Release notes for DIPY version 1.8#
GitHub stats for 2023/04/23 - 2023/12/13 (tag: 1.7.0)
These lists are automatically generated, and may be incomplete or contain duplicates.
The following 28 authors contributed 733 commits.
Ariel Rokem
Atharva Shah
Bramsh Qamar
Charles Poirier
Dimitri Papadopoulos
Eleftherios Garyfallidis
Emmanuelle Renauld
Eric Larson
Francois Rheault
Gabriel Girard
Javier Guaje
John Kruper
Jon Haitz Legarreta Gorroño
Jong Sung Park
Maharshi Gor
Michael R. Crusoe
Nicolas Delinte
Paul Camacho
Philippe Karan
Rafael Neto Henriques
Sam Coveney
Samuel St-Jean
Serge Koudoro
Shilpi Prasad
Theodore Ni
Vara Lakshmi Bayanagari
dependabot[bot]
Étienne Mollier
We closed a total of 327 issues, 130 pull requests and 197 regular issues;
this is the full list (generated with the script
tools/github_stats.py):
Pull Requests (129):
PR #3009: [DOC] Update installation instruction [ci skip]
PR #2999: TEST: Set explicitly CLARABEL as the CVXPY solver
PR #2943: BF: Fix bundlewarp shape analysis profile values for all False mask
PR #2992: RGB support for images
PR #2989: BF: Mask 1 values in leveraged, residual matrix computation
PR #3007: [RF] Define minimum version for some optional packages
PR #3006: [NF] Introduce minimum version in optional_package
PR #3002: [RF] Improve scripts and import management
PR #3005: Bump actions/setup-python from 4 to 5
PR #3004: TEST: Check and filter PCA dimensionality problem warning
PR #2996: RF: Fix b0 threshold warnings
PR #2995: [MTN] remove custom module _importlib
PR #2998: TEST: Filter SciPy 0.18.0 1-D affine transform array warning in test
PR #3001: RF: Create PCA denoising utils methods
PR #3000: RF: Prefer raising sklearn package warnings when required
PR #2997: TEST: Filter warning about resorting to OLS fitting method
PR #2991: MTN: fix byte swap ordering for numpy 2.0
PR #2987: STYLE: Make cvxpy-dependent test checking consistent in test_mcsd
PR #2990: STYLE: Use .astype() on uninitialized array casting
PR #2984: DOC: Miscellaneous documentation improvements
PR #2988: STYLE: Remove unused import in dipy/core/gradients.py
PR #2985: Bump conda-incubator/setup-miniconda from 2 to 3
PR #2986: DOC: Fix typos and grammar in lcr_matrix function documentation
PR #2983: STYLE: Fix boolean variable negation warnings
PR #2981: [MTN] replace the deprecated sctypes
PR #2980: [FIX] int_t to npy_intp
PR #2978: DOC: Fix issue template [ci skip]
PR #2976: [MTN] Update index url for PRE-Wheels dependencies
PR #2975: connectivity_matrix code speed up
PR #2715: Enable building DIPY with Meson
PR #2964: RF: Moving to numpy.random.Generator from numpy.random
PR #2963: NF: Updating EVAC+ model and adding util function
PR #2974: [MTN] Disable github check annotations
PR #2956: Adding support for btens to multi_shell_fiber_response function
PR #2969: bugfix for –force issue
PR #2967: Feature/opacity checkbox
PR #2966: volume slider fix
PR #2958: TEST: Filter legacy SH bases warnings in bootstrap direction getter test
PR #2944: [DOC] Remove ..figure directive in examples
PR #2961: fixes for pep8 in previous PR
PR #2922: synchronized-slicers for same size
PR #2924: Additional check for horizon
PR #2957: STYLE: Fix typo in msdki reconstruction test name
PR #2941: TEST: Fix NumPy array to scalar value conversion warning
PR #2932: OPT - Optimized pmfgen
PR #2929: Stabilizing some test functions with set random seeds
PR #2954: TEST: Bring back Python 3.8 testing to GHA workflows
PR #2946: RF: Refactor duplicate code in qtdmri to mapmri coeff computation
PR #2947: RF - BootDirectionGetter
PR #2945: DOC: Fix miscellaneous docstrings
PR #2940: TEST: Filter legacy SH bases warnings in PTT direction getter test
PR #2938: TEST: Adding random generator with seed to icm tests
PR #2942: OPT: Delegate to NumPy creating a random matrix
PR #2939: DOC: Update jhlegarreta affiliation in developers
PR #2933: fixed bug with fit extra returns
PR #2930: Update of the tutorial apply image-based registration to streamlines
PR #2759: TRX integration
PR #2923: [DOC] Large documentation update
PR #2825: NF - add initial directions to local tracking
PR #2892: BF - fixed random generator seed value too large to convert to int error
PR #2926: ENH: MSMT CSD module unique b-val tolerance parameter improvements
PR #2927: DOC: Fix package name in documentation config file comment
PR #2925: STYLE: Fix miscellaneous Numpy warnings
PR #2781: Small fixes in functions
PR #2910: STYLE: f-strings
PR #2921: [FIX] tiny fix to HBN fetcher to also grab T1 for each subject
PR #2906: [FIX] Pin scipy for the conda failing CI’s
PR #2920: Mark Python3 files as such
PR #2919: fix various grammar errors
PR #2916: Build(deps): Bump codespell-project/actions-codespell from 1 to 2
PR #2914: GitHub Actions
PR #2816: Correlation Tensor Imaging
PR #2912: MAINT: the symbol for second is s, not sec.
PR #2902: Short import for horizon
PR #2904: Apply refurb suggestions
PR #2899: DOC: Fix typos newly found by codespell
PR #2891: Apply pyupgrade suggestions
PR #2898: Remove zip operation in transform_tracking_output
PR #2897: BF: Bug when downloading hbn data.
PR #2893: Remove consecutive duplicate words
PR #2894: Get rid of trailing spaces in text files
PR #2889: Apply pyupgrade suggestions
PR #2888: Fix typos newly found by codespell
PR #2887: Update shm.py
PR #2814: [Fix] Horizon: Binary image loading
PR #2885: [ENH] Add minimum length to streamline generator
PR #2875: Increased PTT performances
PR #2879: Add fetcher for a sample CTI dataset
PR #2882: Change license_file to license_files in setup.cfg
PR #2804: Adding diffusion data descriptions from references to reconstruction table
PR #2730: Fix weighted Jacobians, return extra fit data, add adjacency function
PR #2821: NF - added pft min wm parameter
PR #2876: Introduction of pydata theme for sphinx
PR #2846: Vara’s Week 8 & Week 9 blog
PR #2870: Vara’s Week 12 and Week 13 blog
PR #2865: Shilpi’s Week0&Week1 combined
PR #2868: Submitting Week13.rst file
PR #2871: Corrected paths to static files
PR #2863: Shilpi’s Week12 Blog.
PR #2856: Adding Week 11 Blog
PR #2849: Shilpi’s 10th Blog
PR #2847: Pushing Week 8 + 9 blog
PR #2836: Shilpi’s Week 5 blog
PR #2864: Change internal space/origin when using sft.to_x() with an empty sft.
PR #2806: BF - initial backward orientation of local tracking
PR #2862: Vara’s Week 10 & Week 11 blog
PR #2843: Pushing 7th_blog
PR #2841: Vara’s Week 6 & Week 7 blog
PR #2835: Vara’s week 5 blog
PR #2829: Pushing 3rd blog
PR #2828: Vara’s week 3 blog
PR #2860: Updates HCP fetcher dataset_description to be compatible with current BIDS
PR #2831: Vara’s week 4 blog
PR #2833: Pushing 4thBlog
PR #2840: Shilpi’s Week6 Blog
PR #2839: make order_from_ncoef return an int
PR #2844: doc/tools/: fix trailing dot in version number.
PR #2832: BundleWarp: added tutorial and fixed a small bug
PR #2818: Vara’s week 0 blog
PR #2823: submitting clearn PR for 2nd blog
PR #2813: First Blog
PR #2808: [DOC] Fix cross referencing
PR #2798: Move evac+ to new module nn
PR #2797: remove Nibabel InTemporaryDirectory
PR #2800: Remove the Deprecating nisext
PR #2795: bump dependencies minimal version
PR #2792: Add patch_radius parameter to Patch2Self denoise workflow
PR #2761: [UPCOMING] Release 1.7.0 - workshop release
Issues (197):
#3009: [DOC] Update installation instruction [ci skip]
#2999: TEST: Set explicitly CLARABEL as the CVXPY solver
#2943: BF: Fix bundlewarp shape analysis profile values for all False mask
#2992: RGB support for images
#2989: BF: Mask 1 values in leveraged, residual matrix computation
#3007: [RF] Define minimum version for some optional packages
#3006: [NF] Introduce minimum version in optional_package
#1256: script path can not be found on OSX
#3002: [RF] Improve scripts and import management
#3005: Bump actions/setup-python from 4 to 5
#3004: TEST: Check and filter PCA dimensionality problem warning
#2996: RF: Fix b0 threshold warnings
#2995: [MTN] remove custom module _importlib
#2998: TEST: Filter SciPy 0.18.0 1-D affine transform array warning in test
#3001: RF: Create PCA denoising utils methods
#3000: RF: Prefer raising sklearn package warnings when required
#2997: TEST: Filter warning about resorting to OLS fitting method
#2979: Prerelease wheels not NumPy 2.0.0.dev compatible
#2991: MTN: fix byte swap ordering for numpy 2.0
#2987: STYLE: Make cvxpy-dependent test checking consistent in test_mcsd
#2990: STYLE: Use .astype() on uninitialized array casting
#2984: DOC: Miscellaneous documentation improvements
#2988: STYLE: Remove unused import in dipy/core/gradients.py
#2985: Bump conda-incubator/setup-miniconda from 2 to 3
#2986: DOC: Fix typos and grammar in lcr_matrix function documentation
#2905: base tests
#2983: STYLE: Fix boolean variable negation warnings
#2981: [MTN] replace the deprecated sctypes
#2980: [FIX] int_t to npy_intp
#2978: DOC: Fix issue template [ci skip]
#2976: [MTN] Update index url for PRE-Wheels dependencies
#2975: connectivity_matrix code speed up
#2514: Reshape our packaging system
#2715: Enable building DIPY with Meson
#2964: RF: Moving to numpy.random.Generator from numpy.random
#2736: dipy_horizon needs –force option if there is tmp.png
#2960: add type annotation in io module
#2803: Type annotations integration
#2963: NF: Updating EVAC+ model and adding util function
#2974: [MTN] Disable github check annotations
#2956: Adding support for btens to multi_shell_fiber_response function
#2969: bugfix for –force issue
#2967: Feature/opacity checkbox
#2965: Pip installation issues with python 3.12
#2968: Pip installation issues with python 3.12
#2966: volume slider fix
#2958: TEST: Filter legacy SH bases warnings in bootstrap direction getter test
#2801: Some left-overs from sphinx-gallery conversion
#2944: [DOC] Remove ..figure directive in examples
#2961: fixes for pep8 in previous PR
#2922: synchronized-slicers for same size
#2878: DIPY reinstall doesn’t automatically update needed dependencies
#2924: Additional check for horizon
#2957: STYLE: Fix typo in msdki reconstruction test name
#2941: TEST: Fix NumPy array to scalar value conversion warning
#2932: OPT - Optimized pmfgen
#2929: Stabilizing some test functions with set random seeds
#2954: TEST: Bring back Python 3.8 testing to GHA workflows
#2953: [WIP] Nlmeans update
#2946: RF: Refactor duplicate code in qtdmri to mapmri coeff computation
#2955: set_number_of_points function not found for dipy 1.7.0
#2947: RF - BootDirectionGetter
#2952: Delete dipy/denoise/nlmeans.py
#2949: HBN fetcher failed
#2945: DOC: Fix miscellaneous docstrings
#718: Create an example of multi b-value SFM
#2523: Doc generation failed
#2940: TEST: Filter legacy SH bases warnings in PTT direction getter test
#2928: test_icm_square failing on and off
#2938: TEST: Adding random generator with seed to icm tests
#2942: OPT: Delegate to NumPy creating a random matrix
#2939: DOC: Update jhlegarreta affiliation in developers
#2933: fixed bug with fit extra returns
#2936: Automatic Fiber Bundle Extraction with RecoBundles in DIPY 1.7 broken?
#2934: demo code not working
#2787: Adds a pyproject file.
#2786: “Image based streamlines_registration: unable to warp streamlines into template”
#2400: Applying image-based deformations to streamlines example
#2703: Image based streamlines_registration: unable to warp streamlines into template space
#2930: Update of the tutorial apply image-based registration to streamlines
#2759: TRX integration
#2931: Add caption to sphinx gallery figure
#2560: MCSD Tutorial failed with cvxpy>=1.1.15
#2794: Add a search box to the DIPY documentation
#2815: Reconstruction table of content doesn’t connect to MAP+
#2923: [DOC] Large documentation update
#2790: DTI fitting function with NLLS method raises an error.
#2872: Website image (not showing up or wrong tag showing)
#2884: WIP: trx integration
#2825: NF - add initial directions to local tracking
#2892: BF - fixed random generator seed value too large to convert to int error
#2926: ENH: MSMT CSD module unique b-val tolerance parameter improvements
#2927: DOC: Fix package name in documentation config file comment
#2925: STYLE: Fix miscellaneous Numpy warnings
#2777: Error using dipy_motion_correct
#2781: Small fixes in functions
#2648: Issues with dipy_align_syn
#2900: format → f-strings?
