init
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mario
14
.scripts/dev.sh
Executable file
14
.scripts/dev.sh
Executable file
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#!/bin/bash
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# https://github.com/shelljs/shelljs
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# https://github.com/shelljs/shelljs#exclude-options
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PROJECT=$1
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if [ -z "$PROJECT" ]
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then
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# Default
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npx lerna run dev:viewer
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else
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eval "npx lerna run dev:$PROJECT"
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fi
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read -p 'Press [Enter] key to continue...'
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273
.scripts/dicom-json-generator.js
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273
.scripts/dicom-json-generator.js
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/*
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* This script uses nodejs to generate a JSON file from a DICOM study folder.
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* You need to have dcmjs installed in your project.
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* The JSON file can be used to load the study into the OHIF Viewer. You can get more detail
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* in the DICOM JSON Data source on docs.ohif.org
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*
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* Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> <optional scheme>
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*
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* params:
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* - studyFolder: path to the study folder which contains the DICOM files
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* - urlPrefix: prefix to the url that will be used to load the study into the viewer. For instance
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* we use https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data as the urlPrefix for the
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* example since the data is hosted on S3 and each study is in a folder. So the url in the generated
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* json file for the first instance of the first series of the first study will be
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* dicomweb:https://ohif-assets.s3.us-east-2.amazonaws.com/dicom-json/data/Series1/Instance1
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*
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* as you see the dicomweb is a prefix that is used to load the data into the viewer, which is suited when
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* the .dcm file is hosted statically and can be accessed via a URL (like our example above)
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* However, you can specify a new scheme bellow.
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*
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* - outputJSONPath: path to the output JSON file
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* - scheme: default dicomweb if not provided
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*/
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const dcmjs = require('dcmjs');
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const path = require('path');
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const fs = require('fs').promises;
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const args = process.argv.slice(2);
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const [studyDirectory, urlPrefix, outputPath, scheme = 'dicomweb'] = args;
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if (args.length < 3 || args.length > 4) {
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console.error(
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'Usage: node dicom-json-generator.js <studyFolder> <urlPrefix> <outputJSONPath> [scheme]'
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);
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process.exit(1);
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}
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const model = {
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studies: [],
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};
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async function convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme) {
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try {
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const files = await recursiveReadDir(studyDirectory);
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console.debug('Processing...');
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for (const file of files) {
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if (!file.includes('.DS_Store') && !file.includes('.xml')) {
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const arrayBuffer = await fs.readFile(file);
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const dicomDict = dcmjs.data.DicomMessage.readFile(arrayBuffer.buffer);
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const instance = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomDict.dict);
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instance.fileLocation = createImageId(file, urlPrefix, studyDirectory, scheme);
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processInstance(instance);
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}
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}
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console.log('Successfully loaded data');
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model.studies.forEach(study => {
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study.NumInstances = findInstancesNumber(study);
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study.Modalities = findModalities(study).join('/');
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});
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await fs.writeFile(outputPath, JSON.stringify(model, null, 2));
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console.log('JSON saved');
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} catch (error) {
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console.error(error);
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}
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}
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async function recursiveReadDir(dir) {
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let results = [];
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const list = await fs.readdir(dir);
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for (const file of list) {
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const filePath = path.resolve(dir, file);
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const stat = await fs.stat(filePath);
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if (stat.isDirectory()) {
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const res = await recursiveReadDir(filePath);
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results = results.concat(res);
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} else {
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results.push(filePath);
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}
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}
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return results;
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}
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function createImageId(fileLocation, urlPrefix, studyDirectory, scheme) {
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const relativePath = path.relative(studyDirectory, fileLocation);
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const normalizedPath = path.normalize(relativePath).replace(/\\/g, '/');
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return `${scheme}:${urlPrefix}${normalizedPath}`;
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}
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function processInstance(instance) {
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const { StudyInstanceUID, SeriesInstanceUID } = instance;
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let study = getStudy(StudyInstanceUID);
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if (!study) {
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study = createStudyMetadata(StudyInstanceUID, instance);
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model.studies.push(study);
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}
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let series = getSeries(StudyInstanceUID, SeriesInstanceUID);
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if (!series) {
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series = createSeriesMetadata(instance);
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study.series.push(series);
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}
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const instanceMetaData =
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instance.NumberOfFrames > 1
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? createInstanceMetaDataMultiFrame(instance)
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: createInstanceMetaData(instance);
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series.instances.push(...[].concat(instanceMetaData));
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}
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function getStudy(StudyInstanceUID) {
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return model.studies.find(study => study.StudyInstanceUID === StudyInstanceUID);
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}
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function getSeries(StudyInstanceUID, SeriesInstanceUID) {
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const study = getStudy(StudyInstanceUID);
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return study
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? study.series.find(series => series.SeriesInstanceUID === SeriesInstanceUID)
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: undefined;
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}
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const findInstancesNumber = study => {
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let numInstances = 0;
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study.series.forEach(aSeries => {
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numInstances = numInstances + aSeries.instances.length;
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});
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return numInstances;
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};
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const findModalities = study => {
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let modalities = new Set();
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study.series.forEach(aSeries => {
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modalities.add(aSeries.Modality);
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});
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return Array.from(modalities);
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};
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function createStudyMetadata(StudyInstanceUID, instance) {
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return {
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StudyInstanceUID,
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StudyDescription: instance.StudyDescription,
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StudyDate: instance.StudyDate,
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StudyTime: instance.StudyTime,
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PatientName: instance.PatientName,
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PatientID: instance.PatientID || '1234', // this is critical to have
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AccessionNumber: instance.AccessionNumber,
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PatientAge: instance.PatientAge,
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PatientSex: instance.PatientSex,
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PatientWeight: instance.PatientWeight,
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series: [],
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};
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}
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function createSeriesMetadata(instance) {
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return {
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SeriesInstanceUID: instance.SeriesInstanceUID,
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SeriesDescription: instance.SeriesDescription,
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SeriesNumber: instance.SeriesNumber,
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SeriesTime: instance.SeriesTime,
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Modality: instance.Modality,
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SliceThickness: instance.SliceThickness,
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instances: [],
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};
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}
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function commonMetaData(instance) {
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return {
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Columns: instance.Columns,
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Rows: instance.Rows,
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InstanceNumber: instance.InstanceNumber,
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SOPClassUID: instance.SOPClassUID,
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AcquisitionNumber: instance.AcquisitionNumber,
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PhotometricInterpretation: instance.PhotometricInterpretation,
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BitsAllocated: instance.BitsAllocated,
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BitsStored: instance.BitsStored,
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PixelRepresentation: instance.PixelRepresentation,
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SamplesPerPixel: instance.SamplesPerPixel,
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PixelSpacing: instance.PixelSpacing,
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HighBit: instance.HighBit,
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ImageOrientationPatient: instance.ImageOrientationPatient,
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ImagePositionPatient: instance.ImagePositionPatient,
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FrameOfReferenceUID: instance.FrameOfReferenceUID,
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ImageType: instance.ImageType,
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Modality: instance.Modality,
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SOPInstanceUID: instance.SOPInstanceUID,
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SeriesInstanceUID: instance.SeriesInstanceUID,
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StudyInstanceUID: instance.StudyInstanceUID,
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WindowCenter: instance.WindowCenter,
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WindowWidth: instance.WindowWidth,
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RescaleIntercept: instance.RescaleIntercept,
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RescaleSlope: instance.RescaleSlope,
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};
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}
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function conditionalMetaData(instance) {
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return {
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...(instance.ConceptNameCodeSequence && {
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ConceptNameCodeSequence: instance.ConceptNameCodeSequence,
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}),
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...(instance.SeriesDate && { SeriesDate: instance.SeriesDate }),
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...(instance.ReferencedSeriesSequence && {
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ReferencedSeriesSequence: instance.ReferencedSeriesSequence,
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}),
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...(instance.SharedFunctionalGroupsSequence && {
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SharedFunctionalGroupsSequence: instance.SharedFunctionalGroupsSequence,
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}),
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...(instance.PerFrameFunctionalGroupsSequence && {
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PerFrameFunctionalGroupsSequence: instance.PerFrameFunctionalGroupsSequence,
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}),
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...(instance.ContentSequence && { ContentSequence: instance.ContentSequence }),
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...(instance.ContentTemplateSequence && {
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ContentTemplateSequence: instance.ContentTemplateSequence,
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}),
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...(instance.CurrentRequestedProcedureEvidenceSequence && {
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CurrentRequestedProcedureEvidenceSequence: instance.CurrentRequestedProcedureEvidenceSequence,
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}),
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...(instance.CodingSchemeIdentificationSequence && {
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CodingSchemeIdentificationSequence: instance.CodingSchemeIdentificationSequence,
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}),
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...(instance.RadiopharmaceuticalInformationSequence && {
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RadiopharmaceuticalInformationSequence: instance.RadiopharmaceuticalInformationSequence,
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}),
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...(instance.ROIContourSequence && {
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ROIContourSequence: instance.ROIContourSequence,
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}),
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...(instance.StructureSetROISequence && {
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StructureSetROISequence: instance.StructureSetROISequence,
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}),
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...(instance.ReferencedFrameOfReferenceSequence && {
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ReferencedFrameOfReferenceSequence: instance.ReferencedFrameOfReferenceSequence,
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}),
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...(instance.CorrectedImage && { CorrectedImage: instance.CorrectedImage }),
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...(instance.Units && { Units: instance.Units }),
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...(instance.DecayCorrection && { DecayCorrection: instance.DecayCorrection }),
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...(instance.AcquisitionDate && { AcquisitionDate: instance.AcquisitionDate }),
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...(instance.AcquisitionTime && { AcquisitionTime: instance.AcquisitionTime }),
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...(instance.PatientWeight && { PatientWeight: instance.PatientWeight }),
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...(instance.NumberOfFrames && { NumberOfFrames: instance.NumberOfFrames }),
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...(instance.FrameTime && { FrameTime: instance.FrameTime }),
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...(instance.EncapsulatedDocument && { EncapsulatedDocument: instance.EncapsulatedDocument }),
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...(instance.SequenceOfUltrasoundRegions && {
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SequenceOfUltrasoundRegions: instance.SequenceOfUltrasoundRegions,
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}),
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};
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}
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function createInstanceMetaData(instance) {
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const metadata = {
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...commonMetaData(instance),
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...conditionalMetaData(instance),
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};
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return { metadata, url: instance.fileLocation };
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}
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function createInstanceMetaDataMultiFrame(instance) {
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const instances = [];
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const commonData = commonMetaData(instance);
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const conditionalData = conditionalMetaData(instance);
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for (let i = 1; i <= instance.NumberOfFrames; i++) {
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const metadata = { ...commonData, ...conditionalData };
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const result = { metadata, url: instance.fileLocation + `?frame=${i}` };
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instances.push(result);
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}
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return instances;
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}
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convertDICOMToJSON(studyDirectory, urlPrefix, outputPath, scheme);
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