class NeuroptikonApp(wx.App):
def __init__(self, *args, **keywordArgs):
self._networks = set([])
self.preferences = None
self.inspector = None
self.config = None
self._console = None
# Keep track of open frames so we can close them on quit.
# TODO: use wxWidget's document/view framework instead
self._frames = []
self._customizationDocSetId = wx.NewId()
self._dataMgmtDocSetId = wx.NewId()
self._scriptingDocSetId = wx.NewId()
self._uiDocSetId = wx.NewId()
wx.App.__init__(self, *args, **keywordArgs)
def OnInit(self):
import Inspectors, Layouts, Shapes # pylint: disable=W0612
neuroptikon.library = Library()
self._loadDefaultLibraryItems()
neuroptikon.config = wx.Config('Neuroptikon')
if platform.system() == 'Darwin':
wx.MenuBar.MacSetCommonMenuBar(self.menuBar())
neuroptikon.scriptLocals = self.scriptLocals
self.preferences = Preferences()
self.inspector = InspectorFrame()
self.SetExitOnFrameDelete(False)
startupScript = neuroptikon.config.Read('Startup Script', '')
try:
exec startupScript in self.scriptLocals()
except:
(exceptionType, exceptionValue,
exceptionTraceback) = sys.exc_info()
frames = traceback.extract_tb(exceptionTraceback)[1:]
message = gettext(
'An error occurred while running the startup script:')
subMessage = str(
exceptionValue
) + ' (' + exceptionType.__name__ + ')' + '\n\nTraceback:\n' + ''.join(
traceback.format_list(frames))
if platform.system() == 'Darwin':
wx.MessageBox(subMessage, message, style=wx.ICON_ERROR | wx.OK)
else:
wx.MessageBox(message + '\n\n' + subMessage,
'Neuroptikon',
parent=self,
style=wx.ICON_ERROR | wx.OK)
# open an empty network by default
# TODO: pref to re-open last doc?
self.onNewNetwork()
return True
def _loadDefaultLibraryItems(self):
neuroptikon.library.add(
Neurotransmitter('ACh', gettext('Acetylcholine')))
neuroptikon.library.add(Neurotransmitter('DA', gettext('Dopamine')))
neuroptikon.library.add(
Neurotransmitter('epinephrine', gettext('Epinephrine')))
neuroptikon.library.add(
Neurotransmitter('GABA', gettext('Gamma-aminobutyric acid'),
gettext('GABA')))
neuroptikon.library.add(Neurotransmitter('GLU', gettext('Glutamate')))
neuroptikon.library.add(Neurotransmitter('glycine',
gettext('Glycine')))
neuroptikon.library.add(
Neurotransmitter('histamine', gettext('Histamine')))
neuroptikon.library.add(
Neurotransmitter('norepinephrine', gettext('Norepinephrine')))
neuroptikon.library.add(Neurotransmitter('5-HT', gettext('Serotonin')))
# pylint: disable=E1101
neuroptikon.library.add(
NeuronClass(identifier='basket',
name=gettext('Basket cell'),
polarity=Neuron.Polarity.MULTIPOLAR,
functions=[Neuron.Function.INTERNEURON],
activation='inhibitory',
neurotransmitters=[
neuroptikon.library.neurotransmitter('GABA')
]))
neuroptikon.library.add(
NeuronClass(identifier='pyramidal',
name=gettext('Pyramidal cell'),
polarity=Neuron.Polarity.MULTIPOLAR,
activation='excitatory',
neurotransmitters=[
neuroptikon.library.neurotransmitter('glutamate')
]))
neuroptikon.library.add(
NeuronClass(
identifier='RSad pyramidal',
name=gettext('RSad Pyramidal cell'),
parentClass=neuroptikon.library.neuronClass('pyramidal')))
neuroptikon.library.add(
NeuronClass(
identifier='RSna pyramidal',
name=gettext('RSna Pyramidal cell'),
parentClass=neuroptikon.library.neuronClass('pyramidal')))
neuroptikon.library.add(
NeuronClass(
identifier='IB pyramidal',
name=gettext('IB Pyramidal cell'),
