Implemented independant dialog for setting ud that are not plugins

anymore.

MDANSE/App/GUI/ComboWidgets/AtomSelectionDialog.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 14, 2015
+
+:author: Eric C. Pellegrini
+'''
+
+import collections
+import os
+
+import wx
+
+from MDANSE import LOGGER, REGISTRY
+from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser, AtomSelectionParserError
+from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
+
+from MDANSE.App.GUI.ComboWidgets.UserDefinitionsDialog import UserDefinitionsDialog
+from MDANSE.App.GUI.Framework.Plugins.DataPlugin import get_data_plugin 
+
+class Query(object):
+        
+    def __init__(self):
+        
+        self._list = []
+        
+        self._parser = None
+
+    def get_expression(self):
+
+        s = []
+                 
+        for v in self._list:
+            
+            if isinstance(v, list):
+                keyword,arguments = v
+                arguments = ",".join([str(val) for val in arguments])
+                s.append("%s %s" % (keyword,arguments))
+            else:
+                s.append(v)
+        
+        return "".join(s)
+        
+    @property
+    def list(self):
+        return self._list
+    
+    @property
+    def parser(self):
+        return self._parser
+
+    def add_operator(self, operator):
+
+        if operator == "(":
+            if self._list:
+                if self._list[-1] == ")" or isinstance(self._list[-1], list):
+                    return
+            self._list.append("(")
+            
+        elif operator == ")":
+            if self._list:
+                if self._list[-1] == ")" or isinstance(self._list[-1], list):
+                    if self._list.count(")") < self._list.count("("):
+                        self._list.append(")")
+        
+        elif operator == "not":
+            if self._list:
+                if self._list[-1] == ")":
+                    return
+            self._list.append(" not ")
+            
+        elif operator in ["and","or"]:       
+            if self._list:
+                if self._list[-1] == ")" or isinstance(self._list[-1], list):
+                    self._list.append(" %s " % operator)
+    
+    def add_query(self, query):
+
+        if not self._list:
+            if query is not None:
+                self._list.append(query)            
+        else:
+            
+            keyword, values = query
+
+            if isinstance(self._list[-1], list):
+
+                if self._list[-1][0] == keyword:
+                    if values:
+                        self._list[-1] = query
+                    else:
+                        del self._list[-1]
+                else:
+                    self._list.extend([' or ', query])
+                        
+            elif isinstance(self._list[-1], basestring):
+                if self._list[-1] in [' and ',' or ','(',' not ']:
+                    self._list.append(query)                    
+
+    def clear(self):
+        self._list = []
+        
+    def is_empty(self):
+        
+        return len(self._list) == 0
+            
+    def parse(self):
+        
+        if self._parser is None:
+            return []
+                            
+        try:
+            expression = self.get_expression()
+            selection = self._parser.parse(expression)
+        except AtomSelectionParserError:
+            return ("",[])
+        else:
+            return (expression,selection)
+            
+    def pop(self):
+        return self._list.pop()
+    
+    def set_parser(self, parser):
+        
+        self._parser = parser
+
+class AtomSelectionDialog(UserDefinitionsDialog):
+    
+    def __init__(self, parent, trajectory, *args, **kwargs):
