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Refactor template alignments to keep a fixed parcellation #116

Merged
merged 24 commits into from
Dec 18, 2024
Merged

Refactor template alignments to keep a fixed parcellation #116

merged 24 commits into from
Dec 18, 2024

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pbarbarant
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@pbarbarant pbarbarant commented Dec 8, 2024 •
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Closes #86. Uses the new backend to distribute template computations across parcels.

  • Docstrings
  • Unit tests
  • Adapt examples/plot_template_alignment.py

Pierre-Louis Barbarant added 18 commits December 7, 2024 02:00
Add index_by_parcel
1749a3a
Modify fit method
00751ab
Replace _create_template by _fit_local_template
916fdfc
Add template reconstruction + history
9f9fe29
Rename get_parcellation method to get_parcellation_img for clarity
7c1cc25
Rename transform parameter from X to img for clarity and update relat…
22d2b6e 
…ed references
Rename test_get_parcellation to test_get_parcellation_img
931511c
Refactor transform method in TemplateAlignment for clarity and functi…
5612e75 
…onality; add get_parcellation method to retrieve parcellation masker details.
Remove unused _map_template_to_image function to streamline codebase
169fd45
Remove unused _predict_from_template_and_mapping function
3bf5571
Add tests for parcellation retrieval in TemplateAlignment
a88606c
Refactor variable names in TemplateAlignment for clarity in parcel da…
218fa6c 
…ta processing
Rename index_by_parcel function to _index_by_parcel for clarity and u…
bf33bbd 
…pdate parameter name for consistency
Set default values for parameters in _fit_local_template function for…
1d32ad7 
… improved usability
Add unit tests for template alignment functions and parcellation proc…
885a05b 
…essing
Add function to sample subjects data for testing purposes
5883e48
Update documentation for image processing functions to clarify parame…
9411aee 
…ter types and improve readability
Enhance tutorial on template-based prediction by improving clarity an…
e55d982 
…d detail, correcting typos, and updating variable names for consistency
@pbarbarant pbarbarant marked this pull request as ready for review December 9, 2024 15:08
@pbarbarant
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I refactored the template example to close #100 . Template is now Procrustes-based.

@pbarbarant
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The doc build is now around 10min instead of over 30min, which is acceptable if we want to showcase examples with realistic use cases. @emdupre do you think we can close #92 ?

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emdupre commented Dec 9, 2024

Yes, that seems reasonable to me ! Thank you, @pbarbarant !

bthirion
bthirion reviewed Dec 17, 2024
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LGT

examples/plot_template_alignment.py Outdated Show resolved Hide resolved
examples/plot_template_alignment.py Outdated Show resolved Hide resolved
@pbarbarant pbarbarant merged commit 51b01ff into main Dec 18, 2024
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@pbarbarant pbarbarant deleted the feat/one-parcellation-template branch December 18, 2024 01:59
@pbarbarant pbarbarant mentioned this pull request Jan 2, 2025
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Keep a fixed parcellation when computing templates
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@pbarbarant @emdupre @bthirion