parentClass=neuroptikon.library.neuronClass('pyramidal')))
neuroptikon.library.add(
NeuronClass(
identifier='betz',
name=gettext('Betz cell'),
parentClass=neuroptikon.library.neuronClass('pyramidal'),
functions=[Neuron.Function.MOTOR]))
neuroptikon.library.add(
NeuronClass(identifier='medium spiny',
name=gettext('Medium spiny neuron'),
polarity=Neuron.Polarity.MULTIPOLAR,
activation='inhibitory',
neurotransmitters=[
neuroptikon.library.neurotransmitter('GABA')
]))
neuroptikon.library.add(
NeuronClass(identifier='purkinje',
name=gettext('Purkinje cell'),
polarity=Neuron.Polarity.MULTIPOLAR,
activation='inhibitory',
neurotransmitters=[
neuroptikon.library.neurotransmitter('GABA')
]))
neuroptikon.library.add(
NeuronClass(identifier='renshaw',
name=gettext('Renshaw cell'),
polarity=Neuron.Polarity.MULTIPOLAR,
functions=[Neuron.Function.INTERNEURON],
activation='inhibitory',
neurotransmitters=[
neuroptikon.library.neurotransmitter('glycine')
]))
neuroptikon.library.add(
NeuronClass(identifier='anterior horn',
name=gettext('Anterior horn cell')))
# pylint: enable=E1101
neuroptikon.library.add(Modality('light', gettext('Light')))
neuroptikon.library.add(Modality('odor', gettext('Odor')))
neuroptikon.library.add(Modality('sound', gettext('Sound')))
neuroptikon.library.add(Modality('taste', gettext('Taste')))
# Load any ontologies in <root>/Ontologies
try:
for fileName in os.listdir(neuroptikon.rootDir + os.sep +
'Ontologies'):
if fileName.endswith('.obo'):
identifier = os.path.splitext(fileName)[0]
ontology = Ontology(identifier)
try:
ontology.importOBO(neuroptikon.rootDir + os.sep +
'Ontologies' + os.sep + fileName)
neuroptikon.library.add(ontology)
except:
(exceptionType, exceptionValue,
exceptionTraceback_) = sys.exc_info()
print 'Could not import ontology ' + fileName + ' (' + str(
exceptionValue
) + ' (' + exceptionType.__name__ + ')' + ')'
except:
(exceptionType, exceptionValue,
exceptionTraceback_) = sys.exc_info()
print 'Could not import ontologies (' + str(
exceptionValue) + ' (' + exceptionType.__name__ + ')' + ')'
# Load any textures in <root>/Textures
try:
for fileName in os.listdir(neuroptikon.rootDir + os.sep +
'Textures'):
if fileName != '.svn':
identifier = os.path.splitext(fileName)[0]
texture = Texture(identifier, gettext(identifier))
if texture.loadImage(neuroptikon.rootDir + os.sep +
'Textures' + os.sep + fileName):
neuroptikon.library.add(texture)
except:
(exceptionType, exceptionValue,
exceptionTraceback_) = sys.exc_info()
print 'Could not import textures (' + str(
exceptionValue) + ' (' + exceptionType.__name__ + ')' + ')'
def onQuit(self, event_):
continueQuit = True
for frame in list(self._frames):
if frame.isModified():
frame.Raise()
if not frame.Close():
continueQuit = False
break
if continueQuit and not any(
self._frames) and platform.system() == 'Darwin':
self.ExitMainLoop()
def menuBar(self, frame=None):
menuBar = wx.MenuBar()
fileMenu = wx.Menu()
self.Bind(
wx.EVT_MENU, self.onNewNetwork,
fileMenu.Append(wx.ID_NEW, gettext('New Network\tCtrl-N'),
gettext('Open a new network window')))
self.Bind(
wx.EVT_MENU, self.onOpenNetwork,
fileMenu.Append(wx.ID_OPEN, gettext('Open Network...\tCtrl-O'),
gettext('Open a previously saved network')))
closeItem = fileMenu.Append(
wx.ID_CLOSE, gettext('Close Network\tCtrl-W'),
gettext('Close the current network window'))
if frame:
frame.Bind(wx.EVT_MENU, frame.onCloseWindow, closeItem)
else:
closeItem.Enable(False)
saveItem = fileMenu.Append(wx.ID_SAVE,
gettext('Save Network...\tCtrl-S'),
gettext('Save the current network'))
if frame:
frame.Bind(wx.EVT_MENU, frame.onSaveNetwork, saveItem)
else:
saveItem.Enable(False)
saveAsItem = fileMenu.Append(wx.ID_SAVEAS,
gettext('Save As...\tCtrl-Shift-S'),
gettext('Save to a new file'))
if frame:
frame.Bind(wx.EVT_MENU, frame.onSaveNetworkAs, saveAsItem)
else:
saveAsItem.Enable(False)
fileMenu.AppendSeparator()
runScriptItem = fileMenu.Append(wx.NewId(),
gettext('Run Script...\tCtrl-R'),
gettext('Run a console script file'))
if frame:
frame.Bind(wx.EVT_MENU, frame.onRunScript, runScriptItem)
else:
runScriptItem.Enable(False)
self.Bind(
wx.EVT_MENU, self.onBrowseLibrary,
fileMenu.Append(wx.NewId(),
gettext('Browse the Library\tCtrl-Alt-L'),
gettext('Open the Library window')))
self.Bind(
wx.EVT_MENU, self.onOpenConsole,
fileMenu.Append(wx.NewId(),
gettext('Open the Console\tCtrl-Alt-O'),
gettext('Open the Console window')))
self.Bind(
wx.EVT_MENU, self.onOpenPreferences,
fileMenu.Append(wx.ID_PREFERENCES, gettext('Settings'),
gettext('Change Neuroptikon preferences')))
fileMenu.AppendSeparator()
self.Bind(
wx.EVT_MENU, self.onQuit,
fileMenu.Append(wx.ID_EXIT, gettext('E&xit\tCtrl-Q'),
gettext('Exit the Neuroptikon application')))
menuBar.Append(fileMenu, gettext('&File'))
helpMenu = wx.Menu()
self.Bind(
wx.EVT_MENU, self.onShowDocumentation,
helpMenu.Append(
self._customizationDocSetId,
gettext('Customizing Neuroptikon'),
gettext('Show the documentation on customizing Neuroptikon')))
self.Bind(
wx.EVT_MENU, self.onShowDocumentation,
helpMenu.Append(
self._dataMgmtDocSetId, gettext('Data Management'),
gettext(
'Show the documentation on managing Neuroptikon data')))
self.Bind(
wx.EVT_MENU, self.onShowDocumentation,
helpMenu.Append(
self._scriptingDocSetId, gettext('Scripting Interface'),
gettext('Show the documentation on scripting Neuroptikon')))
self.Bind(
wx.EVT_MENU, self.onShowDocumentation,
helpMenu.Append(
self._uiDocSetId, gettext('User Interface'),
gettext(
'Show the documentation on interacting with Neuroptikon')))
helpMenu.AppendSeparator()
self.Bind(
wx.EVT_MENU, self.onSendFeedback,
helpMenu.Append(wx.NewId(), gettext('Report Bug or Enhancement'),
gettext('Report a bug or request a new feature')))
if platform.system() != 'Darwin':
helpMenu.AppendSeparator()
self.Bind(
wx.EVT_MENU, self.onAboutNeuroptikon,
helpMenu.Append(wx.ID_ABOUT, gettext('About Neuroptikon'),
gettext('Information about this program')))
menuBar.Append(helpMenu, gettext('&Help'))
return menuBar
def scriptLocals(self):
layoutClasses = {}
for layoutClass in display.layout.layoutClasses():
layoutClasses[layoutClass.name()] = layoutClass
shapeClasses = {}
for shapeClass in display.shape.shapeClasses():
shapeClasses[shapeClass.__name__] = shapeClass
scriptLocals = {
'createNetwork': self.createNetwork,
'displayNetwork': self.displayNetwork,
'openNetwork': self.openNetwork,
'networks': self.networks,
'library': neuroptikon.library,
'Neurotransmitter': Neurotransmitter,
'NeuronClass': NeuronClass,
'Modality': Modality,
'Ontology': Ontology,
'Texture': Texture,
'NeuralPolarity': Neuron.Polarity, # DEPRECATED: remove soon...
'NeuralFunction': Neuron.Function, # DEPRECATED: remove soon...
