Gradienthealth/rebase viewer to v3.10.1

.github/workflows/deploy_ghpages.yml

@@ -0,0 +1,110 @@
+name: Deploy viewer to github pages
+
+on:
+  push:
+    branches: ['gradienthealth/rebase-viewer-to-v3.10.1']
+  #pull_request:
+  #branches: [ "main" ]
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [20.9.x]
+
+    steps:
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+
+      - name: Checkout cornerstone3D
+        uses: actions/checkout@v3
+        with:
+          repository: gradienthealth/cornerstone3D-beta
+          ref: gradienthealth/rebase-viewer-to-v3.10.1
+          path: ./cornerstone3D
+
+      - name: Build cornerstone3D
+        run: |
+          cd ./cornerstone3D
+          yarn install
+          yarn build:all
+
+      - name: Checkout GradientExtensionsAndModes
+        uses: actions/checkout@v3
+        with:
+          repository: gradienthealth/GradientExtensionsAndModes
+          ref: gradienthealth/rebase-viewer-to-v3.10.1
+          path: ./GradientExtensionsAndModes
+
+      #- name: Build GradientExtensionsAndModes
+      #  run: |
+      #   cd ./GradientExtensionsAndModes/extensions/ohif-gradienthealth-extension
+      #   yarn install
+      #   yarn build:package
+      #   cd ./modes/cohort
+      #   yarn install
+      #   yarn build:package
+
+      - name: Checkout Viewers
+        uses: actions/checkout@v3
+        with:
+          repository: gradienthealth/Viewers
+          path: ./Viewers
+
+      - name: Link
+        run: |
+          cd ./cornerstone3D/packages/adapters/dist
+          yarn link
+          cd ../../ai/dist
+          yarn link
+          cd ../../core/dist
+          yarn link
+          cd ../../dicomImageLoader/dist
+          yarn link
+          cd ../../labelmap-interpolation/dist
+          yarn link
+          #cd ../../nifti-volume-loader/dist
+          #yarn link
+          cd ../../polymorphic-segmentation/dist
+          yarn link
+          cd ../../tools/dist
+          yarn link
+          cd ../../../../Viewers
+          yarn link @cornerstonejs/adapters
+          yarn link @cornerstonejs/ai
+          yarn link @cornerstonejs/core
+          yarn link @cornerstonejs/dicom-image-loader
+          #yarn link @cornerstonejs/nifti-volume-loader
+          yarn link @cornerstonejs/labelmap-interpolation
+          yarn link @cornerstonejs/polymorphic-segmentation
+          yarn link @cornerstonejs/tools
+          yarn install
+          yarn run cli link-extension ../GradientExtensionsAndModes/extensions/ohif-gradienthealth-extension
+          yarn run cli link-mode ../GradientExtensionsAndModes/modes/breast-density-mode
+          yarn run build:gradient
+
+      - name: Checkout gh page
+        uses: actions/checkout@v3
+        with:
+          repository: gradienthealth/gradienthealth.github.io
+          path: ./gradienthealth.github.io
+          token: ${{ secrets.GH_DEPLOY_TOKEN }}
+
+      - name: Copy
+        run: |
+          mv ./gradienthealth.github.io/.git /tmp/
+          rm -r ./gradienthealth.github.io
+          cp -r ./Viewers/platform/app/dist/ ./gradienthealth.github.io
+          mv /tmp/.git ./gradienthealth.github.io
+          cd ./gradienthealth.github.io
+          cp index.html 404.html
+          git config --global user.name "Adithyan-Dinesh-Trenser"
+          git config --global user.email "adithyan.dinesh@trenser.com"
+          git remote set-url origin https://Adithyan-Dinesh-Trenser:${{ secrets.GH_DEPLOY_TOKEN }}@github.com/gradienthealth/gradienthealth.github.io
+          git add .
+          git commit -a -m "publishing viewer"
+          git push -u origin

extensions/default/package.json

@@ -48,6 +48,7 @@
     "@babel/runtime": "^7.20.13",
     "@cornerstonejs/calculate-suv": "^1.1.0",
     "lodash.get": "^4.4.2",
-    "lodash.uniqby": "^4.7.0"
+    "lodash.uniqby": "^4.7.0",
+    "cod-dicomweb-server": "^1.3.4"
   }
 }

