2.2.1

Welcome to our new scilpy release 2.2.1 🥳

Most of the work completed for this release was carried out in preparation for the publication of the SCILPY paper.
It's minor revision that includes a lot of fixes and a major upgrade of our documentation.

You should definitively visit our brand new documentation: https://scilpy.readthedocs.io/en/latest/

Enjoy and see you soon 😉

What's Changed

• Fix inversed tests files by @EmmaRenauld in #1240
• Update documentation by @arnaudbore in #1243
• [ENH][DOC] new organization documentation by @arnaudbore in #1246
• Vocab and screenshot fixes for tutorial (paper) by @frheault in #1244
• Copy-paste text associated with figures 2 - 5 from scilpy paper by @EmmaRenauld in #1247
• ENH: reconst tutorial by @AntoineTheb in #1248
• Add instructions for ssst and msmt fODFs by @karanphil in #1249
• Docs for Q-ball and asymmetric ODF by @CHrlS98 in #1251
• Add MTI documentation to scilpy by @Manonedde in #1252
• Doc add section and fix documentation compile errors by @EmmaRenauld in #1255
• [FIX] Removing some warnings in the doc by @EmmaRenauld in #1256
• Doc: prevent changes on disk by @EmmaRenauld in #1259
• Fix of codecov components paths by @AlexVCaron in #1245
• Doc reorganize by @EmmaRenauld in #1261
• DOC: Working with Arnaud by @EmmaRenauld in #1263
• Doc add bash equivalents by @EmmaRenauld in #1257
• scil_search_keywords .hidden missing file verification by @guichoquette in #1253
• Doc add tutorial figure3 by @EmmaRenauld in #1260
• Doc add tutorial figure2 by @EmmaRenauld in #1262
• ENH: tractometer-style volume compare by @AntoineTheb in #1242
• First unit tests in tractoanalysis module by @EmmaRenauld in #1235
• Fix links by @EmmaRenauld in #1268
• Prevent input=output in tractogram compress by @EmmaRenauld in #1269
• Adding script to restride data and bvecs by @karanphil in #1254
• Adding option in custom-color for coverage by @EmmaRenauld in #1271
• Nicer print_info. Now ~ the same for all data types! by @EmmaRenauld in #1272

New Contributors

• @guichoquette made their first contribution in #1253

Full Changelog: 2.2.0...2.2.1

2.2.0

Release 2.2.0

Here it is — the brand new shiny Scilpy 2.2.0! 🎉🥳
This release is a big step forward: we’re saying goodbye to the old script names and the outdated code organization.
We’re also closer than ever to reaching our 75% code coverage goal, and of course, we squashed a few bugs 🐛 🐛 along the way.

Thank you everybody !
Let's go !

What's Changed

• [HOTFIX] Install vtk-osmesa in workflow, not provided by runner anymore by @AlexVCaron in #1202
• Feature/python 3.12 by @frheault in #1196
• Handle empty labels by @frheault in #1200
• Ignore some cov viz by @EmmaRenauld in #1137
• harmonzie labels for longitudinal lesions by @frheault in #1039
• [BG] tractogram_filter_by _roi - fix filtering_list by @arnaudbore in #1205
• Unit tests connectivity + FIX MAP_COORDINATES USAGE by @EmmaRenauld in #1102
• [ENH] Change repo organization by @arnaudbore in #1201
• Update test-ml by @arnaudbore in #1215
• [FIX] Still save empty file for scil_tractogram_math.py by @levje in #1212
• Add final viz tests (after PR1137) by @EmmaRenauld in #1213
• [FIX] Erroneous normalization of bvecs on rows by @AlexVCaron in #1211
• Bundles: part 1 by @EmmaRenauld in #1214
• [ENH] Road to scilpy 2.2.0 by @arnaudbore in #1210
• [BF] Fix check when resampling with a ref by @arnaudbore in #1219
• Fixing doc string of scil_tractogram_dps_math by @karanphil in #1224
• Update to most recent Pop Average atlas by @EmmaRenauld in #1225
• [FIX] Fix issue when testing search keywords by @arnaudbore in #1228
• Adding mask and median options to fodf max in ventricles script by @karanphil in #1221
• Bump deepdiff from 6.3.0 to 8.6.1 by @dependabot[bot] in #1223
• Update runners by @AlexVCaron in #1232
• [ENH] Remove old mention of .py scripts by @arnaudbore in #1234
• Bundles: part 2 by @EmmaRenauld in #1216
• Clarified bundle scoring scripts. Added options by @EmmaRenauld in #1231
• Avoid numerical shenanigans by @frheault in #1237
• volume_math Add warning and always convert to fload IF slope/intercept by @frheault in #1226
• Saving DPS and DPP in BundleSeg by @frheault in #1233
• ENH: BundleParc - continuous and distance-based parcellation by @AntoineTheb in #1194

