def run(self, **inputs):
"""Execute this interface.
This interface will not raise an exception if runtime.returncode is
non-zero.
Parameters
----------
inputs : allows the interface settings to be updated
Returns
-------
results : an InterfaceResult object containing a copy of the instance
that was executed, provenance information and, if successful, results
"""
from ...utils.profiler import ResourceMonitor
enable_rm = config.resource_monitor and self.resource_monitor
force_raise = not getattr(self.inputs, 'ignore_exception', False)
self.inputs.trait_set(**inputs)
self._check_mandatory_inputs()
self._check_version_requirements(self.inputs)
interface = self.__class__
self._duecredit_cite()
# initialize provenance tracking
store_provenance = str2bool(
config.get('execution', 'write_provenance', 'false'))
env = deepcopy(dict(os.environ))
if self._redirect_x:
env['DISPLAY'] = config.get_display()
runtime = Bunch(cwd=os.getcwd(),
returncode=None,
duration=None,
environ=env,
startTime=dt.isoformat(dt.utcnow()),
endTime=None,
platform=platform.platform(),
hostname=platform.node(),
version=self.version)
mon_sp = None
if enable_rm:
mon_freq = float(
config.get('execution', 'resource_monitor_frequency', 1))
proc_pid = os.getpid()
iflogger.debug(
'Creating a ResourceMonitor on a %s interface, PID=%d.',
self.__class__.__name__, proc_pid)
mon_sp = ResourceMonitor(proc_pid, freq=mon_freq)
mon_sp.start()
# Grab inputs now, as they should not change during execution
inputs = self.inputs.get_traitsfree()
outputs = None
try:
runtime = self._run_interface(runtime)
outputs = self.aggregate_outputs(runtime)
except Exception as e:
import traceback
# Retrieve the maximum info fast
runtime.traceback = traceback.format_exc()
# Gather up the exception arguments and append nipype info.
exc_args = e.args if getattr(e, 'args') else tuple()
exc_args += (
'An exception of type %s occurred while running interface %s.'
% (type(e).__name__, self.__class__.__name__), )
if config.get('logging', 'interface_level',
'info').lower() == 'debug':
exc_args += ('Inputs: %s' % str(self.inputs), )
runtime.traceback_args = ('\n'.join(
['%s' % arg for arg in exc_args]), )
if force_raise:
raise
finally:
# This needs to be done always
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
runtime.duration = (timediff.days * 86400 + timediff.seconds +
timediff.microseconds / 1e6)
results = InterfaceResult(interface,
runtime,
inputs=inputs,
outputs=outputs,
provenance=None)
# Add provenance (if required)
if store_provenance:
# Provenance will only throw a warning if something went wrong
results.provenance = write_provenance(results)
# Make sure runtime profiler is shut down
if enable_rm:
import numpy as np
mon_sp.stop()
runtime.mem_peak_gb = None
runtime.cpu_percent = None
# Read .prof file in and set runtime values
vals = np.loadtxt(mon_sp.fname, delimiter=',')
if vals.size:
vals = np.atleast_2d(vals)
runtime.mem_peak_gb = vals[:, 1].max() / 1024
runtime.cpu_percent = vals[:, 2].max()
runtime.prof_dict = {
'time': vals[:, 0].tolist(),
'cpus': vals[:, 1].tolist(),
'rss_GiB': (vals[:, 2] / 1024).tolist(),
'vms_GiB': (vals[:, 3] / 1024).tolist(),
}
return results
def run(self, cwd=None, **inputs):
"""Execute this interface.
This interface will not raise an exception if runtime.returncode is
non-zero.
Parameters
----------
cwd : specify a folder where the interface should be run
inputs : allows the interface settings to be updated
Returns
-------
results : an InterfaceResult object containing a copy of the instance
that was executed, provenance information and, if successful, results
"""
from ...utils.profiler import ResourceMonitor
# Tear-up: get current and prev directories
syscwd = rgetcwd(error=False) # Recover when wd does not exist
if cwd is None:
cwd = syscwd
os.chdir(cwd) # Change to the interface wd
enable_rm = config.resource_monitor and self.resource_monitor
self.inputs.trait_set(**inputs)
self._check_mandatory_inputs()
self._check_version_requirements(self.inputs)
interface = self.__class__
self._duecredit_cite()
# initialize provenance tracking
store_provenance = str2bool(
config.get('execution', 'write_provenance', 'false'))
env = deepcopy(dict(os.environ))
if self._redirect_x:
env['DISPLAY'] = config.get_display()
runtime = Bunch(
cwd=cwd,
prevcwd=syscwd,
returncode=None,
duration=None,
environ=env,
startTime=dt.isoformat(dt.utcnow()),
endTime=None,
platform=platform.platform(),
hostname=platform.node(),
version=self.version)
mon_sp = None
if enable_rm:
mon_freq = float(
config.get('execution', 'resource_monitor_frequency', 1))
proc_pid = os.getpid()
iflogger.debug(
'Creating a ResourceMonitor on a %s interface, PID=%d.',
self.__class__.__name__, proc_pid)
mon_sp = ResourceMonitor(proc_pid, freq=mon_freq)
mon_sp.start()
# Grab inputs now, as they should not change during execution
inputs = self.inputs.get_traitsfree()
outputs = None
try:
runtime = self._run_interface(runtime)
outputs = self.aggregate_outputs(runtime)
except Exception as e:
import traceback
# Retrieve the maximum info fast
runtime.traceback = traceback.format_exc()
# Gather up the exception arguments and append nipype info.
exc_args = e.args if getattr(e, 'args') else tuple()
exc_args += (
'An exception of type %s occurred while running interface %s.'
% (type(e).__name__, self.__class__.__name__), )
if config.get('logging', 'interface_level',
'info').lower() == 'debug':
exc_args += ('Inputs: %s' % str(self.inputs), )
runtime.traceback_args = ('\n'.join(
['%s' % arg for arg in exc_args]), )
if not self.ignore_exception:
raise
finally:
# This needs to be done always
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
runtime.duration = (timediff.days * 86400 + timediff.seconds +
timediff.microseconds / 1e6)
results = InterfaceResult(
interface,
runtime,
inputs=inputs,
outputs=outputs,
provenance=None)
# Add provenance (if required)
if store_provenance:
# Provenance will only throw a warning if something went wrong
results.provenance = write_provenance(results)
# Make sure runtime profiler is shut down
if enable_rm:
import numpy as np
mon_sp.stop()
runtime.mem_peak_gb = None
runtime.cpu_percent = None
# Read .prof file in and set runtime values
vals = np.loadtxt(mon_sp.fname, delimiter=',')
if vals.size:
vals = np.atleast_2d(vals)
runtime.mem_peak_gb = vals[:, 1].max() / 1024
runtime.cpu_percent = vals[:, 2].max()
runtime.prof_dict = {
'time': vals[:, 0].tolist(),
'cpus': vals[:, 1].tolist(),
'rss_GiB': (vals[:, 2] / 1024).tolist(),
'vms_GiB': (vals[:, 3] / 1024).tolist(),
}
os.chdir(syscwd)
return results
def run(self, cwd=None, ignore_exception=None, **inputs):
"""Execute this interface.
This interface will not raise an exception if runtime.returncode is
non-zero.
Parameters
----------
cwd : specify a folder where the interface should be run
inputs : allows the interface settings to be updated
Returns
-------
results : :obj:`nipype.interfaces.base.support.InterfaceResult`
A copy of the instance that was executed, provenance information and,
if successful, results
"""
from ...utils.profiler import ResourceMonitor
# if ignore_exception is not provided, taking self.ignore_exception
if ignore_exception is None:
ignore_exception = self.ignore_exception
# Tear-up: get current and prev directories
syscwd = rgetcwd(error=False) # Recover when wd does not exist
if cwd is None:
cwd = syscwd
os.chdir(cwd) # Change to the interface wd
enable_rm = config.resource_monitor and self.resource_monitor
self.inputs.trait_set(**inputs)
self._check_mandatory_inputs()
self._check_version_requirements(self.inputs)
interface = self.__class__
self._duecredit_cite()
# initialize provenance tracking
store_provenance = str2bool(
config.get("execution", "write_provenance", "false"))
env = deepcopy(dict(os.environ))
if self._redirect_x:
env["DISPLAY"] = config.get_display()
runtime = Bunch(
cwd=cwd,
prevcwd=syscwd,
returncode=None,
duration=None,
environ=env,
startTime=dt.isoformat(dt.utcnow()),
endTime=None,
platform=platform.platform(),
hostname=platform.node(),
version=self.version,
)
runtime_attrs = set(runtime.dictcopy())
mon_sp = None
if enable_rm:
mon_freq = float(
config.get("execution", "resource_monitor_frequency", 1))
proc_pid = os.getpid()
iflogger.debug(
"Creating a ResourceMonitor on a %s interface, PID=%d.",
self.__class__.__name__,
proc_pid,
)
mon_sp = ResourceMonitor(proc_pid, freq=mon_freq)
mon_sp.start()
# Grab inputs now, as they should not change during execution
inputs = self.inputs.get_traitsfree()
outputs = None
try:
runtime = self._pre_run_hook(runtime)
runtime = self._run_interface(runtime)
runtime = self._post_run_hook(runtime)
outputs = self.aggregate_outputs(runtime)
except Exception as e:
import traceback
# Retrieve the maximum info fast
runtime.traceback = traceback.format_exc()
# Gather up the exception arguments and append nipype info.
exc_args = e.args if getattr(e, "args") else tuple()
exc_args += (
"An exception of type %s occurred while running interface %s."
% (type(e).__name__, self.__class__.__name__), )
if config.get("logging", "interface_level",
"info").lower() == "debug":
exc_args += ("Inputs: %s" % str(self.inputs), )
runtime.traceback_args = ("\n".join(
["%s" % arg for arg in exc_args]), )
if not ignore_exception:
raise
finally:
if runtime is None or runtime_attrs - set(runtime.dictcopy()):
raise RuntimeError("{} interface failed to return valid "
"runtime object".format(
interface.__class__.__name__))
# This needs to be done always
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
runtime.duration = (timediff.days * 86400 + timediff.seconds +
timediff.microseconds / 1e6)
results = InterfaceResult(interface,
runtime,
inputs=inputs,
outputs=outputs,
provenance=None)
# Add provenance (if required)
if store_provenance:
# Provenance will only throw a warning if something went wrong
results.provenance = write_provenance(results)
# Make sure runtime profiler is shut down
if enable_rm:
import numpy as np
mon_sp.stop()
runtime.mem_peak_gb = None
runtime.cpu_percent = None
# Read .prof file in and set runtime values
vals = np.loadtxt(mon_sp.fname, delimiter=",")
if vals.size:
vals = np.atleast_2d(vals)
runtime.mem_peak_gb = vals[:, 2].max() / 1024
runtime.cpu_percent = vals[:, 1].max()
runtime.prof_dict = {
"time": vals[:, 0].tolist(),
"cpus": vals[:, 1].tolist(),
"rss_GiB": (vals[:, 2] / 1024).tolist(),
"vms_GiB": (vals[:, 3] / 1024).tolist(),
}
os.chdir(syscwd)
return results
