/usr/share/pyshared/nipype/interfaces/base.py is in python-nipype 0.9.2-1.
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# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Package contains interfaces for using existing functionality in other packages
Exaples FSL, matlab/SPM , afni
Requires Packages to be installed
"""
from ConfigParser import NoOptionError
from copy import deepcopy
import datetime
import errno
import os
import re
import platform
from socket import getfqdn
from string import Template
import select
import subprocess
import sys
from textwrap import wrap
from datetime import datetime as dt
from dateutil.parser import parse as parseutc
from warnings import warn
from .traits_extension import (traits, Undefined, TraitDictObject,
TraitListObject, TraitError,
isdefined, File, Directory,
has_metadata)
from ..utils.filemanip import (md5, hash_infile, FileNotFoundError,
hash_timestamp, save_json,
split_filename)
from ..utils.misc import is_container, trim, str2bool
from ..utils.provenance import write_provenance
from .. import config, logging, LooseVersion
from .. import __version__
nipype_version = LooseVersion(__version__)
iflogger = logging.getLogger('interface')
__docformat__ = 'restructuredtext'
def load_template(name):
"""Load a template from the script_templates directory
Parameters
----------
name : str
The name of the file to load
Returns
-------
template : string.Template
"""
full_fname = os.path.join(os.path.dirname(__file__),
'script_templates', name)
template_file = open(full_fname)
template = Template(template_file.read())
template_file.close()
return template
class Bunch(object):
"""Dictionary-like class that provides attribute-style access to it's items.
A `Bunch` is a simple container that stores it's items as class
attributes. Internally all items are stored in a dictionary and
the class exposes several of the dictionary methods.
Examples
--------
>>> from nipype.interfaces.base import Bunch
>>> inputs = Bunch(infile='subj.nii', fwhm=6.0, register_to_mean=True)
>>> inputs
Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=True)
>>> inputs.register_to_mean = False
>>> inputs
Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=False)
Notes
-----
The Bunch pattern came from the Python Cookbook:
.. [1] A. Martelli, D. Hudgeon, "Collecting a Bunch of Named
Items", Python Cookbook, 2nd Ed, Chapter 4.18, 2005.
"""
def __init__(self, *args, **kwargs):
self.__dict__.update(*args, **kwargs)
def update(self, *args, **kwargs):
"""update existing attribute, or create new attribute
Note: update is very much like HasTraits.set"""
self.__dict__.update(*args, **kwargs)
def items(self):
"""iterates over bunch attributes as key, value pairs"""
return self.__dict__.items()
def iteritems(self):
"""iterates over bunch attributes as key, value pairs"""
warn('iteritems is deprecated, use items instead')
return self.items()
def get(self, *args):
'''Support dictionary get() functionality
'''
return self.__dict__.get(*args)
def set(self, **kwargs):
'''Support dictionary get() functionality
'''
return self.__dict__.update(**kwargs)
def dictcopy(self):
"""returns a deep copy of existing Bunch as a dictionary"""
return deepcopy(self.__dict__)
def __repr__(self):
"""representation of the sorted Bunch as a string
Currently, this string representation of the `inputs` Bunch of
interfaces is hashed to determine if the process' dirty-bit
needs setting or not. Till that mechanism changes, only alter
this after careful consideration.
"""
outstr = ['Bunch(']
first = True
for k, v in sorted(self.items()):
if not first:
outstr.append(', ')
outstr.append('%s=%r' % (k, v))
first = False
outstr.append(')')
return ''.join(outstr)
def _hash_infile(self, adict, key):
# Inject file hashes into adict[key]
stuff = adict[key]
if not is_container(stuff):
stuff = [stuff]
file_list = []
for afile in stuff:
if os.path.isfile(afile):
md5obj = md5()
fp = file(afile, 'rb')
while True:
data = fp.read(8192)
if not data:
break
md5obj.update(data)
fp.close()
md5hex = md5obj.hexdigest()
else:
md5hex = None
file_list.append((afile, md5hex))
return file_list
def _get_bunch_hash(self):
"""Return a dictionary of our items with hashes for each file.
Searches through dictionary items and if an item is a file, it
calculates the md5 hash of the file contents and stores the
file name and hash value as the new key value.
However, the overall bunch hash is calculated only on the hash
value of a file. The path and name of the file are not used in
the overall hash calculation.
Returns
-------
dict_withhash : dict
Copy of our dictionary with the new file hashes included
with each file.
hashvalue : str
The md5 hash value of the `dict_withhash`
"""
infile_list = []
for key, val in self.items():
if is_container(val):
# XXX - SG this probably doesn't catch numpy arrays
# containing embedded file names either.
if isinstance(val, dict):
# XXX - SG should traverse dicts, but ignoring for now
item = None
else:
if len(val) == 0:
raise AttributeError('%s attribute is empty' % key)
item = val[0]
else:
item = val
try:
if os.path.isfile(item):
infile_list.append(key)
except TypeError:
# `item` is not a file or string.
continue
dict_withhash = self.dictcopy()
dict_nofilename = self.dictcopy()
for item in infile_list:
dict_withhash[item] = self._hash_infile(dict_withhash, item)
dict_nofilename[item] = [val[1] for val in dict_withhash[item]]
# Sort the items of the dictionary, before hashing the string
# representation so we get a predictable order of the
# dictionary.
sorted_dict = str(sorted(dict_nofilename.items()))
return (dict_withhash, md5(sorted_dict).hexdigest())
def __pretty__(self, p, cycle):
'''Support for the pretty module
pretty is included in ipython.externals for ipython > 0.10'''
if cycle:
p.text('Bunch(...)')
else:
p.begin_group(6, 'Bunch(')
first = True
for k, v in sorted(self.items()):
if not first:
p.text(',')
p.breakable()
p.text(k + '=')
p.pretty(v)
first = False
p.end_group(6, ')')
class InterfaceResult(object):
"""Object that contains the results of running a particular Interface.
Attributes
----------
version : version of this Interface result object (a readonly property)
interface : class type
A copy of the `Interface` class that was run to generate this result.
inputs : a traits free representation of the inputs
outputs : Bunch
An `Interface` specific Bunch that contains all possible files
that are generated by the interface. The `outputs` are used
as the `inputs` to another node when interfaces are used in
the pipeline.
runtime : Bunch
Contains attributes that describe the runtime environment when
the `Interface` was run. Contains the attributes:
* cmdline : The command line string that was executed
* cwd : The directory the ``cmdline`` was executed in.
* stdout : The output of running the ``cmdline``.
* stderr : Any error messages output from running ``cmdline``.
* returncode : The code returned from running the ``cmdline``.
"""
def __init__(self, interface, runtime, inputs=None, outputs=None,
provenance=None):
self._version = 2.0
self.interface = interface
self.runtime = runtime
self.inputs = inputs
self.outputs = outputs
self.provenance = provenance
@property
def version(self):
return self._version
class BaseTraitedSpec(traits.HasTraits):
"""Provide a few methods necessary to support nipype interface api
The inputs attribute of interfaces call certain methods that are not
available in traits.HasTraits. These are provided here.
new metadata:
* usedefault : set this to True if the default value of the trait should be
used. Unless this is set, the attributes are set to traits.Undefined
new attribute:
* get_hashval : returns a tuple containing the state of the trait as a dict
and hashvalue corresponding to dict.
XXX Reconsider this in the long run, but it seems like the best
solution to move forward on the refactoring.
"""
def __init__(self, **kwargs):
""" Initialize handlers and inputs"""
# NOTE: In python 2.6, object.__init__ no longer accepts input
# arguments. HasTraits does not define an __init__ and
# therefore these args were being ignored.
#super(TraitedSpec, self).__init__(*args, **kwargs)
super(BaseTraitedSpec, self).__init__(**kwargs)
traits.push_exception_handler(reraise_exceptions=True)
undefined_traits = {}
for trait in self.copyable_trait_names():
if not self.traits()[trait].usedefault:
undefined_traits[trait] = Undefined
self.trait_set(trait_change_notify=False, **undefined_traits)
self._generate_handlers()
self.set(**kwargs)
def items(self):
""" Name, trait generator for user modifiable traits
"""
for name in sorted(self.copyable_trait_names()):
yield name, self.traits()[name]
def __repr__(self):
""" Return a well-formatted representation of the traits """
outstr = []
for name, value in sorted(self.trait_get().items()):
outstr.append('%s = %s' % (name, value))
return '\n' + '\n'.join(outstr) + '\n'
def _generate_handlers(self):
"""Find all traits with the 'xor' metadata and attach an event
handler to them.
