Removed unused modules

Bug fixes with user definition related widgets

MDANSE/App/GUI/ComboWidgets/ConfigurationPanel.py

@@ -2,6 +2,8 @@ import wx
 
 from MDANSE import REGISTRY
 
+from MDANSE.Framework.Configurators.IConfigurator import ConfiguratorError
+
 class ConfigurationPanel(wx.Panel):
     
     def __init__(self, parent, configurable):
@@ -44,21 +46,21 @@ class ConfigurationPanel(wx.Panel):
         
         return dict([(k,v.get_value()) for k,v in self._widgets.items()])
     
-#     def validate(self):
-# 
-#         for w in self._widgets.values():
-#             w.SetBackgroundColour(wx.NullColour)
-#             w.Refresh()
-#              
-#         try:
-#             self._configurable.parameters = self.get_value()
-#         except ConfiguratorError as e:
-#             d = wx.MessageDialog(self, str(e), style=wx.ICON_ERROR|wx.STAY_ON_TOP|wx.CENTRE)
-#             d.ShowModal()
-#             w = self._widgets[e.configurator.name]
-#             w.SetBackgroundColour("Pink")
-#             w.Refresh()
-#             w.SetFocus()
-#             return False
-#         else:
-#             return True
+    def validate(self):
+ 
+        for w in self._widgets.values():
+            w.SetBackgroundColour(wx.NullColour)
+            w.Refresh()
+              
+        parameters = {}
+        try:
+            parameters.update(self.get_value())
+        except ConfiguratorError as e:
+            d = wx.MessageDialog(self, str(e), style=wx.ICON_ERROR|wx.STAY_ON_TOP|wx.CENTRE)
+            d.ShowModal()
+            w = self._widgets[e.configurator.name]
+            w.SetBackgroundColour("Pink")
+            w.Refresh()
+            w.SetFocus()
+        finally:
+            return parameters

MDANSE/App/GUI/Framework/Plugins/JobPlugin.py

@@ -100,7 +100,10 @@ class JobPlugin(ComponentPlugin):
                          
     def on_run(self, event=None):
 
-        parameters = self._parametersPanel.get_value()
+        parameters = self._parametersPanel.validate()
+        
+        if not parameters:
+            return
         
         name = self._jobClass.set_name()
         
@@ -123,10 +126,10 @@ class JobPlugin(ComponentPlugin):
         
     def on_save(self, event=None):
 
-        if not self._parametersPanel.validate():
+        parameters = self._parametersPanel.validate()
+        
+        if not parameters:
             return
-
-        parameters = self._parametersPanel.get_value()
         
         d = wx.FileDialog(self, "Save MDANSE python script", style = wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT, wildcard = "Python files (*.py)|*.py")
         

MDANSE/App/GUI/Framework/Widgets/AtomSelectionWidget.py

@@ -151,6 +151,8 @@ class Query(object):
 
 class AtomSelectionDialog(UserDefinitionsDialog):
     
+    type = 'atom_selection'
+    
     def __init__(self, parent, trajectory, *args, **kwargs):
 
         self._query = Query()
@@ -167,7 +169,7 @@ class AtomSelectionDialog(UserDefinitionsDialog):
         
         target = os.path.basename(self._trajectory.filename)
         
-        UserDefinitionsDialog.__init__(self, parent, target, 'atom_selection', wx.ID_ANY, title="Atom selection dialog",style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
+        UserDefinitionsDialog.__init__(self, parent, target, wx.ID_ANY, title="Atom selection dialog",style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
 
         pub.subscribe(self.on_select_atoms_from_viewer, ('select_atoms_from_viewer'))       
                  
@@ -367,16 +369,18 @@ class AtomSelectionDialog(UserDefinitionsDialog):
                 
     def set_selection(self):
 
-        _, selection = self._query.parse()
+        _, self._selection = self._query.parse()
                 
-        pub.sendMessage("set_selection", message = (self,selection))
+        pub.sendMessage("set_selection", message = (self,self._selection))
         
     def validate(self):
 
-        if not self._ud:
+        if not self._selection:
             LOGGER("The current selection is empty", "error", ["dialog"])
             return None
         
