xnat-rest

Implement the operations to communicate with xnat via REST api

Usage no npm install needed!

<script type="module">
  import xnatRest from 'https://cdn.skypack.dev/xnat-rest';
</script>

README

xnat-rest

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

Usage:

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();

Help:

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

Documentation:

Usage simplified:

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);
    });

Get all images from a given session

    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..
            });
    });

Upload a dicom directory to xnat

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 ProjectIdInXNAT

User login to xnat instance:


    var user = {
        user: "username",
        password: "password"
    }

    xnat.login(user)
    .then(function(){
        console.log("User is logged in.")
    })
    .catch(function(err){
        console.error("Login failed")
    });

Dump dicom file in JSON format

    xnat.dicomDump(filename)
    .then(function(jsonfile){
        console.log(jsonfile);
    });

Get XNAT projects

Get projects from xnat in json format

    xnat.getProjects()
    .then(function(projects){
        console.log(projects);
    })

Get XNAT subjects

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

Get XNAT experiments, projectid is optional

    xnat.getExperiments(projectid)
    .then(function(experiments){
        console.log(experiments);
    });

Create subject

    xnat.createSubject(projectid, subjectid)
    .then(function(res){
        console.log(res);
    })

Upload dicom image

    xnat.uploadImage(projectid, subjectid, sessionid, filename)
    .then(function(res){
        console.log(res);
    })

Logout from xnat

    xnat.logout()
    .then(function(){
        console.log("logout");
    })