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feat(WADO) Allow WADO / QIDO requests to originate from client (#222)

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This commit is contained in:
Erik Ziegler authored and GitHub committed 2018-07-17 13:03:36 +02:00
1 parent 92408d4c86
commit ebe0a40f3e
43 files changed
+519 -571
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Packages/ohif-studies/imports/server/index.js
-1
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@@ -1,3 +1,2 @@
import './lib';
import './methods';
import './services';
Packages/ohif-studies/imports/server/lib/encodeQueryData.js
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@@ -1,18 +0,0 @@
/**
* Converts the properties to URL query parameters. Based on:
* http://stackoverflow.com/questions/111529/create-query-parameters-in-javascript
*
* @param data
* @returns {string}
*/
encodeQueryData = function(data) {
var ret = [];
for (var d in data) {
if (data[d]) {
ret.push(encodeURIComponent(d) + '=' + encodeURIComponent(data[d]));
}
}
return ret.join('&');
};
Packages/ohif-studies/imports/server/lib/index.js
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@@ -1 +0,0 @@
import './encodeQueryData.js';
Packages/ohif-studies/imports/server/lib/parseFloatArray.js
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export const parseFloatArray = function(obj) {
var result = [];
if (!obj) {
return result;
}
var objs = obj.split("\\");
for (var i = 0; i < objs.length; i++) {
result.push(parseFloat(objs[i]));
}
return result;
};
Packages/ohif-studies/imports/server/services/dimse/instances.js
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@@ -5,6 +5,7 @@ import { OHIF } from 'meteor/ohif:core';
* an array of series that are present in the study
*
* @param resultData
* @param studyInstanceUid
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(resultData, studyInstanceUid) {
Packages/ohif-studies/imports/server/services/dimse/retrieveMetadata.js
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@@ -1,5 +1,5 @@
import { OHIF } from 'meteor/ohif:core';
import { parseFloatArray } from 'meteor/ohif:studies/imports/server/lib/parseFloatArray';
import { parseFloatArray } from 'meteor/ohif:studies/imports/both/lib/parseFloatArray';
/**
* Returns the value of the element (e.g. '00280009')
Packages/ohif-studies/imports/server/services/index.js
-5
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@@ -1,10 +1,5 @@
import './namespace.js';
// DICOMWeb instance, study, and metadata retrieval
import './qido/instances.js';
import './qido/studies.js';
import './wado/retrieveMetadata.js';
// DIMSE instance, study, and metadata retrieval
import './dimse/instances.js';
import './dimse/studies.js';
Packages/ohif-studies/imports/server/services/namespace.js
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@@ -1,8 +1,3 @@
import { OHIF } from 'meteor/ohif:core';
const Services = {};
Services.QIDO = {};
Services.WADO = {};
Services.DIMSE = {};
OHIF.studies.services = Services;
OHIF.studies.services.DIMSE = {};
Packages/ohif-studies/imports/server/services/qido/instances.js
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import { OHIF } from 'meteor/ohif:core';
/**
* Creates a QIDO URL given the server settings and a study instance UID
* @param server
* @param studyInstanceUid
* @returns {string} URL to be used for QIDO calls
*/
function buildUrl(server, studyInstanceUid) {
return server.qidoRoot + '/studies/' + studyInstanceUid + '/instances';
}
/**
* Parses data returned from a QIDO search and transforms it into
* an array of series that are present in the study
*
* @param server The DICOM server
* @param studyInstanceUid
* @param resultData
* @returns {Array} Series List
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
resultData.forEach(function(instance) {
// Use seriesMap to cache series data
// If the series instance UID has already been used to
// process series data, continue using that series
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
var series = seriesMap[seriesInstanceUid];
// If no series data exists in the seriesMap cache variable,
// process any available series data
if (!series) {
series = {
seriesInstanceUid: seriesInstanceUid,
seriesNumber: DICOMWeb.getString(instance['00200011']),
instances: []
};
// Save this data in the seriesMap cache variable
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
// The uri for the dicomweb
// NOTE: DCM4CHEE seems to return the data zipped
// NOTE: Orthanc returns the data with multi-part mime which cornerstoneWADOImageLoader doesn't
// know how to parse yet
//var uri = DICOMWeb.getString(instance['00081190']);
//uri = uri.replace('wado-rs', 'dicom-web');
// manually create a WADO-URI from the UIDs
// NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + '&contentType=application%2Fdicom';
// Add this instance to the current series
series.instances.push({
sopClassUid: DICOMWeb.getString(instance['00080016']),
sopInstanceUid: sopInstanceUid,
uri: uri,
instanceNumber: DICOMWeb.getString(instance['00200013'])
});
});
return seriesList;
}
/**
* Retrieve a set of instances using a QIDO call
* @param server
* @param studyInstanceUid
* @throws ECONNREFUSED
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
*/
OHIF.studies.services.QIDO.Instances = function(server, studyInstanceUid) {
var url = buildUrl(server, studyInstanceUid);
try {
var result = DICOMWeb.getJSON(url, server.requestOptions);
return {
wadoUriRoot: server.wadoUriRoot,
studyInstanceUid: studyInstanceUid,
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
};
} catch (error) {
OHIF.log.trace();
throw error;
}
};
Packages/ohif-studies/imports/server/services/qido/studies.js
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import { OHIF } from 'meteor/ohif:core';
/**
* Creates a QIDO date string for a date range query
* Assumes the year is positive, at most 4 digits long.
*
* @param date The Date object to be formatted
* @returns {string} The formatted date string
*/
function dateToString(date) {
if (!date) return '';
let year = date.getFullYear().toString();
let month = (date.getMonth() + 1).toString();
let day = date.getDate().toString();
year = '0'.repeat(4 - year.length).concat(year);
month = '0'.repeat(2 - month.length).concat(month);
day = '0'.repeat(2 - day.length).concat(day);
return ''.concat(year, month, day);
}
/**
* Produces a QIDO URL given server details and a set of specified search filter
* items
*
* @param server
* @param filter
* @returns {string} The URL with encoded filter query data
*/
function filterToQIDOURL(server, filter) {
const commaSeparatedFields = [
'00081030', // Study Description
'00080060' //Modality
// Add more fields here if you want them in the result
].join(',');
const parameters = {
PatientName: filter.patientName,
PatientID: filter.patientId,
AccessionNumber: filter.accessionNumber,
StudyDescription: filter.studyDescription,
ModalitiesInStudy: filter.modalitiesInStudy,
limit: filter.limit,
includefield: server.qidoSupportsIncludeField ? 'all' : commaSeparatedFields
};
// build the StudyDate range parameter
if (filter.studyDateFrom || filter.studyDateTo) {
const dateFrom = dateToString(new Date(filter.studyDateFrom));
const dateTo = dateToString(new Date(filter.studyDateTo));
parameters.StudyDate = `${dateFrom}-${dateTo}`;
}
// Build the StudyInstanceUID parameter
if (filter.studyInstanceUid) {
let studyUids = filter.studyInstanceUid;
studyUids = Array.isArray(studyUids) ? studyUids.join() : studyUids;
studyUids = studyUids.replace(/[^0-9.]+/g, '\\');
parameters.StudyInstanceUID = studyUids;
}
return server.qidoRoot + '/studies?' + encodeQueryData(parameters);
}
/**
* Parses resulting data from a QIDO call into a set of Study MetaData
*
* @param resultData
* @returns {Array} An array of Study MetaData objects
*/
function resultDataToStudies(resultData) {
const studies = [];
if (!resultData || !resultData.length) return;
resultData.forEach(study => studies.push({
studyInstanceUid: DICOMWeb.getString(study['0020000D']),
// 00080005 = SpecificCharacterSet
studyDate: DICOMWeb.getString(study['00080020']),
studyTime: DICOMWeb.getString(study['00080030']),
accessionNumber: DICOMWeb.getString(study['00080050']),
referringPhysicianName: DICOMWeb.getString(study['00080090']),
// 00081190 = URL
patientName: DICOMWeb.getName(study['00100010']),
patientId: DICOMWeb.getString(study['00100020']),
patientBirthdate: DICOMWeb.getString(study['00100030']),
patientSex: DICOMWeb.getString(study['00100040']),
studyId: DICOMWeb.getString(study['00200010']),
numberOfStudyRelatedSeries: DICOMWeb.getString(study['00201206']),
numberOfStudyRelatedInstances: DICOMWeb.getString(study['00201208']),
studyDescription: DICOMWeb.getString(study['00081030']),
// modality: DICOMWeb.getString(study['00080060']),
// modalitiesInStudy: DICOMWeb.getString(study['00080061']),
modalities: DICOMWeb.getString(DICOMWeb.getModalities(study['00080060'], study['00080061']))
}));
return studies;
}
OHIF.studies.services.QIDO.Studies = (server, filter) => {
const url = filterToQIDOURL(server, filter);
try {
const result = DICOMWeb.getJSON(url, server.requestOptions);
return resultDataToStudies(result.data);
} catch (error) {
OHIF.log.trace();
throw error;
}
};
Packages/ohif-studies/imports/server/services/wado/retrieveMetadata.js
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import { OHIF } from 'meteor/ohif:core';
import { parseFloatArray } from '../../lib/parseFloatArray';
/**
* Simple cache schema for retrieved color palettes.
*/
const paletteColorCache = {
count: 0,
maxAge: 24 * 60 * 60 * 1000, // 24h cache?
entries: {},
isValidUID: function (paletteUID) {
return typeof paletteUID === 'string' && paletteUID.length > 0;
},
get: function (paletteUID) {
let entry = null;
if (this.entries.hasOwnProperty(paletteUID)) {
entry = this.entries[paletteUID];
// check how the entry is...
if ((Date.now() - entry.time) > this.maxAge) {
// entry is too old... remove entry.
delete this.entries[paletteUID];
this.count--;
entry = null;
}
}
return entry;
},
add: function (entry) {
if (this.isValidUID(entry.uid)) {
let paletteUID = entry.uid;
if (this.entries.hasOwnProperty(paletteUID) !== true) {
this.count++; // increment cache entry count...
}
entry.time = Date.now();
this.entries[paletteUID] = entry;
// @TODO: Add logic to get rid of old entries and reduce memory usage...
}
}
};
/**
* Creates a URL for a WADO search
*
* @param server
* @param studyInstanceUid
* @returns {string}
*/
function buildUrl(server, studyInstanceUid) {
return server.wadoRoot + '/studies/' + studyInstanceUid + '/metadata';
}
/** Returns a WADO url for an instance
*
* @param studyInstanceUid
* @param seriesInstanceUid
* @param sopInstanceUid
* @returns {string}
*/
function buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
const params = [];
params.push('requestType=WADO');
params.push(`studyUID=${studyInstanceUid}`);
params.push(`seriesUID=${seriesInstanceUid}`);
params.push(`objectUID=${sopInstanceUid}`);
params.push('contentType=application/dicom');
params.push('transferSyntax=*');
const paramString = params.join('&');
const uri = encodeURIComponent(paramString);
return `${server.wadoUriRoot}?${uri}`;
}
function buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid) {
return `${server.wadoRoot}/studies/${studyInstanceUid}/series/${seriesInstanceUid}/instances/${sopInstanceUid}`
}
function buildInstanceFrameWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid, frame) {
const baseWadoRsUri = buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
frame = frame != null || 1;
return `${baseWadoRsUri}/frames/${frame}`
}
/**
* Parses the SourceImageSequence, if it exists, in order
* to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
* is used to refer to this image in any accompanying DICOM-SR documents.
*
* @param instance
* @returns {String} The ReferenceSOPInstanceUID
*/
function getSourceImageInstanceUid(instance) {
// TODO= Parse the whole Source Image Sequence
// This is a really poor workaround for now.
// Later we should probably parse the whole sequence.
var SourceImageSequence = instance['00082112'];
if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
return SourceImageSequence.Value[0]['00081155'].Value[0];
}
}
function getPaletteColor(server, instance, tag, lutDescriptor) {
const lut = [];
const numLutEntries = lutDescriptor[0];
const bits = lutDescriptor[2];
const uri = WADOProxy.convertURL(instance[tag].BulkDataURI, server)
const data = DICOMWeb.getBulkData(uri);
for (var i = 0; i < numLutEntries; i++) {
if(bits === 16) {
lut[i] = data.readUInt16LE(i*2);
} else {
lut[i] = data.readUInt8(i);
}
}
return lut;
}
/**
* Fetch palette colors for instances with "PALETTE COLOR" photometricInterpretation.
*
* @param server {Object} Current server;
* @param instance {Object} The retrieved instance metadata;
* @returns {String} The ReferenceSOPInstanceUID
*/
function getPaletteColors(server, instance, lutDescriptor) {
let entry = null,
paletteUID = DICOMWeb.getString(instance['00281199']);
if (paletteColorCache.isValidUID(paletteUID)) {
entry = paletteColorCache.get(paletteUID);
} else {
paletteUID = null;
}
if (!entry) {
// no entry on cache... Fetch remote data.
try {
let r, g, b;
r = getPaletteColor(server, instance, '00281201', lutDescriptor);
g = getPaletteColor(server, instance, '00281202', lutDescriptor);;
b = getPaletteColor(server, instance, '00281203', lutDescriptor);;
entry = { red: r, green: g, blue: b };
if (paletteUID !== null) {
// when paletteUID is present, the entry can be cached...
entry.uid = paletteUID;
paletteColorCache.add(entry);
}
} catch (error) {
OHIF.log.error(`(${error.name}) ${error.message}`);
}
}
return entry;
}
function getFrameIncrementPointer(element) {
const frameIncrementPointerNames = {
'00181065': 'frameTimeVector',
'00181063': 'frameTime'
};
if(!element || !element.Value || !element.Value.length) {
return;
}
const value = element.Value[0];
return frameIncrementPointerNames[value];
}
function getRadiopharmaceuticalInfo(instance) {
const modality = DICOMWeb.getString(instance['00080060']);
if (modality !== 'PT') {
return;
}
const radiopharmaceuticalInfo = instance['00540016'];
if ((radiopharmaceuticalInfo === undefined) || !radiopharmaceuticalInfo.Value || !radiopharmaceuticalInfo.Value.length) {
return;
}
const firstPetRadiopharmaceuticalInfo = radiopharmaceuticalInfo.Value[0];
return {
radiopharmaceuticalStartTime: DICOMWeb.getString(firstPetRadiopharmaceuticalInfo['00181072']),
radionuclideTotalDose: DICOMWeb.getNumber(firstPetRadiopharmaceuticalInfo['00181074']),
radionuclideHalfLife: DICOMWeb.getNumber(firstPetRadiopharmaceuticalInfo['00181075'])
};
}
/**
* Parses result data from a WADO search into Study MetaData
* Returns an object populated with study metadata, including the
* series list.
*
* @param server
* @param studyInstanceUid
* @param resultData
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
var seriesMap = {};
var seriesList = [];
if (!resultData.length) {
return;
}
var anInstance = resultData[0];
if (!anInstance) {
return;
}
var studyData = {
seriesList: seriesList,
patientName: DICOMWeb.getName(anInstance['00100010']),
patientId: DICOMWeb.getString(anInstance['00100020']),
patientAge: DICOMWeb.getNumber(anInstance['00101010']),
patientSize: DICOMWeb.getNumber(anInstance['00101020']),
patientWeight: DICOMWeb.getNumber(anInstance['00101030']),
accessionNumber: DICOMWeb.getString(anInstance['00080050']),
studyDate: DICOMWeb.getString(anInstance['00080020']),
modalities: DICOMWeb.getString(anInstance['00080061']),
studyDescription: DICOMWeb.getString(anInstance['00081030']),
imageCount: DICOMWeb.getString(anInstance['00201208']),
studyInstanceUid: DICOMWeb.getString(anInstance['0020000D']),
institutionName: DICOMWeb.getString(anInstance['00080080'])
};
resultData.forEach(function(instance) {
var seriesInstanceUid = DICOMWeb.getString(instance['0020000E']);
var series = seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesDescription: DICOMWeb.getString(instance['0008103E']),
modality: DICOMWeb.getString(instance['00080060']),
seriesInstanceUid: seriesInstanceUid,
seriesNumber: DICOMWeb.getNumber(instance['00200011']),
seriesDate: DICOMWeb.getString(instance['00080021']),
seriesTime: DICOMWeb.getString(instance['00080031']),
instances: []
};
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
const wadouri = buildInstanceWadoUrl(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
const baseWadoRsUri = buildInstanceWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
const wadorsuri = buildInstanceFrameWadoRsUri(server, studyInstanceUid, seriesInstanceUid, sopInstanceUid);
var instanceSummary = {
imageType: DICOMWeb.getString(instance['00080008']),
sopClassUid: DICOMWeb.getString(instance['00080016']),
modality: DICOMWeb.getString(instance['00080060']),
sopInstanceUid: sopInstanceUid,
instanceNumber: DICOMWeb.getNumber(instance['00200013']),
