Subject id depracated

CHANGES

@@ -19,6 +19,11 @@ Bugs fixed
 
 * Workflow engine
   - allows workflows to be relocatable
+
+API changes
+-----------
+
+* subject_id in ModelSpec is now deprecated
 
 Release 0.3.2 (Aug 03, 2010)
 ============================

examples/fsl_tutorial2.py

@@ -131,10 +131,10 @@ def getmiddlevolume(func):
 Plot the estimated motion parameters
 """
 
-plotmotion = ps.MapNode(interface=fsl.PlotMotionParameters(in_source='fsl'),
-                        name='plotmotion',
+plot_motion = pe.MapNode(interface=fsl.PlotMotionParams(in_source='fsl'),
+                        name='plot_motion',
                         iterfield=['in_file'])
-plotmotion.iterables = ('plot_type', ['rotations', 'translations'])
+plot_motion.iterables = ('plot_type', ['rotations', 'translations'])
 preproc.connect(motion_correct, 'par_file', plot_motion, 'in_file')
 
 """
@@ -620,8 +620,7 @@ def subjectinfo(subject_id):
 l1pipeline.config = dict(crashdump_dir=os.path.abspath('./fsl/crashdumps'))
 
 l1pipeline.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
-                    (infosource, firstlevel, [(('subject_id', subjectinfo), 'modelfit.modelspec.subject_info'),
-                                              ('subject_id', 'modelfit.modelspec.subject_id')]),
+                    (infosource, firstlevel, [(('subject_id', subjectinfo), 'modelfit.modelspec.subject_info')]),
                     (datasource, firstlevel, [('struct','preproc.inputspec.struct'),
                                               ('func', 'preproc.inputspec.func'),
                                               ]),

examples/spm_auditory_tutorial.py

@@ -352,8 +352,7 @@ def makelist(item):
 level1.base_dir = os.path.abspath('spm_auditory_tutorial/workingdir')
 
 level1.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
-                (datasource,l1pipeline,[('struct', 'preproc.coregister.source')]),
-                (infosource,l1pipeline,[('subject_id','analysis.modelspec.subject_id')]),
+                (datasource,l1pipeline,[('struct', 'preproc.coregister.source')])
                 ])
 if merge_to_4d:
     level1.connect([(datasource,l1pipeline,[('func','preproc.merge.in_files')])])

examples/spm_face_tutorial.py

@@ -438,9 +438,7 @@ def makelist(item):
 
 level1.connect([(infosource, datasource, [('subject_id', 'subject_id')]),
                 (datasource,l1pipeline,[('struct', 'preproc.coregister.source'),
-                                        ('func','preproc.realign.in_files')]),
-                (infosource,l1pipeline,[('subject_id','analysis.modelspec.subject_id'),
-                                        ('subject_id','paramanalysis.modelspec.subject_id')]),
+                                        ('func','preproc.realign.in_files')])
                 ])
 
 

examples/spm_tutorial.py

@@ -275,8 +275,7 @@ def subjectinfo(subject_id):
 		  (datasource,normalize,[('struct', 'source')]),
 		  (coregister, normalize, [('coregistered_files','apply_to_files')]),
 		  (normalize, smooth, [('normalized_files', 'in_files')]),
-                  (infosource,modelspec,[('subject_id','subject_id'),
-                                         (('subject_id', subjectinfo),
+                  (infosource,modelspec,[(('subject_id', subjectinfo),
                                           'subject_info')]),
                   (realign,modelspec,[('realignment_parameters','realignment_parameters')]),
                   (smooth,modelspec,[('smoothed_files','functional_runs')]),

examples/spm_tutorial2.py

@@ -374,8 +374,7 @@ def subjectinfo(subject_id):
                 (datasource,l1pipeline,[('func','preproc.realign.in_files'),
                                         ('struct', 'preproc.coregister.target'),
                                         ('struct', 'preproc.normalize.source')]),
-                (infosource,l1pipeline,[('subject_id','analysis.modelspec.subject_id'),
-                                        (('subject_id', subjectinfo),
+                (infosource,l1pipeline,[(('subject_id', subjectinfo),
                                           'analysis.modelspec.subject_info')]),
                 ])
 

nipype/algorithms/modelgen.py

@@ -22,11 +22,10 @@
  InputMultiPath, traits, File
 from nipype.utils.misc import isdefined
 from nipype.utils.filemanip import filename_to_list, loadflat
-from nipype.interfaces.spm import scans_for_fnames
 
 class SpecifyModelInputSpec(TraitedSpec):
-    subject_id = traits.Either(traits.Str(),traits.Int(),mandatory=True,
-        desc ="Subject identifier used as a parameter to the subject_info_func.")
+    subject_id = traits.Either(traits.Str(),traits.Int(),
+        desc ="This input is deprecated and will be removed in the future releases. Update your code.")
     subject_info = traits.List(mandatory=True,
                           desc= "List subject specific condition information")
     """    . If all