upload_scans_new_project.py

#!/usr/bin/env python

# Script written by Lorena Escudero (Department of Radiology, University of Cambridge) 
# to upload in batch .zip files containing scans - April 2020 
#
# Usage: edit xnathost/project/user and give as input a .txt file containing a line per patient+session
# in the form  'subject_id:session_id:/path/to/scans.zip' 
#
# Based on xnatpy/examples/upload_data.py

import xnat
import os
import getpass

def upload_scans(session, project_id, subject_id, experiment_id, scans_path):
    xnat_project = session.projects[project_id]
    # We create the subject with the following line: 
    xnat_subject = session.classes.SubjectData(parent=xnat_project, label=subject_id)
    # And now we upload with the import_ method - the experiment will be created in this step
    session.services.import_dir(scans_path,overwrite=None, quarantine=False, destination='/archive', trigger_pipelines=None,project=project_id, subject=subject_id, experiment=experiment_id)
 
# ---------------------------------------------------------------------------------------------------------------------   

if __name__ == '__main__':

    xnathost   = 'URL'
    project_id = 'NEW_PROJECT'
    
    user_id    = 'USER'
    pwd        = getpass.getpass("Password for user name : %s = " % user_id)
    
    input_path = '/path/to/anon/files/old/project'
    
    subjects = os.listdir(input_path)
    with xnat.connect(xnathost, user=user_id, password=pwd) as session:
    
        for subject in subjects:
            subject_id = subject
            experiment_id = subject
            scans_path = input_path + os.sep + subject + '/DICOM/'
            
            upload_scans(session, project_id, subject_id, experiment_id, scans_path)