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This behavior can be disabled with `settings.insert_icc_profile_if_missing = False` -## [0.12.1] - 2023-01-12 +## [0.12.1] - 2024-01-12 ### Fixed - Fixed missing support for Python 3.12. -## [0.12.0] - 2023-01-12 +## [0.12.0] - 2024-01-12 ### Changed @@ -241,7 +248,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Initial release of wsidicomizer -[Unreleased]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.14.0..HEAD +[Unreleased]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.14.1..HEAD +[0.14.1]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.14.0..0.14.1 [0.14.0]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.13.2..0.14.0 [0.13.2]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.13.1..0.13.2 [0.13.1]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.13.0..0.13.1 diff --git a/poetry.lock b/poetry.lock index 0d8a330..7961cb9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -23,33 +23,33 @@ 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{file = "wsidicom-0.20.3-py3-none-any.whl", hash = "sha256:cde5fac11ea0286da659f4cf0c882210fea6903456a9eac518610681a6c8c8e1"}, - {file = "wsidicom-0.20.3.tar.gz", hash = "sha256:265c53f2abd35c882616e712899b291619a11fd4c4389a6fb1a4e5adcaa43949"}, + {file = "wsidicom-0.20.4-py3-none-any.whl", hash = "sha256:6760af7d4e6ecc322c5c23ac2e1aad8f6ee904e126d8c840da90210d95ee0aeb"}, + {file = "wsidicom-0.20.4.tar.gz", hash = "sha256:3d4df665b325e3c990b573258a2cfb974f68ee6d977ce74e9c97fbc6ab8c3663"}, ] [package.dependencies] @@ -1475,20 +1555,20 @@ test = ["pre-commit", "pytest", "pytest-benchmark", "pytest-cov"] [[package]] name = "zarr" -version = "2.17.1" +version = "2.17.2" description = "An implementation of chunked, compressed, N-dimensional arrays for Python" optional = false python-versions = ">=3.9" files = [ - {file = "zarr-2.17.1-py3-none-any.whl", hash = "sha256:e25df2741a6e92645f3890f30f3136d5b57a0f8f831094b024bbcab5f2797bc7"}, - {file = "zarr-2.17.1.tar.gz", hash = "sha256:564b3aa072122546fe69a0fa21736f466b20fad41754334b62619f088ce46261"}, + {file = "zarr-2.17.2-py3-none-any.whl", hash = "sha256:70d7cc07c24280c380ef80644151d136b7503b0d83c9f214e8000ddc0f57f69b"}, + {file = "zarr-2.17.2.tar.gz", hash = "sha256:2cbaa6cb4e342d45152d4a7a4b2013c337fcd3a8e7bc98253560180de60552ce"}, ] [package.dependencies] asciitree = "*" fasteners = {version = "*", markers = "sys_platform != \"emscripten\""} numcodecs = ">=0.10.0" -numpy = ">=1.21.1" +numpy = ">=1.23" [package.extras] docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"] diff --git a/pyproject.toml b/pyproject.toml index 84fe822..6eb0001 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "wsidicomizer" -version = "0.14.0" +version = "0.14.1" description = "Tool for reading WSI files from proprietary formats and optionally convert them to to DICOM" authors = ["Erik O Gabrielsson "] license = "Apache-2.0" diff --git a/tests/conftest.py b/tests/conftest.py index dc71c3d..23a205c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -129,7 +129,13 @@ "level": 0, "size": {"width": 200, "height": 200}, "md5": "aa9e76930398facc8c7910e053a7f418", - } + }, + { + "location": {"x": 30720, "y": 25600}, + "level": 0, + "size": {"width": 512, "height": 512}, + "md5": "ac145933f80f64abac8d69eeb2ea537b", + }, ], "read_region_openslide": [], "read_thumbnail": [], diff --git a/wsidicomizer/__init__.py b/wsidicomizer/__init__.py index 26597e7..b6eff57 100644 --- a/wsidicomizer/__init__.py +++ b/wsidicomizer/__init__.py @@ -14,6 +14,6 @@ from wsidicomizer.wsidicomizer import WsiDicomizer -__version__ = "0.14.0" +__version__ = "0.14.1" __all__ = ["WsiDicomizer"] diff --git a/wsidicomizer/sources/czi/czi_image_data.py b/wsidicomizer/sources/czi/czi_image_data.py index 4d2379d..3e8b2d0 100644 --- a/wsidicomizer/sources/czi/czi_image_data.py +++ b/wsidicomizer/sources/czi/czi_image_data.py @@ -18,7 +18,7 @@ from dataclasses import dataclass from functools import cached_property, lru_cache from pathlib import Path -from threading import Lock +from threading import RLock from typing import Dict, List, Optional, Tuple import numpy as np @@ -78,7 +78,7 @@ def __init__( self._tile_size = Size(tile_size, tile_size) assert isinstance(self._czi.filtered_subblock_directory, list) self._block_directory = self._czi.filtered_subblock_directory - self._block_locks: Dict[int, Lock] = defaultdict(Lock) + self._block_locks: Dict[int, RLock] = defaultdict(RLock) if self._merged_metadata.pixel_spacing is None: raise ValueError("Could not determine pixel spacing for czi image.") @@ -157,7 +157,7 @@ def tile_directory(self) -> Dict[Tuple[Point, float, str], List[CziBlock]]: block_start, block_size, z, c = self._get_block_dimensions(block) tile_region = Region.from_points( block_start // self.tile_size, - (block_start + block_size) // self.tile_size, + (block_start + block_size).ceil_div(self.tile_size), ) for tile in tile_region.iterate_all(): tile_directory[tile, z, c].append( @@ -202,9 +202,8 @@ def _get_tile(self, tile_point: Point, z: float, path: str) -> np.ndarray: # should already have checked). return image_data + # For each block covering the tile for block in self.tile_directory[tile_point, z, path]: - # For each block covering the tile - # Start and end coordinates for block and tile block_end = block.start + block.size tile_start = tile_point * self.tile_size @@ -318,17 +317,21 @@ def _get_tile_data(self, block_index: int) -> np.ndarray: prevent multiple threads proceseing the same tile, use a lock for each block.""" block_lock = self._block_locks[block_index] - if block_lock.locked(): - # Another thread is already reading the block. Wait for lock and - # read from cache. - with block_lock: + try: + # Try to lock block. + aquired = block_lock.acquire(blocking=False) + if not aquired: + # Another thread is already reading the block. + # Wait for lock and hopefully read from cache. + aquired = block_lock.acquire(blocking=True) return self._get_tile_data(block_index) - - with block_lock: - # Lock block and read from block. - block = self.block_directory[block_index] - data = block.data_segment().data() - return data + else: + # Read the block data. + block = self.block_directory[block_index] + return block.data_segment().data() + finally: + if aquired: + block_lock.release() def _get_block_dimensions( self, block: DirectoryEntryDV