Merge pull request #1132 from nipy/enh/cleanup_dcm2nii

Enh/cleanup dcm2nii

Author: blakedewey

CHANGES

@@ -57,6 +57,7 @@ Next release
 * FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
 * ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
 * FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
+* ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
 
 Release 0.10.0 (October 10, 2014)
 ============

nipype/interfaces/dcm2nii.py

@@ -16,6 +16,7 @@
 from nipype.utils.filemanip import split_filename
 import re
 
+
 class Dcm2niiInputSpec(CommandLineInputSpec):
     source_names = InputMultiPath(File(exists=True), argstr="%s", position=-1,
                                   copyfile=False, mandatory=True, xor=['source_dir'])
@@ -37,13 +38,15 @@ class Dcm2niiInputSpec(CommandLineInputSpec):
     convert_all_pars = traits.Bool(True, argstr='-v', usedefault=True)
     reorient_and_crop = traits.Bool(False, argstr='-x', usedefault=True)
 
+
 class Dcm2niiOutputSpec(TraitedSpec):
     converted_files = OutputMultiPath(File(exists=True))
     reoriented_files = OutputMultiPath(File(exists=True))
     reoriented_and_cropped_files = OutputMultiPath(File(exists=True))
     bvecs = OutputMultiPath(File(exists=True))
     bvals = OutputMultiPath(File(exists=True))
 
+
 class Dcm2nii(CommandLine):
     """Uses MRICRON's dcm2nii to convert dicom files
 
@@ -55,14 +58,12 @@ class Dcm2nii(CommandLine):
     >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']
     >>> converter.inputs.gzip_output = True
     >>> converter.inputs.output_dir = '.'
-    >>> converter.cmdline #doctest: +ELLIPSIS
+    >>> converter.cmdline
     'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm'
-    >>> converter.run() # doctest: +SKIP
     """
 
-    input_spec=Dcm2niiInputSpec
-    output_spec=Dcm2niiOutputSpec
-
+    input_spec = Dcm2niiInputSpec
+    output_spec = Dcm2niiOutputSpec
     _cmd = 'dcm2nii'
 
     def _format_arg(self, opt, spec, val):
@@ -81,12 +82,14 @@ def _format_arg(self, opt, spec, val):
         return super(Dcm2nii, self)._format_arg(opt, spec, val)
 
     def _run_interface(self, runtime):
-
+        self._config_created = False
         new_runtime = super(Dcm2nii, self)._run_interface(runtime)
         (self.output_files,
          self.reoriented_files,
          self.reoriented_and_cropped_files,
          self.bvecs, self.bvals) = self._parse_stdout(new_runtime.stdout)
+        if self._config_created:
+            os.remove('config.ini')
         return new_runtime
 
     def _parse_stdout(self, stdout):
@@ -99,22 +102,21 @@ def _parse_stdout(self, stdout):
         last_added_file = None
         for line in stdout.split("\n"):
             if not skip:
-                file = None
+                out_file = None
                 if line.startswith("Saving "):
-                    file = line[len("Saving "):]
+                    out_file = line[len("Saving "):]
                 elif line.startswith("GZip..."):
-                    #for gzipped outpus files are not absolute
+                    # for gzipped outpus files are not absolute
                     if isdefined(self.inputs.output_dir):
                         output_dir = self.inputs.output_dir
                     else:
                         output_dir = self._gen_filename('output_dir')
-                    file = os.path.abspath(os.path.join(output_dir,
-                                                        line[len("GZip..."):]))
+                    out_file = os.path.abspath(os.path.join(output_dir, line[len("GZip..."):]))
                 elif line.startswith("Number of diffusion directions "):
                     if last_added_file:
                         base, filename, ext = split_filename(last_added_file)
-                        bvecs.append(os.path.join(base,filename + ".bvec"))
-                        bvals.append(os.path.join(base,filename + ".bval"))
+                        bvecs.append(os.path.join(base, filename + ".bvec"))
+                        bvals.append(os.path.join(base, filename + ".bval"))
                 elif re.search('.*-->(.*)', line):
                     val = re.search('.*-->(.*)', line)
                     val = val.groups()[0]
@@ -123,11 +125,11 @@ def _parse_stdout(self, stdout):
                     else:
                         output_dir = self._gen_filename('output_dir')
                     val = os.path.join(output_dir, val)
-                    file = val
+                    out_file = val
 
-                if file:
-                    files.append(file)
-                    last_added_file = file
+                if out_file:
+                    files.append(out_file)
+                    last_added_file = out_file
                     continue
 
                 if line.startswith("Reorienting as "):
@@ -156,11 +158,11 @@ def _gen_filename(self, name):
         if name == 'output_dir':
             return os.getcwd()
         elif name == 'config_file':
+            self._config_created = True
             config_file = "config.ini"
             f = open(config_file, "w")
             # disable interactive mode
             f.write("[BOOL]\nManualNIfTIConv=0\n")
             f.close()
             return config_file
         return None
-