CHANGELOG.md

cuCIM 24.04.00 (10 Apr 2024)

🐛 Bug Fixes

• Require click as a wheel dependency (#719) @jakirkham
• Fix docs upload directory (#714) @raydouglass
• Fix popd indent in run (#693) @jakirkham
• Re-run ci/release/update-version.sh 24.04.00 (#690) @jakirkham

🚀 New Features

• Support CUDA 12.2 (#672) @jameslamb

🛠️ Improvements

• Use conda env create --yes instead of --force (#716) @bdice
• Add upper bound to prevent usage of NumPy 2 (#712) @bdice
• Remove hard-coding of RAPIDS version (#711) @KyleFromNVIDIA
• Switch pytest-xdist algorithm to worksteal (#708) @bdice
• Simplify version update script (#705) @jakirkham
• Add support for Python 3.11, require NumPy 1.23+ (#704) @jameslamb
• target branch-24.04 for GitHub Actions workflows (#702) @jameslamb
• Refactor CUDA libraries in dependencies.yaml (#699) @bdice
• Update ops-bot.yaml (#694) @AyodeAwe
• add rapids-dependency-file-generator pre-commmit hook (#682) @jameslamb

cuCIM 24.02.00 (12 Feb 2024)

🐛 Bug Fixes

• Fix CUDA trove classifiers & update README install instructions (#695) @jakirkham
• Exclude PyTest 8 (#689) @jakirkham
• Update OpenJPEG to 2.5.0 (#685) @jakirkham
• Fix CI (pt. 2) (#680) @jakirkham
• Fix CI issues (#676) @jakirkham
• Remove update to symlink (#674) @raydouglass
• Add 3rd party license file in Conda packages (#654) @jakirkham
• Fix style issue in docs/source/conf.py (#648) @jakirkham

🛠️ Improvements

• Consolidate test requirements in dependencies.yaml (#683) @jakirkham
• Remove usages of rapids-env-update (#673) @KyleFromNVIDIA
• refactor CUDA versions in dependencies.yaml (#671) @jameslamb
• minor updates/fixes for consistency with scikit-image 0.22 (#670) @grlee77
• Update CODEOWNERS (#669) @ajschmidt8
• remove redundant notebook (#668) @grlee77
• remove .idea folder (CLion IDE configuration) (#667) @grlee77
• Cleanup old ci and docs subfolders and related files under python/cucim (#666) @grlee77
• remove various files related to old wheel building mechanism (#665) @grlee77
• Relax openslide pin (#653) @jakirkham
• install imagecodecs and openslide-python dependencies so additional tests will run (#634) @grlee77

cuCIM 23.12.00 (6 Dec 2023)

🐛 Bug Fixes

• Retag wheels to be cpXY (#644) @jakirkham
• remove leftover pyproject_.toml file (#632) @grlee77
• update version string (e.g. for CHANGELOG link) in pyproject.toml (#630) @grlee77
• fix import order in test case (#624) @grlee77
• Standardize on rng over seed and fix miscellaneous deprecation warnings (#621) @grlee77
• Fix iterator-related memory issues (#620) @gigony

🚀 New Features

• build wheels on CI (#619) @grlee77

🛠️ 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

• minor updates to release 23.08 changelog (#605) @grlee77

🛠️ Improvements

• Update image names (#609) @AyodeAwe
• Use copy-pr-bot (#606) @ajschmidt8

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

• Support Python 3.9 build/tests (#547) @shwina

🐛 Bug Fixes

• Fix SHA256 check failure in test suite (#564) @grlee77
• Handle space character in ./run download_testdata (#556) @gigony
• Fix return_error='always' 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

• Allow numpy 1.24. (#563) @bdice
• run docs nightly too (#560) @AyodeAwe
• Update cupy dependency (#558) @vyasr
• Remove libjpeg dependency (#557) @gigony
• Enable sccache hits from local builds (#551) @AyodeAwe
• Revert shared workflows branch (#550) @ajschmidt8
• Support Python 3.9 build/tests (#547) @shwina
• Remove usage of rapids-get-rapids-version-from-git (#546) @jjacobelli
• Use ARC V2 self-hosted runners for GPU jobs (#538) @jjacobelli
• Remove underscore in build string. (#528) @bdice

cuCIM 23.04.01 (14 Apr 2023)

