feat: cornerstone3D stack and volume viewports (#2787)

* feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: cs3d tools and toolGroups (#20) * add more tools to work with cs3d mode * fix hotkeys * add stack manager usage for stach viewports * add image scrollbar * wip viewport overlay * fix toAnnotation schema for tools * fix the unnecessary size change that triggered resize * hanging protocol improvement to allow unmatched errors * study description matching for hanging protocol * fix the displaysetOptions to work * fix handle the active tool when a new viewport is added * fix separate toolGroups for mode * apply review comments * apply review comments * yarn lock * feat: overlay component (#21) * fix default displayset options * add viewport overlay * apply review comments * feat: loading and orientation indicators (#22) * add loading indicator * add orientation marker initial work * apply review comments * fix: orientation markers (#23) * finished the orientation markers * fix various broken cypress tests * apply review comments * update yarn lock * feat: re-working measurement tracking mode with cornerstone3d (#2805) * feat: cs3d working stack viewport and tools (#19) * Squashed everything * fix weird react issue * fix eslint / prettier stuff * thumbnails work now with cpu rendering * feat: use new loadImageToCanvas in cs3d * make jump to measurement work * fix active thumbnail * fix measurement delete * fix window level presets * remove segmentation and sync groups for now * fix the dicom pdf and dicom video * fix cornerstone window assignment for cypress * apply review comments Co-authored-by: Erik <erik.sweed@gmail.com> * feat: Add Measurement tracking mode with cs3D (#2789) * feat: first render for cornerstone3d tracked viewport * make tool active work * wip for SR extension * renamed dicom sr to cornerstone dicom sr * remove cornerstone from dicom pdf and video * move dicom sr logic to sr extension * feat: Add hydration for the length tool * fix SR display tool for length using cs3d * fix default config * fix: various bugs with sr viewport and tracking * fix promptying to continue tracking for when SR is created * feat: add keep trackign of unique identifiers * fix hydration for same imageIds * feat: Add SR toolGroup creation on modeEnter * feat: remove the need for separate mapper for SR hydration * add SR display for ellipse * handle hydration of elliptical ROI tool * remove cornerstone extension * add arrow mapping * feat: Add ArrowAnnotate SR display and hydration * apply review comments * apply review comments * move viewport labels to the viewportData * apply review comments * fix: integration cypress tests with cornerstone3D and add CINE tool (#2795) * fix: integration cypress tests with cornerstone3D * revert to addOrUpdate as it makes more sense * fix local drag and drop * fix tests * move dicomLoaderService to cornerstone extension * fix various import bugs * fix bug for local PT series * fix various unit tests * bump cs3d versions * add angle and magnify tool * bump dependencies to avoid broken peerDeps * feat: add initial work for capture using cs3d * feat: show annotations on the image capture * feat: add svg layer export * feat: Add CINE Tool * feat: remove unnecessary viewport rendering for cine state changes Co-authored-by: Erik Ziegler <erik.sweed@gmail.com> * docs: modify and improve documentation (#2800) * cleanup docs versionings * feat: Add all version explanations * version docs for 3.0 * wip for changing docs * wip for updated docs * add utility module documentation * fix demo with nohoisting of history * add slides and video to resources * apply review comments * fix: drag and drop SR into SR viewport (#2803) * update yarn lock Co-authored-by: Erik <erik.sweed@gmail.com> * update pathnames to match v3-stable * update the e2e pathname * fix: various bugs with regard to tracking workflow (#2811) * fix: various issues with measurement panel * fix: update default tool style for annotations * fix: annotatoin label getting removed * feat: Add backward compatibility for SR hydration with legacy cornerstone * fix: cursors and ellipse ROI max style * fix: ArrowAnnotate SRDisplay * apply review comments * bump package versions * fix: bugin rehydration of SR * fix: e2e tests * fix active viewport thickness and arrowTool ui * add readme for measurement tracking * use uploaded image for readme * add back images * try to fix e2e test * fix: window level presets hotkeys * Update README.md * update yarn lock * feat: volume api and TMTV mode (#2817) * feat: volumeAPI and TMTV mode * feat: use cs3d cache service to obtain viewportData * wip for volume api * wip: fusion viewport * feat: add blend mode option * wip for image scrollbar * fix drag and drop thumbnail * wip for image scrollbar for voluems * fix: element mismatch bug for scroll * feat: Add image scrollbar to volumes * feat: add syncGroups to volume api * feat: add tmtv mode initial setup * feat: add initial image options for the stack viewports * feat: Add custom load strategy for volume viewports via HP * apply review comments fix: Jump presets cs3d (#2812) * feat: Add JumpPreset to OHIF for Cornerstone3D * fix: accessing viewport service from servicesManager feat: volume API and TMTV mode (#2814) * fix: do not display overlays on mip viewports * feat: add optional disableCommands for toggle buttons * fix: toggleCrossharis * feat: config the crosshairs * feat: add PetSUV Panel for changing metadata * feat: initial work for the rectangleROIThreshold panel * wip: measurement service * roi threshold working * feat: Add displayText to segmentations * feat: add remove segmentation * feat: add csv export * feat: add RT export for annotations in tmtv mode * fix: fusion to use pt in tmtv mode and measuremet mappings * fix: various bugs * apply review comments * apply review comments * feat: add fusion color maps * add readme to tmtv mode * Update README.md * fix: try to fix build * fix unit tests * Update README.md * feat: add about to the panel * fix: changing strategy in roi panel * apply review comments * update package versions * wip for stackPrefetch * fix: cornerstone3d hydration and renaming (#2818) * update readme * renamed cornerstone extension * wip for renaming cornerstone3D variables * wip for renaming cornerstone3D variables * wip for fixing bugs for SR viewport * fix: jumpToMeasurement and initial label after hydration * fix: fileName capitalization * feat: use the new prefetch stack in the cs3d (#2820) * feat: use the new prefetch stack in the cs3d * use viewport scroll api for stack viewport * fix cine stop when scrollbar changes * feat: use new prefetch events * fix loading state to not show repeatedly * fix: various bugs for tmtv mode thresholding and new icons (#2823) * feat: make tmtv mode available in worklist * feat: add new icons for tmtv mode * feat: add fusion color icon * fix: parallel scale calculation * fix: bump Cornerstone to get large image support working * fix: Fix issues with CPU viewport flipping, including config files * fix: bump cornerstone to fix magnify tool * fix: Bump Cornerstone version to fix resetCamera issue in StackViewport * ci: Add _headers file to enable CORS headers for Netlify Drag/Drop deploys * fix: WADO-URI was not working. PET Metadata was coming from the wrong place. Fixed some minor React errors * feat(OHIF):Allow modes and extensions to be added after commpile time. (#2838) Also works with the compile time add that the existing cli uses, so that both build types work. Eric and I agreed this doesn't change existing functionality, but is almost entirely build issues/fixes. * bump: dependency versions to fix hydration bugs (#2848) * bump: dcmjs version to fix hydration bugs * try to fix tests * bump dependency versions Co-authored-by: Alireza <ar.sedghi@gmail.com> Co-authored-by: Bill Wallace <wayfarer3130@gmail.com>
2022-07-27 12:39:04 -04:00
1 parent 86dcaf6293
commit bd1c38c00c
@@ -0,0 +1,262 @@
+import AnnotationToPointData from './measurements/AnnotationToPointData';
+import dcmjs from 'dcmjs';
+import { DicomMetadataStore } from '@ohif/core';
+
+const { DicomMetaDictionary } = dcmjs.data;
+
+export default class RTSSReport {
+  constructor() {}
+
+  /**
+   * Convert handles to RTSSReport report object containing the dcmjs dicom dataset.
+   *
+   * Note: The tool data needs to be formatted in a specific way, and currently
+   * it is limited to the RectangleROIStartEndTool in the Cornerstone.
+   *
+   * @param annotations Array of Cornerstone tool annotation data
+   * @param metadataProvider Metadata provider
+   * @param options report generation options
+   * @returns Report object containing the dataset
+   */
+  static generateReport(annotations, metadataProvider, options) {
+    let dataset = initializeDataset(annotations, metadataProvider);
+
+    annotations.forEach((annotation, index) => {
+      const ContourSequence = AnnotationToPointData.convert(
+        annotation,
+        index,
+        metadataProvider,
+        options
+      );
+
+      dataset.StructureSetROISequence.push(
+        getStructureSetModule(annotation, index, metadataProvider)
+      );
+
+      dataset.ROIContourSequence.push(ContourSequence);
+      dataset.RTROIObservationsSequence.push(
+        getRTROIObservationsSequence(annotation, index, metadataProvider)
+      );
+
+      // ReferencedSeriesSequence
+      // Todo: handle more than one series
+      dataset.ReferencedSeriesSequence = getReferencedSeriesSequence(
+        annotation,
+        index,
+        metadataProvider
+      );
+
+      // ReferencedFrameOfReferenceSequence
+      dataset.ReferencedFrameOfReferenceSequence = getReferencedFrameOfReferenceSequence(
+        annotation,
+        metadataProvider,
+        dataset
+      );
+    });
+
+    const fileMetaInformationVersionArray = new Uint8Array(2);
+    fileMetaInformationVersionArray[1] = 1;
+
+    const _meta = {
+      FileMetaInformationVersion: {
+        Value: [fileMetaInformationVersionArray.buffer],
+        vr: 'OB',
+      },
+      TransferSyntaxUID: {
+        Value: ['1.2.840.10008.1.2.1'],
+        vr: 'UI',
+      },
+      ImplementationClassUID: {
+        Value: [DicomMetaDictionary.uid()], // TODO: could be git hash or other valid id
+        vr: 'UI',
+      },
+      ImplementationVersionName: {
+        Value: ['dcmjs'],
+        vr: 'SH',
+      },
+    };
+
+    dataset._meta = _meta;
+
+    return dataset;
+  }
+
+  /**
+   * Generate Cornerstone tool state from dataset
+   * @param {object} dataset dataset
+   * @param {object} hooks
+   * @param {function} hooks.getToolClass Function to map dataset to a tool class
+   * @returns
+   */
+  static generateToolState(dataset, hooks = {}) {
+    // Todo
+    console.warn('RTSSReport.generateToolState not implemented');
+  }
+}
+
+function initializeDataset(annotations, metadataProvider) {
+  const rtSOPInstanceUID = DicomMetaDictionary.uid();
+
+  // get the first annotation data
+  const {
+    referencedImageId: imageId,
+    FrameOfReferenceUID,
+  } = annotations[0].metadata;
+
+  const { studyInstanceUID } = metadataProvider.get(
+    'generalSeriesModule',
+    imageId
+  );
+
+  const patientModule = getPatientModule(imageId, metadataProvider);
+  const rtSeriesModule = getRTSeriesModule(imageId, metadataProvider);
+
+  return {
+    StructureSetROISequence: [],
+    ROIContourSequence: [],
+    RTROIObservationsSequence: [],
+    ReferencedSeriesSequence: [],
+    ReferencedFrameOfReferenceSequence: [],
+    ...patientModule,
+    ...rtSeriesModule,
+    StudyInstanceUID: studyInstanceUID,
+    SOPClassUID: '1.2.840.10008.5.1.4.1.1.481.3', // RT Structure Set Storage
+    SOPInstanceUID: rtSOPInstanceUID,
+    Manufacturer: 'dcmjs',
+    Modality: 'RTSTRUCT',
+    FrameOfReferenceUID,
+    PositionReferenceIndicator: '',
+    StructureSetLabel: '',
+    StructureSetName: '',
+    ReferringPhysicianName: '',
+    OperatorsName: '',
+    StructureSetDate: DicomMetaDictionary.date(),
+    StructureSetTime: DicomMetaDictionary.time(),
+  };
+}
+
+function getPatientModule(imageId, metadataProvider) {
+  const generalSeriesModule = metadataProvider.get(
+    'generalSeriesModule',
+    imageId
+  );
+  const generalStudyModule = metadataProvider.get(
+    'generalStudyModule',
+    imageId
+  );
