resume overwrite cmdline

Author: bpinsard

nipype/interfaces/base.py

@@ -1377,16 +1377,13 @@ def _run_interface(self, runtime, correct_return_codes=[0]):
         setattr(runtime, 'command_path', cmd_path)
         setattr(runtime, 'dependencies', get_dependencies(executable_name,
                                                           runtime.environ))
-        runtime = self._run_command(runtime,output=self.inputs.terminal_output)
+        runtime = run_command(runtime, output=self.inputs.terminal_output)
         if runtime.returncode is None or \
                         runtime.returncode not in correct_return_codes:
             self.raise_exception(runtime)
 
         return runtime
 
-    def _run_command(self, runtime, output):
-        return run_command(runtime, output=output)
-
     def _exists_in_path(self, cmd, environ):
         '''
         Based on a code snippet from

nipype/interfaces/freesurfer/preprocess.py

@@ -748,7 +748,14 @@ def _list_outputs(self):
         outputs['subjects_dir'] = subjects_dir
         return outputs
 
-    def _resume_cmdline(self):
+    
+    def cmdline(self):
+        subjects_dir = self.inputs.subjects_dir
+        if not isdefined(subjects_dir):
+            subjects_dir = self._gen_subjects_dir()
+        if not os.path.isdir(
+            os.path.join(subjects_dir,self.inputs.subject_id,'mri')):
+            return super(ReconAll, self).cmdline
         self._check_mandatory_inputs()
         skip = ['T1_files']
         subjects_dir = self.inputs.subjects_dir
@@ -770,20 +777,10 @@ def _resume_cmdline(self):
         self.inputs.directive = directive
         allargs = self._parse_inputs(skip=skip)
         allargs.insert(0, self.cmd)
-        return ' '.join(allargs)
+        cmd = ' '.join(allargs)
+        iflogger.info('resume recon-all : %s'%cmd)
+        return cmd
 
-    def _run_command(self, runtime, output):
-        if isdefined(self.inputs.subjects_dir):
-            subjects_dir = self.inputs.subjects_dir
-        else:
-            subjects_dir = self._gen_subjects_dir()
-        if os.path.isdir(os.path.join(subjects_dir,
-                                      self.inputs.subject_id,'mri')):
-            setattr(runtime, 'cmdline', self._resume_cmdline())
-            iflogger.info('resume recon-all : %s'%runtime.cmdline)
-        runtime = run_command(runtime, output=self.inputs.terminal_output)
-        return super(ReconAll,self)._run_command(runtime, output)
-
 
 class BBRegisterInputSpec(FSTraitedSpec):
     subject_id = traits.Str(argstr='--s %s',

nipype/interfaces/freesurfer/utils.py

@@ -1048,7 +1048,7 @@ class ExtractMainComponent(CommandLine):
     >>> from nipype.interfaces.freesurfer import ExtractMainComponent
     >>> mcmp = ExtractMainComponent(in_file='lh.white')
     >>> mcmp.cmdline
-    'mris_extract_main_component lh.white'
+    'mris_extract_main_component lh.white lh.white_maincmp'
 
     """