itkNaryMaximumImageFilter definition

itkNaryMaximumImageFilter.py

import os

from nipype.interfaces.base import (CommandLine, CommandLineInputSpec,
                                    TraitedSpec, File,
                                    InputMultiPath, traits)
from nipype.utils.misc import isdefined
from nipype.utils.filemanip import fname_presuffix

class ITKNaryMaximumImageFilterInputSpec(CommandLineInputSpec):
    tcl_script = File(exists=True, argstr = '-b %s', position = 1,
                      desc='Full path to itkNary tcl script', mandatory = True)
    in_files = InputMultiPath(File(exists=True), argstr='%s...', sep=',',
                              desc = "List of images", mandatory = True, position = 2)
    file_mode = traits.Str(argstr='%s', desc = "fileMode", exists = True,
                           mandatory = True, position = -2)
    out_file = File(argstr = '%s', desc = "output filename",
                   position = -1, genfile=True)

class ITKNaryMaximumImageFilterOutputSpec(TraitedSpec):
    out_file = File(exists = True, desc = "outFilename")

class ITKNaryMaximumImageFilter(CommandLine):
    input_spec = ITKNaryMaximumImageFilterInputSpec
    output_spec = ITKNaryMaximumImageFilterOutputSpec
    _cmd = "brains3"

    def _gen_outfilename(self):
        outfile = self.inputs.out_file
        if not isdefined(outfile):
            outfile = fname_presuffix(self.inputs.in_files[0],suffix='_out')
        return outfile

    def _gen_filename(self, name):
        if name == 'out_file':
            return self._gen_outfilename()
        return None

    def _list_outputs(self):
        outputs = self.output_spec().get()
        outputs['out_file'] = self._gen_outfilename()
        return outputs

usage

In [35]: filter = itktest.ITKNaryMaximumImageFilter()

In [36]: filter.inputs.tcl_script = os.path.abspath('script.tcl')

In [37]: filter.inputs.in_files = ['img1.nii','img2.nii', 'img3.nii']

In [38]: filter.inputs.file_mode = 'x'

In [39]: filter.cmdline
Out[39]: 'brains3 -b /software/temp/nipype-tutorial/temp/script.tcl img1.nii,img2.nii,img3.nii x img1_out.nii'