Instance metadata/metadata providers overhaul (#1481)
* Instance metadata plus metadata provider overhaul. Fix consumption of wado-uri urls fallbacks + datatype agnosticism. WIP DICOMify things. fix various issues with naturalized variable naming migration. Remove metadata provider. Fix consumption of multiframe images and addition of CWIL metadata. Fix strange build issues. Fix CWIL style windowWidth to array from naturalized DICOM. Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs. Move color palette fetching down to the natuaralized JSON level. Remove unused StudyMetadataSummary Remove redundant dicom metadata dictionary. Working local + json routes. Fix SR read. Finished first round of testing + cleaned up debugging etc. * data => metadata for instance naturalizedJSON * Update dcmjs version * Correct github isssues. * Fix erroneously replaced files. * Danny's recommended changes. * Instance metadata plus metadata provider overhaul. Fix consumption of wado-uri urls fallbacks + datatype agnosticism. WIP DICOMify things. fix various issues with naturalized variable naming migration. Remove metadata provider. Fix consumption of multiframe images and addition of CWIL metadata. Fix strange build issues. Fix CWIL style windowWidth to array from naturalized DICOM. Fix PT, CT, CR and DX issues for cornerstone + DX issues for vtkjs. Move color palette fetching down to the natuaralized JSON level. Remove unused StudyMetadataSummary Remove redundant dicom metadata dictionary. Working local + json routes. Fix SR read. Finished first round of testing + cleaned up debugging etc. * data => metadata for instance naturalizedJSON * Update dcmjs version * Correct github isssues. * Fix erroneously replaced files. * Danny's recommended changes. * Update JSON CI * Update casing of import. * Fix jump for SR. * Fix unit tests for measurements service * Fix json CI test. * fix: update yarn lock * Fix local non-encapsulated pdf view * CI updated to new sucess message. Co-authored-by: Danny <danny.ri.brown@gmail.com>
This commit is contained in:
James PettsandDanny authored and GitHub committed
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@@ -34,7 +34,7 @@
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"@ohif/ui": "^0.50.0",
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"cornerstone-core": "^2.2.8",
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"cornerstone-wado-image-loader": "^3.0.0",
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"dcmjs": "^0.8.2",
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"dcmjs": "^0.10.1",
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"dicom-parser": "^1.8.3",
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"i18next": "^17.0.3",
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"i18next-browser-languagedetector": "^3.0.1",
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@@ -54,7 +54,7 @@
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"devDependencies": {
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"@ohif/core": "^2.5.2",
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"@ohif/ui": "^1.3.2",
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"cornerstone-tools": "^4.12.0",
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"cornerstone-tools": "4.12.0",
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"cornerstone-wado-image-loader": "^3.0.0",
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"dicom-parser": "^1.8.3",
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"gh-pages": "^2.0.1",
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@@ -1,6 +1,5 @@
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import React, { Component } from 'react';
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import { getImageData, loadImageData } from 'react-vtkjs-viewport';
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import ConnectedVTKViewport from './ConnectedVTKViewport';
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import LoadingIndicator from './LoadingIndicator.js';
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import OHIF from '@ohif/core';
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@@ -13,15 +12,7 @@ import vtkVolume from 'vtk.js/Sources/Rendering/Core/Volume';
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import vtkVolumeMapper from 'vtk.js/Sources/Rendering/Core/VolumeMapper';
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const { StackManager } = OHIF.utils;
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// Metadata configuration
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const metadataProvider = new OHIF.cornerstone.MetadataProvider();
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cornerstone.metaData.addProvider(
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metadataProvider.provider.bind(metadataProvider)
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);
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StackManager.setMetadataProvider(metadataProvider);
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const style = { width: '100%', height: '100%', position: 'relative' };
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const SOP_CLASSES = {
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SEGMENTATION_STORAGE: '1.2.840.10008.5.1.4.1.1.66.4',
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@@ -68,10 +59,10 @@ class OHIFVTKViewport extends Component {
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viewportData: PropTypes.shape({
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studies: PropTypes.array,
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displaySet: PropTypes.shape({
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studyInstanceUid: PropTypes.string,
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displaySetInstanceUid: PropTypes.string,
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sopClassUids: PropTypes.arrayOf(PropTypes.string),
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sopInstanceUid: PropTypes.string,
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StudyInstanceUID: PropTypes.string,
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displaySetInstanceUID: PropTypes.string,
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sopClassUIDs: PropTypes.arrayOf(PropTypes.string),
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SOPInstanceUID: PropTypes.string,
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frameIndex: PropTypes.number,
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}),
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}),
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@@ -97,18 +88,18 @@ class OHIFVTKViewport extends Component {
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static getCornerstoneStack(
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studies,
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studyInstanceUid,
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displaySetInstanceUid,
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sopInstanceUid,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPInstanceUID,
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frameIndex
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) {
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// Create shortcut to displaySet
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const study = studies.find(
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study => study.studyInstanceUid === studyInstanceUid
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study => study.StudyInstanceUID === StudyInstanceUID
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);
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const displaySet = study.displaySets.find(set => {
