enh: add c3d and c4d interface

Author: mgxd

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 +59,126 @@ 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
+        # by default, does not want to override file, so we define a new output file
+        if not isdefined(self.inputs.out_file) and not isdefined(self.inputs.out_files):
+            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
+        assert not os.path.exists(os.path.abspath(self.inputs.out_file))
+        iflogger.info("Generating out_file to avoid overwriting")
+
+    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 not len(self.inputs.out_files) > 1:
+                _out_files = glob(os.path.abspath(self.inputs.out_files[0]))
+            else:
+                _out_files = [os.path.abspath(fl) for fl in self.inputs.out_files
+                              if os.path.exists(os.path.abspath(fl))]
+            outputs["out_files"] = _out_files
+
+        return outputs