Recent Releases of siibra
siibra - v1.0.1-alpha.10
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.9...v1.0.1-alpha.10
- Python
Published by AhmetNSimsek 6 months ago
siibra - v1.0.1-alpha.9
What's Changed
- fix: plotly figures not rendering on docs by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/670
- Add von Economo Koskinas atlas to examples by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/675
- fix: explorer component by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/676
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.8...v1.0.1-alpha.9
- Python
Published by AhmetNSimsek 6 months ago
siibra - v1.0.1-alpha.8
What's Changed
- fix: subfragmented ngmesh fetch by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/666
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.7...v1.0.1-alpha.8
- Python
Published by AhmetNSimsek 9 months ago
siibra - v1.0.1-alpha.7
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.4...v1.0.1-alpha.7
- Python
Published by AhmetNSimsek 9 months ago
siibra - v0.4a90
What's Changed
- fix: update spatial backend URL by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/664
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a89...v0.4a90
Includes prerelease of marmoset atlas
- Python
Published by AhmetNSimsek 9 months ago
siibra - v1.0.1-alpha.4
What's Changed
- Maint location space property by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/653
- Add support for species Common Marmoset (see #654) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/657
- Maint paper nbs by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/655
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.2...v1.0.1-alpha.4
- Python
Published by AhmetNSimsek 10 months ago
siibra - v1.0.1-alpha.5
What's Changed
- Maint location space property by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/653
- Add support for species Common Marmoset (see #654) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/657
- Maint paper nbs by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/655
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.2...v1.0.1-alpha.5
- Python
Published by AhmetNSimsek 10 months ago
siibra - v0.4a88
What's Changed
- Added support for species Common Marmoset (CALLITHRIX_JACCHUS) by @baishi in https://github.com/FZJ-INM1-BDA/siibra-python/pull/654
- updated object storage
New Contributors
- @baishi made their first contribution in https://github.com/FZJ-INM1-BDA/siibra-python/pull/654
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a87...v0.4a88
- Python
Published by AhmetNSimsek 10 months ago
siibra - v1.0.1-alpha.2
What's Changed
- Enh patch sampling by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/644
- Maint imports and packages by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/646
- Maint pep8 import order by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/647
- Doc showcase paper nbs by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/645
- check all gene exp measurements at once for intersection by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/648
- Rounding scheme for neuroglancer fetching needs revision by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/642
- Revise Figure 5 code example by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/652
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.1...v1.0.1-alpha.2
- Python
Published by AhmetNSimsek 12 months ago
siibra - v0.4a87
What's Changed
- v0.4 EOL - match region specs of features to higher level regions by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/640
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a86...v0.4a87
- Python
Published by AhmetNSimsek about 1 year ago
siibra - v1.0.1-alpha.1
What's Changed
- maint:
region.supported_spacesandregion.mapped_in_space()by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/635 - Add codespell support (config, workflow to detect/not fix) and make it fix few typos by @yarikoptic in https://github.com/FZJ-INM1-BDA/siibra-python/pull/638
- Fix: query BigBrainProfileIntensity with locations by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/637
- Allow random cmap creation for
map.get_color_mapby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/641
New Contributors
- @yarikoptic made their first contribution in https://github.com/FZJ-INM1-BDA/siibra-python/pull/638
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.1-alpha.0...v1.0.1-alpha.1
- Python
Published by AhmetNSimsek about 1 year ago
siibra - v1.0.1-alpha.0
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0.0-alpha.1...v1.0.1-alpha.0
Same changelog as https://github.com/FZJ-INM1-BDA/siibra-python/releases/tag/v1.0.0-alpha.1.
