CHANGES.rst

25.1.0 (September 22, 2025)

A new feature release in the 25.1.x series.

Version 25.0.1 introduced a backwards-incompatible transposition of coordinate arrays. That version will be yanked from PyPI, which will mean that installers will skip over it unless specifically requested.

This version requires NumPy 2.0, SciPy 1.10 and h5py 3.11 or later.

CHANGES

• FIX: apply() fails with 4D singleton images by @oesteban in #278
• FIX: Respect singleton 4th-D by @oesteban in #279
• FIX: Remove "densification" of B-Spline transforms in apply() by @oesteban in #280
• MNT: Relax dependencies to numpy 2.0 compatibility by @effigies in #284

Full Changelog: https://github.com/nipy/nitransforms/compare/25.0.1...25.1.0

25.0.1 (August 14, 2025)

A patch release addressing a critical issue in the ImageGrid class relating coordinates, and bolstered the testing of ANTs' generated displacements fields by cross-comparing against antsApplyTransformsToPoints in several new tests.

CHANGES

• FIX: ImageGrid._coords was somehow overwritten + re-enable tests by @oesteban in #276
• FIX: Revision of index and RAS coordinate grids generation by @oesteban in #271
• ENH: Implement ITK densefields checks vs antsApplyTransformsToPoints by @oesteban in #277
• ENH: Add unit test on dense fields (extracted from #266) by @oesteban in #274
• RF: Move tests to better locations by @oesteban in #272
• MNT: Minimal housekeeping of tests by @oesteban in #275
• MNT: Fix coverage XML path in CircleCI by @oesteban in #265
• MNT: Add test cases demonstrating ordering bug reading composite ITK's HDF5 files by @oesteban in #263
• STY: Run ruff at the source root by @oesteban in #273

Full Changelog: https://github.com/nipy/nitransforms/compare/25.0.0...25.0.1

25.0.0 (July 22, 2025)

A new major release introducing critical fixes and important new functionality. Most notably, it includes a hotfix for 4D resampling (also backported to 24.1.4) and adds experimental support for the X5 format (BIDS). The X5 support enables I/O for linear and nonlinear transforms and includes partial support for transformation chains—marking a first step toward full BIDS interoperability. This release also drops support for Python 3.9 and earlier, aligning with modern Python standards and paving the way for future improvements.

CHANGES

• FIX: BSpline mapping of individual points by @oesteban in #256
• FIX: Remove implementation of an abstract class by @oesteban in #255
• FIX: Add test for DenseFieldTransform handling of OOB points by @oesteban in #254
• ENH: X5 read/write support of TransformChain by @oesteban in #253
• ENH: Loading of X5 (linear) transforms by @oesteban in #243
• ENH: Implement X5 representation and output to filesystem by @oesteban in #241
• DOC: Fix references to os.PathLike by @oesteban in #242
• MNT: Drop Python 3.9 by @oesteban in #259
• MNT: Increase coverage by testing edge cases and adding docstrings by @oesteban in #248
• MNT: Refactor io/lta to reduce one partial line by @oesteban in #246
• MNT: Move flake8 config into pyproject.toml by @oesteban in #245
• MNT: Configure coverage to omit tests by @oesteban in #244

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.4...25.0.0

24.1.4 (July 20, 2025)

Hotfix release addressing an issue in dense displacements fields.

CHANGES

• FIX: Backport #251 into 24.1.x series by @oesteban in #252

24.1.3 (July 19, 2025)

Hotfix release addressing the issues when resampling 4D data.

CHANGES

• FIX: Broken 4D resampling by @oesteban in #247

24.1.2 (June 02, 2025)

New patch release that addresses a crash when applying a 3D transform to a 4D image.

New Contributors

• @coryshain made their first contribution in #236

CHANGES

• FIX: Patch for crash when applying 3D transform to 4D image (#236)
• MNT: Switch from zenodo.json to CITATION.cff, add contributors (#237)

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.1...24.1.2

24.1.1 (December 18, 2024)

New patch release that adds nitransforms.resampling.apply as a top-level import, and removes the pkg_resources dependency.

CHANGES

• RF: Add nitransforms.resamping.apply to top module imports in #227
• FIX: Remove pkg_resources dependency in #230

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.0...24.1.1

24.1.0 (November 17, 2024)

New feature release in the 24.1.x series.

This release has the same code as 24.0.2, but the package has been tested with Numpy 2.0 and Python 3.13 and the metadata updated accordingly.

CHANGES

• MAINT: Transition to pyproject.toml and tox, support numpy 2, python 3.13 by @effigies in #228

Full Changelog: https://github.com/nipy/nitransforms/compare/24.0.2...24.1.0

24.0.2 (September 21, 2024)

Bug-fix release in the 24.0.x series.