+
+        self._query = Query()
+
+        self._selectors = {}
+                                        
+        self._expression = None
+
+        self._selection = None
+
+        self._selectionParser = None
+
+        self._trajectory = trajectory
+        
+        self._query.set_parser(AtomSelectionParser(self._trajectory.universe))
+
+        self._atoms = sorted_atoms(self._trajectory.universe)  
+        
+        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)
+
+        pub.subscribe(self.on_select_atoms_from_viewer, ('select_atoms_from_viewer'))       
+                 
+    def build_dialog(self):
+                                                
+        panel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
+        panel.SetScrollbars(20,20,50,50)
+
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        
+        settingsPanel = wx.Panel(panel,wx.ID_ANY)
+                
+        # Build the widgets used to build a selection from selection strings and operators
+        self._queryPanel = wx.Panel(settingsPanel)
+                              
+        self.filterTree = wx.TreeCtrl(self._queryPanel, 1, wx.DefaultPosition, style=wx.TR_HIDE_ROOT|wx.TR_HAS_BUTTONS)
+          
+        root = self.filterTree.AddRoot("filters")
+        filters = self.filterTree.AppendItem(root, "Filter by")
+        selectors = REGISTRY["selector"].values()
+        self.__filters = collections.OrderedDict()
+        for selector in selectors:            
+            if selector.section is not None:
+                if self.__filters.has_key(selector.section):
+                    self.__filters[selector.section].append(selector.type)
+                else:
+                    self.__filters[selector.section] = [selector.type]
+         
+        for section, subsections in sorted(self.__filters.items()):
+            section_node = self.filterTree.AppendItem(filters, section)
+            for subsection in sorted(subsections):
+                self.filterTree.AppendItem(section_node,subsection)
+         
+        self.values = wx.ListBox(self._queryPanel, wx.ID_ANY, style = wx.LB_MULTIPLE|wx.LB_NEEDED_SB)
+                                 
+        leftBraceLinker = wx.Button(self._queryPanel, wx.ID_ANY, label = "(")        
+        rightBraceLinker = wx.Button(self._queryPanel, wx.ID_ANY, label = ")")
+        andLinker = wx.Button(self._queryPanel, wx.ID_ANY, label = "and")
+        orLinker = wx.Button(self._queryPanel, wx.ID_ANY, label = "or")
+        notLinker = wx.Button(self._queryPanel, wx.ID_ANY, label = "not")
+
+        selectionStringSizer = wx.BoxSizer(wx.VERTICAL)
+        keywordsValuesSizer = wx.BoxSizer(wx.HORIZONTAL)
+        keywordsValuesSizer.Add(self.filterTree, 1, wx.ALIGN_CENTER_VERTICAL|wx.LEFT|wx.RIGHT|wx.EXPAND, 2)
+        keywordsValuesSizer.Add(self.values, 3, wx.ALIGN_CENTER_VERTICAL|wx.LEFT|wx.RIGHT|wx.EXPAND, 2)
+        linkersSizer = wx.BoxSizer(wx.HORIZONTAL)
+        linkersSizer.Add(leftBraceLinker, 1, flag=wx.ALL|wx.EXPAND)
+        linkersSizer.Add(rightBraceLinker, 1, flag=wx.ALL|wx.EXPAND)
+        linkersSizer.Add(andLinker, 1, flag=wx.ALL|wx.EXPAND)
+        linkersSizer.Add(orLinker, 1, flag=wx.ALL|wx.EXPAND)
+        linkersSizer.Add(notLinker, 1, flag=wx.ALL|wx.EXPAND)
+        selectionStringSizer.Add(keywordsValuesSizer,1,wx.ALL|wx.EXPAND,5)
+        selectionStringSizer.Add(linkersSizer,0,wx.ALL|wx.EXPAND,5)
+        self._queryPanel.SetSizer(selectionStringSizer)
+                                         
+        selectionSizer = wx.BoxSizer(wx.VERTICAL)
+        selectionSizer.Add(self._queryPanel,1,wx.ALL|wx.EXPAND,5)
+         
+        settingsPanel.SetSizer(selectionSizer)
+
+        # The widgets related to the selection being performed        
+        selectionExpressionStaticBox = wx.StaticBox(panel, wx.ID_ANY, label = "Selection")                
+        selectionExpressionStaticBoxSizer = wx.StaticBoxSizer(selectionExpressionStaticBox, wx.HORIZONTAL)
+
+        self.selectionTextCtrl = wx.TextCtrl(panel, wx.ID_ANY, style = wx.TE_READONLY)
+        clearButton  = wx.Button(panel, wx.ID_ANY, label="Clear")
+        
+        self._selectionExpressionSizer = wx.GridBagSizer(5,5)        
+        self._selectionExpressionSizer.AddGrowableCol(0)
+        self._selectionExpressionSizer.Add(self.selectionTextCtrl, pos=(0,0), span=(1,2),flag=wx.ALL|wx.EXPAND)
+        self._selectionExpressionSizer.Add(clearButton, pos=(0,2), flag=wx.ALL)
+        selectionExpressionStaticBoxSizer.Add(self._selectionExpressionSizer,1,wx.ALL|wx.EXPAND,5)
+                    
+        self._selectionSummary = wx.TextCtrl(panel,wx.ID_ANY,style=wx.TE_LINEWRAP|wx.TE_MULTILINE|wx.TE_READONLY)  
+                                                   
+        sizer.Add(settingsPanel, 2, wx.ALL|wx.EXPAND, 5)
+        sizer.Add(selectionExpressionStaticBoxSizer, 0, wx.ALL|wx.EXPAND, 5)
+        sizer.Add(self._selectionSummary, 1, wx.ALL|wx.EXPAND, 5)
+
+        panel.SetSizer(sizer)
+                                                                              
+        self._mainSizer.Add(panel, 1, wx.EXPAND|wx.ALL, 5)
+                                                                              
+        self.Bind(wx.EVT_TREE_SEL_CHANGED, self.on_display_keyword_values, self.filterTree)
+        self.Bind(wx.EVT_LISTBOX, self.on_insert_keyword_values, self.values)
+  
+        self.Bind(wx.EVT_BUTTON, self.on_add_operator, leftBraceLinker)
+        self.Bind(wx.EVT_BUTTON, self.on_add_operator, rightBraceLinker)
+        self.Bind(wx.EVT_BUTTON, self.on_add_operator, orLinker)
+        self.Bind(wx.EVT_BUTTON, self.on_add_operator, andLinker)
+        self.Bind(wx.EVT_BUTTON, self.on_add_operator, notLinker)
+            
+        self.Bind(wx.EVT_BUTTON, self.on_clear, clearButton)
+                        
+    def display_selection_summary(self):
+        
+        self._selectionSummary.Clear()
+        
+        nSelectedAtoms = len(self._selection)
+        
+        self._selectionSummary.AppendText("Number of selected atoms: %d\n\n" % nSelectedAtoms)
+        
+        if nSelectedAtoms == 0:
+            return
+        
+        self._selectionSummary.AppendText("List of selected atoms:\n")
+        for idx in self._selection:
+            self._selectionSummary.AppendText("\t%s (MMTK index: %d)\n" % (self._atoms[idx].fullName(),self._atoms[idx].index))
+
+    def insert_keyword_values(self, keyword, values):
+
+        self._query.add_query([keyword,values])
+                
+        self.set_selection()
+
+        self.selectionTextCtrl.SetValue(self._query.get_expression())
+        
+        self.display_selection_summary()
+
+    def on_add_operator(self, event=None):
+
+        operator = event.GetEventObject().GetLabel()
+
+        self._query.add_operator(operator)        
+                
+        self.selectionTextCtrl.SetValue(self._query.get_expression())
+        
+        self.values.DeselectAll()
+
+    def on_browse_python_script(self, event):
+        
+        dlg = wx.FileDialog(self, "Browse python selection script", defaultDir=os.getcwd(), wildcard="Python files (*.py)|*.py",style=wx.FD_OPEN|wx.FD_MULTIPLE)
+
+        if dlg.ShowModal() == wx.ID_OK:        
+            self.insert_keyword_values("pythonscript", dlg.GetPaths())
+                                                                                                                                                           
+    def on_clear(self, event=None):
+        
