Integrating OHIF with Orthanc & MONAI Label (Docker Compose)

[fisherboneee]

CONFIGURATION SETUP

Hi, I wanted to integrate OHIF Viewer with Orthanc & MONAI Label server. Orthanc and OHIF Viewer integrated successfully but I can't get MONAI Label server to connect with OHIF Viewer via Orthanc DICOMWeb.

I use this code sample to integrate Orthanc with OHIF Viewer.

And then in the compose.yaml, I modified it to include MONAI Label installation in the Docker Compose.

services:
    nginx:
        build: nginx
        restart: unless-stopped
        ports:
            - 80:80
            - 81:81
        depends_on:
            - orthanc

    orthanc:
        image: osimis/orthanc:master-unstable
        restart: unless-stopped
        environment:
            ORTHANC__NAME: 'Orthanc for OHIF'

            DICOM_WEB_PLUGIN_ENABLED: 'true'

            ORTHANC__ORTHANC_EXPLORER_2__UI_OPTIONS__ENABLE_OPEN_IN_OHIF_VIEWER: 'true'
            ORTHANC__ORTHANC_EXPLORER_2__UI_OPTIONS__OHIF_VIEWER_PUBLIC_ROOT: 'http://localhost:81/Viewer/'

            ORTHANC__DICOM_WEB__ENABLE: 'true'

            ORTHANC__REGISTERED_USERS: |
                {"demo": "demo"}

            VERBOSE_STARTUP: 'true'

    monailabel-server: # Project Name
        container_name: monailabel-container # Container Name
        image: projectmonai/monailabel # Image that being pulled from Docker Hub, it will use local image instead if already pulled
        # This is the same as passing `--gpus all` command when running Docker CLI
        deploy:
            resources:
                reservations:
                    devices:
                        - capabilities: [gpu]
        stdin_open: true # docker run -i flag
        tty: true # docker run -t flag
        # Expose port to access from host
        ports:
            - 8000:8000
        # IPC set to host
        ipc: 'host'

        # Attach volume to a path that need to be save
        volumes:
            - orthanc-storage:/var/lib/orthanc/db/
            - monailabel_volume:/opt/monai # Volume name and directory wants to be save, must match the volume name below

volumes:
    orthanc-storage:
    monailabel_volume:

After that, I ran docker compose up -d --build to start the service.

When the service is up, I type in docker exec -it monailabel-container /bin/bash to get inside the container.

From there, I ran monailabel apps --download --name radiology --output apps command to download Radiology sample apps.

Lastly, I ran monailabel start_server --app apps/radiology --studies http://127.0.0.1:80/dicom-web --conf models deepedit

THE PROBLEM

I am able to upload data in Orthanc through this URL: http://localhost/ui/app/
and access it with the OHIF Viewer by navigating through http://localhost:81 or clicking "View in OHIF" button in Orthanc

HOWEVER
I am not able to access http://localhost:8000/ohif and it says

{"detail":"Resource NOT Found"}

But I am able to access http://localhost:8000 and it will give me the list of MONAI Label API.

Can someone help me?

[SachidanandAlle]

If you are using monailabel via GitHub check out.. you need to build ohif.. more details can be found on plugins/ohif

[diazandr3s]

Hi @fisherboneee,

As Sachi suggested, please build OHIF like it is highlighted here: https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif#development-setup

[fisherboneee]

Hi @SachidanandAlle & @diazandr3s, thank you for your answer!

I want to emphasize that I'm using Docker Compose and configuration is as above.

From my understanding, I have to build OHIF inside MONAI Label container correct? I already have OHIF inside different container, how do I connect them?

And just for testing, I already build OHIF Viewer inside MONAI Label container by navigating to /opt/conda/monailabel/plugins/ohif and ran sh build.sh command. But then, I realized that when I started MONAI Label Server by running monailabel start_server --app apps/radiology --studies http://127.0.0.1:80/dicom-web --conf models deepedit then I navigate to http://localhost:8000/ohif, it still says the same thing.

{"detail":"Resource NOT Found"}

But in the terminal I saw the server actually fetching the OHIF in this directory instead:

/opt/conda/lib/python3.8/site-packages/monailabel/endpoints/static/ohif/index.html

So I thought, I need to reconfigure where build.sh need to install OHIF Viewer, so I change the install_dir variable to:

install_dir=/opt/conda/lib/python3.8/site-packages/monailabel/endpoints/static/ohif

Then I ran sh build.sh again & run the server again.

This time I am able to access http://localhost:8000/ohif, but it gave me blank display. When I look into the terminal, it throws me with bunch of error logs:

