Ohifv3 (#1562)

* Add extension and mode for MONAI Label Signed-off-by: Andres <[email protected]> * Add toolGroups to mode Signed-off-by: Andres <[email protected]> * Extension and model working in class format Signed-off-by: Andres <[email protected]> * Connection to MONAI Label server and label fetching are working now Signed-off-by: Andres <[email protected]> * Add probe tool Signed-off-by: Andres <[email protected]> * add segmentation load/rendering for OHIF v3 (#1525) * working segmentation load * segmentation panel * add frame of reference uid to monai segs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Andres Diaz-Pinto <[email protected]> * Update segmentatio reader function Signed-off-by: Andres <[email protected]> * Model inference and label rendering working Signed-off-by: Andres <[email protected]> * Convert points from world to ijk - remove all clicks Signed-off-by: Andres <[email protected]> * Increase caching files when connecting to DICOM server Signed-off-by: Andres <[email protected]> * Add active learning tab Signed-off-by: Andres <[email protected]> * Update style for active learning tab Signed-off-by: Andres <[email protected]> * Hide the right panel Signed-off-by: Andres <[email protected]> * Send centroids to viewer Signed-off-by: Andres <[email protected]> * Send segmentation to DICOM Web Signed-off-by: Andres <[email protected]> * Fix centroids - json compatible Signed-off-by: Andres <[email protected]> * Update gitignore - add build script Signed-off-by: Andres <[email protected]> * feat(ohifv3): parse segment centroids for jump and make smartEdit work (#1531) * working segmentation load * segmentation panel * add frame of reference uid to monai segs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make probe tool grab color for selected segment * parse centroids and add to segmentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Andres Diaz-Pinto <[email protected]> * Fix indexes for centroids Signed-off-by: Andres <[email protected]> * Add image Signed-off-by: Andres <[email protected]> * Add segmentation panel Signed-off-by: Andres <[email protected]> * DICOM-SEG writer is working Signed-off-by: Andres <[email protected]> * DeepEdit working on OHIFv3 Signed-off-by: Andres <[email protected]> * Update tab name Signed-off-by: Andres <[email protected]> * Update gitignore Signed-off-by: Andres <[email protected]> * OHIFv3 working Signed-off-by: Andres <[email protected]> * Update bash scrip to build OHIFv3 Signed-off-by: Andres <[email protected]> * COOP solved - using orthanc instead of proxy Signed-off-by: Andres <[email protected]> * Update print statement Signed-off-by: Andres <[email protected]> * Change tab background Signed-off-by: Andres <[email protected]> * feat(segmentation tools): working new segmentation panel and brushes (#1545) * working segmentation load * segmentation panel * add frame of reference uid to monai segs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make probe tool grab color for selected segment * parse centroids and add to segmentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * initial commit for toolbox * fix merge * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Andres Diaz-Pinto <[email protected]> * feat(labels): add initial labels from the server as starting point (#1546) * working segmentation load * segmentation panel * add frame of reference uid to monai segs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * make probe tool grab color for selected segment * parse centroids and add to segmentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * initial commit for toolbox * fix merge * add initial segments from the server * fix after pull * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Andres Diaz-Pinto <[email protected]> * Add batch infer Signed-off-by: Andres <[email protected]> * Change background colors and fix click edition Signed-off-by: Andres <[email protected]> * change ohif image Signed-off-by: Andres <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Proxy Headers Signed-off-by: Andres <[email protected]> --------- Signed-off-by: Andres <[email protected]> Signed-off-by: Andres Diaz-Pinto <[email protected]> Co-authored-by: Alireza <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Project-MONAI · Oct 10, 2023 · d4209ce · d4209ce
1 parent d2a9bae
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Showing 69 changed files with 6,237 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -166,3 +166,7 @@ junit
 test-output.xml
 studies
 tests/data
+yarn.lock
+# Packages
+node_modules
+yarn.lock
diff --git a/monailabel/config.py b/monailabel/config.py
@@ -62,7 +62,7 @@ class Settings(BaseSettings):
     MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME: bool = False
     MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI: bool = True
     MONAI_LABEL_DICOMWEB_SEARCH_FILTER: Dict[str, Any] = {"Modality": "CT"}
-    MONAI_LABEL_DICOMWEB_CACHE_EXPIRY: int = 180
+    MONAI_LABEL_DICOMWEB_CACHE_EXPIRY: int = 7200
     MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT: float = 30.0
     MONAI_LABEL_DICOMWEB_READ_TIMEOUT: float = 5.0
 

diff --git a/monailabel/datastore/utils/convert.py b/monailabel/datastore/utils/convert.py
@@ -60,7 +60,7 @@ def dicom_to_nifti(series_dir, is_seg=False):
     return output_file
 
