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Commit 3f553546 authored by eric pellegrini's avatar eric pellegrini
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Modified deeply the UD based widgets such that all of the can be 

alunched as standalone widget of used as a plugin
parent e9aa2ee7
Hide whitespace changes
Inline Side-by-side
MDANSE/Framework/Widgets/AtomSelectionWidget.py
View file @ 3f553546
......@@ -34,13 +34,14 @@ import collections
import os
import wx
import wx.aui as wxaui
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.Framework.Widgets.UserDefinitionWidget import UserDefinitionsDialog, UserDefinitionWidget
from MDANSE.Framework.Widgets.UserDefinitionWidget import UDDialog, UDPlugin, UserDefinitionWidget
from MDANSE.Framework.Plugins.DataPlugin import get_data_plugin
class Query(object):
......@@ -148,12 +149,16 @@ class Query(object):
def set_parser(self, parser):
self._parser = parser
class AtomSelectionDialog(UserDefinitionsDialog):
class AtomSelectionPlugin(UDPlugin):
type = 'atom_selection'
def __init__(self, parent, trajectory, *args, **kwargs):
label = "Atom selection"
ancestor = ["molecular_viewer"]
def __init__(self, parent, *args, **kwargs):
self._query = Query()
......@@ -161,19 +166,11 @@ class AtomSelectionDialog(UserDefinitionsDialog):
self._selection = []
self._trajectory = trajectory
self._query.set_parser(AtomSelectionParser(self._trajectory.universe))
pub.subscribe(self.on_select_atoms_from_viewer, ('msg_select_atoms_from_viewer'))
self._atoms = sorted_atoms(self._trajectory.universe)
target = os.path.basename(self._trajectory.filename)
UDPlugin.__init__(self,parent,size=(800,500))
UserDefinitionsDialog.__init__(self, parent, target, 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, ('msg_select_atoms_from_viewer'))
def build_dialog(self):
def build_panel(self):
self._mainPanel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
self._mainPanel.SetScrollbars(20,20,50,50)
......@@ -250,9 +247,14 @@ class AtomSelectionDialog(UserDefinitionsDialog):
sizer.Add(self._selectionSummary, 1, wx.ALL|wx.EXPAND, 5)
self._mainPanel.SetSizer(sizer)
self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)
self._mainSizer = wx.BoxSizer(wx.VERTICAL)
self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self._mainSizer)
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)
......@@ -263,7 +265,25 @@ class AtomSelectionDialog(UserDefinitionsDialog):
self.Bind(wx.EVT_BUTTON, self.on_add_operator, notLinker)
self.Bind(wx.EVT_BUTTON, self.on_clear, clearButton)
def plug(self):
self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
self.parent.mgr.Update()
self.set_trajectory(self.dataproxy.data)
def set_trajectory(self,trajectory):
self._trajectory = trajectory
self._query.set_parser(AtomSelectionParser(self._trajectory.universe))
self._atoms = sorted_atoms(self._trajectory.universe)
self._target = os.path.basename(self._trajectory.filename)
def display_selection_summary(self):
self._selectionSummary.Clear()
......@@ -317,10 +337,6 @@ class AtomSelectionDialog(UserDefinitionsDialog):
self._selectionSummary.Clear()
pub.sendMessage('msg_clear_selection',message=self)
def on_close(self, event=None):
self.Destroy()
def on_display_keyword_values(self, event=None):
......@@ -378,25 +394,17 @@ class AtomSelectionDialog(UserDefinitionsDialog):
if not self._selection:
LOGGER("The current selection is empty", "error", ["dialog"])
return None
self._ud['indexes'] = self._selection
return self._ud
return {'indexes':self._selection}
class AtomSelectionWidget(UserDefinitionWidget):
type = "atom_selection"
def on_new_user_definition(self,event):
dlg = AtomSelectionDialog(self,self._trajectory)
dlg.Show()
def get_widget_value(self):
ud = self._availableUDs.GetStringSelection()
if not ud:
return 'all'
else:
......@@ -406,11 +414,13 @@ if __name__ == "__main__":
from MMTK.Trajectory import Trajectory
t = Trajectory(None,"../../../../../Data/Trajectories/MMTK/protein_in_periodic_universe.nc","r")
from MDANSE import PLATFORM
t = Trajectory(None,os.path.join(PLATFORM.example_data_directory(),"Trajectories","MMTK","protein_in_periodic_universe.nc"),"r")
app = wx.App(False)
p = AtomSelectionDialog(None,t)
p = UDDialog(None,t,'atom_selection')
p.SetSize((800,800))
......