🛠️ Improvements

• Pin libwebp-base (#541) @ajschmidt8

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

• allow scikit-image 0.20 as well (#536) @grlee77
• Pass AWS_SESSION_TOKEN and SCCACHE_S3_USE_SSL vars to conda build (#525) @ajschmidt8
• Update aarch64 to GCC 11 (#524) @bdice
• Update to GCC 11 (#522) @bdice
• Upgrade dockcross and pybind11 (#519) @gigony
• Binary morphology: omit weights array when possible (#517) @grlee77
• Fix inefficiency in handling clipping of image range in resize and other transforms (#516) @grlee77
• Fix GHA build workflow (#515) @AjayThorve
• Reduce error handling verbosity in CI tests scripts (#511) @AjayThorve
• Update shared workflow branches (#510) @ajschmidt8
• Remove gpuCI scripts. (#505) @bdice
• Move date to build string in conda recipe (#497) @ajschmidt8

cuCIM 23.02.00 (9 Feb 2023)

🚨 Breaking Changes

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

🐛 Bug Fixes

• apply bug fix to vendored ndimage code (#494) @grlee77
• Closes #490 -- fixes bug in hue jitter (#491) @benlansdell
• Fix random seed used in test_3d_similarity_estimation (#472) @grlee77

📖 Documentation

• Fix documentation author (#475) @bdice

🚀 New Features

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

🛠️ Improvements

• Update shared workflow branches (#501) @ajschmidt8
• Update isort version to 5.12.0 (#492) @ajschmidt8
• Improve rank filtering performance by removing use of footprint kernel when possible (#485) @grlee77
• use vendored version of cupy.pad with added performance optimizations (#482) @grlee77
• add docs builds to Github Actions (#481) @AjayThorve
• Update numpy version specifier (#480) @ajschmidt8
• Build CUDA 11.8 and Python 3.10 Packages (#476) @ajschmidt8
• Add GitHub Actions Workflows. (#471) @bdice
• Fix conflicts in "Forward-merge branch-22.12 to branch-23.02" (#468) @jakirkham
• Enable copy_prs. (#465) @bdice

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

• update pypi CHANGELOG.md for releases 22.08.00 and 22.08.01 (#404) @grlee77
• Update README.md (#396) @HesAnEasyCoder

🚀 New Features

• Allow cupy 11 (#399) @galipremsagar
• Add cucim.skimage.feature.match_descriptors (#338) @grlee77

🛠️ Improvements

• Merge docs and add links (#415) @jakirkham
• Add benchmarks for scikit-image functions introduced in 22.08 (#378) @grlee77

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

• Defer loading of custom.js (#383) @galipremsagar
• add cucim.core.morphology to API docs + other docstring fixes (#367) @grlee77
• Update README.md (#361) @HesAnEasyCoder
• remove unimplemented functions from See Also and fix version numbers in deprecation warnings (#356) @grlee77
• Forward-merge branch-22.06 to branch-22.08 (#344) @grlee77
• Update README.md (#315) @HesAnEasyCoder
• Update index.rst (#314) @HesAnEasyCoder
• Update PyPI package documentation for v22.06.00 (#311) @gigony

🚀 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

• Revert "Allow CuPy 11" (#362) @galipremsagar
• Fix issues with day & night modes in python docs (#360) @galipremsagar
• Allow CuPy 11 (#357) @jakirkham
• more efficient separable convolution (#355) @grlee77
• Support resolution and spacing metadata (#349) @gigony
• Performance optimizations to morphological segmentation functions (#340) @grlee77
• benchmarks: avoid use of deprecated pandas API (#339) @grlee77
• Reduce memory overhead and improve performance of normalize_colors_pca (#328) @grlee77
• Protect against obscure divide by zero error in edge case of normalize_colors_pca (#327) @grlee77
• complete parametrization of cucim.skimage benchmarks (#324) @grlee77
• parameterization of filters and features benchmarks (v2) (#322) @grlee77
• Add a fast histogram-based median filter (#317) @grlee77
• Remove custom compiler environment variables (#307) @ajschmidt8

cuCIM 22.06.00 (7 Jun 2022)

🚨 Breaking Changes

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

🐛 Bug Fixes

• Populate correct channel names for RGBA image (#294) @gigony
• Merge branch-22.04 into branch-22.06 (#258) @jakirkham

📖 Documentation

• update outdated links to example data (#289) @grlee77
• Add missing API docs (#275) @grlee77

🚀 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

• Update to use DLPack v0.6 (#295) @gigony
• Remove plugin-related messages temporarily (#291) @gigony
• Simplify recipes (#286) @Ethyling
• Use cupy.fuse to improve efficiency hessian_matrix_eigvals (#280) @grlee77
• Promote small integer types to single rather than double precision (#278) @grlee77
• improve efficiency of histogram-based thresholding functions (#276) @grlee77
• Remove unused dependencies in GPU tests job (#268) @Ethyling
• Enable footprint decomposition for morphology (#274) @grlee77
• Use conda compilers (#232) @Ethyling
• Build packages using mambabuild (#216) @Ethyling