+        self._ud['indexes'] = self._selection
+        
         return self._ud
 
 class AtomSelectionWidget(UserDefinitionWidget):

MDANSE/App/GUI/Framework/Widgets/AtomTransmutationWidget.py

@@ -39,6 +39,8 @@ from MDANSE.App.GUI.Framework.Widgets.AtomSelectionWidget import AtomSelectionDi
 
 class AtomTransmutationDialog(AtomSelectionDialog):
     
+    type = 'atom_transmutation'
+    
     def build_dialog(self):
         
         AtomSelectionDialog.build_dialog(self)
@@ -54,12 +56,15 @@ class AtomTransmutationDialog(AtomSelectionDialog):
     def validate(self):
         
         if not self._selection:
-            LOGGER("No atoms selected.", "error", ["dialog"])
+            LOGGER("The current selection is empty", "error", ["dialog"])
             return None
 
         element = self._elements.GetStringSelection()
         
-        return {'transmutation' : {'element' : element, 'selection' : self._selection}}
+        self._ud['element'] = element
+        self._ud['indexes'] = self._selection
+        
+        return self._ud
         
 class AtomTransmutationWidget(UserDefinitionWidget):
         

MDANSE/App/GUI/Framework/Widgets/AtomsListWidget.py

@@ -39,7 +39,7 @@ from MDANSE.App.GUI.Framework.Widgets.UserDefinitionWidget import UserDefinition
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict
 
 class AtomsListDialog(UserDefinitionsDialog):
-
+    
     def __init__(self, parent, trajectory, nAtoms):
         
         self._parent = parent
@@ -53,10 +53,10 @@ class AtomsListDialog(UserDefinitionsDialog):
         self._selection = []
                 
         target = os.path.basename(self._trajectory.filename)
-        
-        section = "%d_atoms_list" % self._nAtoms
 
-        UserDefinitionsDialog.__init__(self, parent, target, section, wx.ID_ANY, title="%d Atoms selection dialog" % nAtoms,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
+        self.type = "%d_atoms_list" % self._nAtoms
+        
+        UserDefinitionsDialog.__init__(self, parent, target, wx.ID_ANY, title="%d Atoms selection dialog" % nAtoms,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
                         
     def build_dialog(self):
 
@@ -154,23 +154,26 @@ class AtomsListDialog(UserDefinitionsDialog):
     def validate(self):
 
         if not self._selection:
+            LOGGER("The current selection is empty", "error", ["dialog"])
             return None
+        
+        self._ud['indexes'] = self._selection
                         
-        return {'selection' : self._selection}
+        return self._ud
 
 class AtomListWidget(UserDefinitionWidget):
-        
-    type = "atoms_list"
     
+    type = 'atoms_list'
+            
     def initialize(self):
+
+        self.type = "%d_atoms_list" % self._configurator._nAtoms
         
         UserDefinitionWidget.initialize(self)
-        
-        self.type = "%d_atoms_list" % self._configurator.nAtoms
-        
+                
     def on_new_user_definition(self,event):
         
-        atomsListDlg = AtomsListDialog(self,self._trajectory,self.configuration[self._name].nAtoms)
+        atomsListDlg = AtomsListDialog(self,self._trajectory,self._configurator._nAtoms)
         
         atomsListDlg.ShowModal()
             

