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Recent Releases of NiTransforms

NiTransforms - 25.0.1

Release Notes

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

What's changed

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

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

Scientific Software - Peer-reviewed - Python
Published by oesteban 7 months ago

NiTransforms - 25.0.0

What's Changed

  • ENH: Implement X5 representation and output to filesystem by @oesteban in https://github.com/nipy/nitransforms/pull/241
  • DOC: Fix references to os.PathLike by @oesteban in https://github.com/nipy/nitransforms/pull/242
  • ENH: X5 read/write support of TransformChain by @oesteban in https://github.com/nipy/nitransforms/pull/253
  • TST: Add test for DenseFieldTransform handling of OOB points by @oesteban in https://github.com/nipy/nitransforms/pull/254
  • FIX: Remove implementation of an abstract class by @oesteban in https://github.com/nipy/nitransforms/pull/255
  • MNT: Drop Python 3.9 by @oesteban in https://github.com/nipy/nitransforms/pull/259
  • FIX: BSpline mapping of individual points by @oesteban in https://github.com/nipy/nitransforms/pull/256

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

Scientific Software - Peer-reviewed - Python
Published by oesteban 7 months ago

NiTransforms - 24.1.4

What's Changed

  • FIX: Backport #251 into 24.1.x series by @oesteban in https://github.com/nipy/nitransforms/pull/252

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.3...24.1.4

Scientific Software - Peer-reviewed - Python
Published by oesteban 7 months ago

NiTransforms - 24.1.3

Hotfix release addressing the issues when resampling 4D data.

What's new

  • FIX: Broken 4D resampling by @oesteban in https://github.com/nipy/nitransforms/pull/247

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.2...24.1.3

Scientific Software - Peer-reviewed - Python
Published by oesteban 8 months ago

NiTransforms - 25.0.0rc0

What's Changed

  • ENH: Implement X5 representation and output to filesystem by @oesteban in https://github.com/nipy/nitransforms/pull/241
  • DOC: Fix references to os.PathLike by @oesteban in https://github.com/nipy/nitransforms/pull/242
  • Configure coverage to omit tests by @oesteban in https://github.com/nipy/nitransforms/pull/244
  • Move flake8 config into pyproject by @oesteban in https://github.com/nipy/nitransforms/pull/245
  • ENH: Loading of X5 (linear) transforms by @oesteban in https://github.com/nipy/nitransforms/pull/243
  • TST: Refactor io/lta to reduce one partial line by @oesteban in https://github.com/nipy/nitransforms/pull/246
  • FIX: Broken 4D resampling by @oesteban in https://github.com/nipy/nitransforms/pull/247
  • MAINT: Increase coverage by testing edge cases and adding docstrings by @oesteban in https://github.com/nipy/nitransforms/pull/248

Full Changelog: https://github.com/nipy/nitransforms/compare/24.1.2...25.0.0rc0

Scientific Software - Peer-reviewed - Python
Published by oesteban 8 months ago

NiTransforms - 24.1.2

What's Changed

  • FIX: Patch for crash when applying 3D transform to 4D image by @coryshain in https://github.com/nipy/nitransforms/pull/236
  • MNT: bump astral-sh/setup-uv from 4 to 5 by @dependabot[bot] in https://github.com/nipy/nitransforms/pull/234
  • MNT: bump astral-sh/setup-uv from 5 to 6 by @dependabot[bot] in https://github.com/nipy/nitransforms/pull/235
  • MNT: Fix doc builds and pacify linter by @effigies in https://github.com/nipy/nitransforms/pull/238
  • MNT: Switch from zenodo.json to CITATION.cff, add contributors by @effigies in https://github.com/nipy/nitransforms/pull/237

New Contributors

  • @coryshain made their first contribution in https://github.com/nipy/nitransforms/pull/236

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

Scientific Software - Peer-reviewed - Python
Published by oesteban 8 months ago

NiTransforms - 24.1.1

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

What's Changed

  • RF: Add nitransforms.resamping.apply to top module imports in https://github.com/nipy/nitransforms/pull/227
  • FIX: Remove pkg_resources dependency in https://github.com/nipy/nitransforms/pull/230

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

Scientific Software - Peer-reviewed - Python
Published by effigies 9 months ago

NiTransforms - 24.1.0

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

  • chore: Transition to pyproject.toml and tox, support numpy 2, python 3.13 by @effigies in https://github.com/nipy/nitransforms/pull/228

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

Scientific Software - Peer-reviewed - Python
Published by effigies over 1 year ago

NiTransforms - 24.0.2

Bug-fix release in the 24.0.x series.

