Release notes for DIPY version 1.5#

GitHub stats for 2021/05/06 - 2022/03/10 (tag: 1.4.1)

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

The following 22 authors contributed 573 commits.

  • Ariel Rokem

  • Dan Bullock

  • David Romero-Bascones

  • Derek Pisner

  • Eleftherios Garyfallidis

  • Eric Larson

  • Francis Jerome

  • Francois Rheault

  • Gabriel Girard

  • Giulia Bertò

  • Javier Guaje

  • Jon Haitz Legarreta Gorroño

  • Joshua Newton

  • Kenji Marshall

  • Leevi Kerkela

  • Leon Weninger

  • Lucas Da Costa

  • Nasim Anousheh

  • Rafael Neto Henriques

  • Sam Coveney

  • Serge Koudoro

  • Shreyas Fadnavis

We closed a total of 200 issues, 72 pull requests and 128 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (72):

  • PR #2561: [FIX] Motion correction tutorial

  • PR #2520: Resdnn inference

  • PR #2558: BUG: Fix errant warning about starting_affine

  • PR #2557: MAINT: Fix version

  • PR #2556: [FIX] Update dipy.segment tutorials

  • PR #2554: Support .vtp files

  • PR #2555: Limit peaks_from_model number of processes in examples

  • PR #2539: Adds utilities for embarrassingly parallel loops.

  • PR #2545: Stateful Tractogram DPS and DPP keys ordering

  • PR #2548: Add timeout + concurrency to GHA

  • PR #2549: [ENH] Clarify reconst_sh tutorial

  • PR #2550: [ENH] Add sigma to DTI/DKI RESTORE workflow

  • PR #2551: [MNT] Update minimal dependencies version

  • PR #2536: Random colors fix in horizon

  • PR #2533: [FIX] Docstring cleaning: wrong underline length…

  • PR #2342: NF: q-space trajectory imaging

  • PR #2512: Masking for affine registration

  • PR #2526: TEST: Filter legacy SH bases warnings in tests

  • PR #2534: TEST: Remove unnecessary main method definition in tests

  • PR #2532: STYLE: Remove unused import statements

  • PR #2529: STYLE: Remove unused import statements

  • PR #2528: TEST: Remove legacy nose-related dead testing code

  • PR #2527: TEST: Fix intermittent RUMBA test check failure

  • PR #2493: Fury dependency resolution

  • PR #2522: ENH: Miscellaneous cleanup

  • PR #2521: DOC: Use GitHub actions status badge in README

  • PR #2420: Documentation corrections

  • PR #2482: ENH: Improve SH bases warning messages

  • PR #2423: NF: rumba reconst

  • PR #2518: Migrations from Azure Pipeline to Github Actions

  • PR #2515: Default to False output for null streamlines in streamline_near_roi

  • PR #2513: [MNT] Drop distutils

  • PR #2506: Horizon FURY update

  • PR #2510: Optimize sfm (reboot)

  • PR #2487: ENH: Better error message

  • PR #2442: [NF] Add Motion correction workflow

  • PR #2470: Add utilities functions: radius curvature <–> maximum deviation angle

  • PR #2485: DOC: Small updates.

  • PR #2481: ENH: Import ABCs from collections.abc

  • PR #2480: STYLE: Make sklearn import warning messages consistent

  • PR #2478: ENH: Deal appropriately with user warnings

  • PR #2479: STYLE: Improve style in misc files

  • PR #2475: ENH: Fix complex type NumPy alias deprecation warnings

  • PR #2476: ENH: Fix dipy.io.bvectxt deprecation warning

  • PR #2472: ENH: Return unique invalid streamline removal indices

  • PR #2471: DOC: Fix coding style guideline link

  • PR #2468: [MNT] Use windows-latest on azure pipeline

  • PR #2467: [ENH] Add fit_method option in DTI and DKI CLI

  • PR #2466: deprecate dipy.io.bvectxt module

  • PR #2453: make it compatible when number of volume is 2

  • PR #2413: Azure pipeline: from ubuntu 1604 to 2004

  • PR #2447: reduce_rois: Force input array type to bool to avoid bitwise or errors

