Update pydicom to version 3

pixl_dcmd/pyproject.toml

@@ -9,11 +9,11 @@ classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
     "core==0.2.0rc0",
     "arrow==1.4.0",
-    "deid==0.3.25",
-    "dicom-anonymizer==1.0.13.post1",
+    "deid==0.4.12",
+    "dicom-anonymizer==2.0.0",
     "dicom-validator==0.7.3",
     "logger==1.4",
-    "pydicom==2.4.5",
+    "pydicom==3.0.2",
     "pydicom-data",
     "python-decouple==3.8",
     "requests==2.33.0",

pixl_dcmd/tests/test_tagrecording.py

@@ -21,7 +21,7 @@
 
 def test_record_dicom_headers(tmpdir, mock_header_record_path):
     ds = generate_dicom_dataset()
-    ds.save_as(str(tmpdir / "test.dcm"), write_like_original=False)
+    ds.save_as(str(tmpdir / "test.dcm"), enforce_file_format=True)
     with open(str(tmpdir / "test.dcm"), "rb") as f:
         ds_bytes = f.read()
         record_dicom_headers(ds_bytes)

pixl_imaging/pyproject.toml

@@ -10,7 +10,7 @@ dependencies = [
     "core==0.2.0rc0",
     "aiohttp==3.13.4",
     "alembic==1.18.4",
-    "pydicom==2.4.5",
+    "pydicom==3.0.2",
     "uvicorn==0.44.0",
 ]
 

pytest-pixl/pyproject.toml

@@ -9,7 +9,7 @@ classifiers = [
     "Programming Language :: Python :: 3"
 ]
 dependencies = [
-    "pydicom==2.4.5",
+    "pydicom==3.0.2",
     "pyftpdlib==2.2.0",
     "pyOpenSSL==26.0.0",
     "python-decouple==3.8",

pytest-pixl/src/pytest_pixl/dicom.py

@@ -46,10 +46,10 @@ def write_volume(filename_pattern: str) -> None:
     variables = json.loads(dicom_variables_path.open("r").read())
     rng = np.random.default_rng(0)
     for i, slice_info in enumerate(variables):
-        slice_info["pixel_data"] = rng.random(size=(256, 256))
+        slice_info["pixel_data"] = (rng.random(size=(256, 256)) * 65535).astype(np.uint16)
         ds = generate_dicom_dataset(slice_info)
         file_name = filename_pattern.format(slice=i)
-        ds.save_as(file_name, write_like_original=False)
+        ds.save_as(file_name, enforce_file_format=True)
 
 
 TAGS_DICT = {
@@ -101,7 +101,7 @@ def generate_dicom_dataset(tag_values: dict = TAGS_DICT, **kwargs: Any) -> Datas
     pixel_data = tag_values["pixel_data"]
 
     if pixel_data is None:
-        pixel_data = np.zeros((256, 256))
+        pixel_data = np.zeros((256, 256), dtype=np.uint16)
 
     ds = _generate_default_dicom_dataset()
     ds.InstanceCreationTime = instance_creation_time
@@ -131,7 +131,8 @@ def generate_dicom_dataset(tag_values: dict = TAGS_DICT, **kwargs: Any) -> Datas
     # Convert Dataset to FileDataset
     # Note: required for image operations using deid which requires FileDataset
     with tempfile.NamedTemporaryFile(suffix=".dcm") as tmp:
-        ds.save_as(tmp.name, write_like_original=False)
+        # a from_json dataset has no transfer syntax, so state the encoding here
+        ds.save_as(tmp.name, enforce_file_format=True, implicit_vr=True, little_endian=True)
         return dcmread(tmp.name)
 
 
@@ -144,11 +145,7 @@ def _generate_default_dicom_dataset() -> Dataset:
         "data/default_dicom_tags.json"
     )
     variables = json.loads(default_variables_path.open("r").read())
-    ds = Dataset.from_json(variables)
-    # Not sure why these weren't carried over to the JSON
-    ds.is_implicit_VR = True
-    ds.is_little_endian = True
-    return ds
+    return Dataset.from_json(variables)
 
 
 def _create_default_json(json_file: Path) -> None:  # noqa: PLR0915 (too many statements)
@@ -159,7 +156,7 @@ def _create_default_json(json_file: Path) -> None:  # noqa: PLR0915 (too many st
 
     :param json_file: The path to save the JSON file to.
     """
-    pixel_data = np.zeros((256, 256))
+    pixel_data = np.zeros((256, 256), dtype=np.uint16)
 
     # File meta info data elements
     file_meta = FileMetaDataset()
@@ -408,8 +405,6 @@ def _create_default_json(json_file: Path) -> None:  # noqa: PLR0915 (too many st
     ds.PixelData = pixel_data.tobytes()
 
     ds.file_meta = file_meta
-    ds.is_implicit_VR = True
-    ds.is_little_endian = True
 
     # Export as JSON dictionary
     with Path(json_file, encoding="utf-8").open("w") as f:

test/conftest.py

@@ -142,8 +142,8 @@ def _upload_dicom_instance(dicom_dir: Path, **kwargs: Any) -> None:
         dicom_dir
         / f"{kwargs['PatientID']}_{kwargs['AccessionNumber']}_{kwargs['SeriesDescription']}.dcm"
     )
-    ds.save_as(str(test_dcm_file), write_like_original=False)
     # I think we can skip writing to disk!
+    ds.save_as(str(test_dcm_file), enforce_file_format=True)
     _upload_to_vna(test_dcm_file)