Initial commit

skills/pydicom/scripts/anonymize_dicom.py

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+#!/usr/bin/env python3
+"""
+Anonymize DICOM files by removing or replacing Protected Health Information (PHI).
+
+Usage:
+    python anonymize_dicom.py input.dcm output.dcm
+    python anonymize_dicom.py input.dcm output.dcm --patient-id ANON001
+"""
+
+import argparse
+import sys
+from pathlib import Path
+
+try:
+    import pydicom
+except ImportError:
+    print("Error: pydicom is not installed. Install it with: pip install pydicom")
+    sys.exit(1)
+
+
+# Tags commonly containing PHI (Protected Health Information)
+PHI_TAGS = [
+    'PatientName', 'PatientID', 'PatientBirthDate', 'PatientBirthTime',
+    'PatientSex', 'PatientAge', 'PatientSize', 'PatientWeight',
+    'PatientAddress', 'PatientTelephoneNumbers', 'PatientMotherBirthName',
+    'MilitaryRank', 'EthnicGroup', 'Occupation', 'PatientComments',
+    'InstitutionName', 'InstitutionAddress', 'InstitutionalDepartmentName',
+    'ReferringPhysicianName', 'ReferringPhysicianAddress',
+    'ReferringPhysicianTelephoneNumbers', 'ReferringPhysicianIdentificationSequence',
+    'PerformingPhysicianName', 'PerformingPhysicianIdentificationSequence',
+    'OperatorsName', 'PhysiciansOfRecord', 'PhysiciansOfRecordIdentificationSequence',
+    'NameOfPhysiciansReadingStudy', 'PhysiciansReadingStudyIdentificationSequence',
+    'StudyDescription', 'SeriesDescription', 'AdmittingDiagnosesDescription',
+    'DerivationDescription', 'RequestingPhysician', 'RequestingService',
+    'RequestedProcedureDescription', 'ScheduledPerformingPhysicianName',
+    'PerformedLocation', 'PerformedStationName',
+]
+
+
+def anonymize_dicom(input_path, output_path, patient_id='ANONYMOUS', patient_name='ANONYMOUS'):
+    """
+    Anonymize a DICOM file by removing or replacing PHI.
+
+    Args:
+        input_path: Path to input DICOM file
+        output_path: Path to output anonymized DICOM file
+        patient_id: Replacement patient ID (default: 'ANONYMOUS')
+        patient_name: Replacement patient name (default: 'ANONYMOUS')
+    """
+    try:
+        # Read DICOM file
+        ds = pydicom.dcmread(input_path)
+
+        # Track what was anonymized
+        anonymized = []
+
+        # Remove or replace sensitive data
+        for tag in PHI_TAGS:
+            if hasattr(ds, tag):
+                if tag == 'PatientName':
+                    ds.PatientName = patient_name
+                    anonymized.append(f"{tag}: replaced with '{patient_name}'")
+                elif tag == 'PatientID':
+                    ds.PatientID = patient_id
+                    anonymized.append(f"{tag}: replaced with '{patient_id}'")
+                elif tag == 'PatientBirthDate':
+                    ds.PatientBirthDate = '19000101'
+                    anonymized.append(f"{tag}: replaced with '19000101'")
+                else:
+                    delattr(ds, tag)
+                    anonymized.append(f"{tag}: removed")
+
+        # Anonymize UIDs if present (optional - maintains referential integrity)
+        # Uncomment if you want to anonymize UIDs as well
+        # if hasattr(ds, 'StudyInstanceUID'):
+        #     ds.StudyInstanceUID = pydicom.uid.generate_uid()
+        # if hasattr(ds, 'SeriesInstanceUID'):
+        #     ds.SeriesInstanceUID = pydicom.uid.generate_uid()
+        # if hasattr(ds, 'SOPInstanceUID'):
+        #     ds.SOPInstanceUID = pydicom.uid.generate_uid()
+
+        # Save anonymized file
+        ds.save_as(output_path)
+
+        return True, anonymized
+
+    except Exception as e:
+        return False, str(e)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Anonymize DICOM files by removing or replacing PHI',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python anonymize_dicom.py input.dcm output.dcm
+  python anonymize_dicom.py input.dcm output.dcm --patient-id ANON001
+  python anonymize_dicom.py input.dcm output.dcm --patient-id ANON001 --patient-name "Anonymous^Patient"
+        """
+    )
+
+    parser.add_argument('input', type=str, help='Input DICOM file')
+    parser.add_argument('output', type=str, help='Output anonymized DICOM file')
+    parser.add_argument('--patient-id', type=str, default='ANONYMOUS',
+                       help='Replacement patient ID (default: ANONYMOUS)')
+    parser.add_argument('--patient-name', type=str, default='ANONYMOUS',
+                       help='Replacement patient name (default: ANONYMOUS)')
+    parser.add_argument('-v', '--verbose', action='store_true',
+                       help='Show detailed anonymization information')
+
+    args = parser.parse_args()
+
+    # Validate input file exists
+    input_path = Path(args.input)
+    if not input_path.exists():
+        print(f"Error: Input file '{args.input}' not found")
+        sys.exit(1)
+
+    # Anonymize the file
+    print(f"Anonymizing: {args.input}")
+    success, result = anonymize_dicom(args.input, args.output,
+                                     args.patient_id, args.patient_name)
+
+    if success:
+        print(f"✓ Successfully anonymized DICOM file: {args.output}")
+        if args.verbose:
+            print(f"\nAnonymized {len(result)} fields:")
+            for item in result:
+                print(f"  - {item}")
+    else:
+        print(f"✗ Error: {result}")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()