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@Remi-Gau Remi-Gau released this 09 Apr 09:15
· 18 commits to main since this release
0.10.4
4f47301
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Learn about vigilant mode.

Released April 2024

HIGHLIGHTS

  • Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).

  • Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).

  • Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).

  • Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).

Fixes

  • Fix plotting of carpet plot due to a change in the coming version of matplolib (3.9.0) (#4279 by Rémi Gau).

  • Fix errant warning when using stat_type in nilearn.glm.compute_contrast (#4257 by Eric Larson).

  • Fix when thresholding is applied to images by GLM reports (#4258 by Rémi Gau).

  • Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).

  • Make masker report tables horizontally scrollable (#4308 by Rémi Gau).-

  • Masker reports tables do not overlap with report image (#4308 by Rémi Gau).

  • Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).

  • Ensure that region_names_ can be generated by nilearn.maskers.NiftiSpheresMasker.transform_single_imgs for deterministic atlases that use floats or non-consecutive values as region_ids whether they include background in their labels or not (#4274 by Rémi Gau).

  • Ensure that nilearn.interfaces.bids.save_glm_to_bids serializes numpy arrays to list used as GLM parameters before saving them to JSON (#4325 by Rémi Gau).

  • Check that the view parameter in surface plotting functions is a pair of int or float when it is not a string (#4297 by Rémi Gau).

  • Fix positions of the markers on the images on the sphere masker reports (#4285 by Rémi Gau).

  • Fix cut position in nifti maps maskers to match displayed map maximum (#4304 by Rémi Gau).

  • Make sure that nilearn.maskers.NiftiSpheresMasker reports displays properly when it contains only 1 sphere (#4269 by Rémi Gau).

  • Miscellaneous fixes in GLM reports (only display FIR delay if FIR is used, display color bar “Z score” legend…) (#4266 by Rémi Gau).

  • Fix minor typos in documentation (glossary and connectivity/parcellating) (#4343 by Florent Pollet).

  • Update minor information on the Code of Conduct page (#4318 and #4320 by Himanshu Aggarwal).

Enhancements

  • Add an avg_method parameter to nilearn.plotting.plot_surf_stat_map (#4298 by Rémi Gau).

  • Advertise nilearn’s in built globbing capability in an example (#4334 by Himanshu Aggarwal).

Changes

  • Throw warnings when passing parameters to surface plotting functions that are not used by the plotly engine (#4298 by Rémi Gau).

  • Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).

  • Change the colormap to gray for the background image in the nilearn.maskers.NiftiSpheresMasker (#4269 by Rémi Gau).

  • Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).

  • Use red to blue color map in the GLM reports (#4266 by Rémi Gau).

  • nilearn.maskers.NiftiSpheresMasker will throw warnings if the labels passed to it is not a list of str, or if the number of items in the list of labels does not match the number of regions in the label image (#4274 by Rémi Gau).

  • Copy headers from user-specified image to the result of nilearn.image.math_img (#4337 by Himanshu Aggarwal).

  • Render the description of the templates, atlases and datasets of the nilearn.datasets as part of the documentation (#4232 by Rémi Gau).

  • Render examples of GLM and masker reports as part of the documentation (#4267 and #4295 by Rémi Gau).

  • HTML, CSS are now linted using prettier. (#4302, by Rémi Gau).