Full Changelog: 2.1.2...2.2.0

2.1.2

Release 2.1.2

🔥 HOT FIX for tractometry_flow

What's Changed

• Avoid numerical shenanigans by @frheault in #1236

Full Changelog: 2.1.1...2.1.2

2.2.0rc1

pre-release 2.2.0rc1

First try at our new Scilpy release. RC1

What's Changed

• [HOTFIX] Install vtk-osmesa in workflow, not provided by runner anymore by @AlexVCaron in #1202
• Feature/python 3.12 by @frheault in #1196
• Handle empty labels by @frheault in #1200
• Ignore some cov viz by @EmmaRenauld in #1137
• harmonzie labels for longitudinal lesions by @frheault in #1039
• [BG] tractogram_filter_by _roi - fix filtering_list by @arnaudbore in #1205
• Unit tests connectivity + FIX MAP_COORDINATES USAGE by @EmmaRenauld in #1102
• [ENH] Change repo organization by @arnaudbore in #1201
• Update test-ml by @arnaudbore in #1215
• [FIX] Still save empty file for scil_tractogram_math.py by @levje in #1212
• Add final viz tests (after PR1137) by @EmmaRenauld in #1213
• [FIX] Erroneous normalization of bvecs on rows by @AlexVCaron in #1211
• Bundles: part 1 by @EmmaRenauld in #1214
• [ENH] Road to scilpy 2.2.0 by @arnaudbore in #1210
• [BF] Fix check when resampling with a ref by @arnaudbore in #1219

Full Changelog: 2.1.1...2.2.0rc1

2.1.1

Minor modification for a new release 🎉

• Fix scil_bundle_label_map.py
• New BundleParc v2

What's Changed

• ENH: BundleParc v2 by @AntoineTheb in #1179
• ENH: shorten scil_fodf_bundleparc.py --help by @AntoineTheb in #1189
• ENH: Add miscellaneous tractogram extensions to header check by @jhlegarreta in #1191
• Test energy_comparison by @karanphil in #1190
• NF - Region-Adaptive Propagation (RAP) tractography by @gabknight in #1192
• [BF] Improve scil_bundle_label_map add filtering by @arnaudbore in #1197
• Update version + typo by @arnaudbore in #1198

Full Changelog: 2.1.0...2.1.1

2.1.0

Release 2.1.0

It's here, it's shiny and it comes with a ton of new features 🎉 and less bugs 🐛 .
Don't hesitate to take a look at the API.

Thank you everybody !

