Added DICOM text SR assets and updated all operator test functions.

Author: MMelQin

monai/deploy/core/domain/dicom_sop_instance.py

@@ -21,9 +21,9 @@
 Dataset_, dataset_ok_ = optional_import("pydicom", name="Dataset")
 # Dynamic class is not handled so make it Any for now: https://github.com/python/mypy/issues/2477
 Dataset: Any = Dataset_ if dataset_ok_ else Any
-TagType_, tagtype_ok_ = optional_import("pydicom.tag", name="TagType")
+Tag_, tag_ok_ = optional_import("pydicom.tag", name="Tag")
 # Dynamic class is not handled so make it Any for now: https://github.com/python/mypy/issues/2477
-TagType: Any = TagType_ if tagtype_ok_ else Any
+Tag: Any = Tag_ if tag_ok_ else Any
 
 
 class DICOMSOPInstance(Domain):
@@ -39,7 +39,7 @@ def __init__(self, native_sop):
     def get_native_sop_instance(self):
         return self._sop
 
-    def __getitem__(self, key: Union[int, slice, TagType]) -> Union[Dataset, DataElement]:
+    def __getitem__(self, key: Union[int, slice, Tag]) -> Union[Dataset, DataElement]:
         return self._sop.__getitem__(key)
 
     def get_pixel_array(self):

monai/deploy/operators/__init__.py

@@ -26,6 +26,7 @@
 from .dicom_seg_writer_operator import DICOMSegmentationWriterOperator
 from .dicom_series_selector_operator import DICOMSeriesSelectorOperator
 from .dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
+from .dicom_text_sr_writer_operator import DICOMTestSRWriterOperator, EquipmentInfo, ModelInfo
 from .inference_operator import InferenceOperator
 from .monai_seg_inference_operator import MonaiSegInferenceOperator
 from .png_converter_operator import PNGConverterOperator

monai/deploy/operators/dicom_data_loader_operator.py

@@ -245,16 +245,50 @@ def populate_series_attributes(self, series, sop_instance):
 
 
 def test():
-    data_path = "../../../examples/ai_spleen_seg_data/dcm"
+    current_file_dir = Path(__file__).parent.resolve()
+    data_path = current_file_dir.joinpath("../../../examples/ai_spleen_seg_data/dcm")
 
     loader = DICOMDataLoaderOperator()
-    study_list = loader.load_data_to_studies(Path(data_path).absolute())
+    study_list = loader.load_data_to_studies(data_path.absolute())
 
     for study in study_list:
         print("###############################")
         print(study)
         for series in study.get_all_series():
             print(series)
+        for series in study.get_all_series():
+            for sop in series.get_sop_instances():
+                print("Demonstrating ways to access DICOM attributes in a SOP instance.")
+                # No need to get the native_ds = sop.get_native_sop_instance()
+                # sop = sop.get_native_sop_instance()
+                print(f"   'StudyInstanceUID': {sop['StudyInstanceUID'].repval}")
+                print(f"     (0x0020, 0x000D): {sop[0x0020, 0x000D].repval}")
+                print(f"  'SeriesInstanceUID': {sop['SeriesInstanceUID'].value.name}")
+                print(f"     (0x0020, 0x000E): {sop[0x0020, 0x000E].value.name}")
+                print(f"     'SOPInstanceUID': {sop['SOPInstanceUID'].value.name}")
+                print(f"          (0008,0018): {sop[0x0008, 0x0018].value.name}")
+                try:
+                    print(f"     'InstanceNumber': {sop['InstanceNumber'].repval}")
+                    print(f"         (0020, 0013): {sop[0x0020, 0x0013].repval}")
+                except KeyError:
+                    pass
+                # Need to get pydicom dataset to use properties and get method of a dict.
+                ds = sop.get_native_sop_instance()
+                print(f"   'StudyInstanceUID': {ds.StudyInstanceUID if ds.StudyInstanceUID else ''}")
+                print(f"  'SeriesDescription': {ds.SeriesDescription if ds.SeriesDescription else ''}")
+                print(
+                    f"  'IssuerOfPatientID': {ds.get('IssuerOfPatientID', '').repval if ds.get('IssuerOfPatientID', '') else '' }"
+                )
+                try:
+                    print(f"  'IssuerOfPatientID': {ds.IssuerOfPatientID if ds.IssuerOfPatientID else '' }")
+                except AttributeError:
+                    print(
+                        "    If the IssuerOfPatientID does not exist, ds.IssuerOfPatientID would throw AttributeError."
+                    )
+                    print("    Use ds.get('IssuerOfPatientID', '') instead.")
+
+                break
+            break
 
 
 if __name__ == "__main__":

monai/deploy/operators/dicom_seg_writer_operator.py

@@ -660,17 +660,17 @@ def test():
     from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
     from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
 