- Python
Published by AhmetNSimsek about 1 year ago
siibra - v1.0.0-alpha.1
What's Changed
- Raise if
get_mapcan't find any maps instead of logging and returning None by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/618 - Maint sparseindex by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/525
- fix: cell density profile by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/617
- Docs: do not fail doc build if allen api is not fully functional by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/626
- Deprecate restrict_space kwarg and allow features queries with space instances by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/628
- introduce
map.get_volume()which returns aFilteredVolumeby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/624 - Raise when a
PointSetis initialized empty by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/627 VolumesubclassBrainStructureby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/630- Maint: parc.findregions as module method. clarify findregions by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/517
- Test region id uniqueness by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/631
- Consider neuroglancer transform half a voxel shift when fetching the affine by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/623
- Change default of findtopmost in `parcellation.getregion` to False by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/632
- Rename pointset to pointcloud by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/633
- fix ci for pythons version <= 3.8 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/634
- Doc: use book theme for docs and general maint by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/584
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a19...v1.0.0-alpha.1
- Python
Published by AhmetNSimsek about 1 year ago
siibra - v1.0a19
What's Changed
- Fix boundingbox transformation by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/591
- Fix: get_region(spec) exact match if spec is a region key by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/598
- clip voi to template's to if voi lies partially outside of the template by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/606
- fix bbox planar intersection by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/609
- Use precalculated bounding boxes of image-features to speed up image feature query by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/583
- Fix nifti fetch voi by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/611
- Fix ng voi shape by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/615
- Use codecov-action@v4 and use codecov secret by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/616
- maint: unify centroid computation by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/610
- Prevent the intersection of volumes from different spaces by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/620
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a14...v1.0a19
- Python
Published by AhmetNSimsek over 1 year ago
siibra - v1.0a11
What's Changed
- Test: add cron job to test tutorials regularly by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/585
- Use
nilearn.resample_to_imgfor merging fragments by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/572 - fix: python closure is weird by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/587
- fix: add assertion error message by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/588
- test: fast ci if regular branch, full suite if PR to main by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/590
- fix: memory usage when warming the cache by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/589
- Introduce merging Neuroglancer fragments by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/561
- feat: update how related regions are fetched by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/582
- Read freesurfer .annot files as fsaverage mesh labels by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/575
- Reformat
feature.nameand reintorudcedataandplot()forCompoundFeatures by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/568 - Test examples as a part of e2e. Create docs on push/PR to main and on publish by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/592
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a09...v1.0a11
- Python
Published by AhmetNSimsek almost 2 years ago
siibra - v1.0a09
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a08...v1.0a09
- Fixed
commonns.connected_componentsnot masking statistical maps- Fixed assignment of volumes to sparsemaps (which was broken due to 1fccb91b9c2c113a415a961e34d81a14cb9db042)
- Added tests to prevent regression
- Fixed minor bugs and typos
- Python
Published by AhmetNSimsek almost 2 years ago
siibra - v1.0a08
What's Changed
- Exclude background from connected_components by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/567
- Use Github repo connector for configurations by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/543
- Print versions in version validation and fix bug by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/570
- urls -> doiorurl and returns a list of string by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/571
- Fix: fetch specific label from gii labels by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/574
- fix: allen gene exp query w a list of genes by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/576
- fix: pointset intersection with boundingbox fails if no points inside by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/577
- use datasets of the spaces if templates don't have any specified by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/578
- Add Volume.evaluatepoints() and fix voxel access for _pointsinside by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/566
- New: experimental module, with draft classes for cortical patch sampling by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/579
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a06...v1.0a08
- Python
Published by AhmetNSimsek almost 2 years ago
siibra - v1.0a06
What's Changed
- fix: takes long time to retrieve feature.dataset.name by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/547
- fix: cancel previous workflows by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/548
- Use codecov v3 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/550
- Neuroglancer volume fetching by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/549
- Maint:
volume.fetchby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/562 - feat: add encode URL point by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/559