extensions/default/src/DicomWebDataSource/codDicomWebServerWrapper.js

@@ -0,0 +1,235 @@
+import { CodDicomWebServer } from 'cod-dicomweb-server';
+
+const Properties = {
+  StudyUID: '0020000D',
+  SeriesUID: '0020000E',
+};
+
+class CodDicomWebServerClient {
+  /**
+   * @param {Object} config
+   */
+  constructor(config) {
+    this.baseURL = config.url;
+    this.qidoURL = this.baseURL;
+    this.wadoURL = this.baseURL;
+    this.config = config;
+    this.headers = config.headers;
+    this.errorInterceptor = config.errorInterceptor;
+
+    this._codServer = new CodDicomWebServer({ domain: parseDomainFromBaseURL(this.baseURL) });
+    this.deidStudyInstanceUIDMap = new Map(); // Map of study instance UIDs to deid study instance UIDs
+  }
+
+  /**
+   * @param {URLSearchParams} queryParams
+   */
+  async fetchStudiesMetadata(queryParams) {
+    this._studiesMetadata = await this.filesFromStudyInstanceUID({
+      wadoURL: this.wadoURL,
+      bucketName: queryParams.get('bucket'),
+      prefix: queryParams.get('bucket-prefix'),
+      studyuids: queryParams.getAll('StudyInstanceUIDs'),
+      headers: this.headers,
+    })
+      .then(studies => {
+        return studies.filter(study => {
+          study.series = study.series.filter(aSeries => {
+            if (aSeries.instances.length) {
+              return true;
+            }
+
+            console.warn('No instance found in series ' + aSeries.deidSeriesInstanceUID);
+            return false;
+          });
+
+          if (study.series.length) {
+            const studyUID = study.series[0].instances[0]['0020000D'].Value[0];
+            this.deidStudyInstanceUIDMap.set(study.deidStudyInstanceUID, studyUID);
+            return true;
+          }
+
+          return false;
+        });
+      })
+      .catch(error => {
+        this.errorInterceptor(error);
+        return [];
+      });
+  }
+
+  /**
+   * @param {string} deidStudyInstanceUID
+   */
+  getStudyUIDForDeidStudyUID(deidStudyInstanceUID) {
+    const studyWithDeidStudyUID = this._studiesMetadata.find(
+      study => (study.deidStudyInstanceUID = deidStudyInstanceUID)
+    );
+
+    return this._getProperty(studyWithDeidStudyUID, Properties.StudyUID);
+  }
+
+  /**
+   * @param {Object} data
+   * @param {string} property
+   */
+  _getProperty(data, property) {
+    if (!data) {
+      return;
+    }
+
+    return (
+      data[property]?.Value[0] ||
+      data.instances?.[0][property].Value[0] ||
+      data.series?.[0].instances[0][property].Value[0]
+    );
+  }
+
+  /**
+   * @param {Object[]} studies
+   * @param {string} studyInstanceUID
+   */
+  _findStudy(studies = [], studyInstanceUID) {
+    return studies.find(
+      study => this._getProperty(study, Properties.StudyUID) === studyInstanceUID
+    );
+  }
+
+  /**
+   * @param {Object[]} series
+   * @param {string} seriesInstanceUID
+   */
+  _findSeries(series = [], seriesInstanceUID) {
+    return series.find(
+      series => this._getProperty(series, Properties.SeriesUID) === seriesInstanceUID
+    );
+  }
+
+  /**
+   * @param {Object} options
+   * @param {string} options.studyInstanceUID
+   * @param {string} options.seriesInstanceUID
+   */
+  retrieveSeriesMetadata({ studyInstanceUID, seriesInstanceUID }) {
+    const studyFound = this._findStudy(this._studiesMetadata, studyInstanceUID);
+    const seriesFound = this._findSeries(studyFound?.series, seriesInstanceUID);
+
+    return new Promise((resolve, reject) => {
+      if (seriesFound) {
+        resolve(seriesFound.instances);
+      } else {
+        reject();
+      }
+    });
+  }
+
+  /**
+   * @param {Object} options
+   * @param {string} options.studyInstanceUID
+   */
+  retrieveStudyMetadata({ studyInstanceUID }) {
+    const studyFound = this._findStudy(this._studiesMetadata, studyInstanceUID);
+
+    return new Promise((resolve, reject) => {
+      if (studyFound) {
+        resolve(studyFound.series.flatMap(aSeries => aSeries.instances));