-    data_path = "../../../examples/ai_spleen_seg_data/dcm"
-    out_path = "../../../examples/output_seg_op/dcm_seg_test.dcm"
+    current_file_dir = Path(__file__).parent.resolve()
+    data_path = current_file_dir.joinpath("../../../examples/ai_spleen_seg_data/dcm")
+    out_path = current_file_dir.joinpath("../../../examples/output_seg_op/dcm_seg_test.dcm")
 
-    files = []
     loader = DICOMDataLoaderOperator()
     series_selector = DICOMSeriesSelectorOperator()
     dcm_to_volume_op = DICOMSeriesToVolumeOperator()
     seg_writer = DICOMSegmentationWriterOperator()
 
     # Testing with more granular functions
-    study_list = loader.load_data_to_studies(Path(data_path).absolute())
+    study_list = loader.load_data_to_studies(data_path.absolute())
     series = study_list[0].get_all_series()[0]
 
     dcm_to_volume_op.prepare_series(series)
@@ -682,10 +682,10 @@ def test():
     seg_writer.create_dicom_seg(image_numpy, series, Path(out_path).absolute())
 
     # Testing with the main entry functions
-    study_list = loader.load_data_to_studies(Path(data_path).absolute())
-    _, study_selected_series_list = series_selector.filter(None, study_list)
+    study_list = loader.load_data_to_studies(data_path.absolute())
+    study_selected_series_list = series_selector.filter(None, study_list)
     image = dcm_to_volume_op.convert_to_image(study_selected_series_list)
-    seg_writer.process_images(image, study_selected_series_list, Path(out_path).parent.absolute())
+    seg_writer.process_images(image, study_selected_series_list, out_path.parent.absolute())
 
 
 if __name__ == "__main__":

monai/deploy/operators/dicom_series_selector_operator.py

@@ -277,14 +277,15 @@ def test():
 
     from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
 
-    data_path = "../../../examples/ai_spleen_seg_data/dcm-multi"
+    current_file_dir = Path(__file__).parent.resolve()
+    data_path = current_file_dir.joinpath("../../../examples/ai_spleen_seg_data/dcm-multi")
 
     loader = DICOMDataLoaderOperator()
-    study_list = loader.load_data_to_studies(Path(data_path).absolute())
+    study_list = loader.load_data_to_studies(data_path.absolute())
     selector = DICOMSeriesSelectorOperator()
     sample_selection_rule = json_loads(Sample_Rules_Text)
     print(f"Selection rules in JSON:\n{sample_selection_rule}")
-    series_list, study_selected_seriee_list = selector.filter(sample_selection_rule, study_list)
+    study_selected_seriee_list = selector.filter(sample_selection_rule, study_list)
 
     for sss_obj in study_selected_seriee_list:
         _print_instance_properties(sss_obj, pre_fix="", print_val=False)
@@ -314,7 +315,7 @@ def test():
                 _print_instance_properties(ss_obj, pre_fix)
                 print(f"{pre_fix}===============================")
 
-    print(f"Total # of series selected: {len(series_list)}")
+        print(f"  A total of {len(sss_obj.selected_series)} series selected for study {study.StudyInstanceUID}")
 
 
 # Sample rule used for testing

monai/deploy/operators/dicom_series_to_volume_operator.py

@@ -346,12 +346,13 @@ def test():
     from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
     from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
 
-    data_path = "../../../examples/ai_spleen_seg_data/dcm"
+    current_file_dir = Path(__file__).parent.resolve()
+    data_path = current_file_dir.joinpath("../../../examples/ai_spleen_seg_data/dcm")
     loader = DICOMDataLoaderOperator()
     study_list = loader.load_data_to_studies(Path(data_path).absolute())
 
     series_selector = DICOMSeriesSelectorOperator()
-    _, study_selected_series_list = series_selector.filter(None, study_list)
+    study_selected_series_list = series_selector.filter(None, study_list)
 
     op = DICOMSeriesToVolumeOperator()
     image = op.convert_to_image(study_selected_series_list)