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Recent Releases of pycortex

pycortex - 1.2.11

What's Changed

  • NF: add config option for uniform lighting by @MShinkle in https://github.com/gallantlab/pycortex/pull/561
  • FIX: Python 3.13 compatibility, and upgrade to Cython 3 by @kroq-gar78 in https://github.com/gallantlab/pycortex/pull/564

Dependabot

  • Bump JamesIves/github-pages-deploy-action from 4.6.3 to 4.6.4 by @dependabot in https://github.com/gallantlab/pycortex/pull/554
  • Bump JamesIves/github-pages-deploy-action from 4.6.4 to 4.6.8 by @dependabot in https://github.com/gallantlab/pycortex/pull/555
  • Bump JamesIves/github-pages-deploy-action from 4.6.8 to 4.6.9 by @dependabot in https://github.com/gallantlab/pycortex/pull/558
  • Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/gallantlab/pycortex/pull/559
  • Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.2 by @dependabot in https://github.com/gallantlab/pycortex/pull/562

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.10...1.2.11

- JavaScript
Published by mvdoc over 1 year ago

pycortex - 1.2.10

What's Changed

  • MNT Remove dependency on distutils by @kroq-gar78 in https://github.com/gallantlab/pycortex/pull/553

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.9...1.2.10

- JavaScript
Published by mvdoc over 1 year ago

pycortex - 1.2.9

What's Changed

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

Full Changelog: https://github.com/gallantlab/pycortex/compare/1.2.8...1.2.9

- JavaScript
Published by mvdoc almost 2 years ago

pycortex - 1.2.8

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

- JavaScript
Published by mvdoc about 2 years ago

pycortex - 1.2.7

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 getdata to getfdata 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 fixgeodesicpath 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

- JavaScript
Published by mvdoc almost 3 years ago

pycortex - 1.2.6

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 getroisurfs 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

- JavaScript
Published by mvdoc over 3 years ago

pycortex - 1.2.5

What's Changed

Fixes * FIX: fixed bug in save3dviews 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 getroimasks 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

- JavaScript
Published by mvdoc almost 4 years ago

pycortex - 1.2.4

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

- JavaScript
Published by mvdoc about 4 years ago

pycortex - 1.2.3a

FIX: GitHub actions pushing to pypi

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

- JavaScript
Published by mvdoc over 4 years ago

pycortex - 1.2.3

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

- JavaScript
Published by mvdoc over 4 years ago

pycortex - 1.2.2

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

- JavaScript
Published by mvdoc over 4 years ago

pycortex - 1.2.1

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)

- JavaScript
Published by mvdoc about 5 years ago

pycortex - 1.2.0

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)

- JavaScript
Published by mvdoc almost 6 years ago

pycortex - 1.1.1

Fixed

  • Installation fix for PyPi

- JavaScript
Published by mvdoc over 6 years ago

pycortex - 1.1.0

Added

  • Added function cortex.utils.download_subject to download new subjects for pycortex from web URLs. This function allows users to download FreeSurfer's fsaverage surface, with a flatmap and ROI labels made by Mark Lescroart (#344)
  • Vertex objects have a new method .map() that allows mapping from one surface to another (#334)
  • Add cortex.freesurfer.get_mri_surf2surf_matrix to create a sparse matrix implementing the mri_surf2surf command (#334 )
  • Add function to plot and save 3D views and plot panels (#337 )
  • Axis object can be passed to quickshow (#325)
  • Help menu for the 3D WebGL viewer can be accessed with a shortcut (#319, #321)
  • New keyboard shortcuts (list)
  • Convenience function to import data preprocessed with fmriprep (#301 )
  • Added option to use FreeSurfer's BBR for automatic alignment and function to use Freeview for manual alignment

Fixed

  • Fix DataView2D to allow plotting of 2D datasets with quickflat
  • Fix VertexRGB and VolumeRGB when alpha is not set
  • Allow arbitrary positioning of the colorbar with quickflat
  • Make quickflat more robust to extraneous polygons (#333)
  • Fix mouse behavior when unfold > 0.5 in WebGL viewer (#330 )
  • Sub surfaces fixes (#307)
  • Firefox compatibility fixes (#306 )
  • Miscellaneous python 3 fixes

- JavaScript
Published by mvdoc over 6 years ago

pycortex - 1.0

- JavaScript
Published by sslivkoff almost 8 years ago