"""
has_xor = dict(xor=lambda t: t is not None)
xors = self.trait_names(**has_xor)
for elem in xors:
self.on_trait_change(self._xor_warn, elem)
has_requires = dict(requires=lambda t: t is not None)
requires = self.trait_names(**has_requires)
for elem in requires:
self.on_trait_change(self._requires_warn, elem)
has_deprecation = dict(deprecated=lambda t: t is not None)
deprecated = self.trait_names(**has_deprecation)
for elem in deprecated:
self.on_trait_change(self._deprecated_warn, elem)
def _xor_warn(self, obj, name, old, new):
""" Generates warnings for xor traits
"""
if isdefined(new):
trait_spec = self.traits()[name]
# for each xor, set to default_value
for trait_name in trait_spec.xor:
if trait_name == name:
# skip ourself
continue
if isdefined(getattr(self, trait_name)):
self.trait_set(trait_change_notify=False,
**{'%s' % name: Undefined})
msg = ('Input "%s" is mutually exclusive with input "%s", '
'which is already set') % (name, trait_name)
raise IOError(msg)
def _requires_warn(self, obj, name, old, new):
"""Part of the xor behavior
"""
if isdefined(new):
trait_spec = self.traits()[name]
msg = None
for trait_name in trait_spec.requires:
if not isdefined(getattr(self, trait_name)):
if not msg:
msg = 'Input %s requires inputs: %s' \
% (name, ', '.join(trait_spec.requires))
if msg:
warn(msg)
def _deprecated_warn(self, obj, name, old, new):
"""Checks if a user assigns a value to a deprecated trait
"""
if isdefined(new):
trait_spec = self.traits()[name]
msg1 = ('Input %s in interface %s is deprecated.' %
(name,
self.__class__.__name__.split('InputSpec')[0]))
msg2 = ('Will be removed or raise an error as of release %s'
% trait_spec.deprecated)
if trait_spec.new_name:
if trait_spec.new_name not in self.copyable_trait_names():
raise TraitError(msg1 + ' Replacement trait %s not found' %
trait_spec.new_name)
msg3 = 'It has been replaced by %s.' % trait_spec.new_name
else:
msg3 = ''
msg = ' '.join((msg1, msg2, msg3))
if LooseVersion(str(trait_spec.deprecated)) < nipype_version:
raise TraitError(msg)
else:
warn(msg)
if trait_spec.new_name:
warn('Unsetting %s and setting %s.' % (name,
trait_spec.new_name))
self.trait_set(trait_change_notify=False,
**{'%s' % name: Undefined,
'%s' % trait_spec.new_name: new})
def _hash_infile(self, adict, key):
""" Inject file hashes into adict[key]"""
stuff = adict[key]
if not is_container(stuff):
stuff = [stuff]
file_list = []
for afile in stuff:
if is_container(afile):
hashlist = self._hash_infile({'infiles': afile}, 'infiles')
hash = [val[1] for val in hashlist]
else:
if config.get('execution',
'hash_method').lower() == 'timestamp':
hash = hash_timestamp(afile)
elif config.get('execution',
'hash_method').lower() == 'content':
hash = hash_infile(afile)
else:
raise Exception("Unknown hash method: %s" %
config.get('execution', 'hash_method'))
file_list.append((afile, hash))
return file_list
def get(self, **kwargs):
""" Returns traited class as a dict
Augments the trait get function to return a dictionary without
notification handles
"""
out = super(BaseTraitedSpec, self).get(**kwargs)
out = self._clean_container(out, Undefined)
return out
def get_traitsfree(self, **kwargs):
""" Returns traited class as a dict
Augments the trait get function to return a dictionary without
any traits. The dictionary does not contain any attributes that
were Undefined
"""
out = super(BaseTraitedSpec, self).get(**kwargs)
out = self._clean_container(out, skipundefined=True)
return out
def _clean_container(self, object, undefinedval=None, skipundefined=False):
"""Convert a traited obejct into a pure python representation.
"""
if isinstance(object, TraitDictObject) or isinstance(object, dict):
out = {}
for key, val in object.items():
if isdefined(val):
out[key] = self._clean_container(val, undefinedval)
else:
if not skipundefined:
out[key] = undefinedval
elif (isinstance(object, TraitListObject) or isinstance(object, list)
or isinstance(object, tuple)):
out = []
for val in object:
if isdefined(val):
out.append(self._clean_container(val, undefinedval))
else:
if not skipundefined:
out.append(undefinedval)
else:
out.append(None)
if isinstance(object, tuple):
out = tuple(out)
else:
if isdefined(object):
out = object
else:
if not skipundefined:
out = undefinedval
return out
def get_hashval(self, hash_method=None):
"""Return a dictionary of our items with hashes for each file.
Searches through dictionary items and if an item is a file, it
calculates the md5 hash of the file contents and stores the
file name and hash value as the new key value.
However, the overall bunch hash is calculated only on the hash
value of a file. The path and name of the file are not used in
the overall hash calculation.
Returns
-------
dict_withhash : dict
Copy of our dictionary with the new file hashes included
with each file.
hashvalue : str
The md5 hash value of the traited spec
"""
dict_withhash = {}
dict_nofilename = {}
for name, val in sorted(self.get().items()):
if isdefined(val):
trait = self.trait(name)
if has_metadata(trait.trait_type, "nohash", True):
continue
hash_files = (not has_metadata(trait.trait_type, "hash_files",
False)
and not has_metadata(trait.trait_type,
"name_source"))
dict_nofilename[name] = \
self._get_sorteddict(val, hash_method=hash_method,
hash_files=hash_files)
dict_withhash[name] = \
self._get_sorteddict(val, True, hash_method=hash_method,
hash_files=hash_files)
return (dict_withhash, md5(str(dict_nofilename)).hexdigest())
def _get_sorteddict(self, object, dictwithhash=False, hash_method=None,
hash_files=True):
if isinstance(object, dict):
out = {}
for key, val in sorted(object.items()):
if isdefined(val):
out[key] = \
self._get_sorteddict(val, dictwithhash,
hash_method=hash_method,
hash_files=hash_files)
elif isinstance(object, (list, tuple)):
out = []
for val in object:
if isdefined(val):
out.append(self._get_sorteddict(val, dictwithhash,
hash_method=hash_method,
hash_files=hash_files))
if isinstance(object, tuple):
out = tuple(out)
else:
if isdefined(object):
if (hash_files and isinstance(object, str) and
os.path.isfile(object)):
if hash_method is None:
hash_method = config.get('execution', 'hash_method')
if hash_method.lower() == 'timestamp':
hash = hash_timestamp(object)
elif hash_method.lower() == 'content':
hash = hash_infile(object)
else:
raise Exception("Unknown hash method: %s" % hash_method)
if dictwithhash:
out = (object, hash)
else:
out = hash
elif isinstance(object, float):
out = '%.10f' % object
else:
out = object
return out
class DynamicTraitedSpec(BaseTraitedSpec):
""" A subclass to handle dynamic traits
This class is a workaround for add_traits and clone_traits not
functioning well together.
