sty: pep8 and better error messages

Author: mgxd

nipype/interfaces/c3.py

@@ -62,62 +62,80 @@ class C3dAffineTool(SEMLikeCommandLine):
 
 
 class C3dInputSpec(CommandLineInputSpec):
-    in_file = InputMultiPath(File(),
+    in_file = InputMultiPath(
+        File(),
         position=1,
         argstr="%s",
         mandatory=True,
-        desc="Input file (wildcard and multiple are supported)")
-    out_file = File(exists=False,
+        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(),
+        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",
+    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(),
+        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(),
+        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",
+    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,
+        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,
+    is_4d = traits.Bool(
+        False,
         usedefault=True,
-        desc="Changes command to support 4D file operations (default is false).")
+        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:
+    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
 
 
@@ -153,8 +171,10 @@ def _is_4d(self):
 
     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):
+        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
@@ -163,11 +183,14 @@ def _run_interface(self, 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")
+            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")
+        # 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()
@@ -177,8 +200,9 @@ def _list_outputs(self):
             if 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))]
+                _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
+