Philis tiff metadata (#75)

* Fix pixel spacing for philips tiff

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] -
 
+## [0.10.4] - 2023-11-30
+
+### Fixed
+
+- Order of pixel spacing for philips tiff files.
+
 ## [0.10.3] - 2023-09-01
 
 ### Fixed
@@ -161,7 +167,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of opentile.
 
-[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.10.3..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.10.4..HEAD
+[0.10.4]: https://github.com/imi-bigpicture/opentile/compare/v0.10.3..v0.10.4
 [0.10.3]: https://github.com/imi-bigpicture/opentile/compare/v0.10.2..v0.10.3
 [0.10.2]: https://github.com/imi-bigpicture/opentile/compare/v0.10.1..v0.10.2
 [0.10.1]: https://github.com/imi-bigpicture/opentile/compare/v0.10.0..v0.10.1

opentile/__init__.py

@@ -15,4 +15,4 @@
 from opentile.opentile import OpenTile
 from opentile.metadata import Metadata
 
-__version__ = "0.10.3"
+__version__ = "0.10.4"

opentile/formats/philips/philips_tiff_metadata.py

@@ -52,19 +52,19 @@ def __init__(self, tiff_file: TiffFile):
 
         metadata = ElementTree.fromstring(tiff_file.philips_metadata)
         self._tags: Dict[str, Optional[str]] = {tag: None for tag in self.TAGS}
-        for element in metadata.iter():
-            if element.tag == "Attribute" and element.text is not None:
-                name = element.attrib["Name"]
-                if name in self._tags and self._tags[name] is None:
-                    self._tags[name] = element.text
+        for element in metadata.iter("Attribute"):
+            if element.text is None:
+                continue
+            name = element.attrib["Name"]
+            if name in self._tags and self._tags[name] is None:
+                self._tags[name] = element.text
 
     @property
     def scanner_manufacturer(self) -> Optional[str]:
         return self._tags["DICOM_MANUFACTURER"]
 
     @cached_property
     def scanner_software_versions(self) -> Optional[List[str]]:
-        print(self._tags["DICOM_SOFTWARE_VERSIONS"])
         if self._tags["DICOM_SOFTWARE_VERSIONS"] is None:
             return None
         return self._split_and_cast_text(self._tags["DICOM_SOFTWARE_VERSIONS"], str)
@@ -88,9 +88,8 @@ def aquisition_datetime(self) -> Optional[datetime]:
     def pixel_spacing(self) -> Optional[Tuple[float, float]]:
         if self._tags["DICOM_PIXEL_SPACING"] is None:
             return None
-        return tuple(
-            self._split_and_cast_text(self._tags["DICOM_PIXEL_SPACING"], float)[0:2]
-        )
+        values = self._split_and_cast_text(self._tags["DICOM_PIXEL_SPACING"], float)
+        return values[1], values[0]
 
     @cached_property
     def properties(self) -> Dict[str, Any]:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "opentile"
-version = "0.10.3"
+version = "0.10.4"
 description = "Read tiles from wsi-TIFF files"
 authors = ["Erik O Gabrielsson <[email protected]>"]
 license = "Apache-2.0"