dicomlock 0.7.0__py3-none-any.whl

dicomlock-0.7.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: dicomlock
+Version: 0.7.0
+Summary: Open-source, self-hosted DICOM file-security scanner + Content Disarm & Reconstruction (CDR)
+Author: Vijay Thakore
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://dicomlock.com
+Project-URL: Repository, https://github.com/vthakore23/dicomlock
+Project-URL: Issues, https://github.com/vthakore23/dicomlock/issues
+Keywords: dicom,security,cdr,content-disarm,medical-imaging,pacs,polyglot
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Security
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydicom>=2.4.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: python-gdcm>=3.0.0
+Requires-Dist: pylibjpeg>=2.0.0
+Requires-Dist: pylibjpeg-libjpeg>=2.0.0
+Requires-Dist: pylibjpeg-openjpeg>=2.0.0
+Provides-Extra: server
+Requires-Dist: fastapi>=0.110.0; extra == "server"
+Requires-Dist: uvicorn>=0.29.0; extra == "server"
+Requires-Dist: python-multipart>=0.0.9; extra == "server"
+Provides-Extra: full
+Requires-Dist: scipy>=1.11.0; extra == "full"
+Requires-Dist: scikit-image>=0.21.0; extra == "full"
+Requires-Dist: Pillow>=10.0.0; extra == "full"
+Requires-Dist: PyWavelets>=1.4.0; extra == "full"
+Dynamic: license-file
+
+# DicomLock
+
+Open-source, self-hosted security for DICOM medical-image files. It scans a file for the ways it can be weaponized, then disarms it by rebuilding a clean, clinically identical copy.
+
+[![PyPI](https://img.shields.io/pypi/v/dicomlock.svg)](https://pypi.org/project/dicomlock/)
+[![License: Apache 2.0](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+
+A DICOM file is not just a picture. It is input for a parser, and hospital software has to read and decode all of it before anyone sees an image. That step is the attack surface. DicomLock checks the file for polyglot malware, parser-exploit constructions, and pixel data that routes through vulnerable image or video codecs, then rebuilds a clean version before the file reaches a PACS, viewer, or model. It runs inside your network, so no patient data leaves the building.
+
+This is Content Disarm and Reconstruction (CDR) for DICOM, built to be open and auditable.
+
+## Install
+
+```bash
+pip install dicomlock
+```
+
+The core install pulls in the decoder backends (gdcm and pylibjpeg) so disarm works out of the box. Two optional extras:
+
+```bash
+pip install "dicomlock[server]"   # web UI and REST API
+pip install "dicomlock[full]"     # PHI / de-identification audit and legacy forensics
+```
+
+Python 3.10 or newer.
+
+## Usage
+
+```bash
+dicomlock file.dcm                 # scan one file
+dicomlock folder/                  # scan every .dcm in a folder
+dicomlock folder/ --disarm         # scan, then disarm or quarantine each file
+dicomlock file.dcm --deid          # add the PHI / de-identification audit
+```
+
+As a library:
+
+```python
+from scanner.pipeline import run_security_scan, disarm_or_quarantine, is_dangerous
+
+report = run_security_scan("file.dcm")
+if is_dangerous(report):
+    result = disarm_or_quarantine("file.dcm")   # {"action": "disarmed" | "quarantined", ...}
+```
+
+Web UI and API:
+
+```bash
+python server.py    # http://localhost:8899
+```
+
+Uploads are scanned in a temp directory and deleted right after, so PHI is never persisted.
+
+## How it works
+
+1. **Scan.** Deterministic, rule-based checks, no ML: preamble and polyglot signatures, length amplification, sequence-nesting depth, pixel-dimension and decompression bombs, private-tag payloads, codec-CVE exposure, and metadata integrity.
