Release notes for DIPY version 1.9#

GitHub stats for 2023/12/14 - 2024/03/07 (tag: 1.8.0)

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

The following 17 authors contributed 175 commits.

  • Ariel Rokem

  • Atharva Shah

  • Ebrahim Ebrahim

  • Eleftherios Garyfallidis

  • Gabriel Girard

  • John Shen

  • Jon Haitz Legarreta Gorroño

  • Jong Sung Park

  • Maharshi Gor

  • Matthew Feickert

  • Philippe Karan

  • Praitayini Kanakaraj

  • Sam Coveney

  • Sandro

  • Serge Koudoro

  • dependabot[bot]

  • Étienne Mollier

We closed a total of 139 issues, 60 pull requests and 81 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (60):

  • PR #3095: [UPCOMING] Release preparation for 1.9.0

  • PR #3086: [RF] Fix spherical harmonic terminology swap

  • PR #3105: [doc] improve some tutorials rendering

  • PR #3109: [BF] convert_tractogram fix

  • PR #3108: enabled trx support with correct header

  • PR #3107: enabled trx support for viz

  • PR #3033: [RF] fix dki mask for nlls

  • PR #3104: Dkimaskfix

  • PR #3106: volume slices visibility fixed

  • PR #3102: Bugfix for peaks slices and synchronization.

  • PR #3078: return S0 from dki fit

  • PR #3101: [BF] Uniformize cython version

  • PR #3097: Feature/surface

  • PR #3048: [TEST] Adds support of cython for pytest

  • PR #3053: [NF] Add workflow to convert tensors in different formats

  • PR #3073: [NF] Add DSI workflow

  • PR #3099: [DOC] fix some typo [ci skip]

  • PR #3098: Removing tensorflow addon from DL models

  • PR #2973: Tab names for slice tabs as file names.

  • PR #3081: NF: Adding N4 bias correction deep learning model

  • PR #3092: Feature: volume synchronizing

  • PR #3059: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors

  • PR #3090: RF - changed memory view to double* trilinear_interpolation_4d

  • PR #3080: Adding SH basis legacy option support to peaks_from_model

  • PR #3087: backward compatibility fixed

  • PR #3088: [TEST] Pin pytest

  • PR #3084: fixed 4d slice issue

  • PR #3083: Np.unique check removed.

  • PR #3082: Add Fedora installation instructions [ci skip]

  • PR #3076: [CI] Update scientific-python/upload-nightly-action to 0.5.0

  • PR #3070: [DOC] Fix installation link in README [ci skip]

  • PR #3069: [DOC] Fix DTI Tutorial [ci skip]

  • PR #3063: [RF] remove cpdef in PmfGen

  • PR #3054: [DOC] Fix some links [ci skip]

  • PR #3060: Bump codecov/codecov-action from 3 to 4

  • PR #3061: [OPT] Enable openmp for macOS wheel and CI’s

  • PR #3049: [MTN] code cleaning: remove some dependencies version checking

  • PR #3050: [RF] Move dipy.boots.resampling to dipy.stats.resampling

  • PR #3051: [RF] Remove dipy.io.bvectxt module

  • PR #3052: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874

  • PR #3045: [DOC] fix multi_shell_fiber_response docstring array dims [ci skip]

  • PR #3041: [NF] Add convert tractograms flow

  • PR #3040: [BW] Remove some python2 reference

  • PR #3039: [TEST] Add setup_module and teardown_module

  • PR #3038: [NF] Update dipy_info: allow tractogram files format

  • PR #3043: d/d/t/test_data.py: endian independent dtype.

  • PR #3042: pyproject.toml: no cython at run time.

  • PR #3027: [NF] Add Concatenate tracks workflows

  • PR #3008: NF: add SH basis conversion between dipy and mrtrix3

  • PR #3025: [TEST] Manage http errors for stateful tractograms

  • PR #3031: Bugfix: Horizon image’s dtype validation

  • PR #3021: [MTN] Remove 3.8 Ci’s

  • PR #3026: [RF] Fix cython 3 warnings

  • PR #3022: [DOC] Fix logo size and link [ci skip]

  • PR #3013: Added Fibonacci spiral and test for it

  • PR #3019: DOC: Fix link to toolchain roadmap page in README

  • PR #3012: DOC: Document observance for Scientific Python min supported versions

  • PR #3018: Bump actions/download-artifact from 3 to 4

  • PR #3017: Bump actions/upload-artifact from 3 to 4

  • PR #3014: Update release1.8.rst

Issues (81):

  • #2970: spherical harmonic degree/order terminology swapped

  • #3105: [doc] improve some tutorials rendering

  • #3109: [BF] convert_tractogram fix

  • #3108: enabled trx support with correct header

  • #3107: enabled trx support for viz

  • #2994: DKI masking

  • #3033: [RF] fix dki mask for nlls

  • #3104: Dkimaskfix

  • #3106: volume slices visibility fixed

  • #3102: Bugfix for peaks slices and synchronization.

