Basic OHIF Plugin support for monailabel (Project-MONAI#252)

* by default allow all for cors Signed-off-by: SACHIDANAND ALLE <[email protected]> * ohif plugin+integration for monailabel Signed-off-by: Sachidanand Alle <[email protected]> * add eslint config Signed-off-by: Sachidanand Alle <[email protected]> * Fix Interface + others Signed-off-by: Sachidanand Alle <[email protected]> * Fix build Signed-off-by: Sachidanand Alle <[email protected]> * fix build and buttons Signed-off-by: Sachidanand Alle <[email protected]> * enable download option to save labelmap as .nrrd Signed-off-by: Sachidanand Alle <[email protected]> * Support ohif build during package Signed-off-by: Sachidanand Alle <[email protected]> * Auto code fix Signed-off-by: Sachidanand Alle <[email protected]> * Fix OHIF build Signed-off-by: Sachidanand Alle <[email protected]> * Skip OHIF build for Pull Requests Signed-off-by: Sachidanand Alle <[email protected]> * Fix build Signed-off-by: Sachidanand Alle <[email protected]> * Add ohif readme Signed-off-by: Sachidanand Alle <[email protected]> * implement next sample action Signed-off-by: Sachidanand Alle <[email protected]> * enable download option from get endpoint for slicer Signed-off-by: Sachidanand Alle <[email protected]> * fix save label Signed-off-by: Sachidanand Alle <[email protected]> * mock to create dicom seg and upload to orthanc Signed-off-by: Sachidanand Alle <[email protected]> * fix after testing Signed-off-by: Sachidanand Alle <[email protected]> * rename func param Signed-off-by: Sachidanand Alle <[email protected]> * fix segment idx for multi-label SegmentAttribute Signed-off-by: Sachidanand Alle <[email protected]> * Fix rgb type while saving the label Signed-off-by: Sachidanand Alle <[email protected]> * Enable OHIF through DICOMWeb interface (infer/save/train works) Signed-off-by: Sachidanand Alle <[email protected]> * fix unit tests Signed-off-by: Sachidanand Alle <[email protected]> * fix training etc... Signed-off-by: Sachidanand Alle <[email protected]> * Fix code check Signed-off-by: Sachidanand Alle <[email protected]> * support start/stop training action Signed-off-by: Sachidanand Alle <[email protected]> * show dicom meta info when next sample is fetched Signed-off-by: Sachidanand Alle <[email protected]> * support auth to connect to remote dicomweb via proxy + readme Signed-off-by: Sachidanand Alle <[email protected]> * Fix readme Signed-off-by: Sachidanand Alle <[email protected]> * update readme Signed-off-by: Sachidanand Alle <[email protected]> * minor updates Signed-off-by: Alvin Ihsani <[email protected]> * adding prefix Signed-off-by: Alvin Ihsani <[email protected]> * autofix Signed-off-by: Sachidanand Alle <[email protected]> Co-authored-by: Sachidanand Alle <[email protected]> Co-authored-by: Alvin Ihsani <[email protected]>
lionM · Sep 1, 2021 · 5060051 · 5060051
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diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
@@ -84,6 +84,7 @@ jobs:
           echo "$root_dir"
 
           # build tar.gz and wheel
+          export BUILD_OHIF=false
           python setup.py check -m -s
           python setup.py sdist bdist_wheel
           python -m twine check dist/*

diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "plugins/ohif/Viewers"]
+	path = plugins/ohif/Viewers
+	url = https://github.com/OHIF/Viewers.git
diff --git a/README.md b/README.md
@@ -13,21 +13,23 @@ principles with [MONAI](https://github.com/Project-MONAI).
 