 
-def binary_to_image(reference_image, label, dtype=np.uint16, file_ext=".nii.gz"):
+def binary_to_image(reference_image, label, dtype=np.uint8, file_ext=".nii.gz"):
     start = time.time()
 
     image_np, meta_dict = LoadImage(image_only=False)(reference_image)

diff --git a/monailabel/endpoints/ohif.py b/monailabel/endpoints/ohif.py
@@ -38,8 +38,17 @@ def get_ohif(path: str):
     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))
 
+    # headers = {
+    #     "Cross-Origin-Opener-Policy": "same-origin",
+    #     "Cross-Origin-Embedder-Policy": "require-corp",
+    #     "Cross-Origin-Resource-Policy": "same-site",
+    # }
+
+    # return FileResponse(file, media_type=get_mime_type(file), headers=headers)
+
 
 @router.get("/{path:path}", include_in_schema=False)
 async def api_get_ohif(path: str, user: User = Depends(RBAC(settings.MONAI_LABEL_AUTH_ROLE_USER))):

diff --git a/monailabel/endpoints/proxy.py b/monailabel/endpoints/proxy.py
@@ -65,6 +65,9 @@ async def proxy_dicom(op: str, path: str, response: Response):
         )
 
         # some version of ohif requests metadata using qido so change it to wado
+        print(
+            f"This is the server {server} - This is the op {op} - This is the prefix {prefix} - This is the path {path}"
+        )
         if path.endswith("metadata") and op == "qido":
             prefix = settings.MONAI_LABEL_WADO_PREFIX
 
@@ -78,10 +81,16 @@ async def proxy_dicom(op: str, path: str, response: Response):
             settings.MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT,
             read=settings.MONAI_LABEL_DICOMWEB_READ_TIMEOUT,
         )
+
+        print(f"This is the proxy path: {proxy_path}")
         proxy = await client.get(proxy_path, timeout=timeout)
 
     response.body = proxy.content
     response.status_code = proxy.status_code
+    # response.headers["Cross-Origin-Opener-Policy"] = "same-origin"
+    # response.headers["Cross-Origin-Embedder-Policy"] = "require-corp"
+    # response.headers["Cross-Origin-Resource-Policy"] = "same-site"
+    # response.headers["Cross-Origin-Resource-Policy"] = "cross-origin"
     return response
 
 

diff --git a/monailabel/tasks/infer/basic_infer.py b/monailabel/tasks/infer/basic_infer.py
@@ -355,6 +355,17 @@ def __call__(
             "transform": data.get("latencies"),
         }
 
+        # Add Centroids to the result json to consume in OHIF v3
+        centroids = data.get("centroids", None)
+        if centroids is not None:
+            centroids_dict = dict()
+            for c in centroids:
+                all_items = list(c.items())
+                centroids_dict[all_items[0][0]] = [str(i) for i in all_items[0][1]]  # making it json compatible
+            result_json["centroids"] = centroids_dict
+        else:
+            result_json["centroids"] = dict()
+
         if result_file_name is not None and isinstance(result_file_name, str):
             logger.info(f"Result File: {result_file_name}")
         logger.info(f"Result Json Keys: {list(result_json.keys())}")

diff --git a/plugins/ohif/monai-label/src/components/MonaiLabelPanel.js b/plugins/ohif/monai-label/src/components/MonaiLabelPanel.js
@@ -39,6 +39,10 @@ export default class MonaiLabelPanel extends Component {
     super(props);
 
     const { viewports, studies, activeIndex } = props;
+    /* setTimeout(() => {
+      this.viewConstants = this.getViewConstants(viewports, studies, activeIndex);
+    }, 2000) */
+
     this.viewConstants = this.getViewConstants(viewports, studies, activeIndex);
     console.debug(this.viewConstants);
 

