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Commit 1420c57e authored by eric pellegrini's avatar eric pellegrini
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Removed unused plugins

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MDANSE/App/GUI/Framework/Plugins/AtomSelectionPlugin.py deleted 100644 → 0
View file @ a7286933
#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
import wx.aui as wxaui
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
from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
class AtomSelectionPluginError(Error):
pass
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[-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 AtomSelectionPlugin(ComponentPlugin):
type = "atom_selection"
label = "Atom selection"
ancestor = "molecular_viewer"
def __init__(self, parent, *args, **kwargs):
self._query = Query()
self._selectors = {}
self._expression = None
self._selection = None
self._selectionParser = None
ComponentPlugin.__init__(self, parent, size = (500,450), *args, **kwargs)
def build_panel(self):
self._mainPanel = wx.Panel(self, wx.ID_ANY, size=self.GetSize())
self._notebook = wxaui.AuiNotebook(self._mainPanel, wx.ID_ANY, style=wxaui.AUI_NB_DEFAULT_STYLE&~wxaui.AUI_NB_CLOSE_ON_ACTIVE_TAB&~wxaui.AUI_NB_TAB_MOVE)
settingsPanel = wx.Panel(self._mainPanel,wx.ID_ANY)
self.keywordsRadioButton = wx.RadioButton(settingsPanel, wx.ID_ANY, label = "Keywords")
self.keywordsRadioButton.SetValue(True)
self.pythonScriptRadioButton = wx.RadioButton(settingsPanel, wx.ID_ANY, label = "Python script")
self.mouseClickRadioButton = wx.RadioButton(settingsPanel, wx.ID_ANY, label = "Mouse click")
self.boxWidgetRadioButton = wx.RadioButton(settingsPanel, wx.ID_ANY, label = "Box widget")
# 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")
self._pythonScript = wx.Button(settingsPanel,wx.ID_ANY,label="Browse")
self._pythonScript.Disable()
self._selectionSummary = wx.TextCtrl(self._mainPanel,wx.ID_ANY,style=wx.TE_LINEWRAP|wx.TE_MULTILINE|wx.TE_READONLY)
self._notebook.AddPage(settingsPanel, "settings")
self._notebook.AddPage(self._selectionSummary, "selection")
selectionExpressionStaticBox = wx.StaticBox(self._mainPanel, wx.ID_ANY, label = "Selection")
# The widgets related to the selection being performed
self.selectionTextCtrl = wx.TextCtrl(self._mainPanel, wx.ID_ANY, style = wx.TE_READONLY)
clearButton = wx.Button(self._mainPanel, wx.ID_ANY, label="Clear")
undoButton = wx.Button(self._mainPanel, wx.ID_ANY, label="Undo")
# The panel related to user definition control
self._udPanel = UserDefinitionsPanel(self._mainPanel)
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.GridBagSizer(5,5)
selectionSizer.AddGrowableCol(1)
selectionSizer.AddGrowableRow(1)
selectionSizer.Add(self.keywordsRadioButton,pos=(0,0),span=(1,2))
selectionSizer.Add((20,-1),pos=(1,0),flag=wx.EXPAND)
selectionSizer.Add(self._queryPanel,pos=(1,1),flag=wx.EXPAND)
selectionSizer.Add(self.pythonScriptRadioButton,pos=(2,0),span=(1,2))
selectionSizer.Add((20,-1),pos=(3,0),flag=wx.EXPAND)
selectionSizer.Add(self._pythonScript,pos=(3,1))
selectionSizer.Add(self.mouseClickRadioButton,pos=(4,0),span=(1,2))
selectionSizer.Add(self.boxWidgetRadioButton,pos=(5,0),span=(1,2))
settingsPanel.SetSizer(selectionSizer)
selectionExpressionStaticBoxSizer = wx.StaticBoxSizer(selectionExpressionStaticBox, wx.HORIZONTAL)
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)
self._selectionExpressionSizer.Add(undoButton, pos=(0,3), flag=wx.ALL)
selectionExpressionStaticBoxSizer.Add(self._selectionExpressionSizer,1,wx.ALL|wx.EXPAND,5)
# Add to main sizer
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(self._notebook, 1, wx.ALL|wx.EXPAND, 5)
mainSizer.Add(selectionExpressionStaticBoxSizer, 0, wx.ALL|wx.EXPAND, 5)
mainSizer.Add(self._udPanel, 0, wx.ALL|wx.EXPAND, 5)
self._mainPanel.SetSizer(mainSizer)
mainSizer.Fit(self._mainPanel)
self._mainPanel.Layout()
self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
self._mgr.Update()
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_RADIOBUTTON, self.on_source_selection, self.keywordsRadioButton)
self.Bind(wx.EVT_RADIOBUTTON, self.on_source_selection, self.pythonScriptRadioButton)
self.Bind(wx.EVT_RADIOBUTTON, self.on_source_selection, self.mouseClickRadioButton)
self.Bind(wx.EVT_RADIOBUTTON, self.on_source_selection, self.boxWidgetRadioButton)
