Fixes (#119)

* Add thread_safe property

* Replace lossy_compressed with lossy_compression property

* Pin zarr to <3.0

* Test openslide cross platform

* Update changelog

* Update version and packages

* Fix openslide checksums

* Skip openslide test on mac on mirax

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.16.0] - 2025-01-29
+
 ### Added
 
 - Support for reading isyntax files using pyisyntax.
@@ -15,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Reading correct image size in pyramid series in Bioformats reader.
 - Skip non-dyadic pyramid series in Bioformats reader.
+- Missing values in `LossyImageCompressionRatio` and `LossyImageCompressionMethod` when converting without re-encoding.
+- Pin zarr to <3.0 to fix import exception.
 
 ## [0.15.1] - 2025-01-07
 
@@ -285,7 +289,8 @@ 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/0.15.1..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.16.0..HEAD
+[0.16.0]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.16.0..0.16.0
 [0.15.1]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.15.0..0.15.1
 [0.15.0]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.14.2..0.15.0
 [0.14.2]: https://github.com/imi-bigpicture/wsidicomizer/compare/0.14.1..0.14.2

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "wsidicomizer"
-version = "0.15.1"
+version = "0.16.0"
 description = "Tool for reading WSI files from proprietary formats and optionally convert them to to DICOM"
 authors = ["Erik O Gabrielsson <[email protected]>"]
 license = "Apache-2.0"
@@ -18,8 +18,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "^3.10"
-wsidicom = "^0.22.0"
-opentile = "^0.13.1"
+wsidicom = "^0.23.0"
+opentile = "^0.14.0"
 numpy = ">=1.22.0"
 pydicom = ">=3.0.0"
 czifile = "^2019.7.2"
@@ -29,6 +29,7 @@ scyjava = { version = "^1.8.1", optional = true }
 ome-types = {version = "^0.5.0", optional = true }
 pyisyntax = {version = "^0.1.2", optional = true }
 imagecodecs = { version = "^2024.12.30",  optional = true }
+zarr = ">=2.11.0, <3.0"
 
 [tool.poetry.extras]
 openslide = ["openslide-python"]

tests/conftest.py

@@ -157,31 +157,18 @@
             "image_coordinate_system": {"x": 2.3061675, "y": 20.79015},
             "icc_profile": False,
             "read_region": [
-                # OpenSlide produces different results across platforms
-                # {
-                #     "location": {
-                #         "x": 50,
-                #         "y": 100
-                #     },
-                #     "level": 6,
-                #     "size": {
-                #         "width": 500,
-                #         "height": 500
-                #     },
-                #     "md5": "fe29e76f5904d65253d8eb742b244789"
-                # },
-                # {
-                #     "location": {
-                #         "x": 400,
-                #         "y": 500
-                #     },
-                #     "level": 4,
-                #     "size": {
-                #         "width": 500,
-                #         "height": 500
-                #     },
-                #     "md5": "4f4c904ed9257e385fc8f0818337d9e7"
-                # }
+                {
+                    "location": {"x": 50, "y": 100},
+                    "level": 6,
+                    "size": {"width": 500, "height": 500},
+                    "md5": "b9052fc1ebbe99582906c575511fe944",
+                },
+                {
+                    "location": {"x": 400, "y": 500},
+                    "level": 4,
+                    "size": {"width": 500, "height": 500},
+                    "md5": "a11881460a4fae78ddfef1100339cac0",
+                },
             ],
             "read_region_openslide": [
                 {
@@ -196,6 +183,7 @@
                 },
             ],
             "read_thumbnail": [],
+            "skip_hash_test_platforms": ["Darwin"],
         }
     },
     "ndpi": {

wsidicomizer/__init__.py

@@ -14,6 +14,6 @@
 
 from wsidicomizer.wsidicomizer import WsiDicomizer
 
-__version__ = "0.15.1"
+__version__ = "0.16.0"
 
 __all__ = ["WsiDicomizer"]

wsidicomizer/extras/bioformats/bioformats_image_data.py

@@ -94,6 +94,10 @@ def photometric_interpretation(self) -> str:
         data."""
         return self.encoder.photometric_interpretation
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
     def _get_tile(
         self, tile_point: Point, z: float, path: str
     ) -> ContextManager[np.ndarray]:

wsidicomizer/extras/isyntax/isyntax_image_data.py

@@ -116,6 +116,10 @@ def blank_color(self) -> Union[int, Tuple[int, int, int]]:
     def image_coordinate_system(self) -> ImageCoordinateSystem:
         return ImageCoordinateSystem(PointMm(0, 0), 0)
 
