Merge branch 'master' into enh/JSONFileInterface

Conflicts:
	CHANGES

Author: oesteban

CHANGES

@@ -2,6 +2,7 @@ Next release
 ============
 
 * ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
+* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
 * ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 
 	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
 	   (https://github.com/nipy/nipype/pull/990/files)
@@ -12,6 +13,7 @@ Next release
 * FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is 
 	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
 * FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
+* FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
 
 Release 0.10.0 (October 10, 2014)
 ============

nipype/interfaces/ants/legacy.py

@@ -94,16 +94,21 @@ class antsIntroduction(ANTSCommand):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
+        transmodel = self.inputs.transformation_model
+
+        # When transform is set as 'RI'/'RA', wrap fields should not be expected 
+        # The default transformation is GR, which outputs the wrap fields
+        if not isdefined(transmodel) or (isdefined(transmodel) and transmodel not in ['RI', 'RA']):
+            outputs['warp_field'] = os.path.join(os.getcwd(),
+                                 self.inputs.out_prefix +
+                                 'Warp.nii.gz')
+            outputs['inverse_warp_field'] = os.path.join(os.getcwd(),
+                                     self.inputs.out_prefix +
+                                     'InverseWarp.nii.gz')
 
         outputs['affine_transformation'] = os.path.join(os.getcwd(),
                                                         self.inputs.out_prefix +
                                                         'Affine.txt')
-        outputs['warp_field'] = os.path.join(os.getcwd(),
-                                             self.inputs.out_prefix +
-                                             'Warp.nii.gz')
-        outputs['inverse_warp_field'] = os.path.join(os.getcwd(),
-                                                     self.inputs.out_prefix +
-                                                     'InverseWarp.nii.gz')
         outputs['input_file'] = os.path.join(os.getcwd(),
                                              self.inputs.out_prefix +
                                              'repaired.nii.gz')

nipype/interfaces/base.py

@@ -757,17 +757,12 @@ def _get_trait_desc(self, inputs, name, spec):
 
         manhelpstr = ['\t%s' % name]
 
-        try:
-            setattr(inputs, name, None)
-        except TraitError as excp:
-            def_val = ''
-            if getattr(spec, 'usedefault'):
-                def_arg = getattr(spec, 'default_value')()[1]
-                def_val = ', nipype default value: %s' % str(def_arg)
-            line = "(%s%s)" % (excp.info, def_val)
-            manhelpstr = wrap(line, 70,
-                              initial_indent=manhelpstr[0]+': ',
-                              subsequent_indent='\t\t ')
+        type_info = spec.full_info(inputs, name, None) 
+        default = ', nipype default value: %s' % spec.default_value()[1]
+        line = "(%s%s)" % (type_info, default if spec.usedefault else '')
+        manhelpstr = wrap(line, 70, 
+                          initial_indent=manhelpstr[0]+': ',
+                          subsequent_indent='\t\t ')
 
         if desc:
             for line in desc.split('\n'):

nipype/interfaces/spm/preprocess.py

@@ -497,20 +497,24 @@ def _list_outputs(self):
                 outputs['normalized_files'] = self.inputs.apply_to_files
             outputs['normalized_source'] = self.inputs.source
         elif 'write' in self.inputs.jobtype:
+            if isdefined(self.inputs.write_preserve) and self.inputs.write_preserve:
+                prefixNorm = ''.join(['m', self.inputs.out_prefix])
+            else:
+                prefixNorm = self.inputs.out_prefix
             outputs['normalized_files'] = []
             if isdefined(self.inputs.apply_to_files):
                 filelist = filename_to_list(self.inputs.apply_to_files)
                 for f in filelist:
                     if isinstance(f, list):
-                        run = [fname_presuffix(in_f, prefix=self.inputs.out_prefix) for in_f in f]
+                        run = [fname_presuffix(in_f, prefix=prefixNorm) for in_f in f]
                     else:
-                        run = [fname_presuffix(f, prefix=self.inputs.out_prefix)]
+                        run = [fname_presuffix(f, prefix=prefixNorm)]
                     outputs['normalized_files'].extend(run)
             if isdefined(self.inputs.source):
                 outputs['normalized_source'] = []
                 for imgf in filename_to_list(self.inputs.source):
                     outputs['normalized_source'].append(fname_presuffix(imgf,
-                                                        prefix=self.inputs.out_prefix))
+                                                        prefix=prefixNorm))
 
         return outputs