# 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.