Alibertia

Bug fix for binarized masks in mask_image - now updated to return a float image type.

What's Changed

• COMP: Version bump by @cookpa in #887
• Docker version tags by @cookpa in #889
• DOC: document imagetype in apply_transforms by @cookpa in #890
• ENH: Assume mm,sec units if nifti units unknown by @cookpa in #892

Full Changelog: v0.6.2...v0.6.3

Alfaroa

Several fixes for apply_transforms with vector and tensor data. ITK updated to 5.4.5.

Nibabel import / export overhauled, should work more consistently now.

New feature: utilities to handle NIFTI transforms and allow more user control over whether to use the qform or sform.

What's Changed

• BUG: Same bias field across modalities. by @ntustison in #831
• ENH: Bump ANTs so that tensor I/O works by @cookpa in #834
• WIP: Allow for enforcing deterministic behavior. by @ntustison in #835
• BUG: Remove isolated deterministic handling. by @ntustison in #836
• BUG: Need to clone to float by @cookpa in #839
• Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 in /.github/workflows by @dependabot[bot] in #850
• fix: setting incorrect direction raises descriptive error by @galenlynch in #848
• BUG: label_geometry_measures with uint32 labels by @cookpa in #853
• ENH: Read ITK metadata from image on disk by @cookpa in #855
• BUG: RGB images could not return number of components by @cookpa in #857
• BUG: exported function names in nifti_utils.py by @cookpa in #858
• PERF: Only clone on read if needed by @cookpa in #859
• DOC: Registration transform convention by @cookpa in #860
• BUG: mask_image should apply the mask to the input by @cookpa in #861
• DOC: Documentation for nifti_utils by @cookpa in #865
• Rtd fixes by @cookpa in #868
• BUG: DOn't normalize. by @ntustison in #869
• CI: Update mac Intel runner by @cookpa in #872
• CI: Update wheels_faster for macos-15-intel by @cookpa in #873
• DOC: Add license string to pyproject.toml by @cookpa in #875
• ENH: nibabel support by @cookpa in #877
• ENH: Support 5D nibabel conversion by @cookpa in #878
• BUG: Remove deprecated numpy calls to reshape by @cookpa in #879
• COMP: Update ITK, ANTs, roll back numpy changes by @cookpa in #884
• Test vector reorient by @cookpa in #886

New Contributors

• @dependabot[bot] made their first contribution in #850
• @galenlynch made their first contribution in #848

Full Changelog: v0.6.1...v0.6.2

Aiouea

Apologies for the lack of Windows wheels on the previous release. This patch release restores Windows distribution along with other changes to make our uploads to PyPI more reliable.

What's Changed

• Fix def grad windows by @cookpa in #828
• Pypi workflow by @cookpa in #829

Full Changelog: v0.6.0...v0.6.1

Aesculus

Quite a few changes in this one, including SimpleITK compatibility, optimizations to improve performance in registration, and bug fixes for Jacobian calculation.