What's Changed

• Tractogram scripts parts4 by @EmmaRenauld in #961
• Tractogram scripts part 5 by @EmmaRenauld in #983
• Tractogram scripts part6 by @EmmaRenauld in #991
• Tractogram scripts part7: segmentation scripts by @EmmaRenauld in #993
• [FIX] 10 colors in BASE10 colors for visualization by @AlexVCaron in #999
• [FIX] Empty remaining indices when filtering for a bundle by @levje in #1002
• Removing xform from convert script by @frheault in #1001
• Generate HDF5 from TRKs by @frheault in #985
• [FIX] Typo in scil_dti_metrics script by @AlexVCaron in #1000
• Update COMMIT AMICO - use args.processes by @arnaudbore in #998
• ENH: tractogram add dps by @AntoineTheb in #1006
• Update to work with Trimeshpy 0.0.4 by @frheault in #1003
• ENH: rework scil_tractogram_cut_streamlines + scil_labels_from_mask by @AntoineTheb in #1009
• Add create surface by @arnaudbore in #1005
• [FIX] Missing parameter for background viz by @levje in #1012
• [ENH] Add script normalize bvec by @arnaudbore in #1011
• [BF] Fix surfaces lib by @arnaudbore in #1014
• [ENH] Bundle fixel analysis script by @karanphil in #1004
• Removing unused argument in scil_bundle_fixel_analysis.py by @karanphil in #1018
• Alter tractogram (trim, cut, replace, subsample, transform) by @frheault in #992
• Modify lesions_info to support labels instead of mask by @frheault in #1020
• New script to compute similarity between mask and atlas (nii) by @frheault in #994
• [ENH] Uniformize surface apply transformation by @arnaudbore in #1015
• Distance map by @frheault in #1023
• Fix tests by @arnaudbore in #1028
• Tractograms: more unit tests by @EmmaRenauld in #1027
• ENH: Pad or crop volume using scil_volume_reshape.py by @AntoineTheb in #1019
• WIP "Fake" ambiant occlusion for MI-Brain by @frheault in #1030
• Nawm generation based on distance map by @frheault in #1026
• return option min_vol_lesion by @ThoumyreStanislas in #1036
• [BF] Fix save FODF add header info from i_dwi by @arnaudbore in #1037
• ENH: cut streamlines min length by @AntoineTheb in #1040
• [ENH][BF] Update json conversion to excel used in tractometry_flow by @arnaudbore in #1041
• [FIX] pyproject.toml and right build dependencies. by @levje in #1048
• Denoise nl_means script by @EmmaRenauld in #972
• Scilpy bot v2 by @frheault in #1033
• ENH: better bundle endpoints maps by @AntoineTheb in #1047
• Add no norm option to scil_bundle_fixel_analysis by @karanphil in #1032
• [ENH] Add mrds scripts part 3 by @arnaudbore in #1046
• Keep old space by @frheault in #1050
• [ENH] Add mrds scripts part 1 by @arnaudbore in #1021
• [ENH] Add mrds scripts part 2 by @arnaudbore in #1022
• FIX: ratio arg in volume pairwise comparison by @AntoineTheb in #1051
• Fibertube Tracking by @VincentBeaud in #971
• Connectivity: compute_matrices script by @EmmaRenauld in #1031
• Improve coverage in multiprocessing cases by @EmmaRenauld in #1053
• Fix doc by @EmmaRenauld in #1056
• [ENH] Fix resample local_tracking_dev accepts close iso voxels by @arnaudbore in #1055
• [ENH] Add precision to FRF scripts by @AlexVCaron in #1057
• Create new script compute_simple_matrix by @EmmaRenauld in #1045
• ENH: add interpolation to scil_volume_apply_transform by @AntoineTheb in #1065
• [BF] Tractogram filter by multiples ROIs - Crash by @arnaudbore in #1052
• Add Fibertube_tracking.rst to the read-the-docs by @CHrlS98 in #1070
• Fibertube tracking - New endpoint scoring by @VincentBeaud in #1064
• New Endpoint Scoring - Charles' suggestions by @VincentBeaud in #1075
• Script dps math by @VincentBeaud in #1066
• Add test single shell NODDI by @karanphil in #1080
• Adding ref to scil_freewater_maps by @karanphil in #1083
• Clarify doc to differentiate dpp_math with dps mode and dps_math by @VincentBeaud in #1081
• Avoid scalar with dim > 0 by squeezing. Passes test and pep8 no warning. by @VincentBeaud in #1078
• Fix merge queue by @AlexVCaron in #1109
• Tracking local custom seeds by @VincentBeaud in #1069
• [FIX]: Return rejected streamlines with empty sft by @levje in #1076
• [DOC] Add documentation for grid_intersections by @CHrlS98 in #1079
• Switch to loops simple connectivity by @frheault in #1082
• FIX: Filter streamlines by length, use the "save rejection" argument. by @levje in #1090
• Fix the hdf5 error when dpp are present by @gagnonanthony in #1092
• Fix Fury upcoming deprecation call by @AlexVCaron in #1085
• BF for asymmetric peaks by @CHrlS98 in #1077
• Move plot residuals into viz - plot by @zinelya in #1088
• Fixing bug in gradients_generate_sampling by @karanphil in #1094
• DOC - fixed updated script name by @gabknight in #1107
• Next connectivity scripts by @EmmaRenauld in #1063
• FIX: Division by 0 in scil_dti_metrics by @AntoineTheb in #1089
• Update script scil_viz_gradients_screenshot by @karanphil in #1097
• Condense distance matrix that was not. Pep8 + test pass by @VincentBeaud in #1084
• Cleaning the connectivity pairwise agreement script by @EmmaRenauld in #1087
• update to dipy 1.10 by @arnaudbore in #1114
• Fixing the skip_b0_check function by @karanphil in #1113
• Cythonization warnings by @CHrlS98 in #1101
• [BF] NODDI map catch error by @arnaudbore in #1115
• [ENH] Allow extra option for topup and eddy by @arnaudbore in #1117
• Adding support for list of lists of paths in assert_inputs_exist by @karanphil in #1086
• Final connectivity scripts PR by @EmmaRenauld in #1099
• Small fix (issue 1123) by @EmmaRenauld in #1126
• Support .tck for commit by @EmmaRenauld in #1125
• RF - Input to volume stats scripts by @gabknight in #1068
• Add script to validate gradient tables by @karanphil in #1110
• Fibertube Density by @VincentBeaud in #1112
• Add Scilpy version - part 1 by @zinelya in #1100
• Add Scilpy version - part 2 by @zinelya in #1106
• BF - fixed voxel bundary conditions in uncompress streamlines by @gabknight in #1098
• Delete script fix_trk by @EmmaRenauld in #984
• [ENH] Add positionnal arguments by @arnaudbore in #1118
• DOC - renamed the uncompress fct to streamlines_to_voxel_coordinates by @gabknight in #1103
• bids_validate func get_data -> changed clean: Boolean definition from… by @Desk3505 in https://gi...

2.1.0rc1

New scilpy release coming up

First release candidate - published on pypi

2.0.2

SCILPY release 2.0.2 🎉

I didn't think I'd be back here so quickly.
Again a couple of issues have been fixed .

See you soon—I hope it's not too soon, though.

What's Changed

• [FIX] fixed typo in surface convert script by @grahamlittlephd in #989
• [BF] Fix mask type - dwi apply bias field by @arnaudbore in #990

Full Changelog: 2.0.1...2.0.2

2.0.1

SCILPY release 2.0.1 🎉

I told you 😂
A couple of issues have been fixed and it makes scilpy even better than before. 💯
See you soon 😉

What's Changed

• Easy tests reconst by @EmmaRenauld in #982
• Fix verifications in volume_resample by @EmmaRenauld in #986
• Add param sub_sphere to tracking_local_dev by @arnaudbore in #987
• Volumes test by @EmmaRenauld in #942
• Fix wrong import in legacy file by @EmmaRenauld in #988

Full Changelog: 2.0.0...2.0.1

2.0.0

⚠️ New SCILPY release 2.0.0 ⚠️

This is huge step for scilpy and our community !

This is a major refactoring of the code.
All our scripts are now organized into categories, I encourage you to check the new documentation https://scilpy.readthedocs.io/en/latest/
As always a lot of new features, unit tests and bug fixes.

Thank you to our new contributors ! 🎉
BIG thank you to all contributors especially @EmmaRenauld , @karanphil , @CHrlS98 , @AlexVCaron 🥳

