interfaces.base.core

BaseInterface

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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.

Relevant Interface attributes

input_spec points to the traited class for the inputs output_spec points to the traited class for the outputs _redirect_x should be set to True when the interface requires

connecting to a $DISPLAY (default is False).
resource_monitor if False prevents resource-monitoring this
interface, if True monitoring will be enabled IFF the general Nipype config is set on (resource_monitor = true).

Inputs:

None

Outputs:

None

CommandLine

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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

>>> 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'

Inputs:

[Optional]
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

None

LibraryBaseInterface

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Inputs:

None

Outputs:

None

MpiCommandLine

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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'

Inputs:

[Optional]
use_mpi: (a boolean, nipype default value: False)
        Whether or not to run the command with mpiexec
n_procs: (an integer (int or long))
        Num processors to specify to mpiexec. Do not specify if this is
        managed externally (e.g. through SGE)
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

None

SEMLikeCommandLine

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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.

Inputs:

[Optional]
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

None

SimpleInterface

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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

Inputs:

None

Outputs:

None

StdOutCommandLine

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Inputs:

[Optional]
out_file: (a file name)
        argument: ``> %s``, position: -1
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

None