bru2nii.py

"""The bru2nii module provides basic functions for dicom conversion
"""

import os
from .base import (
    CommandLine,
    CommandLineInputSpec,
    traits,
    TraitedSpec,
    isdefined,
    File,
    Directory,
)


class Bru2InputSpec(CommandLineInputSpec):
    input_dir = Directory(
        desc="Input Directory", exists=True, mandatory=True, position=-1, argstr="%s"
    )
    actual_size = traits.Bool(
        argstr="-a",
        desc="Keep actual size - otherwise x10 scale so animals match human.",
    )
    force_conversion = traits.Bool(
        argstr="-f",
        desc="Force conversion of localizers images (multiple slice orientations).",
    )
    compress = traits.Bool(argstr="-z", desc='gz compress images (".nii.gz").')
    append_protocol_name = traits.Bool(
        argstr="-p", desc="Append protocol name to output filename."
    )
    output_filename = traits.Str(
        argstr="-o %s",
        desc='Output filename (".nii" will be appended, or ".nii.gz" if the "-z" compress option is selected)',
        genfile=True,
    )


class Bru2OutputSpec(TraitedSpec):
    nii_file = File(exists=True)


class Bru2(CommandLine):
    """Uses bru2nii's Bru2 to convert Bruker files

    Examples
    ========

    >>> from nipype.interfaces.bru2nii import Bru2
    >>> converter = Bru2()
    >>> converter.inputs.input_dir = "brukerdir"
    >>> converter.cmdline  # doctest: +ELLIPSIS
    'Bru2 -o .../data/brukerdir brukerdir'
    """

    input_spec = Bru2InputSpec
    output_spec = Bru2OutputSpec
    _cmd = "Bru2"

    def _list_outputs(self):
        outputs = self._outputs().get()
        if isdefined(self.inputs.output_filename):
            output_filename1 = os.path.abspath(self.inputs.output_filename)
        else:
            output_filename1 = self._gen_filename("output_filename")
        if self.inputs.compress:
            outputs["nii_file"] = output_filename1 + ".nii.gz"
        else:
            outputs["nii_file"] = output_filename1 + ".nii"
        return outputs

    def _gen_filename(self, name):
        if name == "output_filename":
            outfile = os.path.join(
                os.getcwd(), os.path.basename(os.path.normpath(self.inputs.input_dir))
            )
            return outfile