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[EHN] Implement signal.clean to SurfaceMasker #4117

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merged 1 commit into from Nov 24, 2023
Merged

[EHN] Implement signal.clean to SurfaceMasker #4117

merged 1 commit into from Nov 24, 2023

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htwangtw
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@htwangtw htwangtw commented Nov 24, 2023 •
edited

  • Closes #

Changes proposed in this pull request:

This is an initial attempt to implement signal.clean to SurfaceMasker.
Concerns (generalisable to niftimaskers):

  • clean_kwargs - should filter out confounds and sample mask to prevent
    user adding those parameters upon creating the masker
  • all the cleaning related parameters - what do we want to choose to
    expose?

If we set on the solution I will expand this to SurfaceLabelsMasker

@htwangtw
[EHN] Implement signal.clean to SurfMasker
f43c09a 
This is an inital attempt to implement signal.clean to SurfMasker
Concerns:
  clean_kwarg  - should filter out confounds and sample mask to prevent
user adding those parameters upon creating the masker
  all the cleaning related parameters - what do we want to choose to
expose?
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👋 @htwangtw Thanks for creating a PR!

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codecov bot commented Nov 24, 2023 •
edited

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (b607726) 91.80% compared to head (f43c09a) 91.81%.

Files Patch % Lines
nilearn/experimental/surface/_maskers.py 96.00% 1 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #4117      +/-   ##
==========================================
+ Coverage   91.80%   91.81%   +0.01%     
==========================================
  Files         144      144              
  Lines       16152    16172      +20     
  Branches     3359     3360       +1     
==========================================
+ Hits        14829    14849      +20     
  Misses        781      781              
  Partials      542      542
Flag Coverage Δ
macos-latest_3.10_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
macos-latest_3.11_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
macos-latest_3.12_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
macos-latest_3.8_test_plotting 91.60% <96.00%> (+0.01%) ⬆️
macos-latest_3.9_test_plotting 91.61% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.10_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.11_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.12_test_plotting 91.64% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.12_test_pre 91.64% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.8_test_min 69.16% <96.00%> (+0.03%) ⬆️
ubuntu-latest_3.8_test_plot_min 91.36% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.8_test_plotting 91.60% <96.00%> (+0.01%) ⬆️
ubuntu-latest_3.9_test_plotting 91.61% <96.00%> (+0.01%) ⬆️
windows-latest_3.10_test_plotting 91.62% <96.00%> (+0.01%) ⬆️
windows-latest_3.11_test_plotting 91.62% <96.00%> (+0.01%) ⬆️
windows-latest_3.12_test_plotting 91.62% <96.00%> (+0.01%) ⬆️
windows-latest_3.8_test_plotting 91.58% <96.00%> (+0.01%) ⬆️
windows-latest_3.9_test_plotting 91.58% <96.00%> (+0.01%) ⬆️

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bthirion
bthirion reviewed Nov 24, 2023
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Looks good so far.

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You probably want to add tests ?

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htwangtw commented Nov 24, 2023 •
edited

You probably want to add tests ?

When I look at the NiftiMasker objects, it seems that they deliberately did not test out all the signal cleaning part and just assumed all the parameters are passed to signal.clean correctly.
I am not sure what's the best thing to do.

@htwangtw htwangtw marked this pull request as ready for review November 24, 2023 16:02
ymzayek
ymzayek approved these changes Nov 24, 2023
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LGTM!

bthirion
bthirion approved these changes Nov 24, 2023
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Thx !

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merging...

@htwangtw htwangtw merged commit d6d822d into nilearn:main Nov 24, 2023
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@htwangtw htwangtw deleted the surface/signal-cleaning branch November 24, 2023 16:47
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ymzayek commented Dec 11, 2023

linking to #4027 to keep track

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@bthirion bthirion bthirion approved these changes

@ymzayek ymzayek ymzayek approved these changes

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