chore(prettier): full repo linting and code reformatting once and for all (#3627)

extensions/tmtv/src/utils/calculateSUVPeak.ts

@@ -41,21 +41,12 @@ function calculateSuvPeak(
   }
 
   if (labelmap.scalarData.length !== referenceVolume.scalarData.length) {
-    throw new Error(
-      'labelmap and referenceVolume must have the same number of pixels'
-    );
+    throw new Error('labelmap and referenceVolume must have the same number of pixels');
   }
 
-  const {
-    scalarData: labelmapData,
-    dimensions,
-    imageData: labelmapImageData,
-  } = labelmap;
+  const { scalarData: labelmapData, dimensions, imageData: labelmapImageData } = labelmap;
 
-  const {
-    scalarData: referenceVolumeData,
-    imageData: referenceVolumeImageData,
-  } = referenceVolume;
+  const { scalarData: referenceVolumeData, imageData: referenceVolumeImageData } = referenceVolume;
 
   let boundsIJK;
   // Todo: using the first annotation for now
@@ -69,10 +60,7 @@ function calculateSuvPeak(
       return ijk as Types.Point3;
     });
 
-    boundsIJK = utilities.boundingBox.getBoundingBoxAroundShape(
-      rectangleCornersIJK,
-      dimensions
-    );
+    boundsIJK = utilities.boundingBox.getBoundingBoxAroundShape(rectangleCornersIJK, dimensions);
   }
 
   let max = 0;
@@ -96,16 +84,9 @@ function calculateSuvPeak(
     }
   };
 
-  utilities.pointInShapeCallback(
-    labelmapImageData,
-    () => true,
-    callback,
-    boundsIJK
-  );
+  utilities.pointInShapeCallback(labelmapImageData, () => true, callback, boundsIJK);
 
-  const direction = labelmapImageData
-    .getDirection()
-    .slice(0, 3) as Types.Point3;
+  const direction = labelmapImageData.getDirection().slice(0, 3) as Types.Point3;
 
   /**
    * 2. Find the bottom and top of the great circle for the second sphere (1cc sphere)
@@ -120,10 +101,7 @@ function calculateSuvPeak(
   referenceVolumeImageData.indexToWorld(maxIJK as vec3, secondaryCircleWorld);
   vec3.scaleAndAdd(bottomWorld, secondaryCircleWorld, direction, -diameter / 2);
   vec3.scaleAndAdd(topWorld, secondaryCircleWorld, direction, diameter / 2);
-  const suvPeakCirclePoints = [bottomWorld, topWorld] as [
-    Types.Point3,
-    Types.Point3
-  ];
+  const suvPeakCirclePoints = [bottomWorld, topWorld] as [Types.Point3, Types.Point3];
 
   /**
    * 3. Find the Mean and Max of the 1cc sphere centered on the suv Max of the previous

extensions/tmtv/src/utils/calculateTMTV.ts

@@ -11,10 +11,7 @@ import { utilities } from '@cornerstonejs/tools';
  * @param {number} segmentIndex
  * @returns {number} TMTV in ml
  */
-function calculateTMTV(
-  labelmaps: Array<Types.IImageVolume>,
-  segmentIndex = 1
-): number {
+function calculateTMTV(labelmaps: Array<Types.IImageVolume>, segmentIndex = 1): number {
   const volumeId = 'mergedLabelmap';
 
   const mergedLabelmap = utilities.segmentation.createMergedLabelmapForIndex(
@@ -24,10 +21,7 @@ function calculateTMTV(
   );
 
   const { imageData, spacing } = mergedLabelmap;
-  const values = imageData
-    .getPointData()
-    .getScalars()
-    .getData();
+  const values = imageData.getPointData().getScalars().getData();
 
   // count non-zero values inside the outputData, this would
   // consider the overlapping regions to be only counted once

extensions/tmtv/src/utils/createAndDownloadTMTVReport.js

@@ -1,7 +1,4 @@
-export default function createAndDownloadTMTVReport(
-  segReport,
-  additionalReportRows
-) {
+export default function createAndDownloadTMTVReport(segReport, additionalReportRows) {
   const firstReport = segReport[Object.keys(segReport)[0]];
   const columns = Object.keys(firstReport);
   const csv = [columns.join(',')];
@@ -11,9 +8,7 @@ export default function createAndDownloadTMTVReport(
     columns.forEach(column => {
       // if it is array then we need to replace , with space to avoid csv parsing error
       row.push(
-        Array.isArray(segmentation[column])
-          ? segmentation[column].join(' ')
-          : segmentation[column]
+        Array.isArray(segmentation[column]) ? segmentation[column].join(' ') : segmentation[column]
       );
     });
     csv.push(row.join(','));

extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/RTSSReport.js

@@ -98,15 +98,9 @@ function initializeDataset(annotations, metadataProvider) {
   const rtSOPInstanceUID = DicomMetaDictionary.uid();
 
   // get the first annotation data
-  const {
-    referencedImageId: imageId,
-    FrameOfReferenceUID,
-  } = annotations[0].metadata;
+  const { referencedImageId: imageId, FrameOfReferenceUID } = annotations[0].metadata;
 