- fix: write lock for warmup by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/563
- fix citation.CFF file
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a05...v1.0a06
- Python
Published by AhmetNSimsek about 2 years ago
siibra - v1.0a05
What's Changed
- Fix: from_pointset kde volume calculation by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/529
- feat: obtain colorscale of a connectivity profile by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/532
- Fix assigning uncertain points to labelled maps #526 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/531
- Hotfix allen api paging by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/536
- refactor: warm cache by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/537
- Fix image query by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/538
- fix: info uses siibra.retrieval module for local file cache by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/544
- Increase intensity profile compounding speed by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/510
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a04...v1.0a05
- Python
Published by AhmetNSimsek about 2 years ago
siibra - v1.0a03
What's Changed
- Prerelease maint by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/522
- Maint: feature module by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/521
- Add the first location example by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/523
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a02...v1.0a03
- Python
Published by AhmetNSimsek about 2 years ago
siibra - v1.0a02
What's Changed
provider.boundingbox->provider.get_boundingbox()by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/515- Doc: runstaleexamples locally by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/514
- Add support for python 3.11 and 3.12 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/519
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v1.0a01...v1.0a02
- Python
Published by AhmetNSimsek about 2 years ago
siibra - v1.0a01
What's Changed
- Introduce image volumes as an input for feature query by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/480
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.5a02...v1.0a01
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.5a02
What's Changed
- Maint: ebrains datasets, detail property should be private (#444) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/504
- feat: add siibra-explorer module by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/503
- Feature: introduce CompoundFeatures by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/479
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a77...v0.5a02
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a76
What's Changed
- Labelled maps with multiple volumes can be fetched wo args as a joint volume by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/446
- maint: add license, authors, doiorurl to concepts by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/498
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a75...v0.4a76
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a75
What's Changed
- replace
factory.BUILD_FUNCTIONSwithbuild_typedecorator by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/490 - fix: return all related regions, not just first matching by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/491
- check point assignment voxel validity (fixes #492 ) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/493
- Fix bounds check when sampling volumes with points by @ch-schiffer in https://github.com/FZJ-INM1-BDA/siibra-python/pull/495
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a74...v0.4a75
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a74
What's Changed
- add ids for openminds species by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/485
- maint: fix ebrains ref by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/487
- Fix: map.compute_centroids fail for maps with no fragments by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/486
- Fix use of local configurations on windows by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/482
- Add DTI volume of interest by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/488
- use 'channel' kwarg to get a neuroglancer color channel by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/484
- WIP: query related regions (e.g. homologies) by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/448
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a71...v0.4a74
- Python
Published by AhmetNSimsek over 2 years ago
siibra - Fix bug in from_json for polygon structures
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/0.4a68...v0.4a69
- Python
Published by dickscheid over 2 years ago
siibra - v0.4a68
What's Changed
- Display yerr label on tabular feature plots by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/478
- Introduce LSFMVolumeOfInterest modality by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/481
- Use dict.fromkeys for removing duplicates in feature query (for reproducible results order) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/483
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a66...0.4a68
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a66
What's Changed
- Update dev doc by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/439
- General maintainance of doc examples and adding a new example for BOLD signals by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/445
- Local repository by @i-Zaak in https://github.com/FZJ-INM1-BDA/siibra-python/pull/472
- Add GenericDataset for publication data of features by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/473
New Contributors
- @i-Zaak made their first contribution in https://github.com/FZJ-INM1-BDA/siibra-python/pull/472
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a64...v0.4a66
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a63
What's Changed
- Hide dataframe property from InstanceTables for classes by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/443
- Refactor bigbrain livequery to streamline results and data sources by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/456
- feat: extend base volume definition to allow ... by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/447
- feat: add export to feature by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/450
- fix: correctly use Parcellation.find_regions in anchor by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/454
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a62...v0.4a63