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return set.displaySetInstanceUid === displaySetInstanceUid;
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return set.displaySetInstanceUID === displaySetInstanceUID;
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});
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// Get stack from Stack Manager
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@@ -119,17 +110,14 @@ class OHIFVTKViewport extends Component {
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if (frameIndex !== undefined) {
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stack.currentImageIdIndex = frameIndex;
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} else if (sopInstanceUid) {
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} else if (SOPInstanceUID) {
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const index = stack.imageIds.findIndex(imageId => {
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const sopCommonModule = cornerstone.metaData.get(
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'sopCommonModule',
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const imageIdSOPInstanceUID = cornerstone.metaData.get(
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'SOPInstanceUID',
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imageId
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);
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if (!sopCommonModule) {
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return;
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}
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return sopCommonModule.sopInstanceUID === sopInstanceUid;
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return imageIdSOPInstanceUID === SOPInstanceUID;
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});
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if (index > -1) {
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@@ -144,31 +132,31 @@ class OHIFVTKViewport extends Component {
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getViewportData = (
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studies,
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studyInstanceUid,
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displaySetInstanceUid,
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sopClassUid,
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sopInstanceUid,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPClassUID,
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SOPInstanceUID,
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frameIndex
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) => {
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const stack = OHIFVTKViewport.getCornerstoneStack(
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studies,
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studyInstanceUid,
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displaySetInstanceUid,
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sopClassUid,
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sopInstanceUid,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPClassUID,
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SOPInstanceUID,
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frameIndex
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);
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let imageDataObject;
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let labelmapDataObject;
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switch (sopClassUid) {
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switch (SOPClassUID) {
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case SOP_CLASSES.SEGMENTATION_STORAGE:
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throw new Error('Not yet implemented');
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/*
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const data = handleSegmentationStorage(
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stack.imageIds,
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displaySetInstanceUid
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displaySetInstanceUID
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);
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imageDataObject = data.referenceDataObject;
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@@ -182,7 +170,7 @@ class OHIFVTKViewport extends Component {
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});
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*/
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default:
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imageDataObject = getImageData(stack.imageIds, displaySetInstanceUid);
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imageDataObject = getImageData(stack.imageIds, displaySetInstanceUID);
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return imageDataObject;
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}
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@@ -194,25 +182,31 @@ class OHIFVTKViewport extends Component {
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* @param {object} imageDataObject
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* @param {object} imageDataObject.vtkImageData
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* @param {object} imageDataObject.imageMetaData0
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* @param {number} [imageDataObject.imageMetaData0.windowWidth] - The volume's initial windowWidth
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* @param {number} [imageDataObject.imageMetaData0.windowCenter] - The volume's initial windowCenter
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* @param {string} imageDataObject.imageMetaData0.modality - CT, MR, PT, etc
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* @param {string} displaySetInstanceUid
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* @param {number} [imageDataObject.imageMetaData0.WindowWidth] - The volume's initial WindowWidth
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* @param {number} [imageDataObject.imageMetaData0.WindowCenter] - The volume's initial WindowCenter
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* @param {string} imageDataObject.imageMetaData0.Modality - CT, MR, PT, etc
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* @param {string} displaySetInstanceUID
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* @returns vtkVolumeActor
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* @memberof OHIFVTKViewport
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*/
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getOrCreateVolume(imageDataObject, displaySetInstanceUid) {
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if (volumeCache[displaySetInstanceUid]) {
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return volumeCache[displaySetInstanceUid];
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getOrCreateVolume(imageDataObject, displaySetInstanceUID) {
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if (volumeCache[displaySetInstanceUID]) {
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return volumeCache[displaySetInstanceUID];
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}
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const { vtkImageData, imageMetaData0 } = imageDataObject;
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const { windowWidth, windowCenter, modality } = imageMetaData0;
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// TODO -> Should update react-vtkjs-viewport and react-cornerstone-viewports
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// internals to use naturalized DICOM JSON names.
