Fix missing to close file handle (#98)

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.13.1] - 2023-02-22
+
+### Fixed
+
+- Updated version of `WsiDicom` to 0.20.1 to fix missing to close file handle.
+
 ## [0.13.0] - 2023-02-15
 
 ### Added

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "wsidicomizer"
-version = "0.13.0"
+version = "0.13.1"
 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"
@@ -18,8 +18,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-wsidicom = "^0.18.2"
-opentile = "^0.11.1"
+wsidicom = "^0.20.1"
+opentile = "^0.12.0"
 numpy = "^1.22.0"
 pydicom = ">=2.1.0"
 czifile = ">=2019.7.2"

wsidicomizer/__init__.py

@@ -14,6 +14,6 @@
 
 from wsidicomizer.wsidicomizer import WsiDicomizer
 
-__version__ = "0.13.0"
+__version__ = "0.13.1"
 
 __all__ = ["WsiDicomizer"]

wsidicomizer/extras/openslide/openslide_source.py

@@ -16,11 +16,8 @@
 
 import math
 from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import List, Optional
 
-from fsspec.core import url_to_fs
-from fsspec.implementations.local import LocalFileSystem
-from upath import UPath
 from wsidicom.codec import Encoder
 from wsidicom.metadata.wsi import WsiMetadata
 
@@ -38,18 +35,15 @@
 class OpenSlideSource(DicomizerSource):
     def __init__(
         self,
-        filepath: UPath,
+        filepath: Path,
         encoder: Encoder,
         tile_size: int = 512,
         metadata: Optional[WsiMetadata] = None,
         default_metadata: Optional[WsiMetadata] = None,
         include_confidential: bool = True,
-        file_options: Optional[Dict[str, Any]] = None,
     ) -> None:
-        fs, path = url_to_fs(str(filepath), **file_options or {})
-        if not isinstance(fs, LocalFileSystem):
-            raise ValueError("OpenSlideSource only supports local files.")
-        self._slide = OpenSlide(path)
+        self._slide = OpenSlide(filepath)
+
         self._pyramid_levels = self._get_pyramid_levels(self._slide)
         self._base_metadata = OpenSlideMetadata(self._slide)
         super().__init__(
@@ -59,7 +53,6 @@ def __init__(
             metadata,
             default_metadata,
             include_confidential,
-            file_options,
         )
 
     def close(self) -> None:

wsidicomizer/wsidicomizer.py

@@ -117,7 +117,7 @@ def open(
             include_confidential,
             **source_args,
         )
-        return cls(source)
+        return cls(source, True)
 
     @classmethod
     def convert(