  • PR #2444: [DOC] : Added citation for IVIM dataset

  • PR #2434: MAINT: Update import from ndimage

  • PR #2435: BUG: Backward compat support for pipeline

  • PR #2436: MAINT: Bump tolerance

  • PR #2438: BUG: Fix misplaced comma in warn() call from patch2self.py

  • PR #2374: ROIs visualizer

  • PR #2390: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling

  • PR #2417: OPT: Initialize Shape struct

  • PR #2419: Fixes the default option in the command line for Patch2Self ‘ridge’ -> ‘ols’

  • PR #2406: Manage Approx_polygon_track with repeated points

  • PR #2411: [FIX] c_compress_streamline discard identical points

  • PR #2416: OPT: Prefer using a typed index to get the PMF value

  • PR #2415: Implementation multi_voxel_fit progress bar

  • PR #2410: [ENH] Improve Shore Tests

  • PR #2409: NF - Sample PMF for an input position and direction

  • PR #2405: Small correction on KFA

  • PR #2407: from random to deterministic test for deform_streamlines

  • PR #2392: Add decomposition

  • PR #2389: [Fix] bundles_distances_mdf asymmetric values

  • PR #2368: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.

Issues (128):

  • #2561: [FIX] Motion correction tutorial

  • #2123: WIP: Residual Deep NN

  • #2520: Resdnn inference

  • #2558: BUG: Fix errant warning about starting_affine

  • #2557: MAINT: Fix version

  • #2489: MAINT: Get Python 3.10 binaries up on scipy-wheels-nightly

  • #2556: [FIX] Update dipy.segment tutorials

  • #2554: Support .vtp files

  • #2525: Support Opening .vtp files

  • #2555: Limit peaks_from_model number of processes in examples

  • #2539: Adds utilities for embarrassingly parallel loops.

  • #2509: Easy robustness for streamline_near_roi and near_roi for empty streamlines?

  • #2543: StatefulTractogram.are_compatible compare data_per_point keys as list instead of set

  • #2545: Stateful Tractogram DPS and DPP keys ordering

  • #2548: Add timeout + concurrency to GHA

  • #2549: [ENH] Clarify reconst_sh tutorial

  • #2546: Confusing import in ‘reconst_sh`

  • #2550: [ENH] Add sigma to DTI/DKI RESTORE workflow

  • #2542: DTI workflow should allow user-defined fitting method

  • #2551: [MNT] Update minimal dependencies version

  • #2477: Numpy min dependency update

  • #2541: Issue with coverage and pytests for numpy.min()

  • #2507: kernel died when use dipy.viz

  • #2536: Random colors fix in horizon

  • #2533: [FIX] Docstring cleaning: wrong underline length…

  • #2422: WIP-Adding math in SLR tutorial

  • #2342: NF: q-space trajectory imaging

  • #2512: Masking for affine registration

  • #1969: imaffine mask support

  • #2526: TEST: Filter legacy SH bases warnings in tests

  • #2456: Horizon tests failing

  • #2534: TEST: Remove unnecessary main method definition in tests

  • #2532: STYLE: Remove unused import statements

  • #2524: Add concurrency + timeout to Github Actions (GHA)

  • #2529: STYLE: Remove unused import statements

  • #2528: TEST: Remove legacy nose-related dead testing code

  • #2527: TEST: Fix intermittent RUMBA test check failure

  • #2493: Fury dependency resolution

  • #2522: ENH: Miscellaneous cleanup

  • #2521: DOC: Use GitHub actions status badge in README

  • #2420: Documentation corrections

  • #2482: ENH: Improve SH bases warning messages

  • #2449: Nonsense deprecation warning

  • #2423: NF: rumba reconst

  • #2179: NF: Complete masking implementation in affine registration with MI

  • #2518: Migrations from Azure Pipeline to Github Actions

  • #2492: Move to GitHub actions / reusable actions

  • #2515: Default to False output for null streamlines in streamline_near_roi

  • #2497: Remove python 3.6 from Azure pipelines

  • #2495: Remove Distutils (deprecated)

  • #2513: [MNT] Drop distutils

  • #2506: Horizon FURY update

  • #2305: [WIP] Brain Tumor Image Segmentation Code

  • #2499: Problem generating Connectivity Matrix: “Slice step cannot be zero”

  • #2510: Optimize sfm (reboot)

  • #2488: Minimize memory footprint wherever possible, add joblib support for …

  • #2504: Why are there many small dots on the fwdwi image?

