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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
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