+  const patientStudyModule = metadataProvider.get(
+    'patientStudyModule',
+    imageId
+  );
+  const patientModule = metadataProvider.get('patientModule', imageId);
+  const patientDemographicModule = metadataProvider.get(
+    'patientDemographicModule',
+    imageId
+  );
+
+  return {
+    Modality: generalSeriesModule.modality,
+    PatientID: patientModule.patientId,
+    PatientName: patientModule.patientName,
+    PatientBirthDate: '',
+    PatientAge: patientStudyModule.patientAge,
+    PatientSex: patientDemographicModule.patientSex,
+    PatientWeight: patientStudyModule.patientWeight,
+    StudyDate: generalStudyModule.studyDate,
+    StudyTime: generalStudyModule.studyTime,
+    StudyID: 'ToDo',
+    AccessionNumber: generalStudyModule.accessionNumber,
+  };
+}
+
+function getReferencedFrameOfReferenceSequence(
+  toolData,
+  metadataProvider,
+  dataset
+) {
+  const { referencedImageId: imageId, FrameOfReferenceUID } = toolData.metadata;
+  const instance = metadataProvider.get('instance', imageId);
+  const { SeriesInstanceUID } = instance;
+
+  const { ReferencedSeriesSequence } = dataset;
+
+  return [
+    {
+      FrameOfReferenceUID,
+      RTReferencedStudySequence: [
+        {
+          ReferencedSOPClassUID: dataset.SOPClassUID,
+          ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
+          RTReferencedSeriesSequence: [
+            {
+              SeriesInstanceUID,
+              ContourImageSequence: [
+                ...ReferencedSeriesSequence[0].ReferencedInstanceSequence,
+              ],
+            },
+          ],
+        },
+      ],
+    },
+  ];
+}
+
+function getReferencedSeriesSequence(toolData, index, metadataProvider) {
+  // grab imageId from toolData
+  const { referencedImageId: imageId } = toolData.metadata;
+  const instance = metadataProvider.get('instance', imageId);
+  const { SeriesInstanceUID, StudyInstanceUID } = instance;
+
+  const ReferencedSeriesSequence = [];
+  if (SeriesInstanceUID) {
+    const series = DicomMetadataStore.getSeries(
+      StudyInstanceUID,
+      SeriesInstanceUID
+    );
+
+    const ReferencedSeries = {
+      SeriesInstanceUID,
+      ReferencedInstanceSequence: [],
+    };
+
+    series.instances.forEach(instance => {
+      const { SOPInstanceUID, SOPClassUID } = instance;
+      ReferencedSeries.ReferencedInstanceSequence.push({
+        ReferencedSOPClassUID: SOPClassUID,
+        ReferencedSOPInstanceUID: SOPInstanceUID,
+      });
+    });
+
+    ReferencedSeriesSequence.push(ReferencedSeries);
+  }
+
+  return ReferencedSeriesSequence;
+}
+
+function getRTSeriesModule(imageId, metadataProvider) {
+  return {
+    SeriesInstanceUID: DicomMetaDictionary.uid(), // generate a new series instance uid
+    SeriesNumber: '99', // Todo:: what should be the series number?
+  };
+}
+
+function getStructureSetModule(toolData, index, metadataProvider) {
+  const { FrameOfReferenceUID } = toolData.metadata;
+
+  return {
+    ROINumber: index + 1,
+    ROIName: `Todo: name ${index + 1}`,
+    ROIDescription: `Todo: description ${index + 1}`,
+    ROIGenerationAlgorithm: 'Todo: algorithm',
+    ReferencedFrameOfReferenceUID: FrameOfReferenceUID,
+  };
+}
+
+function getRTROIObservationsSequence(toolData, index, metadataProvider) {
+  return {
+    ObservationNumber: index + 1,
+    ReferencedROINumber: index + 1,
+    RTROIInterpretedType: 'Todo: type',
+    ROIInterpreter: 'Todo: interpreter',
+  };
+}
@@ -0,0 +1,15 @@
+import RTSSReport from './RTSSReport';
+import dcmjs from 'dcmjs';
+import { classes } from '@ohif/core';
+
+const { datasetToBlob } = dcmjs.data;
+const metadataProvider = classes.MetadataProvider;
+
+export default function dicomRTAnnotationExport(annotations) {
+  const dataset = RTSSReport.generateReport(annotations, metadataProvider);
+  const reportBlob = datasetToBlob(dataset);
+
+  //Create a URL for the binary.
+  var objectUrl = URL.createObjectURL(reportBlob);
+  window.location.assign(objectUrl);
+}
@@ -0,0 +1,3 @@
+import dicomRTAnnotationExport from './dicomRTAnnotationExport';
+
+export default dicomRTAnnotationExport;
@@ -0,0 +1,58 @@
+import RectangleROIStartEndThreshold from './RectangleROIStartEndThreshold';
+
+function validateAnnotation(annotation) {
+  if (!annotation?.data) {
+    throw new Error('Tool data is empty');
+  }
+
+  if (!annotation.metadata || annotation.metadata.referenceImageId) {
+    throw new Error('Tool data is not associated with any imageId');
+  }
+}
+
+class AnnotationToPointData {
+  constructor() {}
+
+  static convert(annotation, index, metadataProvider) {
+    validateAnnotation(annotation);
+
+    const { toolName } = annotation.metadata;
+    const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
+
+    if (!toolClass) {
+      throw new Error(
+        `Unknown tool type: ${toolName}, cannot convert to RTSSReport`
+      );
+    }
+
+    // Each toolData should become a list of contours, ContourSequence
+    // contains a list of contours with their pointData, their geometry
+    // type and their length.
+    const ContourSequence = toolClass.getContourSequence(
+      annotation,
+      metadataProvider
+    );
+
+    // Todo: random rgb color for now, options should be passed in
+    const color = [
+      Math.floor(Math.random() * 255),
+      Math.floor(Math.random() * 255),
+      Math.floor(Math.random() * 255),
+    ];
+
+    return {
+      ReferencedROINumber: index + 1,
+      ROIDisplayColor: color,
+      ContourSequence,
+    };
+  }
+
+  static register(toolClass) {
+    AnnotationToPointData.TOOL_NAMES[toolClass.toolName] = toolClass;
+  }
+}
+
+AnnotationToPointData.TOOL_NAMES = {};
+AnnotationToPointData.register(RectangleROIStartEndThreshold);
+
+export default AnnotationToPointData;
@@ -0,0 +1,56 @@
+// comment
+class RectangleROIStartEndThreshold {
+  constructor() {}
+
+  static getContourSequence(toolData, metadataProvider) {
+    const { data } = toolData;
+    const { projectionPoints, projectionPointsImageIds } = data.cachedStats;
+
+    return projectionPoints.map((point, index) => {
+      const ContourData = getPointData(point);
+      const ContourImageSequence = getContourImageSequence(
+        projectionPointsImageIds[index],
+        metadataProvider
+      );
+
+      return {
+        NumberOfContourPoints: ContourData.length / 3,
+        ContourImageSequence,
+        ContourGeometricType: 'CLOSED_PLANAR',
+        ContourData,
+      };
+    });
+  }
+}
+
+RectangleROIStartEndThreshold.toolName = 'RectangleROIStartEndThreshold';
+
+function getPointData(points) {
+  // Since this is a closed contour, the order of the points is important.
+  // re-order the points to be in the correct order clockwise
+  // Spread to make sure Float32Arrays are converted to arrays
+  const orderedPoints = [
+    ...points[0],
+    ...points[1],
+    ...points[3],
+    ...points[2],
+  ];
+  const pointsArray = orderedPoints.flat();
+
+  // reduce the precision of the points to 2 decimal places
+  const pointsArrayWithPrecision = pointsArray.map(point => {
+    return point.toFixed(2);
+  });
+
+  return pointsArrayWithPrecision;
+}
+
+function getContourImageSequence(imageId, metadataProvider) {
+  const sopCommon = metadataProvider.get('sopCommonModule', imageId);
+
+  return {
+    ReferencedSOPClassUID: sopCommon.sopClassUID,
+    ReferencedSOPInstanceUID: sopCommon.sopInstanceUID,
+  };
+}
+export default RectangleROIStartEndThreshold;