Getting AttributeError when receving Matlab output using nipype

[balandongiv]

Great work from the team.

Moving forward, I would like to link nipype with Matlab. Specifically, the objective is to submit some argument from Python through nipype to a Matlab script and, submit the Matlab output back to Python.

Working with an extension of the example, in this case, we have a .m (i.e., name get_print) file which has been set to be under Matlab search path.

The .m file is

function opt=get_print(ipt_str)

opt = 1 + 1;
if_possible_return_multiple_output=3 % Suggestion to return multiple output is welcome
end

Then, the Python script is as below

def _my_script(self): 
    """This is where you implement your script"""
    script = """
    %s=get_print(%s)
    """ % (self.inputs.name, self.output.val)
    return script

When execute the Python script, the Python compiler return an error;

AttributeError: ‘HelloWorld’ object has no attribute ‘output’

May I know how solve this issue when expecting an output from Matlab operation?

The complete Python code is

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):

    input_spec = HelloWorldInputSpec
    output_spec = HelloWorldOutputSpec

    def _my_script(self): # similar to _bipolar_reference
        """This is where you implement your script"""
        script = """
        %s=get_print(%s)
        """ % (self.inputs.name, self.output.val)
        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


hello = HelloWorld()
hello.inputs.name = 'hello_world'
out = hello.run()
output_matlab=out.outputs.matlab_output