  • #2281: Black Output for pam5 file with dipy_horizon

  • #3078: return S0 from dki fit

  • #3101: [BF] Uniformize cython version

  • #3097: Feature/surface

  • #2719: pytest and cdef functions

  • #3048: [TEST] Adds support of cython for pytest

  • #3053: [NF] Add workflow to convert tensors in different formats

  • #3073: [NF] Add DSI workflow

  • #3099: [DOC] fix some typo [ci skip]

  • #3098: Removing tensorflow addon from DL models

  • #2973: Tab names for slice tabs as file names.

  • #3081: NF: Adding N4 bias correction deep learning model

  • #3092: Feature: volume synchronizing

  • #3093: Can I use a different sort of dataset and also what if I don’t have a bval , I use . mat images format PATCH2Self

  • #3059: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors

  • #3090: RF - changed memory view to double* trilinear_interpolation_4d

  • #3080: Adding SH basis legacy option support to peaks_from_model

  • #3085: Viz Tests failing

  • #3087: backward compatibility fixed

  • #3088: [TEST] Pin pytest

  • #3074: Horizon for large datasets - concerns regarding np.unique

  • #3075: Horizon - 4D data support - slicing on the 4-th dim

  • #3084: fixed 4d slice issue

  • #3083: Np.unique check removed.

  • #3082: Add Fedora installation instructions [ci skip]

  • #3065: Add s390x test workflow

  • #3076: [CI] Update scientific-python/upload-nightly-action to 0.5.0

  • #3070: [DOC] Fix installation link in README [ci skip]

  • #3069: [DOC] Fix DTI Tutorial [ci skip]

  • #3066: Dipy website incorrect image

  • #3063: [RF] remove cpdef in PmfGen

  • #3054: [DOC] Fix some links [ci skip]

  • #3060: Bump codecov/codecov-action from 3 to 4

  • #3061: [OPT] Enable openmp for macOS wheel and CI’s

  • #3057: Using the atlas HCP1065 in DIPY

  • #3055: [RF] replace Bunch by Enum

  • #3049: [MTN] code cleaning: remove some dependencies version checking

  • #3050: [RF] Move dipy.boots.resampling to dipy.stats.resampling

  • #3051: [RF] Remove dipy.io.bvectxt module

  • #3052: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874

  • #2789: Horizon image’s dtype validation

  • #3047: “Editable” installation broken

  • #3045: [DOC] fix multi_shell_fiber_response docstring array dims [ci skip]

  • #3041: [NF] Add convert tractograms flow

  • #3040: [BW] Remove some python2 reference

  • #3039: [TEST] Add setup_module and teardown_module

  • #3038: [NF] Update dipy_info: allow tractogram files format

  • #3043: d/d/t/test_data.py: endian independent dtype.

  • #3042: pyproject.toml: no cython at run time.

  • #3027: [NF] Add Concatenate tracks workflows

  • #3035: If I want to use 6D array in “actor.odf_slicer”, how can i do?

  • #2993: Add conversion utility between DIPY and MRtrix3 spherical harmonic basis

  • #3008: NF: add SH basis conversion between dipy and mrtrix3

  • #3025: [TEST] Manage http errors for stateful tractograms

  • #3031: Bugfix: Horizon image’s dtype validation

  • #3032: Consider moving your nightly wheel away from the scipy-wheel-nightly (old location) to scientific-python-nightly-wheels

  • #3021: [MTN] Remove 3.8 Ci’s

  • #3003: DIPY installation raises Cython warnings

  • #3026: [RF] Fix cython 3 warnings

  • #2852: Different behavior regarding color channels of horizon

  • #2378: A novice’s request for advice on loading very large tractograms (.tck)

  • #2064: How to register MR to CT of the same person?

  • #2601: read_bvals_bvecs can’t read double volume dwi

  • #3022: [DOC] Fix logo size and link [ci skip]

  • #3013: Added Fibonacci spiral and test for it

  • #3020: load_nifti import doesn’t work if using submodule directly

  • #3019: DOC: Fix link to toolchain roadmap page in README

  • #3012: DOC: Document observance for Scientific Python min supported versions

  • #3018: Bump actions/download-artifact from 3 to 4

  • #3017: Bump actions/upload-artifact from 3 to 4

  • #3014: Update release1.8.rst

  • #1525: Clang-omp moved to boneyard on brew