See you soon 😉

What's Changed

• Volumes modules by @EmmaRenauld in #747
• Streamline operations tests by @EmmaRenauld in #762
• Create a assert_roi_radii_format function for FRF scripts by @karanphil in #771
• Connectomics module by @EmmaRenauld in #764
• Removing frf_table option by @karanphil in #772
• Move load img by @karanphil in #775
• Noddi clean up by @mdesco in #770
• Dti clean up by @mdesco in #773
• Module Gradient by @EmmaRenauld in #779
• add mti.py in reconst by @Manonedde in #768
• Asym clean up by @mdesco in #776
• fodf cleanup, deleted obselete and more by @mdesco in #788
• DWI module by @mdesco in #781
• Modify mti by @Manonedde in #786
• Support multiple input to merge (for PR in connectoflow) by @frheault in #761
• RF - changed tracking default sphere from symmetric724 to repulsion724 by @gabknight in #769
• Adding volume operations tests by @gagnonanthony in #783
• [BF] fix trk space when filter by length by @arnaudbore in #796
• Gradient sampling refactor, part2 by @EmmaRenauld in #790
• FIX: bug in scil_score_bundles.py by @AntoineTheb in #798
• [ENH] Add fix trk startrack by @arnaudbore in #797
• Fix flip startrack by @arnaudbore in #800
• Move bvec_bval_tool from utils to gradients module by @EmmaRenauld in #799
• Add test volume_math by @frheault in #778
• scil_convert_fdf.py by @arnaudbore in #801
• ENH: Adding option to skip randomization of seed. + other fixes by @EmmaRenauld in #757
• Simple framework to port scripts into legacy by @AlexVCaron in #807
• scil_merge_json move function into module by @arnaudbore in #803
• adding vtk legacy options to scil_convert_surface script by @ThoumyreStanislas in #795
• FIX/ENH: Streamline (and mask) operations refactor by @AntoineTheb in #774
• Final check main of script 1) dwi 2) gradient by @EmmaRenauld in #802
• ENH: Add Parallel Transport Tractography to scil_compute_local_tracking by @AntoineTheb in #750
• Cleaning reconst module by @karanphil in #806
• Fix round_bvals_to_shell by @karanphil in #811
• Move valid inputs from reorder_philips into module gradients by @arnaudbore in #787
• BF - metadata version when using editable install by @gabknight in #812
• Fixing scil_visualize_bundles_mosaic.py with Pillow 10.0.* by @karanphil in #814
• RF - Tracking/Tractogram Scripts by @gabknight in #815
• Legacy installation by @arnaudbore in #824
• Rename labels scripts and deprecate old by @EmmaRenauld in #819
• Rename dwi scripts by @karanphil in #823
• [Fix] Change wrong help description by @EmmaRenauld in #825
• ENH: refactor scil_compute_local_tracking by @AntoineTheb in #813
• FIX: scil_cut_streamlines now properly handles loops by @AntoineTheb in #817
• Rename connectomics and deprecate old by @EmmaRenauld in #820
• FIX import new main by @EmmaRenauld in #832
• Rename volume scripts by @arnaudbore in #829
• Rename surface scripts by @arnaudbore in #827
• Rename reconst scripts by @karanphil in #822
• Add legacy test (help) by @EmmaRenauld in #833
• Rename convert scripts by @arnaudbore in #828
• Rename reorder_dwi by @arnaudbore in #835
• Rename gradients scripts by @karanphil in #834
• [FIX] Use numbers rather than letters in scil_gradients_modify_axes by @EmmaRenauld in #821
• RF - Tractogram Scripts Renaming by @gabknight in #837
• Moving OP out of the default output files from scil_btensor_metrics.py. by @karanphil in #836
• General testing for all legacy scripts by @gabknight in #838
• Rename tractometry by @EmmaRenauld in #842
• Rename denoising by @EmmaRenauld in #847
• fix_surface_renaming by @frheault in #849
• Add throttling to jenkins pipeline by @AlexVCaron in #851
• TST - remove legacy warnings by @gabknight in #848
• RF - Scripts Renaming by @gabknight in #856
• Adding tolerance argument to fodf msmt by @karanphil in #839
• Rename some tractogram scripts by @EmmaRenauld in #846
• Rename scripts by @arnaudbore in #845
• DOC - tracking by @gabknight in #861
• [WIP] Add_verbose_arg by @ThoumyreStanislas in #850
• [WIP] Add_version_scilpy by @ThoumyreStanislas in #868
• [ENH] Add coverage by @arnaudbore in #869
• Rename small utils by @EmmaRenauld in #852
• Improved docstring and renaming by @frheault in #857
• Rename "lobe-specific metrics" to "Bingham metrics" by @CHrlS98 in #863
• Add multiple fs folder subject possibility by @arnaudbore in #844
• ENH: merge gradients convert by @AntoineTheb in #854
• Merge asymmetric filtering scripts by @CHrlS98 in #855
• Update help prompts to fit new name + add formerly: line for old script name. by @gagnonanthony in #860
• Fix basename compute dwi snr by @Manonedde in #873
• Update doc surface by @grahamlittlephd in #864
• [BF] tractoflow filter by roi by @arnaudbore in #876
• [ENH] Add pull request template by @arnaudbore in #875
• Update to dipy 1.8 by @arnaudbore in #853
• fix gdrive endpoint for tests by @AlexVCaron in #877
• Update memsmt fodf script [requires dipy 1.8.0] by @karanphil in #791
• OPT - map sh to sf before tracking [requires dipy 1.8.0] by @gabknight in #782
• Fix the script for unequal bval by @frheault in #881
• rename some scripts by @arnaudbore in #878
• Bump pillow from 10.0.1 to 10.2.0 by @dependabot in #882
• Bump pillow from 10.0.1 to 10.2.0 in /docs by @dependabot in #883
• add step to publish coverage to codecov.io by @AlexVCaron in #886
• Add Otsu threshold to scil_volume_math.py by @CHrlS98 in #887
• Fix bad commit in codecov by @AlexVCaron in #888
• Robustify the coloring by @EmmaRenauld in #890
• [WIP] Kill Jenkins by @AlexVCaron in #892
• Cancel previous concurrent build by @AlexVCaron in #893
• run workflow on PR head by @AlexVCaron in #897
• pass fetcher to DVC by @AlexVCaron in #895
• FIX: scil_visualize_connectivity text rotation by @AntoineTheb in #894
• Add perpendicular diffusi...