Czi fixes (#105)

* Fix missing tiles in  block directory

* Fix lock re-entry when block data is not cached

.github/workflows/pytest.yaml

@@ -66,7 +66,10 @@ jobs:
         run: sudo apt-get install -y libturbojpeg libopenslide0
       - name: Set up OSX
         if: matrix.os == 'macos-latest'
-        run: brew install jpeg-turbo openslide
+        run: |
+          echo OS_TAG=macos >> $GITHUB_ENV
+          echo DYLD_LIBRARY_PATH=/opt/homebrew/lib >> $GITHUB_ENV
+          brew install jpeg-turbo openslide
       - name: Set up Windows
         shell: pwsh
         if: matrix.os == 'windows-latest'

CHANGELOG.md

@@ -7,7 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.14.0] - 2023-04-15
+## [0.14.1] - 2024-05-07
+
+### Fixed
+
+- Fix stripes with missing image data for czi source.
+- Fix possible cache deadlock for czi source.
+
+## [0.14.0] - 2024-04-15
 
 ### Added
 
@@ -18,33 +25,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Missing ´label` parameter in bioformats cli.
 - Change to empty `WsiDicomizerMetadata` for bioformat source.
 
-## [0.13.2] - 2023-03-20
+## [0.13.2] - 2024-03-20
 
 ### Fixed
 
 - Missing handling of pyramid index when creating WsiInstance using create_instance().
 
-## [0.13.1] - 2023-02-22
+## [0.13.1] - 2024-02-22
 
 ### Fixed
 
 - Updated version of `WsiDicom` to 0.20.1 to fix missing to close file handle.
 
-## [0.13.0] - 2023-02-15
+## [0.13.0] - 2024-02-15
 
 ### Added
 
 - Support for incorporating ICC profiles from source image if available. This is currently limited to images read by the `OpenTile` and `OpenSlide` source, and only for supported formats (primarily `Aperio svs`).
 
 - If no ICC profile is present in the source file or the provided metadata, an empty profile will be used if the photometric interpretation requires it for DICOM compatibility. 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

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 <erik.o.gabrielsson@sectra.com>"]
 license = "Apache-2.0"

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": [],

wsidicomizer/__init__.py

@@ -14,6 +14,6 @@
 
 from wsidicomizer.wsidicomizer import WsiDicomizer
 
-__version__ = "0.14.0"
+__version__ = "0.14.1"
 
 __all__ = ["WsiDicomizer"]

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