  • #2502: Can i read specific b-values from my own multishell data?

  • #2500: MAP issue

  • #2490: [BUG] MRI-CT alignment failure

  • #2487: ENH: Better error message

  • #2402: Dipy 1.4.1 breaks nipype.interfaces.dipy.dipy_to_nipype_interface

  • #2486: Wrong doc in interpolation

  • #2442: [NF] Add Motion correction workflow

  • #2470: Add utilities functions: radius curvature <–> maximum deviation angle

  • #2485: DOC: Small updates.

  • #2484: [ENH] Add grid search to AffineRegistration.optimize

  • #2483: [DOC] Stable/Latest Documentation Structure

  • #2481: ENH: Import ABCs from collections.abc

  • #2480: STYLE: Make sklearn import warning messages consistent

  • #2478: ENH: Deal appropriately with user warnings

  • #2479: STYLE: Improve style in misc files

  • #2475: ENH: Fix complex type NumPy alias deprecation warnings

  • #2476: ENH: Fix dipy.io.bvectxt deprecation warning

  • #2472: ENH: Return unique invalid streamline removal indices

  • #2471: DOC: Fix coding style guideline link

  • #2468: [MNT] Use windows-latest on azure pipeline

  • #2467: [ENH] Add fit_method option in DTI and DKI CLI

  • #2463: DTI RESTORE on the CLI

  • #2466: deprecate dipy.io.bvectxt module

  • #2460: Deprecate and Remove dipy.io.bvectxt

  • #2429: random_colors flag in dipy_horizon does not work as before

  • #2461: Patch2Self: Less than 10 3D Volumes Bug

  • #2464: Typo on the homepage

  • #2453: make it compatible when number of volume is 2

  • #2457: Choosing sigma_diff and radius parameters for SyN registration

  • #2413: Azure pipeline: from ubuntu 1604 to 2004

  • #2454: Can I show fiber with vtk?

  • #2446: Use of bitwise or with non-bool inputs results in ufunc ‘bitwise_or’ error

  • #2447: reduce_rois: Force input array type to bool to avoid bitwise or errors

  • #2444: [DOC] : Added citation for IVIM dataset

  • #2443: Citation for IVIM dataset not present in docs

  • #2434: MAINT: Update import from ndimage

  • #2441: Horizon error - disk position outside the slider line

  • #2435: BUG: Backward compat support for pipeline

  • #2436: MAINT: Bump tolerance

  • #2438: BUG: Fix misplaced comma in warn() call from patch2self.py

  • #2430: dipy.align.reslice

  • #2431: dipy.align.reslice interpolation order for downsampling

  • #2432: How to apply MI metric in dipy？

  • #2374: ROIs visualizer

  • #2390: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling

  • #2417: OPT: Initialize Shape struct

  • #2419: Fixes the default option in the command line for Patch2Self ‘ridge’ -> ‘ols’

  • #2406: Manage Approx_polygon_track with repeated points

  • #2314: Approx_polygon_track with repeated points gives an error

  • #2411: [FIX] c_compress_streamline discard identical points

  • #1805: c_compress_streamline keeps identical points when it shouldn’t

  • #2418: kernel failure when importing mask from dipy.segment

  • #2416: OPT: Prefer using a typed index to get the PMF value

  • #2415: Implementation multi_voxel_fit progress bar

  • #2410: [ENH] Improve Shore Tests

  • #365: Code review items for dipy.reconst.shore

  • #2409: NF - Sample PMF for an input position and direction

  • #2404: Change affine in StatefulTractogram

  • #2405: Small correction on KFA

  • #2407: from random to deterministic test for deform_streamlines

  • #2392: Add decomposition

  • #717: Download each shell of the CENIR data separately?

  • #2209: _pytest.pathlib.ImportPathMismatchError:

  • #1934: Random lpca denoise

  • #2312: DIPY open group meetings, Spring 2021

  • #2383: error in mcsd model fitting (DCPError)

  • #2391: error performing cross-validation on diffusion HCP data

  • #2393: Add a function to read streamline from the result generated by the command “probtrackx2” in FMRIB’s Diffusion Toolbox

  • #2389: [Fix] bundles_distances_mdf asymmetric values

  • #2310: bundles_distances_mdf asymmetric values

  • #2368: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.