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cucim 24.12.00 (11 Dec 2024)

🚨 Breaking Changes

  • Deprecations: carry out removals scheduled for release 24.12 (#786) @grlee77

🛠️ Improvements

  • allow path conflicts in conda builds (#801) @jameslamb
  • enforce wheel size limits, README formatting in CI (#797) @jameslamb
  • build wheels without build isolation, print sccache stats in builds (#792) @jameslamb
  • make conda installs in CI stricter (#791) @jameslamb
  • Deprecations: carry out removals scheduled for release 24.12 (#786) @grlee77

cucim 24.10.00 (9 Oct 2024)

🐛 Bug Fixes

  • Use cupy to measure memory leak (#777) @bdice
  • Fix wheel tests for Rocky Linux 8. (#774) @bdice
  • Disable custom 2D separable filtering kernels on windows (#770) @grlee77
  • chan_vese: pass all constants to _fused_variance_kernel2 as device scalars (#764) @grlee77
  • Fix "compatibility" spelling in CHANGELOG (#759) @jakirkham
  • Fix error in dependencies.yaml causing incomplete pyproject.toml generation (#757) @grlee77

🛠️ Improvements

cucim 24.08.00 (7 Aug 2024)

🛠️ Improvements

cucim 24.06.00 (5 Jun 2024)

🚨 Breaking Changes

  • The output argument of cucim.skimage.filters.gaussian has been renamed to out. The old name is deprecated and will be removed in release 25.02 (#727)
  • Renamed get_xyz_coords function is now removed (use skimage.color.xyz_tristimulus_values instead) (#724)
  • Removed deprecated return_error kwarg from phase_cross_correlation (the error is now always returned) (#724)
  • Removed deprecated random_state kwarg from medial_axis (it was renamed to rng previously) (#724)

🐛 Bug Fixes

  • Use SciPy's KDTree instead of deprecated cKDTree (#733) @grlee77
  • Binary and grayscale morphology functions have bug fixes in the case of even-sized/non-symmetric footprints (for details see upstream MR: scikit-image/scikit-image#6695) (#728)

🚀 New Features

  • cucim.skimage.measure.regionprops (and regionprops_table) support one new region property: intensity_std (#727)
  • cucim.skimage.segmentation.expand_labels now supports a spacing keyword argument to take a pixel's physical dimensions into account (#727)
  • binary morphology functions have a new mode argument that controls how values outside the image boundaries are interpreted (#728)
  • grayscale morphology functions have new mode and cval arguments that control how boundaries are extended (#728)

🛠️ Improvements

  • Enable FutureWarnings/DeprecationWarnings as errors (#734) @mroeschke
  • Migrate to {{ stdlib("c") }} (#731) @hcho3
  • Implement upstream changes from scikit-image 0.23 (part 2 of 2: morphology) (#728) @grlee77
  • Implement upstream changes from scikit-image 0.23 (part 1 of 2) (#727) @grlee77
  • Update the test criteria for test_read_random_region_cpu_memleak (#726) @gigony
  • Remove code needed to support Python < 3.9 and apply ruff's pyupgrade rules (#725) @grlee77
  • removal of deprecated functions/kwargs scheduled for release 24.06 (#724) @grlee77
  • Enable all tests for arm jobs (#717) @galipremsagar
  • prevent path conflict (#713) @AyodeAwe
  • Updated cuCIM APIs for consistency with scikit-image 0.23.2 (#727 and #728)
  • Additional modules use __init__.pyi instead of just __init__.py (#727)
  • Some grayscale tests now compare directly to skimage CPU outputs instead fetching previously saved values (#728)
  • Refactored some test cases to better use pytest.mark.parametrize (#728)
  • Bumped version pinning for scikit-image to allow 0.23.x to be installed (#728)

📖 Documentation

  • Various fixes to documentation strings (consistent shape notation, etc.) (#727)

cuCIM 24.04.00 (10 Apr 2024)

🐛 Bug Fixes

🚀 New Features

🛠️ Improvements

cuCIM 24.02.00 (12 Feb 2024)

