# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Nipype interfaces core
......................
Defines the ``Interface`` API and the body of the
most basic interfaces.
The I/O specifications corresponding to these base
interfaces are found in the ``specs`` module.
"""
from copy import deepcopy
from datetime import datetime as dt
import os
import platform
import subprocess as sp
import shlex
import sys
import simplejson as json
from dateutil.parser import parse as parseutc
from traits.trait_errors import TraitError
from ... import config, logging, LooseVersion
from ...utils.provenance import write_provenance
from ...utils.misc import str2bool, rgetcwd
from ...utils.filemanip import split_filename, which, get_dependencies
from ...utils.subprocess import run_command
from ...external.due import due
from .traits_extension import traits, isdefined
from .specs import (
BaseInterfaceInputSpec,
CommandLineInputSpec,
StdOutCommandLineInputSpec,
MpiCommandLineInputSpec,
get_filecopy_info,
)
from .support import Bunch, InterfaceResult, NipypeInterfaceError, format_help
iflogger = logging.getLogger("nipype.interface")
VALID_TERMINAL_OUTPUT = [
"stream",
"allatonce",
"file",
"file_split",
"file_stdout",
"file_stderr",
"none",
]
__docformat__ = "restructuredtext"
[docs]class Interface(object):
"""This is an abstract definition for Interface objects.
It provides no functionality. It defines the necessary attributes
and methods all Interface objects should have.
"""
input_spec = None # A traited input specification
output_spec = None # A traited output specification
_can_resume = False # See property below
_always_run = False # See property below
@property
def can_resume(self):
"""Defines if the interface can reuse partial results after interruption.
Only applies to interfaces being run within a workflow context."""
return self._can_resume
@property
def always_run(self):
"""Should the interface be always run even if the inputs were not changed?
Only applies to interfaces being run within a workflow context."""
return self._always_run
@property
def version(self):
"""interfaces should implement a version property"""
raise NotImplementedError
@classmethod
def _outputs(cls):
""" Initializes outputs"""
raise NotImplementedError
[docs] @classmethod
def help(cls, returnhelp=False):
""" Prints class help """
allhelp = format_help(cls)
if returnhelp:
return allhelp
print(allhelp)
return None # R1710
[docs] def __init__(self):
"""Subclasses must implement __init__"""
raise NotImplementedError
[docs] def run(self):
"""Execute the command."""
raise NotImplementedError
[docs] def aggregate_outputs(self, runtime=None, needed_outputs=None):
"""Called to populate outputs"""
raise NotImplementedError
def _list_outputs(self):
""" List expected outputs"""
raise NotImplementedError
@classmethod
def _get_filecopy_info(cls):
"""Provides information about file inputs to copy or link to cwd.
Necessary for pipeline operation
"""
iflogger.warning(
"_get_filecopy_info member of Interface was deprecated "
"in nipype-1.1.6 and will be removed in 1.2.0"
)
return get_filecopy_info(cls)
class BaseInterface(Interface):
"""Implement common interface functionality.
* Initializes inputs/outputs from input_spec/output_spec
* Provides help based on input_spec and output_spec
* Checks for mandatory inputs before running an interface
* Runs an interface and returns results
* Determines which inputs should be copied or linked to cwd
This class does not implement aggregate_outputs, input_spec or
output_spec. These should be defined by derived classes.
This class cannot be instantiated.
Attributes
----------
input_spec: :obj:`nipype.interfaces.base.specs.TraitedSpec`
points to the traited class for the inputs
output_spec: :obj:`nipype.interfaces.base.specs.TraitedSpec`
points to the traited class for the outputs
_redirect_x: bool
should be set to ``True`` when the interface requires
connecting to a ``$DISPLAY`` (default is ``False``).
resource_monitor: bool
If ``False``, prevents resource-monitoring this interface
If ``True`` monitoring will be enabled IFF the general
Nipype config is set on (``resource_monitor = true``).
