register_atlas() and multilabel() aren't connecting properly -- print…

…ing multilabel's annot_files list as ['U','U']
nipy · May 30, 2012 · 4fbef6e · 4fbef6e
1 parent 9e985af
commit 4fbef6e
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Showing 2 changed files with 19 additions and 21 deletions.
diff --git a/atlases.py b/atlases.py
@@ -315,12 +315,15 @@ def vote_labels(label_lists):
 
     return labels_max, label_votes, label_counts
 
-def multilabel(hemi, subject_id, surface_file, annot_files):
+def multilabel(surface_file, annot_files):
     """
     Load VTK surfaces and write majority vote labels as VTK files, 
     according to multiple labelings (atlas_annot_name).
     """
+    print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
+    print(surface_file)
     print(annot_files)
+    print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
     """
     from os import path, getcwd
     import pyvtk

diff --git a/pipeline.py b/pipeline.py
@@ -103,6 +103,7 @@
 mbflow.connect([(infosource, datasource, 
                  [('subject_id','subject_id'),
                   ('hemi','hemi')])])
+#mbflow.add_nodes([datasink])
 
 ##############################################################################
 #   Surface input and conversion
@@ -142,13 +143,6 @@
 template_reg.inputs.templates_path = templates_path
 template_reg.inputs.template_reg_name = template_reg_name
 
-flo1.add_nodes([template_reg])
-mbflow.connect([(infosource, flo1, 
-                 [('hemi', 'Register_template.hemi')])])
-mbflow.connect([(datasource, flo1, 
-                 [('sph_surface_files', 
-                   'Register_template.sph_surface_file')])])
-
 # Atlas registration
 atlas_reg = pe.MapNode(util.Function(input_names=['hemi',
                                                   'subject_id',
@@ -164,27 +158,28 @@
 atlas_reg.inputs.atlases_path = atlases_path
 atlas_reg.inputs.atlas_annot_name = atlas_annot_name
 
-flo1.add_nodes([atlas_reg])
-mbflow.connect([(infosource, flo1, 
-                 [('hemi', 'Register_atlases.hemi'),
-                  ('subject_id', 'Register_atlases.subject_id')])])
-flo1.connect([(template_reg, atlas_reg, 
-               [('template_reg_name', 'template_reg_name')])])
-
 # Majority vote labeling
-majority_vote = pe.Node(util.Function(input_names=['hemi',
-                                                   'subject_id',
-                                                   'surface_file',
+majority_vote = pe.Node(util.Function(input_names=['surface_file',
                                                    'annot_files'],
                                       output_names=['output_files'],
                                       function = multilabel),
                         name='Vote_majority')
 
-flo1.add_nodes([majority_vote])
+# Add and connect the above nodes
+flo1.add_nodes([template_reg, atlas_reg, majority_vote])
+
+mbflow.connect([(infosource, flo1,
+                 [('hemi', 'Register_template.hemi')]),
+                (datasource, flo1, 
+                 [('sph_surface_files',
+                   'Register_template.sph_surface_file')])])
 
 mbflow.connect([(infosource, flo1, 
-                 [('hemi', 'Vote_majority.hemi'),
-                  ('subject_id', 'Vote_majority.subject_id')])])
+                 [('hemi', 'Register_atlases.hemi'),
+                  ('subject_id', 'Register_atlases.subject_id')])])
+flo1.connect([(template_reg, atlas_reg, 
+               [('template_reg_name', 'template_reg_name')])])
+
 if use_freesurfer_surfaces:
     mbflow.connect([(surface_conversion, flo1, 
                      [('converted', 'Vote_majority.surface_file')])])