Developing Python Rest API for downloading and uploading the Data into XNAT

Question

I am developing a python Rest API to XNAT for transferring the data locally or to server. I am trying to download all experiments(data format eg:CT,MR,ECOG,MEEG) those are associated with one subject of Project from XNAT to my local file system. But I am able to download only the experiment with data format of MR &CT sessions(Dicom files) of that subject. Below you can see my python code and please let me know for the changes I have to make.

import xnat
import os
#creating a session
session = xnat.connect('https://xnat.prj.ae.mpg.de', user='xxxx', password='xxxx')
test_project = session.projects["Test"] #loading a project Test
test_subject = test_project.subjects #loading subjects of project
download_folder = os.path.expanduser(r"C:\Users\rkls\Documents\Python-Restapi") # download path
print('Your data is downladed in this directory {} '.format(download_folder))
if not os.path.exists(download_folder):
    os.makedirs(download_folder)
test_project.subjects['S2_RS'].download_dir(download_folder) # using download_dir() to download subject S2_RS
session.disconnect()

Now the above code gives me only experiment with CT, MR session data (DICOM files) but not ECOG and MEEG session data(EDF & FIF files). How do I download all the experiments associated within single subject of a project?

score 0 · Answer 1 · answered Oct 08 '20 at 22:52

What kind of experiments are the ECOG and MEEG session data contained in, i.e. what is the data type? Or are they just resources associated with the subject?

I created a subject with an associated MR session as well as some resources (e.g. open Manage Files on the subject page, create a resource folder, and upload a couple of PDFs to the new resource folder). The download_dir() function on the SubjectData class only downloads the experiments and not the resources associated with the subject. For that you need to iterate the resources directly:

# Set subject to variable for convenience
s2_rs = test_project.subjects['S2_RS']
s2_rs.download_dir(download_folder) # Download experiment data
for resource_id in s2_rs.resources: # Iterate subject resources
    # Download resources for 
    s2_rs.resources.data[resource_id].download_dir(download_folder)

I created a resource folder named FOO on my subject then uploaded a couple of PDFs there. In my download folder, I got the following:

S2_RS/resources/FOO/files/foo-1.pdf
S2_RS/resources/FOO/files/foo-2.pdf
S2_RS/S2_RS_MR01/...

S2_RS_MR01 is the MR session I uploaded so there are a bunch of files under that folder.

It would be nice if the download_dir() function included the resources as well but for now this should work around that issue for you.

Developing Python Rest API for downloading and uploading the Data into XNAT

1 Answers1