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

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This commit is contained in:
Alireza authored and GitHub committed 2023-09-01 16:19:39 -04:00
1 parent 01500a2d4c
commit 9045ddaedc
656 files changed
+21737 -20628
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extensions/dicom-microscopy/src/utils/RoiAnnotation.js
+3 -13
View File
@@ -13,13 +13,7 @@ const EVENTS = {
* Represents a single annotation for the Microscopy Viewer
*/
class RoiAnnotation extends PubSubService {
constructor(
roiGraphic,
studyInstanceUID,
seriesInstanceUID,
label = '',
viewState = null
) {
constructor(roiGraphic, studyInstanceUID, seriesInstanceUID, label = '', viewState = null) {
super(EVENTS);
this.uid = roiGraphic.uid;
this.roiGraphic = roiGraphic;
@@ -34,9 +28,7 @@ class RoiAnnotation extends PubSubService {
const roiGraphic = this.roiGraphic;
const roiGraphicSymbols = Object.getOwnPropertySymbols(roiGraphic);
const _scoord3d = roiGraphicSymbols.find(
s => String(s) === 'Symbol(scoord3d)'
);
const _scoord3d = roiGraphicSymbols.find(s => String(s) === 'Symbol(scoord3d)');
return roiGraphic[_scoord3d];
}
@@ -45,9 +37,7 @@ class RoiAnnotation extends PubSubService {
const scoord3d = this.getScoord3d();
const scoord3dSymbols = Object.getOwnPropertySymbols(scoord3d);
const _coordinates = scoord3dSymbols.find(
s => String(s) === 'Symbol(coordinates)'
);
const _coordinates = scoord3dSymbols.find(s => String(s) === 'Symbol(coordinates)');
const coordinates = scoord3d[_coordinates];
return coordinates;
extensions/dicom-microscopy/src/utils/areaOfPolygon.js
+1 -3
View File
@@ -5,9 +5,7 @@ export default function areaOfPolygon(coordinates) {
let j = n - 1;
for (let i = 0; i < n; i++) {
area +=
(coordinates[j][0] + coordinates[i][0]) *
(coordinates[j][1] - coordinates[i][1]);
area += (coordinates[j][0] + coordinates[i][0]) * (coordinates[j][1] - coordinates[i][1]);
j = i; // j is previous vertex to i
}
extensions/dicom-microscopy/src/utils/callInputDialog.tsx
+1 -1
View File
@@ -53,7 +53,7 @@ export default function callInputDialog({
label="Enter your annotation"
labelClassName="text-white text-[14px] leading-[1.2]"
autoFocus
className="bg-black border-primary-main"
className="border-primary-main bg-black"
type="text"
value={value.defaultValue}
onChange={event => {
extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts
+5 -19
View File
@@ -35,9 +35,7 @@ export default function cleanDenaturalizedDataset(
}
): any {
if (Array.isArray(obj)) {
const newAry = obj.map(o =>
isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)
);
const newAry = obj.map(o => (isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)));
return newAry;
} else if (isPrimitive(obj)) {
return obj;
@@ -47,31 +45,19 @@ export default function cleanDenaturalizedDataset(
delete obj[key].Value;
} else if (Array.isArray(obj[key].Value) && obj[key].vr) {
if (obj[key].Value.length === 1 && obj[key].Value[0].BulkDataURI) {
dicomWebUtils.fixBulkDataURI(
obj[key].Value[0],
options,
options.dataSourceConfig
);
dicomWebUtils.fixBulkDataURI(obj[key].Value[0], options, options.dataSourceConfig);
obj[key].BulkDataURI = obj[key].Value[0].BulkDataURI;
// prevent mixed-content blockage
if (
window.location.protocol === 'https:' &&
obj[key].BulkDataURI.startsWith('http:')
) {
obj[key].BulkDataURI = obj[key].BulkDataURI.replace(
'http:',
'https:'
);
if (window.location.protocol === 'https:' && obj[key].BulkDataURI.startsWith('http:')) {
obj[key].BulkDataURI = obj[key].BulkDataURI.replace('http:', 'https:');
}
delete obj[key].Value;
} else if (vrNumerics.includes(obj[key].vr)) {
obj[key].Value = obj[key].Value.map(v => +v);
} else {
obj[key].Value = obj[key].Value.map(entry =>
cleanDenaturalizedDataset(entry, options)
);
obj[key].Value = obj[key].Value.map(entry => cleanDenaturalizedDataset(entry, options));
}
}
});
extensions/dicom-microscopy/src/utils/constructSR.ts
+36 -59
View File
@@ -9,11 +9,7 @@ import DEVICE_OBSERVER_UID from './DEVICE_OBSERVER_UID';
*
* @return Comprehensive3DSR dataset
*/
export default function constructSR(
metadata,
{ SeriesDescription, SeriesNumber },
annotations
) {
export default function constructSR(metadata, { SeriesDescription, SeriesNumber }, annotations) {
// Handle malformed data
if (!metadata.SpecimenDescriptionSequence) {
metadata.SpecimenDescriptionSequence = {
@@ -31,11 +27,9 @@ export default function constructSR(
schemeDesignator: 'DCM',
meaning: 'Person',
}),
observerIdentifyingAttributes: new dcmjs.sr.templates.PersonObserverIdentifyingAttributes(
{
name: '@ohif/extension-dicom-microscopy',
}
),
observerIdentifyingAttributes: new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({
name: '@ohif/extension-dicom-microscopy',
}),
}),
observerDeviceContext: new dcmjs.sr.templates.ObserverContext({
observerType: new dcmjs.sr.coding.CodedConcept({
@@ -43,11 +37,9 @@ export default function constructSR(
schemeDesignator: 'DCM',
meaning: 'Device',
}),
observerIdentifyingAttributes: new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes(
{
uid: DEVICE_OBSERVER_UID,
}
),
observerIdentifyingAttributes: new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes({
uid: DEVICE_OBSERVER_UID,
}),
}),
subjectContext: new dcmjs.sr.templates.SubjectContext({
subjectClass: new dcmjs.sr.coding.CodedConcept({
@@ -55,28 +47,18 @@ export default function constructSR(
schemeDesignator: 'DCM',
meaning: 'Specimen',
}),
subjectClassSpecificContext: new dcmjs.sr.templates.SubjectContextSpecimen(
{
uid: SpecimenDescriptionSequence.SpecimenUID,
identifier:
SpecimenDescriptionSequence.SpecimenIdentifier ||
metadata.SeriesInstanceUID,
containerIdentifier:
metadata.ContainerIdentifier || metadata.SeriesInstanceUID,
}
),
subjectClassSpecificContext: new dcmjs.sr.templates.SubjectContextSpecimen({
uid: SpecimenDescriptionSequence.SpecimenUID,
identifier: SpecimenDescriptionSequence.SpecimenIdentifier || metadata.SeriesInstanceUID,
containerIdentifier: metadata.ContainerIdentifier || metadata.SeriesInstanceUID,
}),
}),
});
const imagingMeasurements = [];
for (let i = 0; i < annotations.length; i++) {
const { roiGraphic: roi, label } = annotations[i];
let {
measurements,
evaluations,
marker,
presentationState,
} = roi.properties;
let { measurements, evaluations, marker, presentationState } = roi.properties;
console.debug('[SR] storing marker...', marker);
console.debug('[SR] storing measurements...', measurements);
@@ -97,9 +79,7 @@ export default function constructSR(
? measurement.MeasuredValueSequence[0]
: measurement.MeasuredValueSequence;
const MeasuredValueUnits = Array.isArray(
MeasuredValue.MeasurementUnitsCodeSequence
)
const MeasuredValueUnits = Array.isArray(MeasuredValue.MeasurementUnitsCodeSequence)
? MeasuredValue.MeasurementUnitsCodeSequence[0]
: MeasuredValue.MeasurementUnitsCodeSequence;
@@ -136,29 +116,27 @@ export default function constructSR(
});
const identifier = `ROI #${i + 1}`;
const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations(
{
trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({
uid: roi.uid,
identifier: presentationState
? identifier.concat(`(${JSON.stringify(presentationState)})`)
: identifier,
}),
referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({
graphicType: roi.scoord3d.graphicType,
graphicData: roi.scoord3d.graphicData,
frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID,
}),
findingType: new dcmjs.sr.coding.CodedConcept({
value: label,
schemeDesignator: '@ohif/extension-dicom-microscopy',
meaning: 'FREETEXT',
}),
/** Evaluations will conflict with current tracking identifier */
/** qualitativeEvaluations: evaluations, */
measurements,
}
);
const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations({
trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({
uid: roi.uid,
identifier: presentationState
? identifier.concat(`(${JSON.stringify(presentationState)})`)
: identifier,
}),
referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({
graphicType: roi.scoord3d.graphicType,
graphicData: roi.scoord3d.graphicData,
frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID,
}),
findingType: new dcmjs.sr.coding.CodedConcept({
value: label,
schemeDesignator: '@ohif/extension-dicom-microscopy',
meaning: 'FREETEXT',
}),
/** Evaluations will conflict with current tracking identifier */
/** qualitativeEvaluations: evaluations, */
measurements,
});
imagingMeasurements.push(...group);
}
@@ -180,8 +158,7 @@ export default function constructSR(
evidence: [metadata],
seriesInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),
seriesNumber: SeriesNumber,
seriesDescription:
SeriesDescription || 'Whole slide imaging structured report',
seriesDescription: SeriesDescription || 'Whole slide imaging structured report',
sopInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),
instanceNumber: 1,
manufacturer: 'dcmjs-org',
extensions/dicom-microscopy/src/utils/coordinateFormatScoord3d2Geometry.js
+1 -4
View File
@@ -3,10 +3,7 @@ import { inv, multiply } from 'mathjs';
// TODO -> This is pulled out of some internal logic from Dicom Microscopy Viewer,
// We should likely just expose this there.
export default function coordinateFormatScoord3d2Geometry(
coordinates,
pyramid
) {
export default function coordinateFormatScoord3d2Geometry(coordinates, pyramid) {
let transform = false;
if (!Array.isArray(coordinates[0])) {
coordinates = [coordinates];
extensions/dicom-microscopy/src/utils/dicomWebClient.ts
+7 -22
View File
@@ -15,10 +15,7 @@ DICOMwebClient._buildMultipartAcceptHeaderFieldValue = () => {
* @param param0
* @returns
*/
export default function getDicomWebClient({
extensionManager,
servicesManager,
}) {
export default function getDicomWebClient({ extensionManager, servicesManager }) {
const dataSourceConfig = window.config.dataSources.find(
ds => ds.sourceName === extensionManager.activeDataSource
);
@@ -55,29 +52,19 @@ export default function getDicomWebClient({
//
client.retrieveInstanceFrames = async options => {
if (!('studyInstanceUID' in options)) {
throw new Error(
'Study Instance UID is required for retrieval of instance frames'
);
throw new Error('Study Instance UID is required for retrieval of instance frames');
}
if (!('seriesInstanceUID' in options)) {
throw new Error(
'Series Instance UID is required for retrieval of instance frames'
);
throw new Error('Series Instance UID is required for retrieval of instance frames');
}
if (!('sopInstanceUID' in options)) {
throw new Error(
'SOP Instance UID is required for retrieval of instance frames'
);
throw new Error('SOP Instance UID is required for retrieval of instance frames');
}
if (!('frameNumbers' in options)) {
throw new Error(
'frame numbers are required for retrieval of instance frames'
);
throw new Error('frame numbers are required for retrieval of instance frames');
}
console.log(
`retrieve frames ${options.frameNumbers.toString()} of instance ${
options.sopInstanceUID
}`
`retrieve frames ${options.frameNumbers.toString()} of instance ${options.sopInstanceUID}`
);
const instance = DicomMetadataStore.getInstance(
@@ -91,9 +78,7 @@ export default function getDicomWebClient({
: options.frameNumbers.split(',');
return frameNumbers.map(fr =>
Array.isArray(instance.PixelData)
? instance.PixelData[+fr - 1]
: instance.PixelData
Array.isArray(instance.PixelData) ? instance.PixelData[+fr - 1] : instance.PixelData
);
};
}
extensions/dicom-microscopy/src/utils/getSourceDisplaySet.js
+3 -9
View File
@@ -5,24 +5,18 @@
* @param {*} microscopySRDisplaySet
* @returns
*/
export default function getSourceDisplaySet(
allDisplaySets,
microscopySRDisplaySet
) {
export default function getSourceDisplaySet(allDisplaySets, microscopySRDisplaySet) {
const { ReferencedFrameOfReferenceUID } = microscopySRDisplaySet;
const otherDisplaySets = allDisplaySets.filter(
ds =>
ds.displaySetInstanceUID !== microscopySRDisplaySet.displaySetInstanceUID
ds => ds.displaySetInstanceUID !== microscopySRDisplaySet.displaySetInstanceUID
);
const referencedDisplaySet = otherDisplaySets.find(
displaySet =>
displaySet.Modality === 'SM' &&
