OHIF-326, export as CSV. (#1976)

extensions/cornerstone/package.json

@@ -33,7 +33,7 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.3.0",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.19.1",
+    "cornerstone-tools": "4.20.1",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dcmjs": "0.16.1",
     "dicom-parser": "^1.8.3",

extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalRoi.js

@@ -33,7 +33,9 @@ const EllipticalRoi = {
       SeriesInstanceUID
     );
 
-    const { start, end } = measurementData.handles;
+    const { cachedStats, handles } = measurementData;
+
+    const { start, end } = handles;
 
     const halfXLength = Math.abs(start.x - end.x) / 2;
     const halfYLength = Math.abs(start.y - end.y) / 2;
@@ -60,6 +62,20 @@ const EllipticalRoi = {
       points.push({ x: center.x + halfXLength, y: center.y });
     }
 
+    let meanSUV;
+    let stdDevSUV;
+
+    if (
+      cachedStats &&
+      cachedStats.meanStdDevSUV &&
+      cachedStats.meanStdDevSUV.mean !== 0
+    ) {
+      const { meanStdDevSUV } = cachedStats;
+
+      meanSUV = meanStdDevSUV.mean;
+      stdDevSUV = meanStdDevSUV.stdDev;
+    }
+
     return {
       id: measurementData.id,
       SOPInstanceUID,
@@ -70,10 +86,11 @@ const EllipticalRoi = {
       label: measurementData.label,
       description: measurementData.description,
       unit: measurementData.unit,
-      area:
+      area: cachedStats && cachedStats.area,
-        measurementData.cachedStats &&
+      mean: cachedStats && cachedStats.mean,
-        measurementData.cachedStats
+      stdDev: cachedStats && cachedStats.stdDev,
-          .area /* TODO: Add concept names instead (descriptor) */,
+      meanSUV,
+      stdDevSUV,
       type: getValueTypeFromToolType(tool),
       points,
     };

extensions/dicom-rt/package.json

@@ -30,7 +30,7 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.19.1",
+    "cornerstone-tools": "4.20.1",
     "dcmjs": "0.16.1",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

extensions/dicom-segmentation/package.json

@@ -30,7 +30,7 @@
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
     "cornerstone-core": "^2.2.8",
-    "cornerstone-tools": "4.19.0",
+    "cornerstone-tools": "4.20.1",
     "dcmjs": "0.16.1",
     "prop-types": "^15.6.2",
     "react": "^16.8.6",

extensions/dicom-sr/package.json

@@ -33,7 +33,7 @@
     "@ohif/ui": "^0.50.0",
     "cornerstone-core": "^2.3.0",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.19.1",
+    "cornerstone-tools": "4.20.1",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dcmjs": "0.16.1",
     "dicom-parser": "^1.8.3",

extensions/measurement-tracking/package.json

@@ -28,7 +28,7 @@
   },
   "peerDependencies": {
     "@ohif/core": "^0.50.0",
-    "cornerstone-tools": "4.19.0",
+    "cornerstone-tools": "4.20.1",
     "dcmjs": "0.16.1",
     "prop-types": "^15.6.2",
     "react": "^16.13.1",