"""
def __deepcopy__(self, memo):
""" bug in deepcopy for HasTraits results in weird cloning behavior for
added traits
"""
id_self = id(self)
if id_self in memo:
return memo[id_self]
dup_dict = deepcopy(self.get(), memo)
# access all keys
for key in self.copyable_trait_names():
_ = getattr(self, key)
# clone once
dup = self.clone_traits(memo=memo)
for key in self.copyable_trait_names():
try:
_ = getattr(dup, key)
except:
pass
# clone twice
dup = self.clone_traits(memo=memo)
dup.set(**dup_dict)
return dup
class TraitedSpec(BaseTraitedSpec):
""" Create a subclass with strict traits.
This is used in 90% of the cases.
"""
_ = traits.Disallow
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 # defines if the interface can reuse partial results
# after interruption
@property
def can_resume(self):
return self._can_resume
_always_run = False # should the interface be always run even if the
# inputs were not changed?
@property
def always_run(self):
return self._always_run
def __init__(self, **inputs):
"""Initialize command with given args and inputs."""
raise NotImplementedError
@classmethod
def help(cls):
""" Prints class help"""
raise NotImplementedError
@classmethod
def _inputs_help(cls):
""" Prints inputs help"""
raise NotImplementedError
@classmethod
def _outputs_help(cls):
""" Prints outputs help"""
raise NotImplementedError
@classmethod
def _outputs(cls):
""" Initializes outputs"""
raise NotImplementedError
@property
def version(self):
raise NotImplementedError
def run(self):
"""Execute the command."""
raise NotImplementedError
def aggregate_outputs(self, runtime=None, needed_outputs=None):
"""Called to populate outputs"""
raise NotImplementedError
def _list_outputs(self):
""" List expected outputs"""
raise NotImplementedError
def _get_filecopy_info(self):
""" Provides information about file inputs to copy or link to cwd.
Necessary for pipeline operation
"""
raise NotImplementedError
class BaseInterfaceInputSpec(TraitedSpec):
ignore_exception = traits.Bool(False, desc="Print an error message instead \
of throwing an exception in case the interface fails to run", usedefault=True,
nohash=True)
class BaseInterface(Interface):
"""Implements common interface functionality.
Implements
----------
* 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.
"""
input_spec = BaseInterfaceInputSpec
_version = None
_additional_metadata = []
def __init__(self, **inputs):
if not self.input_spec:
raise Exception('No input_spec in class: %s' %
self.__class__.__name__)
self.inputs = self.input_spec(**inputs)
@classmethod
def help(cls, returnhelp=False):
""" Prints class help
"""
if cls.__doc__:
#docstring = cls.__doc__.split('\n')
#docstring = [trim(line, '') for line in docstring]
docstring = trim(cls.__doc__).split('\n') + ['']
else:
docstring = ['']
allhelp = '\n'.join(docstring + cls._inputs_help() + [''] +
cls._outputs_help() + [''])
if returnhelp:
return allhelp
else:
print(allhelp)
@classmethod
def _get_trait_desc(self, inputs, name, spec):
desc = spec.desc
xor = spec.xor
requires = spec.requires
manhelpstr = ['\t%s' % name]
try:
setattr(inputs, name, None)
except TraitError as excp:
def_val = ''
if getattr(spec, 'usedefault'):
def_arg = getattr(spec, 'default_value')()[1]
def_val = ', nipype default value: %s' % str(def_arg)
line = "(%s%s)" % (excp.info, def_val)
manhelpstr = wrap(line, 70,
initial_indent=manhelpstr[0]+': ',
subsequent_indent='\t\t ')
if desc:
for line in desc.split('\n'):
line = re.sub("\s+", " ", line)
manhelpstr += wrap(line, 70,
initial_indent='\t\t',
subsequent_indent='\t\t')
if xor:
line = '%s' % ', '.join(xor)
manhelpstr += wrap(line, 70,
initial_indent='\t\tmutually_exclusive: ',
subsequent_indent='\t\t ')
if requires:
others = [field for field in requires if field != name]
line = '%s' % ', '.join(others)
manhelpstr += wrap(line, 70,
initial_indent='\t\trequires: ',
subsequent_indent='\t\t ')
return manhelpstr
@classmethod
def _inputs_help(cls):
""" Prints description for input parameters
"""
helpstr = ['Inputs::']
inputs = cls.input_spec()
if len(inputs.traits(transient=None).items()) == 0:
helpstr += ['', '\tNone']
return helpstr
manhelpstr = ['', '\t[Mandatory]']
mandatory_items = inputs.traits(mandatory=True)
for name, spec in sorted(mandatory_items.items()):
manhelpstr += cls._get_trait_desc(inputs, name, spec)
opthelpstr = ['', '\t[Optional]']
for name, spec in sorted(inputs.traits(transient=None).items()):
if spec in mandatory_items:
continue
opthelpstr += cls._get_trait_desc(inputs, name, spec)
if manhelpstr:
helpstr += manhelpstr
if opthelpstr:
helpstr += opthelpstr
return helpstr
@classmethod
def _outputs_help(cls):
""" Prints description for output parameters
"""
helpstr = ['Outputs::', '']
if cls.output_spec:
outputs = cls.output_spec()
for name, spec in sorted(outputs.traits(transient=None).items()):
helpstr += cls._get_trait_desc(outputs, name, spec)
if len(helpstr) == 2:
helpstr += ['\tNone']
return helpstr
def _outputs(self):
""" Returns a bunch containing output fields for the class
"""
outputs = None
if self.output_spec:
outputs = self.output_spec()
return outputs
@classmethod
def _get_filecopy_info(cls):
""" Provides information about file inputs to copy or link to cwd.
Necessary for pipeline operation
"""
info = []
if cls.input_spec is None:
return info
metadata = dict(copyfile=lambda t: t is not None)
for name, spec in sorted(cls.input_spec().traits(**metadata).items()):
info.append(dict(key=name,
copy=spec.copyfile))
return info
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):
msg = ("%s requires a value for input '%s' because one of %s "
"is set. For a list of required inputs, see %s.help()" %
(self.__class__.__name__, name,
', '.join(spec.requires), 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 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 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 = []
version = LooseVersion(str(self.version))
if not version:
return
# check minimum version
check = dict(min_ver=lambda t: t is not None)
names = trait_object.trait_names(**check)
for name in names:
min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
if min_ver > version:
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 = dict(max_ver=lambda t: t is not None)
names = trait_object.trait_names(**check)
for name in names:
max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
if max_ver < version:
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 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
"""
self.inputs.set(**inputs)
self._check_mandatory_inputs()
self._check_version_requirements(self.inputs)
interface = self.__class__
# initialize provenance tracking
env = deepcopy(os.environ.data)
runtime = Bunch(cwd=os.getcwd(),
returncode=None,
duration=None,
environ=env,
startTime=dt.isoformat(dt.utcnow()),
endTime=None,
platform=platform.platform(),
hostname=getfqdn(),
version=self.version)
try:
runtime = self._run_interface(runtime)
outputs = self.aggregate_outputs(runtime)
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
runtime.duration = timediff.days * 86400 + timediff.seconds + \
timediff.microseconds/100000.
results = InterfaceResult(interface, runtime,
inputs=self.inputs.get_traitsfree(),
outputs=outputs)
prov_record = None
if str2bool(config.get('execution', 'write_provenance')):
prov_record = write_provenance(results)
results.provenance = prov_record
except Exception, e:
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
runtime.duration = timediff.days * 86400 + timediff.seconds + \
timediff.microseconds/100000.
if len(e.args) == 0:
e.args = ("")
message = "\nInterface %s failed to run." % self.__class__.__name__
if config.has_option('logging', 'interface_level') and \
config.get('logging', 'interface_level').lower() == 'debug':
inputs_str = "Inputs:" + str(self.inputs) + "\n"
else:
inputs_str = ''
if len(e.args) == 1 and isinstance(e.args[0], str):
e.args = (e.args[0] + " ".join([message, inputs_str]),)
else:
e.args += (message, )
if inputs_str != '':
e.args += (inputs_str, )
#exception raising inhibition for special cases
import traceback
runtime.traceback = traceback.format_exc()
runtime.traceback_args = e.args
inputs = None
try:
inputs = self.inputs.get_traitsfree()
except Exception, e:
pass
results = InterfaceResult(interface, runtime, inputs=inputs)
prov_record = None
if str2bool(config.get('execution', 'write_provenance')):
try:
prov_record = write_provenance(results)
except Exception:
prov_record = None
results.provenance = prov_record
if hasattr(self.inputs, 'ignore_exception') and \
isdefined(self.inputs.ignore_exception) and \
self.inputs.ignore_exception:
pass
else:
raise
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 check for existence
"""
predicted_outputs = self._list_outputs()
outputs = self._outputs()
if predicted_outputs:
_unavailable_outputs = []
if outputs:
_unavailable_outputs = \
self._check_version_requirements(self._outputs())
for key, val in predicted_outputs.items():
if needed_outputs and key not in needed_outputs:
continue
if key in _unavailable_outputs:
raise KeyError(('Output trait %s not available in version '
'%s of interface %s. Please inform '
'developers.') % (key, self.version,
self.__class__.__name__))
try:
setattr(outputs, key, val)
_ = getattr(outputs, key)
except TraitError, error:
if hasattr(error, 'info') and \
error.info.startswith("an existing"):
msg = ("File/Directory '%s' not found for %s output "
"'%s'." % (val, self.__class__.__name__, key))
raise FileNotFoundError(msg)
else:
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
class Stream(object):
"""Function to capture stdout and stderr streams with timestamps
stackoverflow.com/questions/4984549/merge-and-sync-stdout-and-stderr/5188359
"""
def __init__(self, name, impl):
self._name = name
self._impl = impl
self._buf = ''
self._rows = []
self._lastidx = 0
def fileno(self):
"Pass-through for file descriptor."