+    @property
+    def thread_safe(selt) -> bool:
+        return False
+
     def stitch_tiles(self, region: Region, path: str, z: float, threads: int) -> Image:
         """Overrides ImageData stitch_tiles() to read reagion directly from
         ISyntax object.
@@ -302,6 +306,10 @@ def pyramid_index(self) -> int:
     def image_coordinate_system(self) -> ImageCoordinateSystem:
         return ImageCoordinateSystem(PointMm(0, 0), 0)
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
     def _get_encoded_tile(self, tile: Point, z: float, path: str) -> bytes:
         if z not in self.focal_planes or path not in self.optical_paths:
             raise WsiDicomNotFoundError(

wsidicomizer/extras/openslide/openslide_image_data.py

@@ -98,6 +98,10 @@ def optical_paths(self) -> List[str]:
     def blank_color(self) -> Union[int, Tuple[int, int, int]]:
         return self._blank_color
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
     def _get_blank_color(
         self, photometric_interpretation: str
     ) -> Union[int, Tuple[int, int, int]]:

wsidicomizer/image_data.py

@@ -16,11 +16,13 @@
 files."""
 
 from abc import ABCMeta, abstractmethod
+from typing import List, Optional, Tuple
 
 import numpy as np
 from PIL import Image as Pillow
 from PIL.Image import Image
 from wsidicom import ImageData
+from wsidicom.codec import LossyCompressionIsoStandard
 from wsidicom.geometry import PointMm, Size
 from wsidicom.metadata import ImageCoordinateSystem
 
@@ -49,9 +51,11 @@ def bits(self) -> int:
         return self.encoder.bits
 
     @property
-    def lossy_compressed(self) -> bool:
-        # TODO: This should be set from encoder and base file.
-        return True
+    def lossy_compression(
+        self,
+    ) -> Optional[List[Tuple[LossyCompressionIsoStandard, float]]]:
+        """Return None as image compression is for most format not known."""
+        return None
 
     def _encode(self, image_data: np.ndarray) -> bytes:
         """Return image data encoded in jpeg using set quality and subsample

wsidicomizer/sources/czi/czi_image_data.py

@@ -103,6 +103,10 @@ def photometric_interpretation(self) -> str:
     def pixel_spacing(self) -> SizeMm:
         return self._pixel_spacing
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
     @cached_property
     def image_size(self) -> Size:
         """The pixel size of the image."""

wsidicomizer/sources/opentile/opentile_image_data.py

@@ -14,14 +14,14 @@
 
 """Image data for opentile compatible file."""
 
-from typing import Iterable, Iterator, List, Optional
+from typing import Iterable, Iterator, List, Optional, Tuple
 
 from opentile.tiff_image import TiffImage
 from PIL import Image as Pillow
 from PIL.Image import Image
 from pydicom.uid import JPEG2000, UID, JPEG2000Lossless, JPEGBaseline8Bit
 from tifffile import COMPRESSION, PHOTOMETRIC
-from wsidicom.codec import Encoder
+from wsidicom.codec import Encoder, LossyCompressionIsoStandard
 from wsidicom.geometry import Point, Size, SizeMm
 from wsidicom.metadata import Image as ImageMetadata
 from wsidicom.metadata import ImageCoordinateSystem
@@ -138,6 +138,25 @@ def photometric_interpretation(self) -> str:
     def samples_per_pixel(self) -> int:
         return self._tiff_image.samples_per_pixel
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
+    @property
+    def lossy_compression(
+        self,
+    ) -> Optional[List[Tuple[LossyCompressionIsoStandard, float]]]:
+        """Return lossy compression method and compression ratio if lossy compressed."""
+        iso = LossyCompressionIsoStandard.transfer_syntax_to_iso(self.transfer_syntax)
+        if iso is None:
+            return None
+        uncompressed_size = (
+            self.image_size.area * self.samples_per_pixel * self.bits // 8
+        )
+        compressed_size = self._tiff_image.compressed_size
+        compression_ratio = round(compressed_size / uncompressed_size, 2)
+        return [(iso, compression_ratio)]
+
     def _get_encoded_tile(self, tile: Point, z: float, path: str) -> bytes:
         """Return image bytes for tile. Returns transcoded tile if
         non-supported encoding.

wsidicomizer/sources/tiffslide/tiffslide_image_data.py

@@ -86,6 +86,10 @@ def optical_paths(self) -> List[str]:
     def blank_color(self) -> Union[int, Tuple[int, int, int]]:
         return self._blank_color
 
+    @property
+    def thread_safe(self) -> bool:
+        return True
+
     def _get_blank_color(
         self, photometric_interpretation: str
     ) -> Union[int, Tuple[int, int, int]]: