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chore(cleanup) Remove OrthancRemote service which is not being used

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This commit is contained in:
Erik Ziegler 2018-07-13 10:19:20 +02:00
parent f2c509b6af
commit 30ed1911fb
9 changed files with 0 additions and 421 deletions
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5
Packages/ohif-studies/imports/server/services/index.js
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@ -10,8 +10,3 @@ import './dimse/instances.js';
import './dimse/studies.js';
import './dimse/retrieveMetadata.js';
import './dimse/setup.js';
// Study, instance, and metadata retrieval from remote PACS via Orthanc as a proxy
import './remote/instances.js';
import './remote/studies.js';
import './remote/retrieveMetadata.js';

1
Packages/ohif-studies/imports/server/services/namespace.js
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@ -4,7 +4,6 @@ const Services = {};
Services.QIDO = {};
Services.WADO = {};
Services.DIMSE = {};
Services.REMOTE = {};
OHIF.studies.services = Services;

85
Packages/ohif-studies/imports/server/services/remote/instances.js
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@ -1,85 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
import { remoteGetValue } from '../../lib/remoteGetValue';
/**
* 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 = remoteGetValue(instance['0020,000e']);
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 : parseFloat(remoteGetValue(instance['0020,0011'])),
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 = remoteGetValue(instance['0008,0018']);
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: remoteGetValue(instance['0008,0016']),
sopInstanceUid: sopInstanceUid,
uri: uri,
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013']))
});
});
return seriesList;
}
/**
* Retrieve a set of instances using a QIDO call
* @param server
* @param studyInstanceUid
* @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
*/
OHIF.studies.services.REMOTE.Instances = function(server, studyInstanceUid) {
var parameters = {
PatientName: "",
PatientID: "",
AccessionNumber: "",
SeriesInstanceUID: "",
SeriesNumber : "",
SOPClassUID : "",
InstanceNumber : ""
};
var remote = new OrthancRemote(server.root, server.sourceAE);
return {
wadoUriRoot: server.wadoUriRoot,
studyInstanceUid: studyInstanceUid,
seriesList: resultDataToStudyMetadata(server, studyInstanceUid, remote.findInstances(server.modality, studyInstanceUid, null, parameters))
};
};

