Initial commit

skills/pydicom/scripts/extract_metadata.py

@@ -0,0 +1,173 @@
+#!/usr/bin/env python3
+"""
+Extract and display DICOM metadata in a readable format.
+
+Usage:
+    python extract_metadata.py file.dcm
+    python extract_metadata.py file.dcm --output metadata.txt
+    python extract_metadata.py file.dcm --format json --output metadata.json
+"""
+
+import argparse
+import sys
+import json
+from pathlib import Path
+
+try:
+    import pydicom
+except ImportError:
+    print("Error: pydicom is not installed. Install it with: pip install pydicom")
+    sys.exit(1)
+
+
+def format_value(value):
+    """Format DICOM values for display."""
+    if isinstance(value, bytes):
+        try:
+            return value.decode('utf-8', errors='ignore')
+        except:
+            return str(value)
+    elif isinstance(value, pydicom.multival.MultiValue):
+        return ', '.join(str(v) for v in value)
+    elif isinstance(value, pydicom.sequence.Sequence):
+        return f"Sequence with {len(value)} item(s)"
+    else:
+        return str(value)
+
+
+def extract_metadata_text(ds, show_sequences=False):
+    """Extract metadata as formatted text."""
+    lines = []
+    lines.append("=" * 80)
+    lines.append("DICOM Metadata")
+    lines.append("=" * 80)
+
+    # File Meta Information
+    if hasattr(ds, 'file_meta'):
+        lines.append("\n[File Meta Information]")
+        for elem in ds.file_meta:
+            lines.append(f"{elem.name:40s} {format_value(elem.value)}")
+
+    # Patient Information
+    lines.append("\n[Patient Information]")
+    patient_tags = ['PatientName', 'PatientID', 'PatientBirthDate',
+                   'PatientSex', 'PatientAge', 'PatientWeight']
+    for tag in patient_tags:
+        if hasattr(ds, tag):
+            value = getattr(ds, tag)
+            lines.append(f"{tag:40s} {format_value(value)}")
+
+    # Study Information
+    lines.append("\n[Study Information]")
+    study_tags = ['StudyInstanceUID', 'StudyDate', 'StudyTime',
+                 'StudyDescription', 'AccessionNumber', 'StudyID']
+    for tag in study_tags:
+        if hasattr(ds, tag):
+            value = getattr(ds, tag)
+            lines.append(f"{tag:40s} {format_value(value)}")
+
+    # Series Information
+    lines.append("\n[Series Information]")
+    series_tags = ['SeriesInstanceUID', 'SeriesNumber', 'SeriesDescription',
+                  'Modality', 'SeriesDate', 'SeriesTime']
+    for tag in series_tags:
+        if hasattr(ds, tag):
+            value = getattr(ds, tag)
+            lines.append(f"{tag:40s} {format_value(value)}")
+
+    # Image Information
+    lines.append("\n[Image Information]")
+    image_tags = ['SOPInstanceUID', 'InstanceNumber', 'ImageType',
+                 'Rows', 'Columns', 'BitsAllocated', 'BitsStored',
+                 'PhotometricInterpretation', 'SamplesPerPixel',
+                 'PixelSpacing', 'SliceThickness', 'ImagePositionPatient',
+                 'ImageOrientationPatient', 'WindowCenter', 'WindowWidth']
+    for tag in image_tags:
+        if hasattr(ds, tag):
+            value = getattr(ds, tag)
+            lines.append(f"{tag:40s} {format_value(value)}")
+
+    # All other elements
+    if show_sequences:
+        lines.append("\n[All Elements]")
+        for elem in ds:
+            if elem.VR != 'SQ':  # Skip sequences for brevity
+                lines.append(f"{elem.name:40s} {format_value(elem.value)}")
+            else:
+                lines.append(f"{elem.name:40s} {format_value(elem.value)}")
+
+    return '\n'.join(lines)
+
+
+def extract_metadata_json(ds):
+    """Extract metadata as JSON."""
+    metadata = {}
+
+    # File Meta Information
+    if hasattr(ds, 'file_meta'):
+        metadata['file_meta'] = {}
+        for elem in ds.file_meta:
+            metadata['file_meta'][elem.keyword] = format_value(elem.value)
+
+    # All data elements (excluding sequences for simplicity)
+    metadata['dataset'] = {}
+    for elem in ds:
+        if elem.VR != 'SQ':
+            metadata['dataset'][elem.keyword] = format_value(elem.value)
+
+    return json.dumps(metadata, indent=2)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Extract and display DICOM metadata',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python extract_metadata.py file.dcm
+  python extract_metadata.py file.dcm --output metadata.txt
+  python extract_metadata.py file.dcm --format json --output metadata.json
+  python extract_metadata.py file.dcm --show-sequences
+        """
+    )
+
+    parser.add_argument('input', type=str, help='Input DICOM file')
+    parser.add_argument('--output', '-o', type=str, help='Output file (default: print to console)')
+    parser.add_argument('--format', type=str, choices=['text', 'json'], default='text',
+                       help='Output format (default: text)')
+    parser.add_argument('--show-sequences', action='store_true',
+                       help='Include all data elements including sequences')
+
+    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)
+
+    try:
+        # Read DICOM file
+        ds = pydicom.dcmread(args.input)
+
+        # Extract metadata
+        if args.format == 'json':
+            output = extract_metadata_json(ds)
+        else:
+            output = extract_metadata_text(ds, args.show_sequences)
+
+        # Write or print output
+        if args.output:
+            with open(args.output, 'w') as f:
+                f.write(output)
+            print(f"✓ Metadata extracted to: {args.output}")
+        else:
+            print(output)
+
+    except Exception as e:
+        print(f"✗ Error: {e}")
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()