 [Brief Demo](https://youtu.be/gzAR-Ix31Gs)
 
-<img src="https://raw.githubusercontent.com/Project-MONAI/MONAILabel/main/docs/images/demo.png" width="800"/>
+![DEMO](docs/images/demo.png)
 
 ## Features
+
 > _The codebase is currently under active development._
 
 - framework for developing and deploying MONAI Label Apps to train and infer AI models
 - compositional & portable APIs for ease of integration in existing workflows
 - customizable design for varying user expertise
 - 3DSlicer support
 
-
 ## Installation
+
 MONAI Label supports following OS with **GPU/CUDA** enabled.
- - Ubuntu
- - [Windows](https://docs.monai.io/projects/label/en/latest/installation.html#windows)
+
+- Ubuntu
+- [Windows](https://docs.monai.io/projects/label/en/latest/installation.html#windows)
 
 To install the current release, you can simply run:
 
@@ -43,28 +45,46 @@ To install the current release, you can simply run:
 
 ```
 
-For **_prerequisites_**, other installation methods (using the default GitHub branch, using Docker, etc.), please refer to the [installation guide](https://docs.monai.io/projects/label/en/latest/installation.html).
+For **_prerequisites_**, other installation methods (using the default GitHub branch, using Docker, etc.), please refer
+to the [installation guide](https://docs.monai.io/projects/label/en/latest/installation.html).
 
-> Once you start the MONAI Label Server, by default it will be up and serving at http://127.0.0.1:8000/. Open the serving
-  URL in browser. It will provide you the list of Rest APIs available.
+> Once you start the MONAI Label Server, by default it will be up and serving at http://127.0.0.1:8000/. Open the serving URL in browser. It will provide you the list of Rest APIs available.
 
 ### 3D Slicer
 
-Download **Preview Release** from https://download.slicer.org/ and install MONAI Label plugin from Slicer Extension Manager.
+Download **Preview Release** from https://download.slicer.org/ and install MONAI Label plugin from Slicer Extension
+Manager.
 
 Refer [3D Slicer plugin](plugins/slicer) for other options to install and run MONAI Label plugin in 3D Slicer.
-> To avoid accidentally using an older Slicer version, you may want to _uninstall_ any previously installed 3D Slicer package. 
+> To avoid accidentally using an older Slicer version, you may want to _uninstall_ any previously installed 3D Slicer package.
+
+### OHIF
 
+MONAI Label comes with pre-built plugin for [OHIF Viewer](https://github.com/OHIF/Viewers).
+> Please install [Orthanc](https://www.orthanc-server.com/download.php) before using OHIF Viewer.
+> For Ubuntu 20.x, Orthanc can be installed as `apt-get install orthanc orthanc-dicomweb`. However, you have to **upgrade to latest version** by following steps mentioned [here](https://book.orthanc-server.com/users/debian-packages.html#replacing-the-package-from-the-service-by-the-lsb-binaries)
+>
+> You can use [PlastiMatch](https://plastimatch.org/plastimatch.html#plastimatch-convert) to convert NIFTI to DICOM
+
+> OHIF Viewer will be accessible at http://127.0.0.1:8000/ohif/
+> For development OHIF can be built by running 
+
+![OHIF](docs/images/ohif.png)
 
 ## Contributing
+
 For guidance on making a contribution to MONAI Label, see the [contributing guidelines](CONTRIBUTING.md).
 
 ## Community
-Join the conversation on Twitter [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
 
-Ask and answer questions over on [MONAI Label's GitHub Discussions tab](https://github.com/Project-MONAI/MONAILabel/discussions).