diff --git a/plugins/ohifv3/README.md b/plugins/ohifv3/README.md
@@ -0,0 +1,149 @@
+<!--
+Copyright (c) MONAI Consortium
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+    http://www.apache.org/licenses/LICENSE-2.0
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+## MONAI Label Plugin for OHIF Viewer
+The Open Health Imaging Foundation (OHIF) Viewer is an open-source, web-based platform for medical imaging. OHIF Viewer provides a framework for building complex imaging applications with user-friendly interfaces. MONAI Label supports the web-based OHIF viewer with connectivity to a remote DICOM server via DICOMweb.
+
+<img src="./images/ohifv3.png" width=90% />
+
+### Table of Contents
+- [Supported Applications](#supported-applications)
+- [Installing OHIF](#installing-ohif)
+- [Installing Orthanc](#installing-orthanc-dicomweb)
+- [Converting NIFTI Images to DICOM](#converting-nifti-images-to-dicom)
+- [Converting NIFTI Annotations to DICOM-SEG](#converting-nifti-annotations-to-dicom-seg)
+- [Uploading DICOM to Orthanc](#uploading-dicom-to-orthanc)
+
+### Supported Applications
+Supported applications can be found in the [sample-apps](../../sample-apps/radiology/) folder under the radiology section. These applications include models like DeepEdit, DeepGrow, Segmentation, and more, which can be used to create and refine labels for various medical imaging tasks.
+
+### Installing OHIF
+When installing MONAI Label with `pip install monailabel`, a version of OHIF that is pre-built with the MONAI Label library is automatically installed. OHIF will be accessible at http://127.0.0.1:8000/ohif/ when you start the MONAI Label server and connect to local/remote DICOM-web storage.
+
+#### Development setup
+
+To build the OHIF plugin for development, follow these steps:
+  ```bash
+  sudo sh requirements.sh # installs yarn
+  sh build.sh
+  ```
+
+To run Orthanc from the submodule and avoid building the OHIF package for every code change, use the following commands:
+```bash
+cd plugins/ohif/Viewers
+
+yarn run dev:orthanc
+
+# OHIF will run at http://127.0.0.1:3000/
+```
+You can then visit http://127.0.0.1:3000/ on your browser to see the running OHIF.
+
+### Installing Orthanc (DICOMWeb)
+
+#### Ubuntu 20.x
+
+```bash
+# Install Orthanc and DICOMweb plugin
+sudo apt-get install orthanc orthanc-dicomweb -y
+
+# Install Plastimatch
+sudo apt-get install plastimatch -y
+```
+
+However, you must upgrade to the latest version by following the steps mentioned on the [Orthanc Installation Guide](https://book.orthanc-server.com/users/debian-packages.html#replacing-the-package-from-the-service-by-the-lsb-binaries)
+
+```bash
+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 images to DICOM
+To use Orthanc, your files need to be in DICOM format. You can convert any Nifti files to DICOM using the following command:
+```bash
+plastimatch convert --patient-id patient1 --input image.nii.gz --output-dicom test
+```
+- `plastimatch convert`: This is the command to run the conversion tool.
+- `--patient-id patient1`: This option specifies the ID of the patient to be associated with the DICOM files. In this example, it is set to `patient1`.
+- `--input image.nii.gz`: This option specifies the path to the input Nifti file that you want to convert to DICOM. In this example, the input file is `image.nii.gz`.
+- `--output-dicom test`: This option specifies the path to the output folder where the DICOM files will be saved. In this example, the output folder is named `test`.
+
+When you run this command, plastimatch will read the input Nifti file and convert it to a series of DICOM files with the specified patient ID. These files will be saved in the test folder in DICOM format, which can be uploaded to an Orthanc server.
+
+### Converting NIFTI Annotations to DICOM-SEG
+
+If you want to upload image annotations to the DICOMWeb server (such as Orthanc), you should use DICOM-SEG format. DICOM-SEG is a DICOM standard format for image segmentation. To convert NIFTI annotations to DICOM-SEG, you can use the itkimage2segimage tool from ITK (Insight Toolkit).
+
+Here's how to use itkimage2segimage to convert NIFTI annotations to DICOM-SEG:
