Small changes in a few configurators

MDANSE/Framework/Configurators/AtomsListConfigurator.py

@@ -30,10 +30,6 @@ Created on Mar 30, 2015
 :author: Eric C. Pellegrini
 '''
 
-import collections
-
-import numpy
-
 from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
@@ -98,72 +94,6 @@ class AtomsListConfigurator(IConfigurator):
         
         self['n_values'] = len(self['atoms'])
                                     
-    @staticmethod                                                                                                                        
-    def find_parent(atom, level):
-        '''
-        Retrieve recursively the parent of a given MMTK atom at a given level.
-        For example, a level of 1 will return the direct parent of the atom. 
-        
-        :note: this is a static method
-        
-        :param atom: the atom for which the parent is searched for
-        :type atom: MMTK.Atom object
-        :param level: the level of the parent
-        :type level: int
-        '''
-        
-        for _ in range(level):
-            atom = atom.parent
-            
-        return atom
-    
-    def group(self, atoms, level="atom"):
-        '''
-        Group the selected atoms according to a given granularity and update
-        the configurator with the grouping results.
-        
-        :param atoms: the atoms for 
-        :type atoms: list of MMTK.Atom
-        :param level: the level of granularity at which the atoms should be grouped
-        :type level: str
-        '''
-                                        
-        groups = collections.OrderedDict()
-        
-        for at in atoms:
-            lvl = LEVELS[level][at.topLevelChemicalObject().__class__.__name__.lower()]
-            parent = self.find_parent(at,lvl)        
-            groups.setdefault(parent,[]).append(at.index)
-        
-        self["groups"] = groups.values()
-            
-        self["n_groups"] = len(self["groups"])
-        
-        if level != "atom":
-            self["elements"] = [["dummy"]]*self["n_groups"]
-                                        
-        self["level"] = level
-                
-        self.set_contents()
-                        
-    def set_contents(self):
-        '''
-        Sets the contents of the atom selection.
-        '''
-                    
-        self["contents"] = collections.OrderedDict()
-        self['index_to_symbol'] = collections.OrderedDict()
-        for i, group in enumerate(self["elements"]):
-            for j, el in enumerate(group):
-                self["contents"].setdefault(el,[]).append(self["groups"][i][j])
-                self['index_to_symbol'][self["groups"][i][j]] = el
-                 
-        for k,v in self["contents"].items():
-            self["contents"][k] = numpy.array(v,dtype=numpy.int32)
-            
-        self["n_atoms_per_element"] = dict([(k,len(v)) for k,v in self["contents"].items()])              
-        self['n_selected_elements'] = len(self["contents"])
-                        
     def get_information(self):
         '''
         Returns some informations the atom selection.
@@ -172,13 +102,10 @@ class AtomsListConfigurator(IConfigurator):
         :rtype: str
         '''
 
-        if not self.has_key("n_selected_atoms"):
+        if not self.has_key("atoms"):
             return "No configured yet"
         
         info = []
-        info.append("Number of selected atoms:%d" % self["n_selected_atoms"])
-        info.append("Level of selection:%s" % self["level"])
-        info.append("Number of selected groups:%d" % self["n_groups"])
-        info.append("Selected elements:%s" % self["contents"].keys())
+        info.append("Number of selected %d-tuplets:%d" % (self._nAtoms,self["n_values"]))
         
         return "\n".join(info)
\ No newline at end of file

MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py

@@ -50,9 +50,7 @@ class InterpolationOrderConfigurator(SingleChoiceConfigurator):
     
     _default = "no interpolation"
         
-    orders = ["no interpolation","1st order","2nd order","3rd order","4th order","5th order"] 
-    
-    def __init__(self, name, **kwargs):
+    def __init__(self, name, orders=None,**kwargs):
         '''
         Initializes the configurator.
         
@@ -60,7 +58,10 @@ class InterpolationOrderConfigurator(SingleChoiceConfigurator):
         :type name: str.
         '''
 
-        SingleChoiceConfigurator.__init__(self, name, choices=InterpolationOrderConfigurator.orders, **kwargs)
+        if orders is None:
+            orders = ["no interpolation","1st order","2nd order","3rd order","4th order","5th order"] 
+                
+        SingleChoiceConfigurator.__init__(self, name, choices=orders, **kwargs)
 
     def configure(self, configuration, value):
         '''

MDANSE/Framework/Configurators/OutputFilesConfigurator.py

@@ -63,7 +63,7 @@ class OutputFilesConfigurator(IConfigurator):
                         
         IConfigurator.__init__(self, name, **kwargs)
 
-        self._formats = formats if formats is not None else ["netcdf"]
+        self._formats = formats if formats is not None else OutputFilesConfigurator._default[2]
     
     def configure(self, configuration, value):
         '''