MDANSE/Framework/Widgets/AtomTransmutationWidget.py
View file @ 3f553546
......@@ -35,18 +35,20 @@ import wx
from MDANSE import ELEMENTS, LOGGER
from MDANSE.Framework.Widgets.UserDefinitionWidget import UserDefinitionWidget
from MDANSE.Framework.Widgets.AtomSelectionWidget import AtomSelectionDialog
from MDANSE.Framework.Widgets.AtomSelectionWidget import AtomSelectionPlugin
class AtomTransmutationDialog(AtomSelectionDialog):
class AtomTransmutationPlugin(AtomSelectionPlugin):
type = 'atom_transmutation'
label = "Atom transmutation"
ancestor = ["molecular_viewer"]
def build_dialog(self):
AtomSelectionDialog.build_dialog(self)
self.SetTitle("Atom transmutation dialog")
AtomSelectionPlugin.build_dialog(self)
self._elements = wx.ComboBox(self._mainPanel, wx.ID_ANY, value="Transmutate to", choices=ELEMENTS.elements)
self._selectionExpressionSizer.Add(self._elements, pos=(0,3), flag=wx.EXPAND|wx.ALIGN_CENTER_VERTICAL)
......@@ -67,39 +69,14 @@ class AtomTransmutationDialog(AtomSelectionDialog):
return self._ud
class AtomTransmutationWidget(UserDefinitionWidget):
type = "atom_transmutation"
def on_new_user_definition(self,event):
dlg = AtomTransmutationDialog(self,self._trajectory)
dlg.Show()
def get_widget_value(self):
ud = self._availableUDs.GetStringSelection()
if not ud:
return None
else:
return str(ud)
if __name__ == "__main__":
from MMTK.Trajectory import Trajectory
t = Trajectory(None,"../../../../../Data/Trajectories/MMTK/protein_in_periodic_universe.nc","r")
app = wx.App(False)
p = AtomTransmutationDialog(None,t)
p.SetSize((800,800))
p.ShowModal()
p.Destroy()
app.MainLoop()
\ No newline at end of file
return str(ud)
\ No newline at end of file
MDANSE/Framework/Widgets/AtomsListWidget.py
View file @ 3f553546
......@@ -33,9 +33,10 @@ Created on Jun 30, 2015
import os
import wx
import wx.aui as wxaui
from MDANSE import LOGGER
from MDANSE.Framework.Widgets.UserDefinitionWidget import UserDefinitionsDialog, UserDefinitionWidget
from MDANSE.Framework.Widgets.UserDefinitionWidget import UDPlugin, UserDefinitionWidget, UDDialog
from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict
class AtomNameDropTarget(wx.TextDropTarget):
......@@ -68,56 +69,57 @@ class AtomNameDropTarget(wx.TextDropTarget):
self._atoms.Append([data])
class AtomsListDialog(UserDefinitionsDialog):
class AtomsListPlugin(UDPlugin):
def __init__(self, parent, trajectory, nAtoms):
type = 'atoms_list'
label = "Atoms list"
ancestor = ["molecular_viewer"]
def __init__(self, parent, *args, **kwargs):
self._parent = parent
self._trajectory = trajectory
self._nAtoms = nAtoms
self._nAtoms = 1
self._selectedAtoms = []
self._selection = []
target = os.path.basename(self._trajectory.filename)
self.type = "%d_atoms_list" % self._nAtoms
UserDefinitionsDialog.__init__(self, parent, target, wx.ID_ANY, title="%d Atoms selection dialog" % nAtoms,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