+2. **Disarm.** For files that are dangerous but recoverable, it zeroes the preamble, transcodes compressed pixels to native off the vulnerable codec (in a sandboxed subprocess), and filters private tags against a vendor allowlist. Lossless sources come out bit-exact. Lossy sources are decoded once with no new compression.
+3. **Quarantine.** Anything it cannot safely rebuild, such as length bombs and files no backend can decode, is held back. It re-scans its own output, so it never emits a file that still fails a check.
+
+The point of CDR is that it rebuilds from a validated canonical form instead of matching a known signature, so it neutralizes attacks it has never seen. That is the defense that holds up when vulnerabilities turn up faster than anyone can patch them, which is the situation for the systems a patch cycle reaches slowly: legacy and embedded medical devices, and software locked behind FDA recertification.
+
+## Why this is a real problem
+
+The 128-byte preamble can hold an executable header, so one file can be a valid scan and working malware at the same time (CVE-2019-11687, extended to Linux devices by ELFDICOM). Attacker-controlled length fields turn a 140-byte file into a multi-gigabyte allocation request. Encapsulated pixel and video data decodes through libjpeg, OpenJPEG, CharLS, and FFmpeg-class libraries that carry long CVE histories. Live examples in clinical software include the Orthanc auth bypass (CVE-2025-0896, CVSS 9.8) and MicroDicom remote code execution (CVE-2025-5943).
+
+DicomLock works on the file. It does not break or weaken encryption and makes no claim to.
+
+## Results
+
+All reproducible from the scripts in [`_attack_test/`](_attack_test/):
+
+- Zero false positives across 575 real clinical CT files, and zero on a separate mixed-compression corpus spanning 12 transfer syntaxes.
+- 20 of 20 crafted attack fixtures flagged by the expected check.
+- pydicom, GDCM, and dcmtk accept the weaponized files without complaint; DicomLock flags every one.
+- Disarmed pixels are bit-exact against two independent decoders (GDCM and pylibjpeg) on every lossless sample.
+- The codec decode is sandboxed, so a crashing or hanging decoder is contained and the file is quarantined, not the tool.
+
+The attack fixtures in this repo are inert. Polyglots carry only magic bytes, and payload tags carry a header plus zero padding. No working malware ships here.
+
+## Where it fits
+
+Commercial DICOM CDR already exists (OPSWAT, Votiro), and there is academic prior art, so "nobody does this" is not the pitch. DicomLock's reason to exist is that it is open, self-hosted, auditable, and PACS-depth. The transcoding, the vendor allowlist, and the parser-bomb rejection are all readable in source and run inside your network. The natural first users are research-imaging and data-engineering teams that already ingest untrusted external DICOM.
+
+It is a security and sanitization tool, not a medical device. It carries no diagnostic claim and no FDA clearance. See [THREAT_MODEL.md](THREAT_MODEL.md) for what it does and does not defend.
+
+## Documentation
+
+- [THREAT_MODEL.md](THREAT_MODEL.md), attacks defended and explicit non-claims
+- [ARCHITECTURE.md](ARCHITECTURE.md), module specs
+- [CONTRIBUTING.md](CONTRIBUTING.md), how to help with the CVE map, vendor allowlist, and codecs
+- [SECURITY.md](SECURITY.md), vulnerability disclosure
+
+## License
+
+[Apache-2.0](LICENSE), © 2026 Vijay Thakore. Provided as is, without warranty. DicomLock is a sanitization tool, not a medical device, and makes no diagnostic claim. Validate disarmed files in your own environment before any clinical use, and run on de-identified data where you can.