"""
input_spec = BaseInterfaceInputSpec
_version = None
_additional_metadata = []
_redirect_x = False
references_ = []
resource_monitor = True # Enabled for this interface IFF enabled in the config
_etelemetry_version_data = None
def __init__(
self, from_file=None, resource_monitor=None, ignore_exception=False, **inputs
):
if (
config.getboolean("execution", "check_version")
and "NIPYPE_NO_ET" not in os.environ
):
from ... import check_latest_version
if BaseInterface._etelemetry_version_data is None:
BaseInterface._etelemetry_version_data = check_latest_version()
if not self.input_spec:
raise Exception("No input_spec in class: %s" % self.__class__.__name__)
self.inputs = self.input_spec(**inputs)
self.ignore_exception = ignore_exception
if resource_monitor is not None:
self.resource_monitor = resource_monitor
if from_file is not None:
self.load_inputs_from_json(from_file, overwrite=True)
for name, value in list(inputs.items()):
setattr(self.inputs, name, value)
def _outputs(self):
""" Returns a bunch containing output fields for the class
"""
outputs = None
if self.output_spec:
outputs = self.output_spec()
return outputs
def _check_requires(self, spec, name, value):
""" check if required inputs are satisfied
"""
if spec.requires:
values = [
not isdefined(getattr(self.inputs, field)) for field in spec.requires
]
if any(values) and isdefined(value):
if len(values) > 1:
fmt = (
"%s requires values for inputs %s because '%s' is set. "
"For a list of required inputs, see %s.help()"
)
else:
fmt = (
"%s requires a value for input %s because '%s' is set. "
"For a list of required inputs, see %s.help()"
)
msg = fmt % (
self.__class__.__name__,
", ".join("'%s'" % req for req in spec.requires),
name,
self.__class__.__name__,
)
raise ValueError(msg)
def _check_xor(self, spec, name, value):
""" check if mutually exclusive inputs are satisfied
"""
if spec.xor:
values = [isdefined(getattr(self.inputs, field)) for field in spec.xor]
if not any(values) and not isdefined(value):
msg = (
"%s requires a value for one of the inputs '%s'. "
"For a list of required inputs, see %s.help()"
% (
self.__class__.__name__,
", ".join(spec.xor),
self.__class__.__name__,
)
)
raise ValueError(msg)
def _check_mandatory_inputs(self):
""" Raises an exception if a mandatory input is Undefined
"""
for name, spec in list(self.inputs.traits(mandatory=True).items()):
value = getattr(self.inputs, name)
self._check_xor(spec, name, value)
if not isdefined(value) and spec.xor is None:
msg = (
"%s requires a value for input '%s'. "
"For a list of required inputs, see %s.help()"
% (self.__class__.__name__, name, self.__class__.__name__)
)
raise ValueError(msg)
if isdefined(value):
self._check_requires(spec, name, value)
for name, spec in list(
self.inputs.traits(mandatory=None, transient=None).items()
):
self._check_requires(spec, name, getattr(self.inputs, name))
def _check_version_requirements(self, trait_object, raise_exception=True):
""" Raises an exception on version mismatch
"""
unavailable_traits = []
# check minimum version
check = dict(min_ver=lambda t: t is not None)
names = trait_object.trait_names(**check)
if names and self.version:
version = LooseVersion(str(self.version))
for name in names:
min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
try:
too_old = min_ver > version
except TypeError as err:
msg = (
f"Nipype cannot validate the package version {version!r} for "
f"{self.__class__.__name__}. Trait {name} requires version >={min_ver}."
)
iflogger.warning(f"{msg}. Please verify validity.")
if config.getboolean("execution", "stop_on_unknown_version"):
raise ValueError(msg) from err
continue
if too_old:
unavailable_traits.append(name)
if not isdefined(getattr(trait_object, name)):
continue
if raise_exception:
raise Exception(
"Trait %s (%s) (version %s < required %s)"
% (name, self.__class__.__name__, version, min_ver)
)
# check maximum version
check = dict(max_ver=lambda t: t is not None)
names = trait_object.trait_names(**check)
if names and self.version:
version = LooseVersion(str(self.version))
for name in names:
max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
try:
too_new = max_ver < version
except TypeError as err:
msg = (
f"Nipype cannot validate the package version {version!r} for "
f"{self.__class__.__name__}. Trait {name} requires version <={max_ver}."
