How to wrap a MATLAB script

Example 1

This is a minimal script for wrapping MATLAB code. You should replace the MATLAB code template, and define approriate inputs and outputs.

from nipype.interfaces.matlab import MatlabCommand
from nipype.interfaces.base import TraitedSpec, \
    BaseInterface, BaseInterfaceInputSpec, File
import os
from string import Template


class ConmapTxt2MatInputSpec(BaseInterfaceInputSpec):
    in_file = File(exists=True, mandatory=True)
    out_file = File('cmatrix.mat', usedefault=True)


class ConmapTxt2MatOutputSpec(TraitedSpec):
    out_file = File(exists=True)


class ConmapTxt2Mat(BaseInterface):
    input_spec = ConmapTxt2MatInputSpec
    output_spec = ConmapTxt2MatOutputSpec

    def _run_interface(self, runtime):
        d = dict(in_file=self.inputs.in_file,
                 out_file=self.inputs.out_file)
        # This is your MATLAB code template
        script = Template("""in_file = '$in_file';
                             out_file = '$out_file';
                             ConmapTxt2Mat(in_file, out_file);
                             exit;
                          """).substitute(d)

        # mfile = True  will create an .m file with your script and executed.
        # Alternatively
        # mfile can be set to False which will cause the matlab code to be
        # passed
        # as a commandline argument to the matlab executable
        # (without creating any files).
        # This, however, is less reliable and harder to debug
        # (code will be reduced to
        # a single line and stripped of any comments).
        mlab = MatlabCommand(script=script, mfile=True)
        result = mlab.run()
        return result.runtime

    def _list_outputs(self):
        outputs = self._outputs().get()
        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
        return outputs

Example source code

You can download the source code of this example.

Example 2

By subclassing nipype.interfaces.matlab.MatlabCommand for your main class, and nipype.interfaces.matlab.MatlabInputSpec for your input and output spec, you gain access to some useful MATLAB hooks

from nipype.interfaces.base import traits
from nipype.interfaces.base import TraitedSpec
from nipype.interfaces.matlab import MatlabCommand, MatlabInputSpec


class HelloWorldInputSpec(MatlabInputSpec):
    name = traits.Str(mandatory=True,
                      desc='Name of person to say hello to')


class HelloWorldOutputSpec(TraitedSpec):
    matlab_output = traits.Str()


class HelloWorld(MatlabCommand):
    """Basic Hello World that displays Hello <name> in MATLAB

    Returns
    -------

    matlab_output : capture of matlab output which may be
                    parsed by user to get computation results

    Examples
    --------

    >>> hello = HelloWorld()
    >>> hello.inputs.name = 'hello_world'
    >>> out = hello.run()
    >>> print out.outputs.matlab_output
    """
    input_spec = HelloWorldInputSpec
    output_spec = HelloWorldOutputSpec

    def _my_script(self):
        """This is where you implement your script"""
        script = """
        disp('Hello %s Python')
        two = 1 + 1
        """ % (self.inputs.name)
        return script

    def run(self, **inputs):
        # Inject your script
        self.inputs.script = self._my_script()
        results = super(MatlabCommand, self).run(**inputs)
        stdout = results.runtime.stdout
        # Attach stdout to outputs to access matlab results
        results.outputs.matlab_output = stdout
        return results

    def _list_outputs(self):
        outputs = self._outputs().get()
        return outputs

Example source code

You can download the source code of this example.