with open(data_config_file, 'w') as f:
noalias_dumper = yaml.dumper.SafeDumper
noalias_dumper.ignore_aliases = lambda self, data: True
yaml.dump(sub_list, f, default_flow_style=False, Dumper=noalias_dumper)
if args.analysis_level in ["participant", "test_config"]:
# build pipeline easy way
from CPAC.utils.monitoring import monitor_server
import CPAC.pipeline.cpac_runner
monitoring = None
if args.monitoring:
try:
monitoring = monitor_server(
c['pipeline_setup']['pipeline_name'],
c['pipeline_setup']['log_directory']['path'])
except:
pass
plugin_args = {
'n_procs':
int(c['pipeline_setup']['system_config']
['max_cores_per_participant']),
'memory_gb':
int(c['pipeline_setup']['system_config']
['maximum_memory_per_participant']),
}
print("Starting participant level processing")
CPAC.pipeline.cpac_runner.run(
if args.analysis_level == "test_config":
print(
'This has been a test run, the pipeline and data configuration files should'
' have been written to {0} and {1} respectively.'
' CPAC will not be run.'.format(pipeline_config_file,
data_config_file))
elif args.analysis_level == "participant":
# build pipeline easy way
from CPAC.utils.monitoring import monitor_server
import CPAC.pipeline.cpac_runner
monitoring = None
if args.monitoring:
try:
monitoring = monitor_server(c['pipelineName'],
c['logDirectory'])
except:
pass
plugin_args = {
'n_procs': int(c['maxCoresPerParticipant']),
'memory_gb': int(c['maximumMemoryPerParticipant']),
}
print("Starting participant level processing")
CPAC.pipeline.cpac_runner.run(
data_config_file,
pipeline_config_file,
plugin='MultiProc' if plugin_args['n_procs'] > 1 else 'Linear',
plugin_args=plugin_args,
tracking=not args.tracking_opt_out)
# Avoid dict/list references
noalias_dumper = yaml.dumper.SafeDumper
noalias_dumper.ignore_aliases = lambda self, data: True
yaml.dump(sub_list, f, default_flow_style=False, Dumper=noalias_dumper)
if args.analysis_level == "participant":
# build pipeline easy way
import CPAC
from CPAC.utils.monitoring import log_nodes_cb, monitor_server
monitoring = None
if args.monitoring:
try:
monitoring = monitor_server(c['pipelineName'], c['logDirectory'])
except:
pass
plugin_args = {'n_procs': int(c['maxCoresPerParticipant']),
'memory_gb': int(c['maximumMemoryPerParticipant']),
'status_callback': log_nodes_cb}
print ("Starting participant level processing")
CPAC.pipeline.cpac_runner.run(config_file, data_config_file,
plugin='MultiProc', plugin_args=plugin_args,
tracking=not args.tracking_opt_out)
if monitoring:
monitoring.join(10)
else: