Recent Releases of hf-deepali

hf-deepali - 0.6.4

What's Changed

enh: Adopt axisangle naming instead of angleaxis from newer kornia versions by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/160
fix: Import of joinkwargsin_sequence in FFD example by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/156
fix: Replace use of deprecated pkg_resources by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/158
fix: Linter a few warnings by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/159
fix: Rotation applied in surfaceimagestencil() based on image orientation by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/147
doc: Replace HeartFlow by Heartflow by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/161
ci: First publish to Test PyPI without attestations by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/151
ci: Update GitHub actions of workflow to publish docs by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/157

Full Changelog: https://github.com/BioMedIA/deepali/compare/0.6.3...0.6.4

- Python
Published by aschuh-hf 7 months ago

hf-deepali - 0.6.3

What's Changed

[core] Multiply input by 'scale' even when 'steps=0' in expv() by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/144
[utils] Support MetaImage files with unspecified HeaderSize by @sgerber-hf in https://github.com/BioMedIA/deepali/pull/149
[doc] Add TorchIR to list of related projects by @aschuh-hf in https://github.com/BioMedIA/deepali/pull/146

New Contributors

@sgerber-hf made their first contribution in https://github.com/BioMedIA/deepali/pull/149

Full Changelog: https://github.com/BioMedIA/deepali/compare/0.6.2...0.6.3

- Python
Published by aschuh-hf over 1 year ago

hf-deepali - 0.6.2

Maintenance release.

[losses] Fix MI loss to allow sample ratio of 1 (#139)
[doc] Fix regularization weights of pairwise registration tutorial (#142)
[ci] Update used GitHub actions to latest versions using Node.js 20 (#143)

- Python
Published by aschuh-hf about 2 years ago

hf-deepali - 0.6.1

[core] Fix spatial derivatives when using mode="bspline" or mode="gaussian" (#135).
[core] Rename SpatialDerivativeKeys all() and unmixed() argument ndim to spatial_dims (#132).
[data] Fix exception when passing a FlowFields batch tensor to F.grid_sample() (#134).
[losses] Add spacing option to flow field loss modules (#136).
[spatial] Reverse stride order when subsampling DenseVectorFieldTransform (#133).

- Python
Published by aschuh-hf about 2 years ago

hf-deepali - 0.6.0

Modify mi_loss() to allow use of num_samples to limit maximum number when using a sample_ratio (#121).
Ensure Gaussian kernel tensor is 1-dimensional even when sigma=0 (#122).
Fix compose_flows() to compute composite displacement field (#128, #129).
Add compose_svfs() to compose velocity fields using Baker-Campbell-Hausdorff (BCH) formula (#129, #130).
Add lie_bracket() of vector fields which is required for BCH formula (#129).
Add logv(), the inverse map of expv(), based on the algorithm proposed by Bossa & Olsom (2008) (#131).
Switch from .vscode/ folder to deepali.code-workspace file (#123).

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.5.2

Maintenance release.

Fix calculation of flow field Jacobian determinant (#120).
Add add_identity option to jacobian_det() (#120).

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.5.1

Maintenance release.

[core] Ignore error in deepali.core.pathlib.delete() of failed deletion of non-empty directory
[utils] Fix check if path exists in deepali.utils.simpleitk.imageio.read_image()
[utils] Force pull file from cloud storage in deepali.utils.vtk.polydata.read_polydata()
[ci] Update action/checkout to v4

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.5.0

Maintenance release with some minor breaking changes.

Fix DataclassConfig.from_path() when argument is a URI (#111)
Fix and extend flow field derivative based losses (#117)
- Add flow_derivatives() with default spacing for finite differences assuming a normalized flow field.
- Add curl(), divergence(), and divergence_free_flow() functions to core library.
- Modify finite_differences() to pad input using replicate instead of padding output with zeros.
- Add mode='forward_central_backward' to avoid padding using replicate or constant values.
- Add mode='bspline' to spatial_derivatives().
- Generalize cubic_bspline_jacobian_*() to jacobian_*() functions for all mode values.
- Fix bending energy, curvature, and divergence loss functions.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.4.3

Maintenance release.

Move deepali.utils.storage module to deepali.core.
Add EulerRotation.matrix_() setter.
Add LogLevel convenience initialization methods.
Fix setting default log_level in configure_logging().
Fix flattening of direction cosines matrix in write_sitk_iamge().
Remove pyyaml dependency, only use ruamel.yaml instead.
Install conda-devenv and conda-lock in conda environment.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.4.2

Maintenance release.

Modified spatial.ImageTransformer to allow target grid domain to differ from transform.grid() domain.
Change image tensor creation functions to return non-batched image tensor when num=0 is passed.
Fix assertion condition when comparing data tensor shape to MetaImage DimSize metadata.
Fix torch.from_numpy() warning that NumPy array is read-only when reading MetaImage from data blob.
Fix circle_image() and cshape_image() functions used to create synthetic 2D registration example images.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.4.1

Minor refactoring of deepali.core and deepali.utils with a few breaking changes.

Renamed deepali.core.path to deepali.core.pathlib
- Moved functions make_temp_dir(), temp_dir(), and temp_file() to deepali.core.tempfile.
Renamed deepali.core.types to deepali.core.typing.
- Moved TensorCollections related functions to deepali.core.collections.
Move deepali.utils.cli modules to deepali.core such as
- deepali.core.argparse
- deepali.core.environ
- deepali.core.logging
Added deepali.utils.imageio library.
- If installed, use nibabel to read/write NIfTI images instead of SimpleITK.
- Support direct streaming of .mha MetaImage files from cloud storage (AWS S3).
- Keep using SimpleITK for all other image file formats.
Modified Image.read() and Image.write() methods to use deepali.utils.imageio library.
Use absolute imports between deepali.* packages, relative imports only within.
Added software citation using Zenodo.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.4.0

Minor refactoring of deepali.core and deepali.utils with a few breaking changes.

Renamed deepali.core.path to deepali.core.pathlib
- Moved functions make_temp_dir(), temp_dir(), and temp_file() to deepali.core.tempfile.
Renamed deepali.core.types to deepali.core.typing.
- Moved TensorCollections related functions to deepali.core.collections.
Move deepali.utils.cli modules to deepali.core such as
- deepali.core.argparse
- deepali.core.environ
- deepali.core.logging
Added deepali.utils.imageio library.
- If installed, use nibabel to read/write NIfTI images instead of SimpleITK.
- Support direct streaming of .mha MetaImage files from cloud storage (AWS S3).
- Keep using SimpleITK for all other image file formats.
Modified Image.read() and Image.write() methods to use deepali.utils.imageio library.
Use absolute imports between deepali.* packages, relative imports only within.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.3.2

Maintenance release with fix of ImageBatch.__getitem__ handling of int index along channel dimension. Includes support of more batch tensor indexing. Added an introductory tutorial notebook to walk through an image registration with different spatial transforms.

- Python
Published by aschuh-hf over 2 years ago

hf-deepali - 0.3.1

First release of the deepali library with upload of hf-deepali package to PyPI.

- Python
Published by aschuh-hf over 2 years ago