Nitransforms

======================
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)

======================
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)

=======================
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)

==========================
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)

===========================
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)