The main new functionality is the label image registration from @ntustison

Thanks to all contributors

What's Changed

• COMP: version bump by @cookpa in #722
• WIP: Fix nanobind memory leaks by @cookpa in #734
• DOC: explain reg transform options by @cookpa in #735
• DOC: example typo by @cookpa in #736
• Build template: delete temporary files by @dyollb in #731
• ENH: Throw exception if image cannot be read by @cookpa in #738
• add SimpleITK.Image to ANTsImage conversion by @dyollb in #726
• DOC: initial transform option by @cookpa in #739
• ENH: Add label iamge registration and tests. by @ntustison in #743
• Make precision (--float) configurable for registration by @evertdeman in #741
• ENH: Test reg precision by @cookpa in #744
• Update mac runner by @cookpa in #745
• BUG: Python str objects don't have astype() by @cookpa in #746
• ENH: Prevent pandas type conversion warning by @cookpa in #748
• COMP: Bump ITK for Windows by @cookpa in #750
• ENH: Change variable name by @ntustison in #751
• ENH: Add functionality for specifying def. xfrm by @ntustison in #752
• WIP: Don't do COM initialization for "syn-only" reg by @cookpa in #757
• DOC: Windows runtime requirements by @cookpa in #759
• DOC: Update conf.py by @cookpa in #756
• ENH: Add explicit identity linear transform. by @ntustison in #761
• Allow numpy datatypes in image_clone by @cookpa in #765
• Neatened things up to be more reader-friendly by @DeanTM in #766
• ENH: Change gradient and radius defaults. by @ntustison in #770
• Turn off hard-coded histogram matching in registration by @cookpa in #768
• No swap numpy dims by @cookpa in #774
• fix: vertical line (xyz-lines) in sagittal image of plot_ortho is flipped by @sai8951 in #762
• fix: vertical line in sagittal view is flipped by @sai8951 in #763
• Fix mac wheels by @cookpa in #749
• BUG: Fix some logic issues. by @ntustison in #777
• ENH: Update ITK Tag. by @ntustison in #778
• ENH: Prevent attempts to iterate over antsImage by @cookpa in #780
• Update ants by @cookpa in #782
• CI: Python 3.13 wheels by @cookpa in #785
• Label geom test by @cookpa in #784
• CI: Build all the wheels weekly by @cookpa in #786
• STYLE: Clean up old build files by @cookpa in #788
• COMP: Update Windows ITK to match others by @cookpa in #789
• DOC: Registration usage by @cookpa in #792
• BUG: Fix logic by @ntustison in #793
• ENH: Subsume typeOfLinearTransform in initialTransforms. by @ntustison in #794
• COMP: Nanobind version limit for older Python by @cookpa in #796
• Probable typo in docstring by @arovai in #799
• CI: Send all wheels to pypi by @cookpa in #800
• ENH: Migrate ANTsPyNet functionality by @ntustison in #802
• DOC: Adding all to get functions added to documentation by @cookpa in #804
• COMP: Install SimpleITK to test by @cookpa in #805
• More sitk imports and tests by @cookpa in #806
• CI: Pin simpleitk to 2.4.1 for Linux, seems 2.5.0 doesn't build by @cookpa in #807
• ENH: one-hot xfrms by @ntustison in #808
• ENH: Remove deprecated variable. by @ntustison in #809
• COMP: Allow modern numpy by @cookpa in #816
• added conda installation instructions by @sarthakpati in #815
• DOC: Updating broken links in README by @lankabelgezogen in #817
• ENH: Add polar decomposition and convergence monitoring. by @ntustison in #819
• ENH: Non-symmetrization. by @ntustison in #820
• COMP: don't use latest scipy by @cookpa in #825
• Jacobian fixes by @cookpa in #823
• ENH: Expand jacobian tests by @cookpa in #826
• COMP: Version bump for release by @cookpa in #801

New Contributors

• @dyollb made their first contribution in #731
• @evertdeman made their first contribution in #741
• @DeanTM made their first contribution in #766
• @sai8951 made their first contribution in #762
• @arovai made their first contribution in #799
• @sarthakpati made their first contribution in #815
• @lankabelgezogen made their first contribution in #817

Full Changelog: v0.5.4...v0.6.0

Acer

Improved compile time optimization makes speed of ANTsPy operations much closer to the comparable command-line ANTs call.

Various bug fixes including adding ants.ANTsImage back to the namespace.

What's Changed

• ENH: Add ants.ANTsImage back to namespace by @cookpa in #700
• CI: Push more wheels to pypi, document Mac compatibility issues by @cookpa in #697
• COMP: downgrade numpy for arm64 by @cookpa in #702
• ENH: Default to 2 voxel radius for denoise_image.py by @cookpa in #704
• PERF: more optimization at compile time by @cookpa in #705
• DISP: Address pd warning. by @ntustison in #713
• BUG: label_image_centroids only worked with sequential labels 1..N by @cookpa in #714
• DOC: remove reference to ants/lib which no longer exists by @cookpa in #720
• BUG: Fix slicing. More consistent with numpy by @cookpa in #721

Full Changelog: v0.5.3...v0.5.4

Sassafras

Big computational changes in this release: the move from pybind11 to nanobind massively reduces wheel size, which makes for faster builds and will enable us to keep more releases on pypi.

