add_qyscore_analysis_from_dicom

#!/usr/bin/env python

import argparse
import os
import tempfile
import shutil
import json

import dicom
import requests

from soma.archive import pack, unpack

from commons.helpers.analyses import get_analyses_dir
from commons.helpers.api_calls import ApiInformation
from qynapse.dicom.dataset import Dataset
from qynapse.dicom.clinical_info import compute_clinical_info


def add_qyscore_analysis(directory, storescu, aec, user, apiUrl, apiHost):
    application = 'QyScore'
    patient = None
    acquisition = None
    clinicalInfos = None
    for root, dirs, files in os.walk(directory):
        for filename in files:
            try:
                ds = dicom.read_file(os.path.join(root, filename))
                patient = Dataset.get_patient_name(ds)
                chars_to_remove = ['\x00', '\x09', '\x20']
                patient = patient.translate(None, ''.join(chars_to_remove))
                acquisition = Dataset.get_study_date_and_time(ds)
                clinicalInfos = compute_clinical_info(ds)
            except:
                continue

    if patient is None or acquisition is None:
        raise ValueError('Could not find required data in input files.')

    inputDict = {
        'analysis': {
            'inputs': {
                'subject_name': patient,
                'subject_age': clinicalInfos['subject'][
                    'subject_age'],
                'subject_sex': clinicalInfos['subject'][
                    'subject_sex'],
                'acquisition': acquisition,
                'user': user,
                'aec': aec,
                'storescu': storescu
            }
        },
        'mode': 'single',
        'application': application,
        'patient': patient,
        'acquisition': acquisition,
    }
    analysisResponse = requests.post(
        apiUrl + '/analyses', json=inputDict, headers={'API-Host': apiHost}, verify=False)
    analysis = json.loads(analysisResponse.text.encode('utf-8'))['analysis']
    try:
        analysisId = analysis['id']
        analysisPath = os.path.join(get_analyses_dir(), str(analysisId))
        pack(os.path.join(analysisPath, 'input_dicom.zip'),
             os.path.abspath(directory))
    except Exception as e:
        raise e


def main():
    parser = argparse.ArgumentParser(description='''Run QyScore.''')
    parser.add_argument('-i', '--input', help='ZIP input')
    parser.add_argument('-d', '--directory', help='Directory input')
    parser.add_argument('-s', '--storescu', help='Request storescu',
                        action='store_true', dest='storescu', default=False)
    parser.add_argument('-c', '--aec', help='Called AE')
    parser.add_argument('-u', '--user', help='User')
    parser.add_argument('-e', '--envPath', help='QyScore env path',
                        required=True)
    args = parser.parse_args()

    directory = args.directory
    deleteDirectory = False
    if args.input is not None:
        directory = tempfile.mktemp()
        unpack(args.input, directory)
        deleteDirectory = True

    apiInfo = ApiInformation()
    add_qyscore_analysis(directory,
                         args.storescu, args.aec, args.user,
                         apiInfo.get_url(), apiInfo.get_ip_address())

    if deleteDirectory:
        shutil.rmtree(directory)


if __name__ == '__main__':
    main()