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
@@ -11,10 +11,8 @@ import { DicomMetadataStore, utils } from '@ohif/core';
 import { useDebounce } from '@hooks';
 import ActionButtons from './ActionButtons';
 import { useTrackedMeasurements } from '../../getContextModule';
-import createReportDialogPrompt from '../../_shared/createReportDialogPrompt';
-import RESPONSES from '../../_shared/PROMPT_RESPONSES';
-import downloadCSVReport from '../../_shared/downloadCSVReport';

+const { downloadCSVReport } = utils;
 const { formatDate } = utils;

 const DISPLAY_STUDY_SUMMARY_INITIAL_VALUE = {
@@ -146,29 +144,24 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
        trackedSeries.includes(m.referenceSeriesUID)
    );

-    downloadCSVReport(
-      trackedMeasurements,
-      trackedStudy,
-      trackedSeries,
-      MeasurementService
-    );
+    downloadCSVReport(trackedMeasurements, MeasurementService);
  }

-  const jumpToImage = ({ id, isActive }) => {
-    MeasurementService.jumpToMeasurement(viewportGrid.activeViewportIndex, id);
+  const jumpToImage = ({ uid, isActive }) => {
+    MeasurementService.jumpToMeasurement(viewportGrid.activeViewportIndex, uid);

-    onMeasurementItemClickHandler({ id, isActive });
+    onMeasurementItemClickHandler({ uid, isActive });
  };

-  const onMeasurementItemEditHandler = ({ id, isActive }) => {
-    const measurement = MeasurementService.getMeasurement(id);
-    jumpToImage({ id, isActive });
+  const onMeasurementItemEditHandler = ({ uid, isActive }) => {
+    const measurement = MeasurementService.getMeasurement(uid);
+    jumpToImage({ uid, isActive });

    const onSubmitHandler = ({ action, value }) => {
      switch (action.id) {
        case 'save': {
          MeasurementService.update(
-            id,
+            uid,
            {
              ...measurement,
              ...value,
@@ -225,12 +218,12 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
    });
  };

-  const onMeasurementItemClickHandler = ({ id, isActive }) => {
+  const onMeasurementItemClickHandler = ({ uid, isActive }) => {
    if (!isActive) {
      const measurements = [...displayMeasurements];
-      const measurement = measurements.find(m => m.id === id);
+      const measurement = measurements.find(m => m.uid === uid);

-      measurements.forEach(m => (m.isActive = m.id !== id ? false : true));
+      measurements.forEach(m => (m.isActive = m.uid !== uid ? false : true));
      measurement.isActive = true;
      setDisplayMeasurements(measurements);
    }
@@ -245,8 +238,10 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {

  return (
    <>
-      <div className="overflow-x-hidden overflow-y-auto invisible-scrollbar"
-           data-cy={"trackedMeasurements-panel"}>
+      <div
+        className="overflow-x-hidden overflow-y-auto invisible-scrollbar"
+        data-cy={'trackedMeasurements-panel'}
+      >
        {displayStudySummary.key && (
          <StudySummary
            date={formatDate(displayStudySummary.date)}
@@ -320,17 +315,9 @@ function _mapMeasurementToDisplay(measurement, types, DisplaySetService) {
    );
  }

-  const { PixelSpacing, SeriesNumber, InstanceNumber } = instance;
-  const displayText = _getDisplayText(
-    measurement,
-    PixelSpacing,
-    SeriesNumber,
-    InstanceNumber,
-    types
-  );
-
+  const { displayText } = measurement;
  return {
-    id: measurement.id,
+    uid: measurement.uid,
    label: measurement.label || '(empty)',
    measurementType: measurement.type,
    displayText: displayText || [],
@@ -338,67 +325,4 @@ function _mapMeasurementToDisplay(measurement, types, DisplaySetService) {
  };
 }