#2910: STYLE: f-strings
#2921: [FIX] tiny fix to HBN fetcher to also grab T1 for each subject
#2906: [FIX] Pin scipy for the conda failing CI’s
#2920: Mark Python3 files as such
#2919: fix various grammar errors
#2896: Interactive examples for dipy
#2901: patch2self question
#2916: Build(deps): Bump codespell-project/actions-codespell from 1 to 2
#2914: GitHub Actions
#2816: Correlation Tensor Imaging
#2912: MAINT: the symbol for second is s, not sec.
#2913: DOC: fix links
#2902: Short import for horizon
#2908: Voxel correspondence between Non-Linearly aligned Volumes
#2890: Attempt to fix error in conda jobs
#2907: Temp - Gab PR
#2904: Apply refurb suggestions
#2903: Typo in the skills required section (Project 2) of Project Ideas
#2899: DOC: Fix typos newly found by codespell
#2891: Apply pyupgrade suggestions
#2898: Remove zip operation in transform_tracking_output
#2897: BF: Bug when downloading hbn data.
#2893: Remove consecutive duplicate words
#2894: Get rid of trailing spaces in text files
#2889: Apply pyupgrade suggestions
#2888: Fix typos newly found by codespell
#2887: Update shm.py
#2814: [Fix] Horizon: Binary image loading
#2885: [ENH] Add minimum length to streamline generator
#1372: Change direction getter dictionary keys from floats[3] to int
#2805: Incorrect initial direction for the backward segment of local tracking
#2875: Increased PTT performances
#2883: Adding last,Week14Blog
#2879: Add fetcher for a sample CTI dataset
#2769: DOC example for data_per_streamline usage
#2774: Added a tutorial in doc folder for saving labels.
#2882: Change license_file to license_files in setup.cfg
#2881: Adding fetcher in the test_file for #2879
#2867: Bug in PFT when changing the random function
#2804: Adding diffusion data descriptions from references to reconstruction table
#2820: fixed bug for nlls fitting
#2746: Weighted Non-Linear Fitting may be wrong
#2730: Fix weighted Jacobians, return extra fit data, add adjacency function
#2821: NF - added pft min wm parameter
#2876: Introduction of pydata theme for sphinx
#2846: Vara’s Week 8 & Week 9 blog
#2870: Vara’s Week 12 and Week 13 blog
#2865: Shilpi’s Week0&Week1 combined
#2868: Submitting Week13.rst file
#2871: Corrected paths to static files
#2873: Motion estimate
#2863: Shilpi’s Week12 Blog.
#2856: Adding Week 11 Blog
#2849: Shilpi’s 10th Blog
#2847: Pushing Week 8 + 9 blog
#2836: Shilpi’s Week 5 blog
#2864: Change internal space/origin when using sft.to_x() with an empty sft.
#2806: BF - initial backward orientation of local tracking
#2862: Vara’s Week 10 & Week 11 blog
#2843: Pushing 7th_blog
#2841: Vara’s Week 6 & Week 7 blog
#2835: Vara’s week 5 blog
#2829: Pushing 3rd blog
#2828: Vara’s week 3 blog
#2860: Updates HCP fetcher dataset_description to be compatible with current BIDS
#2831: Vara’s week 4 blog
#1883: Interesting dataset for linear, planar, spherical encoding
#2491: ENH: Extend Horizon to visualize 2 volumes simultaneously
#2812: Patch2self denoising followed by topup and eddy corrections worsens distortions in the orbitofrontal region
#2833: Pushing 4thBlog
#2858: Odffp
#2857: Odffp
#2840: Shilpi’s Week6 Blog
#2838: Reconstruction issues using MAP-MRI model (RTOP, RTAP, RTPP)
#2845: MAP ODF issues
#2851: How to use “synb0” in Dipy for preprocessing
#2839: make order_from_ncoef return an int
#2844: doc/tools/: fix trailing dot in version number.
#2827: BundleWarp CLI Tutorial - Missing from Website
#2832: BundleWarp: added tutorial and fixed a small bug
#1627: WIP - NF - Tracking with Initial Directions and other tracking parameters
#2818: Vara’s week 0 blog
#2823: submitting clearn PR for 2nd blog
#2822: Pushing 2nd blog,
#2813: First Blog
#2808: [DOC] Fix cross referencing
#2798: Move evac+ to new module nn
#2797: remove Nibabel InTemporaryDirectory
#2706: FYI: Deprecating nisext in nibabel
#2800: Remove the Deprecating nisext
#2689: Installing DIPY fails with current conda version
#2718: StatefulTractogram
#2795: bump dependencies minimal version
#2747: Cannot set dipy as a dependency
#2791: Update Patch2Self CLI
#2792: Add patch_radius parameter to Patch2Self denoise workflow
#2771: BUG: Missing Python 3.11 macOS wheels
#2761: [UPCOMING] Release 1.7.0 - workshop release