Standardize sub-workflow creation.

qipipe/pipeline/mask.py

@@ -23,10 +23,10 @@ def run(subject, session, scan, time_series, **opts):
         parameters
     :return: the mask file location
     """
-    wf_gen = MaskWorkflow(**opts)
+    workflow = MaskWorkflow(**opts)
 
     # Run the workflow.
-    return wf_gen.run(subject, session, scan, time_series)
+    return workflow.run(subject, session, scan, time_series)
 
 
 class MaskWorkflow(WorkflowBase):

qipipe/pipeline/modeling.py

@@ -223,6 +223,7 @@ def run(self, subject, session, scan, time_series, **opts):
         :param time_series: the 4D modeling input time series file
             location
         :param opts: the following keyword parameters:
+        :option bolus_arrival_index: the bolus uptake volume index
         :option mask: the XNAT mask resource name
         :return: the modeling result dictionary
         """
@@ -321,10 +322,10 @@ def _create_workflow(self, **opts):
         # parent_opt = '.'.join(modules[:-1])
         # child_opt = modules[-1]
         # if parent_opt:
-        #     wf_gen = __import__(parent_opt, globals(), locals(), [child_opt])
+        #     workflow = __import__(parent_opt, globals(), locals(), [child_opt])
         # else:
-        #     wf_gen = __import__(child_opt)
-        # child_wf = wf_gen.create_workflow(**opts)
+        #     workflow = __import__(child_opt)
+        # child_wf = workflow.create_workflow(**opts)
         #
         if self.technique == 'bolero':
             child_wf = self._create_bolero_workflow(**opts)

qipipe/pipeline/registration.py

@@ -266,7 +266,7 @@ def _create_execution_workflow(self, reference, dest, recursive=False):
 
         # The execution workflow.
         exec_wf = pe.Workflow(
-            name='reg_exec', base_dir=self.workflow.base_dir
+            name='registration', base_dir=self.workflow.base_dir
         )
 
         # The registration workflow input.
@@ -405,7 +405,7 @@ def _create_realignment_workflow(self, **opts):
 
         # The workflow.
         base_dir = opts.get('base_dir', tempfile.mkdtemp(prefix='qipipe_'))
-        realign_wf = pe.Workflow(name='registration', base_dir=self.base_dir)
+        realign_wf = pe.Workflow(name=self.technique, base_dir=self.base_dir)
 
         # The workflow input.
         in_fields = ['subject', 'session', 'scan', 'moving_image',

qipipe/pipeline/staging.py

@@ -99,7 +99,7 @@ def run(subject, session, scan, *in_dirs, **opts):
         # Look for the 3D volume output in the workflow base directory
         # work area directly instead.
         vol_file = ("%s/staging/stack/volume%03d.nii.gz" %
-                    (base_dir, volume))
+                    (stg_wf.base_dir, volume))
         if os.path.exists(vol_file):
             vol_nii_files.append(vol_file)
         elif not stg_wf.dry_run: