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Gradienthealth/load dicom from tar file using offsets #9

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db0b26a
Supports relative filepaths and added FileOffsets to the instance met…
Adithyan-Dinesh-Trenser Sep 20, 2024
6b83cff
Changed the usage of ExtendedOffsetTable to CustomOffsetTable and cha…
Adithyan-Dinesh-Trenser Oct 1, 2024
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119 changes: 95 additions & 24 deletions extensions/ohif-gradienthealth-extension/src/DicomJSONDataSource/index.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,18 @@ import getImageId from '../DicomWebDataSource/utils/getImageId';
import _ from 'lodash';

const metadataProvider = classes.MetadataProvider;
const { datasetToBlob } = dcmjs.data;
const { datasetToBlob, DicomMetaDictionary } = dcmjs.data;

const mappings = {
studyInstanceUid: 'StudyInstanceUID',
patientId: 'PatientID',
};

const GH_CUSTOM_TAGS = {
CustomOffsetTable: '60011002',
CustomOffsetTableLengths: '60011003',
};

let _store = {
urls: [],
studyInstanceUIDMap: new Map(), // map of urls to array of study instance UIDs
Expand All @@ -37,13 +42,23 @@ const getMetaDataByURL = url => {
return _store.urls.find(metaData => metaData.url === url);
};

const getInstanceUrl = (url, prefix) => {
let modifiedUrl = prefix
? url.replace(
const getInstanceUrl = (url, prefix, bucket, bucketPrefix) => {
let modifiedUrl = url;

const schemaPresent = !!url.match(/^(dicomweb:|dicomzip:|wadouri:)/)
if (!schemaPresent) {
const filePath = url.split('studies/')[1];
modifiedUrl = `dicomweb:https://storage.googleapis.com/${bucket}/${
bucketPrefix ? bucketPrefix + '/' : ''
}studies/${filePath}`;
}

modifiedUrl = prefix
? modifiedUrl.replace(
'https://storage.googleapis.com',
`https://storage.googleapis.com/${prefix}`
)
: url;
: modifiedUrl;

const dicomwebRegex = /^dicomweb:/
modifiedUrl = modifiedUrl.includes(":zip//")
Expand All @@ -53,13 +68,56 @@ const getInstanceUrl = (url, prefix) => {
return modifiedUrl;
}

const naturalizeMetadata = (metadata) => {
return {
...DicomMetaDictionary.naturalizeDataset(metadata),
CustomOffsetTable: metadata[GH_CUSTOM_TAGS.CustomOffsetTable]?.Value,
CustomOffsetTableLengths:
metadata[GH_CUSTOM_TAGS.CustomOffsetTableLengths]?.Value,
};
};

const mergeInstanceProperties = (instance) => {
return {
...instance.metadata,
...(instance.headers.start_byte &&
instance.headers.end_byte && {
FileOffsets: {
startByte: instance.headers.start_byte,
endByte: instance.headers.end_byte,
},
}),
};
};

const getProperty = (serieMetadata, property) => {
return (
serieMetadata[property] || serieMetadata.instances[0].metadata[property]
);
};

const getMetadataFromRows = (rows, prefix, seriesuidArray) => {
const getMetadataFromRows = (data, prefix, seriesuidArray) => {
const rows = data.flatMap(({ metadata }) =>
metadata.map((seriesMetadata) => ({
...seriesMetadata,
instances: seriesMetadata.instances.map((instance) => ({
...instance,
metadata: naturalizeMetadata(instance.metadata),
url: instance.url || instance.uri,
})),
}))
);
const bucketMap = data.reduce(
(dataMap, { bucket, bucketPrefix, metadata }) => {
metadata.forEach(({ instances }) =>
instances.forEach(({ url, uri }) => {
dataMap[url || uri] = { bucket, bucketPrefix };
})
);
return dataMap;
},
{}
);
// TODO: bq should not have dups
let filteredRows = rows.map(row => {
row.instances = _.uniqBy(row.instances, (x)=>x.url)
Expand All @@ -74,7 +132,7 @@ const getMetadataFromRows = (rows, prefix, seriesuidArray) => {

const rowsByStudy = Object.values(
filteredRows.reduce((rowsByStudy, row) => {
const studyuid = row['StudyInstanceUID'];
const studyuid = getProperty(row, 'StudyInstanceUID');
if (!rowsByStudy[studyuid]) rowsByStudy[studyuid] = [];
rowsByStudy[studyuid].push(row);
return rowsByStudy;
Expand All @@ -88,20 +146,27 @@ const getMetadataFromRows = (rows, prefix, seriesuidArray) => {

const series = rows.map(row => {
return {
SeriesInstanceUID: row['SeriesInstanceUID'],
Modality: row['Modality'],
SeriesDescription: row['SeriesDescription'] || 'No description',
StudyInstanceUID: row['StudyInstanceUID'],
SeriesNumber: row['SeriesNumber'],
SeriesDate: row['SeriesDate'],
SeriesTime: row['SeriesTime'],
NumInstances: isNaN(parseInt(row['NumInstances']))
SeriesInstanceUID: getProperty(row, 'SeriesInstanceUID'),
Modality: getProperty(row, 'Modality'),
SeriesDescription:
getProperty(row, 'SeriesDescription') || 'No description',
StudyInstanceUID: getProperty(row, 'StudyInstanceUID'),
SeriesNumber: getProperty(row, 'SeriesNumber'),
SeriesDate: getProperty(row, 'SeriesDate'),
SeriesTime: getProperty(row, 'SeriesTime'),
NumInstances: isNaN(parseInt(getProperty(row, 'NumInstances')))
? 0
: parseInt(row['NumInstances']),
instances: row['instances'].map(instance => {
: parseInt(getProperty(row, 'NumInstances')),
instances: row['instances'].map((instance) => {
const url = instance.url;
return {
metadata: instance.metadata,
url: getInstanceUrl(instance.url, prefix),
metadata: mergeInstanceProperties(instance),
url: getInstanceUrl(
url,
prefix,
bucketMap[url].bucket,
bucketMap[url].bucketPrefix
),
};
}),
};
Expand Down Expand Up @@ -195,7 +260,7 @@ const filesFromStudyInstanceUID = async ({bucketName, prefix, studyuids, headers
const files = res.items || [];
const folders = res.prefixes || [];
const series = folders.map(async (folderPath)=>{
const objectName = `${folderPath}metadata`;
const objectName = `${folderPath}metadata.json`;
const apiUrl = `https://storage.googleapis.com/storage/v1/b/${bucketName}/o/${encodeURIComponent(objectName)}?alt=media`;
const response = await fetch(apiUrl, { headers });
return response.json()
Expand Down Expand Up @@ -313,7 +378,7 @@ const storeDicomSeg = async (naturalizedReport, headers, displaySetService) => {
const compressedFile = pako.gzip(JSON.stringify(segSeries));

return fetch(
`https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/metadata&contentEncoding=gzip`,
`https://storage.googleapis.com/upload/storage/v1/b/${segBucket}/o?uploadType=media&name=${segPrefix}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/metadata.json&contentEncoding=gzip`,
{
method: 'POST',
headers: {
Expand Down Expand Up @@ -381,14 +446,20 @@ function createDicomJSONApi(dicomJsonConfig, servicesManager) {

const studyMetadata = [];
for (let i = 0; i < buckets.length; i++) {
const bucket = buckets[i],
bucketPrefix = query.get('bucket-prefix') || 'dicomweb';
const metadataPerBucket = await filesFromStudyInstanceUID({
bucketName: buckets[i],
prefix: query.get('bucket-prefix') || 'dicomweb',
bucketName: bucket,
prefix: bucketPrefix,
studyuids: query.getAll('StudyInstanceUID'),
headers: UserAuthenticationService.getAuthorizationHeader(),
});

studyMetadata.push(...metadataPerBucket);
studyMetadata.push({
bucket,
bucketPrefix,
metadata: metadataPerBucket.flatMap(e=>e),
});
}

const data = getMetadataFromRows(
Expand Down