+Join the conversation on Twitter [@ProjectMONAI](https://twitter.com/ProjectMONAI) or join
+our [Slack channel](https://forms.gle/QTxJq3hFictp31UM9).
+
+Ask and answer questions over
+on [MONAI Label's GitHub Discussions tab](https://github.com/Project-MONAI/MONAILabel/discussions).
 
 ## Links
+
 - Website: https://monai.io/
 - API documentation: https://docs.monai.io/projects/label
 - Code: https://github.com/Project-MONAI/MONAILabel

diff --git a/docs/images/ohif.png b/docs/images/ohif.png
diff --git a/monailabel/config.py b/monailabel/config.py
@@ -30,8 +30,6 @@ class Settings(BaseSettings):
     DATASTORE_AUTO_RELOAD: bool = True
     DATASTORE_FILE_EXT: List[str] = ["*.nii.gz", "*.nii"]
 
-    DICOM_WEB: str = "http://localhost:8042"
-
     CORS_ORIGINS: List[AnyHttpUrl] = []
 
     class Config:

diff --git a/monailabel/endpoints/activelearning.py b/monailabel/endpoints/activelearning.py
@@ -47,7 +47,9 @@ async def sample(strategy: str, params: Optional[dict] = None):
     image_id = result["id"]
     image_info = instance.datastore().get_image_info(image_id)
 
-    return {
+    result = {
         "id": image_id,
         **image_info,
     }
+    logger.info(f"Next sample: {result}")
+    return result
diff --git a/monailabel/endpoints/ohif.py b/monailabel/endpoints/ohif.py
@@ -0,0 +1,29 @@
+import logging
+import os
+
+from fastapi import APIRouter, HTTPException
+from fastapi.responses import FileResponse
+
+from monailabel.utils.others.generic import get_mime_type
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(
+    prefix="/ohif",
+    tags=["Others"],
+    responses={404: {"description": "Not found"}},
+)
+
+
+@router.get("/{path:path}", include_in_schema=False)
+async def get_ohif(path: str):
+    ohif_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "..", "static", "ohif")
+    file = os.path.join(ohif_dir, "index.html")
+    if path:
+        path = os.path.join(ohif_dir, path.replace("/", os.pathsep))
+        file = path if os.path.exists(path) else file
+
+    if not os.path.exists(file):
+        logger.info(file)
+        raise HTTPException(status_code=404, detail="Resource NOT Found")
+    return FileResponse(file, media_type=get_mime_type(file))
diff --git a/monailabel/endpoints/proxy.py b/monailabel/endpoints/proxy.py
@@ -0,0 +1,32 @@
+import logging
+
+import httpx
+from fastapi import APIRouter
+from fastapi.responses import Response
+
+from monailabel.config import settings
+
+logger = logging.getLogger(__name__)
+
+router = APIRouter(
+    prefix="/proxy",
+    tags=["Others"],
+    responses={404: {"description": "Not found"}},
+)
+
+
+@router.get("/dicom/{path:path}", include_in_schema=False)
+async def proxy(path: str, response: Response):
+    auth = (
+        (settings.DICOMWEB_USERNAME, settings.DICOMWEB_PASSWORD)
+        if settings.DICOMWEB_USERNAME and settings.DICOMWEB_PASSWORD
+        else None
+    )
+
+    async with httpx.AsyncClient(auth=auth) as client:
+        proxy_path = f"{settings.STUDIES.lstrip('/')}/{path}"
+        logger.debug(f"Proxy conneting to {proxy_path}")
+        proxy = await client.get(proxy_path)
+    response.body = proxy.content
+    response.status_code = proxy.status_code
+    return response
diff --git a/monailabel/main.py b/monailabel/main.py
@@ -26,7 +26,7 @@
 from starlette.middleware.cors import CORSMiddleware
 
 from monailabel.config import settings
-from monailabel.endpoints import activelearning, batch_infer, datastore, infer, info, logs, scoring, train