)
iflogger.warning(f"{msg}. Please verify validity.")
if config.getboolean("execution", "stop_on_unknown_version"):
raise ValueError(msg) from err
continue
if too_new:
unavailable_traits.append(name)
if not isdefined(getattr(trait_object, name)):
continue
if raise_exception:
raise Exception(
"Trait %s (%s) (version %s > required %s)"
% (name, self.__class__.__name__, version, max_ver)
)
return unavailable_traits
def _run_interface(self, runtime):
""" Core function that executes interface
"""
raise NotImplementedError
def _duecredit_cite(self):
""" Add the interface references to the duecredit citations
"""
for r in self.references_:
r["path"] = self.__module__
due.cite(**r)
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
def _list_outputs(self):
""" List the expected outputs
"""
if self.output_spec:
raise NotImplementedError
else:
return None
def aggregate_outputs(self, runtime=None, needed_outputs=None):
"""Collate expected outputs and apply output traits validation."""
outputs = self._outputs() # Generate an empty output spec object
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
if not predicted_outputs:
return outputs
# Precalculate the list of output trait names that should be aggregated
aggregate_names = set(predicted_outputs)
if needed_outputs is not None:
aggregate_names = set(needed_outputs).intersection(aggregate_names)
if aggregate_names: # Make sure outputs are compatible
_na_outputs = self._check_version_requirements(outputs)
na_names = aggregate_names.intersection(_na_outputs)
if na_names:
# XXX Change to TypeError in Nipype 2.0
raise KeyError(
"""\
Output trait(s) %s not available in version %s of interface %s.\
"""
% (", ".join(na_names), self.version, self.__class__.__name__)
)
for key in aggregate_names: # Final aggregation
val = predicted_outputs[key]
try:
setattr(outputs, key, val)
except TraitError as error:
if "an existing" in getattr(error, "info", "default"):
msg = (
"No such file or directory '%s' for output '%s' of a %s interface"
% (val, key, self.__class__.__name__)
)
raise FileNotFoundError(msg)
raise error
return outputs
@property
def version(self):
if self._version is None:
if str2bool(config.get("execution", "stop_on_unknown_version")):
raise ValueError(
"Interface %s has no version information" % self.__class__.__name__
)
return self._version
def load_inputs_from_json(self, json_file, overwrite=True):
"""
A convenient way to load pre-set inputs from a JSON file.
"""
with open(json_file) as fhandle:
inputs_dict = json.load(fhandle)
def_inputs = []
if not overwrite:
def_inputs = list(self.inputs.get_traitsfree().keys())
new_inputs = list(set(list(inputs_dict.keys())) - set(def_inputs))
for key in new_inputs:
if hasattr(self.inputs, key):
setattr(self.inputs, key, inputs_dict[key])
def save_inputs_to_json(self, json_file):
"""
A convenient way to save current inputs to a JSON file.
"""
inputs = self.inputs.get_traitsfree()
iflogger.debug("saving inputs %s", inputs)
with open(json_file, "w") as fhandle:
json.dump(inputs, fhandle, indent=4, ensure_ascii=False)
def _pre_run_hook(self, runtime):
"""
Perform any pre-_run_interface() processing
Subclasses may override this function to modify ``runtime`` object or
interface state
MUST return runtime object
"""
return runtime
def _post_run_hook(self, runtime):
"""
Perform any post-_run_interface() processing
Subclasses may override this function to modify ``runtime`` object or
interface state
MUST return runtime object
"""
return runtime
class SimpleInterface(BaseInterface):
""" An interface pattern that allows outputs to be set in a dictionary
called ``_results`` that is automatically interpreted by
``_list_outputs()`` to find the outputs.
When implementing ``_run_interface``, set outputs with::
self._results[out_name] = out_value
This can be a way to upgrade a ``Function`` interface to do type checking.
Examples
--------
>>> from nipype.interfaces.base import (
... SimpleInterface, BaseInterfaceInputSpec, TraitedSpec)
>>> def double(x):
... return 2 * x
...
>>> class DoubleInputSpec(BaseInterfaceInputSpec):
... x = traits.Float(mandatory=True)
...
>>> class DoubleOutputSpec(TraitedSpec):
... doubled = traits.Float()
...
>>> class Double(SimpleInterface):
... input_spec = DoubleInputSpec
... output_spec = DoubleOutputSpec
...