dicomlock-0.7.0.dist-info/RECORD

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dicomlock-0.7.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

dicomlock-0.7.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+dicomlock = scanner.cli:main

dicomlock-0.7.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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dicomlock-0.7.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+scanner

scanner/_resources.py

@@ -0,0 +1,20 @@
+"""Locate packaged config data (codec-CVE map, vendor allowlist).
+
+Resolves to scanner/data/<name> whether running from source or pip-installed. Falls back to a
+project-root data/ dir so legacy/custom copies still work.
+"""
+
+import os
+
+_HERE = os.path.dirname(os.path.abspath(__file__))
+
+
+def data_file(name: str) -> str:
+    candidates = [
+        os.path.join(_HERE, "data", name),                       # packaged (canonical)
+        os.path.join(os.path.dirname(_HERE), "data", name),      # project-root fallback
+    ]
+    for path in candidates:
+        if os.path.exists(path):
+            return path
+    return candidates[0]

scanner/_sandbox.py

@@ -0,0 +1,107 @@
+"""
+DicomLock — sandboxed pixel decode for CDR.
+
+This is the ONE place DicomLock invokes a third-party image codec (libjpeg / OpenJPEG /
+CharLS / OpenJPH / RLE) on untrusted bytes. Decoding compressed pixel data is the deep
+memory-safety attack surface (the codec CVE class). We never run it in the tool's own process:
+the decode happens in a resource-limited child process, so a codec segfault, OOM, or hang kills
+the worker, and the caller quarantines the file instead of crashing the scanner.
+
+This makes the "tool must not become the victim" property in THREAT_MODEL.md real rather than
+just a deployment recommendation. Allocation/length/decompression bombs are still rejected by the
+header-level checks BEFORE this worker is ever spawned; the rlimits here are defense in depth and
+the timeout/signal handling is what contains a genuine codec memory fault.
+
+The worker is invoked by file path (`python3 scanner/_sandbox.py <in> <out>`), so it has no
+dependency on DicomLock's package imports and stays self-contained.
+"""
+
+import os
+import subprocess
+import sys
+
+# A codec decode on real clinical data is fast (ms). A worker that needs more than this much
+# wall-clock or memory is treating the input as hostile; we kill it and quarantine.
+TIMEOUT_S = 30
+MEM_LIMIT_BYTES = 2 * 1024 ** 3  # 2 GiB address-space cap per worker
+
+# The child script the parent spawns. Module-level so a containment self-test can point it at a
+# deliberately crashing/hanging worker without shipping a vulnerable codec (see test_sandbox.py).
+_WORKER = os.path.abspath(__file__)
+
+
+def _limit_resources():
+    """Run in the child between fork and exec: cap address space + CPU time. Best-effort
+    (RLIMIT_AS is weakly enforced on some platforms); the subprocess timeout and signal-exit
+    detection below are the portable backstops for hang and crash."""
+    try:
+        import resource
+        resource.setrlimit(resource.RLIMIT_AS, (MEM_LIMIT_BYTES, MEM_LIMIT_BYTES))
+        resource.setrlimit(resource.RLIMIT_CPU, (TIMEOUT_S, TIMEOUT_S))
+    except Exception:
+        pass
+
+
+def safe_transcode_to_native(in_path: str, out_path: str, timeout: int = TIMEOUT_S):
+    """Decode `in_path` and rewrite it as native Explicit VR LE at `out_path`, in a sandboxed
+    child process. Returns (ok: bool, reason: str).
+
+    ok=False means the codec crashed, hung, exhausted memory, or otherwise failed — the file is
+    NOT disarmable and the caller MUST quarantine it (we never trust a file whose decode
+    misbehaved). ok=True means `out_path` is a clean native file the parent can safely re-open
+    without ever invoking a codec again.
+    """
+    argv = [sys.executable, _WORKER, in_path, out_path]
+    try:
+        proc = subprocess.run(
+            argv, capture_output=True, timeout=timeout,
+            preexec_fn=_limit_resources if os.name == "posix" else None,
+        )
+    except subprocess.TimeoutExpired:
+        _unlink(out_path)
+        return False, f"sandboxed decode hung (> {timeout}s) — denial-of-service codec input"
+
+    if proc.returncode == 0 and os.path.exists(out_path) and os.path.getsize(out_path) > 0:
+        return True, "ok"
+
+    _unlink(out_path)
+    if proc.returncode < 0:
+        return False, (f"sandboxed decode crashed (killed by signal {-proc.returncode}) — "
+                       "codec memory fault; file quarantined")
+    last = (proc.stderr.decode("utf-8", "ignore").strip().splitlines() or ["decode failed"])[-1]
+    return False, f"sandboxed decode failed: {last[:200]}"
+
+
+def _unlink(path: str):
+    try:
+        os.unlink(path)
+    except OSError:
+        pass
+
+
+def _worker(in_path: str, out_path: str) -> int:
+    """Child entry point: decode pixels (the dangerous codec call) and save native. Any failure
+    exits non-zero so the parent quarantines; a memory fault exits via signal, also caught."""
+    import pydicom
+    from pydicom.uid import ExplicitVRLittleEndian
+
+    ds = pydicom.dcmread(in_path, force=True)
+    try:
+        ds.decompress()  # primary path: decode + set TransferSyntaxUID = Explicit VR LE
+    except Exception:
+        # Fallback: decode to an array and store raw uncompressed.
+        arr = ds.pixel_array
+        ds.PixelData = arr.tobytes()
+        ds.file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
+        ds["PixelData"].VR = "OW" if int(getattr(ds, "BitsAllocated", 16)) > 8 else "OB"
+
+    try:
+        ds.save_as(out_path)
+    except TypeError:
+        ds.save_as(out_path, enforce_file_format=False)
+    return 0
+
+
+if __name__ == "__main__":
+    _limit_resources()
+    sys.exit(_worker(sys.argv[1], sys.argv[2]))

scanner/calibration.py

@@ -0,0 +1,157 @@
+"""
+DicomLock — Calibration Pipeline
+
+Runs feature extraction on a corpus of known-real DICOM files to establish
+per-modality baselines. These baselines define "what normal looks like"
+so the scanner can flag statistical outliers.
+
+Usage:
+    from scanner.calibration import calibrate, load_baselines
+
+    # Build baselines from a directory of real DICOM files
+    calibrate("path/to/real/dicoms", "data/baselines.json")
+
+    # Load baselines for use in scanning
+    baselines = load_baselines("data/baselines.json")
+"""
+
+import json
+import os
+import sys
+from collections import defaultdict
+from pathlib import Path
+
+import numpy as np
+import pydicom
+
+from scanner.pixel_advanced import extract_all_features
+
+
+def calibrate(dicom_dir: str, output_path: str, verbose: bool = True) -> dict:
+    """
+    Run feature extraction on all DICOM files in a directory
+    and compute per-modality baseline statistics.
+
+    Args:
+        dicom_dir: Path to directory containing real DICOM files
+        output_path: Where to save the baselines JSON
+        verbose: Print progress
+
+    Returns:
+        The baselines dict (also saved to output_path)
+    """
+    # Collect all DICOM files
+    dcm_files = sorted(Path(dicom_dir).rglob("*.dcm"))
+    if verbose:
+        print(f"Found {len(dcm_files)} DICOM files in {dicom_dir}")
+
+    # Extract features from every file, grouped by modality
+    modality_features = defaultdict(list)
+    errors = 0
+    skipped = 0
+
+    for i, filepath in enumerate(dcm_files):
+        try:
+            ds = pydicom.dcmread(str(filepath), force=True)
+            features = extract_all_features(ds)
+
+            if features is None:
+                skipped += 1
+                continue
+
+            modality = features.pop("modality", "UNKNOWN")
+            # Remove non-numeric fields
+            features.pop("rows", None)
+            features.pop("cols", None)
+
+            modality_features[modality].append(features)
+
+            if verbose and (i + 1) % 50 == 0:
+                print(f"  Processed {i + 1}/{len(dcm_files)} files...")
+        except Exception as e:
+            errors += 1
+            if verbose:
+                print(f"  Error on {filepath.name}: {e}")
+
+    if verbose:
+        print(f"\nExtraction complete:")
+        for mod, feats in sorted(modality_features.items()):
+            print(f"  {mod}: {len(feats)} files")
+        if skipped:
+            print(f"  Skipped (no pixel data): {skipped}")
+        if errors:
+            print(f"  Errors: {errors}")
+
+    # Compute statistics for each feature within each modality
+    baselines = {}
+    for modality, feature_list in modality_features.items():
+        if len(feature_list) < 3:
+            if verbose:
+                print(f"\n  Skipping {modality} — too few samples ({len(feature_list)})")
+            continue
+
+        baselines[modality] = {
+            "_sample_count": len(feature_list),
+        }
+
+        # Get all feature keys
+        all_keys = set()
+        for f in feature_list:
+            all_keys.update(f.keys())
+
+        for key in sorted(all_keys):
+            values = [f[key] for f in feature_list if key in f and np.isfinite(f[key])]
+            if len(values) < 3:
+                continue
+
+            arr = np.array(values)
+            baselines[modality][key] = {
+                "mean": float(np.mean(arr)),
+                "std": float(np.std(arr)),
+                "median": float(np.median(arr)),
+                "min": float(np.min(arr)),
+                "max": float(np.max(arr)),
+                "p5": float(np.percentile(arr, 5)),
+                "p95": float(np.percentile(arr, 95)),
+                "n": len(values),
+            }
+
+    # Save
+    os.makedirs(os.path.dirname(output_path) or ".", exist_ok=True)
+    with open(output_path, "w") as f:
+        json.dump(baselines, f, indent=2)
+
+    if verbose:
+        total_features = sum(
+            len([k for k in v if not k.startswith("_")])
+            for v in baselines.values()
+        )
+        print(f"\nBaselines saved to {output_path}")
+        print(f"  {len(baselines)} modalities, {total_features} total feature baselines")
+
+    return baselines
+
+
+def load_baselines(path: str) -> dict:
+    """Load baselines from a JSON file."""
+    if not os.path.exists(path):
+        return {}
+    with open(path) as f:
+        return json.load(f)
+
+
+# ---------------------------------------------------------------------------
+# CLI entry point
+# ---------------------------------------------------------------------------
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python -m scanner.calibration <dicom_dir> [output.json]")
+        print("  Scans all .dcm files in <dicom_dir> and computes baselines.")
+        print("  Default output: data/baselines.json")
+        sys.exit(1)
+
+    dicom_dir = sys.argv[1]
+    output = sys.argv[2] if len(sys.argv) > 2 else "data/baselines.json"
+
+    calibrate(dicom_dir, output)