List of pull requests

  • [MAINT] Post release 0.10.3 by @Remi-Gau in #4246
  • [MAINT] Refactor test reporting by @Remi-Gau in #4247
  • [MAINT] remove date from copyright by @Remi-Gau in #4249
  • [FIX] numpy 2 compatibility by @Remi-Gau in #4251
  • [DOC] Add datasets description to the documentation by @Remi-Gau in #4232
  • [FIX] Replace remaining contrast_type by stat_type by @larsoner in #4257
  • [DOC] Add versionadded directive to two_sided parameter of binarize_img function by @NicolasGensollen in #4262
  • [DOC] Improve warnings for BIDS folders by @Remi-Gau in #4253
  • [DOC] clean citation and bibliography in the documentation by @Remi-Gau in #4254
  • [STY] fix doc strings flake8 errors that were ignored until now by @Remi-Gau in #4264
  • [FIX] read only problem with numpy 2 by @Remi-Gau in #4265
  • [FIX] threshold images right before ploting in GLM reports by @Remi-Gau in #4258
  • [FIX] Make sure that NiftiSphereMaskers reports display properly for only 1 sphere by @Remi-Gau in #4269
  • [FIX] use proper grid spec when plotting carpet plots by @Remi-Gau in #4279
  • [FIX] fix positions markers on images on sphere masker reports by @Remi-Gau in #4285
  • [DOC] add documentation about kwargs in nilearn.plotting by @Remi-Gau in #4270
  • [DOC] update doc strings of the maskers by @Remi-Gau in #4286
  • [FIX] improve colorbar in mosaic display by @Remi-Gau in #4284
  • [FIX] Fix color bar handling with color map with only 1 level by @Remi-Gau in #4256
  • [DOC] render reports in the documentation by @Remi-Gau in #4267
  • [FIX] fixes several plotting details in glm reports by @Remi-Gau in #4266
  • [FIX] force views in surface plotting to be pairs of int or float when not a string by @Remi-Gau in #4297
  • [FIX] fix cut position in nifti maps maskers by @Remi-Gau in #4304
  • [FIX] remove conftest for externals by @Remi-Gau in #4306
  • [MAINT] add script to check duration of test suite by @Remi-Gau in #4231
  • [DOC] display all masker reports in the doc by @Remi-Gau in #4295
  • Revert "[FIX] remove conftest for externals" by @Remi-Gau in #4311
  • [ENH] Add avg_method to plot_surf_stat_map by @Remi-Gau in #4298
  • [FIX] make masker report tables horizontally scrollable and not overlap with masker report images by @Remi-Gau in #4308
  • [FIX] use the proper html template for mutli maps and label masker by @Remi-Gau in #4310
  • [DOC] Update drop-in hour information on contributing page by @man-shu in #4318
  • [MAINT] Use prettier to format HTML and CSS by @Remi-Gau in #4302
  • [DOC] Refer to nilearn datasets module by @man-shu in #4320
  • [DOC] Adding Himanshu to authors by @man-shu in #4322
  • [FIX] check data format passed to surface plotting functions by @Remi-Gau in #4323
  • [FIX] serialize numpy arrays to list before saving to json by @Remi-Gau in #4325
  • [FIX] make identifying region names more robust by @Remi-Gau in #4289
  • [DOC] Advertise nilearn's in built globbing by @man-shu in #4334
  • [MAINT] Refactor test nifti label maskers by @Remi-Gau in #4333
  • [MAINT] add test to resampling_target = None for nifti label maskers by @Remi-Gau in #4336
  • [DOC] Fix typos doc by @florian6973 in #4343
  • [BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in #4348
  • [ENH] relax requirements for test_sampling_affine by @Remi-Gau in #4349
  • [DOC] Fix typo and docstring formatting in glm.first_level.first_level_from_bids by @michellewang in #4352
  • [FIX] change "grey" to "gray" in doc/visual_testing/reporter_visual_inspection_suite.py for older Matplotlib versions by @michellewang in #4353
  • [DOC] Update release section of maintainence page by @man-shu in #4356
  • [FIX] resolve numpy2 compatibility related to ambiguity when broadcasting in np.solve by @Remi-Gau in #4350
  • [FIX] Headers not carried over by math_img by @man-shu in #4337
  • REL 0.10.4 by @man-shu in #4354
  • [MAINT] Post release 0.10.4 by @Remi-Gau in #4366

New Contributors

Full Changelog: 0.10.3...0.10.4

Contributors

larsoner, NicolasGensollen, and 4 other contributors
Assets 4