extensions/measurement-tracking/src/_shared/downloadCSVReport.js

@@ -0,0 +1,164 @@
+import { DicomMetadataStore } from '@ohif/core';
+
+export default function downloadCSVReport(
+  measurementData,
+  StudyInstanceUID,
+  referencedSeriesInstanceUIDs,
+  MeasurementService
+) {
+  const { VALUE_TYPES } = MeasurementService;
+
+  if (measurementData.length === 0) {
+    // Prevent download of report with no measurements.
+    return;
+  }
+
+  const seriesMetadataMap = {};
+
+  referencedSeriesInstanceUIDs.forEach(SeriesInstanceUID => {
+    seriesMetadataMap[SeriesInstanceUID] = DicomMetadataStore.getSeries(
+      StudyInstanceUID,
+      SeriesInstanceUID
+    );
+  });
+
+  const rows = [
+    [
+      'Patient ID',
+      'Patient Name',
+      'Study UID',
+      'Series UID',
+      'SOP Instance UID',
+      'Label',
+      'Long Axis (mm)',
+      'Short Axis (mm)',
+      'Length (mm)',
+      'Area (mmˆ2)',
+      'Mean',
+      'StDev',
+      'Units',
+    ],
+  ];
+
+  measurementData.forEach(measurement => {
+    switch (measurement.type) {
+      case VALUE_TYPES.BIDIRECTIONAL:
+        rows.push(_getBidirectionalRow(measurement, seriesMetadataMap));
+        break;
+      case VALUE_TYPES.ELLIPSE:
+        rows.push(_getEllipseRow(measurement, seriesMetadataMap));
+        break;
+      case VALUE_TYPES.POINT:
+        rows.push(_getAdditionalFindingRow(measurement, seriesMetadataMap));
+        break;
+      case VALUE_TYPES.POLYLINE:
+        rows.push(_getLengthRow(measurement, seriesMetadataMap));
+    }
+  });
+
+  let csvContent =
+    'data:text/csv;charset=utf-8,' + rows.map(row => row.join(',')).join('\n');
+
+  _createAndDownloadFile(csvContent);
+}
+
+function _getBidirectionalRow(measurement, seriesMetadataMap) {
+  const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
+
+  return [
+    ...commonRowItems,
+    measurement.longestDiameter, // Long Axis (mm)
+    measurement.shortestDiameter, // Short Axis (mm)
+  ];
+}
+
+function _getCommonRowItems(measurement, seriesMetadataMap) {
+  const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
+  const firstInstance = seriesMetadata.instances[0];
+
+  const row = [
+    firstInstance.PatientID, // Patient ID
+    firstInstance.PatientName.Alphabetic, // PatientName
+    measurement.referenceStudyUID, // StudyInstanceUID
+    measurement.referenceSeriesUID, // SeriesInstanceUID
+    measurement.SOPInstanceUID, // SOPInstanceUID
+    measurement.label || '', // Label
+  ];
+
+  return row;
+}
+
+function _getAdditionalFindingRow(measurement, seriesMetadataMap) {
+  const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
+
+  return [...commonRowItems];
+}
+
+function _getEllipseRow(measurement, seriesMetadataMap) {
+  const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
+  const blankColumns = ['', '', ''];
+
+  const { area, mean, stdDev, unit } = _getEllipseStatsWithUnits(
+    measurement,
+    seriesMetadataMap
+  );
+
+  return [
+    ...commonRowItems,
+    ...blankColumns,
+    area, // Area (mmˆ2)
+    mean, // Mean
+    stdDev, // StDev
+    unit,
+  ];
+}
+
+function _getEllipseStatsWithUnits(measurement, seriesMetadataMap) {
+  const seriesMetadata = seriesMetadataMap[measurement.referenceSeriesUID];
+  const firstInstance = seriesMetadata.instances[0];
+  const modality = firstInstance.Modality;
+
+  switch (modality) {
+    case 'CT':
+      return {
+        mean: `${measurement.mean.toFixed(1)}`,
+        stdDev: `${measurement.stdDev.toFixed(1)}`,
+        area: measurement.area.toFixed(1),
+        unit: 'HU',
+      };
+    case 'PT':
+      if (measurement.meanSUV) {
+        return {
+          mean: `${measurement.meanSUV.toFixed(1)}`,
+          stdDev: `${measurement.stdDevSUV.toFixed(1)}`,
+          area: measurement.area.toFixed(1),
+          unit: 'SUV',
+        };
+      }
+    // If no SUV calculation then fallback to default.
+    default:
+      return {
+        mean: `${measurement.mean.toFixed(1)}`,
+        stdDev: `${measurement.stdDev.toFixed(1)}`,
+        area: measurement.area.toFixed(1),
+        unit: 'Pixel Values',
+      };
+  }
+}
+
+function _getLengthRow(measurement, seriesMetadataMap) {
+  const commonRowItems = _getCommonRowItems(measurement, seriesMetadataMap);
+  const blankColumns = ['', ''];
+
+  return [...commonRowItems, ...blankColumns, measurement.length.toFixed(1)];
+}
+
+function _createAndDownloadFile(csvContent) {
+  const encodedUri = encodeURI(csvContent);
+
+  const link = document.createElement('a');
+  link.setAttribute('href', encodedUri);
+  link.setAttribute('download', 'MeasurementReport.csv');
+  document.body.appendChild(link);
+  link.click();
+}

extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/ActionButtons.jsx

@@ -6,15 +6,9 @@ function ActionButtons({ onExportClick, onCreateReportClick }) {
   return (
     <React.Fragment>
       <ButtonGroup color="black" size="inherit">
-        <Button className="text-base px-2 py-2" onClick={onExportClick}>Export</Button>
+        <Button className="text-base px-2 py-2" onClick={onExportClick}>
-        <IconButton
+          Export
-          className="px-2"
+        </Button>
-          color="black"
-          size="initial"
-          variant="outlined"
-        >
-          <Icon name="arrow-down" />
-        </IconButton>
       </ButtonGroup>
       <Button
         className="ml-2 text-base"

extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/index.js

@@ -7,12 +7,13 @@ import {
   Input,
   useViewportGrid,
 } from '@ohif/ui';
-import { DicomMetadataStore, DICOMSR, utils } from '@ohif/core';
+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 { formatDate } = utils;
 
