def _agg(objekt, runtime):
outputs = Bunch(tissue_class_map=os.path.join(
datadir, 'testFASTRPT-tissue_class_map.nii.gz'),
tissue_class_files=[
os.path.join(datadir, 'testFASTRPT-tissue_class_files0.nii.gz'),
os.path.join(datadir, 'testFASTRPT-tissue_class_files1.nii.gz'),
os.path.join(datadir, 'testFASTRPT-tissue_class_files2.nii.gz')]
)
return outputs
def _agg(objekt, runtime):
outputs = Bunch(out_lta_file=os.path.join(
datadir, 'testBBRegisterRPT-out_lta_file.lta'), )
return outputs
def _agg(objekt, runtime):
outputs = Bunch(warped_image=os.path.join(
datadir, 'testANTSRegistrationRPT-warped_image.nii.gz'))
return outputs
def _agg(objekt, runtime):
outputs = Bunch(warped_image=os.path.join(
datadir, 'testRobustMNINormalizationRPTMovingWarpedImage.nii.gz'))
return outputs
def upload_qc_metrics(in_iqms,
loc,
path='',
scheme='http',
port=None,
email=None):
"""
Upload qc metrics to remote repository.
:param str in_iqms: Path to the qc metric json file as a string
:param str scheme: the protocol (either http or https)
:param str email: email address to be included with the metric submission
:param bool upload_strict: the client should fail if it's strict mode
:return: either the response object if a response was successfully sent
or it returns the string "No Response"
:rtype: object
"""
from json import load, dumps
import requests
from io import open
from copy import deepcopy
if port is None:
port = 443 if scheme == 'https' else 80
with open(in_iqms, 'r') as input_json:
in_data = load(input_json)
# Extract metadata and provenance
meta = in_data.pop('bids_meta')
prov = in_data.pop('provenance')
# At this point, data should contain only IQMs
data = deepcopy(in_data)
# Check modality
modality = meta.get('modality', 'None')
if modality not in ('T1w', 'bold', 'T2w'):
errmsg = (
'Submitting to MRIQCWebAPI: image modality should be "bold", "T1w", or "T2w", '
'(found "%s")' % modality)
return Bunch(status_code=1, text=errmsg)
# Filter metadata values that aren't in whitelist
data['bids_meta'] = {k: meta[k] for k in META_WHITELIST if k in meta}
# Filter provenance values that aren't in whitelist
data['provenance'] = {k: prov[k] for k in PROV_WHITELIST if k in prov}
# Hash fields that may contain personal information
data['bids_meta'] = _hashfields(data['bids_meta'])
if email:
data['provenance']['email'] = email
if path and not path.endswith('/'):
path += '/'
if path.startswith('/'):
path = path[1:]
headers = {'Authorization': SECRET_KEY, "Content-Type": "application/json"}
webapi_url = '{}://{}:{}/{}{}'.format(scheme, loc, port, path, modality)
IFLOGGER.info('MRIQC Web API: submitting to <%s>', webapi_url)
try:
# if the modality is bold, call "bold" endpoint
response = requests.post(webapi_url, headers=headers, data=dumps(data))
except requests.ConnectionError as err:
errmsg = 'QC metrics failed to upload due to connection error shown below:\n%s' % err
return Bunch(status_code=1, text=errmsg)
return response
def _agg(objekt, runtime):
outputs = Bunch(BrainExtractionMask=os.path.join(
datadir, 'testBrainExtractionRPTBrainExtractionMask.nii.gz')
)
return outputs