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const {
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windowWidth: WindowWidth,
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windowCenter: WindowCenter,
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modality: Modality,
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} = imageMetaData0;
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const { lower, upper } = _getRangeFromWindowLevels(
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windowWidth,
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windowCenter,
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modality
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WindowWidth,
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WindowCenter,
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Modality
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);
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const volumeActor = vtkVolume.newInstance();
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const volumeMapper = vtkVolumeMapper.newInstance();
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@@ -236,7 +230,7 @@ class OHIFVTKViewport extends Component {
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// TODO: maybe we should auto adjust samples to 1000.
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volumeMapper.setMaximumSamplesPerRay(4000);
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volumeCache[displaySetInstanceUid] = volumeActor;
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volumeCache[displaySetInstanceUID] = volumeActor;
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return volumeActor;
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}
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@@ -244,26 +238,26 @@ class OHIFVTKViewport extends Component {
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setStateFromProps() {
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const { studies, displaySet } = this.props.viewportData;
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const {
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studyInstanceUid,
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displaySetInstanceUid,
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sopClassUids,
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sopInstanceUid,
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StudyInstanceUID,
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displaySetInstanceUID,
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sopClassUIDs,
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SOPInstanceUID,
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frameIndex,
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} = displaySet;
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if (sopClassUids.length > 1) {
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if (sopClassUIDs.length > 1) {
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console.warn(
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'More than one SOPClassUid in the same series is not yet supported.'
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'More than one SOPClassUID in the same series is not yet supported.'
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);
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}
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const sopClassUid = sopClassUids[0];
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const SOPClassUID = sopClassUIDs[0];
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const imageDataObject = this.getViewportData(
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studies,
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studyInstanceUid,
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displaySetInstanceUid,
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sopClassUid,
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sopInstanceUid,
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StudyInstanceUID,
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displaySetInstanceUID,
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SOPClassUID,
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SOPInstanceUID,
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frameIndex
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);
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@@ -277,7 +271,7 @@ class OHIFVTKViewport extends Component {
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const volumeActor = this.getOrCreateVolume(
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imageDataObject,
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displaySetInstanceUid
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displaySetInstanceUID
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);
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this.setState({
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@@ -317,9 +311,9 @@ class OHIFVTKViewport extends Component {
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const prevDisplaySet = prevProps.viewportData.displaySet;
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if (
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displaySet.displaySetInstanceUid !==
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prevDisplaySet.displaySetInstanceUid ||
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displaySet.sopInstanceUid !== prevDisplaySet.sopInstanceUid ||
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displaySet.displaySetInstanceUID !==
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prevDisplaySet.displaySetInstanceUID ||
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displaySet.SOPInstanceUID !== prevDisplaySet.SOPInstanceUID ||
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displaySet.frameIndex !== prevDisplaySet.frameIndex
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) {
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this.setStateFromProps();
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@@ -331,7 +325,7 @@ class OHIFVTKViewport extends Component {
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const { isLoading, insertPixelDataPromises } = imageDataObject;
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const numberOfFrames = insertPixelDataPromises.length;
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const NumberOfFrames = insertPixelDataPromises.length;
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if (!isLoading) {
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this.setState({ isLoaded: true });
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@@ -341,7 +335,7 @@ class OHIFVTKViewport extends Component {
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insertPixelDataPromises.forEach(promise => {
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promise.then(numberProcessed => {
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const percentComplete = Math.floor(
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(numberProcessed * 100) / numberOfFrames
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(numberProcessed * 100) / NumberOfFrames
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);
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if (percentComplete !== this.state.percentComplete) {
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@@ -373,8 +367,6 @@ class OHIFVTKViewport extends Component {
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});
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}
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const style = { width: '100%', height: '100%', position: 'relative' };
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return (
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<>
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<div style={style}>
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@@ -409,21 +401,21 @@ class OHIFVTKViewport extends Component {
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* @private
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* @param {number} [width] - the width of our window
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* @param {number} [center] - the center of our window
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* @param {string} [modality] - 'PT', 'CT', etc.
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* @param {string} [Modality] - 'PT', 'CT', etc.