What's Changed

• ENH: support resampling multi-channel images by @ncullen93 in #609
• DOC: document reg initial transform by @cookpa in #616
• update tests; remove contrib by @ncullen93 in #618
• add more tests by @ncullen93 in #619
• Add tests; Remove labelimage + invariant image similarity by @ncullen93 in #620
• ENH: move c++ wrapping from pybind11 to nanobind by @ncullen93 in #621
• CLEAN: remove unused top files and update readme by @ncullen93 in #623
• FIX: overlay plot background is masked by @ncullen93 in #631
• ENH: Update CI and scikit-build-core by @cookpa in #628
• ENH: initialize ANTsImage with pointer only by @ncullen93 in #634
• ENH: check for transform instance before writing to file by @ncullen93 in #636
• Ants read warp transform by @cookpa in #638
• ENH: simpler imports, image decorator, and better code organization by @ncullen93 in #637
• DOCS: update docs by @ncullen93 in #640
• ENH: Verbose tests by @cookpa in #639
• FIX: remove listfunc from `matrix_to_image´ by @ncullen93 in #642
• DOC: Clarify return type of apply_transforms by @cookpa in #644
• FIX: image indexing returns image where possible by @ncullen93 in #645
• ENH: Threshold mask in images_to_matrix by @cookpa in #646
• ENH: Hoping to stop the windows access violation errors by @cookpa in #647
• ENH: support 2d images on slice_image function by @ncullen93 in #649
• FIX: new_image_like arg typo by @ncullen93 in #650
• FIX: compose multi type transforms by @ncullen93 in #652
• Fix: raise for bad slice axis; ENH: support slicing vector images by @ncullen93 in #653
• CI: Trying to use bash on windows by @cookpa in #654
• ENH: squeeze data_weights if necessary by @ncullen93 in #656
• ENH: support channels first for vector images by @ncullen93 in #657
• DOC: Fix license by @cookpa in #659
• ENH: support pickle and deepcopy for images by @ncullen93 in #658
• BUG: Return variable. by @ntustison in #661
• TESTS: add test for bspline zeros bug by @ncullen93 in #662
• TESTS: expand tests for ops and plotting by @ncullen93 in #663
• FIX: cast unsupported numpy dtypes in ants.from_numpy() by @ncullen93 in #665
• ENH: crop vector images by @ncullen93 in #669
• COMP: Docker build suddenly stopped working, needs classic solver by @cookpa in #673
• BUG: Remove deprecated np.math by @cookpa in #674
• CI: Update action versions by @cookpa in #675
• CI: Don't push PRs to dockerhub by @cookpa in #677
• ENH: Update cibuildwheel linux by @cookpa in #679
• WIP: import hessian objectness itk filter. by @ntustison in #681
• ENH: Add hessian objectness test. by @ntustison in #682
• BUG: fix paste error from R, arg is type_of_transform by @cookpa in #687
• Update test_core_ants_image.py by @cookpa in #689
• fix typo in affine_initializer() by @FeynmanDNA in #690
• CI: Update Dockerfile by @cookpa in #691
• Fix apply transform to image by @cookpa in #692

New Contributors

• @FeynmanDNA made their first contribution in #690

Full Changelog: v0.5.2...v0.5.3

Alder

Fixes incorrect version information in version 0.5.1. Changelog here shown relative to 0.5.0.

What's Changed

• ENH: Multiple CI changes by @cookpa in #580
• Use double precision by default in apply_transforms computations by @cookpa in #585
• BUG: Overly strict floating point test by @cookpa in #587
• ENH: Reset index after ITK filters, keep ITK object and python interface consistent by @cookpa in #588
• ENH: Bump ITK and ANTs, initialize all memory allocated for images by @cookpa in #590
• ENH: Update coveralls version by @cookpa in #592
• ENH: Use XML for coverage by @cookpa in #593
• ENH: Test coverage on PRs by @cookpa in #595
• BUG: Cache key had wrong path to config scripts by @cookpa in #599
• ENH: Version bump to fix imath segfault by @cookpa in #598
• ENH: Add Mattes. by @ntustison in #603
• ENH: Add masked/bspline fitting variant of Nyul histogram matching. by @ntustison in #607
• FIX: remove plot_ortho return statement by @ncullen93 in #608

Full Changelog: v0.5.0...v0.5.2

Birkenshaw

EDIT: Apologies for the incorrect version information in the wheels below. Please update to 0.5.2.

This is a bug fix release. ITK and ANTs are updated to fix intermittent errors caused by uninitialized memory (see #579 and #583).

The apply_transforms function now uses double precision by default, to avoid lossy resampling of Allen brain atlas labels.