+
+1. Install ITK: You can download and install ITK from their website, or use a package manager such as pip or conda to install it.
+2. Convert NIFTI annotations to NIFTI-Segmentations: Use the `plastimatch convert` command to convert the NIFTI annotations to NIFTI-Segmentations format. This format is required as an input to `itkimage2segimage`. The command is similar to the one used to convert NIFTI images to DICOM, but with an additional option:
+
+```bash
+plastimatch convert --input annotations.nii.gz --output-nifti-seg annotations-seg.nii.gz
+```
+This command will convert the NIFTI annotations file named `annotations.nii.gz` to NIFTI-Segmentations format and save the result in a file named `annotations-seg.nii.gz`.
+
+3. Convert NIFTI-Segmentations to DICOM-SEG: Use the `itkimage2segimage` command to convert the NIFTI-Segmentations file to DICOM-SEG format. Here's an example command:
+
+```bash
+itkimage2segimage --inputImage annotations-seg.nii.gz --outputDICOM annotations-seg.dcm --patientID patient1
+```
+This command will convert the `annotations-seg.nii.gz` file to DICOM-SEG format and save the result in a file named `annotations-seg.dcm`. The `--patientID` option specifies the ID of the patient to be associated with the DICOM-SEG file.
+
+After conversion, you can upload the DICOM-SEG file to the DICOMWeb server such as Orthanc.
+
+
+### Uploading DICOM to Orthanc
+
+#### Use Orthanc Browser
+You can use the Orthanc browser located at http://127.0.0.1:8042/app/explorer.html#upload to upload files.
+
+#### Using STORE SCP/SCU
+To upload files using STORE SCP/SCU, you need to enable AET by editing the `orthanc.json` file:
+`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]
+```
+Then, restart Orthanc:
+
+```
+sudo service orthanc restart
+```
+
+#### Upload Files
+To upload files, use the following command:
+
+```bash
+python -m pynetdicom storescu 127.0.0.1 4242 test -aet MONAILABEL -r
+```
+That's it! With these steps, you should have successfully installed MONAI Label with the OHIF viewer plugin and connected it to a remote DICOM server via DICOMweb.
diff --git a/plugins/ohifv3/build.sh b/plugins/ohifv3/build.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+curr_dir="$(pwd)"
+my_dir="$(dirname "$(readlink -f "$0")")"
+
+echo "Installing requirements..."
+sh $my_dir/requirements.sh
+
+install_dir=${1:-$my_dir/../../monailabel/endpoints/static/ohif}
+
+echo "Current Dir: ${curr_dir}"
+echo "My Dir: ${my_dir}"
+echo "Installing OHIF at: ${install_dir}"
+
+cd ${my_dir}
+rm -rf Viewers
+git clone https://github.com/OHIF/Viewers.git
+cd Viewers
+git checkout feat/monai-label
+
+
+sed -i "s|routerBasename: '/'|routerBasename: '/ohif/'|g" ./platform/app/public/config/default.js
+sed -i "s|name: 'aws'|name: 'Orthanc'|g" ./platform/app/public/config/default.js
+sed -i "s|wadoUriRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb'|wadoUriRoot: 'http://localhost/dicom-web'|g" ./platform/app/public/config/default.js
+sed -i "s|wadoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb'|wadoRoot: 'http://localhost/dicom-web'|g" ./platform/app/public/config/default.js
+sed -i "s|qidoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb'|qidoRoot: 'http://localhost/dicom-web'|g" ./platform/app/public/config/default.js
+
+sed -i "s|PUBLIC_URL=/|PUBLIC_URL=/ohif/|g" ./platform/app/.env
+
+
+yarn install
+
+# Link the mode and extension HERE
+echo "Linking extension and mode at: $(pwd)"
+yarn run cli link-extension ../extension-monai-label
+yarn run cli link-mode ../mode-monai-label
+
+cd ../extension-monai-label
+
+echo "Running install again at: $(pwd)"
+
+yarn install
+
+echo "Moving nrrd-js and itk node modules to Viewersnode_modules/"
+
+cp -r ./node_modules/nrrd-js ../Viewers/node_modules/
+
+cp -r ./node_modules/itk ../Viewers/node_modules/
+
+echo "Moving to Viewers folder to build OHIF"
+
+cd ../Viewers
+
+echo "Viewers folder before building OHIF $(pwd)"
+
+QUICK_BUILD=true yarn run build
+
+rm -rf ${install_dir}
+mv ./platform/app/dist/ ${install_dir}
+echo "Copied OHIF to ${install_dir}"
+
+rm -rf ../Viewers
+
+cd ${curr_dir}