matlab_interface_devel.rst

How to wrap a MATLAB script

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

.. testcode::

        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