v1.3.0

v1.3.0

This release brings major improvements to pycortex's rendering and RGB visualization workflows. The new headless webviewer lets you generate 3D brain snapshots entirely from scripts, notebooks, and CI pipelines; no browser window required. The RGB color range API has been overhauled to support per-channel vmin/vmax control, giving you much finer control over how multi-channel data is displayed. Several long-standing issues with the webviewer crashing Jupyter kernels have also been resolved.

Enhancements

• Headless webviewer for automated save_3d_views (#604, @kroq-gar78). Playwright-backed headless rendering lets you run cortex.export.save_3d_views and cortex.export.plot_panels without a browser window. It works in CI, scripts, and Jupyter notebooks. Install with pip install pycortex[headless].
• Unified VolumeRGB / VertexRGB signatures (#599, @mvdoc). Fixes #579.
• More useful error message for missing surfaces (#593, @kroq-gar78).
• Type annotations for the frontend (#597, @kroq-gar78).

⚠️ Breaking change

VolumeRGB / VertexRGB: new color range API (#603). The arguments shared_range, shared_vmin, and shared_vmax have been replaced with autorange, vmin, and vmax.

Before (v1.2.x):

cortex.VolumeRGB(red, green, blue, shared_range=True, shared_vmin=-3, shared_vmax=3)

After (v1.3.0):

cortex.VolumeRGB(red, green, blue, autorange="shared", vmin=-3, vmax=3)

autorange accepts "shared" or "individual". vmin/vmax now accept either a single float (applied to all channels) or a 3-tuple for per-channel control. When vmin/vmax are provided, they override autorange. See #603 for details.

Bug fixes

• Fix save_3d_views crashing IPython/Jupyter kernels (#602, @kroq-gar78).
• Fix pickerfun Python callback (#600, @kroq-gar78).

Maintenance

• Bump actions/upload-artifact from 6 to 7 (#596, @dependabot).
• Bump actions/download-artifact from 7 to 8 (#595, @dependabot).

Full Changelog: v1.2.14...v1.3.0

v1.2.14

MNT fixing release action

Full Changelog: v1.2.13...v1.2.14

v1.2.13

What's Changed

• FIX error if unsupported kwargs in make_figure by @kroq-gar78 in #585
• FIX pass freesurfer_subject_dir to get_surf() in cut_surface() (#591) by @mvdoc in #592
• MNT Automate version management with setuptools-scm and simplify release workflow by @Copilot in #587
• Bump actions/checkout from 5 to 6 by @dependabot[bot] in #582
• Bump JamesIves/github-pages-deploy-action from 4.7.3 to 4.7.4 by @dependabot[bot] in #581
• Bump JamesIves/github-pages-deploy-action from 4.7.4 to 4.7.6 by @dependabot[bot] in #589
• Bump actions/cache from 4 to 5 by @dependabot[bot] in #588
• Bump JamesIves/github-pages-deploy-action from 4.7.6 to 4.8.0 by @dependabot[bot] in #590

Full Changelog: 1.2.12...v1.2.13

1.2.12

What's Changed

• Bump JamesIves/github-pages-deploy-action from 4.7.2 to 4.7.3 by @dependabot[bot] in #565
• FIX make parse_curve also compatible with NumPy 2.0 by @evi-hendrikx in #570
• FIX deprecated ndarray.tostring() -> tobytes() by @hmac213 in #571
• Colormap additions by @tknapen in #574
• Clipping sliceplanes by @alexhuth in #556
• Minor fix to manual align by @marklescroart in #575
• Bump actions/checkout from 4 to 5 by @dependabot[bot] in #576
• Fix xdrlib import compatibility for Python 3.12+ and Blender by @sjshim in #577
• Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #578
• Blender flattening support by @dmitry-mli in #572
• Handle NumPy 2.x hash compatibility for WebGL data by @Copilot in #584

New Contributors

• @evi-hendrikx made their first contribution in #570
• @hmac213 made their first contribution in #571
• @tknapen made their first contribution in #574
• @sjshim made their first contribution in #577
• @dmitry-mli made their first contribution in #572
• @Copilot made their first contribution in #584

Full Changelog: 1.2.11...1.2.12

1.2.11

What's Changed

• NF: add config option for uniform lighting by @MShinkle in #561
• FIX: Python 3.13 compatibility, and upgrade to Cython 3 by @kroq-gar78 in #564

Dependabot

• Bump JamesIves/github-pages-deploy-action from 4.6.3 to 4.6.4 by @dependabot in #554
• Bump JamesIves/github-pages-deploy-action from 4.6.4 to 4.6.8 by @dependabot in #555
• Bump JamesIves/github-pages-deploy-action from 4.6.8 to 4.6.9 by @dependabot in #558
• Bump codecov/codecov-action from 4 to 5 by @dependabot in #559
• Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.2 by @dependabot in #562

