Renamed IJob.configurators class attribute to IJob.settings to avoid

conflicts
Refactored many GUI related module to make the main app restartable

MDANSE/App/GUI/ComboWidgets/ConfigurationPanel.py

@@ -5,11 +5,11 @@ from MDANSE.Framework.Configurators.IConfigurator import ConfiguratorError
 
 class ConfigurationPanel(wx.Panel):
     
-    def __init__(self, parent, configuration):
+    def __init__(self, parent, configurable):
         
         wx.Panel.__init__(self, parent, wx.ID_ANY)
         
-        self._configuration = configuration
+        self._configurable = configurable
         
         self._widgets = {}
         
@@ -19,13 +19,13 @@ class ConfigurationPanel(wx.Panel):
         
         self.panelSizer = wx.BoxSizer(wx.VERTICAL)
 
-        for cfg in self._configuration.configurators.values():
+        for cfgName, cfg in self._configurable.settings.items():
 
-            widgetClass = REGISTRY["configurator_widget"][cfg.widget]
+            widgetClass = REGISTRY["widget"][cfg[0]]
                         
-            self._widgets[cfg.name] = widgetClass(self, cfg.name, self._configuration)
+            self._widgets[cfgName] = widgetClass(self, cfgName, self._configurable)
             
-            self.panelSizer.Add(self._widgets[cfg.name], 0, wx.ALL|wx.EXPAND, 5)
+            self.panelSizer.Add(self._widgets[cfgName], 0, wx.ALL|wx.EXPAND, 5)
                   
         self.SetSizer(self.panelSizer)
                                    

MDANSE/App/GUI/ComboWidgets/ProgressBar.py

+import wx
+import wx.lib.agw.pygauge as pygauge
+
+from nMOLDYN.Core.Status import StatusHandler
+from nMOLDYN.GUI.Resources.Icons import ICONS, scaled_bitmap
+        
+class ProgressBar(wx.Panel,StatusHandler):
+    
+    def __init__(self, *args, **kwargs):
+        
+        wx.Panel.__init__(self,*args, **kwargs)
+        StatusHandler.__init__(self)
+                                
+        sizer = wx.BoxSizer(wx.HORIZONTAL)
+        
+        self._progress = pygauge.PyGauge(self, wx.ID_ANY)
+        self._stop = wx.BitmapButton(self, wx.ID_ANY, scaled_bitmap(ICONS["stop"], 24, 24))
+        
+        sizer.Add(self._progress,1,wx.ALL|wx.EXPAND,5)
+        sizer.Add(self._stop,0,wx.ALL|wx.EXPAND,5)
+        
+        self.SetSizer(sizer)
+        
+        self.Layout()
+                
+        self.Bind(wx.EVT_BUTTON,self.on_stop,self._stop)
+                
+    def finish_status(self,message):
+
+        status = message
+        
+        if status != self._status:
+            return
+        
+        self._progress.SetBarColor(wx.BLUE)
+        self._progress.Refresh()
+        self._stop.Disable()
+        
+    def on_stop(self,event):
+
+        d = wx.MessageDialog(None, 'This will stop the current task. Do you really want to stop it ?', 'Question', wx.YES_NO|wx.YES_DEFAULT|wx.ICON_WARNING)
+                 
+        if d.ShowModal() == wx.ID_NO:
+            return
+         
+        self._stop.Disable()        
+        self._status.stop()
+                        
+    def start_status(self, message):
+        
+        status = message
+        
+        if status != self._status:
+            return
+
+        self._stop.Enable()        
+        self._progress.SetValue(self._status.currentStep)
+        self._progress.SetRange(self._status.nSteps)
+        self._progress.SetBarColor(wx.GREEN)    
+
+    def stop_status(self, message):
+        
+        status = message
+        
+        if status != self._status:
+            return
+        
+        self._progress.SetBarColor(wx.RED)
+        self._progress.Refresh()   
+        
+    def update_status(self,message):
+        
+        status = message
+        
+        if status != self._status:
+            return
+        
+        self._progress.SetValue(self._status.currentStep)
+        self._progress.Refresh()   

MDANSE/App/GUI/Framework/Handlers/ConsoleHandler.py

@@ -38,9 +38,9 @@ from MDANSE.Framework.Handlers.IHandler import IHandler
 from MDANSE.Logging.Formatters import Formatter
   
 class ConsoleHandler(IHandler, logging.Handler):
-    """Sets up a GUI handler for the nMOLDYN logger.
+    """Sets up a GUI handler for the MDANSE logger.
     