UDPlugin.__init__(self,parent,size=(800,500))
self.SetSize((400,400))
def build_dialog(self):
def build_panel(self):
panel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
panel.SetScrollbars(20,20,50,50)
self._mainPanel = wx.ScrolledWindow(self, wx.ID_ANY, size=self.GetSize())
self._mainPanel.SetScrollbars(20,20,50,50)
sizer = wx.BoxSizer(wx.VERTICAL)
self._nAtomsSelectionSizer = wx.BoxSizer(wx.HORIZONTAL)
label = wx.StaticText(self._mainPanel, wx.ID_ANY, label="Number of atoms")
self._nAtomsSpinCtrl = wx.SpinCtrl(self._mainPanel,wx.ID_ANY,style=wx.SP_ARROW_KEYS|wx.SP_WRAP)
self._nAtomsSpinCtrl.SetRange(1,100)
self._nAtomsSpinCtrl.SetValue(self._nAtoms)
self._nAtomsSelectionSizer.Add(label,0,wx.ALL|wx.ALIGN_CENTRE_VERTICAL,5)
self._nAtomsSelectionSizer.Add(self._nAtomsSpinCtrl,1,wx.ALL|wx.EXPAND,5)
gbSizer = wx.GridBagSizer(5,5)
label1 = wx.StaticText(panel, wx.ID_ANY, label="Molecules")
label2 = wx.StaticText(panel, wx.ID_ANY, label="Selected atoms")
label1 = wx.StaticText(self._mainPanel, wx.ID_ANY, label="Molecules")
label2 = wx.StaticText(self._mainPanel, wx.ID_ANY, label="Selected atoms")
gbSizer.Add(label1, (0,0), flag=wx.EXPAND)
gbSizer.Add(label2, (0,1), flag=wx.EXPAND)
self._molecules = wx.TreeCtrl(panel, wx.ID_ANY, style=wx.TR_DEFAULT_STYLE|wx.LB_HSCROLL|wx.LB_NEEDED_SB^wx.TR_HIDE_ROOT)
self._molecularContents = get_chemical_objects_dict(self._trajectory.universe)
root = self._molecules.AddRoot('')
for mname in sorted(self._molecularContents.keys()):
molnode = self._molecules.AppendItem(root,mname)
atomsList = self._molecularContents[mname][0].atomList()
atomNames = sorted(set([at.name for at in atomsList]))
for aname in atomNames:
self._molecules.AppendItem(molnode,aname)
self._atoms = wx.ListCtrl(panel, wx.ID_ANY)
self._molecules = wx.TreeCtrl(self._mainPanel, wx.ID_ANY, style=wx.TR_DEFAULT_STYLE|wx.LB_HSCROLL|wx.LB_NEEDED_SB^wx.TR_HIDE_ROOT)
self._atoms = wx.ListCtrl(self._mainPanel, wx.ID_ANY)
dt = AtomNameDropTarget(self._molecules,self._atoms)
self._atoms.SetDropTarget(dt)
......@@ -129,21 +131,71 @@ class AtomsListDialog(UserDefinitionsDialog):
gbSizer.AddGrowableCol(0)
gbSizer.AddGrowableCol(1)
setButton = wx.Button(panel, wx.ID_ANY, label="Set")
self._resultsTextCtrl = wx.TextCtrl(panel, wx.ID_ANY, style=wx.TE_READONLY|wx.TE_MULTILINE)
setButton = wx.Button(self._mainPanel, wx.ID_ANY, label="Set")
self._resultsTextCtrl = wx.TextCtrl(self._mainPanel, wx.ID_ANY, style=wx.TE_READONLY|wx.TE_MULTILINE)
sizer.Add(self._nAtomsSelectionSizer, 0, wx.EXPAND|wx.ALL, 5)
sizer.Add(gbSizer, 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._mainPanel.SetSizer(sizer)
self._mainSizer.Add(panel, 1, wx.EXPAND|wx.ALL, 5)
self._mainSizer = wx.BoxSizer(wx.VERTICAL)
self._mainSizer.Add(self._mainPanel, 1, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self._mainSizer)
self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
self._mgr.Update()
