DICOM Text SR Writer Updates

monai/deploy/operators/dicom_seg_writer_operator.py

@@ -1,4 +1,4 @@
-# Copyright 2021-2025 MONAI Consortium
+# Copyright 2021-2026 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -382,7 +382,7 @@ def create_dicom_seg(self, image: np.ndarray, dicom_series: DICOMSeries, output_
             seg_purpose_of_reference_code = Dataset()
             seg_purpose_of_reference_code.CodeValue = "Newcode1"
             seg_purpose_of_reference_code.CodingSchemeDesignator = "99IHE"
-            seg_purpose_of_reference_code.CodeMeaning = '"Processing Algorithm'
+            seg_purpose_of_reference_code.CodeMeaning = "Processing Algorithm"
             seq_purpose_of_reference_code.append(seg_purpose_of_reference_code)
 
             seq_contributing_equipment = PyDicomSequence()

monai/deploy/operators/dicom_text_sr_writer_operator.py

@@ -1,4 +1,4 @@
-# Copyright 2021-2022 MONAI Consortium
+# Copyright 2021-2026 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -96,6 +96,7 @@ def __init__(
         #   "SR" for Structured Report.
         # Media Storage SOP Class UID, e.g.,
         #   "1.2.840.10008.5.1.4.1.1.88.11" for Basic Text SR Storage
+        #   "1.2.840.10008.5.1.4.1.1.88.22" for Enhanced SR
         #   "1.2.840.10008.5.1.4.1.1.104.1" for Encapsulated PDF Storage,
         #   "1.2.840.10008.5.1.4.1.1.88.34" for Comprehensive 3D SR IOD
         #   "1.2.840.10008.5.1.4.1.1.66.4" for Segmentation Storage
@@ -192,8 +193,12 @@ def write(self, content_text, dicom_series: Optional[DICOMSeries], output_dir: P
         )
 
         # SR specific
+        ds.CompletionFlag = "COMPLETE"  # Estimated degree of completeness.
         ds.VerificationFlag = "UNVERIFIED"  # Not attested by a legally accountable person.
 
+        ds.ReferencedPerformedProcedureStepSequence = Sequence([])  # Required by SR Document Series
+        ds.PerformedProcedureCodeSequence = Sequence([])  # Required by SR Document General
+
         # Per recommendation of IHE Radiology Technical Framework Supplement
         # AI Results (AIR) Rev1.1 - Trial Implementation
         # Specifically for Qualitative Findings,

monai/deploy/operators/dicom_utils.py

@@ -1,4 +1,4 @@
-# Copyright 2022 MONAI Consortium
+# Copyright 2022-2026 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -198,8 +198,8 @@ def write_common_modules(
 
     # File meta info data set
     file_meta = Dataset()
-    file_meta.FileMetaInformationGroupLength = 198
-    file_meta.FileMetaInformationVersion = bytes("01", "utf-8")  # '\x00\x01'
+    # file_meta.FileMetaInformationGroupLength = 198
+    file_meta.FileMetaInformationVersion = b"\x00\x01"  # '\x00\x01'
 
     file_meta.MediaStorageSOPClassUID = sop_class_uid
     file_meta.MediaStorageSOPInstanceUID = my_sop_instance_uid
@@ -282,7 +282,7 @@ def write_common_modules(
         ds_purpose_of_reference_code = Dataset()
         ds_purpose_of_reference_code.CodeValue = "Newcode1"
         ds_purpose_of_reference_code.CodingSchemeDesignator = "99IHE"
-        ds_purpose_of_reference_code.CodeMeaning = '"Processing Algorithm'
+        ds_purpose_of_reference_code.CodeMeaning = "Processing Algorithm"
         seq_purpose_of_reference_code.append(ds_purpose_of_reference_code)
 
         seq_contributing_equipment = Sequence()

requirements-min.txt

@@ -1,5 +1,5 @@
 # Requirements for minimal tests
 -r requirements.txt
-setuptools>=59.5.0
+setuptools>=59.5.0,<81.0.0 # pkg_resources deprecation
 coverage>=5.5
 parameterized

tests/fixtures/runner_fixtures.py

@@ -36,8 +36,7 @@ def sample_map_name():
 
 @pytest.fixture(scope="session")
 def faux_app_manifest():
-    app_manifest = json.loads(
-        """{
+    app_manifest = json.loads("""{
         "command": "/usr/bin/python3 -u /opt/monai/app/main.py",
         "input": {
             "path": "input",
@@ -63,15 +62,13 @@ def faux_app_manifest():
         },
         "timeout": 600,
         "working-directory": "/var/monai"
-        }"""
-    )
+        }""")
     yield app_manifest
 
 
 @pytest.fixture(scope="session")
 def faux_pkg_manifest_with_gpu():
-    pkg_manifest = json.loads(
-        """{
+    pkg_manifest = json.loads("""{
         "sdk-version": "0.0.0",
         "models": [
             {
@@ -85,15 +82,13 @@ def faux_pkg_manifest_with_gpu():
             "memory": "4Gi"
         }
         }
-    """
-    )
+    """)
     yield pkg_manifest
 
 
 @pytest.fixture(scope="session")
 def faux_pkg_manifest():
-    pkg_manifest = json.loads(
-        """{
+    pkg_manifest = json.loads("""{
         "sdk-version": "0.0.0",
         "models": [
             {
@@ -106,16 +101,14 @@ def faux_pkg_manifest():
             "memory": "4Gi"
         }
         }
-    """
-    )
+    """)
     yield pkg_manifest
 
 
 @pytest.fixture(scope="session")
 def faux_app_manifest_with_absolute_path():
     """App manifest with absolute input and output paths"""
-    app_manifest = json.loads(
-        """{
+    app_manifest = json.loads("""{
         "command": "/usr/bin/python3 -u /opt/monai/app/main.py",
         "input": {
             "path": "/input",
@@ -141,8 +134,7 @@ def faux_app_manifest_with_absolute_path():
         },
         "timeout": 600,
         "working-directory": "/var/monai"
-        }"""
-    )
+        }""")
     yield app_manifest
 
 

tools/pipeline-generator/tests/test_cli.py

@@ -142,13 +142,11 @@ def test_list_command_with_config(self):
         with self.runner.isolated_filesystem():
             # Create a test config file
             with open("test_config.yaml", "w") as f:
-                f.write(
-                    """
+                f.write("""
 endpoints:
   - organization: "TestOrg"
     description: "Test organization"
-"""
-                )
+""")
 
             # Run command with config file
             with patch("pipeline_generator.cli.main.HuggingFaceClient") as mock_client_class: