Release notes for DIPY version 1.6#

GitHub stats for 2022/03/11 - 2023/01/12 (tag: 1.5.0)

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

The following 15 authors contributed 242 commits.

  • Ariel Rokem

  • David Romero-Bascones

  • Deneb Boito

  • Eleftherios Garyfallidis

  • Emmanuelle Renauld

  • Eric Larson

  • Francois Rheault

  • Jacob Roberts

  • Jon Haitz Legarreta Gorroño

  • Malinda Dilhara

  • Omar Ocegueda

  • Sam Coveney

  • Serge Koudoro

  • Shreyas Fadnavis

  • Tom Dela Haije

We closed a total of 116 issues, 41 pull requests and 75 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (41):

  • PR #2710: small fixes for tutorials

  • PR #2711: [FIX] use tempfile module instead of nibabel for TemporaryDirectory

  • PR #2702: One more small fix to the hcp fetcher.

  • PR #2704: MAINT: Fixes for 3.11 and sdist

  • PR #2701: FIX: Don’t print a progbar for downloading unless you need to.

  • PR #2700: [FIX] incompatible type in numpy array

  • PR #2694: NF: Add RUMBA-SD reconstruction workflow

  • PR #2697: NF: Adds a fetcher for HCP data.

  • PR #2692: RF: Improve multi-shell RUMBA test WM response parameterization

  • PR #2693: TEST: Fix Node.js warnings linked to GitHub actions

  • PR #2687: DOC: Fix typos in SH theory documentation page

  • PR #2690: STYLE: Remove unnecessary b-val print in CSD reconstruction flow

  • PR #2688: DOC: Document Dirac delta generation method missing member

  • PR #2683: DOC: Adds missing documentation for a kwarg.

  • PR #2668: ENH: Make the DTI fit CLI metric saving message accurate

  • PR #2674: Improve doc (tensor values’ order)

  • PR #2670: ENH: Allow non-default parameters to Patch2Self CLI

  • PR #2672: DOC: Miscellaneous docstring fixes

  • PR #2669: DOC: Remove inaccurate patch2self docstring default values

  • PR #2664: DOC: Fix DTI fit CLI docstring

  • PR #2553: NF: Unbiased groupwise linear bundle registration

  • PR #2369: Transform points with DiffeormorphicMap

  • PR #2631: [FIX] Allow patch size parameter to be an int on denoise Workflow

  • PR #2630: [DOC] Remove search index

  • PR #2629: [FIX ] Handle save VTP

  • PR #2618: Use np.linalg.multi_dot instead of multiple np.dot routines

  • PR #2606: STYLE: Fix miscellaneous Python warnings

  • PR #2600: Pin Ray

  • PR #2531: NF: MAP+ constraints

  • PR #2589: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module

  • PR #2577: Add positivity constraints to QTI

  • PR #2595: Temporary skip Cython 0.29.29

  • PR #2591: STYLE: Avoid array-like mutable default argument values

  • PR #2592: STYLE: Fix miscellaneous Python warnings

  • PR #2579: Generalized PCA to less than 3 spatial dims

  • PR #2584: transform_streamlines changes dtype to float64

  • PR #2566: [FIX] Update tests for the deprecated dipy.io.bvectxt module

  • PR #2581: Fix logger in SFT

  • PR #2580: DOC: Fix typos and grammar

  • PR #2576: DOC: Documentation fixes

  • PR #2568: DOC: Fix the docstring of write_mapping

Issues (75):

  • #2710: small fixes for tutorials

  • #2711: [FIX] use tempfile module instead of nibabel for TemporaryDirectory

  • #2709: DiffeomorphicMap object on github not the same as recent release

  • #2708: Provide the dataset of this code

  • #2699: WIP: Single shell/noreg redux

  • #2702: One more small fix to the hcp fetcher.

  • #2704: MAINT: Fixes for 3.11 and sdist

  • #2701: FIX: Don’t print a progbar for downloading unless you need to.

  • #2700: [FIX] incompatible type in numpy array

  • #2694: NF: Add RUMBA-SD reconstruction workflow

  • #2696: Port HCP fetcher from pyAFQ into here

  • #2697: NF: Adds a fetcher for HCP data.

  • #2692: RF: Improve multi-shell RUMBA test WM response parameterization

  • #2693: TEST: Fix Node.js warnings linked to GitHub actions

  • #1418: Adding parallel_voxel_fit decorator

  • #2687: DOC: Fix typos in SH theory documentation page

  • #2690: STYLE: Remove unnecessary b-val print in CSD reconstruction flow

  • #2688: DOC: Document Dirac delta generation method missing member

  • #2683: DOC: Adds missing documentation for a kwarg.

  • #2679: Problems with a .nii.gz file when loading and floating

  • #2676: Does `convert_sh_to_legacy` work as intended ?

  • #2668: ENH: Make the DTI fit CLI metric saving message accurate

  • #2674: Improve doc (tensor values’ order)

  • #2670: ENH: Allow non-default parameters to Patch2Self CLI

  • #2673: ENH: Doc: DTI format

  • #2667: Defaults for Patch2Self

  • #2672: DOC: Miscellaneous docstring fixes

  • #2669: DOC: Remove inaccurate patch2self docstring default values

  • #2662: Update cmd_line dipy_fit_dti

  • #2664: DOC: Fix DTI fit CLI docstring

  • #2658: Any chance of arm64 wheels for Mac / Python 3.10?

  • #2659: Angle var

  • #2649: IVIM VarPro fitting running error

  • #2553: NF: Unbiased groupwise linear bundle registration

  • #2424: Transforming individual points with SDR

  • #2327: Diffeomorphic transformation of coordinates

  • #2313: deform_streamlines for wholebrain tractogram doesn’t function properly

  • #936: WIP: coordinate mapping with DiffeomorphicMap

  • #2369: Transform points with DiffeormorphicMap

  • #2616: dti TensorModel fitting issue

  • #2627: Free-Water Analysis Gradient Table Error

  • #2635: get_flexi_tvis_affine(tvis_hdr, nii_aff)

  • #2634: Fix small difference between pdfs dense 2d/3d

  • #2559: CLI denoise patch_size error

  • #2631: [FIX] Allow patch size parameter to be an int on denoise Workflow

  • #2564: Search, index, module links not working in the doc

  • #2630: [DOC] Remove search index

  • #2572: Saving vtp file error

  • #2629: [FIX ] Handle save VTP

  • #2622: Error with Illustrating Electrostatic Repulsion

  • #2618: Use np.linalg.multi_dot instead of multiple np.dot routines

  • #2617: DKI model fit shape broadcast error

  • #2606: STYLE: Fix miscellaneous Python warnings

  • #2602: Dear experts, how can I set different number of fiber tracks before generating streamlines?

  • #2603: Dear experts, how to save dti_peaks?

  • #2600: Pin Ray

  • #2531: NF: MAP+ constraints

  • #2587: Thread safety concerns with reliance on nibabel.tmpdirs.InTemporaryDirectory

  • #2589: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module

  • #2577: Add positivity constraints to QTI

  • #2450: [NF] New tracking Algorithm: Parallel Transport Tractography (PTT)

  • #2594: DIPY compilation fails with the last release of cython (0.29.29)

  • #2595: Temporary skip Cython 0.29.29

  • #2591: STYLE: Avoid array-like mutable default argument values

  • #2592: STYLE: Fix miscellaneous Python warnings

  • #2579: Generalized PCA to less than 3 spatial dims

  • #2584: transform_streamlines changes dtype to float64

  • #2566: [FIX] Update tests for the deprecated dipy.io.bvectxt module

  • #2581: Fix logger in SFT

  • #2580: DOC: Fix typos and grammar

  • #2576: DOC: Documentation fixes

  • #2573: Cannot Import “Feature” From “dipy.segment.metric”

  • #2568: DOC: Fix the docstring of write_mapping

  • #2567: This should be a 1

  • #2565: compress_streamlines() not available anymore