ENH: Replace pydicom deprecated usage of get_frame_offsets

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
     "requests>=2.18",
     "retrying>=1.3.3",
     "Pillow>=8.3",
-    "pydicom>=2.2",
+    "pydicom>=3.0.0",
     "typing-extensions>=4.0; python_version < '3.8.0'",
 ]
 

src/dicomweb_client/file.py

@@ -32,7 +32,7 @@
 from pydicom.datadict import dictionary_VR, keyword_for_tag, tag_for_keyword
 from pydicom.dataelem import DataElement
 from pydicom.dataset import Dataset, FileMetaDataset
-from pydicom.encaps import encapsulate, get_frame_offsets
+from pydicom.encaps import encapsulate, parse_basic_offsets
 from pydicom.errors import InvalidDicomError
 from pydicom.filebase import DicomFileLike
 from pydicom.filereader import data_element_offset_to_value, dcmread
@@ -350,7 +350,7 @@ def _read_bot(fp: DicomFileLike) -> np.ndarray:
         fp.is_implicit_VR, 'OB'
     )
     fp.seek(pixel_data_element_value_offset - 4, 1)
-    is_empty, offsets = get_frame_offsets(fp)
+    offsets = parse_basic_offsets(fp)
     return np.array(offsets, dtype=np.uint32)
 
 

src/dicomweb_client/web.py

@@ -29,6 +29,7 @@
 )
 
 import pydicom
+from pydicom.valuerep import INT_VR, FLOAT_VR, VR
 import requests
 import retrying
 
@@ -60,7 +61,7 @@ def _load_xml_dataset(dataset: Element) -> pydicom.dataset.Dataset:
     for element in dataset:
         keyword = element.attrib['keyword']
         vr = element.attrib['vr']
-        value: Optional[Union[List[Any], str]]
+        value: Optional[Union[List[Any], str, int, float]]
         if vr == 'SQ':
             value = [
                 _load_xml_dataset(item)
@@ -74,6 +75,26 @@ def _load_xml_dataset(dataset: Element) -> pydicom.dataset.Dataset:
                 value = [v.text.strip() for v in value]
             else:
                 value = None
+
+            # Convert string values to appropriate Python types for
+            # numeric VRs to satisfy pydicom 3.0+ stricter type validation
+            if value is not None:
+                try:
+                    vr_enum = VR(vr)
+                    if vr_enum in INT_VR:
+                        if isinstance(value, list):
+                            value = [int(v) for v in value]
+                        else:
+                            value = int(value)
+                    elif vr_enum in FLOAT_VR:
+                        if isinstance(value, list):
+                            value = [float(v) for v in value]
+                        else:
+                            value = float(value)
+                except ValueError:
+                    # VR not recognized, leave value as-is
+                    pass
+
         setattr(ds, keyword, value)
     return ds
 

tests/test_web.py

@@ -776,10 +776,20 @@ def test_retrieve_instance_singlepart(httpserver, client, cache_dir):
     cache_filename = str(cache_dir.joinpath('file.dcm'))
     with open(cache_filename, 'rb') as f:
         data = f.read()
+    media_type = 'application/dicom'
+    boundary = 'boundary'
     headers = {
-        'content-type': 'application/dicom'
+        'content-type': (
+            'multipart/related; '
+            f'type="{media_type}"; '
+            f'boundary="{boundary}"'
+        ),
     }
-    httpserver.serve_content(content=data, code=200, headers=headers)
+    message = DICOMwebClient._encode_multipart_message(
+        content=[data],
+        content_type=headers['content-type']
+    )
+    httpserver.serve_content(content=message, code=200, headers=headers)
     study_instance_uid = '1.2.3'
     series_instance_uid = '1.2.4'
     sop_instance_uid = '1.2.5'
@@ -1285,8 +1295,8 @@ def test_retrieve_instance_frames_rendered_png(httpserver, client, cache_dir):
 
 def test_store_instance_error_with_retries(httpserver, client, cache_dir):
     dataset = pydicom.Dataset.from_json({})
-    dataset.is_little_endian = True
-    dataset.is_implicit_VR = True
+    dataset.file_meta = pydicom.dataset.FileMetaDataset()
+    dataset.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
     max_attempts = 2
     client.set_http_retry_params(
         retry=True,
@@ -1311,8 +1321,8 @@ def test_store_instance_error_with_retries_and_additional_params(
     httpserver, client, cache_dir
 ):
     dataset = pydicom.Dataset.from_json({})
-    dataset.is_little_endian = True
-    dataset.is_implicit_VR = True
+    dataset.file_meta = pydicom.dataset.FileMetaDataset()
+    dataset.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
     max_attempts = 2
     client.set_http_retry_params(
         retry=True,
@@ -1339,8 +1349,8 @@ def test_store_instance_error_with_retries_and_additional_params(
 
 def test_store_instance_error_with_no_retries(httpserver, client, cache_dir):
     dataset = pydicom.Dataset.from_json({})
-    dataset.is_little_endian = True
-    dataset.is_implicit_VR = True
+    dataset.file_meta = pydicom.dataset.FileMetaDataset()
+    dataset.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
     client.set_http_retry_params(retry=False)
     httpserver.serve_content(
         content='',
@@ -1360,8 +1370,8 @@ def test_store_instance_error_with_no_retries_and_additional_params(
     httpserver, client, cache_dir
 ):
     dataset = pydicom.Dataset.from_json({})
-    dataset.is_little_endian = True
-    dataset.is_implicit_VR = True
+    dataset.file_meta = pydicom.dataset.FileMetaDataset()
+    dataset.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian
     client.set_http_retry_params(retry=False)
     httpserver.serve_content(
         content='',
@@ -1527,7 +1537,7 @@ def test_delete_instance_error_with_additional_params(
 
 
 def test_load_json_dataset_da(httpserver, client, cache_dir):
-    value = ['2018-11-21']
+    value = ['20181121']  # DA format must be YYYYMMDD
     dicom_json = {
         '00080020': {
             'vr': 'DA',