... def _run_interface(self, runtime):
... self._results['doubled'] = double(self.inputs.x)
... return runtime
>>> dbl = Double()
>>> dbl.inputs.x = 2
>>> dbl.run().outputs.doubled
4.0
"""
def __init__(self, from_file=None, resource_monitor=None, **inputs):
super(SimpleInterface, self).__init__(
from_file=from_file, resource_monitor=resource_monitor, **inputs
)
self._results = {}
def _list_outputs(self):
return self._results
class CommandLine(BaseInterface):
"""Implements functionality to interact with command line programs
class must be instantiated with a command argument
Parameters
----------
command : str
define base immutable `command` you wish to run
args : str, optional
optional arguments passed to base `command`
Examples
--------
>>> import pprint
>>> from nipype.interfaces.base import CommandLine
>>> cli = CommandLine(command='ls', environ={'DISPLAY': ':1'})
>>> cli.inputs.args = '-al'
>>> cli.cmdline
'ls -al'
>>> # Use get_traitsfree() to check all inputs set
>>> pprint.pprint(cli.inputs.get_traitsfree()) # doctest:
{'args': '-al',
'environ': {'DISPLAY': ':1'}}
>>> cli.inputs.get_hashval()[0][0]
('args', '-al')
>>> cli.inputs.get_hashval()[1]
'11c37f97649cd61627f4afe5136af8c0'
"""
input_spec = CommandLineInputSpec
_cmd_prefix = ""
_cmd = None
_version = None
_terminal_output = "stream"
@classmethod
def set_default_terminal_output(cls, output_type):
"""Set the default terminal output for CommandLine Interfaces.
This method is used to set default terminal output for
CommandLine Interfaces. However, setting this will not
update the output type for any existing instances. For these,
assign the <instance>.terminal_output.
"""
if output_type in VALID_TERMINAL_OUTPUT:
cls._terminal_output = output_type
else:
raise AttributeError("Invalid terminal output_type: %s" % output_type)
def __init__(self, command=None, terminal_output=None, **inputs):
super(CommandLine, self).__init__(**inputs)
self._environ = None
# Set command. Input argument takes precedence
self._cmd = command or getattr(self, "_cmd", None)
# Store dependencies in runtime object
self._ldd = str2bool(config.get("execution", "get_linked_libs", "true"))
if self._cmd is None:
raise Exception("Missing command")
if terminal_output is not None:
self.terminal_output = terminal_output
@property
def cmd(self):
"""sets base command, immutable"""
if not self._cmd:
raise NotImplementedError(
"CommandLineInterface should wrap an executable, but "
"none has been set."
)
return self._cmd
@property
def cmdline(self):
""" `command` plus any arguments (args)
validates arguments and generates command line"""
self._check_mandatory_inputs()
allargs = [self._cmd_prefix + self.cmd] + self._parse_inputs()
return " ".join(allargs)
@property
def terminal_output(self):
return self._terminal_output
@terminal_output.setter
def terminal_output(self, value):
if value not in VALID_TERMINAL_OUTPUT:
raise RuntimeError(
'Setting invalid value "%s" for terminal_output. Valid values are '
"%s." % (value, ", ".join(['"%s"' % v for v in VALID_TERMINAL_OUTPUT]))
)
self._terminal_output = value
def raise_exception(self, runtime):
raise RuntimeError(
(
"Command:\n{cmdline}\nStandard output:\n{stdout}\n"
"Standard error:\n{stderr}\nReturn code: {returncode}"
).format(**runtime.dictcopy())
)
def _get_environ(self):
return getattr(self.inputs, "environ", {})
def version_from_command(self, flag="-v", cmd=None):
iflogger.warning(
"version_from_command member of CommandLine was "
"Deprecated in nipype-1.0.0 and deleted in 1.1.0"
)
if cmd is None:
cmd = self.cmd.split()[0]
env = dict(os.environ)
if which(cmd, env=env):
out_environ = self._get_environ()
env.update(out_environ)
proc = sp.Popen(
" ".join((cmd, flag)),
shell=True,
env=env,
stdout=sp.PIPE,
stderr=sp.PIPE,
)
o, e = proc.communicate()
return o
def _run_interface(self, runtime, correct_return_codes=(0,)):
"""Execute command via subprocess
Parameters
----------
runtime : passed by the run function
Returns
-------
runtime :
updated runtime information
adds stdout, stderr, merged, cmdline, dependencies, command_path
"""
out_environ = self._get_environ()
# Initialize runtime Bunch
runtime.stdout = None
runtime.stderr = None
runtime.cmdline = self.cmdline
runtime.environ.update(out_environ)
# which $cmd
executable_name = shlex.split(self._cmd_prefix + self.cmd)[0]
cmd_path = which(executable_name, env=runtime.environ)
if cmd_path is None:
raise IOError(
'No command "%s" found on host %s. Please check that the '
"corresponding package is installed."
