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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)