-/**
- *
- * @param {*} measurement
- * @param {*} pixelSpacing
- * @param {*} seriesNumber
- * @param {*} instanceNumber
- * @param {*} types
- */
-function _getDisplayText(
-  measurement,
-  pixelSpacing,
-  seriesNumber,
-  instanceNumber,
-  types
-) {
-  const { type, points } = measurement;
-  const hasPixelSpacing =
-    pixelSpacing !== undefined &&
-    Array.isArray(pixelSpacing) &&
-    pixelSpacing.length === 2;
-  const [rowPixelSpacing, colPixelSpacing] = hasPixelSpacing
-    ? pixelSpacing
-    : [1, 1];
-  const unit = hasPixelSpacing ? 'mm' : 'px';
-
-  switch (type) {
-    case types.POLYLINE: {
-      const { length } = measurement;
-      const roundedLength = _round(length, 2);
-
-      return [
-        `${roundedLength} ${unit} (S:${seriesNumber}, I:${instanceNumber})`,
-      ];
-    }
-    case types.BIDIRECTIONAL: {
-      const { shortestDiameter, longestDiameter } = measurement;
-      const roundedShortestDiameter = _round(shortestDiameter, 1);
-      const roundedLongestDiameter = _round(longestDiameter, 1);
-
-      return [
-        `L: ${roundedLongestDiameter} ${unit} (S:${seriesNumber}, I:${instanceNumber})`,
-        `W: ${roundedShortestDiameter} ${unit}`,
-      ];
-    }
-    case types.ELLIPSE: {
-      const { area } = measurement;
-      const roundedArea = _round(area, 2);
-
-      return [
-        `${roundedArea} ${unit}<sup>2</sup> (S:${seriesNumber}, I:${instanceNumber})`,
-      ];
-    }
-    case types.POINT: {
-      const { text } = measurement; // Will display in "short description"
-      return [`(S:${seriesNumber}, I:${instanceNumber})`];
-    }
-  }
-}
-
-function _round(value, decimals) {
-  return parseFloat(value).toFixed(decimals);
-}
-
 export default PanelMeasurementTableTracking;
@@ -47,14 +47,14 @@ function PanelStudyBrowserTracking({
  const [jumpToDisplaySet, setJumpToDisplaySet] = useState(null);

  const onDoubleClickThumbnailHandler = displaySetInstanceUID => {
-    viewportGridService.setDisplaysetForViewport({
+    viewportGridService.setDisplaySetsForViewport({
      viewportIndex: activeViewportIndex,
-      displaySetInstanceUID,
+      displaySetInstanceUIDs: [displaySetInstanceUID],
    });
  };

-  const activeDisplaySetInstanceUID =
-    viewports[activeViewportIndex]?.displaySetInstanceUID;
+  const activeViewportDisplaySetInstanceUIDs =
+    viewports[activeViewportIndex]?.displaySetInstanceUIDs;

  const isSingleViewport = numCols === 1 && numRows === 1;

@@ -260,8 +260,12 @@ function PanelStudyBrowserTracking({
    setExpandedStudyInstanceUIDs(updatedExpandedStudyInstanceUIDs);

    if (!shouldCollapseStudy) {
-      const madeInClient = true
-      requestDisplaySetCreationForStudy(DisplaySetService, StudyInstanceUID, madeInClient);
+      const madeInClient = true;
+      requestDisplaySetCreationForStudy(
+        DisplaySetService,
+        StudyInstanceUID,
+        madeInClient
+      );
    }
  }