self.Bind(wx.EVT_BUTTON, self.on_browse_python_script, self._pythonScript)
self.Bind(wx.EVT_BUTTON, self.on_clear, clearButton)
self.Bind(wx.EVT_BUTTON, self.on_undo, undoButton)
def close(self):
self.parent.selection_box.hide()
self.parent.clear_selection()
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._parent.clear_selection()
def on_close(self, event=None):
self.close()
self.parent.mgr.ClosePane(self.parent.mgr.GetPane(self))
def on_display_keyword_values(self, event=None):
if self._parent.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._parent.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_save(self, event=None):
if not self._selection:
LOGGER("The current selection is empty", "error", ["dialog"])
return
name = self._udPanel.get_selection_name()
if not name:
LOGGER("You must enter a value for the user definition", "error", ["dialog"])
return
target = os.path.basename(self.parent.trajectory.filename)
ud = REGISTRY['user_definition']['atom_selection'](target,expression=self._expression,indexes=self._selection)
UD_STORE.set_definition(target,ud.type,name,ud)
UD_STORE.save()
pub.sendMessage("new_selection", message = (target, name))
def on_select_atoms(self, message):
self.insert_keyword_values("atompicked", message)
def on_show_hide_selection_box(self, event=None):
self._parent.show_hide_selection_box()
def on_source_selection(self, event=None):
selectedSource = str(event.GetEventObject().GetLabelText())
if selectedSource == "Keywords":
self._queryPanel.Enable()
self._pythonScript.Disable()
self._parent.selection_box.hide()
self._parent.disable_picking()
elif selectedSource == "Python script":
self._queryPanel.Disable()
self._pythonScript.Enable()
self._parent.selection_box.hide()
self._parent.disable_picking()
elif selectedSource == "Mouse click":
self._queryPanel.Disable()
self._pythonScript.Disable()
self._parent.selection_box.hide()
self._parent.enable_picking()
elif selectedSource == "Box widget":
self._queryPanel.Disable()
self._pythonScript.Disable()
self._parent.selection_box.show()
self._parent.disable_picking()
def on_undo(self, event=None):
if self._query.is_empty():
return
self._query.pop()
self.set_selection()
self.selectionTextCtrl.SetValue(self._query.get_expression())
def plug(self):
self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
self.parent.mgr.Update()
self._query.set_parser(AtomSelectionParser(self.dataproxy.data.universe))
self._atoms = sorted_atoms(self.dataproxy.data.universe)
pub.subscribe(self.on_select_atoms, ('select atoms'))
def set_selection(self):
self._expression, self._selection = self._query.parse()
self._parent.show_selected_atoms(self._selection)
\ No newline at end of file
MDANSE/App/GUI/Framework/Plugins/AtomTransmutationPlugin.py deleted 100644 → 0
View file @ a7286933
#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 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
class AtomTransmutationPlugin(AtomSelectionPlugin):
type = "atom_transmutation"
label = "Atom transmutation"
ancestor = "molecular_viewer"
def build_panel(self):
AtomSelectionPlugin.build_panel(self)
label = wx.StaticText(self._mainPanel, wx.ID_ANY, style=wx.ALIGN_LEFT, label="Transmute to")
self._elements = wx.Choice(self._mainPanel, wx.ID_ANY, choices=ELEMENTS.elements)
self._elements.SetStringSelection("H[2]")
self._selectionExpressionSizer.Add(label, pos=(1,0), flag=wx.ALIGN_CENTER_VERTICAL)
self._selectionExpressionSizer.Add(self._elements, pos=(1,1), flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL)
self._mainPanel.Layout()
def on_save(self, event=None):
'''
Event handler: validate the selection.
@param event: the event binder
@type event: wx event
'''
if not self._selection:
LOGGER("The current selection is empty", "warning", ["dialog"])
return
name = self._udPanel.get_selection_name()
if not name:
LOGGER("You must enter a value for the user definition", "error", ["dialog"])
return
target = os.path.basename(self.parent.trajectory.filename)
element = self._elements.GetStringSelection()
ud = REGISTRY['user_definition']['atom_transmutation'](target,expression=self._expression,indexes=self._selection,element=element)
UD_STORE.set_definition(target,ud.type,name,ud)
UD_STORE.save()
Publisher.sendMessage("new_transmutation", message = (target, name))
\ No newline at end of file