to avoid circular import error


Missing docstring

EmmaRenauld · 2024-06-24T18:48:39Z

scripts/scil_tractogram_alter.py

+This affect the whole bundle.
+
+The transform operation will apply random transformations to the streamlines
+until the minimum dice is reached. This affect the whole bundle.


In the description of the method, you only mention rotations. Here, you say any transformation. Can you be more precise?

EmmaRenauld · 2024-06-24T18:48:56Z

scripts/tests/test_tractogram_alter.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+def test_help_option(script_runner):


More tests required.

frheault added 2 commits May 16, 2024 14:56

Added docstring

e771d98

Fix test after /0

799b9c1

frheault added 4 commits May 22, 2024 12:08

Add shuffle options

90113f1

Change permission

3e962de

Fix pep8

829c90b

Save matrix

1c25833

arnaudbore requested review from arnaudbore and CHrlS98 June 18, 2024 13:59

Merge upstream, fix conflicts

9eb4594

EmmaRenauld requested changes Jun 24, 2024

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Alter tractogram (trim, cut, replace, subsample, transform) #992

Alter tractogram (trim, cut, replace, subsample, transform) #992

frheault commented May 16, 2024 •

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		def trim_streamlines_alter(sft, min_dice=0.90, epsilon=0.01):
		# Import in function to avoid circular import error

Alter tractogram (trim, cut, replace, subsample, transform) #992

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Alter tractogram (trim, cut, replace, subsample, transform) #992

Conversation

frheault commented May 16, 2024 • edited Loading

Quick description

Type of change

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

Checklist

pep8speaks commented May 16, 2024 • edited Loading

Comment last updated at 2024-06-18 14:03:36 UTC

codecov bot commented May 16, 2024 • edited Loading

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frheault commented May 16, 2024 •

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pep8speaks commented May 16, 2024 •

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