Merge pull request #557 from satra/enh/nodeconfig

Enh/nodeconfig

Author: chrisgorgo

CHANGES

@@ -9,11 +9,12 @@ Next release
        with rotation of the B-matrix, and susceptibility correction for EPI imaging using
        fieldmaps. Updated eddy_correct pipeline to support both dMRI and fMRI, and new parameters.
 * ENH: Minor improvements to FSL's FUGUE and FLIRT interfaces
-* ENH: Added optional dilation of parcels in cmtk.Parcellate 
+* ENH: Added optional dilation of parcels in cmtk.Parcellate
 * ENH: Interpolation mode added to afni.Resample
 * ENH: Function interface can accept a list of strings containing import statements
        that allow external functions to run without their imports defined in the
        function body
+* ENH: Allow node configurations to override master configuration
 
 * FIX: SpecifyModel works with 3D files correctly now.
 

examples/fmri_spm.py

@@ -98,7 +98,7 @@
 datasource.inputs.base_directory = data_dir
 datasource.inputs.template = '%s/%s.nii'
 datasource.inputs.template_args = info
-
+datasource.inputs.sort_filelist = True
 
 """Use :class:`nipype.interfaces.spm.Realign` for motion correction
 and register all images to the mean image.
@@ -194,7 +194,7 @@ def subjectinfo(subject_id):
 """
 
 modelspec = pe.Node(interface=model.SpecifySPMModel(), name= "modelspec")
-modelspec.inputs.concatenate_runs        = True
+modelspec.inputs.concatenate_runs        = False
 modelspec.inputs.input_units             = 'secs'
 modelspec.inputs.output_units            = 'secs'
 modelspec.inputs.time_repetition         = 3.
@@ -223,6 +223,8 @@ def subjectinfo(subject_id):
 
 contrastestimate = pe.Node(interface = spm.EstimateContrast(), name="contrastestimate")
 contrastestimate.inputs.contrasts = contrasts
+contrastestimate.overwrite = True
+contrastestimate.config = {'execution': {'remove_unnecessary_outputs': False}}
 
 """
 Setup the pipeline

nipype/pipeline/engine.py

@@ -143,7 +143,7 @@ def __init__(self, name=None, base_dir=None, **kwargs):
             special characters (e.g., '.', '@').
         """
         self.base_dir = base_dir
-        self.config = deepcopy(config._sections)
+        self.config = None #deepcopy(config._sections)
         if name is None:
             raise Exception("init requires a name for this %s" %
                             self.__class__.__name__)
@@ -215,6 +215,7 @@ class Workflow(WorkflowBase):
     def __init__(self, *args, **kwargs):
         super(Workflow, self).__init__(* args, **kwargs)
         self._graph = nx.DiGraph()
+        self.config = deepcopy(config._sections)
 
     # PUBLIC API
     def clone(self, name):
@@ -657,7 +658,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
         self._set_needed_outputs(flatgraph)
         execgraph = generate_expanded_graph(deepcopy(flatgraph))
         for index, node in enumerate(execgraph.nodes()):
-            node.config = self.config
+            node.config = merge_dict(deepcopy(self.config), node.config)
             node.base_dir = self.base_dir
             node.index = index
             if isinstance(node, MapNode):
@@ -1205,7 +1206,10 @@ def run(self, updatehash=False):
             Update the hash stored in the output directory
         """
         # check to see if output directory and hash exist
-        self.config = merge_dict(deepcopy(config._sections), self.config)
+        if self.config is None:
+            self.config = deepcopy(config._sections)
+        else:
+            self.config = merge_dict(deepcopy(config._sections), self.config)
         if not self._got_inputs:
             self._get_inputs()
             self._got_inputs = True

nipype/pipeline/utils.py

@@ -729,6 +729,8 @@ def merge_dict(d1, d2, merge=lambda x, y: y):
     if not isinstance(d1, dict):
         return merge(d1, d2)
     result = dict(d1)
+    if d2 is None:
+        return result
     for k, v in d2.iteritems():
         if k in result:
             result[k] = merge_dict(result[k], v, merge=merge)