Preprocessing: add option to only pad and never crop (#54)

Preprocessing: add option to only pad and never crop
Update version to 2.1.8

setup.py

@@ -5,7 +5,7 @@
         long_description = fh.read()
 
     setuptools.setup(
-        version='2.1.7',
+        version='2.1.8',
         author_email='[email protected]',
         long_description=long_description,
         long_description_content_type="text/markdown",

src/picai_prep/dcm2mha.py

@@ -661,7 +661,7 @@ def _read_image_pydicom(self, path: Optional[PathLike] = None) -> sitk.Image:
             # collect all available metadata (with DICOM tags, e.g. 0010|1010, as keys)
             value = self.get_pydicom_value(ref, key)
             if value is not None:
-                key = str(key).replace(", ", "|").replace("(", "").replace(")", "")
+                key = str(key).replace(",", "|").replace("(", "").replace(")", "").replace(" ", "")
                 image.SetMetaData(key, value)
 
         return image

src/picai_prep/preprocessing.py

@@ -176,6 +176,7 @@ def crop_or_pad(
     size: Optional[Iterable[int]] = (20, 256, 256),
     physical_size: Optional[Iterable[float]] = None,
     crop_only: bool = False,
+    pad_only: bool = False,
 ) -> "Union[sitk.Image, npt.NDArray[Any]]":
     """
     Resize image by cropping and/or padding
@@ -208,6 +209,9 @@ def crop_or_pad(
             padding[i][0] = (size[i] - shape[i]) // 2
             padding[i][1] = size[i] - shape[i] - padding[i][0]
         else:
+            if pad_only:
+                continue
+
             # create slicer object to crop image
             idx_start = int(np.floor((shape[i] - size[i]) / 2.))
             idx_end = idx_start + size[i]

tests/test_dcm2mha.py

@@ -93,7 +93,7 @@ def test_dcm2mha_commandline(
     ]
 
     # run command
-    subprocess.check_call(cmd, shell=(sys.platform == 'win32'))
+    subprocess.check_call(cmd, shell=(sys.platform == "win32"))
 
     # compare output
     for patient_id, subject_id in [
@@ -148,7 +148,7 @@ def test_resolve_duplicates(
 
     # check if duplicates were resolved
     matched_series = [serie for serie in case.valid_series if "t2w" in serie.mappings]
-    assert len(matched_series) == 1, 'More than one serie after resolving duplicates!'
+    assert len(matched_series) == 1, "More than one serie after resolving duplicates!"
 
 
 def test_value_match_contains(
@@ -185,7 +185,7 @@ def test_value_match_contains(
 
     # check if duplicates were resolved
     matched_series = [serie for serie in case.valid_series if "test" in serie.mappings]
-    assert len(matched_series) == 11, 'Empty lower_strip_contains should match all series!'
+    assert len(matched_series) == 11, "Empty lower_strip_contains should match all series!"
 
 
 def test_value_match_multiple_keys(
@@ -236,7 +236,7 @@ def test_value_match_multiple_keys(
 
     # check if duplicates were resolved
     matched_series = [serie for serie in case.valid_series if "test" in serie.mappings]
-    assert len(matched_series) == 3, 'Should find three diffusion scans!'
+    assert len(matched_series) == 3, "Should find three diffusion scans!"
 
 
 @pytest.mark.parametrize("input_dir", [
@@ -265,7 +265,9 @@ def test_image_reader(input_dir: str):
     metadata_sitk = {key: image_sitk.GetMetaData(key) for key in image_sitk.GetMetaDataKeys()}
     metadata_pydicom = {key: image_pydicom.GetMetaData(key) for key in image_pydicom.GetMetaDataKeys()}
     keys = set(metadata_pydicom.keys()) & set(metadata_sitk.keys())
-    assert len(keys) > 1, 'No metadata found!'
+    assert len(metadata_sitk.keys()) > 1, "No metadata found with SimpleITK!"
+    assert len(metadata_pydicom.keys()) > 1, "No metadata found with pydicom!"
+    assert len(keys) > 1, f"No metadata found! SimpleITK: {list(metadata_sitk.keys())}, pydicom: {list(metadata_pydicom.keys())}"
     assert {k: metadata_sitk[k] for k in keys} == {k: metadata_pydicom[k] for k in keys}
 
 
@@ -298,7 +300,9 @@ def test_image_reader_dicom_zip(input_dir: str):
 
     # compare metadata
     keys = set(metadata1.keys()) & set(metadata2.keys())
-    assert len(keys) > 1, 'No metadata found!'
+    assert len(metadata1.keys()) > 1, "No metadata found with first reader!"
+    assert len(metadata2.keys()) > 1, "No metadata found with second reader!"
+    assert len(keys) > 1, f"No metadata found! First reader: {list(metadata1.keys())}, second reader: {list(metadata2.keys())}"
     assert {k: metadata1[k] for k in keys} == {k: metadata2[k] for k in keys}