+from monailabel.endpoints import activelearning, batch_infer, datastore, infer, info, logs, ohif, proxy, scoring, train
 from monailabel.utils.others.app_utils import app_instance
 from monailabel.utils.others.generic import init_log_config
 
@@ -61,6 +61,8 @@
 app.include_router(scoring.router)
 app.include_router(datastore.router)
 app.include_router(logs.router)
+app.include_router(ohif.router)
+app.include_router(proxy.router)
 
 
 @app.get("/", include_in_schema=False)

diff --git a/monailabel/utils/datastore/dicom/cache.py b/monailabel/utils/datastore/dicom/cache.py
@@ -83,11 +83,12 @@ def get_label_uri(self, label_id: str, label_tag: str, image_id: str = "") -> st
 
     def _dicom_info(self, series_id):
         meta = load_json_dataset(self._client.search_for_series(search_filters={"SeriesInstanceUID": series_id})[0])
-        return {
-            "SeriesInstanceUID": series_id,
-            "StudyInstanceUID": str(meta["StudyInstanceUID"].value),
-            "PatientID": str(meta["PatientID"].value),
-        }
+        fields = ["StudyDate", "StudyTime", "Modality", "RetrieveURL", "PatientID", "StudyInstanceUID"]
+
+        info = {"SeriesInstanceUID": series_id}
+        for f in fields:
+            info[f] = str(meta[f].value)
+        return info
 
     def list_images(self) -> List[str]:
         datasets = self._client.search_for_series(search_filters={"Modality": self._modality})

diff --git a/plugins/ohif/.gitignore b/plugins/ohif/.gitignore
@@ -0,0 +1 @@
+node_modules/
diff --git a/plugins/ohif/README.md b/plugins/ohif/README.md
@@ -0,0 +1,96 @@
+## MONAILabel Plugin for OHIF Viewer
+
+![](Screenshots/1.png)
+
+## Development setup
+
+- Build the OHIF plugin for development:
+
+  `(cd plugins/ohif && ./build.sh)`
+
+- Run App with Orthanc (DICOMWeb):
+
+  `./monailabel/monailabel start_server -a samples/segmentation_spleen -s http://127.0.0.1:8042/dicom-web`
+
+- Access OHIF: http://127.0.0.1:8000/ohif/
+
+```shell
+# If you want to avoid building OHIF package for every code changes, 
+# you can run OHIF Viewer directly in checked-out git submodule
+cd plugins/ohif/Viewers
+
+yarn run dev:orthanc
+
+# in this case ohif will run at http://127.0.0.1:3000/
+xdg-open http://127.0.0.1:3000/
+```
+
+## Installing Orthanc (DICOMWeb)
+
+### Ubuntu 20.x
+
+```shell
+# Install orthanc and dicomweb plugin
+sudo apt-get install orthanc orthanc-dicomweb -y
+
+# Install plastimatch
+sudo apt-get install plastimatch -y
+```
+
+However, you have to **upgrade to latest version** by following steps
+mentioned [here](https://book.orthanc-server.com/users/debian-packages.html#replacing-the-package-from-the-service-by-the-lsb-binaries)
+
+```shell
+sudo service orthanc stop
+sudo wget https://lsb.orthanc-server.com/orthanc/1.9.7/Orthanc --output-document /usr/sbin/Orthanc
+sudo rm -f /usr/share/orthanc/plugins/*.so
+
+sudo wget https://lsb.orthanc-server.com/orthanc/1.9.7/libServeFolders.so --output-document /usr/share/orthanc/plugins/libServeFolders.so
+sudo wget https://lsb.orthanc-server.com/orthanc/1.9.7/libModalityWorklists.so --output-document /usr/share/orthanc/plugins/libModalityWorklists.so
+sudo wget https://lsb.orthanc-server.com/plugin-dicom-web/1.6/libOrthancDicomWeb.so --output-document /usr/share/orthanc/plugins/libOrthancDicomWeb.so
+
+sudo service orthanc restart
+```
+
+### Windows/Others _(latest version)_
+
+- Download and Install Orthanc from https://www.orthanc-server.com/download.php
+
+## Converting NIFTI to DICOM