imagePositionPatient: DICOMWeb.getString(instance['00200032']),
imageOrientationPatient: DICOMWeb.getString(instance['00200037']),
frameOfReferenceUID: DICOMWeb.getString(instance['00200052']),
sliceLocation: DICOMWeb.getNumber(instance['00201041']),
samplesPerPixel: DICOMWeb.getNumber(instance['00280002']),
photometricInterpretation: DICOMWeb.getString(instance['00280004']),
planarConfiguration: DICOMWeb.getNumber(instance['00280006']),
rows: DICOMWeb.getNumber(instance['00280010']),
columns: DICOMWeb.getNumber(instance['00280011']),
pixelSpacing: DICOMWeb.getString(instance['00280030']),
pixelAspectRatio: DICOMWeb.getString(instance['00280034']),
bitsAllocated: DICOMWeb.getNumber(instance['00280100']),
bitsStored: DICOMWeb.getNumber(instance['00280101']),
highBit: DICOMWeb.getNumber(instance['00280102']),
pixelRepresentation: DICOMWeb.getNumber(instance['00280103']),
smallestPixelValue: DICOMWeb.getNumber(instance['00280106']),
largestPixelValue: DICOMWeb.getNumber(instance['00280107']),
windowCenter: DICOMWeb.getString(instance['00281050']),
windowWidth: DICOMWeb.getString(instance['00281051']),
rescaleIntercept: DICOMWeb.getNumber(instance['00281052']),
rescaleSlope: DICOMWeb.getNumber(instance['00281053']),
rescaleType: DICOMWeb.getNumber(instance['00281054']),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: DICOMWeb.getString(instance['00200062']),
viewPosition: DICOMWeb.getString(instance['00185101']),
acquisitionDateTime: DICOMWeb.getString(instance['0008002A']),
numberOfFrames: DICOMWeb.getNumber(instance['00280008']),
frameIncrementPointer: getFrameIncrementPointer(instance['00280009']),
frameTime: DICOMWeb.getNumber(instance['00181063']),
frameTimeVector: parseFloatArray(DICOMWeb.getString(instance['00181065'])),
sliceThickness: DICOMWeb.getNumber(instance['00180050']),
lossyImageCompression: DICOMWeb.getString(instance['00282110']),
derivationDescription: DICOMWeb.getString(instance['00282111']),
lossyImageCompressionRatio: DICOMWeb.getString(instance['00282112']),
lossyImageCompressionMethod: DICOMWeb.getString(instance['00282114']),
echoNumber: DICOMWeb.getString(instance['00180086']),
contrastBolusAgent: DICOMWeb.getString(instance['00180010']),
radiopharmaceuticalInfo: getRadiopharmaceuticalInfo(instance),
baseWadoRsUri: baseWadoRsUri,
wadouri: WADOProxy.convertURL(wadouri, server),
wadorsuri: WADOProxy.convertURL(wadorsuri, server),
imageRendering: server.imageRendering,
thumbnailRendering: server.thumbnailRendering
};
// Get additional information if the instance uses "PALETTE COLOR" photometric interpretation
if (instanceSummary.photometricInterpretation === 'PALETTE COLOR') {
const redPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281101']));
const greenPaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281102']));
const bluePaletteColorLookupTableDescriptor = parseFloatArray(DICOMWeb.getString(instance['00281103']));
const palettes = getPaletteColors(server, instance, redPaletteColorLookupTableDescriptor);
if (palettes) {
if (palettes.uid) {
instanceSummary.paletteColorLookupTableUID = palettes.uid;
}
instanceSummary.redPaletteColorLookupTableData = palettes.red;
instanceSummary.greenPaletteColorLookupTableData = palettes.green;
instanceSummary.bluePaletteColorLookupTableData = palettes.blue;
instanceSummary.redPaletteColorLookupTableDescriptor = redPaletteColorLookupTableDescriptor;
instanceSummary.greenPaletteColorLookupTableDescriptor = greenPaletteColorLookupTableDescriptor;
instanceSummary.bluePaletteColorLookupTableDescriptor = bluePaletteColorLookupTableDescriptor;
}
}
series.instances.push(instanceSummary);
});
return studyData;
}
/**
* Retrieved Study MetaData from a DICOM server using a WADO call
* @param server
* @param studyInstanceUid
* @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
*/
OHIF.studies.services.WADO.RetrieveMetadata = function(server, studyInstanceUid) {
var url = buildUrl(server, studyInstanceUid);
try {
var result = DICOMWeb.getJSON(url, server.requestOptions);
var study = resultDataToStudyMetadata(server, studyInstanceUid, result.data);
if (!study) {
study = {};
}
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
return study;
} catch (error) {
OHIF.log.trace();
throw error;
}
};