Full Changelog: 1.2.10...1.2.11

1.2.10

What's Changed

• MNT Remove dependency on distutils by @kroq-gar78 in #553

Full Changelog: 1.2.9...1.2.10

1.2.9

What's Changed

• MNT,FIX test code on python 3.11, fix matplotlib register cmap by @mvdoc in #536
• Bump JamesIves/github-pages-deploy-action from 4.6.0 to 4.6.1 by @dependabot in #537
• NF Add functions to project volume data to surface while dealing with NaNs. by @mvdoc in #539
• FIX np.product is deprecated in favor of np.prod by @mvdoc in #541
• ENH better handling of temp directory for downloading subjects by @mvdoc in #540
• FIX avoid using wget and use urllib by @mvdoc in #542
• MNT use codecov action with token by @mvdoc in #543
• FIX avoid using jQuery for getting numpy arrays by @mvdoc in #544
• Bump JamesIves/github-pages-deploy-action from 4.6.1 to 4.6.3 by @dependabot in #546
• NF add functions to compute mappers from freesurfer to WebGL by @mvdoc in #547
• NF,DOC improve docstring for show and make_static by @mvdoc in #548
• NF display values at vertex in webgl viewer by @mvdoc in #549
• ENH Add option to specify which sulci to show. by @cchen23 in #550

Full Changelog: 1.2.8...1.2.9

1.2.8

What's Changed

• FIX pass overlay_file arg when creating cutout. by @cchen23 in #496
• FIX update URL of retinotopy dataset by @mvdoc in #499
• ENH allow setting curvature values when starting webgl viewer by @mvdoc in #498
• FIX ensure correct datatype for mri_surf2surf by @mvdoc in #502
• FIX check if shapes exist before setting the labels in the WebGL viewer by @mvdoc in #501
• FIX do not use a default layout selection for multiple volumes by @mvdoc in #503
• FIX Improve masks returned by get_roi_masks and correctly split into left/right hemispheres by @mvdoc in #504
• Add codespell: workflow, config and fix typos it finds by @yarikoptic in #506
• FIX save surf2surf matrix with surface_type in filename by @mvdoc in #510
• FIX do not register colormap if already done by @Matlmr in #512
• MNT specify when to run actions by @mvdoc in #513
• ADD add multiple data at the same time if data is a list by @Matlmr in #514
• ENH,EXA add function to upsample from fsaverageX to fsaverage by @mvdoc in #519
• ENH Add more options for freesurfer's automatic alignment, move code for FSL's automatic alignment by @mvdoc in #528
• FIX,DOC make sure cmap filename ends with png by @mvdoc in #529
• ENH sort subject list and improve repr of transforms by @mvdoc in #530
• DOC Update README.md by @FrancisVila in #527
• FIX,MNT import surfaces generated from volumes with any voxel size by @mvdoc in #531
• FIX allow any character in mask name by @mvdoc in #533

New Contributors

• @Matlmr made their first contribution in #512
• @FrancisVila made their first contribution in #527

Full Changelog: 1.2.7...1.2.8

1.2.7

What's Changed

• MNT use latest ubuntu and more recent actions for publishing to pypi by @mvdoc in #481
• MNT: updated get_data to get_fdata to support latest nibabel (5.0). by @marklescroart in #482
• Removed dependency on 'six' library by @marklescroart in #483
• MNT require cython<3.0 to avoid breaking install by @mvdoc in #491
• EXA make path visible in fix_geodesic_path example by @marklescroart in #487

Full Changelog: 1.2.6...1.2.7

1.2.6

What's Changed

Fixes

• FIX update nibabel deprecated methods by @TomDLT in #457
• FIX Improve robustness of attribute query for JSProxy by @mvdoc in #456
• FIX Correctly handle NaNs in VertexRGB and VolumeRGB by @mvdoc in #458
• FIX add missing params to cortex.export.init by @mvdoc in #460
• FIX force vmin/vmax to 0/1 whenever an array is passed as alpha by @mvdoc in #461
• FIX when shared_range=True, use the alpha that is passed and do not create a Volume from alpha by @ctseng12 in #462
• FIX avoid registering the same colormap twice to matplotlib by @TomDLT in #464
• FIX get_roi_surfs is now py3 compatible and accepts overlay_file by @mvdoc in #467
• FIX git URL for pip install by @kroq-gar78 in #476
• FIX cortex.export.plot_panels correctly shows inflated surfaces for subjects without a flatmap by @mvdoc in #477
• FIX stop using expired deprecation for numpy 1.24 by @TomDLT in #479

Enhancements

• ENH enable loading of pycortex datasets that have old subject names by @marklescroart in #463
• ENH warn non-perceptually-uniform 2D colormap by @TomDLT in #466

Maintenance

• MNT fix typos by @kroq-gar78 in #459
• MNT warn about alpha only if dtype is not uint8 by @mvdoc in #465
• MNT deal with some nibabel deprecation errors by @mvdoc in #471
• MNT bump version to 1.2.6 by @mvdoc in #480

Full Changelog: 1.2.5...1.2.6