dicom-agent-mcp 0.1.0__tar.gz

dicom_agent_mcp-0.1.0/.gitignore

@@ -0,0 +1,24 @@
+# Python environments and generated artifacts
+.venv/
+venv/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.coverage
+.coverage.*
+htmlcov/
+dist/
+build/
+*.egg-info/
+
+# Local medical data
+dicom-cache/
+inbox/
+*.dcm
+
+# Local configuration and secrets
+.env
+.env.*
+!.env.example
+dicom-agent-mcp.yaml
+config.yaml

dicom_agent_mcp-0.1.0/LICENSE

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dicom_agent_mcp-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: dicom-agent-mcp
+Version: 0.1.0
+Summary: MCP server that gives AI agents protocol-neutral DICOM tools (DIMSE and DICOMweb).
+Project-URL: Homepage, https://github.com/arunmk-ms/dicom-agent-mcp
+Project-URL: Repository, https://github.com/arunmk-ms/dicom-agent-mcp
+Project-URL: Issues, https://github.com/arunmk-ms/dicom-agent-mcp/issues
+Author: arunmk-ms
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: ai-agents,dicom,dicomweb,mcp,medical-imaging,model-context-protocol,pacs
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: httpx>=0.27
+Requires-Dist: mcp<2,>=1.9
+Requires-Dist: numpy>=1.24
+Requires-Dist: pillow>=10
+Requires-Dist: pydantic>=2
+Requires-Dist: pydicom>=3.0
+Requires-Dist: pynetdicom>=2.1
+Requires-Dist: pyyaml>=6
+Provides-Extra: codecs
+Requires-Dist: pylibjpeg-libjpeg>=2; extra == 'codecs'
+Requires-Dist: pylibjpeg-openjpeg>=2; extra == 'codecs'
+Requires-Dist: pylibjpeg-rle>=2; extra == 'codecs'
+Requires-Dist: pylibjpeg>=2; extra == 'codecs'
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# dicom-agent-mcp
+
+<!-- mcp-name: io.github.arunmk-ms/dicom-agent-mcp -->
+
+An MCP (Model Context Protocol) server that gives AI agents one set of tools for both **DIMSE** archives (C-ECHO, C-FIND, C-GET, C-MOVE, C-STORE) and **DICOMweb** archives (QIDO-RS, WADO-RS, STOW-RS).
+
+It also includes pixel and geometry tools that work on local files: rendering, statistics, measurement, geometry checks, multiplanar reconstruction (MPR) and de-identification. This is the tool layer for Topic 3 (Validated Tool Execution). The verification loop comes later; see [ROADMAP.md](ROADMAP.md).
+
+> **Not for clinical use.** This is a research scaffold. Use only with test or de-identified data.
+
+## Tools
+
+| Tool | DIMSE node | DICOMweb node | Notes |
+|---|---|---|---|
+| `list_nodes` | – | – | Lists configured nodes; secrets are never returned |
+| `echo` | C-ECHO | `GET /studies?limit=1` | Connectivity check |
+| `search` | C-FIND | QIDO-RS | Levels: patient, study, series, instance. Supports wildcards and date ranges. Paging uses `offset`/`limit`. QIDO has no patient level |
+| `get_metadata` | C-FIND (indexed attributes only) | WADO-RS `/metadata` | Returns keyword-based JSON; bulk data is summarised |
+| `retrieve` | C-GET | WADO-RS | Saves files to `storage_dir/<study>/<series>/<sop>.dcm` |
+| `move` | C-MOVE | – | Destination is a node name or an AE title |
+| `store` | C-STORE | STOW-RS | Accepts files or directories inside the sandbox |
+| `transfer` | retrieve + store | retrieve + store | Works across protocols (e.g. PACS → DICOMweb) |
+| `list_local_files` | – | – | Lists cached or allowed DICOM files |
+| `read_local_metadata` | – | – | Reads a local file header without pixel data |
+
+### Pixel and geometry tools (local files)
+
+| Tool | What it does |
+|---|---|
+| `render_image` | Renders one frame to a PNG and returns it alongside JSON. Windowing comes from explicit centre/width values, a preset (`lung`, `mediastinum`, `soft_tissue`, `abdomen`, `liver`, `bone`, `brain`, `subdural`, `stroke`), the file's window, or 0.5–99.5 percentiles. Corrects for non-square pixels and MONOCHROME1, and labels the edges with patient directions (for example R/L, A/P) |
+| `pixel_statistics` | Reports min, max, mean, standard deviation, percentiles and a voxel count for a frame or a rectangular/elliptical ROI. ROIs can be given in pixels or mm. Values are in modality units (HU for CT) and the ROI area is reported in mm² |
+| `measure_distance` | Measures the in-plane distance in mm between two pixels and returns both points in patient (LPS) coordinates |
+| `check_geometry` | Groups files into series and checks whether each one can be treated as a volume. Issues are reported with codes such as `MISSING_SLICES`, `NON_UNIFORM_SPACING`, `DUPLICATE_POSITIONS`, `MIXED_ORIENTATION`, `OBLIQUE`, `SHEARED_STACK` and `INSTANCE_ORDER_MISMATCH` |
+| `render_mpr` | Renders an axial, coronal or sagittal slice reformatted from a series that passes `check_geometry`. The PNG uses true mm aspect and radiological orientation |
+| `deidentify` | Writes de-identified copies under `storage_dir/deidentified` using a subset of the Basic Profile. See [De-identification](#de-identification) |
+
+Every pixel result includes an `input_fingerprint`: a SHA-256 hash of the decoded pixels and geometry. It does not change with the transfer syntax, and the planned verification loop will use it to bind results to their inputs.