🐛 Bug Fixes

🛠️ Improvements

cuCIM 23.12.00 (6 Dec 2023)

🐛 Bug Fixes

🚀 New Features

🛠️ Improvements

  • carry out removals of previously deprecated functions/kwargs (#631) @grlee77
  • Improve memory leak check stability in test_read_region_cpu_memleak test (#623) @gigony
  • Update linting tool versions and replace isort with ruff (#622) @grlee77
  • Update packages (pybind11 and catch2) and do not use nvidia-docker command (#618) @gigony
  • Replace setup.py with pyproject toml (#617) @grlee77
  • update linters and move their configurations from setup.cfg to pyproject.toml (#616) @grlee77
  • remove versioneer (#615) @grlee77
  • Update shared-action-workflows references (#614) @AyodeAwe
  • Use branch-23.12 workflows. (#613) @bdice
  • cucim: Build CUDA 12.0 ARM conda packages. (#610) @bdice

cuCIM 23.10.00 (11 Oct 2023)

🐛 Bug Fixes

  • Use conda mambabuild not mamba mambabuild (#607) @bdice

📖 Documentation

🛠️ Improvements

cuCIM 23.08.00 (9 Aug 2023)

🚨 Breaking Changes

  • Sync cuCIM API with scikit-image 0.21 (#573) @grlee77
  • The random_state argument of medial_axis and unsupervised_wiener is now deprecated and will be removed in the future. The new argument name, seed, should be used instead. (#573) @grlee77
  • The existing function cucim.skimage.color.get_xyz_coords has been renamed cucim.skimage.color.xyz_tristimulus_values. The former function name is deprecated and will be removed in the future. (#573) @grlee77

🐛 Bug Fixes

  • Remove libwebp-base upper bound. (#599) @bdice
  • Fix ignore_run_exports_from. (#596) @bdice
  • Add ignore_run_exports for CUDA 11 (#593) @raydouglass
  • Use linalg & inline _get_manders_overlap_coeff (#578) @jakirkham
  • Fix canny and butterworth (recent CuPy and NumPy compatibility) (#574) @grlee77
  • A bug was fixed in 2D shear calculations for AffineTransform. (#573) @grlee77
  • A bug was fixed in the energy calculation of cucim.skimage.segmentation.chan_vese. This fix may result in different output from previous versions. (#573) @grlee77

🛠️ Improvements

  • The formerly private function _invariant_denoise has been renamed denoise_invariant and is now part of the public cucim.skimage.restoration API (#573) @grlee77
  • A new return_mapping option was added to cucim.skimage.segmentation.join_segmentations. This provides an additional output with a mapping between the labels in the joined segmentation and the original ones. (#573) @grlee77
  • Added support for y-axis shear to the 2D AffineTransform. (#573) @grlee77
  • Postponed the assessment of GPU memory for testing (#601) @gigony
  • Do not use x86_64 GDS binaries for aarch64 (#590) @gigony
  • remove checks for versions of scikit-image that are no longer supported (#587) @grlee77
  • Allow scikit-image 0.21.0 (#580) @jakirkham
  • Drop unneeded selector on libwebp-base (#579) @jakirkham
  • switch from bundled lazy loading code to the public lazy_loader package (#575) @grlee77
  • Sync cuCIM API with scikit-image 0.21 (#573) @grlee77
  • cuCIM: Build CUDA 12 packages (#572) @jakirkham
  • use rapids-upload-docs script (#570) @AyodeAwe
  • Remove documentation build scripts for Jenkins (#567) @ajschmidt8

cuCIM 23.06.00 (7 Jun 2023)

🚨 Breaking Changes

🐛 Bug Fixes

  • Fix SHA256 check failure in test suite (#564) @grlee77
  • Handle space character in ./run download_testdata (#556) @gigony
  • Fix return_error=&#39;always&#39; behavior in phase_cross_correlation (#549) @grlee77
  • Only load versioned libcufile (#548) @jakirkham
  • add a 20 minute timeout for pytest runs on CI (#545) @grlee77
  • protect against possible out of bounds memory access in 2D distance transform (#540) @grlee77

📖 Documentation

  • Fix doc building via run build_package (#553) @grlee77
  • update changelog for release 23.04.00 and 23.04.01 (#552) @grlee77

🛠️ Improvements

cuCIM 23.04.01 (14 Apr 2023)

🛠️ Improvements

cuCIM 23.04.00 (6 Apr 2023)

🚨 Breaking Changes

  • Fix inefficiency in handling clipping of image range in resize and other transforms (#516) @grlee77

🐛 Bug Fixes

  • Fix bug in median filter with non-uniform footprint (#521) @grlee77
  • use cp.around instead of cp.round for CuPy 10.x compatibility (#508) @grlee77
  • Fix error in LZ4-compressed Zarr writing demo (#506) @grlee77
  • Normalize whitespace. (#474) @bdice

🛠️ Improvements

cuCIM 23.02.00 (9 Feb 2023)

🚨 Breaking Changes

  • Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) (#486) @grlee77

🐛 Bug Fixes

📖 Documentation

🚀 New Features

  • Add colocalization measures (#488) @grlee77
  • Add disambiguation option to phase_cross_correlation (skimage 0.20 feature) (#486) @grlee77

🛠️ Improvements

cuCIM 22.12.00 (8 Dec 2022)

🚨 Breaking Changes

  • Implement additional deprecations carried out for scikit-image 0.20 (#451) @grlee77
  • improved implementation of ridge filters (bug fixes and reduced memory footprint) (#423) @grlee77

🐛 Bug Fixes

  • pin to cmake !3.25.0 on CI to avoid bug with CUDA+conda during build (#444) @grlee77
  • update incorrect argument and deprecated function for tifffile.TiffWriter (#433) @JoohyungLee0106
  • Fix rotate behavior for ndim > 2 (#432) @grlee77

📖 Documentation

  • add whole-slide tiled read/write demos for measuring GPUDirect Storage (GDS) I/O performance (#452) @grlee77
  • Add demo for distance_transform_edt (#394) @grlee77

🚀 New Features

  • Support no-compression method in converter (#443) @gigony
  • add three segmentation metrics (#425) @grlee77
  • add isotropic binary morphology functions (#421) @grlee77
  • Add blob feature detectors (blob_dog, blob_log, blob_doh) (#413) @monzelr

🛠️ Improvements

  • additional minor updates (skimage 0.20) (#455) @grlee77
  • Implement additional deprecations carried out for scikit-image 0.20 (#451) @grlee77
  • Faster hessian_matrix_* and structure_tensor_eigvals via analytical eigenvalues for the 3D case (#434) @grlee77
  • use fused kernels to reduce overhead in corner detector implementations (#426) @grlee77
  • Misc updates for consistency with scikit-image 0.20 (#424) @grlee77
  • improved implementation of ridge filters (bug fixes and reduced memory footprint) (#423) @grlee77
  • analytical moments computations, support pixel spacings in moments and regionprops (#422) @grlee77
  • Forward merge branch-22.10 to branch-22.12 (#420) @grlee77
  • Support sampling kwarg for distance_transform_edt (take pixel/voxel sizes into account) (#407) @grlee77
  • Improve performance of Euclidean distance transform (#406) @grlee77

cuCIM 22.10.00 (12 Oct 2022)

🐛 Bug Fixes

  • Correctly use dtype when computing shared memory requirements of separable convolution (#409) @grlee77
  • Forward-merge branch-22.08 to branch-22.10 (#403) @jakirkham
  • Add missing imports of euler_number and perimeter_crofton (#386) @grlee77

📖 Documentation

🚀 New Features

🛠️ Improvements

cuCIM 22.08.00 (17 Aug 2022)

🚨 Breaking Changes

  • Stain extraction: use a less strict condition across channels when thresholding (#316) @grlee77