MDANSE/App/GUI/Framework/Widgets/AxisSelectionWidget.py

-#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-#------------------------------------------------------------------------------------------
-#Copyright (C)
-#2015- Eric C. Pellegrini Institut Laue-Langevin
-#BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
-#France
-#pellegrini[at]ill.fr
-#goret[at]ill.fr
-#aoun[at]ill.fr
-#
-#This library is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
-#
-#This library is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#Lesser General Public License for more details.
-#
-#You should have received a copy of the GNU Lesser General Public
-#License along with this library; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-''' 
-Created on Mar 30, 2015
-
-:author: Eric C. Pellegrini
-'''
-
-from MDANSE.Externals.pubsub import pub
-from MDANSE.Framework.Configurable import ConfigurationError
-
-from MDANSE.App.GUI.Framework.Widgets.UserDefinitionWidget import UserDefinitionWidget
-
-class AxisSelectionWidget(UserDefinitionWidget):
-        
-    type = "axis_selection"
-        
-    def __init__(self, parent, name, configuration, *args, **kwargs):
-        
-        UserDefinitionWidget.__init__(self,parent, name, configuration, *args, **kwargs)
-                            
-        pub.subscribe(self.msg_set_trajectory, ("set_trajectory"))
-        pub.subscribe(self.msg_new_definition, ("new_axis",))
-            
-    def get_widget_value(self):
-
-        names = self._selections.GetControl().GetCheckedStrings()
-        
-        if len(names) != 1:
-            raise ConfigurationError("Invalid number of axis definitions selected")
-        
-        return names[0]
\ No newline at end of file

MDANSE/App/GUI/Framework/Widgets/BasisSelectionWidget.py

-#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-#------------------------------------------------------------------------------------------
-#Copyright (C)
-#2015- Eric C. Pellegrini Institut Laue-Langevin
-#BP 156
-#6, rue Jules Horowitz
-#38042 Grenoble Cedex 9
-#France
-#pellegrini[at]ill.fr
-#goret[at]ill.fr
-#aoun[at]ill.fr
-#
-#This library is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
-#
-#This library is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-#Lesser General Public License for more details.
-#
-#You should have received a copy of the GNU Lesser General Public
-#License along with this library; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-
-''' 
-Created on Mar 30, 2015
-
-:author: Eric C. Pellegrini
-'''
-
-from MDANSE.Externals.pubsub import pub
-from MDANSE.Framework.Configurable import ConfigurationError
-
-from MDANSE.App.GUI.Framework.Widgets.UserDefinitionWidget import UserDefinitionWidget
-
-class BasisSelectionWidget(UserDefinitionWidget):
-        
-    type = "basis_selection"
-
-    def __init__(self, parent, name, configuration, *args, **kwargs):
-        
-        UserDefinitionWidget.__init__(self,parent, name, configuration, *args, **kwargs)
-                            
-        pub.subscribe(self.msg_set_trajectory, ("set_trajectory"))
-        pub.subscribe(self.msg_new_definition, ("new_basis",))
-        
-    def get_widget_value(self):
-
-        names = self._selections.GetControl().GetCheckedStrings()
-        
-        if len(names) != 1:
-            raise ConfigurationError("Invalid number of basis definitions selected")
-        
-        return names[0]
\ No newline at end of file

MDANSE/App/GUI/Framework/Widgets/QVectorsWidget.py

@@ -154,20 +154,20 @@ class QVectorsPanel(wx.Panel):
         return self._progress
                             
 class QVectorsDialog(UserDefinitionsDialog):
+    
+    type = 'q_vectors'
             
     def __init__(self, parent, trajectory):
 
         self._currentGenerator = None
 
         self._value = None
-        
-        self._qVectors = {}
-        
+                
         self._trajectory = trajectory
         
         target = os.path.basename(self._trajectory.filename)
 
-        UserDefinitionsDialog.__init__(self, parent, target, 'q_vectors', wx.ID_ANY, title="Q vectors generator dialog",style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
+        UserDefinitionsDialog.__init__(self, parent, target, wx.ID_ANY, title="Q vectors generator dialog",style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
         
         self.SetSize((800,700))
                                                                   
@@ -223,10 +223,9 @@ class QVectorsDialog(UserDefinitionsDialog):
             LOGGER("No data is the selected Q vectors tab", "error")
             return
         
-        self._qVectors.clear()
-        self._qVectors['parameters'] = (qPanel.generator.type,qPanel.parameters)
-        self._qVectors['q_vectors'] = qPanel.grid.GetTable().data
-        self._qVectors['is_lattice'] = qPanel.generator.is_lattice
+        self._ud['parameters'] = (qPanel.generator.type,qPanel.parameters)
+        self._ud['q_vectors'] = qPanel.grid.GetTable().data
+        self._ud['is_lattice'] = qPanel.generator.is_lattice
                 
     def on_close(self, event):
         