[2022-10-28 08:03:10,609] [3728] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/anyio/_core/_sockets.py", line 164, in try_connect
    stream = await asynclib.connect_tcp(remote_host, remote_port, local_address)
  File "/opt/conda/lib/python3.8/site-packages/anyio/_backends/_asyncio.py", line 1691, in connect_tcp
    await get_running_loop().create_connection(
  File "/opt/conda/lib/python3.8/asyncio/base_events.py", line 1025, in create_connection
    raise exceptions[0]
  File "/opt/conda/lib/python3.8/asyncio/base_events.py", line 1010, in create_connection
    sock = await self._connect_sock(
  File "/opt/conda/lib/python3.8/asyncio/base_events.py", line 924, in _connect_sock
    await self.sock_connect(sock, address)
  File "/opt/conda/lib/python3.8/asyncio/selector_events.py", line 496, in sock_connect
    return await fut
  File "/opt/conda/lib/python3.8/asyncio/selector_events.py", line 528, in _sock_connect_cb
    raise OSError(err, f'Connect call failed {address}')
ConnectionRefusedError: [Errno 111] Connect call failed ('127.0.0.1', 80)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_exceptions.py", line 8, in map_exceptions
    yield
  File "/opt/conda/lib/python3.8/site-packages/httpcore/backends/asyncio.py", line 109, in connect_tcp
    stream: anyio.abc.ByteStream = await anyio.connect_tcp(
  File "/opt/conda/lib/python3.8/site-packages/anyio/_core/_sockets.py", line 222, in connect_tcp
    raise OSError("All connection attempts failed") from cause
OSError: All connection attempts failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/httpx/_transports/default.py", line 60, in map_httpcore_exceptions
    yield
  File "/opt/conda/lib/python3.8/site-packages/httpx/_transports/default.py", line 353, in handle_async_request
    resp = await self._pool.handle_async_request(req)
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_async/connection_pool.py", line 253, in handle_async_request
    raise exc
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_async/connection_pool.py", line 237, in handle_async_request
    response = await connection.handle_async_request(request)
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_async/connection.py", line 86, in handle_async_request
    raise exc
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_async/connection.py", line 63, in handle_async_request
    stream = await self._connect(request)
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_async/connection.py", line 111, in _connect
    stream = await self._network_backend.connect_tcp(**kwargs)
  File "/opt/conda/lib/python3.8/site-packages/httpcore/backends/auto.py", line 29, in connect_tcp
    return await self._backend.connect_tcp(
  File "/opt/conda/lib/python3.8/site-packages/httpcore/backends/asyncio.py", line 109, in connect_tcp
    stream: anyio.abc.ByteStream = await anyio.connect_tcp(
  File "/opt/conda/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/opt/conda/lib/python3.8/site-packages/httpcore/_exceptions.py", line 12, in map_exceptions
    raise to_exc(exc)
httpcore.ConnectError: All connection attempts failed

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/opt/conda/lib/python3.8/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/opt/conda/lib/python3.8/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/middleware/cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/opt/conda/lib/python3.8/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/opt/conda/lib/python3.8/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/opt/conda/lib/python3.8/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/opt/conda/lib/python3.8/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/opt/conda/lib/python3.8/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/opt/conda/lib/python3.8/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/opt/conda/lib/python3.8/site-packages/monailabel/endpoints/proxy.py", line 95, in proxy_qido
    return await proxy_dicom("qido", path, response)
  File "/opt/conda/lib/python3.8/site-packages/monailabel/endpoints/proxy.py", line 81, in proxy_dicom
    proxy = await client.get(proxy_path, timeout=timeout)
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1751, in get
    return await self.request(
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1527, in request
    return await self.send(request, auth=auth, follow_redirects=follow_redirects)
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1614, in send
    response = await self._send_handling_auth(
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1642, in _send_handling_auth
    response = await self._send_handling_redirects(
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1679, in _send_handling_redirects
    response = await self._send_single_request(request)
  File "/opt/conda/lib/python3.8/site-packages/httpx/_client.py", line 1716, in _send_single_request
    response = await transport.handle_async_request(request)
  File "/opt/conda/lib/python3.8/site-packages/httpx/_transports/default.py", line 353, in handle_async_request
    resp = await self._pool.handle_async_request(req)
  File "/opt/conda/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/opt/conda/lib/python3.8/site-packages/httpx/_transports/default.py", line 77, in map_httpcore_exceptions
    raise mapped_exc(message) from exc
httpx.ConnectError: All connection attempts failed

Any clue?

[SachidanandAlle]

You are running 2 dockers.. they can't connect each other using 127.0.0.1.. you need network sharing.. or simply use direct ip.. something starts with 10.x.. as studies uri.. before you use that make sure you can access it using simple wget/curl inside monailabel docker

Ohif is pre built in monailabel docker.. you don't have to build it

[jlvahldiek]

When trying to open OHIF I also discovered the error {"detail":"Resource NOT Found"}, which is invoked here:

MONAILabel/monailabel/endpoints/ohif.py

Line 39 in 166ff7c

raise HTTPException(status_code=404, detail="Resource NOT Found")

I also consider the path concatenation of install_dir to be probably wrong:

MONAILabel/plugins/ohif/build.sh

Line 20 in 166ff7c

install_dir=${1:-$my_dir/../../monailabel/endpoints/static/ohif}

This leads to the following message when executing plugins/ohif/build.sh in Docker container:
mv: cannot move './Viewers/platform/viewer/dist' to '/opt/conda/monailabel/plugins/ohif/../../monailabel/endpoints/static/ohif': No such file or directory

I also think that install_dir=/opt/conda/lib/python3.8/site-packages/monailabel/endpoints/static/ohif would be more appropriate (successfully tested with latest Docker image).

@SachidanandAlle and @diazandr3s, could you please comment on what would be the correct install_dir path concatenation in build.sh? I can raise an according PR if you like to...

[jlvahldiek]

With the changes of PR #1106 OHIF now builds correctly and is now again available via API endpoint /ohif. No changes to install_dir in build.sh necessary.

[fisherboneee]

Thanks @SachidanandAlle @diazandr3s @jlvahldiek, the issue has been resolved with the changes of PR #1106.

If you're using Docker like me, make sure to pull the latest Docker image by running docker pull projectmonai/monailabel command in your terminal first.

And also just to remind the community that OHIF has already built-in inside of MONAI Label container, so you don't have to build it again. Just follow the steps on the docs and you'll be fine.

Here is the overview for the system: