Tags: nipy/nitransforms
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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**: 24.0.0...24.0.1
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. 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**: 23.0.1...24.0.0
23.0.0 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)
21.0.1 Release Notes ------------- 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 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. * 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 Release Notes ============= A first release of *NiTransforms*. This release accompanies a corresponding `JOSS submission <https://doi.org/10.21105/joss.03459>`__. 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)
20.0.0rc5 A first beta release of NiTransforms with the purpose of integrating it within *fMRIPrep*. This release accompanies the `ISBI2020 preprint <https://doi.org/10.31219/osf.io/8aq7b>`__. * FIX: Accept double precision when reading ANTs' ``.mat`` affines (#102) * 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 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: Update sphinx to latest major (4.0) (#116) * DOC: Initial setup for sphinx-build (#114) * DOC: Add Jupyter notebooks (#93) * DOC: Add figure to JOSS draft / Add @smoia to author list (#61) * DOC: Initial JOSS draft (#47) * MAINT: Move from TravisCI to GHA (#112) * MAINT: Revise tests and Docker image dependencies (#104) * 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)