% (executable_name, runtime.hostname)
)
runtime.command_path = cmd_path
runtime.dependencies = (
get_dependencies(executable_name, runtime.environ)
if self._ldd
else "<skipped>"
)
runtime = run_command(runtime, output=self.terminal_output)
if runtime.returncode is None or runtime.returncode not in correct_return_codes:
self.raise_exception(runtime)
return runtime
def _format_arg(self, name, trait_spec, value):
"""A helper function for _parse_inputs
Formats a trait containing argstr metadata
"""
argstr = trait_spec.argstr
iflogger.debug("%s_%s", name, value)
if trait_spec.is_trait_type(traits.Bool) and "%" not in argstr:
# Boolean options have no format string. Just append options if True.
return argstr if value else None
# traits.Either turns into traits.TraitCompound and does not have any
# inner_traits
elif trait_spec.is_trait_type(traits.List) or (
trait_spec.is_trait_type(traits.TraitCompound) and isinstance(value, list)
):
# This is a bit simple-minded at present, and should be
# construed as the default. If more sophisticated behavior
# is needed, it can be accomplished with metadata (e.g.
# format string for list member str'ification, specifying
# the separator, etc.)
# Depending on whether we stick with traitlets, and whether or
# not we beef up traitlets.List, we may want to put some
# type-checking code here as well
sep = trait_spec.sep if trait_spec.sep is not None else " "
if argstr.endswith("..."):
# repeatable option
# --id %d... will expand to
# --id 1 --id 2 --id 3 etc.,.
argstr = argstr.replace("...", "")
return sep.join([argstr % elt for elt in value])
else:
return argstr % sep.join(str(elt) for elt in value)
else:
# Append options using format string.
return argstr % value
def _filename_from_source(self, name, chain=None):
if chain is None:
chain = []
trait_spec = self.inputs.trait(name)
retval = getattr(self.inputs, name)
source_ext = None
if not isdefined(retval) or "%s" in retval:
if not trait_spec.name_source:
return retval
# Do not generate filename when excluded by other inputs
if any(
isdefined(getattr(self.inputs, field)) for field in trait_spec.xor or ()
):
return retval
# Do not generate filename when required fields are missing
if not all(
isdefined(getattr(self.inputs, field))
for field in trait_spec.requires or ()
):
return retval
if isdefined(retval) and "%s" in retval:
name_template = retval
else:
name_template = trait_spec.name_template
if not name_template:
name_template = "%s_generated"
ns = trait_spec.name_source
while isinstance(ns, (list, tuple)):
if len(ns) > 1:
iflogger.warning("Only one name_source per trait is allowed")
ns = ns[0]
if not isinstance(ns, (str, bytes)):
raise ValueError(
"name_source of '{}' trait should be an input trait "
"name, but a type {} object was found".format(name, type(ns))
)
if isdefined(getattr(self.inputs, ns)):
name_source = ns
source = getattr(self.inputs, name_source)
while isinstance(source, list):
source = source[0]
# special treatment for files
try:
_, base, source_ext = split_filename(source)
except (AttributeError, TypeError):
base = source
else:
if name in chain:
raise NipypeInterfaceError("Mutually pointing name_sources")
chain.append(name)
base = self._filename_from_source(ns, chain)
if isdefined(base):
_, _, source_ext = split_filename(base)
else:
# Do not generate filename when required fields are missing
return retval
chain = None
retval = name_template % base
_, _, ext = split_filename(retval)
if trait_spec.keep_extension and (ext or source_ext):
if (ext is None or not ext) and source_ext:
retval = retval + source_ext
else:
retval = self._overload_extension(retval, name)
return retval
def _gen_filename(self, name):
raise NotImplementedError
def _overload_extension(self, value, name=None):
return value
def _list_outputs(self):
metadata = dict(name_source=lambda t: t is not None)
traits = self.inputs.traits(**metadata)
if traits:
outputs = self.output_spec().trait_get()
for name, trait_spec in list(traits.items()):
out_name = name
if trait_spec.output_name is not None:
out_name = trait_spec.output_name
fname = self._filename_from_source(name)
if isdefined(fname):
outputs[out_name] = os.path.abspath(fname)
return outputs
def _parse_inputs(self, skip=None):
"""Parse all inputs using the ``argstr`` format string in the Trait.
Any inputs that are assigned (not the default_value) are formatted
to be added to the command line.
Returns
-------
all_args : list
A list of all inputs formatted for the command line.