-  const { studyInstanceUID } = metadataProvider.get(
-    'generalSeriesModule',
-    imageId
-  );
+  const { studyInstanceUID } = metadataProvider.get('generalSeriesModule', imageId);
 
   const patientModule = getPatientModule(imageId, metadataProvider);
   const rtSeriesModule = getRTSeriesModule(imageId, metadataProvider);
@@ -136,23 +130,11 @@ function initializeDataset(annotations, metadataProvider) {
 }
 
 function getPatientModule(imageId, metadataProvider) {
-  const generalSeriesModule = metadataProvider.get(
-    'generalSeriesModule',
-    imageId
-  );
-  const generalStudyModule = metadataProvider.get(
-    'generalStudyModule',
-    imageId
-  );
-  const patientStudyModule = metadataProvider.get(
-    'patientStudyModule',
-    imageId
-  );
+  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
-  );
+  const patientDemographicModule = metadataProvider.get('patientDemographicModule', imageId);
 
   return {
     Modality: generalSeriesModule.modality,
@@ -169,11 +151,7 @@ function getPatientModule(imageId, metadataProvider) {
   };
 }
 
-function getReferencedFrameOfReferenceSequence(
-  toolData,
-  metadataProvider,
-  dataset
-) {
+function getReferencedFrameOfReferenceSequence(toolData, metadataProvider, dataset) {
   const { referencedImageId: imageId, FrameOfReferenceUID } = toolData.metadata;
   const instance = metadataProvider.get('instance', imageId);
   const { SeriesInstanceUID } = instance;
@@ -190,9 +168,7 @@ function getReferencedFrameOfReferenceSequence(
           RTReferencedSeriesSequence: [
             {
               SeriesInstanceUID,
-              ContourImageSequence: [
-                ...ReferencedSeriesSequence[0].ReferencedInstanceSequence,
-              ],
+              ContourImageSequence: [...ReferencedSeriesSequence[0].ReferencedInstanceSequence],
             },
           ],
         },
@@ -209,10 +185,7 @@ function getReferencedSeriesSequence(toolData, index, metadataProvider) {
 
   const ReferencedSeriesSequence = [];
   if (SeriesInstanceUID) {
-    const series = DicomMetadataStore.getSeries(
-      StudyInstanceUID,
-      SeriesInstanceUID
-    );
+    const series = DicomMetadataStore.getSeries(StudyInstanceUID, SeriesInstanceUID);
 
     const ReferencedSeries = {
       SeriesInstanceUID,

extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/AnnotationToPointData.js

@@ -20,18 +20,13 @@ class AnnotationToPointData {
     const toolClass = AnnotationToPointData.TOOL_NAMES[toolName];
 
     if (!toolClass) {
-      throw new Error(
-        `Unknown tool type: ${toolName}, cannot convert to RTSSReport`
-      );
+      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
-    );
+    const ContourSequence = toolClass.getContourSequence(annotation, metadataProvider);
 
     // Todo: random rgb color for now, options should be passed in
     const color = [

extensions/tmtv/src/utils/dicomRTAnnotationExport/RTStructureSet/measurements/RectangleROIStartEndThreshold.js

@@ -29,12 +29,7 @@ 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 orderedPoints = [...points[0], ...points[1], ...points[3], ...points[2]];
   const pointsArray = orderedPoints.flat();
 
   // reduce the precision of the points to 2 decimal places

extensions/tmtv/src/utils/getThresholdValue.ts

@@ -3,10 +3,7 @@ import * as csTools from '@cornerstonejs/tools';
 function getRoiStats(referencedVolume, annotations) {
   // roiStats
   const { imageData } = referencedVolume;
-  const values = imageData
-    .getPointData()
-    .getScalars()
-    .getData();
+  const values = imageData.getPointData().getScalars().getData();
 
   // Todo: add support for other strategies
   const { fn, baseValue } = _getStrategyFn('max');
@@ -59,9 +56,10 @@ function getThresholdValues(
   };
 }
 
-function _getStrategyFn(
-  statistic
-): { fn: (a: number, b: number) => number; baseValue: number } {
+function _getStrategyFn(statistic): {
+  fn: (a: number, b: number) => number;
+  baseValue: number;
+} {
   const baseValue = -Infinity;
   const fn = (number, maxValue) => {
     if (number > maxValue) {

extensions/tmtv/src/utils/measurementServiceMappings/RectangleROIStartEndThreshold.js

@@ -10,11 +10,7 @@ const RectangleROIStartEndThreshold = {
    * @param {Object} cornerstone Cornerstone event data
    * @return {Measurement} Measurement instance
    */
-  toMeasurement: (
-    csToolsEventDetail,
-    displaySetService,
-    cornerstoneViewportService
-  ) => {
+  toMeasurement: (csToolsEventDetail, displaySetService, cornerstoneViewportService) => {
     const { annotation, viewportId } = csToolsEventDetail;
     const { metadata, data, annotationUID } = annotation;
 
@@ -30,11 +26,7 @@ const RectangleROIStartEndThreshold = {
       throw new Error('Tool not supported');
     }
 
-    const {
-      SOPInstanceUID,
-      SeriesInstanceUID,
-      StudyInstanceUID,
-    } = getSOPInstanceAttributes(
+    const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = getSOPInstanceAttributes(
       referencedImageId,
       cornerstoneViewportService,
       viewportId