+        self._query.clear()
+
+        self.selectionTextCtrl.Clear()
+                
+        self.values.DeselectAll()
+        
+        self._selectionSummary.Clear()
+
+        pub.sendMessage('clear_selection',message=self)                                
+
+    def on_close(self, event=None):
+        
+        self.Destroy()
+                
+    def on_display_keyword_values(self, event=None):
+        
+        if self._trajectory is None:
+            return
+        
+        item = event.GetItem()
+
+        selectionFilter = self.filterTree.GetItemText(item)
+        
+        if not REGISTRY["selector"].has_key(selectionFilter):
+            return
+                                
+        if not self._selectors.has_key(selectionFilter):
+            self._selectors[selectionFilter] = [str(v) for v in REGISTRY["selector"][selectionFilter](self._trajectory.universe).choices]
+        
+        self.values.Set(self._selectors[selectionFilter])
+
+    def on_insert_keyword_values(self, event):
+                                
+        item = self.filterTree.GetSelection()
+                
+        keyword = str(self.filterTree.GetItemText(item))
+                                
+        values = [str(self.values.GetString(v)) for v in self.values.GetSelections()]
+
+        self.insert_keyword_values(keyword, values)
+
+    def on_mode_selection(self, event=None): 
+        
+        self.selectedMode = str(event.GetEventObject().GetLabelText()).lower()
+        
+        self.keywords.DeselectAll()
+        self.values.DeselectAll()
+
+    def on_select_atoms_from_viewer(self, message):
+
+        dataPlugin,selection = message
+        
+        if dataPlugin != get_data_plugin(self):
+            return
+        
+        self._query.clear()
+        
+        self.insert_keyword_values("atom_picked", selection)
+                
+    def set_selection(self):
+
+        self._expression, self._selection = self._query.parse()
+                
+        pub.sendMessage("set_selection", message = (self,self._selection))
+        
+    def validate(self):
+
+        if not self._selection:
+            LOGGER("The current selection is empty", "error", ["dialog"])
+            return None
+        
+        return self._selection
+        
+if __name__ == "__main__":
+    
+    from MMTK.Trajectory import Trajectory
+    
+    t = Trajectory(None,"../../../../Data/Trajectories/MMTK/protein_in_periodic_universe.nc","r")
+    
+    app = wx.App(False)
+    
+    f = wx.Frame(None)
+            
+    p = AtomSelectionDialog(f,t)
+        
+    p.SetSize((800,800))
+            
+    p.ShowModal()
+    
+    p.Destroy()
+    
+    app.MainLoop()
+    
\ No newline at end of file

MDANSE/App/GUI/ComboWidgets/AtomsListDialog.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 14, 2015
+
+:author: Eric C. Pellegrini
+'''
+
+import os
+
+import wx
+
+from MDANSE import LOGGER
+from MDANSE.App.GUI.ComboWidgets.UserDefinitionsDialog import UserDefinitionsDialog
+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
+
+        self._trajectory = trajectory
+    
+        self._nAtoms = nAtoms
+        
+        self._selectedAtoms = []
+                
+        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)
+                        
+    def build_dialog(self):
+
+        panel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
+        panel.SetScrollbars(20,20,50,50)
+        
+        sizer = wx.BoxSizer(wx.VERTICAL)
+        
+        sb = wx.StaticBox(panel, wx.ID_ANY, label = "Atom selection")
+        sbSizer = wx.StaticBoxSizer(sb, wx.HORIZONTAL)
+        
+        gbSizer = wx.GridBagSizer(5,5)
+        
+        label1 = wx.StaticText(panel, wx.ID_ANY, label="Molecules")
