Tags: feilong/nitransforms
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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 (nipy#176) * FIX: Ensure datatype of generated CIFTI2 file in ``TransformBase`` unit test (nipy#178) * ENH: Read ITK's composite transforms with only affines (nipy#174) * ENH: "Densify" voxel-wise nonlinear mappings with interpolation (nipy#168) * ENH: Extend the nonlinear transforms API (nipy#166) * ENH: API change in ``TransformChain`` - new composition convention (nipy#165) * MAINT: Rotate CircleCI secrets and setup up org-level context (nipy#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 (nipy#162) * FIX: Wrong datatype used for offset when reading ITK's h5 fields. (nipy#161) * ENH: Guess open linear transform formats (nipy#160) * MAINT: Conclude migration ``poldracklab`` -> ``nipy`` (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 (nipy#117) * FIX: Ensure input dtype is kept after resampling (nipy#153) * FIX: Replace deprecated ``_read_mat`` with ``scipy.io.loadmat`` (nipy#151) * FIX: Add FSL-LTA-FSL regression tests (nipy#146) * FIX: Increase FSL serialization precision (nipy#144) * FIX: Refactor of LTA implementation (nipy#145) * FIX: Load arrays of linear transforms from AFNI files (nipy#143) * FIX: Load arrays of linear transforms from FSL files (nipy#142) * FIX: Double-check dtypes within tests and increase RMSE tolerance (nipy#141) * ENH: Base implementation of B-Spline transforms (nipy#138) * ENH: I/O of FSL displacements fields (nipy#51) * MAINT: Fix path to test summaries in CircleCI (nipy#148) * MAINT: Move testdata on to gin.g-node.org & datalad (nipy#140) * MAINT: scipy-1.8, numpy-1.22 require python 3.8 (nipy#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 (nipy#135) * FIX: Add mention to potential alternatives in JOSS submission (nipy#132) * FIX: Misinterpretation of voxel ordering in LTAs (nipy#129) * FIX: Suggested edits to the JOSS submission (nipy#121) * FIX: Invalid DOI (nipy#124) * FIX: Remove the ``--inv`` flag from regression ``mri_vol2vol`` regression test (nipy#78) * FIX: Improve handling of optional fields in LTA (nipy#65) * FIX: LTA conversions (nipy#36) * ENH: Add more comprehensive comments to notebook (nipy#134) * ENH: Add an ``.asaffine()`` member to ``TransformChain`` (nipy#90) * ENH: Read (and apply) *ITK*/*ANTs*' composite HDF5 transforms (nipy#79) * ENH: Improved testing of LTA handling - *ITK*-to-LTA, ``mri_concatenate_lta`` (nipy#75) * ENH: Add *FS* transform regression (nipy#74) * ENH: Add *ITK*-LTA conversion test (nipy#66) * ENH: Support for transforms mappings (e.g., head-motion correction) (nipy#59) * ENH: command line interface (nipy#55) * ENH: Facilitate loading of displacements field transforms (nipy#54) * ENH: First implementation of *AFNI* displacement fields (nipy#50) * ENH: Base implementation of transforms chains (composition) (nipy#43) * ENH: First implementation of loading and applying *ITK* displacements fields (nipy#42) * ENH: Refactor of *AFNI* and *FSL* I/O with ``StringStructs`` (nipy#39) * ENH: More comprehensive implementation of ITK affines I/O (nipy#35) * ENH: Added some minimal test-cases to the Affine class (nipy#33) * ENH: Rewrite load/save utilities for ITK's MatrixOffsetBased transforms in ``io`` (nipy#31) * ENH: Rename ``resample()`` with ``apply()`` (nipy#30) * ENH: Write tests pulling up the coverage of base submodule (nipy#28) * ENH: Add tests and implementation for Displacements fields and refactor linear accordingly (nipy#27) * ENH: Uber-refactor of code style, method names, etc. (nipy#24) * ENH: Increase coverage of linear transforms code (nipy#23) * ENH: FreeSurfer LTA file support (nipy#17) * ENH: Use ``obliquity`` directly from nibabel (nipy#18) * ENH: Setting up a battery of tests (nipy#9) * ENH: Revise doctests and get them ready for more thorough testing. (nipy#10) * DOC: Add *Zenodo* metadata record (nipy#136) * DOC: Better document the *IPython* notebooks (nipy#133) * DOC: Transfer ``CoC`` from *NiBabel* (nipy#131) * DOC: Clarify integration plans with *NiBabel* in the ``README`` (nipy#128) * DOC: Add contributing page to RTD (nipy#130) * DOC: Add ``CONTRIBUTING.md`` file pointing at *NiBabel* (nipy#127) * DOC: Add example notebooks to sphinx documentation (nipy#126) * DOC: Add an *Installation* section (nipy#122) * DOC: Display API per module (nipy#120) * DOC: Add figure to JOSS draft / Add @smoia to author list (nipy#61) * DOC: Initial JOSS draft (nipy#47) * MAINT: Add imports of modules in ``__init__.py`` to workaround nipy#91 (nipy#92) * MAINT: Fix missing ``python3`` binary on CircleCI build job step (nipy#85) * MAINT: Use ``setuptools_scm`` to manage versioning (nipy#83) * MAINT: Split binary test-data out from gh repo (nipy#84) * MAINT: Add Docker image/circle build (nipy#80) * MAINT: Drop Python 3.5 (nipy#77) * MAINT: Better config on ``setup.py`` (binary operator starting line) (nipy#60) * MAINT: add docker build to travis matrix (nipy#29) * MAINT: testing coverage (nipy#16) * MAINT: pep8 complaints (nipy#14) * MAINT: skip unfinished implementation tests (nipy#15) * MAINT: pep8speaks (nipy#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 (nipy#102) * FIX: Remove the ``--inv`` flag from regression ``mri_vol2vol`` regression test (nipy#78) * FIX: Improve handling of optional fields in LTA (nipy#65) * FIX: LTA conversions (nipy#36) * ENH: Add an ``.asaffine()`` member to ``TransformChain`` (nipy#90) * ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms (nipy#79) * ENH: Improved testing of LTA handling - ITK-to-LTA, ``mri_concatenate_lta`` (nipy#75) * ENH: Add FS transform regression (nipy#74) * ENH: Add ITK-LTA conversion test (nipy#66) * ENH: Support for transforms mappings (e.g., head-motion correction) (nipy#59) * ENH: command line interface (nipy#55) * ENH: Facilitate loading of displacements field transforms (nipy#54) * ENH: First implementation of AFNI displacement fields (nipy#50) * ENH: Base implementation of transforms chains (composition) (nipy#43) * ENH: First implementation of loading and applying ITK displacements fields (nipy#42) * ENH: Refactor of AFNI and FSL I/O with StringStructs (nipy#39) * ENH: More comprehensive implementation of ITK affines I/O (nipy#35) * ENH: Added some minimal test-cases to the Affine class (nipy#33) * ENH: Rewrite load/save utilities for ITK's MatrixOffsetBased transforms in ``io`` (nipy#31) * ENH: Rename ``resample()`` with ``apply()`` (nipy#30) * ENH: Write tests pulling up the coverage of base submodule (nipy#28) * ENH: Add tests and implementation for Displacements fields and refactor linear accordingly (nipy#27) * ENH: Uber-refactor of code style, method names, etc. (nipy#24) * ENH: Increase coverage of linear transforms code (nipy#23) * ENH: FreeSurfer LTA file support (nipy#17) * ENH: Use ``obliquity`` directly from nibabel (nipy#18) * ENH: Setting up a battery of tests (nipy#9) * ENH: Revise doctests and get them ready for more thorough testing. (nipy#10) * DOC: Update sphinx to latest major (4.0) (nipy#116) * DOC: Initial setup for sphinx-build (nipy#114) * DOC: Add Jupyter notebooks (nipy#93) * DOC: Add figure to JOSS draft / Add @smoia to author list (nipy#61) * DOC: Initial JOSS draft (nipy#47) * MAINT: Move from TravisCI to GHA (nipy#112) * MAINT: Revise tests and Docker image dependencies (nipy#104) * MAINT: Add imports of modules in ``__init__.py`` to workaround nipy#91 (nipy#92) * MAINT: Fix missing python3 binary on CircleCI build job step (nipy#85) * MAINT: Use setuptools_scm to manage versioning (nipy#83) * MAINT: Split binary test-data out from gh repo (nipy#84) * MAINT: Add docker image/circle build (nipy#80) * MAINT: Drop Python 3.5 (nipy#77) * MAINT: Better config on setup.py (binary operator starting line) (nipy#60) * MAINT: add docker build to travis matrix (nipy#29) * MAINT: testing coverage (nipy#16) * MAINT: pep8 complaints (nipy#14) * MAINT: skip unfinished implementation tests (nipy#15) * MAINT: pep8speaks (nipy#13)
20.0.0rc4 (May 14, 2021) * FIX: Accept double precision when reading ANTs' ``.mat`` affines (nipy#102) * DOC: Add Jupyter notebooks (nipy#93, nipy#96, nipy#97, nipy#98) * MAINT: Revise tests and Docker image dependencies (nipy#104) * MAINT: Add imports of modules in ``__init__.py`` to workaround nipy#91 (nipy#92)
20.0.0rc1 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: Remove the ``--inv`` flag from regression ``mri_vol2vol`` regression test (nipy#78) * FIX: Improve handling of optional fields in LTA (nipy#65) * FIX: LTA conversions (nipy#36) * ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms (nipy#79) * ENH: Improved testing of LTA handling - ITK-to-LTA, ``mri_concatenate_lta`` (nipy#75) * ENH: Add FS transform regression (nipy#74) * ENH: Add ITK-LTA conversion test (nipy#66) * ENH: Support for transforms mappings (e.g., head-motion correction) (nipy#59) * ENH: command line interface (nipy#55) * ENH: Facilitate loading of displacements field transforms (nipy#54) * ENH: First implementation of AFNI displacement fields (nipy#50) * ENH: Base implementation of transforms chains (composition) (nipy#43) * ENH: First implementation of loading and applying ITK displacements fields (nipy#42) * ENH: Refactor of AFNI and FSL I/O with StringStructs (nipy#39) * ENH: More comprehensive implementation of ITK affines I/O (nipy#35) * ENH: Added some minimal test-cases to the Affine class (nipy#33) * ENH: Rewrite load/save utilities for ITK's MatrixOffsetBased transforms in ``io`` (nipy#31) * ENH: Rename ``resample()`` with ``apply()`` (nipy#30) * ENH: Write tests pulling up the coverage of base submodule (nipy#28) * ENH: Add tests and implementation for Displacements fields and refactor linear accordingly (nipy#27) * ENH: Uber-refactor of code style, method names, etc. (nipy#24) * ENH: Increase coverage of linear transforms code (nipy#23) * ENH: FreeSurfer LTA file support (nipy#17) * ENH: Use ``obliquity`` directly from nibabel (nipy#18) * ENH: Setting up a battery of tests (nipy#9) * ENH: Revise doctests and get them ready for more thorough testing. (nipy#10) * DOC: Add figure to JOSS draft / Add @smoia to author list (nipy#61) * DOC: Initial JOSS draft (nipy#47) * MAINT: Fix missing python3 binary on CircleCI build job step (nipy#85) * MAINT: Use setuptools_scm to manage versioning (nipy#83) * MAINT: Split binary test-data out from gh repo (nipy#84) * MAINT: Add docker image/circle build (nipy#80) * MAINT: Drop Python 3.5 (nipy#77) * MAINT: Better config on setup.py (binary operator starting line) (nipy#60) * MAINT: add docker build to travis matrix (nipy#29) * MAINT: testing coverage (nipy#16) * MAINT: pep8 complaints (nipy#14) * MAINT: skip unfinished implementation tests (nipy#15) * MAINT: pep8speaks (nipy#13)