Output a summary of an xnat project

summary.py

# outputs a summary of the data in an xnat project, e.g.:

# 55 subjects, 65 scans, 400 sequences (SNAPSHOTS: 400, DICOM: 400, NIFTI: 200)

# Note that in our lab we talk about "scans" and "sequences" which correspond
# to xnat's "MR Sessions" and "Scans" respectively.

# Parameters:
# 1. url - xnat url
# 2. username - xnat username
# 3. password - xnat password
# 4. project - xnat project

import sys
import xnat # see https://xnat.readthedocs.io/en/latest/
from requests.exceptions import ConnectionError

if len(sys.argv) != 5:
    print "Incorrect number of arguments - expected 4"
    print "Usage: python summary.py xnat_url xnat_username xnat_password project_id"
else:
    host = sys.argv[1]
    user = sys.argv[2]
    password = sys.argv[3]
    project = sys.argv[4]
    try:
        session = xnat.connect(host, user=user, password=password)
        xnatproject = session.projects[project]
        if xnatproject:
            summ = "{} subjects, {} scans, ".format(len(xnatproject.subjects.keys()),len(xnatproject.experiments.keys()))
            tot = 0
            cnt = {}
            for experiment_id in xnatproject.experiments.keys():
                scans = xnatproject.experiments[experiment_id].scans.keys()
                tot = tot + len(scans)
                for scan_id in scans:
                    scan = xnatproject.experiments[experiment_id].scans[scan_id]
                    for resource_id in scan.resources.keys():
                        resource = scan.resources[resource_id]
                        if resource.label in cnt.keys():
                            cnt[resource.label]=cnt[resource.label]+1
                        else:
                            cnt[resource.label]=1
            summ = summ + "{} sequences ".format(tot)
            if tot>0:
                summ = summ + "(" + ', '.join('{}: {}'.format(scantype, cnt[scantype]) for scantype in cnt) + ")"
            print summ
        else:
            print 'Unable to find {} project.  Does the user you supplied have collaborator access?'.format(project)
    except ConnectionError:
        print "Unable to connect to specified xnat instance, {}".format(host)
        print " - is the url valid?"
    except:
        print "Unable to authenticate with specified credientials"