All the analysis are now reintroduced in MDANSE

Splitted the Plotter plugin in several modules

MDANSE/App/GUI/Framework/Plugins/ComponentPlugin.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: Gael Goret, Eric C. Pellegrini
+'''
+
+from MDANSE.App.GUI.Plugins.IPlugin import IPlugin 
+             
+class ComponentPlugin(IPlugin):
+    
+    type = None
+
+    @property
+    def datakey(self):
+        return self.parent.datakey
+
+    @property
+    def dataproxy(self):
+        return self.parent.dataproxy
+

MDANSE/App/GUI/Framework/Plugins/DataPlugin.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: Gael Goret, Eric C. Pellegrini
+'''
+
+import wx
+import wx.aui as wxaui
+
+from MDANSE import REGISTRY
+from MDANSE.Externals.pubsub import pub
+
+from MDANSE.App.GUI import DATA_CONTROLLER
+from MDANSE.App.GUI.Plugins.IPlugin import IPlugin, plugin_parent 
+                    
+class DataPlugin(IPlugin):
+    
+    type = 'data'
+        
+    ancestor = None
+    
+    def __init__(self, parent, datakey):
+        
+        IPlugin.__init__(self, parent, wx.ID_ANY)
+
+        self._datakey = datakey
+        
+        self._dataProxy = DATA_CONTROLLER[self._datakey]
+                                                
+        self._mgr.Bind(wx.EVT_CHILD_FOCUS, self.on_changing_pane)
+        
+        self._currentWindow = self
+         
+    def build_panel(self):
+        pass
+
+    def plug(self, standalone=False):
+        pass
+
+    @property
+    def currentWindow(self):
+        return self._currentWindow
+
+    @property
+    def datakey(self):
+        return self._datakey
+
+    @datakey.setter
+    def datakey(self, key):
+        self._datakey = key
+
+    @property
+    def dataproxy(self):
+        
+        return self._dataProxy
+    
+    def drop(self, pluginName):
+                                        
+        # If no plugin match the name of the dropped plugin, do nothing.
+        plugin = REGISTRY["plugin"].get(pluginName,None)        
+        if plugin is None:
+            return
+        
+        if not issubclass(self.__class__,REGISTRY['plugin'][plugin.ancestor]):
+            return
+                                                    
+        plugin = plugin(self)
+
+        self._mgr.AddPane(plugin, wxaui.AuiPaneInfo().Caption(getattr(plugin, "label", pluginName)))
+
+        self._mgr.Update()
+        
+        plugin.plug()
+        
+        plugin.SetFocus()
+
+    def has_parent(self, window):
+        return False
+    
+    def on_changing_pane(self, event):
+                        
+        window = plugin_parent(event.GetWindow())
+                                        
+        if window is None:
+            return
+        
+        self._currentWindow = window
+                                    
+        pub.sendMessage(('set_plugins_tree'), message= window)

MDANSE/App/GUI/Framework/Plugins/IPlugin.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: Gael Goret, Eric C. Pellegrini
+'''
+
+import abc
+import cPickle
+
+import wx
+import wx.aui as aui
+
+from MDANSE import REGISTRY
+
+def plugin_parent(window):
+                          
+    if window == window.TopLevelParent:
+        return None
+     
+    if isinstance(window,IPlugin):
+        return window
+     
+    else:
+        return plugin_parent(window.Parent)
+
+class PluginDropTarget(wx.DropTarget):
+
+    def __init__(self, targetPanel):
+
+        wx.DropTarget.__init__(self)
+        self._targetPanel = targetPanel
+        
+        self._data = wx.CustomDataObject("Plugin")
+        self.SetDataObject(self._data)
+        
+    @property
+    def target_panel(self):
+        return self._targetPanel
+
+    def OnDrop(self, x, y):
+        return True
+
+    def OnDragOver(self, x, y, d):
+        return wx.DragCopy
+
+    def OnData(self, x, y, d):
+
+        if self.GetData():
+            pluginName = cPickle.loads(self._data.GetData())
+            self._targetPanel.drop(pluginName)
+
+        return d
+
+class IPlugin(wx.Panel):
+    
+    __metaclass__ = REGISTRY
+    
+    type = "plugin"
+        
+    ancestor = None
+    
+    def __init__(self, parent, *args, **kwargs):
+        
+        wx.Panel.__init__(self, parent, *args, **kwargs)
+        
+        self._parent = parent
+        
+        self.SetDropTarget(PluginDropTarget(self))
+        
+        self.build_dialog()
+        
+        self._mgr.Bind(aui.EVT_AUI_PANE_CLOSE, self.on_close_pane)
+                                                        
+    @abc.abstractmethod
+    def build_panel(self):
+        pass
+    
+    @abc.abstractmethod
+    def plug(self, standalone=False):
+        pass
+    
+    @property
+    def mgr(self):
+        return self._mgr
+    
+    @property
+    def parent(self):
+        return self._parent
+    
+    def close_children(self):
+
+        childrenPlugins = [p.window for p in self._mgr.GetAllPanes()]
+        
+        for plugin in childrenPlugins:
+            try:
+                plugin.close_children()
+            except AttributeError:
+                continue
+            
+        self.close()
+        
+    def close(self):
+        pass
+        
+    def on_close_pane(self, event):
+        
+        plugin = event.GetPane().window
+        
+        try:
+            plugin.close_children()
+        except AttributeError:
+            plugin.Close()
+                                
+    def build_dialog(self):
+
+        self.Freeze()
+
+        self._mgr = aui.AuiManager(self)
+
+        self.build_panel()  
+         
+        self._mgr.Update()
+        
+        self.Thaw()
+        
+    def drop(self, pluginName):
+                                        
+        # If no plugin match the name of the dropped plugin, do nothing.
+        plugin = REGISTRY["plugin"].get(pluginName,None)        
+        if plugin is None:
+            return
+        
+        if not issubclass(self.__class__,REGISTRY['plugin'][plugin.ancestor]):
+            self.parent.drop(pluginName)
+            return
+                                               
+        plugin = plugin(self)
+
+        self._mgr.AddPane(plugin, aui.AuiPaneInfo().Caption(getattr(plugin, "label", pluginName)))
+
+        self._mgr.Update()
+        
+        plugin.plug()
+        
+        plugin.SetFocus()
\ No newline at end of file

MDANSE/App/GUI/Framework/Plugins/Plotter/Ticker.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 Apr 13, 2015
+
+@author: Gael Goret, Eric C. Pellegrini
+'''
+
+import matplotlib
+
+class ScaledLocator(matplotlib.ticker.MaxNLocator):
+    """
+    Locates regular intervals along an axis scaled by *dx* and shifted by
+    *x0*. For example, this would locate minutes on an axis plotted in seconds
+    if dx=60.  This differs from MultipleLocator in that an approriate interval
+    of dx units will be chosen similar to the default MaxNLocator.
+    """
+    def __init__(self, dx=1.0, x0=0.0):
+        self.dx = dx
+        self.x0 = x0
+        matplotlib.ticker.MaxNLocator.__init__(self, nbins=9, steps=[1, 2, 5, 10])
+
+    def rescale(self, x):
+        return x * self.dx + self.x0
+    def inv_rescale(self, x):
+        return  (x - self.x0) / self.dx
+
+    def __call__(self): 
+        vmin, vmax = self.axis.get_view_interval()
+        vmin, vmax = self.rescale(vmin), self.rescale(vmax)
+        vmin, vmax = matplotlib.transforms.nonsingular(vmin, vmax, expander = 0.05)
+        locs = self.bin_boundaries(vmin, vmax)
+        locs = self.inv_rescale(locs)
+        prune = self._prune
+        if prune=='lower':
+            locs = locs[1:]
+        elif prune=='upper':
+            locs = locs[:-1]
+        elif prune=='both':
+            locs = locs[1:-1]
+        return self.raise_if_exceeds(locs)
+
+class ScaledFormatter(matplotlib.ticker.OldScalarFormatter):
+    """Formats tick labels scaled by *dx* and shifted by *x0*."""
+    def __init__(self, dx=1.0, x0=0.0, **kwargs):
+        self.dx, self.x0 = dx, x0
+
+    def rescale(self, x):
+        return x * self.dx + self.x0
+
+    def __call__(self, x, pos=None):
+        xmin, xmax = self.axis.get_view_interval()
+        xmin, xmax = self.rescale(xmin), self.rescale(xmax)
+        d = abs(xmax - xmin)
+        x = self.rescale(x)
+        s = self.pprint_val(x, d)
+        return s

MDANSE/Core/ClassRegistry.py

@@ -78,6 +78,8 @@ class ClassRegistry(abc.ABCMeta):
         :type namespace: dict
         '''
         
+        print name, bases, namespace
+        
         super(ClassRegistry, self).__init__(name, bases, namespace)
         
         # Get the typ of the class
@@ -123,8 +125,6 @@ class ClassRegistry(abc.ABCMeta):
      
             moduleName, moduleExt = os.path.splitext(moduleFile)
             
-            print moduleName
-    
             if moduleDir not in sys.path:        
                 sys.path.append(moduleDir)
                       

MDANSE/Core/Preferences.py

@@ -204,6 +204,27 @@ class InputDirectory(PreferencesItem):
             raise PreferencesError('Error when setting input directory %r' % value)
         
         self._value = value
+
+class LoggingLevel(PreferencesItem):
+    
+    type = "logging_level"
+    
+    LOGGING_LEVELS = ["debug","info","warning","error","critical","fatal"]
+    
+    def set_value(self, value):
+        '''
+        Set the value of the logging level preferences item.
+        
+        :param value: the logging level
+        :type value: str
+        '''
+                
+        value = value.lower()
+        
+        if not value in LoggingLevel.LOGGING_LEVELS:
+            raise PreferencesError("Invalid logging level")
+                
+        self._value = value
                 
 class Preferences(collections.OrderedDict):
     '''
@@ -220,12 +241,14 @@ class Preferences(collections.OrderedDict):
         Constructs the preferences
         '''
         