🐛 Bug Fixes

  • create SimilarityTransform using CuPy 9.x-compatible indexing (#365) @grlee77
  • Add __init__.py in cucim.core (#359) @jakirkham
  • Stain extraction: use a less strict condition across channels when thresholding (#316) @grlee77
  • Incorporate bug fixes from skimage 0.19.3 (#312) @grlee77
  • fix RawKernel bug for canny filter when quantiles are used (#310) @grlee77

📖 Documentation

🚀 New Features

  • Add segmentation with the Chan-Vese active contours method (#343) @grlee77
  • Add cucim.skimage.morphology.medial_axis (#342) @grlee77
  • Add cucim.skimage.segmentation.expand_labels (#341) @grlee77
  • Add Euclidean distance transform for images/volumes (#318) @grlee77

🛠️ Improvements

cuCIM 22.06.00 (7 Jun 2022)

🚨 Breaking Changes

  • Promote small integer types to single rather than double precision (#278) @grlee77

🐛 Bug Fixes

📖 Documentation

🚀 New Features

  • add missing cucim.skimage.segmentation.clear_border function (#267) @grlee77
  • add cucim.core.operations.color.stain_extraction_pca and cucim.core.operations.color.normalize_colors_pca for digital pathology H&E stain extraction and normalization (#273) @grlee77, @drbeh

🛠️ Improvements

cuCIM 22.04.00 (6 Apr 2022)

🚨 Breaking Changes

  • Apply fixes to skimage.transform scheduled for scikit-image 0.19.2 (#208) @grlee77

🐛 Bug Fixes

📖 Documentation

🛠️ Improvements

cuCIM 22.02.00 (2 Feb 2022)

🚨 Breaking Changes

  • Update cucim.skimage API to match scikit-image 0.19 (#190) @glee77

🐛 Bug Fixes

  • Fix a bug in v21.12.01 (#191) @gigony
    • Fix GPU memory leak when using nvJPEG API (when device='cuda' parameter is used in read_region method).
  • Fix segfault for preferred_memory_capacity in Python 3.9+ (#214) @gigony

📖 Documentation

🚀 New Features

  • Update cucim.skimage API to match scikit-image 0.19 (#190) @glee77
  • Support multi-threads and batch, and support nvJPEG for JPEG-compressed images (#191) @gigony
  • Allow CuPy 10 (#195) @jakikham

🛠️ Improvements

cuCIM 21.12.00 (9 Dec 2021)

🚀 New Features

🐛 Bug Fixes

📖 Documentation

🛠️ Improvements

cuCIM 21.10.00 (7 Oct 2021)

🐛 Bug Fixes

📖 Documentation

  • Forward-merge branch-21.08 to branch-21.10 (#88) @jakirkham
  • Update PyPI cuCIM v21.08.01 README.md and CHANGELOG.md (#87) @gigony

🚀 New Features

  • Support raw RGB tiled TIFF (#108) @gigony
  • Add a mechanism for user to know the availability of cucim.CuImage (#107) @gigony
  • Enable GDS and Support Runtime Context (enter, exit) for CuFileDriver and CuImage (#106) @gigony
  • Add transforms for Digital Pathology (#100) @shekhardw

🛠️ Improvements

cuCIM 21.08.00 (4 Aug 2021)

🐛 Bug Fixes

  • Remove int-type bug on Windows in skimage.measure.label (#72) @grlee77
  • Fix missing array interface for associated_image() (#65) @gigony
  • Handle zero-padding version string (#59) @gigony
  • Remove invalid conda environment activation (#58) @ajschmidt8

📖 Documentation

🚀 New Features

🛠️ Improvements

  • Add SciPy 2021 to README (#79) @jakirkham
  • Use more descriptive ElementwiseKernel names in cucim.skimage (#75) @grlee77
  • Add initial Python unit/performance tests for TIFF loader module (#62) @gigony
  • Fix 21.08 forward-merge conflicts (#57) @ajschmidt8

cuCIM 21.06.00 (9 Jun 2021)

🐛 Bug Fixes

🛠️ Improvements

cuCIM 0.19.0 (15 Apr 2021)

  • Initial release of cuCIM including cuClaraImage and cupyimg.