dicom-metadata-extract

DICOM Metadata Extract

Purpose

• Used for extracting selected metadata from one DICOM file and flagging standard-tag PHI presence. Not for anonymization or clinical use.
• Use the wrapper exactly as documented; do not replace the upstream entrypoint with a handwritten implementation.
• Manifest I/O: inputs are dicom_path; outputs are metadata_json.

Instructions

• Read skill_manifest.yaml before changing arguments, side effects, or validation gates.
• Run scripts/extract_metadata.py through the documented command below; keep outputs under a caller-provided run directory.
• If a host agent exposes run_script, use run_script("scripts/extract_metadata.py", args=[...]); otherwise run the Bash/Python command shown below.
• Check the emitted JSON and run medagent.verifiers.dicom_metadata_quality_v1 on evidence packs before treating the run as reviewed evidence.

Available Scripts

Script	Purpose	Arguments
scripts/extract_metadata.py	Primary entrypoint declared by skill_manifest.yaml.	PATH_TO_DICOM [--output OUT.json]

Prerequisites

• Runtime requirements: Python packages listed in runtime.side_effects.pip_packages.
• Run commands from the repository root unless an existing section below says otherwise.

Limitations

• Small PS3.15-inspired standard-tag subset only; not a complete Basic Application Confidentiality Profile implementation.
• Private tags not checked
• Burnt-in pixel PHI not detected
• Multi-frame handling minimal
• Not for clinical deployment, regulatory de-identification, autonomous diagnosis, patient-facing use.

Troubleshooting

Error	Cause	Fix
Missing dependency or import error	Runtime package drift from skill_manifest.yaml.	Install the packages declared in the manifest or use the documented setup command.
Empty or schema-invalid output	Wrong input path, unsupported modality, or upstream failure.	Re-run with a known fixture and inspect the wrapper JSON plus stderr.
Validation gate failure	Output violated a declared engineering invariant.	Keep the failed evidence pack and use the gate message to repair inputs or wrapper code.

Reads one DICOM file with pydicom and emits JSON on stdout.

python scripts/extract_metadata.py PATH_TO_DICOM
python scripts/extract_metadata.py PATH_TO_DICOM --output result.json

Output includes transfer_syntax, modality, grouped study/series/image metadata, phi_present, and phi_tags_found.

Use this as the smallest end-to-end example of a Medical AI Skills skill. Do not use it for anonymization, private-tag review, pixel PHI detection, or clinical interpretation.

For second-pass evidence review, generate a trusted run:

python -m eval_engine.run_trusted skills/dicom-metadata-extract \
  --fixture skills/dicom-metadata-extract/fixtures/sample_ct.dcm \
  --out runs/dicom_metadata_trusted