Merge pull request #782 from satra/enh/dcm2nii

fix: make dcm2nii compatible with node for efficient execution, improve docs

Author: chrisgorgo

nipype/interfaces/dcm2nii.py

@@ -1,3 +1,12 @@
+"""The dcm2nii module provides basic functions for dicom conversion
+
+   Change directory to provide relative paths for doctests
+   >>> import os
+   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+   >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+   >>> os.chdir(datadir)
+"""
+
 from nipype.interfaces.base import (CommandLine, CommandLineInputSpec,
                                     InputMultiPath, traits, TraitedSpec,
                                     OutputMultiPath, isdefined,
@@ -8,7 +17,8 @@
 import re
 
 class Dcm2niiInputSpec(CommandLineInputSpec):
-    source_names = InputMultiPath(File(exists=True), argstr="%s", position=10, mandatory=True)
+    source_names = InputMultiPath(File(exists=True), argstr="%s", position=10,
+                                  copyfile=False, mandatory=True)
     gzip_output = traits.Bool(False, argstr='-g', position=0, usedefault=True)
     nii_output = traits.Bool(True, argstr='-n', position=1, usedefault=True)
     anonymize = traits.Bool(argstr='-a', position=2)
@@ -18,7 +28,8 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
     output_dir = Directory(exists=True, argstr='-o %s', genfile=True, position=6)
     config_file = File(exists=True, argstr="-b %s", genfile=True, position=7)
     convert_all_pars = traits.Bool(argstr='-v', position=8)
-    args = traits.Str(argstr='%s', desc='Additional parameters to the command', position=9)
+    args = traits.Str(argstr='%s', desc='Additional parameters to the command',
+                      position=9)
 
 class Dcm2niiOutputSpec(TraitedSpec):
     converted_files = OutputMultiPath(File(exists=True))
@@ -28,6 +39,21 @@ class Dcm2niiOutputSpec(TraitedSpec):
     bvals = OutputMultiPath(File(exists=True))
 
 class Dcm2nii(CommandLine):
+    """Uses MRICRON's dcm2nii to convert dicom files
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces.dcm2nii import Dcm2nii
+    >>> converter = Dcm2nii()
+    >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
+    >>> converter.inputs.gzip_output = True
+    >>> converter.inputs.output_dir = '.'
+    >>> converter.cmdline #doctest: +ELLIPSIS
+    'dcm2nii -g y -n y -i n -o . -b config.ini functional_1.dcm functional_2.dcm'
+    >>> converter.run() # doctest: +SKIP
+    """
+
     input_spec=Dcm2niiInputSpec
     output_spec=Dcm2niiOutputSpec
 

nipype/interfaces/tests/test_auto_Dcm2nii.py

@@ -45,6 +45,7 @@ def test_Dcm2nii_inputs():
     position=5,
     ),
     source_names=dict(argstr='%s',
+    copyfile=False,
     mandatory=True,
     position=10,
     ),