self.Bind(wx.EVT_SPINCTRL,self.on_select_natoms,self._nAtomsSpinCtrl)
self.Bind(wx.EVT_BUTTON, self.on_set_user_definition, setButton)
self.Bind(wx.EVT_TREE_BEGIN_DRAG,self.on_drag_atom_name,self._molecules)
self.Bind(wx.EVT_LIST_KEY_DOWN,self.on_delete_atom_name,self._atoms)
def plug(self):
self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
self.parent.mgr.Update()
self.set_trajectory(self.dataproxy.data)
def enable_natoms_selection(self,state):
self._nAtomsSelectionSizer.ShowItems(state)
def set_natoms(self,nAtoms):
self._nAtoms = nAtoms
self._nAtomsSpinCtrl.SetValue(nAtoms)
def set_trajectory(self,trajectory):
self._trajectory = trajectory
self._target = os.path.basename(self._trajectory.filename)
self._molecularContents = get_chemical_objects_dict(self._trajectory.universe)
root = self._molecules.AddRoot('')
for mname in sorted(self._molecularContents.keys()):
molnode = self._molecules.AppendItem(root,mname)
atomsList = self._molecularContents[mname][0].atomList()
atomNames = sorted(set([at.name for at in atomsList]))
for aname in atomNames:
self._molecules.AppendItem(molnode,aname)
def on_select_natoms(self,event):
self._nAtoms = event.GetInt()
self._atoms.ClearAll()
self._resultsTextCtrl.Clear()
def on_delete_atom_name(self,event):
keycode = event.GetKeyCode()
......@@ -226,38 +278,35 @@ class AtomsListDialog(UserDefinitionsDialog):
class AtomListWidget(UserDefinitionWidget):
type = 'atoms_list'
def initialize(self):
self.type = "%d_atoms_list" % self._configurator._nAtoms
UserDefinitionWidget.initialize(self)
def on_new_user_definition(self,event):
dlg = UDDialog(self,self._trajectory,self.type)
atomsListDlg = AtomsListDialog(self,self._trajectory,self._configurator._nAtoms)
dlg.plugin.set_natoms(self._configurator._nAtoms)
atomsListDlg.ShowModal()
atomsListDlg.Destroy()
dlg.plugin.enable_natoms_selection(False)
if __name__ == "__main__":
from MMTK.Trajectory import Trajectory
from MDANSE import PLATFORM,REGISTRY
LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'](), level="error", start=True)
dlg.ShowModal()
t = Trajectory(None,os.path.join(os.path.dirname(PLATFORM.package_directory()),"Data","Trajectories","MMTK","nagma_in_periodic_universe.nc"),"r")
app = wx.App(False)
p = AtomsListDialog(None,t,4)
p.ShowModal()
p.Destroy()
app.MainLoop()
# if __name__ == "__main__":
#
# from MMTK.Trajectory import Trajectory
#
# from MDANSE import PLATFORM,REGISTRY
#
# LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'](), level="error", start=True)
#
# t = Trajectory(None,os.path.join(os.path.dirname(PLATFORM.package_directory()),"Data","Trajectories","MMTK","nagma_in_periodic_universe.nc"),"r")
#
# app = wx.App(False)
#
# p = AtomsListDialog(None,t,4)
#
# p.ShowModal()
#
# p.Destroy()
#
# app.MainLoop()
\ No newline at end of file
MDANSE/Framework/Widgets/PartialChargesWidget.py
View file @ 3f553546
......@@ -34,37 +34,65 @@ import operator
import os
import wx
import wx.aui as wxaui