-    Emits the logging message to the nMOLDYN GUI console.
+    Emits the logging message to the MDANSE GUI console.
 
     @note: inherits from logging.Handler class that sets a generic handler.
     """

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

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 14, 2015
 
-@author: pellegrini
+@author: Eric C. pellegrini
 '''
 
 import wx

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

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 14, 2015
 
-@author: pellegrini
+@author: Eric C. Pellegrini
 '''
 
 import collections
@@ -40,10 +40,10 @@ from MDANSE import LOGGER, REGISTRY, UD_STORE
 from MDANSE.Core.Error import Error
 from MDANSE.Externals.pubsub import pub
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser, AtomSelectionParserError
+from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
-from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 
 class AtomSelectionPluginError(Error):
     pass
@@ -486,3 +486,4 @@ class AtomSelectionPlugin(ComponentPlugin):
         
         self._parent.show_selected_atoms(self._selection)
     
+print REGISTRY['plugin']

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

@@ -27,15 +27,16 @@
 ''' 
 Created on Apr 14, 2015
 
-@author: pellegrini
+@author: Eric C. Pellegrini
 '''
 import os
 
 import wx
 
-from nMOLDYN import ELEMENTS, LOGGER, REGISTRY, USER_DEFINITIONS
-from nMOLDYN.Externals.pubsub import pub as Publisher
-from nMOLDYN.Framework.Plugins.AtomSelectionPlugin import AtomSelectionPlugin
+from MDANSE import ELEMENTS, LOGGER, REGISTRY
+from MDANSE.Externals.pubsub import pub as Publisher
+
+from MDANSE.App.GUI.Framework.Plugins.AtomSelectionPlugin import AtomSelectionPlugin
 
 class AtomTransmutationPlugin(AtomSelectionPlugin):
 
@@ -85,8 +86,8 @@ class AtomTransmutationPlugin(AtomSelectionPlugin):
                                                              expression=self._expression,
                                                              indexes=self._selection,
                                                              element=element)            
-        USER_DEFINITIONS[name] = ud
-        USER_DEFINITIONS.save()
+        UD_STORE[name] = ud
+        UD_STORE.save()
         
         Publisher.sendMessage("new_transmutation", message = (path, name))
         
\ No newline at end of file

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

@@ -37,7 +37,7 @@ import wx.aui as wxaui
 
 from MDANSE import LOGGER, REGISTRY, UD_STORE
 from MDANSE.Externals.pubsub import pub
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+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

@@ -37,7 +37,7 @@ import wx.aui as wxaui
 
 from MDANSE import LOGGER, REGISTRY, UD_STORE
 from MDANSE.Externals.pubsub import pub
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+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/DataInfoPlugin.py

@@ -33,7 +33,7 @@ Created on Apr 14, 2015
 import wx
 import wx.aui as aui
 
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 
 class DataInfoPlugin(ComponentPlugin):
     

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

@@ -39,7 +39,7 @@ import numpy
 
 from Scientific.IO.NetCDF import NetCDFFile
 
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.Core.Error import Error
 
 class DensitySuperpositionError(Error):

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

@@ -30,7 +30,7 @@ Created on Apr 14, 2015
 @author: pellegrini
 '''
 
-from MDANSE.App.GUI.Framework.Plugins.Plugin import DataPlugin
+from MDANSE.App.GUI.Framework.Plugins.DataPlugin import DataPlugin
 
 class EmptyDataPlugin(DataPlugin):
     

