Put interpolation argument back in. Renamed the input/outputspec.

Author: chrisgorgo

examples/smri_ants_build_template_new.py

@@ -127,21 +127,21 @@
 BeginANTS = buildTemplateIteration1.get_node("BeginANTS")
 BeginANTS.plugin_args={'qsub_args': '-S /bin/bash -pe smp1 8-12 -l mem_free=6000M -o /dev/null -e /dev/null queue_name', 'overwrite': True}
 
-tbuilder.connect(initAvg, 'output_average_image', buildTemplateIteration1, 'InputSpec.fixed_image')
-tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration1, 'InputSpec.ListOfImagesDictionaries')
-tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration1, 'InputSpec.registrationImageTypes')
-tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration1, 'InputSpec.interpolationMapping')
+tbuilder.connect(initAvg, 'output_average_image', buildTemplateIteration1, 'inputspec.fixed_image')
+tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration1, 'inputspec.ListOfImagesDictionaries')
+tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration1, 'inputspec.registrationImageTypes')
+tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration1, 'inputspec.interpolationMapping')
 """
 7. Define the second iteration of template building
 """
 
 buildTemplateIteration2 = antsRegistrationTemplateBuildSingleIterationWF('iteration02')
 BeginANTS = buildTemplateIteration2.get_node("BeginANTS")
 BeginANTS.plugin_args={'qsub_args': '-S /bin/bash -pe smp1 8-12 -l mem_free=6000M -o /dev/null -e /dev/null queue_name', 'overwrite': True}
-tbuilder.connect(buildTemplateIteration1, 'OutputSpec.template', buildTemplateIteration2, 'InputSpec.fixed_image')
-tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration2, 'InputSpec.ListOfImagesDictionaries')
-tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration2, 'InputSpec.registrationImageTypes')
-tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration2, 'InputSpec.interpolationMapping')
+tbuilder.connect(buildTemplateIteration1, 'outputspec.template', buildTemplateIteration2, 'inputspec.fixed_image')
+tbuilder.connect(datasource, 'ListOfImagesDictionaries', buildTemplateIteration2, 'inputspec.ListOfImagesDictionaries')
+tbuilder.connect(datasource, 'registrationImageTypes', buildTemplateIteration2, 'inputspec.registrationImageTypes')
+tbuilder.connect(datasource, 'interpolationMapping', buildTemplateIteration2, 'inputspec.interpolationMapping')
 
 """
 8. Move selected files to a designated results folder

nipype/interfaces/ants/registration.py

@@ -193,6 +193,17 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
 
     use_estimate_learning_rate_once = traits.List(traits.Bool(), desc='')
     use_histogram_matching = traits.List(traits.Bool(argstr='%s'), default=True, usedefault=True)
+    # Interpolation flag  
+    interpolation = traits.Enum('Linear',
+                                'NearestNeighbor',
+                                'CosineWindowedSinc',
+                                'WelchWindowedSinc',
+                                'HammingWindowedSinc',
+                                'LanczosWindowedSinc',
+                                # 'MultiLabel',
+                                # 'Gaussian',
+                                # 'BSpline',
+                                argstr='%s', usedefault = True)
     # Transform flags
     write_composite_transform = traits.Bool(argstr='--write-composite-transform %d', default=False, usedefault=True, desc='')
     transforms = traits.List(traits.Enum('Rigid', 'Affine', 'CompositeAffine',
@@ -323,7 +334,10 @@ def _format_arg(self, opt, spec, val):
             if self.inputs.invert_initial_moving_transform:
                 return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
             else:
-                return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
+                return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform    
+        elif opt == 'interpolation':  
+            # TODO: handle multilabel, gaussian, and bspline options  
+            return '--interpolation %s' % self.inputs.interpolation
         elif opt == 'output_transform_prefix':
             if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:
                 return '--output [ %s, %s, %s ]' % (self.inputs.output_transform_prefix, self.inputs.output_warped_image, self.inputs.output_inverse_warped_image )