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a62
What's Changed
- maint: add typing to anchor by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/422
- fix: adhere to oidc spec for scope by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/424
- Speed up checking conn matrix symmetry by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/426
- Maint: RepositoryConnector.decoderesponse by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/427
- Add preloading preconfigs of modules to memory by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/425
- Sort atlas concepts by their name (within the same class) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/434
- Migrate ebrainsFeature to EbrainsDatasetVersionV3 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/416
- Preserve the style settings of matplotlib for plotly plots by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/429
- fix: parcellation.get_region exact string match by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/437
- Test configured maps to get regions from parcellations by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/373
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a61...v0.4a62
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a61
What's Changed
- HttpRequest.findsuitabledecoder returns None if no suitable decoder found by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/415
- TracerConnectivity to TracingConnectivity by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/420
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a59...v0.4a61
- Python
Published by xgui3783 over 2 years ago
siibra - v0.4a59
What's Changed
- Warn of non-symmetric connectivity matrix on creation of dataframe, and allow getting row profile aside by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/400
- Get resampled template of a map instance by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/409
- Implement plotly by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/388
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a58...v0.4a59
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a58
What's Changed
- Remove sparseinedx url connection. Simplify factory.build_map by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/398
- Allow automatically digesting .gz files of gzipped types listed in
DECODERSby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/401 - Allow digesting Ebrains Dataset V3 information by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/397
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a57...v0.4a58
- Python
Published by xgui3783 over 2 years ago
siibra - v0.4a54
What's Changed
- If no format is given, only try to fetch single format else fail by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/391
- test: add e2e test to ensure labelled/stat map is of expected size by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/367
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a51...v0.4a54
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a51
What's Changed
- Tracer connectivity matrix by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/362
- fix: do not index proxy feature to SUBCLASSES by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/366
- Improve sparse map handling by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/363
- Fix doc failure due to setuptools by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/375
- InstanceDataframe for maps (strictly additive, does not remove InstanceTable) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/364
- Point assignments also have map value by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/378
- add VolumeOfInterest search in example 03_000 by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/380
- Add an examples for fetching 1um bigbrain sections by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/383
- plot_matrix works with region selection by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/382
- example 03_007 last figure layout fix by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/384
- Detect csv delimiter with Python’s builtin sniffer tool by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/381
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a47...v0.4a51
- Python
Published by AhmetNSimsek over 2 years ago
siibra - v0.4a47
What's Changed
- Allow specifying a map candidate of the same kind by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/278
- Fix: dedup feature_id and feature instances by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/288
- fix: file lock in lazy request by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/289
- Fixes malformation of receptor density profiles due to trailing white spaces by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/287
- fix: anchor.regions.values must be anatQuant by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/296
- feat: add feature get instance by id by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/294
Map.colorizeshould take kwargs to allow fetching with further specification by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/293- Add a progressbar function with the ability to disable from logger level by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/277
- chore: fix category of ebrains datafeature (dataset -> other) by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/298
- fix: patch class in FeatureProxy by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/299
- fix: desc and publications for atlas concepts by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/300
- chore: update schema by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/303
- updated name of regional connectivity by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/304
- Implement BOLD acitivity timeseries as a new feature by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/301
- bump version by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/305
- Update the examples for changes in the preconfigurations by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/308
- feat: parse ebrains v3 query datasetversion by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/307
- Remove precision from int value in f-str by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/309
- fix: add datasets to feature.image by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/311
- Feat allow local repo snapshot by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/315
- fix: spatial props sort by volume by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/319