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

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 14, 2015
 
-@author: pellegrini
+@author: Eric C. ellegrini
 '''
 
 import os
@@ -41,7 +41,9 @@ import wx.aui as aui
 
 from MDANSE import PLATFORM,REGISTRY
 from MDANSE.Externals.pubsub import pub
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+
+from MDANSE.App.GUI.ComboWidgets.ConfigurationPanel import ConfigurationPanel
+from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 
 class JobPlugin(ComponentPlugin):
         
@@ -51,17 +53,14 @@ class JobPlugin(ComponentPlugin):
         
         ComponentPlugin.__init__(self, parent, size=wx.Size(800,400), **kwargs)
                 
-                                
     def build_panel(self):
         
         self._main = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
         self._main.SetScrollbars(pixelsPerUnitX= 20, pixelsPerUnitY=20, noUnitsX=500, noUnitsY=500)
                 
         mainSizer = wx.BoxSizer(wx.VERTICAL)
-        
-        from nMOLDYN.GUI.Widgets.ConfigurationPanel import ConfigurationPanel
-        
-        self._parametersPanel = ConfigurationPanel(self._main, self._job.configuration)
+                
+        self._parametersPanel = ConfigurationPanel(self._main, self._job)
                     
         sb = wx.StaticBox(self._main, wx.ID_ANY)
         sbSizer = wx.StaticBoxSizer(sb, wx.HORIZONTAL)
@@ -93,7 +92,6 @@ class JobPlugin(ComponentPlugin):
         self.Bind(wx.EVT_BUTTON, self.on_save, saveButton)
         self.Bind(wx.EVT_BUTTON, self.on_run, runButton)
         
-                 
     def on_help(self, event):
                 
         from nMOLDYN.GUI.Widgets.JobHelpFrame import JobHelpFrame

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

@@ -43,10 +43,10 @@ from MMTK.Trajectory import Trajectory
 from MDANSE import ELEMENTS, LOGGER
 from MDANSE.Core.Error import Error
 from MDANSE.Extensions import fast_calculation 
-from MDANSE.Externals.pubsub import pub as Publisher
+from MDANSE.Externals.pubsub import pub
 from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 
-from MDANSE.App.GUI.Framework.Plugins.Plugin import ComponentPlugin
+from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 
 # The colour for a selected atom (R,G,B,Alpha).
 RGB_COLOURS = {}
@@ -145,12 +145,11 @@ class SelectionBox(vtk.vtkBoxWidget):
         
         self.viewer.pick_atoms(selection)
 
-    
 class MolecularViewerPanel(ComponentPlugin):
     '''
     This class sets up a molecular viewer using vtk functionnalities.
     '''
-    
+        
     type = "molecular_viewer"
     
     label = "Molecular Viewer"
@@ -166,7 +165,6 @@ class MolecularViewerPanel(ComponentPlugin):
         
         ComponentPlugin.__init__(self, parent, *args, **kwargs)
    
-
     def build_panel(self):
                 
         self._iren = MyRenderWindowInteractor(self, wx.ID_ANY, size=self.GetSize())
@@ -196,7 +194,7 @@ class MolecularViewerPanel(ComponentPlugin):
         self._iren.AddObserver("CharEvent", self.on_keyboard_input)
         self._iren.AddObserver("LeftButtonPressEvent", self.emulate_focus)
 
-        Publisher.subscribe(self.check_switch_consistancy, ('Switch'))
+        pub.subscribe(self.check_switch_consistancy, ('Switch'))
         
         self._iren.Bind(wx.EVT_CONTEXT_MENU, self.on_show_popup_menu)
                 
@@ -222,7 +220,6 @@ class MolecularViewerPanel(ComponentPlugin):
         
         self.SetFocusIgnoringChildren()
         
-
     def del_surface(self):
         del self._surface
         self._surface = None
@@ -240,15 +237,13 @@ class MolecularViewerPanel(ComponentPlugin):
     def emulate_focus(self, obj, event):
         
         self.SetFocusIgnoringChildren()
-        
-        
+           
     def close(self):
                 
         self.clear_universe()
         
-        Publisher.unsubscribe(self.check_switch_consistancy, "Switch")
+        pub.unsubscribe(self.check_switch_consistancy, "Switch")
         