import wx.grid as wxgrid
from MDANSE import LOGGER
from MDANSE.Framework.Widgets.UserDefinitionWidget import UserDefinitionsDialog, UserDefinitionWidget
from MDANSE.Framework.Widgets.UserDefinitionWidget import UDPlugin, UDDialog, UserDefinitionWidget
class PartialChargesDialog(UserDefinitionsDialog):
class PartialChargesPlugin(UDPlugin):
def __init__(self, parent, trajectory):
type = 'partial_charges'
label = "Partial charges settings"
ancestor = ["molecular_viewer"]
def __init__(self, parent, *args, **kwargs):
self._parent = parent
self._trajectory = trajectory
self._selectedAtoms = []
target = os.path.basename(self._trajectory.filename)
UserDefinitionsDialog.__init__(self, parent, target, 'partial_charges', wx.ID_ANY, title="Partial charges dialog",style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER|wx.MINIMIZE_BOX|wx.MAXIMIZE_BOX)
def build_dialog(self):
UDPlugin.__init__(self, parent)
def build_panel(self):
self._mainPanel = wx.Panel(self,wx.ID_ANY)
sizer = wx.BoxSizer(wx.VERTICAL)
self._grid = wxgrid.Grid(self._mainPanel)
self._grid = wxgrid.Grid(self)
sizer.Add(self._grid, 1, wx.ALL|wx.EXPAND, 5)
self._mainPanel.SetSizer(sizer)
self._mgr.AddPane(self._mainPanel, wxaui.AuiPaneInfo().DestroyOnClose().Center().Dock().CaptionVisible(False).CloseButton(False).BestSize(self.GetSize()))
self._mgr.Update()
def plug(self):
self.parent.mgr.GetPane(self).Float().Dockable(False).CloseButton(True).BestSize((600,600))
self._grid.CreateGrid(self._trajectory.universe.numberOfAtoms(),3)
self.parent.mgr.Update()
self.set_trajectory(self.dataproxy.data)
def set_trajectory(self,trajectory):
self._trajectory = trajectory
self._target = os.path.basename(self._trajectory.filename)
self._grid.CreateGrid(self._trajectory.universe.numberOfAtoms(),3)
self._grid.SetRowLabelSize(1)
self._grid.SetColFormatNumber(0)
self._grid.SetColFormatNumber(1)
self._grid.SetColFormatNumber(2)
roAttr = wxgrid.GridCellAttr()
roAttr.SetReadOnly(True)
roAttr.SetBackgroundColour(wx.Colour(220,220,220))
......@@ -84,9 +112,7 @@ class PartialChargesDialog(UserDefinitionsDialog):
for idx, at in enumerate(atoms):
self._grid.SetCellValue(idx,0,str(idx))
self._grid.SetCellValue(idx,1,at.name)
self._mainSizer.Add(self._grid, 1, wx.EXPAND|wx.ALL, 5)
def validate(self):
charges = {}
......@@ -105,32 +131,23 @@ class PartialChargesDialog(UserDefinitionsDialog):
class PartialChargesWidget(UserDefinitionWidget):
type = "partial_charges"
def initialize(self):
UserDefinitionWidget.initialize(self)
def on_new_user_definition(self,event):
dlg = PartialChargesDialog(self,self._trajectory)
dlg.ShowModal()
dlg.Destroy()
if __name__ == "__main__":
from MMTK.Trajectory import Trajectory
t = Trajectory(None,"../../../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc","r")
from MDANSE import PLATFORM
t = Trajectory(None,os.path.join(PLATFORM.example_data_directory(),"Trajectories","MMTK","protein_in_periodic_universe.nc"),"r")