+
+```shell
+plastimatch convert --patient-id patient1 --input image.nii.gz --output-dicom test 
+```
+
+## Uploading DICOM to Orthanc
+
+### Use Orthanc Browser
+
+Use orthanc browser located at http://127.0.0.1:8042/app/explorer.html#upload to upload the files.
+
+### Using STORE SCP/SCU
+
+#### Enable AET
+
+`sudo vim /etc/orthanc/orthanc.json`
+
+```json5
+// The list of the known DICOM modalities
+"DicomModalities" : {
+/**
+ * Uncommenting the following line would enable Orthanc to
+ * connect to an instance of the "storescp" open-source DICOM
+ * store (shipped in the DCMTK distribution) started by the
+ * command line "storescp 2000".
+ **/
+"sample": ["MONAILABEL", "127.0.0.1", 104]
+```
+
+`sudo service orthanc restart`
+
+#### Upload Files
+
+```shell
+# If AET 'MONAILABEL' is enabled in Orthanc
+python -m pynetdicom storescu 127.0.0.1 4242 test -aet MONAILABEL -r
+```
diff --git a/plugins/ohif/Screenshots/1.png b/plugins/ohif/Screenshots/1.png
diff --git a/plugins/ohif/Viewers b/plugins/ohif/Viewers
diff --git a/plugins/ohif/build.sh b/plugins/ohif/build.sh
@@ -0,0 +1,55 @@
+#!/bin/bash
+
+curr_dir="$(pwd)"
+my_dir="$(dirname "$(readlink -f "$0")")"
+
+echo "Installing requirements..."
+sh $my_dir/requirements.sh
+
+install_dir=${1:-$my_dir/../../monailabel/static/ohif}
+
+echo "Current Dir: ${curr_dir}"
+echo "My Dir: ${my_dir}"
+echo "Installing OHIF at: ${install_dir}"
+
+cd ${my_dir}
+git submodule update --init
+
+cd Viewers
+
+# Viewers/platform/viewer/public/config/default.js
+git checkout -- ./platform/viewer/public/config/default.js
+sed -i "s|routerBasename: '/'|routerBasename: '/ohif/'|g" ./platform/viewer/public/config/default.js
+sed -i "s|name: 'DCM4CHEE'|name: 'Orthanc'|g" ./platform/viewer/public/config/default.js
+sed -i "s|https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/wado|/proxy/dicom/wado|g" ./platform/viewer/public/config/default.js
+sed -i "s|https://server.dcmjs.org/dcm4chee-arc/aets/DCM4CHEE/rs|/proxy/dicom|g" ./platform/viewer/public/config/default.js
+
+# Viewers/platform/viewer/.env
+git checkout -- ./platform/viewer/.env
+sed -i "s|PUBLIC_URL=/|PUBLIC_URL=/ohif/|g" ./platform/viewer/.env
+
+# monailabel plugin
+cd extensions
+rm monai-label
+ln -s ../../monai-label monai-label
+cd ..
+
+git checkout -- ./platform/viewer/src/index.js
+sed -i "s|let config = {};|import OHIFMONAILabelExtension from '@ohif/extension-monai-label';\nlet config = {};|g" ./platform/viewer/src/index.js
+sed -i "s|defaultExtensions: \[|defaultExtensions: \[OHIFMONAILabelExtension,|g" ./platform/viewer/src/index.js
+
+yarn config set workspaces-experimental true
+yarn install
+rm -rf ./Viewers/platform/viewer/dist
+QUICK_BUILD=true yarn run build
+
+# Reset if you want to run directly from yarn run dev:orthanc (without monailabel server)
+git checkout -- platform/viewer/.env
+git checkout -- platform/viewer/public/config/default.js
+git checkout -- yarn.lock
+cd ..
+
+rm -rf ${install_dir}
+mv ./Viewers/platform/viewer/dist ${install_dir}
+echo "Copied OHIF to ${install_dir}"
+cd ${curr_dir}
diff --git a/plugins/ohif/monai-label/.webpack/webpack.dev.js b/plugins/ohif/monai-label/.webpack/webpack.dev.js
@@ -0,0 +1,8 @@
+const path = require('path');
+const webpackCommon = require('./../../../.webpack/webpack.commonjs.js');
+const SRC_DIR = path.join(__dirname, '../src');
+const DIST_DIR = path.join(__dirname, '../dist');
+
+module.exports = (env, argv) => {
+  return webpackCommon(env, argv, { SRC_DIR, DIST_DIR });
+};