def OnInit(self):
"""OnInit method used by wxwindows. initiates all base
classes and methods
"""
self.model = FlowModel()
self.model.addListener(self.OnModelUpdate)
self.controlFrame = MainFrame(pos=(50, 50))
self.controlFrame.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
self.controlFrame.Show()
self.model.addListener(self.controlFrame.ModelUpdate)
self.controlFrame.AttachModel(self.model)
self.io = Io(self.model, self.controlFrame)
self.io.LoadPlugins()
self.fileMenu = wx.Menu()
self.io.BuildOpenMenu(self.fileMenu)
self.fileMenu.AppendSeparator()
importFCSDir = self.fileMenu.Append(-1, "Load all FCS files in directory")
importCSVDir = self.fileMenu.Append(-1, "Load all delimited files in directory")
self.controlFrame.Bind(wx.EVT_MENU, self.OnImportFCSDir, importFCSDir)
self.controlFrame.Bind(wx.EVT_MENU, self.OnImportCSVDir, importCSVDir)
self.fileMenu.AppendSeparator()
save = self.fileMenu.Append(-1,'Save HDF5 file')
self.controlFrame.Bind(wx.EVT_MENU, self.OnSave, save)
menuquit = self.fileMenu.Append(-1,'Quit')
self.controlFrame.Bind(wx.EVT_MENU, self.OnQuit, menuquit)
self.compensateMenu = wx.Menu()
compensate = self.compensateMenu.Append(-1, 'Apply compensation')
#load_comp = self.compensateMenu.Append(-1, 'Load compensation matrix')
#edit_comp = self.compensateMenu.Append(-1, 'Edit compensation matrix')
self.controlFrame.Bind(wx.EVT_MENU, self.OnCompensate, compensate)
#self.controlFrame.Bind(wx.EVT_MENU, self.OnLoadCompensate, load_comp)
#self.controlFrame.Bind(wx.EVT_MENU, self.OnEditCompensate, edit_comp)
self.graphicsMenu = wx.Menu()
self.visuals = loadFrames("plugins/visual")
self.controlFrame.Visuals = self.visuals
for key in self.visuals:
menuid = self.graphicsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.OnAddWindow, menuid)
self.graphicsMenu.AppendSeparator()
self.statisticsMenu = wx.Menu()
self.statistics = loadstatistics("plugins/statistics")
for key in self.statistics.keys():
menuid = self.statisticsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.Onstatistics, menuid)
self.projectionsMenu = wx.Menu()
self.projections = loadprojections("plugins/projections")
for key in self.projections.keys():
menuid = self.projectionsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.Onprojections, menuid)
menuItems = [(self.fileMenu, 'File'),
(self.controlFrame.edit, 'Tree'),
(self.compensateMenu, 'Compensation'),
(self.controlFrame.filterMenu, 'Sub-Sample'),
(self.controlFrame.transformMenu, 'Transformation'),
(self.graphicsMenu, 'Graphics'),
(self.statisticsMenu, 'Statistics'),
(self.projectionsMenu, 'Projection'),
(self.controlFrame.ontologyMenu, 'Ontology'),
(self.controlFrame.remoteProcessMenu, 'Server')]
for item in menuItems:
self.controlFrame.GetMenuBar().Append(*item)
# help menu
self.helpMenu = wx.Menu()
self.about = self.helpMenu.Append(wx.ID_ABOUT, "&About Flow")
self.help = self.helpMenu.Append(-1, "Flow User Guide")
self.developer = self.helpMenu.Append(-1, "Flow Developer Guide")
# self.tutorial = self.helpMenu.Append(-1, "Flow Tutorial")
self.helpMenu.AppendSeparator()
self.homepage = self.helpMenu.Append(-1, "Flow homepage")
self.bugs = self.helpMenu.Append(-1, "Report bugs")
self.helpMenu.AppendSeparator()
# self.update = self.helpMenu.Append(-1, "Check for updates")
self.controlFrame.GetMenuBar().Append(self.helpMenu, "&Help")
self.Bind(wx.EVT_MENU, self.OnAbout, self.about)
self.Bind(wx.EVT_MENU, self.OnHelp, self.help)
self.Bind(wx.EVT_MENU, self.OnDeveloper, self.developer)
# self.Bind(wx.EVT_MENU, self.OnTutorial, self.tutorial)
self.Bind(wx.EVT_MENU, self.OnHomepage, self.homepage)
self.Bind(wx.EVT_MENU, self.OnBugs, self.bugs)
# self.Bind(wx.EVT_MENU, self.OnUpdate, self.update)
global Visual
self.controlFrame.DoLayout()
self.SetTopWindow(self.controlFrame)
return True
class MainApp(wx.App): #IGNORE:R0902
"""main app class, used to start the whole program """
framelist = []
def OnInit(self):
"""OnInit method used by wxwindows. initiates all base
classes and methods
"""
self.model = FlowModel()
self.model.addListener(self.OnModelUpdate)
self.controlFrame = MainFrame(pos=(50, 50))
self.controlFrame.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
self.controlFrame.Show()
self.model.addListener(self.controlFrame.ModelUpdate)
self.controlFrame.AttachModel(self.model)
self.io = Io(self.model, self.controlFrame)
self.io.LoadPlugins()
self.fileMenu = wx.Menu()
self.io.BuildOpenMenu(self.fileMenu)
self.fileMenu.AppendSeparator()
importFCSDir = self.fileMenu.Append(-1, "Load all FCS files in directory")
importCSVDir = self.fileMenu.Append(-1, "Load all delimited files in directory")
self.controlFrame.Bind(wx.EVT_MENU, self.OnImportFCSDir, importFCSDir)
self.controlFrame.Bind(wx.EVT_MENU, self.OnImportCSVDir, importCSVDir)
self.fileMenu.AppendSeparator()
save = self.fileMenu.Append(-1,'Save HDF5 file')
self.controlFrame.Bind(wx.EVT_MENU, self.OnSave, save)
menuquit = self.fileMenu.Append(-1,'Quit')
self.controlFrame.Bind(wx.EVT_MENU, self.OnQuit, menuquit)
self.compensateMenu = wx.Menu()
compensate = self.compensateMenu.Append(-1, 'Apply compensation')
#load_comp = self.compensateMenu.Append(-1, 'Load compensation matrix')
#edit_comp = self.compensateMenu.Append(-1, 'Edit compensation matrix')
self.controlFrame.Bind(wx.EVT_MENU, self.OnCompensate, compensate)
#self.controlFrame.Bind(wx.EVT_MENU, self.OnLoadCompensate, load_comp)
#self.controlFrame.Bind(wx.EVT_MENU, self.OnEditCompensate, edit_comp)
self.graphicsMenu = wx.Menu()
self.visuals = loadFrames("plugins/visual")
self.controlFrame.Visuals = self.visuals
for key in self.visuals:
menuid = self.graphicsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.OnAddWindow, menuid)
self.graphicsMenu.AppendSeparator()
self.statisticsMenu = wx.Menu()
self.statistics = loadstatistics("plugins/statistics")
for key in self.statistics.keys():
menuid = self.statisticsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.Onstatistics, menuid)
self.projectionsMenu = wx.Menu()
self.projections = loadprojections("plugins/projections")
for key in self.projections.keys():
menuid = self.projectionsMenu.Append(-1, key)
self.controlFrame.Bind(wx.EVT_MENU, self.Onprojections, menuid)
menuItems = [(self.fileMenu, 'File'),
(self.controlFrame.edit, 'Tree'),
(self.compensateMenu, 'Compensation'),
(self.controlFrame.filterMenu, 'Sub-Sample'),
(self.controlFrame.transformMenu, 'Transformation'),
(self.graphicsMenu, 'Graphics'),
(self.statisticsMenu, 'Statistics'),
(self.projectionsMenu, 'Projection'),
(self.controlFrame.ontologyMenu, 'Ontology'),
(self.controlFrame.remoteProcessMenu, 'Server')]
for item in menuItems:
self.controlFrame.GetMenuBar().Append(*item)
# help menu
self.helpMenu = wx.Menu()
self.about = self.helpMenu.Append(wx.ID_ABOUT, "&About Flow")
self.help = self.helpMenu.Append(-1, "Flow User Guide")
self.developer = self.helpMenu.Append(-1, "Flow Developer Guide")
# self.tutorial = self.helpMenu.Append(-1, "Flow Tutorial")
self.helpMenu.AppendSeparator()
self.homepage = self.helpMenu.Append(-1, "Flow homepage")
self.bugs = self.helpMenu.Append(-1, "Report bugs")
self.helpMenu.AppendSeparator()
# self.update = self.helpMenu.Append(-1, "Check for updates")
self.controlFrame.GetMenuBar().Append(self.helpMenu, "&Help")
self.Bind(wx.EVT_MENU, self.OnAbout, self.about)
self.Bind(wx.EVT_MENU, self.OnHelp, self.help)
self.Bind(wx.EVT_MENU, self.OnDeveloper, self.developer)
# self.Bind(wx.EVT_MENU, self.OnTutorial, self.tutorial)
self.Bind(wx.EVT_MENU, self.OnHomepage, self.homepage)
self.Bind(wx.EVT_MENU, self.OnBugs, self.bugs)
# self.Bind(wx.EVT_MENU, self.OnUpdate, self.update)
global Visual
self.controlFrame.DoLayout()
self.SetTopWindow(self.controlFrame)
return True
def OnCompensate(self, event): #IGNORE:W0613
"""Apply compensation matrix to data."""
try:
if hasattr(self.model.GetCurrentGroup(), 'spillover'):
comp = CompensationFrame(self.model, matrix = self.model.GetCurrentGroup().spillover)
else:
comp = CompensationFrame(self.model)
comp.Show()
except ValueError:
dlg = wx.MessageDialog(None, 'Check that ALL columns listed in spillover matrix are present in the data', 'Compensation Error', style=wx.OK)
if dlg.ShowModal() == wx.ID_OK:
dlg.Destroy()
def OnLoadCompensate(self, event): #IGNORE:W0613
"""Loads a compensation file in ASCII format with following structure
n,h_1,...,h_n,a_11,...,a_nn
where n is the number of marker columns requiring compensation
h_i is the header column name and
a_ij are the entries in the spillover matrix
just like 'SPILL' entry in FACSDiva 'SPILL'"""
overwrite = True
if self.model.getSpill():
overwrite = False
dlg = wx.MessageDialog(None,
'Overwrite existing matrix?',
'Load spillover matrix',
style=wx.OK|wx.CANCEL)
if dlg.ShowModal() == wx.ID_OK:
overwrite = True
dlg.Destroy()
if overwrite:
filetype = "Text files (*.txt)|*.txt|CSV files (*.csv)|*.csv|All files (*.*)|*.*"
dialog = wx.FileDialog(None,
"Load compensation matrix",
os.getcwd(),
"" ,
filetype,
wx.OPEN)
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
self.model.setSpill(open(path).read())
dialog.Destroy()
def OnEditCompensate(self, event): #IGNORE:W0613
"""Assumes that spillover matrix is stored within fields as SPILL."""
if self.model.ready:
spill, markers = self.model.getSpill()
if spill:
self.spillFrame = SpillFrame(spill, markers)
self.spillFrame.Show()
def OnImportFCSDir(self, event): #IGNORE:W0613
"""Import all fcs files in directory."""
dlg = wx.DirDialog(None,
"Choose a directory with .fcs files:",
style=wx.DD_DEFAULT_STYLE)
if dlg.ShowModal() == wx.ID_OK:
dir = dlg.GetPath()
fs = glob.glob(dir + '/*.fcs')
for f in fs:
self.io.ReadFCS(f)
self.model.SelectRoot()
dlg.Destroy()
def OnImportCSVDir(self, event): #IGNORE:W0613
"""Import all csv files in directory."""
