Merge pull request #30 from niaid/use_simpleitk_23

Allow SimpleITK 2.3  in requirements.

rap_sitkcore/read_dcm.py

@@ -35,7 +35,6 @@ def _read_dcm_pydicom(filename: Path) -> sitk.Image:
         # use complement to invert the pixel intensity.
         img = sitk.GetImageFromArray(~arr, isVector=False)
     elif ds.PhotometricInterpretation in ["YBR_FULL_422", "YBR_FULL", "RGB"]:
-
         if ds.PhotometricInterpretation != "RGB":
             from pydicom.pixel_data_handlers.util import convert_color_space
 
@@ -49,7 +48,9 @@ def _read_dcm_pydicom(filename: Path) -> sitk.Image:
         if tag in ds:
             de = ds.data_element(tag)
             key = f"{de.tag.group:04x}|{de.tag.elem:04x}"
-            if de.VR == "DS":
+            if de.value is None:
+                img[key] = ""
+            elif de.VR == "DS":
                 if de.VM > 1:
                     img[key] = convert_float_list_to_mv_ds(de.value)
                 else:

requirements.txt

@@ -1,4 +1,4 @@
-SimpleITK >=2.1.0, <2.3
+SimpleITK >=2.1.0, <2.4.0
 
 numpy
 pydicom

test/unit/test_dicom_util.py

@@ -20,7 +20,6 @@ def test_convert1():
 
 
 def test_keyword_to_gdcm_tag():
-
     assert keyword_to_gdcm_tag("PatientName") == "0010|0010"
     assert keyword_to_gdcm_tag("SeriesDescription") == "0008|103e"
     assert keyword_to_gdcm_tag("Modality") == "0008|0060"

test/unit/test_is_dicom_xray.py

@@ -95,6 +95,5 @@ def test_is_dicom_xray4(test_file, is_xray, data_paths):
     ("test_file", "is_xray"), [("1.3.6.1.4.1.25403.163683357445804.11044.20131119114627.12.dcm", True)]
 )
 def test_is_dicom_xray5(test_file, is_xray, remote_data_paths):
-
     url = remote_data_paths[test_file]
     assert rap_sitkcore.is_dicom_xray(url, strict=True) == is_xray

test/unit/test_resize.py

@@ -13,7 +13,6 @@
     ],
 )
 def test_resize_and_scale_uint8_1(file_name, thumbnail_size, md5_hash, data_paths):
-
     filename = data_paths[file_name]
     img = read_dcm(Path(filename))