CHANGELOG.md

cuCIM 22.12.00 (Date TBD)

Please see https://github.com/rapidsai/cucim/releases/tag/v22.12.00a for the latest changes to this development branch.

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.