Use xnat-rest API with this package.
npm install xnat-rest To test this package please download some DICOM files to your directory and modify the test.js script with the folder name. This package was tested with data available at archive.org
Run all tests with
npm test To write your own application and query XNAT Rest API
var xnat = require('xnat-rest'); xnat.start() .then(function(){ //Do operations with XNAT REST points }) .catch(function(err){ console.error("Login failed") });The following operations are supported by this library
xnat.useDCMExtensionOn() xnat.useDCMExtensionOff() xnat.setUseDCMExtension(bool); xnat.setAgentOptions(agentOptions);//Object to pass to the request library documentation is here https://github.com/request/request xnat.setXnatUrl(url);//url = http://localhost:8080/xnat for example xnat.getXnatUrl(); xnat.login(user);//Object with {"user":"username","password":"yourpass"} given to the request lib documentation also in the 'auth' section https://github.com/request/request xnat.dicomDump(filename); xnat.getProjects(); xnat.getSubjects(projectid, subjectid); xnat.getExperiments(projectid); xnat.getSubject(projectid, subjectid); xnat.setSubject(projectid, subjectid, params); xnat.setExperiment(projectid, subjectid, experimentid, params); xnat.getSubjectData(projectid, subjectid); xnat.getSubjectFiles(projectid, subjectid); xnat.getSubjectExperiments(projectid, subjectid); xnat.getSubjectExperiment(projectid, subjectid, experimentid); xnat.getSubjectSession(projectid, subjectid, sessionid); xnat.createSubject(projectid, subjectid); xnat.uploadImage(projectid, subjectid, experimentid, filename); xnat.uploadConvertedImage(projectid, subjectid, experimentid, scanid, filename); xnat.copyResource(projectid, source_subjectid, source_experimentid, source_scanid, source_resourceid, source_filename, dest_subjectid, dest_experimentid, dest_scanid, dest_resourceid, dest_filename); xnat.moveResource(projectid, source_subjectid, source_experimentid, source_scanid, source_resourceid, source_filename, dest_subjectid, dest_experimentid, dest_scanid, dest_resourceid, dest_filename); xnat.deleteResourceFile(projectid, subjectid, experimentid, scanid, resourceid, filename); xnat.createResources(projectid, subjectid, experimentid, scanid, resourceName); xnat.getResourceFiles(projectid, subjectid, experimentid, scanid, resource); xnat.getResources(projectid, subjectid, experimentid, scanid); xnat.uploadResourceFile(projectid, subjectid, experimentid, scanid, resourceid, filename); xnat.search(id); xnat.deleteConvertedImage(projectid, subjectid, experimentid, scanid, filename); xnat.getScanFiles(projectid, subjectid, experimentid, scanid); xnat.getScans(projectid, subjectid, experimentid); xnat.deleteFile(uri); xnat.triggerPipelines(projectid, subjectid, experimentid); xnat.prearchive(); xnat.logout(); xnat.findFiles(directory); xnat.promptUsernamePassword(); xnat.promptXnatUrl(); xnat.writeConfFile(conf); xnat.setScanQualityLabels(projectid, labelfilename); xnat.upload(); xnat.importConverted(); xnat.deleteConverted(); xnat.changeSubjectLabel(); xnat.setXnatUrlAndLogin(server, promptlogin);To upload files using this library create a file (index.js) and add:
var xnat = require('xnat-rest'); xnat.upload();Usage: node index.js -d <directory> -p <project id> Options: -d <DICOM directory>, directory with DICOM files. -p <project id>, project id in XNAT to upload the files. --pid <patient id>, If patient id is specified, the patient id won't be extracted from the DICOM file. --sessid <session id>, If session id is specified, the session id won't be extracted from the DICOM file. --server <server url>, XNAT server url. When server is set, the user will be prompted for username and password --prompt , If set, forces prompt for login information again. It will use the previous server URL saved in the configuration file The function 'xnat.start()' will prompt for the xnat url, e.x., 'http://yourserver.com/xnat', then for username and password You can then query and do operations on your xnat instance after that.
const Promise = require('bluebird'); const _ = require('underscore'); const xnat = require('xnat-rest'); var projectid = "YourProjectId"; var subjectid = "SomeSubjectId"; var sessionid = "SomeSessionId"; xnat.start() .then(function(){ return xnat.getSubjectExperiment(projectid, subjectid, sessionid); }) .then(function(result){ console.log(result); });const xnat = require('xnat-rest'); const _ = require('underscore'); const Promise = require('bluebird'); var projectid = "YourProjectId"; var subjectid = "SomeSubjectId"; var sessionid = "SomeSessionId"; xnat.getSubjectExperiment(projectid, subjectid, sessionid) .then(function(res){ //This will give you the id of the acquired images in that session var scan = []; _.each(res.items, function(item){ _.each(item.children, function(children){ _.each(children.items, function(items){ scan.push(items.data_fields); }); }); }); return scan; }) .then(function(scan_items_data_fields){ //This gives you ALL the available images for a given session // /data/archive/projects/{ID}/subjects/{ID | label}/experiments/{ID | label}/scans/{ID}/files return Promise.map(scan_items_data_fields, function(data_fields){ return xnat.getScanFiles(projectid, subjectid, sessionid, data_fields.ID); }) .then(function(res){ //to have a flat array with all the available files return _.flatten(res); }); }) .then(function(scan_files){ return Promise.map(scan_files, function(files){ return xnat.getFileStream(files.URI) .then(function(fstream){ // Do something with stream, pipe, write etc.. }); });Create a script with the following code
const xnat = require('xnat-rest'); xnat.upload();Call your script
node yourscript.js -d /path/to/dicom/directory -p ProjectIdInXNATvar user = { user: "username", password: "password" } xnat.login(user) .then(function(){ console.log("User is logged in.") }) .catch(function(err){ console.error("Login failed") });xnat.dicomDump(filename) .then(function(jsonfile){ console.log(jsonfile); });Get projects from xnat in json format
xnat.getProjects() .then(function(projects){ console.log(projects); })Optional parameters are projectid and subjectid.
xnat.getSubjects(projectid, subjectid) .then(function(subjects){ console.log(subjects); });Required parameters when using function getSubject
xnat.getSubject(projectid, subjectid) .then(function(subject){ console.log(subject); });Get XNAT experiments, projectid is optional
xnat.getExperiments(projectid) .then(function(experiments){ console.log(experiments); });xnat.createSubject(projectid, subjectid) .then(function(res){ console.log(res); })xnat.uploadImage(projectid, subjectid, sessionid, filename) .then(function(res){ console.log(res); })xnat.logout() .then(function(){ console.log("logout"); })