def test_yaml_template():
config_file = tempfile.mkstemp(suffix='test_yaml_template')[1]
# Create a new YAML configuration file based on the default_pipeline.yml file.
config = yaml.safe_load(open('./data/default_pipeline.yml', 'r'))
new_config = create_yaml_from_template(config,
'./data/default_pipeline.yml')
with open(config_file, 'wb') as f:
f.write(new_config)
# Verify that the output has preserved blank lines, comments
with open(config_file, 'r') as f:
lines = f.readlines()
# Assert first lines starts with a comment
assert lines[0].startswith('# ')
# Assert that there are blank lines
assert lines[6].isspace()
assert lines[7].isspace()
# Assert that regressors configuration written in block style
assert lines[669].startswith('Regressors:')
assert lines[670].startswith('- Bandpass:'******'roiTSOutputs: [true, true]')
def test_yaml_template():
config_file = tempfile.mkstemp(suffix='test_yaml_template')[1]
with open("./default_pipeline.yaml", "r") as f:
config = yaml.load(f)
new_config = create_yaml_from_template(config, "./default_pipeline.yaml")
with open(config_file, "wb") as f:
f.write(new_config)
# TODO test cases
# Test lists, dicts and list of dicts
# Look for who is in flow style and who is not
# Check for default values
# Check for comments
print("Available threads: {0}".format(c['maxCoresPerParticipant']))
print("Number of threads for ANTs: {0}".format(c['num_ants_threads']))
# create a timestamp for writing config files
st = datetime.datetime.now().strftime('%Y-%m-%dT%H-%M-%SZ')
# update config file
if "s3://" not in args.output_dir.lower():
pipeline_config_file = os.path.join(
args.output_dir, "cpac_pipeline_config_{0}.yml".format(st))
else:
pipeline_config_file = os.path.join(
"/scratch", "cpac_pipeline_config_{0}.yml".format(st))
with open(pipeline_config_file, 'w') as f:
f.write(create_yaml_from_template(c, DEFAULT_PIPELINE))
participant_labels = []
if args.participant_label:
participant_labels = [
'sub-' + pt if not pt.startswith('sub-') else pt
for pt in args.participant_label
]
# otherwise we move on to conforming the data configuration
if not args.data_config_file:
from bids_utils import collect_bids_files_configs, bids_gen_cpac_sublist
(file_paths,
config) = collect_bids_files_configs(args.bids_dir,
print("Number of threads for ANTs: {0}".format(
c['pipeline_setup']['system_config']['num_ants_threads']))
# create a timestamp for writing config files
st = datetime.datetime.now().strftime('%Y-%m-%dT%H-%M-%SZ')
# update config file
if "s3://" not in args.output_dir.lower():
pipeline_config_file = os.path.join(
args.output_dir, "cpac_pipeline_config_{0}.yml".format(st))
else:
pipeline_config_file = os.path.join(
DEFAULT_TMP_DIR, "cpac_pipeline_config_{0}.yml".format(st))
open(pipeline_config_file,
'w').write(create_yaml_from_template(c, DEFAULT_PIPELINE, True))
open(f'{pipeline_config_file[:-4]}_min.yml',
'w').write(create_yaml_from_template(c, DEFAULT_PIPELINE, False))
participant_labels = []
if args.participant_label:
participant_labels = [
'sub-' + pt if not pt.startswith('sub-') else pt
for pt in args.participant_label
]
# otherwise we move on to conforming the data configuration
if not args.data_config_file:
sub_list = create_cpac_data_config(args.bids_dir,
args.participant_label,
args.aws_input_creds,
print("Available threads: {0}".format(c['maxCoresPerParticipant']))
print("Number of threads for ANTs: {0}".format(c['num_ants_threads']))
# create a timestamp for writing config files
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y%m%d%H%M%S')
# update config file
if "s3://" not in args.output_dir.lower():
config_file = os.path.join(args.output_dir, "cpac_pipeline_config_{0}.yml".format(st))
else:
config_file = os.path.join("/scratch", "cpac_pipeline_config_{0}.yml".format(st))
with open(config_file, 'w') as f:
f.write(create_yaml_from_template(c, DEFAULT_PIPELINE))
# we have all we need if we are doing a group level analysis
if args.analysis_level == "group":
if not args.group_file or not os.path.exists(args.group_file):
print()
print()
print("No group analysis configuration file was supplied.")
print()
import pkg_resources as p
args.group_file = \
p.resource_filename("CPAC",