- Chore: Logger.warn is depreacted, use warning instead by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/324
- Allow parsing files with varied spaces by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/321
- Chore: clean up the use of region.index property remnants after the refactoring by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/323
- Clarify the uses of
findandfind_regionsby @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/320 - add non jba conn feature to e2e test by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/326
- Return copy with connectivity.getmatrix (and gettable) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/345
- Add docstring to livequery by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/337
- Do not raise a ValueError when comparing a Region to an unknown object type by @ch-schiffer in https://github.com/FZJ-INM1-BDA/siibra-python/pull/343
- Clean region.find() and parcellation.get_region() up by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/331
- test: add connectivity e2e test by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/346
- connectivity assert colnames == rownames (#162) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/347
- When map.get_region takes MapIndex as only argument, it should raise exception by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/325
- Remove overriding assigned point scores by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/351
- Preserve map shape and dtype when a map is merged by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/341
- e2e test for mergedmap shape and dtype (#302) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/353
- test: add test to sparsemapsparseindex by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/357
- Use unique name for the cache of sparseindices by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/356
- maint: change category of bold by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/358
New Contributors
- @ch-schiffer made their first contribution in https://github.com/FZJ-INM1-BDA/siibra-python/pull/343
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a35...v0.4a47
- Python
Published by xgui3783 almost 3 years ago
siibra - v0.3a28 backport KG v1 EOL
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a27...v0.3a28
- Python
Published by xgui3783 almost 3 years ago
siibra - v0.4a35
What's Changed
- Temp fix to autodoc generation timeout problem by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/265
- tests: remove xfail and added unique id test by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/270
- fix: add label to volume where they exist by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/272
- chore: minor rework on if's logic + typing by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/266
- [chore] make error in Map.get_index more specific by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/273
- Get connectivity features' resting-state paradigm from configs by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/275
- feat: add ebrains ds to volumes by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/282
- bugfix: Image should not have configuration folder + misc fixes by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/280
- chore: remove live query of kg v1 by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/281
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a33...v0.4a35
- Python
Published by xgui3783 about 3 years ago
siibra - v0.4a30-rst-fixed
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a29...v0.4a30-rst-fixed
- Python
Published by xgui3783 about 3 years ago
siibra - v0.4a30
What's Changed
- include 1 micron sections and first 1 micron VOIs for BigBrain
- enable building of maps by linear projection from a different space, approximating the nonlinear warps
- bugfix: re-add device flow by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/260
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a29...v0.4a30
- Python
Published by dickscheid about 3 years ago
siibra - Fix profile extraction from connectivity matrices
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.4a27...v0.4a28
- Python
Published by dickscheid about 3 years ago
siibra - Streamlined preconfigurations, live queries and data features
What's Changed
- chore: consolidating configurable (env var) into a single file by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/209
- use preconfigured ebrains info by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/208
- feat: allow multiple gene fetch from allen api by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/211
- misc fixes of typos, typing and type checks by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/207
- WIP migrating pydantic models by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/226
- fix use configuration by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/228
- feat: enable device flow for v0.4 by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/232
- Refactor v0.4 fix tests by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/229
- feat: add schema & verification script by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/227
- Refactor v0.4 layer thickness by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/233
- Added an optional param to get_colormap to get the colormap of a single region by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/238
- UnicodeEncodeError fix (issue for Windows) by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/236
- Simplify device flow for notebooks by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/246
- regex syntax support for region.find(), i.e., '/pattern/flags' by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/251
- Bug fix to keyboard interruption during caching by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/253
- feat: cached ebrains queries by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/254
- chore: unify parcellationmap.fetch and sparsemap.fetch by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/255
- Refactor v0.4 suggestions for feature examples by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/252
- Use
features.ALLfor a dict of all features by @AhmetNSimsek in https://github.com/FZJ-INM1-BDA/siibra-python/pull/258
New Contributors
- @AhmetNSimsek made their first contribution in https://github.com/FZJ-INM1-BDA/siibra-python/pull/233
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a27...v0.4a27
- Python
Published by dickscheid about 3 years ago
siibra - "CM Amygdala" removed from the superficial group
Uses a new tag of siibra-configurations, where "CM (Amygdala)" is removed from the superficial group.