CHANGES

• FIX: Add per-volume transforms as single transform in chain by @effigies in #226

Full Changelog: https://github.com/nipy/nitransforms/compare/24.0.1...24.0.2

24.0.1 (September 17, 2024)

Bug-fix release in the 24.0.x series.

New Contributors

• @shnizzedy made their first contribution in #222

CHANGES

• FIX: Use standard library pathlib by @shnizzedy in #222
• MAINT: Support pre-__or__ types by @effigies in #223
• MAINT: Bump the actions-infrastructure group with 3 updates by @dependabot in #224
• MAINT: Bump codecov/codecov-action from 3 to 4 by @dependabot in #225

Full Changelog: https://github.com/nipy/nitransforms/compare/24.0.0...24.0.1

24.0.0 (August 18, 2024)

A new series incorporating several major changes, including bugfixes and taking on several housekeeping/maintenance actions. One relevant change is the outsourcing of the apply() member out of transformation data structures by @jmarabotto. The method apply() is now a standalone method that operates on one transform and images/surfaces/etc. provided as arguments. A later major development is the adoption of a foundation for surface transforms by @feilong and @Shotgunosine.

New Contributors

• @mvdoc made their first contribution in #194
• @jmarabotto made their first contribution in #197
• @bpinsard made their first contribution in #182
• @jbanusco made their first contribution in #188
• @feilong made their first contribution in #203

CHANGES

• FIX: Inefficient iterative reloading of reference and moving images by @oesteban in #186
• FIX: Postpone coordinate mapping on linear array transforms by @oesteban in #187
• FIX: Remove unsafe cast during TransformBase.apply() by @effigies in #189
• FIX: _is_oblique() by @mvdoc in #194
• FIX: Update implementation of ndim property of transforms by @jmarabotto in #197
• FIX: Output displacement fields by @bpinsard in #182
• FIX: Composition of deformation fields by @jbanusco in #188
• FIX: Indexing disallowed in lists introduced by bugfix by @oesteban in #204
• FIX: Do not transpose (see :obj:`~scipy.ndimage.map_coordinates`) by @oesteban in #207
• FIX: Forgotten test using xfm.apply() by @oesteban in #208
• FIX: Load ITK fields from H5 correctly by @effigies in #211
• FIX: Wrong warning argument name level in warnings.warn by @oesteban in #216
• ENH: Define ndim property on nonlinear transforms by @oesteban in #201
• ENH: Outsource apply() from transform objects by @jmarabotto in #195
• ENH: Restore apply() method, warning of deprecation and calling function by @effigies in #209
• ENH: SurfaceTransform class by @feilong in #203
• ENH: reenable-parallelization-apply-214 (builds on PR #215, solves Issue #214) by @jmarabotto in #217
• ENH: Parallelize serialized 3D+t transforms by @oesteban in #220
• ENH: Implement a memory limitation mechanism in loading data by @oesteban in #221
• ENH: Serialize+parallelize 4D apply() into 3D+t and add 'low memory' loading by @oesteban in #215
• MAINT: Loosen dependencies by @mgxd in #164
• MAINT: Drop Python 3.7 support, test through 3.11 by @effigies in #181
• MAINT: Update CircleCI's infrastructure (machine image and Python version in Docker image) by @oesteban in #206
• MAINT: Fix tests for Python 3.12, numpy 2.0, and pytest-xdist by @effigies in #210
• MAINT: Update ANTs' pinnings by @oesteban in #219

Full Changelog: https://github.com/nipy/nitransforms/compare/23.0.1...24.0.0

23.0.1 (July 10, 2023)

Hotfix release addressing two issues.

CHANGES

• FIX: Load ITK's .mat files with Affine's loaders (#179)
• FIX: numpy deprecation errors after 1.22 (#180)

23.0.0 (June 13, 2023)

A new major release preparing for the finalization of the package and migration into NiBabel, mostly addressing bugfixes and scheduled added new features.

CHANGES

• FIX: Set x-forms on resampled images (#176)
• FIX: Ensure datatype of generated CIFTI2 file in TransformBase unit test (#178)
• ENH: Read ITK's composite transforms with only affines (#174)
• ENH: "Densify" voxel-wise nonlinear mappings with interpolation (#168)
• ENH: Extend the nonlinear transforms API (#166)
• ENH: API change in TransformChain - new composition convention (#165)
• MAINT: Rotate CircleCI secrets and setup up org-level context (#172)

22.0.1 (April 28, 2022)

A patch release after migration into the NiPy organization. This release is aliased as 21.0.1 to flexibilize dependency resolution.

