3dcalc test interface

threedcalc.output

In [2]: dcalc = Threedcalc()

In [3]: dcalc.inputs.infile_a = 'struct.nii'

In [4]: dcalc.inputs.expr = 'a'

In [5]: dcalc.cmdline
Out[5]: '3dcalc -a struct.nii -expr a -prefix /software/temp/struct_3dcalc.nii'

In [6]: dcalc.inputs.start_idx = 1
/software/pysoft/nipype/nipype/interfaces/base.py:349: UserWarning: Input start_idx requires inputs: stop_idx
  warn(msg)

In [7]: dcalc.inputs.stop_idx = 4

In [8]: dcalc.cmdline
Out[8]: '3dcalc -a struct.nii[1...4] -expr a -prefix /software/temp/struct_3dcalc.nii'

threedcalc.py

import os
from nipype.interfaces.base import (CommandLineInputSpec, CommandLine,
                                    TraitedSpec, traits, isdefined, File)
from nipype.utils.filemanip import split_filename
"""
3dcalc -a ${rest}.nii.gz[${TRstart}..${TRend}] -expr 'a' -prefix $
{rest}_dr.nii.gz

3dcalc -a ${rest}_mc.nii.gz -b ${rest}_mask.nii.gz -expr 'a*b' -prefix
${rest}_ss.nii.gz
"""

class ThreedcalcInputSpec(CommandLineInputSpec):
    infile_a = File(desc = 'input file to 3dcalc',
                          argstr = '-a %s', position = 0, mandatory = True)
    infile_b = File(desc = 'operand file to 3dcalc',
                          argstr = ' -b %s', position = 1)
    expr = traits.Str(desc = 'expr', argstr = '-expr %s', position = 2,
                      mandatory = True)
    out_file = File(desc = 'output file from 3dFourier', argstr = '-prefix %s',
                    position = -1, genfile=True)
    start_idx = traits.Int(desc='start index for infile_a',
                           requires=['stop_idx'])
    stop_idx = traits.Int(desc='stop index for infile_a',
                          requires=['start_idx'])
    other = File(desc = 'other options', argstr = '')

class ThreedcalcOutputSpec(TraitedSpec):
    out_file = File(desc = ' output file', exists = True)

class Threedcalc(CommandLine):
    """Merge or edit volumes using AFNI 3dmerge command.

For complete details, see the `3dcalc Documentation.
<http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dcalc.html>`_
"""

    _cmd = '3dcalc'
    input_spec = ThreedcalcInputSpec
    output_spec = ThreedcalcOutputSpec

    def _list_outputs(self):
        outputs = self.output_spec().get()
        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
        if not isdefined(outputs['out_file']):
            outputs['out_file'] = self._gen_filename('out_file')
        return outputs

    def _format_arg(self, name, trait_spec, value):
        if name == 'infile_a':
            arg = trait_spec.argstr%value
            if isdefined(self.inputs.start_idx):
                arg += '[%d...%d]'%(self.inputs.start_idx, self.inputs.stop_idx)
            return arg
        return super(Threedcalc, self)._format_arg(name, trait_spec, value)

    def _parse_inputs(self, skip=None):
        """Skip the arguments without argstr metadata
        """
        return super(Threedcalc, self)._parse_inputs(skip=('start_idx',
                                                           'stop_idx',
                                                           'other'))

    def _gen_filename(self, name):
        """Generate output file name
        """
        if name == 'out_file':
            _, fname, ext = split_filename(self.inputs.infile_a)
            return os.path.join(os.getcwd(), ''.join((fname, '_3dcalc',
                                                        ext)))