@@ -144,21 +145,12 @@ function PanelMeasurementTableTracking({ servicesManager, extensionManager }) {
         trackedSeries.includes(m.referenceSeriesUID)
     );
 
-    const promptResult = await createReportDialogPrompt(UIDialogService);
+    downloadCSVReport(
-
+      trackedMeasurements,
-    if (promptResult.action === RESPONSES.CREATE_REPORT) {
+      trackedStudy,
-      const additionalFindings = ['ArrowAnnotate'];
+      trackedSeries,
-
+      MeasurementService
-      const SeriesDescription =
+    );
-        // isUndefinedOrEmpty
-        promptResult.value === undefined || promptResult.value === ''
-          ? 'Research Derived Series' // default
-          : promptResult.value; // provided value
-
-      DICOMSR.downloadReport(trackedMeasurements, additionalFindings, {
-        SeriesDescription,
-      });
-    }
   }
 
   const jumpToImage = ({ id, isActive }) => {

extensions/vtk/package.json

@@ -57,7 +57,7 @@
     "@ohif/core": "^2.9.6",
     "@ohif/ui": "^2.0.0",
     "cornerstone-core": "^2.3.0",
-    "cornerstone-tools": "4.19.0",
+    "cornerstone-tools": "4.20.1",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dicom-parser": "^1.8.3",
     "gh-pages": "^2.0.1",

platform/core/package.json

@@ -31,7 +31,7 @@
   },
   "peerDependencies": {
     "cornerstone-core": "^2.3.0",
-    "cornerstone-tools": "4.19.1",
+    "cornerstone-tools": "4.20.1",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dicom-parser": "^1.8.3"
   },

platform/core/src/services/MeasurementService/MeasurementService.js

@@ -40,6 +40,8 @@ const MEASUREMENT_SCHEMA_KEYS = [
   'type',
   'unit',
   'area', // TODO: Add concept names instead (descriptor)
+  'mean',
+  'stdDev',
   'length',
   'shortestDiameter',
   'longestDiameter',

platform/viewer/package.json

@@ -68,7 +68,7 @@
     "classnames": "^2.2.6",
     "core-js": "^3.2.1",
     "cornerstone-math": "^0.1.8",
-    "cornerstone-tools": "4.19.1",
+    "cornerstone-tools": "4.20.1",
     "cornerstone-wado-image-loader": "^3.1.2",
     "dcmjs": "0.16.1",
     "dicom-parser": "^1.8.3",

yarn.lock

@@ -7921,18 +7921,10 @@ cornerstone-math@^0.1.8:
   resolved "https://registry.yarnpkg.com/cornerstone-math/-/cornerstone-math-0.1.8.tgz#68ab1f9e4fdcd7c5cb23a0d2eb4263f9f894f1c5"
   integrity sha512-x7NEQHBtVG7j1yeyj/aRoKTpXv1Vh2/H9zNLMyqYJDtJkNng8C4Q8M3CgZ1qer0Yr7eVq2x+Ynmj6kfOm5jXKw==
 
-cornerstone-tools@4.19.0:
+cornerstone-tools@4.20.1:
-  version "4.19.0"
+  version "4.20.1"
-  resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.19.0.tgz#4c1cb0729fdf5ba5f3c2b83172395738dc8a972b"
+  resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.20.1.tgz#90f6c28356622eac037683b19f9175f85d33dff7"
-  integrity sha512-Q8fgx4eN9F0TG84UXprMWjU4YpF/Vhs7ux67b0nV/E5SbyCip7yple4SfDbABB8oxVqzOdKpBnICMNTZNAyyKg==
+  integrity sha512-SyQsrg3bnGHUvWGZpUq7ia7/gj12S9zQFK2VMhpyAYxK9pWz+PRv8HBi0eEe/fWGAo/Vc62IRkdP3uF9MJlqiQ==
-  dependencies:
-    "@babel/runtime" "7.1.2"
-    cornerstone-math "0.1.7"
-
-cornerstone-tools@4.19.1:
-  version "4.19.1"
-  resolved "https://registry.yarnpkg.com/cornerstone-tools/-/cornerstone-tools-4.19.1.tgz#8a3e9473495b83e9f88dcbad99ac79eae65a81d4"
-  integrity sha512-ltobIAUEgnPswhWLSAm05HRP7pw99m07RNBYuoN4NInDD2ctvk3HxAjM1CAV2GO1zv8yMwKOaE/j2m70Na12mQ==
   dependencies:
     "@babel/runtime" "7.1.2"
     cornerstone-math "0.1.7"