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

• Fix ImportError from vendored code (#252) @grlee77
• Fix wrong dimension in metadata (#248) @gigony
• Handle file descriptor ownership and update documents for GDS (#234) @gigony
• Check nullptr of handler in CuFileDriver::close() (#229) @gigony
• Fix docs builds (#218) @ajschmidt8
• Apply fixes to skimage.transform scheduled for scikit-image 0.19.2 (#208) @grlee77

📖 Documentation

• Update PyPI cuCIM v22.02.01 CHANGELOG.md (#249) @gigony
• Update GTC 2021 Spring video links (#227) @gigony
• Update documents for v22.02.00 (#226) @gigony
• Merge branch-22.02 into branch-22.04 (#220) @jakirkham

🛠️ Improvements

• Expose data type of CuImage object for interoperability with NumPy (#246) @gigony
• Temporarily disable new ops-bot functionality (#239) @ajschmidt8
• Add .github/ops-bot.yaml config file (#236) @ajschmidt8
• randomization per image per batch (#231) @shekhardw

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

• PyPI v21.12.00 release (#182) @gigony

🚀 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

• Add missing imports tests (#183) @Ethyling
• Allow installation with CuPy 10 (#197) @glee77
• Upgrade Numpy to 1.18 for Python 3.9 support (#196) @Ethyling
• Upgrade Numpy to 1.19 for Python 3.9 support (#203) @Ethyling

cuCIM 21.12.00 (9 Dec 2021)

🚀 New Features

• Support Aperio SVS with CPU LZW and jpeg2k decoder (#141) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Add NVTX support for performance analysis (#144) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Normalize operation (#150) [@shekhardw](https://github.com/shekhardw](https://github.com/shekhardw))

🐛 Bug Fixes

• Load libcufile.so with RTLD_NODELETE flag (#177) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Remove rmm/nvcc dependencies to fix cudaErrorUnsupportedPtxVersion error (#175) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Do not compile code with nvcc if no CUDA kernel exists (#171) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Fix a segmentation fault due to unloaded libcufile (#158) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Fix thread contention in Cache (#145) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Build with NumPy 1.17 (#148) [@jakirkham](https://github.com/jakirkham](https://github.com/jakirkham))

📖 Documentation

• Add Jupyter notebook for SVS Support (#147) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Update change log for v21.10.01 (#142) [@gigony](https://github.com/gigony](https://github.com/gigony))
• update docs theme to pydata-sphinx-theme (#138) [@quasiben](https://github.com/quasiben](https://github.com/quasiben))
• Update Github links in README.md through script (#132) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Fix GDS link in Jupyter notebook (#131) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Update notebook for the interoperability with DALI (#127) [@gigony](https://github.com/gigony](https://github.com/gigony))

🛠️ Improvements

• Update conda recipes for Enhanced Compatibility effort by (#164) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))
• Fix Changelog Merge Conflicts for branch-21.12 (#156) [@ajschmidt8](https://github.com/ajschmidt8](https://github.com/ajschmidt8))
• Add cucim.kit.cumed plugin with skeleton (#129) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Update initial cpp unittests (#128) [@gigony](https://github.com/gigony](https://github.com/gigony))
• Optimize zoom out implementation with separate padding kernel (#125) [@chirayuG-nvidia](https://github.com/chirayuG-nvidia](https://github.com/chirayuG-nvidia))
• Do not force install linux-64 version of openslide-python (#124) [@Ethyling](https://github.com/Ethyling](https://github.com/Ethyling))

cuCIM 21.10.00 (7 Oct 2021)

🐛 Bug Fixes

• fix failing regionprops test cases (#110) @grlee77

📖 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

• ENH Replace gpuci_conda_retry with gpuci_mamba_retry (#69) @dillon-cullinan

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

• Fix a typo in cache document (#66) @gigony

🚀 New Features

• Pin isort hook to 5.6.4 (#73) @charlesbluca
• Add skimage.morphology.thin (#27) @grlee77

🛠️ 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

• Update update-version.sh (#42) @ajschmidt8

🛠️ Improvements

• Update environment variable used to determine cuda_version (#43) @ajschmidt8
• Update version script to remove bump2version dependency (#41) @gigony
• Update changelog (#40) @ajschmidt8
• Update docs build script (#39) @ajschmidt8

cuCIM 0.19.0 (15 Apr 2021)

• Initial release of cuCIM including cuClaraImage and cupyimg.