"""
all_args = []
initial_args = {}
final_args = {}
metadata = dict(argstr=lambda t: t is not None)
for name, spec in sorted(self.inputs.traits(**metadata).items()):
if skip and name in skip:
continue
value = getattr(self.inputs, name)
if spec.name_source:
value = self._filename_from_source(name)
elif spec.genfile:
if not isdefined(value) or value is None:
value = self._gen_filename(name)
if not isdefined(value):
continue
arg = self._format_arg(name, spec, value)
if arg is None:
continue
pos = spec.position
if pos is not None:
if int(pos) >= 0:
initial_args[pos] = arg
else:
final_args[pos] = arg
else:
all_args.append(arg)
first_args = [el for _, el in sorted(initial_args.items())]
last_args = [el for _, el in sorted(final_args.items())]
return first_args + all_args + last_args
class StdOutCommandLine(CommandLine):
input_spec = StdOutCommandLineInputSpec
def _gen_filename(self, name):
return self._gen_outfilename() if name == "out_file" else None
def _gen_outfilename(self):
raise NotImplementedError
class MpiCommandLine(CommandLine):
"""Implements functionality to interact with command line programs
that can be run with MPI (i.e. using 'mpiexec').
Examples
--------
>>> from nipype.interfaces.base import MpiCommandLine
>>> mpi_cli = MpiCommandLine(command='my_mpi_prog')
>>> mpi_cli.inputs.args = '-v'
>>> mpi_cli.cmdline
'my_mpi_prog -v'
>>> mpi_cli.inputs.use_mpi = True
>>> mpi_cli.inputs.n_procs = 8
>>> mpi_cli.cmdline
'mpiexec -n 8 my_mpi_prog -v'
"""
input_spec = MpiCommandLineInputSpec
@property
def cmdline(self):
"""Adds 'mpiexec' to begining of command"""
result = []
if self.inputs.use_mpi:
result.append("mpiexec")
if self.inputs.n_procs:
result.append("-n %d" % self.inputs.n_procs)
result.append(super(MpiCommandLine, self).cmdline)
return " ".join(result)
class SEMLikeCommandLine(CommandLine):
"""In SEM derived interface all outputs have corresponding inputs.
However, some SEM commands create outputs that are not defined in the XML.
In those cases one has to create a subclass of the autogenerated one and
overload the _list_outputs method. _outputs_from_inputs should still be
used but only for the reduced (by excluding those that do not have
corresponding inputs list of outputs.
"""
def _list_outputs(self):
outputs = self.output_spec().trait_get()
return self._outputs_from_inputs(outputs)
def _outputs_from_inputs(self, outputs):
for name in list(outputs.keys()):
corresponding_input = getattr(self.inputs, name)
if isdefined(corresponding_input):
if isinstance(corresponding_input, bool) and corresponding_input:
outputs[name] = os.path.abspath(self._outputs_filenames[name])
else:
if isinstance(corresponding_input, list):
outputs[name] = [
os.path.abspath(inp) for inp in corresponding_input
]
else:
outputs[name] = os.path.abspath(corresponding_input)
return outputs
def _format_arg(self, name, spec, value):
if name in list(self._outputs_filenames.keys()):
if isinstance(value, bool):
if value:
value = os.path.abspath(self._outputs_filenames[name])
else:
return ""
return super(SEMLikeCommandLine, self)._format_arg(name, spec, value)
class LibraryBaseInterface(BaseInterface):
_pkg = None
imports = ()
def __init__(self, check_import=True, *args, **kwargs):
super(LibraryBaseInterface, self).__init__(*args, **kwargs)
if check_import:
import pkgutil
failed_imports = []
for pkg in (self._pkg,) + tuple(self.imports):
if pkgutil.find_loader(pkg) is None:
failed_imports.append(pkg)
if failed_imports:
iflogger.warning(
"Unable to import %s; %s interface may fail to " "run",
failed_imports,
self.__class__.__name__,
)
@property
def version(self):
if self._version is None:
import importlib
try:
self._version = importlib.import_module(self._pkg).__version__
except (ImportError, AttributeError):
pass
return super(LibraryBaseInterface, self).version
class PackageInfo(object):
_version = None
version_cmd = None
version_file = None
@classmethod
def version(klass):
if klass._version is None:
if klass.version_cmd is not None:
try:
clout = CommandLine(
command=klass.version_cmd,
resource_monitor=False,
terminal_output="allatonce",
).run()
except IOError:
return None
raw_info = clout.runtime.stdout
elif klass.version_file is not None:
try:
with open(klass.version_file, "rt") as fobj:
raw_info = fobj.read()
except OSError:
return None
else:
return None
klass._version = klass.parse_version(raw_info)
return klass._version
@staticmethod
def parse_version(raw_info):
raise NotImplementedError