-
     def set_trajectory(self, trajectory, selection=None, frame=0):
         
         if not isinstance(trajectory,Trajectory):
@@ -287,7 +282,7 @@ class MolecularViewerPanel(ComponentPlugin):
         
         self._trajectoryLoaded = True
 
-        Publisher.sendMessage(('Load trajectory'), message = self)
+        pub.sendMessage(('Load trajectory'), message = self)
 
     def color_string_to_RGB(self, s):
         
@@ -318,7 +313,6 @@ class MolecularViewerPanel(ComponentPlugin):
                     
         return colours, lut
         
-        
     def enable_picking(self):
 
         self.__pickerObserverId = self._iren.AddObserver("LeftButtonPressEvent", self.on_pick)
@@ -333,7 +327,6 @@ class MolecularViewerPanel(ComponentPlugin):
         self._iren.RemoveObserver(self.__pickerObserverId)
         self.__pickerObserverId = None
 
-
     def on_show_popup_menu(self, event):
 
         popupMenu = wx.Menu()
@@ -387,7 +380,6 @@ class MolecularViewerPanel(ComponentPlugin):
     def animation_loop(self):
         return self._animationLoop
 
-
     @property
     def surface(self):
         return self._surface
@@ -400,17 +392,14 @@ class MolecularViewerPanel(ComponentPlugin):
     def current_frame(self):
         return self._currentFrame
 
-
     @property
     def iren(self):
         return self._iren
 
-
     @property
     def max_laps(self):
         return self._maxLaps
 
-
     @property
     def n_frames(self):
         return self._nFrames
@@ -419,24 +408,20 @@ class MolecularViewerPanel(ComponentPlugin):
     def n_atoms(self):
         return self._nAtoms
 
-
     @property
     def selection_box(self):
         return self.__selectionBox
 
-
     @property
     def timer_interval(self):
 
         return self._timerInterval
 
-
     @property
     def trajectory(self):
 
         return self._trajectory
 
-
     @property
     def trajectory_loaded(self):
 
@@ -447,7 +432,6 @@ class MolecularViewerPanel(ComponentPlugin):
         
         return self.__pickedAtoms
 
-
     def change_frame_rate(self, laps):
 
         if not self._trajectoryLoaded:
@@ -457,7 +441,6 @@ class MolecularViewerPanel(ComponentPlugin):
         if self._animationLoop:
             self._iren.CreateRepeatingTimer(self._timerInterval)
 
-
     def create_timer(self):
         
         self._iren.Initialize()    
@@ -466,7 +449,6 @@ class MolecularViewerPanel(ComponentPlugin):
 
         return timerId
 
-
     def set_frame(self, frame):
         
         if not self._trajectoryLoaded:
@@ -477,28 +459,22 @@ class MolecularViewerPanel(ComponentPlugin):
         self._timerCounter = frame
         
         self.set_configuration(frame)
-                
-                
+                                
     def on_clear_labels(self, event=None):
         pass
 
-
     def on_clear_selection(self, event=None):
         pass
 
-
     def on_export(self, event=None):
         pass
 
-
     def on_hide_labels(self, event=None):
         pass
 
-
     def on_select_all(self, event=None):
         pass
 
-
     def on_show_all_atoms(self, event=None):
         pass
 
@@ -506,19 +482,15 @@ class MolecularViewerPanel(ComponentPlugin):
     def on_show_labels(self, event=None):
         pass
 
-
     def on_show_unselected_atoms(self, event=None):
         pass
 
-
     def on_show_selected_atoms(self, event=None):
         pass
 
-
     def on_undo_exclude(self, event=None):
         pass
 
-
     def on_undo_include(self, event=None):
         pass
        
@@ -556,7 +528,6 @@ class MolecularViewerPanel(ComponentPlugin):
         elif key == " ":
             self.start_stop_animation()
 
-
     def on_timer(self, obj=None, event=None):
 
         if self._iren._timer.IsRunning():
@@ -565,8 +536,7 @@ class MolecularViewerPanel(ComponentPlugin):
         self.set_configuration(self._timerCounter)
         self._timerCounter += 1
         
