Release notes for DIPY version 1.11#

GitHub stats for 2024/12/12 - 2025/03/14 (tag: 1.10.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 11 authors contributed 175 commits.

  • Ariel Rokem

  • Atharva Shah

  • Eleftherios Garyfallidis

  • Gabriel Girard

  • Jon Haitz Legarreta Gorroño

  • Jong Sung Park

  • Maharshi Gor

  • Michael R. Crusoe

  • Prajwal Reddy

  • Sam Coveney

  • Serge Koudoro

We closed a total of 120 issues, 47 pull requests and 73 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (47):

  • PR #3487: RF: update tracking cli

  • PR #3490: ENH: Updated the logging info

  • PR #3489: DOC - Renamed fast tracking example

  • PR #3475: NF: add workflow for N4 biasfield

  • PR #3485: DOC: remove modulo in dipy_math docstring

  • PR #3486: RF: Fixed Warnings of Patch2self3

  • PR #3483: ENH: Add use_cuda option to torch models

  • PR #3471: Patch2Self3 skipping b0_denoising error fixed.

  • PR #3477: NF: Add dipy_classify_tissue CLI

  • PR #3461: BF: Handling binary and small intensity value range and Volume slider not be shown if single channel provided.

  • PR #3479: DOC - Updated tracking examples to use the fast tracking framework

  • PR #3482: RF: Avoid crash of optional_package when dirty install

  • PR #3480: RF: Allow hcp and hcp in dipy_fetch CLI

  • PR #3476: BF - generate_tractogram needs seed coordinate in image space

  • PR #3478: RF: Small variable mismatch in the tutorial for DAM classifier

  • PR #3458: NF: Add optional fetcher

  • PR #3438: NF: Add 7 new dipy_fit_* workflows

  • PR #3462: NF: Reset of visualization introduced.

  • PR #3470: RF: Enforce bvecs for the cli extract_b0

  • PR #3472: RF: Rename and Deprecate dipy_sh_convert_mrtrix CLI

  • PR #3449: Adding DeepN4 PyTorch model

  • PR #3465: RF: Import fixes

  • PR #3459: NF: Add default value to docstring for the CLI

  • PR #3446: Dki constraints

  • PR #3467: RF: Changed the matrix

  • PR #3457: DOC: fix markup issues with tracking tutorial

  • PR #3456: Added tissue classification with DAM example

  • PR #3444: NF: Add 3 new dipy_extract_* workflows

  • PR #3089: Parallel Tracking Framework

  • PR #3448: Spelling error in the deprecation warning

  • PR #3442: RF: update of peak_directions to allow nogil

  • PR #3445: DOC: removed title

  • PR #3400: CI: Add python 3.13

  • PR #3440: RF - add pmf_gen argument to peaks_from_positions

  • PR #3441: ENH: Add GitHub CI workflow file to run benchmarks using asv

  • PR #3427: NF: add dipy_math workflow

  • PR #3432: RF: bump tensorflow minimal version to 2.18.0.

  • PR #3436: RF: Update scipy.special deprecated functions

  • PR #3433: TEST: remove skip if not have_delaunay

  • PR #3434: ENH: Transition remaining NumPy RandomState instances to Generator

  • PR #3430: ENH: Add type annotation information

  • PR #3428: DOC: Add implemented tractography method table to tracking example index

  • PR #3426: RF: from relative import to absolute import

  • PR #3423: Make the docs more reproducible

  • PR #3421: CI: remove python3.9 support

  • PR #3422: RF: fix joblib warning in sfm

  • PR #3364: UPCOMING: Release 1.10.0

Issues (73):

  • #3487: RF: update tracking cli

  • #3490: ENH: Updated the logging info

  • #3489: DOC - Renamed fast tracking example

  • #3475: NF: add workflow for N4 biasfield

  • #3485: DOC: remove modulo in dipy_math docstring

  • #3486: RF: Fixed Warnings of Patch2self3

  • #3483: ENH: Add use_cuda option to torch models

  • #3471: Patch2Self3 skipping b0_denoising error fixed.

