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...

1.7.0-dev

This is a temporary pre-release used only for dev purposes.

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YOU SHOULD NOT BE USING THIS VERSION -

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1.6.0

New SCILPY release 1.6.0

First of all congrats to @EliseCos for her first PR 🎉 !!

A lot of new features and bug fixes. Thanks to @EmmaRenauld @CHrlS98 @karanphil @AlexVCaron @frheault !!

Good job everybody !

What's Changed

• [BF] Error message - metrics stats in ROI by @arnaudbore in #702
• [BF] GPU tracking kernel cannot be called main by @CHrlS98 in #701
• Get version script by @frheault in #703
• Adding import matplotlib to assign_custom_color_to_tractogram by @karanphil in #713
• Upgrade dipy to 1.7.0 by @CHrlS98 in #712
• Adding options for normalization in scil_assign_custom_color_to_tractogram by @karanphil in #717
• Adding absolute_peak_values to scil_compute_fodf_metrics.py by @karanphil in #715
• Fix: Add bundle to scores if it was not found by @EmmaRenauld in #709
• Refactor asym_odf_metrics script by @CHrlS98 in #708
• Add angle coloring option + fix bugs by @EmmaRenauld in #718
• Adding legacy options to scil_convert_sh_basis.py by @karanphil in #704
• [ENH] Add soft distance for each filter by @arnaudbore in #719
• Correlation ops by @frheault in #721
• (WIP) Harmonize json by @frheault in #716
• [ENH] Add new parameter to overwrite filter distance by @arnaudbore in #723
• Fix permissions by @frheault in #726
• Upgrade filter overwrite distance - Add criteria by @arnaudbore in #727
• RBx with FSS by @frheault in #707
• Multi centro labels map by @frheault in #728
• BUG: Allow tractogram math script to run as such by @jhlegarreta in #729
• Optional out_indices in scil_extract_dwi_shells.py by @CHrlS98 in #724
• Display masks as contours in screenshots by @AlexVCaron in #705
• ENH: Verbose tracking by @EmmaRenauld in #714
• Fix validate BIDS by @arnaudbore in #710
• Correct ihMTsat by @karanphil in #732
• Make stopping criteria more obvious + more similar to dipy. by @EmmaRenauld in #699
• Unit test tractogram operations by @EmmaRenauld in #706
• Sphere subdivide by @EliseCos in #731
• Working Scilpy development container for VS Code by @AlexVCaron in #733
• Fix filter anatomically by @arnaudbore in #735
• Fix bug with new .gitattributes by @AlexVCaron in #737
• Update citation for RBx -> BundleSeg by @frheault in #738
• Module streamline operations by @EmmaRenauld in #736
• Fix undetected bug after modifying module tractogram. by @EmmaRenauld in #739
• Add rejected streamlines to scil_filter_tractogram_anatomically by @arnaudbore in #740
• Remove pairwise by @frheault in #744
• Fix a few warnings by @EmmaRenauld in #748
• Use hot dipy 1.8.0.dev0 by @arnaudbore in #749
• Custom ROI surface rendering for Laurent by @frheault in #746
• Fix interp surf rendering by @frheault in #753
• Bump pillow from 9.0.1 to 10.0.1 in /docs by @dependabot in #755
• Bump pillow from 9.0.1 to 10.0.1 by @dependabot in #756
• ENH: scil_tractogram_math support for TCKs by @AntoineTheb in #752
• Merge gpu tracking into scil_compute_local_tracking.py by @CHrlS98 in #743
• Update version and README by @arnaudbore in #759

New Contributors

• @EliseCos made their first contribution in #731

Full Changelog: 1.5.0...1.6.0

1.5.0

NEW RELEASE 🎉 🥳

A lot of things have changed since the last version.
Thank you to every single one of you for contributing to scilpy.

What's Changed

• Testing 3 10 upgrade by @frheault in #662
• Fixing unique in dev branch by @frheault in #668
• Python3 10 readme by @frheault in #666
• [ENH] scilpy and python3.10 by @arnaudbore in #678
• Parallelise remove_loops_and_sharp_turns by @arnaudbore in #677
• Change version number by @frheault in #681
• Project streamlines from/to wm/gm by @frheault in #640
• Coloring connectomics by @frheault in #636
• Added OLO to reorder_connectivity by @frheault in #630
• New script: Plot dipy sphere by @EmmaRenauld in #679
• Fix multiprocess in dev tracking by @EmmaRenauld in #676
• Add python3.10-venv to packages to install by @CHrlS98 in #682
• skip init in search_keyword. by @frheault in #683
• Fixing uniform_coloring in scil_visualize_bunldes.py by @karanphil in #672
• Reactivate md5sum in fetcher by @frheault in #684
• uint8 in compute_density when possible by @frheault in #685
• Fix validate bids by @arnaudbore in #674
• Switch to kdtree for uniformize --target by @frheault in #686
• Adding variance to scil_visualize_fodf by @karanphil in #671
• Add check_bbox argument management by @EmmaRenauld in #641
• Adding PCA script for dimension reduction of metrics by @gagnonanthony in #673
• Module tractogram operations by @EmmaRenauld in #658
• fix seed mask empty by @arnaudbore in #687
• Adding small_dims option to scil_compute_fodf_max_in_ventricles by @karanphil in #688
• Adding explanations to scil_compute_fodf_max_in_ventricles by @karanphil in #689
• Fix some deprecated import and fix some tests by @arnaudbore in #690
• Fixing warning always showing up. by @EmmaRenauld in #693
• Fix default sphere tracking by @arnaudbore in #692
• Update to hotdipy + fix load empty sft by @arnaudbore in #694
• [WIP] Adding b-tensor encoding scripts like compute_fodf/frf and metrics by @karanphil in #425
• [ENH] Upload frozen python requirements aside of release assets by @AlexVCaron in #695
• (WIP) Adding script to apply transform to bvecs by @karanphil in #696
• Fix warnings in distortion correction by @arnaudbore in #700

New Contributors

• @gagnonanthony made their first contribution in #673

Full Changelog: 1.4.2...1.5.0

1.5.0-rc3

What's Changed

• [ENH] Upload frozen python requirements aside of release assets by @AlexVCaron in #695
• (WIP) Adding script to apply transform to bvecs by @karanphil in #696
• Fix warnings in distortion correction by @arnaudbore in #700

Full Changelog: 1.5.0-rc2...1.5.0-rc3

1.5.0-rc2

OMG A Big congratulation to @karanphil for his 2y+ PR
That's a guinness scilpy record 👍

We will keep rc-2 for a week or so and if everything adds up we'll release 1.5.0 !!!

What's Changed

• Fixing warning always showing up. by @EmmaRenauld in #693
• Fix default sphere tracking by @arnaudbore in #692
• Update to hotdipy + fix load empty sft by @arnaudbore in #694
• [WIP] Adding b-tensor encoding scripts like compute_fodf/frf and metrics by @karanphil in #425

Full Changelog: 1.5.0-rc1...1.5.0-rc2

1.5.0-rc1

🥳 🎉 🎉 🥳
First of all congratulations to all of you and especially @gagnonanthony who made his first contribution.
This is a big step for scilpy and the scilus since we moved from python 3.7 to 3.10.

Mostly new features and a couple of bug fixes.

What's Changed

• Testing 3 10 upgrade by @frheault in #662
• Fixing unique in dev branch by @frheault in #668
• Python3 10 readme by @frheault in #666
• [ENH] scilpy and python3.10 by @arnaudbore in #678
• Parallelise remove_loops_and_sharp_turns by @arnaudbore in #677
• Change version number by @frheault in #681
• Project streamlines from/to wm/gm by @frheault in #640
• Coloring connectomics by @frheault in #636
• Added OLO to reorder_connectivity by @frheault in #630
• New script: Plot dipy sphere by @EmmaRenauld in #679
• Fix multiprocess in dev tracking by @EmmaRenauld in #676
• Add python3.10-venv to packages to install by @CHrlS98 in #682
• skip init in search_keyword. by @frheault in #683
• Fixing uniform_coloring in scil_visualize_bunldes.py by @karanphil in #672
• Reactivate md5sum in fetcher by @frheault in #684
• uint8 in compute_density when possible by @frheault in #685
• Fix validate bids by @arnaudbore in #674
• Switch to kdtree for uniformize --target by @frheault in #686
• Adding variance to scil_visualize_fodf by @karanphil in #671
• Add check_bbox argument management by @EmmaRenauld in #641
• Adding PCA script for dimension reduction of metrics by @gagnonanthony in #673
• Module tractogram operations by @EmmaRenauld in #658
• fix seed mask empty by @arnaudbore in #687
• Adding small_dims option to scil_compute_fodf_max_in_ventricles by @karanphil in #688
• Adding explanations to scil_compute_fodf_max_in_ventricles by @karanphil in #689
• Fix some deprecated import and fix some tests by @arnaudbore in #690

New Contributors

• @gagnonanthony made their first contribution in #673

Full Changelog: 1.4.2...1.5.0-rc1

1.4.2

scilpy 1.4.1 was supposed to be the last release working on python3.7 but we now have another last version before python 3.10 👍

What's Changed

• Fix the unique len issue by @frheault in #665
• [BF] bids_validate by @arnaudbore in #669

Full Changelog: 1.4.1...1.4.2

1.4.1

A minor release for a major issue fixed when using scil_validate_bids with phase and mag data.

Thank you @EmmaRenauld @frheault @AlexVCaron 🎉

What's Changed

• Creating module 'labels' by @EmmaRenauld in #648
• [ENH] POC : Use mocking to get faster execution of tests by @AlexVCaron in #639
• Unit tests for the new labels module by @frheault in #659
• --no_empty in scil_remove invalid streamlines.py by @frheault in #657
• [ENH][BF] scil_validate_bids by @arnaudbore in #661
• [BF] Bids validate by @arnaudbore in #663

Full Changelog: 1.4.0...1.4.1

1.4.0

Holy 🐮 🐮 🐮 !

🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀
🚀 Congrats everybody for this amazing work ! 🚀
🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀🚀

SCILUS team you rock !! 🎉

🔥 @CHrlS98 🔥
🔥 @EmmaRenauld 🔥
🔥 @AlexVCaron 🔥
🔥 @karanphil 🔥
🔥 @frheault 🔥
🔥 @AntoineTheb 🔥

What's Changed

• Better docstring for scil_validate_and_correct_bvecs by @CHrlS98 in #570
• Improve DOC on scil_resample_tractogram.py by @frheault in #574
• Fix wrong condition for is_voxel_in_bound used in dev tracking by @CHrlS98 in #569
• Small fixes and improvements in tractogram filtering scripts by @EmmaRenauld in #567
• Adding new filtering script by orientation by @EmmaRenauld in #571
• Fix fix dsi studio by @frheault in #572
• Add mask option for bingham fit and metrics by @CHrlS98 in #573
• Fixing coordinate type + decreasing test size in dev tracking by @EmmaRenauld in #581
• Warn user for rk > 1 with prob tracking in dev tracking by @CHrlS98 in #580
• Clean pep8 in the fetcher file by @EmmaRenauld in #582
• Modifying scil_score tractogram by @EmmaRenauld in #568
• Simple GPU tracking by @CHrlS98 in #576
• Small changes in the dev tracker by @EmmaRenauld in #585
• Fixing transform_anatomy by @karanphil in #586
• Add split image script by @karanphil in #584
• Enhance GPU tracking by @CHrlS98 in #587
• Upgrading dipy by @EmmaRenauld in #578
• Fix case with no wpc in scil_score_tractogram by @EmmaRenauld in #595
• Modify scil_cut_streamlines.py by @karanphil in #588
• [BF] Fix arg in invalid streamlines + warning in todi by @arnaudbore in #589
• [BF] Fix bug in scil_concatenate_dwi.py when supplying more than 2 images by @CHrlS98 in #603
• Fix lazy usage with tck files by @EmmaRenauld in #598
• Fix F1 score by @EmmaRenauld in #600
• ENH: Add overlapping volume mosaic screenshot script by @jhlegarreta in #577
• ENH: Adding QBx option in subsampling + cleaning by @EmmaRenauld in #590
• Clarify vox space by @EmmaRenauld in #593
• Update prepare eddy by @arnaudbore in #609
• update jenkins and requirements by @arnaudbore in #611
• ENH: scil scoring unique streamlines by @AntoineTheb in #614
• Added a 'must_pass_mask' by @EmmaRenauld in #599
• [BF] Update bundle metrics - handle NaN by @arnaudbore in #619
• New assign color options by @frheault in #566
• Add a function to verify compatibility by @arnaudbore in #616
• Moving methods by @EmmaRenauld in #621
• New method to get n seeds at once. by @EmmaRenauld in #597
• Add arguments for RGB color ODF and RGB background color by @karanphil in #612
• Change default interpolation for mask by @CHrlS98 in #625
• Fix jenkins by @arnaudbore in #635
• [WIP] Correlate dwi QC by @frheault in #528
• WIP: New labels maps and simplification of tractometry profile scripts by @frheault in #554
• [ENH] Add multiple ID to filter tractogram with atlas by @arnaudbore in #627
• scil_assign_custom_color_to_tractogram.py optional colorbar image output by @CHrlS98 in #629
• Trilinear interpolation + sf threshold for GPU tracking by @CHrlS98 in #613
• ENH: unit test PoC by @AntoineTheb in #631
• Creating new script to score tractogram that is already segmented. by @EmmaRenauld in #622
• Bug fix for scil_swap_gradient_axis by @CHrlS98 in #634
• [ENH] Validate bids by @arnaudbore in #591
• Fix rare division by 0 in f1 by @EmmaRenauld in #642
• Gradient sampling ajustment by @karanphil in #626
• [ENH] Extract gradient scheme from eddy output - for tractoflow by @arnaudbore in #623
• Tensor format by @EmmaRenauld in #637
• [BF] validate BIDS by @arnaudbore in #645
• Fix: names for overreach by @EmmaRenauld in #643
• Add check_bbox_false (only in scil_score_bundles) by @EmmaRenauld in #646
• Fix logging across scilpy by @frheault in #647
• Fix logging for RBx (file handling) by @frheault in #649
• Fix total count by @EmmaRenauld in #650
• [BF] BG color as optional function argument by @CHrlS98 in #651
• Fix fetcher by @EmmaRenauld in #655
• BF validate_bids when full reverse by @arnaudbore in #654

Full Changelog: 1.3.0...1.4.0