(displaySet.FrameOfReferenceUID === ReferencedFrameOfReferenceUID ||
// sometimes each depth instance has the different FrameOfReferenceID
displaySet.othersFrameOfReferenceUID.includes(
ReferencedFrameOfReferenceUID
))
displaySet.othersFrameOfReferenceUID.includes(ReferencedFrameOfReferenceUID))
);
if (!referencedDisplaySet && otherDisplaySets.length >= 1) {
extensions/dicom-microscopy/src/utils/loadSR.js
+14 -35
View File
@@ -3,8 +3,7 @@ import dcmjs from 'dcmjs';
import DCM_CODE_VALUES from './dcmCodeValues';
import toArray from './toArray';
const MeasurementReport =
dcmjs.adapters.DICOMMicroscopyViewer.MeasurementReport;
const MeasurementReport = dcmjs.adapters.DICOMMicroscopyViewer.MeasurementReport;
// Define as async so that it returns a promise, expected by the ViewportGrid
export default async function loadSR(
@@ -16,9 +15,7 @@ export default async function loadSR(
const { StudyInstanceUID, FrameOfReferenceUID } = referencedDisplaySet;
const managedViewers = microscopyService.getManagedViewersForStudy(
StudyInstanceUID
);
const managedViewers = microscopyService.getManagedViewersForStudy(StudyInstanceUID);
if (!managedViewers || !managedViewers.length) {
return;
@@ -26,10 +23,7 @@ export default async function loadSR(
microscopySRDisplaySet.isLoaded = true;
const { rois, labels } = await _getROIsFromToolState(
naturalizedDataset,
FrameOfReferenceUID
);
const { rois, labels } = await _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID);
const managedViewer = managedViewers[0];
@@ -58,9 +52,7 @@ async function _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID) {
/* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer'
);
const measurementGroupContentItems = _getMeasurementGroups(
naturalizedDataset
);
const measurementGroupContentItems = _getMeasurementGroups(naturalizedDataset);
const rois = [];
const labels = [];
@@ -71,17 +63,13 @@ async function _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID) {
const capsToolType = t.toUpperCase();
const measurementGroupContentItemsForTool = measurementGroupContentItems.filter(
mg => {
const imageRegionContentItem = toArray(mg.ContentSequence).find(
ci =>
ci.ConceptNameCodeSequence.CodeValue ===
DCM_CODE_VALUES.IMAGE_REGION
);
const measurementGroupContentItemsForTool = measurementGroupContentItems.filter(mg => {
const imageRegionContentItem = toArray(mg.ContentSequence).find(
ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.IMAGE_REGION
);
return imageRegionContentItem.GraphicType === capsToolType;
}
);
return imageRegionContentItem.GraphicType === capsToolType;
});
toolSpecificToolState.forEach((coordinates, index) => {
const properties = {};
@@ -109,9 +97,7 @@ async function _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID) {
);
const trackingGroup = toArray(measurementGroup.ContentSequence).find(
ci =>
ci.ConceptNameCodeSequence.CodeValue ===
DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER
ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER
);
/**
@@ -138,9 +124,7 @@ async function _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID) {
);
let evaluations = toArray(measurementGroup.ContentSequence).filter(ci =>
[DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER].includes(
ci.ConceptNameCodeSequence.CodeValue
)
[DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER].includes(ci.ConceptNameCodeSequence.CodeValue)
);
/**
@@ -191,17 +175,12 @@ function _getMeasurementGroups(naturalizedDataset) {
const { ContentSequence } = naturalizedDataset;
const imagingMeasurementsContentItem = ContentSequence.find(
ci =>
ci.ConceptNameCodeSequence.CodeValue ===
DCM_CODE_VALUES.IMAGING_MEASUREMENTS
ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.IMAGING_MEASUREMENTS
);
const measurementGroupContentItems = toArray(
imagingMeasurementsContentItem.ContentSequence
).filter(
ci =>
ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.MEASUREMENT_GROUP
);
).filter(ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.MEASUREMENT_GROUP);
return measurementGroupContentItems;
}