Merge pull request #2430 from mgxd/enh/c4d

enh: c3d + c4d interface

Author: satra

nipype/interfaces/c3.py

@@ -10,9 +10,16 @@
 """
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
+import os
+from glob import glob
 
 from .base import (CommandLineInputSpec, traits, TraitedSpec, File,
-                   SEMLikeCommandLine)
+                   SEMLikeCommandLine, InputMultiPath, OutputMultiPath,
+                   CommandLine, isdefined)
+from ..utils.filemanip import split_filename
+from .. import logging
+
+iflogger = logging.getLogger("interface")
 
 
 class C3dAffineToolInputSpec(CommandLineInputSpec):
@@ -52,3 +59,150 @@ class C3dAffineTool(SEMLikeCommandLine):
 
     _cmd = 'c3d_affine_tool'
     _outputs_filenames = {'itk_transform': 'affine.txt'}
+
+
+class C3dInputSpec(CommandLineInputSpec):
+    in_file = InputMultiPath(
+        File(),
+        position=1,
+        argstr="%s",
+        mandatory=True,
+        desc="Input file (wildcard and multiple are supported).")
+    out_file = File(
+        exists=False,
+        argstr="-o %s",
+        position=-1,
+        xor=["out_files"],
+        desc="Output file of last image on the stack.")
+    out_files = InputMultiPath(
+        File(),
+        argstr="-oo %s",
+        xor=["out_file"],
+        position=-1,
+        desc=("Write all images on the convert3d stack as multiple files."
+        " Supports both list of output files or a pattern for the output"
+        " filenames (using %d substituion)."))
+    pix_type = traits.Enum(
+        "float", "char", "uchar", "short", "ushort", "int", "uint", "double",
+        argstr="-type %s",
+        desc=("Specifies the pixel type for the output image. By default,"
+        " images are written in floating point (float) format"))
+    scale = traits.Either(
+        traits.Int(), traits.Float(),
+        argstr="-scale %s",
+        desc=("Multiplies the intensity of each voxel in the last image on the"
+        " stack by the given factor."))
+    shift = traits.Either(
+        traits.Int(), traits.Float(),
+        argstr="-shift %s",
+        desc='Adds the given constant to every voxel.')
+    interp = traits.Enum(
+        "Linear", "NearestNeighbor", "Cubic", "Sinc", "Gaussian",
+        argstr="-interpolation %s",
+        desc=("Specifies the interpolation used with -resample and other"
+        " commands. Default is Linear."))
+    resample = traits.Str(
+        argstr="-resample %s",
+        desc=("Resamples the image, keeping the bounding box the same, but"
+        " changing the number of voxels in the image. The dimensions can be"
+        " specified as a percentage, for example to double the number of voxels"
+        " in each direction. The -interpolation flag affects how sampling is"
+        " performed."))
+    smooth = traits.Str(
+        argstr="-smooth %s",
+        desc=("Applies Gaussian smoothing to the image. The parameter vector"
+        " specifies the standard deviation of the Gaussian kernel."))
+    multicomp_split = traits.Bool(
+        False,
+        usedefault=True,
+        argstr="-mcr",
+        position=0,
+        desc="Enable reading of multi-component images.")
+    is_4d = traits.Bool(
+        False,
+        usedefault=True,
+        desc=("Changes command to support 4D file operations (default is"
+        " false)."))
+
+
+class C3dOutputSpec(TraitedSpec):
+    out_files = OutputMultiPath(File(exists=False))
+
+
+class C3d(CommandLine):
+    """
+    Convert3d is a command-line tool for converting 3D (or 4D) images between
+    common file formats. The tool also includes a growing list of commands for
+    image manipulation, such as thresholding and resampling. The tool can also
+    be used to obtain information about image files. More information on
+    Convert3d can be found at:
+    https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md
+
+
+    Example
+    =======
+
+    >>> from nipype.interfaces.c3 import C3d
+    >>> c3 = C3d()
+    >>> c3.inputs.in_file = "T1.nii"
+    >>> c3.inputs.pix_type = "short"
+    >>> c3.inputs.out_file = "T1.img"
+    >>> c3.cmdline
+    'c3d T1.nii -type short -o T1.img'
+    >>> c3.inputs.is_4d = True
+    >>> c3.inputs.in_file = "epi.nii"
+    >>> c3.inputs.out_file = "epi.img"
+    >>> c3.cmdline
+    'c4d epi.nii -type short -o epi.img'
+    """
+    input_spec = C3dInputSpec
+    output_spec = C3dOutputSpec
+
+    _cmd = "c3d"
+
+    def __init__(self, **inputs):
+        super(C3d, self).__init__(**inputs)
+        self.inputs.on_trait_change(self._is_4d, "is_4d")
+        if self.inputs.is_4d:
+            self._is_4d()
+
+    def _is_4d(self):
+        self._cmd = "c4d" if self.inputs.is_4d else "c3d"
+
+    def _run_interface(self, runtime):
+        cmd = self._cmd
+        if (not isdefined(self.inputs.out_file)
+            and not isdefined(self.inputs.out_files)):
+            # Convert3d does not want to override file, by default
+            # so we define a new output file
+            self._gen_outfile()
+        runtime = super(C3d, self)._run_interface(runtime)
+        self._cmd = cmd
+        return runtime
+
+    def _gen_outfile(self):
+        # if many infiles, raise exception
+        if (len(self.inputs.in_file) > 1) or ("*" in self.inputs.in_file[0]):
+            raise AttributeError("Multiple in_files found - specify either"
+                                 " `out_file` or `out_files`.")
+        _, fn, ext = split_filename(self.inputs.in_file[0])
+        self.inputs.out_file = fn + "_generated" + ext
+        # if generated file will overwrite, raise error
+        if os.path.exists(os.path.abspath(self.inputs.out_file)):
+            raise IOError("File already found - to overwrite, use `out_file`.")
+        iflogger.info("Generating `out_file`.")
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if isdefined(self.inputs.out_file):
+            outputs["out_files"] = os.path.abspath(self.inputs.out_file)
+        if isdefined(self.inputs.out_files):
+            if len(self.inputs.out_files) == 1:
+                _out_files = glob(os.path.abspath(self.inputs.out_files[0]))
+            else:
+                _out_files = [os.path.abspath(f) for f in self.inputs.out_files
+                              if os.path.exists(os.path.abspath(f))]
+            outputs["out_files"] = _out_files
+
+        return outputs
+

nipype/interfaces/tests/test_auto_C3d.py

@@ -0,0 +1,61 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..c3 import C3d
+
+
+def test_C3d_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        in_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=1,
+        ),
+        interp=dict(argstr='-interpolation %s', ),
+        is_4d=dict(usedefault=True, ),
+        multicomp_split=dict(
+            argstr='-mcr',
+            position=0,
+            usedefault=True,
+        ),
+        out_file=dict(
+            argstr='-o %s',
+            position=-1,
+            xor=['out_files'],
+        ),
+        out_files=dict(
+            argstr='-oo %s',
+            position=-1,
+            xor=['out_file'],
+        ),
+        pix_type=dict(argstr='-type %s', ),
+        resample=dict(argstr='-resample %s', ),
+        scale=dict(argstr='-scale %s', ),
+        shift=dict(argstr='-shift %s', ),
+        smooth=dict(argstr='-smooth %s', ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+    )
+    inputs = C3d.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_C3d_outputs():
+    output_map = dict(out_files=dict(), )
+    outputs = C3d.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value