+
+Each tool carries MCP annotations (`readOnlyHint`, `destructiveHint`, `idempotentHint`) so a harness can decide which tools need approval.
+
+## Install
+
+```powershell
+python -m venv .venv
+.venv\Scripts\python -m pip install -e ".[dev]"
+# Optional: decoders for JPEG, JPEG-LS, JPEG 2000 and RLE compressed pixel data
+.venv\Scripts\python -m pip install -e ".[codecs]"
+```
+
+## Configure
+
+No config file is needed. Pass nodes and paths as arguments in the harness config; add a YAML file only for advanced settings.
+
+### Arguments
+
+| Argument | Meaning |
+|---|---|
+| `--node SPEC` | Adds a node. Repeatable. See the node spec below |
+| `--storage-dir DIR` | Local cache for retrieved files and renders. Default `~/.dicom-agent-mcp/cache` |
+| `--allow-path DIR` | Extra directory that the local-file and pixel tools may read. Repeatable |
+| `--calling-ae AE` | AE title this server uses for DIMSE. Default `DICOM_MCP`; register it on your PACS |
+| `--config FILE` | Optional YAML file (see below) |
+| `--print-config` | Prints the resolved settings and exits. Useful for checking a harness setup |
+
+**Node spec:** `name=URL[;option;option…]`
+
+| URL | Node type |
+|---|---|
+| `dimse://AE_TITLE@host:port` | DIMSE (C-FIND, C-GET, C-MOVE, C-STORE) |
+| `http://…` or `https://…` | DICOMweb base URL (QIDO-RS, WADO-RS, STOW-RS) |
+
+| Option | Meaning |
+|---|---|
+| `read-only` | `store`, `move` and `transfer` refuse to write to this node |
+| `token-env=VAR` | DICOMweb bearer token read from environment variable `VAR` |
+| `user=NAME;password-env=VAR` | DICOMweb basic auth; the password is read from `VAR` |
+| `no-verify-tls` | Skip TLS certificate checks (test servers only) |
+| `transfer-syntax=UID` | Transfer syntax requested from WADO-RS. Empty means the server default; the default `*` keeps the stored encoding |
+
+Examples:
+
+```text
+--node orthanc=dimse://ORTHANC@localhost:4242
+--node orthanc-web=http://localhost:8042/dicom-web
+--node "azure=https://<workspace>-<service>.dicom.azurehealthcareapis.com/v2;token-env=AZURE_DICOM_TOKEN;read-only"
+```
+
+**Secrets never go in arguments.** Arguments are visible in process lists and are often committed in `mcp.json`. Put tokens and passwords in environment variables and pass only the variable name.
+
+With no `--node`, the server still starts: the local-file and pixel tools work on files under the allowed paths.
+
+### Environment variables
+
+Every argument has an environment-variable equivalent, which suits Docker and CI:
+
+| Variable | Equivalent |
+|---|---|
+| `DICOM_AGENT_MCP_NODES` | `--node`; several specs separated by spaces |
+| `DICOM_AGENT_MCP_STORAGE_DIR` | `--storage-dir` |
+| `DICOM_AGENT_MCP_ALLOWED_PATHS` | `--allow-path`; several paths separated by `;` on Windows or `:` elsewhere |
+| `DICOM_AGENT_MCP_CALLING_AE` | `--calling-ae` |
+| `DICOM_AGENT_MCP_CONFIG` | `--config` |
+
+### Optional YAML file (advanced)
+
+Use a file for settings that have no argument: timeouts, `max_results`, `max_volume_voxels`, `deid_key_env` and node descriptions. See `config.example.yaml`. If `./dicom-agent-mcp.yaml` exists in the working directory, it is loaded automatically. Relative paths in a file resolve against the file's directory; relative paths in arguments and environment variables resolve against the working directory.