@@ -331,7 +335,7 @@ function PanelStudyBrowserTracking({
      }}
      onClickThumbnail={() => {}}
      onDoubleClickThumbnail={onDoubleClickThumbnailHandler}
-      activeDisplaySetInstanceUID={activeDisplaySetInstanceUID}
+      activeDisplaySetInstanceUIDs={activeViewportDisplaySetInstanceUIDs}
    />
  );
 }
@@ -398,8 +402,12 @@ function _mapDisplaySets(
    const viewportIdentificator = isSingleViewport
      ? []
      : viewports.reduce((acc, viewportData, index) => {
-          if (viewportData.displaySetInstanceUID === ds.displaySetInstanceUID) {
-            acc.push(_viewportLabels[index]);
+          if (
+            viewportData?.displaySetInstanceUIDs?.includes(
+              ds.displaySetInstanceUID
+            )
+          ) {
+            acc.push(viewportData.viewportLabel);
          }
          return acc;
        }, []);
@@ -4,12 +4,10 @@
 */
 function getImageSrcFromImageId(cornerstone, imageId) {
  return new Promise((resolve, reject) => {
-    cornerstone
-      .loadAndCacheImage(imageId)
-      .then(image => {
-        const canvas = document.createElement('canvas');
-        cornerstone.renderToCanvas(canvas, image);
-
+    const canvas = document.createElement('canvas');
+    cornerstone.utilities
+      .loadImageToCanvas(canvas, imageId)
+      .then(imageId => {
        resolve(canvas.toDataURL());
      })
      .catch(reject);
@@ -1,29 +0,0 @@
-async function getStudiesForPatientByStudyInstanceUID(
-  dataSource,
-  StudyInstanceUID
-) {
-  if (StudyInstanceUID === undefined) {
-    return;
-  }
-  // TODO: The `DicomMetadataStore` should short-circuit both of these requests
-  // Data _could_ be here from route query, or if using JSON data source
-  // We could also force this to "await" these values being available in the DICOMStore?
-  // Kind of like promise fulfillment in cornerstone-wado-image-loader when there are multiple
-  // outgoing requests for the same data
-  const getStudyResult = await dataSource.query.studies.search({
-    studyInstanceUid: StudyInstanceUID,
-  });
-
-  // TODO: To Erik's point, the data source likely shouldn't deviate from
-  // Naturalized DICOM JSON when returning. It makes things like this awkward (mrn)
-  if (getStudyResult && getStudyResult.length && getStudyResult[0].mrn) {
-    return dataSource.query.studies.search({
-      patientId: getStudyResult[0].mrn,
-    });
-  }
-  console.log('No mrn found for', getStudyResult);
-  // The original study we KNOW belongs to the same set, so just return it
-  return getStudyResult;
-}
-
-export default getStudiesForPatientByStudyInstanceUID;
@@ -3,9 +3,17 @@ import PropTypes from 'prop-types';
 //
 import PanelStudyBrowserTracking from './PanelStudyBrowserTracking';
 import getImageSrcFromImageId from './getImageSrcFromImageId';
-import getStudiesForPatientByStudyInstanceUID from './getStudiesForPatientByStudyInstanceUID';
 import requestDisplaySetCreationForStudy from './requestDisplaySetCreationForStudy';

+function _getStudyForPatientUtility(extensionManager) {
+  const utilityModule = extensionManager.getModuleEntry(
+    '@ohif/extension-default.utilityModule.common'
+  );
+
+  const { getStudiesForPatientByStudyInstanceUID } = utilityModule.exports;
+  return getStudiesForPatientByStudyInstanceUID;
+}
+
 /**
 * Wraps the PanelStudyBrowser and provides features afforded by managers/services
 *
@@ -19,12 +27,16 @@ function WrappedPanelStudyBrowserTracking({
  servicesManager,
 }) {
  const dataSource = extensionManager.getActiveDataSource()[0];
+
+  const getStudiesForPatientByStudyInstanceUID = _getStudyForPatientUtility(
+    extensionManager
+  );
  const _getStudiesForPatientByStudyInstanceUID = getStudiesForPatientByStudyInstanceUID.bind(
    null,
    dataSource
  );
  const _getImageSrcFromImageId = _createGetImageSrcFromImageIdFn(
-    commandsManager.getCommand.bind(commandsManager)
+    extensionManager
  );
  const _requestDisplaySetCreationForStudy = requestDisplaySetCreationForStudy.bind(
    null,
@@ -56,14 +68,13 @@ function WrappedPanelStudyBrowserTracking({
 * @returns {func} getImageSrcFromImageId - A utility function powered by
 * cornerstone
 */
-function _createGetImageSrcFromImageIdFn(getCommand) {
-  try {
-    const command = getCommand('getCornerstoneLibraries', 'VIEWER');
-    if (!command) {
-      return;
-    }
-    const { cornerstone } = command.commandFn();
+function _createGetImageSrcFromImageIdFn(extensionManager) {
+  const utilities = extensionManager.getModuleEntry(
+    '@ohif/extension-cornerstone.utilityModule.common'
+  );

+  try {
+    const { cornerstone } = utilities.exports.getCornerstoneLibraries();
    return getImageSrcFromImageId.bind(null, cornerstone);
  } catch (ex) {
    throw new Error('Required command not found');