dlg = wx.DirDialog(None,
"Choose a directory with .out and .txt files:",
style=wx.DD_DEFAULT_STYLE)
if dlg.ShowModal() == wx.ID_OK:
dir = dlg.GetPath()
fs = glob.glob(dir + '/*.out')
for f in fs:
self.io.ReadCSV(f)
self.model.SelectRoot()
dlg.Destroy()
def OnQuit(self, event): #IGNORE:W0613
"""Handle quit event"""
try:
if not self.model.isChanged:
self.Exit()
elif self.model.isOpen():
dialog = SaveDialog()
result = dialog.ShowModal()
if result == wx.ID_YES:
self.SaveFile()
self.model.close()
elif result == wx.ID_NO:
self.model.close()
if result == wx.ID_YES or result == wx.ID_NO:
self.Exit()
dialog.Destroy()
except AttributeError:
self.Exit()
def OnSave(self, event): #IGNORE:W0613
"""Save the hdf5 file"""
if self.model.isOpen:
filetype = "HDF5 file (*.h5)|*.h5"
dialog = wx.FileDialog(None,
"Save Working Set",
os.getcwd(),
"" ,
filetype,
wx.SAVE|wx.OVERWRITE_PROMPT)
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
if path.split('.')[-1] == 'h5':
ext = ''
else:
ext = '.h5'
self.model.saveAs(path + ext)
self.model.isChanged = False
dialog.Destroy()
def OnAddWindow(self, event):
"""add a new window frame"""
newWindowType = self.controlFrame.GetMenuBar().FindItemById(event.GetId()).GetLabel() #IGNORE:C0301
newWindow = self.visuals[newWindowType]()
title = newWindow.GetTitle()
title = title + " of " + str(self.model.current_array)
newWindow.SetTitle(title)
newWindow.AttachModel(self.model)
newId = self.graphicsMenu.AppendCheckItem(-1, title)
newId.Check(True)
self.framelist.append((newWindow.GetId(), newId.GetId(), newWindow))
self.controlFrame.Bind(wx.EVT_MENU, self.OnWindowSelect, newId)
newWindow.Bind(wx.EVT_CLOSE, self.OnCloseWindow)
newWindow.Plot()
def OnWindowSelect(self, event):
"""handle selecting a window from the list of windows"""
menuItem = self.controlFrame.GetMenuBar().FindItemById(event.GetId())
for windowId, menuId, window in self.framelist: #IGNORE:W0612
if menuItem.GetId() == menuId:
if menuItem.IsChecked():
window.Show(True)
window.SetFocus()
else:
window.Show(False)
def OnCloseWindow(self, event):
"""on window close event destroy all windows"""
if event.GetId() == self.controlFrame.GetId():
self.OnQuit(event)
else:
for windowId, menuId, window in self.framelist:
if event.GetId() == windowId:
window.Destroy()
self.graphicsMenu.Remove(menuId)
self.framelist.remove((windowId, menuId, window))
def OnModelUpdate(self, model): #IGNORE:W0613
"""on model update do something"""
#print "Model Update Called"
def Onstatistics(self, event):
"""When Statistics menu events are called"""
Name = self.controlFrame.GetMenuBar().FindItemById(event.GetId()).GetLabel() #IGNORE:C0301
statistics = self.statistics[Name]()
statistics.Main(self.model)
def Onprojections(self, event):
"""When projections menu events are called"""
Name = self.controlFrame.GetMenuBar().FindItemById(event.GetId()).GetLabel() #IGNORE:C0301
projections = self.projections[Name]()
projections.Main(self.model)
def OnAbout(self, event):
"""About screen."""
dlg = about.FlowAbout(self.controlFrame)
dlg.ShowModal()
dlg.Destroy()
def OnHelp(self, event):
os_utils.open(os.path.join("..", "docs", "userguide.pdf"))
def OnDeveloper(self, event):
os_utils.open(os.path.join("..", "docs", "developer_guide.pdf"))
def OnTutorial(self, event):
pass
def OnHomepage(self, event):
os_utils.open('http://galen.dulci.org/flow')
def OnBugs(self, event):
os_utils.open('http://galen.dulci.org/flow/newticket')
def OnUpdate(self, event):
pass