Pycortex Versions Save

What's Changed

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

New Contributors

• @Matlmr made their first contribution in https://github.com/gallantlab/pycortex/pull/512
• @FrancisVila made their first contribution in https://github.com/gallantlab/pycortex/pull/527

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.7...1.2.8

What's Changed

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

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.6...1.2.7

What's Changed

Fixes

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

Enhancements

• ENH enable loading of pycortex datasets that have old subject names by @marklescroart in https://github.com/gallantlab/pycortex/pull/463
• ENH warn non-perceptually-uniform 2D colormap by @TomDLT in https://github.com/gallantlab/pycortex/pull/466

Maintenance

• MNT fix typos by @kroq-gar78 in https://github.com/gallantlab/pycortex/pull/459
• MNT warn about alpha only if dtype is not uint8 by @mvdoc in https://github.com/gallantlab/pycortex/pull/465
• MNT deal with some nibabel deprecation errors by @mvdoc in https://github.com/gallantlab/pycortex/pull/471
• MNT bump version to 1.2.6 by @mvdoc in https://github.com/gallantlab/pycortex/pull/480

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.5...1.2.6

What's Changed

Fixes

• FIX: fixed bug in save_3d_views handling custom parameter dicts by @alexhuth in https://github.com/gallantlab/pycortex/pull/439
• FIX Webgl racecondition by @alexhuth in https://github.com/gallantlab/pycortex/pull/440
• FIX,REF Handle different header length for vox2ras tk by @mvdoc in https://github.com/gallantlab/pycortex/pull/442
• FIX attempt to fix random crashes in save_3d_views by @mvdoc in https://github.com/gallantlab/pycortex/pull/445
• FIX copy filestore in wheel by @TomDLT in https://github.com/gallantlab/pycortex/pull/451
• FIX,DOC exception in get_roi_masks by @mvdoc in https://github.com/gallantlab/pycortex/pull/452

New features

• NF new params for a multipanel figure with all views by @mvdoc in https://github.com/gallantlab/pycortex/pull/446

Maintenance

• MNT change default fsl-prefix and 2D colormap by @mvdoc in https://github.com/gallantlab/pycortex/pull/444
• MNT provide a more informative error if attribute not found in JSProxy by @mvdoc in https://github.com/gallantlab/pycortex/pull/450
• MNT update CI badge to github actions by @TomDLT in https://github.com/gallantlab/pycortex/pull/453
• MNT version 1.2.5 by @mvdoc in https://github.com/gallantlab/pycortex/pull/454

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.4...1.2.5

What's Changed

• FIX do not show labels for invisible shapes by @mvdoc in https://github.com/gallantlab/pycortex/pull/429
• MNT Deal with rgb vs rgba for different blender versions. by @cchen23 in https://github.com/gallantlab/pycortex/pull/430
• FIX Check if overlays file exists before unlinking. by @cchen23 in https://github.com/gallantlab/pycortex/pull/431
• FIX change location of filestore during the install by @TomDLT in https://github.com/gallantlab/pycortex/pull/433
• REF Changed name of cortex.align.fs_manual to cortex.align.manual by @marklescroart in https://github.com/gallantlab/pycortex/pull/434
• FIX ignore masked voxels when averaging with nanmean=True by @TomDLT in https://github.com/gallantlab/pycortex/pull/436