CHANGES

• FIX: Orientation of displacements field and header when reading ITK's h5 (#162)
• FIX: Wrong datatype used for offset when reading ITK's h5 fields. (#161)
• ENH: Guess open linear transform formats (#160)
• MAINT: Conclude migration poldracklab -> nipy (#163)

22.0.0 (February 28, 2022)

The first stable release of NiTransforms in 2022. Contains all the new bug-fixes, features, and maintenance executed within the context of the NiBabel EOSS4 grant from the CZI Foundation.

CHANGES

• FIX: Implement AFNI's deoblique operations (#117)
• FIX: Ensure input dtype is kept after resampling (#153)
• FIX: Replace deprecated _read_mat with scipy.io.loadmat (#151)
• FIX: Add FSL-LTA-FSL regression tests (#146)
• FIX: Increase FSL serialization precision (#144)
• FIX: Refactor of LTA implementation (#145)
• FIX: Load arrays of linear transforms from AFNI files (#143)
• FIX: Load arrays of linear transforms from FSL files (#142)
• FIX: Double-check dtypes within tests and increase RMSE tolerance (#141)
• ENH: Base implementation of B-Spline transforms (#138)
• ENH: I/O of FSL displacements fields (#51)
• MAINT: Fix path to test summaries in CircleCI (#148)
• MAINT: Move testdata on to gin.g-node.org & datalad (#140)
• MAINT: scipy-1.8, numpy-1.22 require python 3.8 (#139)

21.0.0 (September 10, 2021)

A first release of NiTransforms. This release accompanies a corresponding JOSS submission.

CHANGES

• FIX: Final edits to JOSS submission (#135)
• FIX: Add mention to potential alternatives in JOSS submission (#132)
• FIX: Misinterpretation of voxel ordering in LTAs (#129)
• FIX: Suggested edits to the JOSS submission (#121)
• FIX: Invalid DOI (#124)
• FIX: Remove the --inv flag from regression mri_vol2vol regression test (#78)
• FIX: Improve handling of optional fields in LTA (#65)
• FIX: LTA conversions (#36)
• ENH: Add more comprehensive comments to notebook (#134)
• ENH: Add an .asaffine() member to TransformChain (#90)
• ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms (#79)
• ENH: Improved testing of LTA handling - ITK-to-LTA, mri_concatenate_lta (#75)
• ENH: Add FS transform regression (#74)
• ENH: Add ITK-LTA conversion test (#66)
• ENH: Support for transforms mappings (e.g., head-motion correction) (#59)
• ENH: command line interface (#55)
• ENH: Facilitate loading of displacements field transforms (#54)
• ENH: First implementation of AFNI displacement fields (#50)
• ENH: Base implementation of transforms chains (composition) (#43)
• ENH: First implementation of loading and applying ITK displacements fields (#42)
• ENH: Refactor of AFNI and FSL I/O with StringStructs (#39)
• ENH: More comprehensive implementation of ITK affines I/O (#35)
• ENH: Added some minimal test-cases to the Affine class (#33)
• ENH: Rewrite load/save utilities for ITK's MatrixOffsetBased transforms in io (#31)
• ENH: Rename resample() with apply() (#30)
• ENH: Write tests pulling up the coverage of base submodule (#28)
• ENH: Add tests and implementation for Displacements fields and refactor linear accordingly (#27)
• ENH: Uber-refactor of code style, method names, etc. (#24)
• ENH: Increase coverage of linear transforms code (#23)
• ENH: FreeSurfer LTA file support (#17)
• ENH: Use obliquity directly from nibabel (#18)
• ENH: Setting up a battery of tests (#9)
• ENH: Revise doctests and get them ready for more thorough testing. (#10)
• DOC: Add Zenodo metadata record (#136)
• DOC: Better document the IPython notebooks (#133)
• DOC: Transfer CoC from NiBabel (#131)
• DOC: Clarify integration plans with NiBabel in the README (#128)
• DOC: Add contributing page to RTD (#130)
• DOC: Add CONTRIBUTING.md file pointing at NiBabel (#127)
• DOC: Add example notebooks to sphinx documentation (#126)
• DOC: Add an Installation section (#122)
• DOC: Display API per module (#120)
• DOC: Add figure to JOSS draft / Add @smoia to author list (#61)
• DOC: Initial JOSS draft (#47)
• MAINT: Add imports of modules in __init__.py to workaround #91 (#92)
• MAINT: Fix missing python3 binary on CircleCI build job step (#85)
• MAINT: Use setuptools_scm to manage versioning (#83)
• MAINT: Split binary test-data out from gh repo (#84)
• MAINT: Add Docker image/circle build (#80)
• MAINT: Drop Python 3.5 (#77)
• MAINT: Better config on setup.py (binary operator starting line) (#60)
• MAINT: add docker build to travis matrix (#29)
• MAINT: testing coverage (#16)
• MAINT: pep8 complaints (#14)
• MAINT: skip unfinished implementation tests (#15)
• MAINT: pep8speaks (#13)