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chrisgorgochrisgorgo
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Merge pull request #795 from chrisfilo/enh/nipypecmd
nipype_cmd - run any Interface from a command line
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‎CHANGES

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============
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* ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
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* FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
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* ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
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* FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
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* ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
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* ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)

‎bin/nipype_cmd

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#!/usr/bin/env python
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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import sys
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from nipype.utils.nipype_cmd import main
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if __name__ == '__main__':
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main(sys.argv)

‎doc/users/index.rst

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saving_workflows
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spmmcr
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mipav
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nipypecmd
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‎doc/users/nipypecmd.rst

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.. _nipypecmd:
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============================================================
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Running Nipype Interfaces from the command line (nipype_cmd)
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============================================================
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The primary use of Nipype_ is to build automated non-interactive pipelines.
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However, sometimes there is a need to run some interfaces quickly from the command line.
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This is especially useful when running Interfaces wrapping code that does not have
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command line equivalents (nipy or SPM). Being able to run Nipype interfaces opens new
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possibilities such as inclusion of SPM processing steps in bash scripts.
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To run Nipype Interafces you need to use the nipype_cmd tool that should already be installed.
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The tool allows you to list Interfaces available in a certain package:
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.. testcode::
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$nipype_cmd nipype.interfaces.nipy
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Available Interfaces:
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SpaceTimeRealigner
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Similarity
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ComputeMask
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FitGLM
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EstimateContrast
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FmriRealign4d
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After selecting a particular Interface you can learn what inputs it requires:
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.. testcode::
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$nipype_cmd nipype.interfaces.nipy ComputeMask --help
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usage:nipype_cmd nipype.interfaces.nipy ComputeMask [-h] [--M M] [--cc CC]
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[--ignore_exception IGNORE_EXCEPTION]
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[--m M]
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[--reference_volume REFERENCE_VOLUME]
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mean_volume
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Run ComputeMask
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positional arguments:
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mean_volume mean EPI image, used to compute the threshold for the
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mask
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optional arguments:
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-h, --help show this help message and exit
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--M M upper fraction of the histogram to be discarded
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--cc CC Keep only the largest connected component
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--ignore_exception IGNORE_EXCEPTION
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Print an error message instead of throwing an
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exception in case the interface fails to run
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--m M lower fraction of the histogram to be discarded
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--reference_volume REFERENCE_VOLUME
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reference volume used to compute the mask. If none is
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give, the mean volume is used.
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Finally you can run run the Interface:
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.. testcode::
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$nipype_cmd nipype.interfaces.nipy ComputeMask mean.nii.gz
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All that from the command line without having to start python interpreter manually.
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.. include:: ../links_names.txt

‎nipype/utils/nipype_cmd.py

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import os
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import argparse
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import inspect
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import sys
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from nipype.interfaces.base import Interface
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def listClasses(module=None):
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if module:
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__import__(module)
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pkg = sys.modules[module]
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print "Available Interfaces:"
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for k,v in pkg.__dict__.items():
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if inspect.isclass(v) and issubclass(v, Interface):
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print "\t%s"%k
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def add_options(parser=None, module=None, function=None):
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interface = None
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if parser and module and function:
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__import__(module)
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interface = getattr(sys.modules[module],function)()
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inputs = interface.input_spec()
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for name, spec in sorted(interface.inputs.traits(transient=None).items()):
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desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:]
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if hasattr(spec, "mandatory") and spec.mandatory:
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parser.add_argument(name, help=desc)
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else:
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parser.add_argument("--%s"%name, dest=name,
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help=desc)
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return parser, interface
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def run_instance(interface, options):
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if interface:
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print "setting function inputs"
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for input_name, _ in interface.inputs.items():
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if getattr(options, input_name) != None:
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value = getattr(options, input_name)
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#traits cannot cast from string to float or int
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try:
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value = float(value)
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except:
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pass
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try:
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setattr(interface.inputs, input_name,
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value)
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except ValueError, e:
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print "Error when setting the value of %s: '%s'"%(input_name, str(e))
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print interface.inputs
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res = interface.run()
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print res.outputs
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def main(argv):
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if len(argv) == 2 and not argv[1].startswith("-"):
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listClasses(argv[1])
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sys.exit(0)
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parser = argparse.ArgumentParser(description='Nipype interface runner', prog=argv[0])
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parser.add_argument("module", type=str, help="Module name")
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parser.add_argument("interface", type=str, help="Interface name")
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parsed = parser.parse_args(args=argv[1:3])
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_, prog = os.path.split(argv[0])
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interface_parser = argparse.ArgumentParser(description="Run %s"%parsed.interface, prog=" ".join([prog] + argv[1:3]))
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interface_parser, interface = add_options(interface_parser, parsed.module, parsed.interface)
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args = interface_parser.parse_args(args=argv[3:])
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run_instance(interface, args)