+        label2 = wx.StaticText(panel, wx.ID_ANY, label="Atoms")
+
+        gbSizer.Add(label1, (0,0), flag=wx.EXPAND)
+        gbSizer.Add(label2, (0,1), flag=wx.EXPAND)
+    
+        self._molecules = wx.ListBox(panel, wx.ID_ANY, style = wx.LB_SINGLE|wx.LB_NEEDED_SB)
+        self._molecularContents = get_chemical_objects_dict(self._trajectory.universe)
+        self._molecules.SetItems(sorted(self._molecularContents.keys()))        
+
+        self._atoms = wx.ListBox(panel, wx.ID_ANY, style = wx.LB_MULTIPLE|wx.LB_NEEDED_SB)
+        
+        gbSizer.Add(self._molecules, (1,0), flag=wx.EXPAND)
+        gbSizer.Add(self._atoms    , (1,1), flag=wx.EXPAND)
+        
+        gbSizer.AddGrowableRow(1)
+        gbSizer.AddGrowableCol(0)
+        gbSizer.AddGrowableCol(1)
+        
+        sbSizer.Add(gbSizer, 1, wx.EXPAND|wx.ALL, 5)
+
+        setButton  = wx.Button(panel, wx.ID_ANY, label="Set")
+        self._resultsTextCtrl  = wx.TextCtrl(panel, wx.ID_ANY, style=wx.TE_READONLY|wx.TE_MULTILINE)
+
+        sizer.Add(sbSizer,1,wx.EXPAND|wx.ALL,5)
+        sizer.Add(setButton,0,wx.EXPAND|wx.ALL,5)
+        sizer.Add(self._resultsTextCtrl,1,wx.EXPAND|wx.ALL,5)
+
+        panel.SetSizer(sizer)
+
+        self._mainSizer.Add(panel, 1, wx.EXPAND|wx.ALL, 5)
+                
+        self.Bind(wx.EVT_BUTTON, self.on_set_user_definition, setButton)
+        self.Bind(wx.EVT_LISTBOX, self.on_select_molecule, self._molecules)
+        self.Bind(wx.EVT_LISTBOX, self.on_select_atom, self._atoms)
+
+    def set_user_definition(self):
+
+        self._ud.clear()
+
+        if len(self._selectedAtoms) != self._nAtoms:
+            LOGGER('You must select %d atoms.' % self._nAtoms,'error',['dialog'])
+            return
+
+        molecule = str(self._molecules.GetStringSelection())
+        atoms = tuple(str(self._atoms.GetString(idx)) for idx in self._selectedAtoms)
+
+        self._ud = {}
+        self._ud['parameters'] = (molecule,atoms)
+        self._ud['indexes'] = find_atoms_in_molecule(self._trajectory.universe,molecule, atoms, True)
+                        
+    def on_set_user_definition(self,event=None):
+
+        self._resultsTextCtrl.Clear()
+        
+        self.set_user_definition()
+        if not self._ud:
+            return
+            
+        molecule,atoms = self._ud['parameters']
+            
+        self._resultsTextCtrl.AppendText('Molecule = %s ; Atoms = %s\nIndexes:\n' % (molecule,atoms))
+        for idxs in self._ud['indexes']:
+            line = "   ;   ".join(["Atom %d : %s" % (i,v) for i,v in enumerate(idxs)])
+            self._resultsTextCtrl.AppendText(line)
+            self._resultsTextCtrl.AppendText('\n')
+        
+    def on_select_atom(self, event):
+        
+        selection = self._atoms.GetSelections()
+                
+        if len(selection) > self._nAtoms:
+            self._atoms.DeselectAll()
+            for idx in self._selectedAtoms:
+                self._atoms.SetSelection(idx,True)
+        else:
+            self._selectedAtoms = selection
+                            
+    def on_select_molecule(self, event):
+        
+        atomsList = self._molecularContents[event.GetString()][0].atomList()
+        atomNames = sorted(set([at.name for at in atomsList]))
+        
+        self._atoms.SetItems(atomNames)
+            
+    def validate(self):
+
+        if not self._ud:
+            return None
+                        
+        return self._ud
+    
+if __name__ == "__main__":
+    
+    from MMTK.Trajectory import Trajectory
+    
+    t = Trajectory(None,"../../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc","r")
+    
+    app = wx.App(False)
+    
+    f = wx.Frame(None)
+            
+    p = AtomsListDialog(f,t,2)
+    
+    f.Show()
+