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* @returns { lower, upper } - range
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*/
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function _getRangeFromWindowLevels(width, center, modality = undefined) {
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function _getRangeFromWindowLevels(width, center, Modality = undefined) {
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// For PET just set the range to 0-5 SUV
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if (Modality === 'PT') {
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return { lower: 0, upper: 5 };
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}
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const levelsAreNotNumbers = isNaN(center) || isNaN(width);
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if (levelsAreNotNumbers) {
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return { lower: 0, upper: 512 };
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}
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|
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// For PET just set the range to 0-5 SUV
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if (modality === 'PT') {
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return { lower: 0, upper: 5 };
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}
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return {
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lower: center - width / 2.0,
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upper: center + width / 2.0,
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@@ -19,8 +19,8 @@ const VTKViewport = props => {
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useEffect(() => {
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const handleScrollEvent = evt => {
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const vtkViewportApiReference = props.onScroll(props.viewportIndex) || {};
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const viewportUid = vtkViewportApiReference.uid;
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const viewportWasScrolled = viewportUid === evt.detail.uid;
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const viewportUID = vtkViewportApiReference.uid;
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const viewportWasScrolled = viewportUID === evt.detail.uid;
|
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|
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if (viewportWasScrolled) {
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setViewportActiveHandler();
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@@ -70,12 +70,9 @@ const commandsModule = ({ commandsManager }) => {
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if (cornerstoneElement) {
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const imageId = cornerstoneElement.image.imageId;
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const { modality } = cornerstone.metaData.get(
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'generalSeriesModule',
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imageId
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);
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const Modality = cornerstone.metaData.get('Modality', imageId);
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|
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if (modality !== 'PT') {
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if (Modality !== 'PT') {
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const { windowWidth, windowCenter } = cornerstoneElement.viewport.voi;
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|
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return {
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@@ -1,42 +1,42 @@
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import * as dcmjs from "dcmjs";
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import * as dcmjs from 'dcmjs';
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|
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import OHIF from "@ohif/core";
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import { api } from "dicomweb-client";
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import OHIF from '@ohif/core';
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import { api } from 'dicomweb-client';
|
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|
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const { StackManager } = OHIF.utils;
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|
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function getDisplaySet(studies, studyInstanceUid, displaySetInstanceUid) {
|
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function getDisplaySet(studies, StudyInstanceUID, displaySetInstanceUID) {
|
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const study = studies.find(
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study => study.studyInstanceUid === studyInstanceUid
|
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study => study.StudyInstanceUID === StudyInstanceUID
|
||||
);
|
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|
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const displaySet = study.displaySets.find(set => {
|
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return set.displaySetInstanceUid === displaySetInstanceUid;
|
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return set.displaySetInstanceUID === displaySetInstanceUID;
|
||||
});
|
||||
|
||||
return displaySet;
|
||||
}
|
||||
|
||||
function getDisplaySetsBySeries(studies, studyInstanceUid, seriesInstanceUid) {
|
||||
function getDisplaySetsBySeries(studies, StudyInstanceUID, SeriesInstanceUID) {
|
||||
const study = studies.find(
|
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study => study.studyInstanceUid === studyInstanceUid
|
||||
study => study.StudyInstanceUID === StudyInstanceUID
|
||||
);
|
||||
|
||||
return study.displaySets.filter(set => {
|
||||
return set.seriesInstanceUid === seriesInstanceUid;
|
||||
return set.SeriesInstanceUID === SeriesInstanceUID;
|
||||
});
|
||||
}
|
||||
|
||||
function getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
|
||||
function getCornerstoneStack(studies, StudyInstanceUID, displaySetInstanceUID) {
|
||||
const study = studies.find(
|
||||
study => study.studyInstanceUid === studyInstanceUid
|
||||
study => study.StudyInstanceUID === StudyInstanceUID
|
||||
);
|
||||
|
||||
// Create shortcut to displaySet
|
||||
const displaySet = getDisplaySet(
|
||||
studies,
|
||||
studyInstanceUid,
|
||||
displaySetInstanceUid
|
||||
StudyInstanceUID,
|
||||
displaySetInstanceUID
|
||||
);
|
||||
|
||||
// Get stack from Stack Manager
|
||||
@@ -52,19 +52,19 @@ function getCornerstoneStack(studies, studyInstanceUid, displaySetInstanceUid) {
|
||||
function retrieveDicomData(
|
||||
studyInstanceUID,
|
||||
seriesInstanceUID,
|
||||
sopInstanceUID,
|
||||
sopInstanceUid,
|
||||
wadoRoot
|
||||
) {
|
||||
const config = {
|
||||
url: wadoRoot,
|
||||
headers: DICOMWeb.getAuthorizationHeader()
|
||||
headers: DICOMWeb.getAuthorizationHeader(),
|
||||
};
|
||||
|
||||
const dicomWeb = new api.DICOMwebClient(config);
|
||||
const options = {
|
||||
studyInstanceUID,
|
||||
seriesInstanceUID,
|
||||
sopInstanceUID
|
||||
sopInstanceUid,
|
||||
};
|
||||
|
||||
return dicomWeb.retrieveInstance(options);
|
||||
@@ -72,30 +72,26 @@ function retrieveDicomData(
|
||||
|
||||
async function handleSegmentationStorage(
|
||||
studies,
|
||||
studyInstanceUid,
|
||||
displaySetInstanceUid
|
||||
StudyInstanceUID,
|
||||
displaySetInstanceUID
|
||||
) {
|
||||
const study = studies.find(
|
||||
study => study.studyInstanceUid === studyInstanceUid
|
||||
study => study.StudyInstanceUID === StudyInstanceUID
|
||||
);
|
||||
const displaySet = getDisplaySet(
|
||||
studies,
|
||||
studyInstanceUid,
|
||||
displaySetInstanceUid
|
||||
StudyInstanceUID,
|
||||
displaySetInstanceUID
|
||||
);
|
||||
|
||||
// TODO: This is terrible but we need to use WADO-RS or we can't retrieve the SEG
|
||||
// from google cloud
|
||||
const wadoRoot = displaySet.images[0].getData().wadoRoot;
|
||||
|
||||
const StudyInstanceUID = displaySet.images[0].getStudyInstanceUID();
|
||||
const SeriesInstanceUID = displaySet.images[0].getSeriesInstanceUID();
|
||||
const SOPInstanceUID = displaySet.images[0].getSOPInstanceUID();
|
||||
|
||||
const arrayBuffer = await retrieveDicomData(
|
||||
StudyInstanceUID,
|
||||
SeriesInstanceUID,
|
||||
SOPInstanceUID,
|
||||
displaySet.images[0].getStudyInstanceUID(),
|
||||
displaySet.images[0].getSeriesInstanceUID(),
|
||||
displaySet.images[0].getSOPInstanceUID(),
|
||||
wadoRoot
|
||||
);
|
||||
|
||||
@@ -108,16 +104,16 @@ async function handleSegmentationStorage(
|
||||
|
||||
dataset._meta = dcmjs.data.DicomMetaDictionary.namifyDataset(dicomData.meta);
|
||||
|
||||
const seriesInstanceUid = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
|
||||
const SeriesInstanceUID = dataset.ReferencedSeriesSequence.SeriesInstanceUID;
|
||||
const displaySets = getDisplaySetsBySeries(
|
||||
studies,
|
||||
studyInstanceUid,
|
||||
seriesInstanceUid
|
||||
StudyInstanceUID,
|
||||
SeriesInstanceUID
|
||||
);
|
||||
|
||||
if (displaySets.length > 1) {
|
||||
console.warn(
|
||||
"More than one display set with the same seriesInstanceUid. This is not supported yet..."
|
||||
'More than one display set with the same SeriesInstanceUID. This is not supported yet...'
|
||||
);
|
||||
}
|
||||
|
||||
@@ -125,7 +121,7 @@ async function handleSegmentationStorage(
|
||||
const imageIds = referenceDisplaySet.images.map(image => image.getImageId());
|
||||
|
||||
if (!results) {
|
||||
throw new Error("Fractional segmentations are not supported");
|
||||
throw new Error('Fractional segmentations are not supported');
|
||||
}
|
||||
|
||||
const cachedStack = StackManager.findOrCreateStack(
|
||||
@@ -137,13 +133,13 @@ async function handleSegmentationStorage(
|
||||
|
||||
return {
|
||||
referenceDataObject,
|
||||
labelmapDataObject
|
||||
labelmapDataObject,
|
||||
};
|
||||
|
||||
return {
|
||||
studyInstanceUid,
|
||||
displaySetInstanceUid,
|
||||
stack
|
||||
StudyInstanceUID,
|
||||
displaySetInstanceUID,
|
||||
stack,
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
@@ -13,21 +13,21 @@ const _isDisplaySetReconstructable = (viewportSpecificData = {}, activeViewportI
|
||||
return false;
|
||||
};
|
||||
|
||||
const { displaySetInstanceUid, studyInstanceUid } = viewportSpecificData[
|
||||
const { displaySetInstanceUID, StudyInstanceUID } = viewportSpecificData[
|
||||
activeViewportIndex
|
||||
];
|
||||
|
||||
const studies = studyMetadataManager.all();
|
||||
|
||||
const study = studies.find(
|
||||
study => study.studyInstanceUID === studyInstanceUid
|
||||
study => study.studyInstanceUID === StudyInstanceUID
|
||||
);
|
||||
|
||||
if (!study) {
|
||||
return false;
|
||||
}
|
||||
|
||||
const displaySet = study._displaySets.find(set => set.displaySetInstanceUid === displaySetInstanceUid);
|
||||
const displaySet = study._displaySets.find(set => set.displaySetInstanceUID === displaySetInstanceUID);
|
||||
|
||||
if (!displaySet) {
|
||||
return false;
|
||||
|
||||
Reference in new issue
Block a user