-        Publisher.sendMessage(("On timer"), message = self)
-
+        pub.sendMessage(("On timer"), message = self)
 
     def set_rendering_mode(self, mode):
         if not self._trajectoryLoaded:
@@ -576,7 +546,6 @@ class MolecularViewerPanel(ComponentPlugin):
             self._rendmod=mode
             self.set_configuration(self._currentFrame)
 
-
     def goto_first_frame(self):
 
         if not self._trajectoryLoaded:
@@ -586,8 +555,7 @@ class MolecularViewerPanel(ComponentPlugin):
 
         self._timerCounter = 0
         self.set_configuration(0)
-        
-                
+                   
     def goto_last_frame(self):
 
         if not self._trajectoryLoaded:
@@ -597,19 +565,16 @@ class MolecularViewerPanel(ComponentPlugin):
         last = self._nFrames-1
         self._timerCounter = last
         self.set_configuration(last)
-        
 
     def show_hide_selection_box(self):
 
         if self._trajectoryLoaded:
             self.__selectionBox.on_off()
-            
         
     def set_timer_interval(self, timerInterval):
 
         self._timerInterval = timerInterval
-        
-        
+          
     def on_pick(self, obj, evt=None):
         
         if not self._trajectoryLoaded:
@@ -647,14 +612,12 @@ class MolecularViewerPanel(ComponentPlugin):
                         
         self.__pickedAtoms.symmetric_difference_update(atomsList)
                         
-        Publisher.sendMessage(('select atoms'), message = list(self.__pickedAtoms))
+        pub.sendMessage(('select atoms'), message = list(self.__pickedAtoms))
             
-
     def show_selected_atoms(self, atomsList):
 
         self.show_selection(atomsList)
         
-
     def clear_selection(self):
         
         if not self._trajectoryLoaded:
@@ -669,7 +632,6 @@ class MolecularViewerPanel(ComponentPlugin):
         
         self._iren.Render()
         
-    
     def show_selection(self, selection):
         
         if not self._trajectoryLoaded:
@@ -696,13 +658,11 @@ class MolecularViewerPanel(ComponentPlugin):
             self._iren.TimerEventResetsTimerOn()
             self._animationLoop = True
 
-
     def stop_animation(self, event=None):
         if self._trajectoryLoaded:
             self._iren.TimerEventResetsTimerOff()
             self._animationLoop = False 
 
-
     def start_stop_animation(self, event=None, check=True):
         
         if not self._trajectoryLoaded:
@@ -716,9 +676,9 @@ class MolecularViewerPanel(ComponentPlugin):
         else:
             self.stop_animation()
         if check: 
-            Publisher.sendMessage(('Switch'), message = self)
+            pub.sendMessage(('Switch'), message = self)
             
-        Publisher.sendMessage(('Animation'), message = self)
+        pub.sendMessage(('Animation'), message = self)
     
     def check_switch_consistancy(self, message):
         
@@ -753,12 +713,10 @@ class MolecularViewerPanel(ComponentPlugin):
         
         return radius, color, int(idx)
     
-    
     def this_atom_is_selected(self,pid):
         _, _, pid = self.get_atom_props(pid)
         return self.atomsColours[pid]==RGB_COLOURS["selection"][0]
-    
-        
+       
     def pick_atom(self,pid):
         if self.this_atom_is_selected(pid):
             self.unpick_atom(pid)
@@ -980,8 +938,7 @@ class MolecularViewerPanel(ComponentPlugin):
         
         # rendering
         self._iren.Render()
-        
-        
+             
     def set_configuration(self, frame):
         '''
         Sets a new configuration.
@@ -1049,7 +1006,6 @@ def ndarray_to_vtkcellarray(array):
 
     return bonds
 
-
 def get_trajectory_filename():
 
     filters = 'NC file (*.nc)|*.nc|All files (*.*)|*.*'

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

-import numpy as np
+#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 Apr 15, 2015
+
+@author: Gael Goret
+