@@ -280,10 +279,11 @@ class QVectorsDialog(UserDefinitionsDialog):
 
         self.set_user_definition()
         
-        if not self._qVectors:
+        if not self._ud['q_vectors']:
+            LOGGER("No Q vectors generated.", "error", ["dialog"])
             return None
         
-        return self._qVectors
+        return self._ud
                 
     def select_generator(self, generatorName):
                          

MDANSE/App/GUI/Framework/Widgets/UserDefinitionWidget.py

@@ -46,7 +46,7 @@ class UserDefinitionsDialog(wx.Dialog):
     
     __metaclass__ = abc.ABCMeta
 
-    def __init__(self, parent, target, section, *args, **kwargs):
+    def __init__(self, parent, target, *args, **kwargs):
         
         wx.Dialog.__init__(self, parent, *args, **kwargs)
 
@@ -54,9 +54,9 @@ class UserDefinitionsDialog(wx.Dialog):
         
         self._target = target
         
-        self._section = section
-
         self._mainSizer = wx.BoxSizer(wx.VERTICAL)
+        
+        self._ud = {}
                                 
         self.build_dialog()
 
@@ -107,15 +107,15 @@ class UserDefinitionsDialog(wx.Dialog):
         if value is None:
             return 
                 
-        if UD_STORE.has_definition(self._target,self._section,name):
-            LOGGER('There is already a user-definition that matches %s,%s,%s' % (self._target,self._section,name),'error',['dialog'])
+        if UD_STORE.has_definition(self._target,self.type,name):
+            LOGGER('There is already a user-definition that matches %s,%s,%s' % (self._target,self.type,name),'error',['dialog'])
             self.EndModal(wx.ID_CANCEL)
             return
                   
-        UD_STORE.set_definition(self._target,self._section,name,value)
+        UD_STORE.set_definition(self._target,self.type,name,value)
         UD_STORE.save()
                  
-        pub.sendMessage("save_definition", message = (self._target, name))
+        pub.sendMessage("save_definition", message = (self._target, self.type, name))
                          
         self.EndModal(wx.ID_OK)
                 
@@ -177,9 +177,12 @@ class UserDefinitionWidget(IWidget):
 
     def on_save_definition(self, message):
          
-        filename, name = message
+        filename, section, name = message
+         
+        if section is not self.type:
+            return
          
         if filename != self._basename:
             return
-
+        
         self._availableUDs.Append(name)

MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -92,16 +92,14 @@ class AtomTransmutationConfigurator(IConfigurator):
                 indexes = parser.parse(element,expression)
                 self.transmutate(configuration, indexes, element)
           
-        # Otherwise, it must be a list of strings that will be found as user-definition keys
-        elif isinstance(value,(list,tuple)):                        
-            for definition in value:
-                
-                if UD_STORE.has_definition(trajConfig["basename"],"atom_transmutation",value):                
-                    ud = UD_STORE.get_definition(trajConfig["basename"],"atom_transmutation",definition)
-                    self.transmutate(configuration, ud["indexes"], ud["element"])
-                else:
-                    raise ConfiguratorError("wrong parameters type:  must be either a dictionary whose keys are an atom selection string and values are the target element \
-                    or a list of string that match an user definition",self)
+        # Otherwise, it must be a string that will be found as a user-definition keys
+        elif isinstance(value,basestring):
+            if UD_STORE.has_definition(trajConfig["basename"],"atom_transmutation",value):                
+                ud = UD_STORE.get_definition(trajConfig["basename"],"atom_transmutation",value)
+                self.transmutate(configuration, ud["indexes"], ud["element"])
+            else:
+                raise ConfiguratorError("wrong parameters type:  must be either a dictionary whose keys are an atom selection string and values are the target element \
+                or a list of string that match an user definition",self)
         else:
             raise ConfiguratorError("wrong parameters type:  must be either a dictionary whose keys are an atom selection string and values are the target element \
             or a list of string that match an user definition",self)

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -120,8 +120,6 @@ class MeanSquareDisplacement(IJob):
          
         series = self.configuration['projection']["projector"](series)
         
-        1/0
-         
         msd = mean_square_displacement(series)
                 
         return index, msd