Merge remote-tracking branch 'nipype_proper/master' into FreeSurfer53

Author: ellisdg

nipype/pipeline/plugins/sge.py

@@ -60,7 +60,7 @@ def is_initializing(self):
         return self._job_queue_state == "initializing"
 
     def is_zombie(self):
-        return self._job_queue_state == "zombie"
+        return self._job_queue_state == "zombie" or self._job_queue_state == "finished"
 
     def is_running(self):
         return self._job_queue_state == "running"

nipype/workflows/smri/freesurfer/autorecon1.py

@@ -1,10 +1,7 @@
-import sys
-import os
-import nipype
 from nipype.interfaces.utility import Function,IdentityInterface
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
-from .utils import copy_file, copy_files
+from .utils import copy_file
 
 
 def checkT1s(T1_files, cw256=False):

nipype/workflows/smri/freesurfer/autorecon2.py

@@ -1,5 +1,3 @@
-import os
-import nipype
 from nipype.interfaces.utility import Function, IdentityInterface, Merge
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *

nipype/workflows/smri/freesurfer/autorecon3.py

@@ -1,10 +1,7 @@
-import os
-import nipype
-from nipype.interfaces.utility import Function, IdentityInterface, Merge
+from nipype.interfaces.utility import IdentityInterface, Merge
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
 from .ba_maps import create_ba_maps_wf
-from .utils import createsrcsubj
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,

nipype/workflows/smri/freesurfer/recode_tables/fs2abc.csv

@@ -79,8 +79,7 @@ def link_masks(subjects_dir, subject_id):
     wf.connect(autorecon_resume, "subject_id", outputnode, "subject_id")
     return wf
 
-def create_reconall_workflow(name="ReconAll", plugin_args=None,
-                             recoding_file=None):
+def create_reconall_workflow(name="ReconAll", plugin_args=None):
     """Creates the ReconAll workflow in nipype.
 
     Example
@@ -554,15 +553,6 @@ def completemethod(datasinked_files, subject_id):
                       (inputspec, completion, [('subject_id', 'subject_id')]),
                       (completion, postds_outputspec, [('subject_id', 'subject_id')])])
 
-
-    #### Workflow additions go here
-    if recoding_file:
-        from utils import create_recoding_wf
-        recode = create_recoding_wf(recoding_file)
-        reconall.connect([(ar3_wf, recode, [('outputspec.aseg', 'inputspec.labelmap')]),
-                          (recode, outputspec, [('outputspec.recodedlabelmap', 'recoded_labelmap')])])
-
-
     return reconall