return self._impl.fileno()
def read(self, drain=0):
"Read from the file descriptor. If 'drain' set, read until EOF."
while self._read(drain) is not None:
if not drain:
break
def _read(self, drain):
"Read from the file descriptor"
fd = self.fileno()
buf = os.read(fd, 4096)
if not buf and not self._buf:
return None
if '\n' not in buf:
if not drain:
self._buf += buf
return []
# prepend any data previously read, then split into lines and format
buf = self._buf + buf
if '\n' in buf:
tmp, rest = buf.rsplit('\n', 1)
else:
tmp = buf
rest = None
self._buf = rest
now = datetime.datetime.now().isoformat()
rows = tmp.split('\n')
self._rows += [(now, '%s %s:%s' % (self._name, now, r), r)
for r in rows]
for idx in range(self._lastidx, len(self._rows)):
iflogger.info(self._rows[idx][1])
self._lastidx = len(self._rows)
def run_command(runtime, output=None, timeout=0.01):
"""Run a command, read stdout and stderr, prefix with timestamp.
The returned runtime contains a merged stdout+stderr log with timestamps
"""
PIPE = subprocess.PIPE
proc = subprocess.Popen(runtime.cmdline,
stdout=PIPE,
stderr=PIPE,
shell=True,
cwd=runtime.cwd,
env=runtime.environ)
result = {}
errfile = os.path.join(runtime.cwd, 'stderr.nipype')
outfile = os.path.join(runtime.cwd, 'stdout.nipype')
if output == 'stream':
streams = [Stream('stdout', proc.stdout), Stream('stderr', proc.stderr)]
def _process(drain=0):
try:
res = select.select(streams, [], [], timeout)
except select.error, e:
iflogger.info(str(e))
if e[0] == errno.EINTR:
return
else:
raise
else:
for stream in res[0]:
stream.read(drain)
while proc.returncode is None:
proc.poll()
_process()
_process(drain=1)
# collect results, merge and return
result = {}
temp = []
for stream in streams:
rows = stream._rows
temp += rows
result[stream._name] = [r[2] for r in rows]
temp.sort()
result['merged'] = [r[1] for r in temp]
if output == 'allatonce':
stdout, stderr = proc.communicate()
result['stdout'] = stdout.split('\n')
result['stderr'] = stderr.split('\n')
result['merged'] = ''
if output == 'file':
stderr = open(errfile, 'wt')
stdout = open(outfile, 'wt')
proc = subprocess.Popen(runtime.cmdline,
stdout=stdout,
stderr=stderr,
shell=True,
cwd=runtime.cwd,
env=runtime.environ)
ret_code = proc.wait()
stderr.flush()
stdout.flush()
result['stdout'] = [line.strip() for line in open(outfile).readlines()]
result['stderr'] = [line.strip() for line in open(errfile).readlines()]
result['merged'] = ''
if output == 'none':
proc.communicate()
result['stdout'] = []
result['stderr'] = []
result['merged'] = ''
runtime.stderr = '\n'.join(result['stderr'])
runtime.stdout = '\n'.join(result['stdout'])
runtime.merged = result['merged']
runtime.returncode = proc.returncode
return runtime
def get_dependencies(name, environ):
"""Return library dependencies of a dynamically linked executable
Uses otool on darwin, ldd on linux. Currently doesn't support windows.