+      } else {
+        reject();
+      }
+    });
+  }
+
+  /**
+   * @param {Object} options
+   * @param {string} options.studyInstanceUID
+   */
+  searchForSeries({ studyInstanceUID }) {
+    const studyFound = this._findStudy(this._studiesMetadata, studyInstanceUID);
+
+    return new Promise(resolve => {
+      if (studyFound) {
+        resolve(studyFound.series.map(aSeries => aSeries.instances[0]));
+      } else {
+        resolve([]);
+      }
+    });
+  }
+
+  /**
+   * @param {Object} options
+   * @param {Object} options.queryParams
+   * @param {string} options.queryParams.StudyInstanceUID
+   */
+  searchForStudies({ queryParams }) {
+    const studyFound = this._studiesMetadata.find(study => {
+      if (this._getProperty(study, Properties.StudyUID) === queryParams.StudyInstanceUID) {
+        return true;
+      }
+
+      const tagFound = Object.entries(queryParams).find(
+        ([tag, value]) => this._getProperty(study, tag) === value
+      );
+      if (tagFound) {
+        return true;
+      }
+
+      return false;
+    });
+
+    return new Promise(resolve => {
+      if (studyFound) {
+        resolve([studyFound.series[0].instances[0]]);
+      } else {
+        resolve([]);
+      }
+    });
+  }
+
+  /**
+   * @param {Object} params
+   * @param {string} params.wadoURL
+   * @param {string} params.bucketName
+   * @param {string[]} params.studyuids
+   * @param {string} params.prefix
+   * @param {Object} params.headers
+   */
+  async filesFromStudyInstanceUID({ wadoURL, bucketName, prefix, studyuids, headers }) {
+    const delimiter = '/';
+    const domain = parseDomainFromBaseURL(wadoURL);
+    const bucketComponents = wadoURL.split(domain + delimiter)[1].split(delimiter);
+    const bucket = bucketName || bucketComponents[0];
+    const bucketPrefix = prefix || bucketComponents.slice(1).join(delimiter) || 'dicomweb';
+    const urlRoot = `${domain}/${bucket}/${bucketPrefix}`;
+
+    const studyMetadata = studyuids.map(async (/** @type {string} */ deidStudyInstanceuid) => {
+      const folderPath = `${bucketPrefix}/studies/${deidStudyInstanceuid}/series/`;
+      const apiUrl = `${domain}/storage/v1/b/${bucket}/o?prefix=${folderPath}&delimiter=${delimiter}`;
+      const response = await fetch(apiUrl, { headers });
+      const res = await response.json();
+      const folders = res.prefixes || [];
+      const series = folders.map(async (/** @type {string} */ folderPath) => {
+        const deidSeriesInstanceUID = folderPath.split('/series/')[1].split(delimiter)[0];
+        const wadoUrl = `${urlRoot}/studies/${deidStudyInstanceuid}/series/${deidSeriesInstanceUID}/metadata`;
+        return {
+          deidSeriesInstanceUID,
+          instances: await this._codServer.fetchCod(wadoUrl, headers),
+        };
+      });
+      return Promise.all(series).then(result => ({
+        deidStudyInstanceUID: deidStudyInstanceuid,
+        series: result,
+      }));
+    });
+    return await Promise.all(studyMetadata);
+  }
+}
+
+/**
+ * @param {string} baseRoot
+ */
+function parseDomainFromBaseURL(baseRoot) {
+  const [firstPart, secondPart] = baseRoot.split('://');
+  return `${firstPart}://${secondPart.split('/')[0]}`;
+}
+
+export default CodDicomWebServerClient;

extensions/default/src/DicomWebDataSource/getCodImageId.js

@@ -0,0 +1,25 @@
+import getWADORSImageId from './utils/getWADORSImageId';
+
+/**
+ * @param {Object} params
+ * @param {Object} params.instance
+ * @param {number} [params.frame]
+ * @param {Object} params.config
+ */
+export default function getCodImageId({ instance, frame, config }) {
+  if (!instance) {
+    return;
+  }
+
+  let wadoRsImageId;
+
+  if (instance.imageId && frame === undefined) {
+    wadoRsImageId = instance.imageId;
+  } else if (instance.url) {
+    wadoRsImageId = instance.url;
+  } else {
+    wadoRsImageId = getWADORSImageId(instance, config, frame);
+  }
+
+  return wadoRsImageId.replace('wadors:', 'cod:');
+}