142
Packages/ohif-studies/imports/server/services/remote/retrieveMetadata.js
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@ -1,142 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
import { remoteGetValue } from '../../lib/remoteGetValue';
import { parseFloatArray } from '../../lib/parseFloatArray';
/**
* 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 = remoteGetValue(instance['0008,2112']);
if (SourceImageSequence && SourceImageSequence.Value && SourceImageSequence.Value.length) {
return SourceImageSequence.Value[0]['0008,1155'].Value[0];
}
}
/**
* 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: remoteGetValue(anInstance['0010,0010']),
patientId: remoteGetValue(anInstance['0010,0020']),
accessionNumber: remoteGetValue(anInstance['0008,0050']),
studyDate: remoteGetValue(anInstance['0008,0020']),
modalities: remoteGetValue(anInstance['0008,0061']),
studyDescription: remoteGetValue(anInstance['0008,1030']),
imageCount: remoteGetValue(anInstance['0020,1208']),
studyInstanceUid: remoteGetValue(anInstance['0020,000d'])
};
resultData.forEach(function(instance) {
var seriesInstanceUid = remoteGetValue(instance['0020,000e']);
var series = seriesMap[seriesInstanceUid];
if (!series) {
series = {
seriesDescription: remoteGetValue(instance['0008,103e']),
modality: remoteGetValue(instance['0008,0060']),
seriesInstanceUid: seriesInstanceUid,
seriesNumber: parseFloat(remoteGetValue(instance['0020,0011'])),
instances: []
};
seriesMap[seriesInstanceUid] = series;
seriesList.push(series);
}
var sopInstanceUid = remoteGetValue(instance['0008,0018']);
var instanceSummary = {
imageType: remoteGetValue(instance['0008,0008']),
sopClassUid: remoteGetValue(instance['0008,0016']),
sopInstanceUid: sopInstanceUid,
instanceNumber: parseFloat(remoteGetValue(instance['0020,0013'])),
imagePositionPatient: remoteGetValue(instance['0020,0032']),
imageOrientationPatient: remoteGetValue(instance['0020,0037']),
frameOfReferenceUID: remoteGetValue(instance['0020,0052']),
sliceLocation: parseFloat(remoteGetValue(instance['0020,1041'])),
samplesPerPixel: parseFloat(remoteGetValue(instance['0028,0002'])),
photometricInterpretation: remoteGetValue(instance['0028,0004']),
rows: parseFloat(remoteGetValue(instance['0028,0010'])),
columns: parseFloat(remoteGetValue(instance['0028,0011'])),
pixelSpacing: remoteGetValue(instance['0028,0030']),
bitsAllocated: parseFloat(remoteGetValue(instance['0028,0100'])),
bitsStored: parseFloat(remoteGetValue(instance['0028,0101'])),
highBit: parseFloat(remoteGetValue(instance['0028,0102'])),
pixelRepresentation: parseFloat(remoteGetValue(instance['0028,0103'])),
windowCenter: remoteGetValue(instance['0028,1050']),
windowWidth: remoteGetValue(instance['0028,1051']),
rescaleIntercept: parseFloat(remoteGetValue(instance['0028,1052'])),
rescaleSlope: parseFloat(remoteGetValue(instance['0028,1053'])),
sourceImageInstanceUid: getSourceImageInstanceUid(instance),
laterality: remoteGetValue(instance['0020,0062']),
viewPosition: remoteGetValue(instance['0018,5101']),
acquisitionDateTime: remoteGetValue(instance['0008,002A']),
numberOfFrames: parseFloat(remoteGetValue(instance['0028,0008'])),
frameIncrementPointer: remoteGetValue(instance['0028,0009']),
frameTime: parseFloat(remoteGetValue(instance['0018,1063'])),
frameTimeVector: parseFloatArray(remoteGetValue(instance['0018,1065'])),
echoNumber: remoteGetValue(instance['0018,0086']),
contrastBolusAgent: remoteGetValue(instance['0018,0010'])
};
var iid = instance['xxxx,0001'].Value;
if (server.imageRendering === 'wadouri') {
instanceSummary.wadouri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
} else if (server.imageRendering == 'orthanc') {
instanceSummary.wadouri = server.root + '/instances/' + iid + '/file';
} else {
instanceSummary.wadorsuri = server.wadoRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
}
series.instances.push(instanceSummary);
});
console.log(studyData.seriesList[0].instances);
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.REMOTE.RetrieveMetadata = function(server, studyInstanceUid) {
var remote = new OrthancRemote(server.root, server.sourceAE);
var study = resultDataToStudyMetadata(server, studyInstanceUid, remote.retrieveMetadata(server.modality, studyInstanceUid));
if (!study) {
study = {};
}
study.wadoUriRoot = server.wadoUriRoot;
study.studyInstanceUid = studyInstanceUid;
return study;
};

53
Packages/ohif-studies/imports/server/services/remote/studies.js
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@ -1,53 +0,0 @@
import { OHIF } from 'meteor/ohif:core';
import { remoteGetValue } from '../../lib/remoteGetValue';
function resultDataToStudies(resultData) {
const studies = [];
resultData.forEach(function(study) {
studies.push({
studyInstanceUid: remoteGetValue(study['0020,000d']),
// 00080005 = SpecificCharacterSet
studyDate: remoteGetValue(study['0008,0020']),
studyTime: remoteGetValue(study['0008,0030']),
accessionNumber: remoteGetValue(study['0008,0050']),
referringPhysicianName: remoteGetValue(study['0008,0090']),
// 00081190 = URL
patientName: remoteGetValue(study['0010,0010']),
patientId: remoteGetValue(study['0010,0020']),
patientBirthdate: remoteGetValue(study['0010,0030']),
patientSex: remoteGetValue(study['0010,0040']),
studyId: remoteGetValue(study['0020,0010']),
numberOfStudyRelatedSeries: parseFloat(remoteGetValue(study['0020,1206'])),
numberOfStudyRelatedInstances: parseFloat(remoteGetValue(study['0020,1208'])),
studyDescription: remoteGetValue(study['0008,1030']),
modalities: remoteGetValue(study['0008,0061'])
});
});
return studies;
}
OHIF.studies.services.REMOTE.Studies = function(server, filter) {
const parameters = {
studyInstanceUID: filter.studyInstanceUid || '',
PatientName: filter.patientName ? filter.patientName : '',
PatientID: filter.patientId,
AccessionNumber: filter.accessionNumber ? filter.accessionNumber : '',
StudyDescription: '',
StudyDate: '',
StudyTime: '',
ReferringPhysicianName: '',
PatientBirthDate: '',
PatientSex: '',
StudyID: '',
NumberOfStudyRelatedSeries: '',
NumberOfStudyRelatedInstances: '',
ModalitiesInStudy: ''
};
const remote = new OrthancRemote(server.root, server.sourceAE);
const data = remote.findStudies(server.modality, parameters);
return resultDataToStudies(data.results);
};

15
Packages/orthanc-remote/package.js
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@ -1,15 +0,0 @@
Package.describe({
name: "orthanc-remote",
summary: "Orthanc Remote",
version: '0.0.1'
});
Package.onUse(function (api) {
api.use("http");
api.addFiles('server/require.js', 'server');
api.addFiles('server/namespace.js', 'server');
api.addFiles('server/lib.js', 'server');
api.export("OrthancRemote", 'server');
});

115
Packages/orthanc-remote/server/lib.js
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@ -1,115 +0,0 @@
OrthancRemote.prototype.findStudies = function(modality, params) {
return this.query(modality, 'Study', params);
}
OrthancRemote.prototype.findSeries = function(modality, studyId, params) {
params = Object.assign({StudyInstanceUID : studyId || ''}, params);
return this.query(modality, 'Series', params);
}
OrthancRemote.prototype.findInstances = function(modality, studyId, seriesId, params) {
params = Object.assign({StudyInstanceUID : studyId || '', SeriesInstanceUID : seriesId || ''}, params);
return this.query(modality, 'Instance', params);
}
OrthancRemote.prototype.query = function(modality, level, params) {
var url = this.root + '/modalities/' + modality + '/query',
postData = {Level : level, Query : params || {}};
var result = HTTP.call('POST', url, {content : JSON.stringify(postData)});
return this.getAnswersFromQuery(result.data['ID']);
}
OrthancRemote.prototype.getAnswersFromQuery = function(id) {
var url = this.root + '/queries/' + id + '/answers',
result = HTTP.call('GET', url);
var resultCount = result.data.length, answers = [], i = 0;
while (i < resultCount) {
var contentUrl = this.root + '/queries/' + id + '/answers/' + result.data[i] + '/content';
//fetch the result
var contentResult = HTTP.call('GET', contentUrl);
answers.push(contentResult.data);
i++;
}
return {
query : id,
length : resultCount,
results : answers
};
}
OrthancRemote.prototype.retrieveAnswer = function(query, index) {
var retrieveUrl = this.root + '/queries/' + query + '/answers/' + index + '/retrieve';
var result = HTTP.call('POST', retrieveUrl, {content : this.localAE});
return result.data;
}
OrthancRemote.prototype.retrieveStudy = function(modality, studyInstanceUID) {
var id = this.findStudyID(studyInstanceUID);
if (id === null) {
//retrieve the study
console.log('RetrieveStudy', studyInstanceUID);
var result = this.findStudies(modality, {"StudyInstanceUID" : studyInstanceUID});
if (result.results.length < 1) {
throw new Meteor.Error(404, "No such study");
}
this.retrieveAnswer(result.query, 0);
//check again
id = this.findStudyID(studyInstanceUID);
if (id === null) {
throw new Meteor.Error(500, "Failed to retrieve remote study");
}
}
return id;
}
OrthancRemote.prototype.retrieveMetadata = function(modality, studyInstanceUID) {
var studyId = this.retrieveStudy(modality, studyInstanceUID),
instances = this.getInstancesByStudy(studyId);
var results = [], length = instances.length;
for (var i = 0;i < length;i++) {
var instanceId = instances[i].ID, metadata = this.getInstanceMetadata(instanceId);
metadata['xxxx,0001'] = {Value : instanceId};
results.push(metadata);
}
return results;
}
OrthancRemote.prototype.getInstancesByStudy = function(studyId) {
var url = this.root + '/studies/' + studyId + '/instances';
var result = this._getCall(url);
return result;
}
OrthancRemote.prototype.getInstanceMetadata = function(instanceId) {
var url = this.root + '/instances/' + instanceId + '/tags';
return this._getCall(url);
}
OrthancRemote.prototype.findStudyID = function(uid) {
var url = this.root + '/tools/lookup';
var result = HTTP.call('POST', url, {content : uid}), len = result.data.length;
for (var i = 0;i < len;i++) {
if (result.data[i].Type == 'Study') {
return result.data[i].ID;
}
}
return null;
}
OrthancRemote.prototype._getCall = function(url) {
return HTTP.call('GET', url).data;
}

4
Packages/orthanc-remote/server/namespace.js
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@ -1,4 +0,0 @@
OrthancRemote = function(root, localAE){
this.root = root || 'http://localhost:8042';
this.localAE = localAE || 'ORTHANCLOCAL';
};

1
Packages/orthanc-remote/server/require.js
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@ -1 +0,0 @@
//http = Npm.require("http");