Version 0.13.0 (#101)

Closes #90

HISTORY.md

@@ -1,5 +1,11 @@
 # History
 
+## 0.13.0 (2023-07-17)
+
+* Increased maximum number of segments to 64
+* Required segmentations to be of type Int8 or UInt8
+* Reduced memory usage
+
 ## 0.12.0 (2023-06-02)
 
 * Add support for conversion of DICOM-WSI files to TIFF

panimg/image_builders/metaio_utils.py

@@ -278,6 +278,12 @@ def load_sitk_image(
 
     headers = validate_and_clean_additional_mh_headers(reader=reader)
 
+    if reader.GetNumberOfComponents() > 4:
+        raise ValidationError(
+            "Images with more than 4 channels not supported. "
+            "For 4D data please use the 4th dimension instead."
+        )
+
     # Header has been validated, read the pixel data
     if reader.GetDimension() in (2, 3, 4):
         sitk_image = reader.Execute()

panimg/models.py

@@ -203,10 +203,6 @@ def depth(self) -> Optional[int]:
 
         return depth or None
 
-    @property
-    def is_4d(self):
-        return len(self.image.GetSize()) == 4
-
     @staticmethod
     def _extract_first_float(value: str) -> float:
         if value.startswith("["):
@@ -273,7 +269,7 @@ def segments(self) -> Optional[FrozenSet[int]]:
 
         im_arr = GetArrayViewFromImage(self.image)
 
-        if self.is_4d:
+        if self.image.GetDimension() == 4:
             segments = set()
             n_volumes = self.image.GetSize()[3]
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "panimg"
-version = "0.12.0"
+version = "0.13.0"
 description = "Conversion of medical images to MHA and TIFF."
 license = "Apache-2.0"
 authors = ["James Meakin <[email protected]>"]

tests/test_models.py

@@ -225,3 +225,23 @@ def test_segments(
 
     image = result.new_images.pop()
     assert image.segments == segments
+
+
+def test_invalid_4d(tmp_path_factory):
+    file = RESOURCE_PATH / "channels" / "5_1_1_1_invalid.mha"
+    result = _build_files(
+        builder=image_builders.image_builder_mhd,
+        files={file},
+        output_directory=tmp_path_factory.mktemp("output"),
+    )
+
+    assert result.consumed_files == set()
+    assert len(result.new_images) == 0
+    assert result.file_errors == {
+        file: [
+            (
+                "Mhd image builder: Images with more than 4 channels not supported. "
+                "For 4D data please use the 4th dimension instead."
+            )
+        ]
+    }