  • #3477: NF: Add dipy_classify_tissue CLI

  • #3484: Default parameter values not shown on DIPY’s CLIs

  • #3371: Horizon miscalculating contrast when returning to previous volume

  • #3112: Horizon fails with a single channel 4D volume

  • #3461: BF: Handling binary and small intensity value range and Volume slider not be shown if single channel provided.

  • #3479: DOC - Updated tracking examples to use the fast tracking framework

  • #3482: RF: Avoid crash of optional_package when dirty install

  • #3480: RF: Allow hcp and hcp in dipy_fetch CLI

  • #3476: BF - generate_tractogram needs seed coordinate in image space

  • #3478: RF: Small variable mismatch in the tutorial for DAM classifier

  • #3190: Allow to define optional file to fetch

  • #3458: NF: Add optional fetcher

  • #3438: NF: Add 7 new dipy_fit_* workflows

  • #3469: horizon - SSLCertVerificationError

  • #3152: Horizon needs a home button which realigns the view to the z slice we are at.

  • #2421: DIPY Horizon Menu

  • #3462: NF: Reset of visualization introduced.

  • #3470: RF: Enforce bvecs for the cli extract_b0

  • #3472: RF: Rename and Deprecate dipy_sh_convert_mrtrix CLI

  • #3449: Adding DeepN4 PyTorch model

  • #3164: Simplify or remove the use of mpl_tri in viz module

  • #3465: RF: Import fixes

  • #3454: Default Value in Workflows docstring

  • #3459: NF: Add default value to docstring for the CLI

  • #3446: Dki constraints

  • #3467: RF: Changed the matrix

  • #3466: Theory for b and q values represent incorrect b matrix

  • #3457: DOC: fix markup issues with tracking tutorial

  • #3463: Remove the warnings from doc build in DIPY docs

  • #3451: How can be the drawing background changed from black to white using actor.odf_slicer

  • #3179: Need specific area zooming for horizon

  • #3359: Bug: Horizon throws errors when changing intensity range and then changing volumes

  • #3460: [WIP] RF: force use of header for fetcher

  • #3394: Create a tutorial for DAM classifier

  • #3456: Added tissue classification with DAM example

  • #3444: NF: Add 3 new dipy_extract_* workflows

  • #1501: Refactoring tracking and checking tutorials and workflows - high priority for next release.

  • #834: Multiprocessing the local tracking?

  • #3089: Parallel Tracking Framework

  • #3448: Spelling error in the deprecation warning

  • #3442: RF: update of peak_directions to allow nogil

  • #3445: DOC: removed title

  • #3443: NF: Replace urllib by requests to improve fetcher stability.

  • #3400: CI: Add python 3.13

  • #3440: RF - add pmf_gen argument to peaks_from_positions

  • #3441: ENH: Add GitHub CI workflow file to run benchmarks using asv

  • #3427: NF: add dipy_math workflow

  • #3432: RF: bump tensorflow minimal version to 2.18.0.

  • #3436: RF: Update scipy.special deprecated functions

  • #3431: Tests with scipy.spatial.Delaunay being skipped

  • #3433: TEST: remove skip if not have_delaunay

  • #3434: ENH: Transition remaining NumPy RandomState instances to Generator

  • #3430: ENH: Add type annotation information

  • #3428: DOC: Add implemented tractography method table to tracking example index

  • #3426: RF: from relative import to absolute import

  • #3423: Make the docs more reproducible

  • #3421: CI: remove python3.9 support

  • #3422: RF: fix joblib warning in sfm

  • #2364: Streamlines get negative coordinates in voxel space

  • #3016: [WIP] NF: Wigner-D Rotation Functions

  • #3276: [Feature] Multithreading support for reading and opening files.

  • #2304: [WIP] DKI ODF redux

  • #2705: WIP: Single-shell FWDTI

  • #3416: support for numpy 2.0 seems missing

  • #3364: UPCOMING: Release 1.10.0