+
+**Precedence:** config file, then environment variables, then arguments. Later sources override single values, nodes are merged by name (a `--node` with the same name replaces the file's node), and allowed paths are combined.
+
+## Run
+
+```powershell
+dicom-agent-mcp --node orthanc=dimse://ORTHANC@localhost:4242                                   # stdio
+dicom-agent-mcp --node orthanc=dimse://ORTHANC@localhost:4242 --transport streamable-http --port 8000
+dicom-agent-mcp --node orthanc=dimse://ORTHANC@localhost:4242 --print-config                    # check settings
+```
+
+### VS Code (`.vscode/mcp.json`)
+
+```json
+{
+  "inputs": [
+    { "id": "azureToken", "type": "promptString", "description": "Azure DICOM access token", "password": true }
+  ],
+  "servers": {
+    "dicom": {
+      "type": "stdio",
+      "command": "${workspaceFolder}/.venv/Scripts/dicom-agent-mcp",
+      "args": [
+        "--node", "orthanc=dimse://ORTHANC@localhost:4242",
+        "--node", "orthanc-web=http://localhost:8042/dicom-web",
+        "--node", "azure=https://<workspace>-<service>.dicom.azurehealthcareapis.com/v2;token-env=AZURE_DICOM_TOKEN;read-only",
+        "--storage-dir", "${workspaceFolder}/dicom-cache",
+        "--allow-path", "${workspaceFolder}/inbox"
+      ],
+      "env": { "AZURE_DICOM_TOKEN": "${input:azureToken}" }
+    }
+  }
+}
+```
+
+### Claude Desktop / Copilot CLI / other harnesses
+
+```json
+{
+  "mcpServers": {
+    "dicom": {
+      "command": "dicom-agent-mcp",
+      "args": [
+        "--node", "orthanc=dimse://ORTHANC@localhost:4242",
+        "--allow-path", "C:/data/dicom-inbox"
+      ]
+    }
+  }
+}
+```
+
+Use absolute paths here: these harnesses may start the server in any working directory. To use a file instead, pass `"args": ["--config", "C:/path/to/dicom-agent-mcp.yaml"]`.
+### Local Orthanc for testing
+
+```powershell
+docker-compose up -d   # DIMSE on 4242, DICOMweb on http://localhost:8042/dicom-web (compose file not yet tested)
+```
+
+## Sample prompts
+
+These prompts assume three nodes: `orthanc` (DIMSE), `orthanc-web` (DICOMweb) and `azure-dicom`, for example:
+
+```text
+--node orthanc=dimse://ORTHANC@localhost:4242 --node orthanc-web=http://localhost:8042/dicom-web
+--node "azure-dicom=https://<workspace>-<service>.dicom.azurehealthcareapis.com/v2;token-env=AZURE_DICOM_TOKEN"
+```
+
+The tool the agent is expected to call is shown after each prompt.
+
+### Nodes and connectivity
+
+| Prompt | Tool |
+|---|---|
+| "Which DICOM nodes are configured, and which ones are read-only?" | `list_nodes` |
+| "Check whether `orthanc` and `azure-dicom` are reachable." | `echo` |
+
+### Search and metadata
+
+| Prompt | Tool |
+|---|---|
+| "Find all CT studies on `orthanc` from the last 30 days." | `search` (C-FIND) |
+| "List the series in study `1.2.840…` on `orthanc-web`, with modality and number of images." | `search` (QIDO-RS) |
+| "Find patients whose name starts with `DOE^`." | `search` at patient level (DIMSE nodes only) |
+| "Show the acquisition parameters for series `1.2.840…`: slice thickness, kVp and pixel spacing." | `get_metadata` |
+
+### Moving data
+
+| Prompt | Tool |
+|---|---|
+| "Download the chest CT series from `orthanc` into the local cache." | `retrieve` |
+| "Send study `1.2.840…` from `orthanc` to the AE title `WORKSTATION1`." | `move` (C-MOVE) |
+| "Upload the files in `./inbox/case42` to `orthanc-web`." | `store` (STOW-RS) |
+| "Copy series `1.2.840…` from `orthanc` to `azure-dicom`." | `transfer` (works across protocols) |
+
+### Local files
+
+| Prompt | Tool |
+|---|---|
+| "What DICOM files do I have locally?" | `list_local_files` |
+| "Read the header of `./dicom-cache/…/x.dcm`. Is it compressed? What is the photometric interpretation?" | `read_local_metadata` |
+
+### Pixels and geometry
+
+| Prompt | Tool |
+|---|---|
+| "Show me slice 40 of that series in a lung window." | `render_image` (preset) |
+| "Render it again with centre 40 and width 400." | `render_image` (explicit window) |
+| "What is the mean HU in a 10 mm circle centred at row 256, column 300?" | `pixel_statistics` (ellipse in mm) |
+| "Give me the minimum, maximum and 95th percentile for the whole frame." | `pixel_statistics` |
+| "How far apart in mm are pixel (120, 200) and pixel (180, 260)?" | `measure_distance` |
+| "Can this series be used as a 3D volume? Report any missing slices or uneven spacing." | `check_geometry` |
+| "Show the middle coronal slice in a bone window." | `render_mpr` |
+| "Show sagittal slice 100." | `render_mpr` |
+
+### De-identification
+
+| Prompt | Tool |
+|---|---|
+| "De-identify the downloaded study, shift the dates and drop private tags." | `deidentify` |
+| "De-identify it but keep the original dates and the series descriptions." | `deidentify` (`date_mode=keep`, `keep_descriptions`) |
+
+### Multi-step workflows
+
+- "Find the latest CT for patient MRN123 on `orthanc`, download it, check its geometry, and show me an axial and a coronal view in a soft-tissue window."