What's Changed

• ENH: Multiple CI changes by @cookpa in #580
• Use double precision by default in apply_transforms computations by @cookpa in #585
• BUG: Overly strict floating point test by @cookpa in #587
• ENH: Reset index after ITK filters, keep ITK object and python interface consistent by @cookpa in #588
• ENH: Bump ITK and ANTs, initialize all memory allocated for images by @cookpa in #590
• ENH: Update coveralls version by @cookpa in #592
• ENH: Use XML for coverage by @cookpa in #593
• ENH: Test coverage on PRs by @cookpa in #595
• BUG: Cache key had wrong path to config scripts by @cookpa in #599
• ENH: Version bump to fix imath segfault by @cookpa in #598

Full Changelog: v0.5.0...v0.5.1

Meadow

ITK and ANTs library updates, and many improvements including boosts to test coverage, visualization fixes, and documentation.

Summary by @ncullen93:

improved testing
minor bug fixes
minor documentation improvements
upgrade to latest ANTs and ITK version
removed deprecated code (VTK-related visualization)
Things to accomplish during v0.5.x

rework docs and tutorials (to ants.dev)
reduce build size
refactor ants.plot function to be simpler
speed up import time (by deferring imports?)

What's Changed

• Affine updates by @seogier in #505
• STYLE: Remove unused CLI mangling code by @cookpa in #516
• COMP: Add support for Python 3.12 by @ravnoor in #510
• Update configure_ANTsPy.sh by @crossmanith in #523
• ENH: allow setting of fixed_parameters when creating a transform by @cookpa in #526
• DOC: Update aff_sampling docstring in interface.py by @dzenanz in #529
• make interpolation case-insensitive by @ncullen93 in #534
• Explicit imports by @ncullen93 in #533
• update reg docs by @ncullen93 in #535
• remove all R_PACKAGE_LIB refs by @ncullen93 in #537
• ENH: Histogram equalization by @ntustison in #539
• Code cov by @ncullen93 in #541
• ENH: allow workflow dispatch by @cookpa in #543
• ENH: Don't need extra parameter for branch by @cookpa in #545
• rightside ops by @ncullen93 in #547
• ENH: Support different segmentation labels in kelly_kapowski by @cookpa in #548
• Test viz png by @cookpa in #551
• ENH: More specific error messages if atropos fails by @cookpa in #556
• DOC: Update issue template by @cookpa in #558
• ENH: ARM64 builds by @cookpa in #557
• ENH: Coordinate with other n4 usage. by @ntustison in #560
• fix small doc typo by @ncullen93 in #563
• fix issue with plotting negative-sum images by @ncullen93 in #562
• change required slice_image args by @ncullen93 in #565
• COMP: Debugging output in runners by @cookpa in #564
• BUG: Check for zero image in plot by @cookpa in #566
• ENH: avoid kelly_kapowski returning GMP by @cookpa in #561
• Add more plotting tests by @ncullen93 in #568
• test plot grid and support 2d images by @ncullen93 in #569
• allow decrop_image to be chained by @ncullen93 in #571

New Contributors

• @crossmanith made their first contribution in #523
• @dzenanz made their first contribution in #529

Full Changelog: v0.4.2...v0.5.0

Cascade

What's Changed

• Generate python 3.11 wheels by @tfmoraes in #445
• WIP: attach wheels to releases by @cookpa in #444
• Support for a slightly more flexible use of masks by @azylbertal in #450
• ENH: Registration masks use all voxels != 0 by @cookpa in #456
• ENH: default n3 / n4 spline mesh size of 1 by @cookpa in #457
• updated build_template with affine shape correction by @richardbeare in #459
• ENH: Add thin-plate splines. by @ntustison in #460
• BUG: Typo by @ntustison in #462
• ENH: Make pcasl available in get_ants_data by @ntustison in #465
• Rewrite Windows tests by @cookpa in #469
• Feat/cbar for ortho plot by @gladomat in #473
• ENH: Support vector images stored as double by @cookpa in #474
• ENH: applytransforms: dont force compose as nii.gz by @MSco in #476
• ENH: Add initial velocity field capabilities. by @ntustison in #477
• Similarity option typo made "ANTSNeighborhoodCorrelation" unreachable by @cookpa in #480
• COMP: Migrate RTD to new config by @cookpa in #483
• ENH: Allow multiple initial transforms by @cookpa in #488
• ENH: Update ANTs git tag. by @ntustison in #489
• corrected docstrings for affine transformations by @seogier in #492

New Contributors

• @azylbertal made their first contribution in #450
• @richardbeare made their first contribution in #459
• @gladomat made their first contribution in #473
• @MSco made their first contribution in #476

Full Changelog: v0.3.8...v0.4.2