- Python
Published by dickscheid over 3 years ago
siibra - v0.3a24
What's Changed
- Fix groupregion decoding & centroid computation by @dickscheid in https://github.com/FZJ-INM1-BDA/siibra-python/pull/202
- bugfix: add desc to waxholm & allen by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/205
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a23...v0.3a24
- Python
Published by xgui3783 over 3 years ago
siibra - v0.3a23
What's Changed
- bugfix: parcellation ebrains doi by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/198
- WIP fix when multiple centroids are available by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/200
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a22...v0.3a23
- Python
Published by xgui3783 over 3 years ago
siibra - v0.3a18
What's Changed
- Fix connectivity model by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/191
- bugfix: cortical cell distribution name/feat: add structure attr to gene exp by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/192
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a17...v0.3a18
- Python
Published by xgui3783 almost 4 years ago
siibra - v0.3a17
What's Changed
- refactor: pydantic lite rewrite by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/154
- feature: addition to pydantic models by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/158
- bugfix: fetch map results in error by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/159
- feat: extend models by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/160
- add tests to all connectivity features (many are buggy) by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/161
- extend pydantic model by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/163
- new function to find a feature by id without the need to provide an a… by @marcenko in https://github.com/FZJ-INM1-BDA/siibra-python/pull/165
- feat: extend models by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/164
- extend region model, catch cases where mapIndex is None by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/167
- feat: auto set ng volume map type by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/172
- fix internal identifier to make it relevant by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/171
- reduce number of features for connectivity test by @marcenko in https://github.com/FZJ-INM1-BDA/siibra-python/pull/166
- feat: unify at_type for pydantic models by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/170
- model fix: refining region internal identifier by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/174
- bugfix: to_model of regions in surface based space by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/175
- chore: unify at_type field name by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/177
- Feat cell density to model by @marcenko in https://github.com/FZJ-INM1-BDA/siibra-python/pull/176
- feat: extend ieeg models to be in_roi, if provided by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/178
- bugfix: use xform in json as defacto xform by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/179
- feat: enforce feature type in feature id by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/180
- fix conn feat instance types by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/181
- tmp fix: jba29 in big brain by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/186
- feat: allow thresholding cont maps for spatialfeat by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/184
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a16...v0.3a17
- Python
Published by xgui3783 almost 4 years ago
siibra - Connectivity code example
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a14...v0.3a15
- Python
Published by dickscheid about 4 years ago
siibra - v0.3a13
What's Changed
- bugfix: checks configuration mirror (fixes #152) by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/153
- feat: add docker image build in CI by @xgui3783 in https://github.com/FZJ-INM1-BDA/siibra-python/pull/145
Full Changelog: https://github.com/FZJ-INM1-BDA/siibra-python/compare/v0.3a11...v0.3a13
- Python
Published by dickscheid about 4 years ago
siibra - v0.3a8
- Qualifications and descriptions of feature links to brain regions, see examples/03datafeatures/000_matchings.py
- Basic support for surface meshes
- remove dependency to cloud-volume in favor of the much more lightweight neuroglancer-scripts
- first implementation of EbrainsPublicDatasetConnector for querying versioned files from datasets in the new EBRAINS Knowledge Graph V3, used for new connectivity datasets (https://github.com/FZJ-INM1-BDA/siibra-python/blob/ff2048d952299b2a8594108c2318d92c0c22f6be/siibra/retrieval/repositories.py#L264)
- first implementation of EbrainsHdgConnector for getting data from the EBRAINS Human Data Gateway (https://github.com/FZJ-INM1-BDA/siibra-python/blob/ff2048d952299b2a8594108c2318d92c0c22f6be/siibra/retrieval/repositories.py#L174)
- many smaller fixes and updates
- Python
Published by dickscheid about 4 years ago
siibra -
- almost full rewrite of documentation with real code snippets from examples/ using sphinx-gallery
- Refactor of
ContinuousParcellationMap.assign()and unify withassign_coordinates(); now returns a pandas dataframe - bring back cell distribution features (fix species spec)
- several bug fixes
- first implementation of a bigbrain sampler
- Python
Published by dickscheid about 4 years ago