What's Changed

  • FIX: Add per-volume transforms as single transform in chain by @effigies in https://github.com/nipy/nitransforms/pull/226

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

Scientific Software - Peer-reviewed - Python
Published by effigies over 1 year ago

NiTransforms - 24.0.1

Bug-fix release in the 24.0.x series.

New Contributors

  • @shnizzedy made their first contribution in https://github.com/nipy/nitransforms/pull/222

CHANGES

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

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

Scientific Software - Peer-reviewed - Python
Published by effigies over 1 year ago

NiTransforms - 24.0.0

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.

What's Changed

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

New Contributors

  • @mvdoc made their first contribution in https://github.com/nipy/nitransforms/pull/194
  • @jmarabotto made their first contribution in https://github.com/nipy/nitransforms/pull/197
  • @bpinsard made their first contribution in https://github.com/nipy/nitransforms/pull/182
  • @jbanusco made their first contribution in https://github.com/nipy/nitransforms/pull/188
  • @feilong made their first contribution in https://github.com/nipy/nitransforms/pull/203

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

Scientific Software - Peer-reviewed - Python
Published by oesteban over 1 year ago

NiTransforms - 23.0.1

What's Changed

  • FIX: numpy deprecation errors after 1.22 by @oesteban in https://github.com/nipy/nitransforms/pull/180
  • FIX: Load ITK's .mat files with Affine's loaders by @oesteban in https://github.com/nipy/nitransforms/pull/179

Full Changelog: https://github.com/nipy/nitransforms/compare/23.0.0...23.0.1

Scientific Software - Peer-reviewed - Python
Published by oesteban over 2 years ago

NiTransforms - 23.0.0

Release Notes

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

What's Changed

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

Full Changelog: https://github.com/nipy/nitransforms/compare/22.0.0...23.0.0

Scientific Software - Peer-reviewed - Python
Published by oesteban over 2 years ago

NiTransforms - 21.0.1

What's Changed

  • Add myself as a contributor by @HippocampusGirl in https://github.com/nipy/nitransforms/pull/159
  • FIX: Wrong datatype used for offset when reading ITK's h5 fields. by @oesteban in https://github.com/nipy/nitransforms/pull/161
  • FIX: Orientation of displacements field and header when reading ITK's h5 by @oesteban in https://github.com/nipy/nitransforms/pull/162
  • MAINT: Conclude migration poldracklab -> nipy by @oesteban in https://github.com/nipy/nitransforms/pull/163
  • ENH: Guess open linear transform formats by @oesteban in https://github.com/nipy/nitransforms/pull/160

Full Changelog: https://github.com/nipy/nitransforms/compare/22.0.0...21.0.1

Scientific Software - Peer-reviewed - Python
Published by oesteban over 2 years ago

NiTransforms - 22.0.0

Release Notes

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)

New Contributors

  • @HippocampusGirl made their first contribution in https://github.com/poldracklab/nitransforms/pull/151

Full Changelog: https://github.com/poldracklab/nitransforms/compare/21.0.1...22.0.0

Scientific Software - Peer-reviewed - Python
Published by oesteban about 4 years ago

NiTransforms - 21.0.0

Release Notes

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)

Scientific Software - Peer-reviewed - Python
Published by oesteban over 4 years ago

NiTransforms - 20.0.0rc5

Scientific Software - Peer-reviewed - Python
Published by oesteban over 4 years ago

NiTransforms - 20.0.0rc4

Scientific Software - Peer-reviewed - Python
Published by oesteban almost 5 years ago

NiTransforms - 20.0.0rc1

Release Notes

A first beta release of NiTransforms with the purpose of integrating it within fMRIPrep. This release accompanies the ISBI2020 preprint.

CHANGES

  • 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: 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 figure to JOSS draft / Add @smoia to author list (#61)
  • DOC: Initial JOSS draft (#47)
  • 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)

Scientific Software - Peer-reviewed - Python
Published by oesteban almost 6 years ago