Merge branch 'philips'

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
   - id: black
     language_version: python3
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.6.1'
+  rev: 'v1.7.1'
   hooks:
   - id: mypy
     additional_dependencies: ["numpy"]

tiffslide/_types.py

@@ -56,10 +56,7 @@ def __getattr__(name: str) -> Any:
         raise AttributeError(name)
 
 
-if sys.version_info >= (3, 9):
-    PathLikeStr: TypeAlias = os.PathLike[str]
-else:
-    PathLikeStr: TypeAlias = os.PathLike
+PathLikeStr: TypeAlias = "os.PathLike[str]"
 
 
 @runtime_checkable

tiffslide/tiffslide.py

@@ -13,6 +13,7 @@
 from typing import Iterator
 from typing import Literal
 from typing import Mapping
+from typing import Optional
 from typing import TypeVar
 from typing import overload
 from warnings import warn
@@ -644,6 +645,7 @@ class _PropertyParser:
         scn="leica",
         bif="ventana",
         ndpi="hamamatsu",
+        philips="philips_tiff"
         # add more when needed
     )
 
@@ -843,6 +845,34 @@ def parse_generic_tiff(self) -> dict[str, Any]:
         md.update(self.collect_level_info(series0))
         return md
 
+    def parse_philips_tiff(self) -> dict[str, Any]:
+        """parse Philips tiff properties"""
+        md = self.parse_generic_tiff()
+        if self._tf.philips_metadata is None:
+            return md
+        philips_metadata = ElementTree.fromstring(self._tf.philips_metadata)
+
+        def get_first_attribute_with_name(
+            root: ElementTree.Element, name: str
+        ) -> str | None:
+            return next(root.iterfind(f".//Attribute[@Name='{name}']")).text
+
+        md[PROPERTY_NAME_VENDOR] = get_first_attribute_with_name(
+            philips_metadata, "DICOM_MANUFACTURER"
+        )
+        pixel_spacing_attribute = get_first_attribute_with_name(
+            philips_metadata, "DICOM_PIXEL_SPACING"
+        )
+        if pixel_spacing_attribute is not None:
+            pixel_spacings = [
+                float(element.strip('"')) * 1000
+                for element in pixel_spacing_attribute.split(" ")
+            ]
+            mpp_x, mpp_y = pixel_spacings[0], pixel_spacings[1]
+            md[PROPERTY_NAME_MPP_X] = mpp_x
+            md[PROPERTY_NAME_MPP_Y] = mpp_y
+        return md
+
 
 def _parse_metadata_aperio(desc: str) -> dict[str, Any]:
     """Aperio SVS metadata"""