Added a generic ASCII trajectory converter

Many bug fixes related to ud

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

@@ -36,9 +36,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Core.Error import Error
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser, AtomSelectionParserError
 from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 

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

@@ -33,8 +33,9 @@ import os
 
 import wx
 
-from MDANSE import ELEMENTS, LOGGER, REGISTRY, UD_STORE
+from MDANSE import ELEMENTS, LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub as Publisher
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 
 from MDANSE.App.GUI.Framework.Plugins.AtomSelectionPlugin import AtomSelectionPlugin
 

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

@@ -35,8 +35,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict

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

@@ -35,8 +35,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict
@@ -124,7 +126,7 @@ class BasisSelectionPlugin(ComponentPlugin):
                 
         self._moleculeNames.SetItems(sorted(self._molecularContents.keys()))        
         
-    def on_close(self, event):
+    def on_close(self, event=None):
         
         self.parent.clear_selection()
         self.parent.mgr.ClosePane(self.parent.mgr.GetPane(self))
@@ -138,7 +140,6 @@ class BasisSelectionPlugin(ComponentPlugin):
         if (not origin) or (not xAxis) or (not yAxis):
             LOGGER("One of the atom selection is empty. Please select some values.", "error", ["dialog"])
             return
-
         
         if (origin == xAxis) or (origin == yAxis) or (xAxis == yAxis):
             LOGGER("A basis can not be set from identical atom selections.", "error", ["dialog"])

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

@@ -33,7 +33,6 @@ Created on Apr 14, 2015
 import os
 import subprocess               
 import sys
-import tempfile
 import time
 
 import wx

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

@@ -37,9 +37,11 @@ import wx.aui as wxaui
 import wx.grid as wxgrid
 from wx.lib.delayedresult import startWorker
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
 
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.ComboWidgets.ConfigurationPanel import ConfigurationPanel
 from MDANSE.App.GUI.ComboWidgets.ProgressBar import ProgressBar
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin

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

@@ -34,7 +34,7 @@ import os
 
 import wx.combo
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 
 from MDANSE.App.GUI.Framework.Widgets.IWidget import IWidget
 from MDANSE.App.GUI.ComboWidgets.ComboCheckbox import ComboCheckbox

MDANSE/App/GUI/Main.py

@@ -13,7 +13,6 @@ class MainApplication(wx.App):
         f.Show()
         self.SetTopWindow(f)
         return True
-        
 
 class PeriodicTableApplication(wx.App):
     
@@ -24,7 +23,6 @@ class PeriodicTableApplication(wx.App):
         self.SetTopWindow(f)
         return True
 
-        
 class PlotterApplication(wx.App):
     
     def OnInit(self):
@@ -42,4 +40,9 @@ class UserDefinitionViewerApplication(wx.App):
         f.Show()
         self.SetTopWindow(f)
         return True
+    
+if __name__ == "__main__":
+    
+    app = MainApplication()
+    app.MainLoop()
     
\ No newline at end of file

MDANSE/App/GUI/MainFrame.py

@@ -57,7 +57,7 @@ class MainFrame(wx.Frame):
         
         # Add some handlers to the loggers
         LOGGER.add_handler("console", REGISTRY['handler']['console'](self._panels["controller"].pages["logger"]), level="info")
-        LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'], level="error")
+        LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'](), level="error")
         LOGGER.start()
                                 
     def build_dialog(self):

MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -35,7 +35,7 @@ import operator
 
 import numpy
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE, UserDefinitionError
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser
 
@@ -91,7 +91,7 @@ class AtomSelectionConfigurator(IConfigurator):
         try:
             ud = UD_STORE[trajConfig["basename"],"atom_selection",value]        
         # The input value is an atom selection string: parse it and update the configuration
-        except UserDefinitionError:
+        except UserDefinitionsStoreError:
             parser = AtomSelectionParser(trajConfig["instance"].universe)
             self["indexes"] = parser.parse(value)
             self["expression"] = value

MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -31,7 +31,7 @@ Created on Mar 30, 2015
 '''
 
 from MDANSE import ELEMENTS
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser
         

MDANSE/Framework/Configurators/AxisSelectionConfigurator.py

@@ -30,7 +30,7 @@ Created on Mar 30, 2015
 @author: Eric C. Pellegrini and Bachir Aoun
 '''
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
         
@@ -73,11 +73,12 @@ class AxisSelection(IConfigurator):
         
         trajConfig = configuration[self._dependencies['trajectory']]
                 
-        ud = UD_STORE[trajConfig["basename"],"axis_selection",value]        
-        if ud is not None:
-            self.update(ud)
-        else:
+        try: 
+            ud = UD_STORE[trajConfig["basename"],"axis_selection",value]
+        except UserDefinitionsStoreError:
             self.update(value)
+        else:
+            self.update(ud)
 
         e1 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['endpoint1'], True)
         e2 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['endpoint2'], True)

MDANSE/Framework/Configurators/BasisSelectionConfigurator.py

@@ -30,7 +30,7 @@ Created on Mar 30, 2015
 @author: Eric C. Pellegrini and Bachir Aoun
 '''
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
 
@@ -74,12 +74,14 @@ class BasisSelection(IConfigurator):
         '''
 
         trajConfig = configuration[self._dependencies['trajectory']]
-
-        ud = UD_STORE[trajConfig["basename"],"basis_selection",value]        
-        if ud is not None:
-            self.update(ud)
-        else:
+            
+        try: 
+            ud = UD_STORE[trajConfig["basename"],"basis_selection",value]
+        except UserDefinitionsStoreError:
             self.update(value)
+        else:
+            self.update(ud)
+            
                 
         e1 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['origin'], True)
         e2 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['x_axis'], True)

MDANSE/Framework/Configurators/QVectorsConfigurator.py

@@ -31,7 +31,7 @@ Created on May 22, 2015
 '''
 
 from MDANSE import REGISTRY
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 
 class QVectorsConfigurator(IConfigurator):
@@ -70,15 +70,11 @@ class QVectorsConfigurator(IConfigurator):
 
         trajConfig = configuration[self._dependencies['trajectory']]
 
-        ud = UD_STORE[trajConfig["basename"],"q_vectors",value]        
-        if ud is not None:
+        try:        
+            ud = UD_STORE[trajConfig["basename"],"q_vectors",value]
             
-            self["parameters"] = ud['parameters']
-            self["type"] = ud['generator']
-            self["is_lattice"] = ud['is_lattice']
-            self["q_vectors"] = ud['q_vectors']
-        
-        else:                        
+        except UserDefinitionsStoreError:
+
             generator, parameters = value
             generator = REGISTRY["q_vectors"][generator](trajConfig["instance"])
             generator.setup(parameters)
@@ -86,6 +82,12 @@ class QVectorsConfigurator(IConfigurator):
                         
             if not data:
                 raise ConfiguratorError("no Q vectors could be generated", self)
+        
+        else:                        
+            self["parameters"] = ud['parameters']
+            self["type"] = ud['generator']
+            self["is_lattice"] = ud['is_lattice']
+            self["q_vectors"] = ud['q_vectors']
 
             self["parameters"] = parameters
             self["type"] = generator.type

MDANSE/Framework/Jobs/IJob.py

@@ -74,7 +74,7 @@ class JobError(Error):
         trace.append("\n%s" % self._message)
 
         trace = '\n'.join(trace)
-        
+                
         LOGGER(trace,'error',[job._name])
 
         if job._status is not None:
@@ -128,7 +128,7 @@ class IJob(Configurable):
                         
         return name
         
-    def __init__(self, status=None):
+    def __init__(self, status=False):
         """
         The base class constructor.        
         """
@@ -143,7 +143,7 @@ class IJob(Configurable):
         
         self._info = ""
                                         
-        if status is not None:
+        if status:
             self._status = JobStatus(self)
         else:
             self._status = None
@@ -467,7 +467,10 @@ class IJob(Configurable):
             if getattr(self,'numberOfSteps', 0) <= 0:
                 raise JobError(self,"Invalid number of steps for job %s" % self._name)
     
-            mode = self.configuration['running_mode']['mode']
+            if self.configuration.has_key('running_mode'):
+                mode = self.configuration['running_mode']['mode']
+            else:
+                mode = 'monoprocessor'
     
             IJob._runner[mode](self)
     

MDANSE/Framework/Status.py

@@ -29,6 +29,8 @@ class Status(object):
         
     def __init__(self):
         
+        self._updateStep = 1
+        
         self._currentStep = 0
         self._nSteps = None
         self._finished = False
@@ -121,10 +123,8 @@ class Status(object):
             return
          
         self._nSteps = nSteps
-         
-        if rate is None:
-            self._updateStep = 1
-        else:
+                 
+        if rate is not None:
             self._updateStep = max(0,int(rate*nSteps))
                   
         Publisher.sendMessage("status_start",message=self)
@@ -137,6 +137,9 @@ class Status(object):
                 
     def update(self,force=False):
         
+        if self._nSteps is None:
+            return
+        
         if self._updateStep == 0:
             return
                 

MDANSE/Framework/UserDefinitionsStore.py

@@ -4,7 +4,6 @@ import os
 from MDANSE import PLATFORM
 from MDANSE.Core.Error import Error
 from MDANSE.Core.Singleton import Singleton
-from MDANSE.Framework.UserDefinitions.AtomSelectionDefinition import AtomSelectionDefinition
 
 class UserDefinitionsStoreError(Error):
     pass
@@ -82,23 +81,18 @@ class UserDefinitionsStore(UnicodeDict):
         if not os.path.exists(UserDefinitionsStore.UD_PATH):
             return
         
-#         # Try to open the UD file.
-#         try:
-#             f = open(UserDefinitionsStore.UD_PATH, "rb")
-#             UD = cPickle.load(f)        
-# 
-#         # If for whatever reason the pickle file loading failed do not even try to restore it
-#         except:
-#             return
-#         
-#         else:
-#             UnicodeDict.update(self,UD)
-#             f.close()
-
-        f = open(UserDefinitionsStore.UD_PATH, "rb")
-        UD = cPickle.load(f)        
-        UnicodeDict.update(self,UD)
-        f.close()
+        # Try to open the UD file.
+        try:
+            f = open(UserDefinitionsStore.UD_PATH, "rb")
+            UD = cPickle.load(f)        
+ 
+        # If for whatever reason the pickle file loading failed do not even try to restore it
+        except:
+            return
+         
+        else:
+            UnicodeDict.update(self,UD)
+            f.close()
                         
     def save(self):
         '''

MDANSE/__init__.py

@@ -41,7 +41,7 @@ from MDANSE.Logging.Logger import LOGGER
 
 from MDANSE.Core.Preferences import PREFERENCES
 
-from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+import Framework
 
 import os