+        collections.OrderedDict.__init__(self)
+        
         self["working_directory"] = InputDirectory("working_directory", "paths", PLATFORM.home_directory())
         self["macros_directory"] = InputDirectory("macros_directory", "paths", os.path.join(PLATFORM.home_directory(), "mdanse_macros"))
                 
         self._parser = ConfigParser.ConfigParser()
 
-        for s in self._items.values():
+        for s in self.values():
             try:
                 self._parser.add_section(s.section)
             except ConfigParser.DuplicateSectionError:
@@ -276,11 +299,11 @@ class Preferences(collections.OrderedDict):
         :type value: any
         '''
         
-        if not self._items.has_key(item):
+        if not self.has_key(item):
             return
 
         try:
-            self._items[item].value = value
+            self[item].value = value
 
         except KeyError:
             raise PreferencesError("The preferences item %r is not valid" % item)
@@ -320,7 +343,7 @@ class Preferences(collections.OrderedDict):
         except (IOError,TypeError) as e:
             raise PreferencesError(e)
 
-        for v in self._items.values():
+        for v in self.values():
             self._parser.set(v.section,v.name,v.value)
                 
         # Write the preferences.

MDANSE/Data/ElementsDatabase.py

@@ -66,7 +66,6 @@ def create_mmtk_atom_entry(name, symbol=None, mass=0.0):
         symbol = name
 
     filename = os.path.join(PLATFORM.local_mmtk_database_directory(),"Atoms", name)
-    print filename
     f = open(filename, 'w')
     # This three entries are compulsory for a MMTK.Atom to be valid
     f.write('name = "%s"\n\n' % name)
@@ -275,19 +274,19 @@ class ElementsDatabase(object):
     
     >>> # Import the database
     >>> from MDANSE import ELEMENTS
-    >>>
+    >>> 
     >>> # Fetch the hydrogen natural element --> get a deep-copy of the its properties
     >>> hydrogen = ELEMENTS["H"]
-    >>>
+    >>> 
     >>> # Fetch the hydrogen H[1] isotope --> get a deep-copy of the its properties
     >>> h1 = ELEMENTS["H[1]"]
-    >>>
+    >>> 
     >>> # Return a list of the properties stored in the database
     >>> l = ELEMENTS.get_properties()
-    >>>
+    >>> 
     >>> # Return the atomic weight of U[235] element
     >>> w = ELEMENTS["U[235]","atomic_weight"]
-    >>>
+    >>> 
     >>> # Returns the elements stored currently in the database
     >>> elements = ELEMENTS.get_elements()
     '''

MDANSE/Framework/Configurable.py

@@ -186,7 +186,9 @@ class Configurable(object):
         
         for name,(typ,kwds) in configurators.items():
             cfg=REGISTRY["configurator"][typ](name, **kwds)
-            doclist.append({'Configurator' : name,'Default value' : repr(cfg.default),'Description' : str(cfg.__doc__)})
+            descr = kwds.get("description","")
+            descr += "\n"+str(cfg.__doc__)
+            doclist.append({'Configurator' : name,'Default value' : repr(cfg.default),'Description' : descr})
                                     
         docstring = "\n:Example:\n\n"
         docstring += ">>> from MDANSE import REGISTRY\n"
@@ -227,8 +229,6 @@ class Configurable(object):
             
         docstring += "\n"
         
-#         print docstring
-            
         return docstring
     
     @classmethod

MDANSE/Framework/Jobs/Castep.py

@@ -100,7 +100,6 @@ class MDFile(dict):
         
         self["instance"].seek(0)           
         
-        
     def read_step(self, step):
         """
         """
@@ -129,12 +128,10 @@ class MDFile(dict):
         
         return timeStep, basisVectors, config
 
-
     def close(self):
         self["instance"].close()
 
-
-class CASTEP_Converter(IJob):
+class CASTEPConverter(IJob):
     """
     Converts a Castep Trajectory into a MMTK NetCDFFile. 
     """

MDANSE/Framework/Jobs/DensityOfStates.py

@@ -35,7 +35,7 @@ import collections
 from MDANSE import ELEMENTS
 from MDANSE.Framework.Jobs.IJob import IJob
 from MDANSE.Mathematics.Arithmetic import weight
-from MDANSE.Mathematics.Signal import correlation, differentiate, normalize, get_spectrum
+from MDANSE.Mathematics.Signal import correlation, differentiate, get_spectrum
 from MDANSE.MolecularDynamics.Trajectory import read_atoms_trajectory
 
 class DensityOfStates(IJob):

MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.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 Fre