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.3...1.2.4

FIX: GitHub actions pushing to pypi

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.3...1.2.3a

What's Changed

• FIX BrainData division overrides for Python 3 by @kroq-gar78 in https://github.com/gallantlab/pycortex/pull/405
• FIX division by 0 in quickflat.utils.make_flatmap_image when nanmean=True by @mvdoc in https://github.com/gallantlab/pycortex/pull/404
• ENH Long-overdue update to Blender 2.8+ by @marklescroart in https://github.com/gallantlab/pycortex/pull/406
• ENH added config file specfication of domain name; blank by default by @marklescroart in https://github.com/gallantlab/pycortex/pull/407
• FIX Tiny blender bug fix by @marklescroart in https://github.com/gallantlab/pycortex/pull/410
• MNT Setup github actions by @mvdoc in https://github.com/gallantlab/pycortex/pull/411
• MNT enable actions on PRs by @mvdoc in https://github.com/gallantlab/pycortex/pull/412
• FIX add downloaded subjects to the cortex database by @TomDLT in https://github.com/gallantlab/pycortex/pull/413
• FIX create intermediate dirs for config file by @mvdoc in https://github.com/gallantlab/pycortex/pull/415
• FIX update sources before apt-get installing by @mvdoc in https://github.com/gallantlab/pycortex/pull/418
• ENH add option for intermediate image in bbregister by @TomDLT in https://github.com/gallantlab/pycortex/pull/417
• FIX keep current sampler when dataview changes by @TomDLT in https://github.com/gallantlab/pycortex/pull/420
• Revert "FIX keep current sampler when dataview changes (#420)" by @mvdoc in https://github.com/gallantlab/pycortex/pull/421
• FIX keep current sampler when dataview changes - v2 by @TomDLT in https://github.com/gallantlab/pycortex/pull/422
• FIX set interpolation and layers only for volumes by @mvdoc in https://github.com/gallantlab/pycortex/pull/423
• FIX ensure c-ordering for flatmap image by @mvdoc in https://github.com/gallantlab/pycortex/pull/424
• ENH add blend_curvature method to Vertex, Vertex2D, and VertexRGB by @TomDLT in https://github.com/gallantlab/pycortex/pull/425
• ENH,FIX add dropout option to make_svg, fix transparency by @mvdoc in https://github.com/gallantlab/pycortex/pull/426

New Contributors

• @kroq-gar78 made their first contribution in https://github.com/gallantlab/pycortex/pull/405

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.2...1.2.3

What's Changed

• FIX add more informative error in get_texture if inkscape is not installed by @mvdoc in https://github.com/gallantlab/pycortex/pull/391
• NF Add Blue/Purple/Red/Orange/Green colormap by @mvdoc in https://github.com/gallantlab/pycortex/pull/395
• ENH Enhancements to cortex.export by @mvdoc in https://github.com/gallantlab/pycortex/pull/394
• DEP Use encodebytes instead of encodestring. by @cchen23 in https://github.com/gallantlab/pycortex/pull/397
• FIX set default imshow interpolation to nearest for composite.add_data by @mvdoc in https://github.com/gallantlab/pycortex/pull/402
• FIX: allow vertex data to be passed to cortex.segment.cut_surface(). … by @marklescroart in https://github.com/gallantlab/pycortex/pull/399
• MNT Release version 1.2.2 by @mvdoc in https://github.com/gallantlab/pycortex/pull/403

New Contributors

• @cchen23 made their first contribution in https://github.com/gallantlab/pycortex/pull/397

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.1...1.2.2

Added

• Allow option to perform automatic alignment with Freesurfer's BBR for volumes without distortion correction (https://github.com/gallantlab/pycortex/commit/5d7d6ca73845986fcc182899289218132be99604)
• Add line_lanczos to available mappers (https://github.com/gallantlab/pycortex/commit/77212535da1ad17930697b8cf2f497ae09d2898b)
• Use Freesurfer's BBR by default for automatic alignment (https://github.com/gallantlab/pycortex/pull/384)

Fixed

• Parameter names for freesurfer.import_flat (https://github.com/gallantlab/pycortex/commit/4371b2633a0b7180e3893484af61a941ba5029b9))
• Fix left/right location of hemispheres for medial-pivot view (https://github.com/gallantlab/pycortex/commit/c3b029e96c7ffa67c8c35c7af47c045e0161abc3)
• Animation functions in webgl.view (https://github.com/gallantlab/pycortex/pull/372)
• Various fixes to 2D volumes
• Installation with numpy < 1.2 (https://github.com/gallantlab/pycortex/pull/385)
• String encoding in openctm.pyx (https://github.com/gallantlab/pycortex/commit/6dc80db6305f0ad97e7b857e083958636fab2233)

Added

• More functionality to import fMRIprep-processed data (#315)
• Function to rotate flatmaps (f88a)
• Option to ignore NaNs when averaging across the thickness of cortex (#355)
• New views for cortex.export.plot_panels and passing of additional kwargs (#361, #362)
• Specify colorbar location with default positionings for quickflat (#364)
• Pass custom colors for VolumeRGB (#366)

Fixed

• Bug with automatic creation of SVGs with ROIs (#340)
• Python 2/3 compatibilities for svgoverlay (#352)
• from_freesurfer/to_freesurfer handling of NIFTI images (#354)
• ROI label display parameters (#356)
• Improve documentation for install and demo (#359)
• Inkscape compatibility with newer versions (#365)
• Use correct contrast for automatic alignment with FreeSurfer's bbregister (39d8)