"""
PIPE = subprocess.PIPE
if sys.platform == 'darwin':
proc = subprocess.Popen('otool -L `which %s`' % name,
stdout=PIPE,
stderr=PIPE,
shell=True,
env=environ)
elif 'linux' in sys.platform:
proc = subprocess.Popen('ldd `which %s`' % name,
stdout=PIPE,
stderr=PIPE,
shell=True,
env=environ)
else:
return 'Platform %s not supported' % sys.platform
o, e = proc.communicate()
return o.rstrip()
class CommandLineInputSpec(BaseInterfaceInputSpec):
args = traits.Str(argstr='%s', desc='Additional parameters to the command')
environ = traits.DictStrStr(desc='Environment variables', usedefault=True,
nohash=True)
terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none',
desc=('Control terminal output: `stream` - '
'displays to terminal immediately, '
'`allatonce` - waits till command is '
'finished to display output, `file` - '
'writes output to file, `none` - output'
' is ignored'),
nohash=True, mandatory=True)
class CommandLine(BaseInterface):
"""Implements functionality to interact with command line programs
class must be instantiated with a command argument
Parameters
----------
command : string
define base immutable `command` you wish to run
args : string, optional
optional arguments passed to base `command`
Examples
--------
>>> from nipype.interfaces.base import CommandLine
>>> cli = CommandLine(command='ls', environ={'DISPLAY': ':1'})
>>> cli.inputs.args = '-al'
>>> cli.cmdline
'ls -al'
>>> cli.inputs.trait_get() # doctest: +NORMALIZE_WHITESPACE
{'ignore_exception': False, 'terminal_output': 'stream',
'environ': {'DISPLAY': ':1'}, 'args': '-al'}
>>> cli.inputs.get_hashval()
({'args': '-al'}, 'a2f45e04a34630c5f33a75ea2a533cdd')
"""
input_spec = CommandLineInputSpec
_cmd = None
_version = None
_terminal_output = 'stream'
def __init__(self, command=None, **inputs):
super(CommandLine, self).__init__(**inputs)
self._environ = None
if not hasattr(self, '_cmd'):
self._cmd = None
if self.cmd is None and command is None:
raise Exception("Missing command")
if command:
self._cmd = command
self.inputs.on_trait_change(self._terminal_output_update,
'terminal_output')
if not isdefined(self.inputs.terminal_output):
self.inputs.terminal_output = self._terminal_output
else:
self._terminal_output_update()
def _terminal_output_update(self):
self._terminal_output = self.inputs.terminal_output
@classmethod
def set_default_terminal_output(cls, output_type):
"""Set the default output type for FSL classes.
This method is used to set the default output type for all fSL
subclasses. However, setting this will not update the output
type for any existing instances. For these, assign the
<instance>.inputs.output_type.
"""
if output_type in ['stream', 'allatonce', 'file', 'none']:
cls._terminal_output = output_type
else:
raise AttributeError('Invalid terminal output_type: %s' %
output_type)
@property
def cmd(self):
"""sets base command, immutable"""
return self._cmd
@property
def cmdline(self):
""" `command` plus any arguments (args)
validates arguments and generates command line"""
self._check_mandatory_inputs()
allargs = self._parse_inputs()
allargs.insert(0, self.cmd)
return ' '.join(allargs)
def raise_exception(self, runtime):
message = "Command:\n" + runtime.cmdline + "\n"
message += "Standard output:\n" + runtime.stdout + "\n"
message += "Standard error:\n" + runtime.stderr + "\n"
message += "Return code: " + str(runtime.returncode)
raise RuntimeError(message)
@classmethod
def help(cls, returnhelp=False):
allhelp = super(CommandLine, cls).help(returnhelp=True)
allhelp = "Wraps command **%s**\n\n" % cls._cmd + allhelp
if returnhelp:
return allhelp
else:
print(allhelp)
def _get_environ(self):
out_environ = {}
try:
display_var = config.get('execution', 'display_variable')
out_environ = {'DISPLAY': display_var}
except NoOptionError:
pass
iflogger.debug(out_environ)
if isdefined(self.inputs.environ):
out_environ.update(self.inputs.environ)
return out_environ
def version_from_command(self, flag='-v'):
cmdname = self.cmd.split()[0]
if self._exists_in_path(cmdname):
env = deepcopy(os.environ.data)
out_environ = self._get_environ()
env.update(out_environ)
proc = subprocess.Popen(' '.join((cmdname, flag)),
shell=True,
env=env,
stdout=subprocess.PIPE,
stderr=subprocess.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
"""
setattr(runtime, 'stdout', None)
setattr(runtime, 'stderr', None)
setattr(runtime, 'cmdline', self.cmdline)
out_environ = self._get_environ()
runtime.environ.update(out_environ)
executable_name = self.cmd.split()[0]
exist_val, cmd_path = self._exists_in_path(executable_name,
runtime.environ)
if not exist_val:
raise IOError("%s could not be found on host %s" %
(self.cmd.split()[0], runtime.hostname))
setattr(runtime, 'command_path', cmd_path)
setattr(runtime, 'dependencies', get_dependencies(executable_name,
runtime.environ))
runtime = run_command(runtime, output=self.inputs.terminal_output)
if runtime.returncode is None or \
runtime.returncode not in correct_return_codes:
self.raise_exception(runtime)
return runtime
def _exists_in_path(self, cmd, environ):
'''
Based on a code snippet from
http://orip.org/2009/08/python-checking-if-executable-exists-in.html
'''
if 'PATH' in environ:
input_environ = environ.get("PATH")
else:
input_environ = os.environ.get("PATH", "")
extensions = os.environ.get("PATHEXT", "").split(os.pathsep)
for directory in input_environ.split(os.pathsep):
base = os.path.join(directory, cmd)
options = [base] + [(base + ext) for ext in extensions]
for filename in options:
if os.path.exists(filename):
return True, filename
return False, None
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, str(value)))
if trait_spec.is_trait_type(traits.Bool) and "%" not in argstr:
if value:
# Boolean options have no format string. Just append options
# if True.
return argstr
else:
return 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 sep is None:
sep = ' '
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):
trait_spec = self.inputs.trait(name)
retval = getattr(self.inputs, name)
if not isdefined(retval) or "%s" in retval:
if not trait_spec.name_source:
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"
if isinstance(trait_spec.name_source, list):
for ns in trait_spec.name_source:
if isdefined(getattr(self.inputs, ns)):
name_source = ns
break
else:
name_source = trait_spec.name_source
source = getattr(self.inputs, name_source)
while isinstance(source, list):
source = source[0]
_, base, _ = split_filename(source)
retval = name_template % base
_, _, ext = split_filename(retval)
if trait_spec.keep_extension and ext:
return retval
return self._overload_extension(retval)
return retval
def _gen_filename(self, name):
raise NotImplementedError
def _overload_extension(self, value):
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().get()
for name, trait_spec in traits.iteritems():
out_name = name
if trait_spec.output_name != None:
out_name = trait_spec.output_name
outputs[out_name] = \
os.path.abspath(self._filename_from_source(name))
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.genfile or spec.name_source:
value = self._filename_from_source(name)
if not isdefined(value):
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 pos >= 0:
initial_args[pos] = arg
else:
final_args[pos] = arg
else:
all_args.append(arg)
first_args = [arg for pos, arg in sorted(initial_args.items())]
last_args = [arg for pos, arg in sorted(final_args.items())]
return first_args + all_args + last_args
class StdOutCommandLineInputSpec(CommandLineInputSpec):
out_file = File(argstr="> %s", position=-1, genfile=True)
class StdOutCommandLine(CommandLine):
input_spec = StdOutCommandLineInputSpec
def _gen_filename(self, name):
if name is 'out_file':
return self._gen_outfilename()
else:
return None
def _gen_outfilename(self):
raise NotImplementedError
class MpiCommandLineInputSpec(CommandLineInputSpec):
use_mpi = traits.Bool(False,
desc="Whether or not to run the command with mpiexec",
usedefault=True)
n_procs = traits.Int(desc="Num processors to specify to mpiexec. Do not "
"specify if this is managed externally (e.g. through "
"SGE)")
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().get()
return self._outputs_from_inputs(outputs)
def _outputs_from_inputs(self, outputs):
for name in 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 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 MultiPath(traits.List):
""" Abstract class - shared functionality of input and output MultiPath
"""
def validate(self, object, name, value):
if not isdefined(value) or \
(isinstance(value, list) and len(value) == 0):
return Undefined
newvalue = value
if not isinstance(value, list) \
or (self.inner_traits()
and isinstance(self.inner_traits()[0].trait_type, traits.List)
and not isinstance(self.inner_traits()[0].trait_type,
InputMultiPath)
and isinstance(value, list)
and value
and not isinstance(value[0], list)):
newvalue = [value]
value = super(MultiPath, self).validate(object, name, newvalue)
if len(value) > 0:
return value
self.error(object, name, value)
class OutputMultiPath(MultiPath):
""" Implements a user friendly traits that accepts one or more
paths to files or directories. This is the output version which
return a single string whenever possible (when it was set to a
single value or a list of length 1). Default value of this trait
is _Undefined. It does not accept empty lists.
XXX This should only be used as a final resort. We should stick to
established Traits to the extent possible.
XXX This needs to be vetted by somebody who understands traits
>>> from nipype.interfaces.base import OutputMultiPath
>>> class A(TraitedSpec):
... foo = OutputMultiPath(File(exists=False))
>>> a = A()
>>> a.foo
<undefined>
>>> a.foo = '/software/temp/foo.txt'
>>> a.foo
'/software/temp/foo.txt'
>>> a.foo = ['/software/temp/foo.txt']
>>> a.foo
'/software/temp/foo.txt'
>>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt']
>>> a.foo
['/software/temp/foo.txt', '/software/temp/goo.txt']
"""
def get(self, object, name):
value = self.get_value(object, name)
if len(value) == 0:
return Undefined
elif len(value) == 1:
return value[0]
else:
return value
def set(self, object, name, value):
self.set_value(object, name, value)
class InputMultiPath(MultiPath):
""" Implements a user friendly traits that accepts one or more
paths to files or directories. This is the input version which
always returns a list. Default value of this trait
is _Undefined. It does not accept empty lists.
XXX This should only be used as a final resort. We should stick to
established Traits to the extent possible.
XXX This needs to be vetted by somebody who understands traits
>>> from nipype.interfaces.base import InputMultiPath
>>> class A(TraitedSpec):
... foo = InputMultiPath(File(exists=False))
>>> a = A()
>>> a.foo
<undefined>
>>> a.foo = '/software/temp/foo.txt'
>>> a.foo
['/software/temp/foo.txt']
>>> a.foo = ['/software/temp/foo.txt']
>>> a.foo
['/software/temp/foo.txt']
>>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt']
>>> a.foo
['/software/temp/foo.txt', '/software/temp/goo.txt']
"""
pass
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