def run(self):
# Get configurations and settings
config = self._config
subject_list = self._sub_dict
cloudify = self._cloudify
ns_at_once = config.get('num_subjects_at_once', 1)
write_report = config.get('write_report', False)
# Create output directory
try:
os.makedirs(config["output_directory"])
except:
if not op.isdir(config["output_directory"]):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % config["output_directory"]
raise Exception(err)
else:
pass
# Create working directory
try:
os.makedirs(config["working_directory"])
except:
if not op.isdir(config["working_directory"]):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % config["working_directory"]
raise Exception(err)
else:
pass
run_name = config['pipeline_config_yaml'].split("/")[-1].split(".")[0]
results = None
if not cloudify:
results = self._run_here(run_name)
else:
results = self._run_cloud(run_name)
# PDF reporting
if write_report:
from qap.viz.reports import workflow_report
logger.info('Writing PDF reports')
qap_type = 'qap_' + config['qap_type']
in_csv = op.join(config['output_directory'], '%s.csv' % qap_type)
reports = workflow_report(in_csv,
qap_type,
run_name,
results,
out_dir=config['output_directory'])
for k, v in reports.iteritems():
if v['success']:
logger.info('Written report (%s) in %s' % (k, v['path']))
def run(self):
# Get configurations and settings
config = self._config
subject_list = self._sub_dict
cloudify = self._cloudify
ns_at_once = config.get('num_subjects_at_once', 1)
write_report = config.get('write_report', False)
# Create output directory
try:
os.makedirs(config["output_directory"])
except:
if not op.isdir(config["output_directory"]):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % config["output_directory"]
raise Exception(err)
else:
pass
# Create working directory
try:
os.makedirs(config["working_directory"])
except:
if not op.isdir(config["working_directory"]):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % config["working_directory"]
raise Exception(err)
else:
pass
run_name = config['pipeline_config_yaml'].split("/")[-1].split(".")[0]
results = None
if not cloudify:
results = self._run_here(run_name)
else:
results = self._run_cloud(run_name)
# PDF reporting
if write_report:
from qap.viz.reports import workflow_report
logger.info('Writing PDF reports')
qap_type = 'qap_' + config['qap_type']
in_csv = op.join(config['output_directory'], '%s.csv' % qap_type)
reports = workflow_report(in_csv, qap_type, run_name, results,
out_dir=config['output_directory'])
for k, v in reports.iteritems():
if v['success']:
logger.info('Written report (%s) in %s' % (k, v['path']))
def main():
import os
import argparse
from qap.script_utils import gather_json_info, json_to_csv
from qap.qap_utils import raise_smart_exception
parser = argparse.ArgumentParser()
parser.add_argument("output_dir", type=str,
help="the main output directory of the QAP run "
"which contains the participant directories")
parser.add_argument("--with_group_reports", action='store_true',
default=False, help="Write a summary report in PDF "
"format.")
parser.add_argument("--with_full_reports", action='store_true',
default=False, help="Write the summary report and "
"the individual participant reports as well.")
args = parser.parse_args()
json_dict = gather_json_info(args.output_dir)
json_to_csv(json_dict)
if args.with_group_reports or args.with_full_reports:
from qap.viz.reports import workflow_report
# TODO: read in combined results dictionary from log JSONs
#logs_dict = gather_json_info("_".join([args.output_dir, "logs"]))
qap_types = ["anatomical_spatial",
"functional_spatial",
"functional_temporal"]
for qap_type in qap_types:
qap_type = "_".join(["qap", qap_type])
run_name = args.output_dir.split("/")[-1]
in_csv = os.path.join(os.getcwd(), '%s.csv' % qap_type)
if not os.path.isfile(in_csv):
continue
reports = workflow_report(in_csv, qap_type, run_name,
out_dir=args.output_dir,
full_reports=args.with_full_reports)
parser = argparse.ArgumentParser()
req = parser.add_argument_group("Required Inputs")
req.add_argument('-i',
'--input_csv',
type=str,
required=True,
help='filepath to csv file generated by qap')
req.add_argument('-m',
'--qap_mode',
type=str,
help='report type',
choices=[
'qap_anatomical_spatial', 'qap_functional_temporal',
'qap_functional_spatial'
],
required=True)
args = parser.parse_args()
in_csv = args.input_csv
out_dir = op.dirname(in_csv)
qap_type = args.qap_mode
reports = workflow_report(in_csv, qap_type, run_name, out_dir=out_dir)
for k, v in reports.iteritems():
if v['success']:
logger.info('Written report (%s) in %s' % (k, v['path']))
# @Last Modified by: oesteban
# @Last Modified time: 2015-10-08 14:53:20
if __name__ == "__main__":
import argparse
import os.path as op
from qap.viz.reports import workflow_report
parser = argparse.ArgumentParser()
req = parser.add_argument_group("Required Inputs")
req.add_argument('-i', '--input_csv', type=str, required=True,
help='filepath to csv file generated by qap')
req.add_argument(
'-m', '--qap_mode', type=str, help='report type',
choices=['qap_anatomical_spatial', 'qap_functional_temporal',
'qap_functional_spatial'], required=True)
args = parser.parse_args()
in_csv = args.input_csv
out_dir = op.dirname(in_csv)
qap_type = args.qap_mode
reports = workflow_report(in_csv, qap_type, run_name,
out_dir=out_dir)
for k, v in reports.iteritems():
if v['success']:
logger.info('Written report (%s) in %s' % (k, v['path']))