‎nipype/utils/tests/test_cmd.py

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#!/usr/bin/env python
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from StringIO import StringIO
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import unittest, sys
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from nipype.utils import nipype_cmd
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from contextlib import contextmanager
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@contextmanager
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def capture_sys_output():
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caputure_out, capture_err = StringIO(), StringIO()
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current_out, current_err = sys.stdout, sys.stderr
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try:
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sys.stdout, sys.stderr = caputure_out, capture_err
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yield caputure_out, capture_err
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finally:
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sys.stdout, sys.stderr = current_out, current_err
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class TestNipypeCMD(unittest.TestCase):
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def test_main_returns_2_on_empty(self):
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with self.assertRaises(SystemExit) as cm:
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with capture_sys_output() as (stdout, stderr):
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nipype_cmd.main(['nipype_cmd'])
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exit_exception = cm.exception
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self.assertEqual(exit_exception.code, 2)
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self.assertEqual(stderr.getvalue(),
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"""usage: nipype_cmd [-h] module interface
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nipype_cmd: error: too few arguments
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""")
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self.assertEqual(stdout.getvalue(), '')
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def test_main_returns_0_on_help(self):
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with self.assertRaises(SystemExit) as cm:
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with capture_sys_output() as (stdout, stderr):
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nipype_cmd.main(['nipype_cmd', '-h'])
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exit_exception = cm.exception
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self.assertEqual(exit_exception.code, 0)
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self.assertEqual(stderr.getvalue(), '')
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self.assertEqual(stdout.getvalue(),
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"""usage: nipype_cmd [-h] module interface
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Nipype interface runner
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positional arguments:
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module Module name
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interface Interface name
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optional arguments:
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-h, --help show this help message and exit
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""")
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def test_list_nipy_interfacesp(self):
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with self.assertRaises(SystemExit) as cm:
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with capture_sys_output() as (stdout, stderr):
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nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy'])
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exit_exception = cm.exception
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self.assertEqual(exit_exception.code, 0)
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self.assertEqual(stderr.getvalue(), '')
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self.assertEqual(stdout.getvalue(),
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"""Available Interfaces:
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SpaceTimeRealigner
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Similarity
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ComputeMask
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FitGLM
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EstimateContrast
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FmriRealign4d
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""")
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def test_run_4d_realign_without_arguments(self):
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with self.assertRaises(SystemExit) as cm:
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with capture_sys_output() as (stdout, stderr):
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nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d'])
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exit_exception = cm.exception
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self.assertEqual(exit_exception.code, 2)
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self.assertEqual(stderr.getvalue(),
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"""usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h]
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[--between_loops BETWEEN_LOOPS]
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[--ignore_exception IGNORE_EXCEPTION]
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[--loops LOOPS]
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[--slice_order SLICE_ORDER]
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[--speedup SPEEDUP]
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[--start START]
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[--time_interp TIME_INTERP]
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[--tr_slices TR_SLICES]
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in_file tr
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nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
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""")
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self.assertEqual(stdout.getvalue(), '')
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def test_run_4d_realign_help(self):
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with self.assertRaises(SystemExit) as cm:
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with capture_sys_output() as (stdout, stderr):
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nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d', '-h'])
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exit_exception = cm.exception
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self.assertEqual(exit_exception.code, 0)
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self.assertEqual(stderr.getvalue(), '')
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self.assertTrue("Run FmriRealign4d" in stdout.getvalue())
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if __name__ == '__main__':
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unittest.main()

‎tools/run_interface.py

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