+- "Measure the mean HU of the liver at slice 60 (a 15 mm circle at row 300, column 180) and report the input fingerprint."
+- "Download study X from `orthanc`, de-identify it, and upload the de-identified copy to `azure-dicom`."
+
+### Prompts the server should refuse
+
+| Prompt | Expected result |
+|---|---|
+| "Store these files to `<a node marked read_only>`." | Refused because the node is read-only |
+| "Read `C:\Windows\System32\config`." | Refused because the path is outside the sandbox |
+| "Render a coronal MPR of a series that has missing slices." | Refused, with the geometry issues listed |
+
+## Safety
+
+- **Path sandbox.** `store`, `list_local_files`, `read_local_metadata` and the pixel tools only accept paths under `storage_dir` or `allowed_paths`.
+- **UID validation.** UIDs are checked before they are used in file paths or URLs.
+- **`read_only` nodes.** `store`, `move` and `transfer` refuse to write to them.
+- **Result caps.** `max_results` limits results; truncation is reported with `truncated: true`.
+- **Pixels in context only by request.** Raw pixel arrays are never returned. `render_image` and `render_mpr` do send a downsampled PNG to the model; a copy is saved under `storage_dir/renders`.
+- **Volume cap.** `render_mpr` refuses series larger than `max_volume_voxels`, and refuses series that fail `check_geometry`.
+
+### De-identification
+
+`deidentify` does the following:
+
+- removes or empties identifying attributes;
+- drops private tags and overlay or curve groups;
+- replaces PatientName and PatientID with pseudonyms;
+- remaps instance UIDs consistently;
+- by default, shifts dates by a per-patient offset of 1 to 730 days.
+
+It records what it did in `DeidentificationMethodCodeSequence`.
+
+To get the same pseudonyms and UIDs across runs, set a secret key in the environment variable named by `deid_key_env` (default `DICOM_AGENT_MCP_DEID_KEY`). Without a key, each call uses a random key and the result reports `linkable: false`.
+
+It does **not** remove text burned into the pixels; affected modalities produce a warning. It is a research aid, not a certified de-identification tool.
+
+## Architecture
+
+```
+server.py  (FastMCP tools)  →  service.py  (routing, sandbox, paging)
+                                   ├── dimse.py     (pynetdicom SCU)
+                                   ├── dicomweb.py  (httpx QIDO/WADO/STOW)
+                                   ├── imaging.py   (windowing, geometry, ROI stats, MPR, fingerprints)
+                                   └── deid.py      (Basic Profile subset)
+```
+
+## Tests
+
+```powershell
+.venv\Scripts\python -m pytest -q
+```
+
+The tests run end to end against an in-process pynetdicom PACS (two AEs so C-MOVE can be tested) and a mocked DICOMweb server. They need no network. The pixel tests use a synthetic CT series with known HU values, spacing and positions.
+
+## Limitations
+
+- STOW-RS builds the whole request in memory, and WADO-RS reads the whole response into memory.
+- DIMSE `get_metadata` only returns attributes that the archive indexes for C-FIND.
+- `retrieve` uses C-GET. Archives that only support C-MOVE need `move` to a storage SCP.
+- No TLS for DIMSE yet.
+- Pixel tools have been tested on synthetic CT and pydicom sample files only. Compressed transfer syntaxes, enhanced multi-frame objects and real-world data are not yet tested.
+- MPR uses nearest-slice sampling and does not resample to isotropic voxels.
+- Pixel tools work on local files; use `retrieve` first.
+
+## Roadmap
+
+See [ROADMAP.md](ROADMAP.md).