'Attribute': Attribute,
'layouts': layoutClasses,
'shapes': shapeClasses,
'Object': Object,
'showMessage': self.showMessage
}
for objectClass in NeuroObject.__subclasses__(): # pylint: disable=E1101
scriptLocals[objectClass.__name__] = objectClass
if 'DEBUG' in os.environ:
scriptLocals['os'] = os
scriptLocals['sys'] = sys
scriptLocals['wx'] = wx
import osg
scriptLocals['osg'] = osg
import gc
scriptLocals['gc'] = gc
scriptLocals['datetime'] = datetime
scriptLocals['date'] = date
scriptLocals['time'] = time
try:
import objgraph
scriptLocals['objgraph'] = objgraph
except ImportError:
pass
from pydispatch import dispatcher
scriptLocals['dispatcher'] = dispatcher
return scriptLocals
def onRunScript(self, event_):
dlg = wx.FileDialog(None, gettext('Choose a script to run'), 'Scripts',
'', '*.py', wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
prevDir = os.getcwd()
os.chdir(os.path.dirname(dlg.GetPath()))
try:
execfile(dlg.GetPath(), self.scriptLocals())
except:
(exceptionType, exceptionValue,
exceptionTraceback) = sys.exc_info()
wx.MessageBox(
str(exceptionValue) + ' (' + exceptionType.__name__ + ')',
gettext('An error occurred at line %d of the script:') %
exceptionTraceback.tb_next.tb_lineno,
style=wx.ICON_ERROR | wx.OK)
os.chdir(prevDir)
dlg.Destroy()
def onOpenConsole(self, event_):
if not self._console:
confDir = wx.StandardPaths.Get().GetUserDataDir()
if not os.path.exists(confDir):
os.mkdir(confDir)
fileName = os.path.join(confDir, 'Console.config')
self.config = wx.FileConfig(localFilename=fileName)
self.config.SetRecordDefaults(True)
self._console = py.shell.ShellFrame(title=gettext('Console'),
config=self.config,
dataDir=confDir,
locals=self.scriptLocals())
#TODO: need to just hide the console window on close or set up some kind of callback to clear _console when the console closes
self._console.Show()
self._console.Raise()
def onNewNetwork(self, event_=None):
network = self.createNetwork()
self.displayNetwork(network)
def createNetwork(self):
network = Network()
#TODO: implement doc/view framework
return network
def openNetwork(self, filePath):
"""
Open the previously saved network at the indicated path.
Any displays will be restored or a default one will be opened.
"""
from neuroptikon_frame import NeuroptikonFrame
# TODO: raise an existing window if the network is already open
try:
xmlTree = ElementTree.parse(filePath)
# Instantiate the network
networkElement = xmlTree.find('Network')
network = Network._fromXMLElement(networkElement)
if network is None:
raise ValueError, gettext('Could not load the network')
network.setSavePath(filePath)
network.setModified(False)
self._networks.add(network)
# Instantiate any displays
for frameElement in xmlTree.findall('DisplayWindow'):
frame = NeuroptikonFrame._fromXMLElement(frameElement,
network=network)
if frame is None:
raise ValueError, gettext(
'Could not create one of the displays')
frame.Show(True)
frame.Raise()
self._frames.append(frame)
# Create a default display if none were specified in the file.
if len(network.displays) == 0:
self.displayNetwork(network).zoomToFit()
except:
raise
def onOpenNetwork(self, event_):
dlg = wx.FileDialog(None, gettext('Choose a saved network to open:'),
'', '', '*.xml', wx.OPEN)
if dlg.ShowModal() == wx.ID_OK:
self.openNetwork(dlg.GetPath())
dlg.Destroy()
def networks(self):
return list(self._networks)
def releaseNetwork(self, network):
if not any(network.displays):
network.removeAllObjects()
self._networks.remove(network)
def displayNetwork(self, network, populateDisplay=True):
"""
Open a new display for the network.
"""
self._networks.add(network)
from neuroptikon_frame import NeuroptikonFrame
frame = NeuroptikonFrame(network=network,
populateDisplay=populateDisplay)
frame.Show(True)
frame.Raise()
self._frames.append(frame)
return frame.display
def displayWasClosed(self, displayFrame):
self._frames.remove(displayFrame)
if len(self._frames) == 0 and platform.system() != 'Darwin':
self.ExitMainLoop()
def onOpenPreferences(self, event_):
self.preferences.Show(True)
self.preferences.Raise()
return self.preferences
def onBrowseLibrary(self, event_):
neuroptikon.library.browse()
def onOpenInspector(self, event_):
self.inspector.Show(True)
self.inspector.Raise()
return self.inspector
def onShowDocumentation(self, event):
if event.GetId() == self._customizationDocSetId:
page = 'Customizing/index.html'
elif event.GetId() == self._dataMgmtDocSetId:
page = 'DataManagement.html'
elif event.GetId() == self._scriptingDocSetId:
page = 'Scripting/index.html'
elif event.GetId() == self._uiDocSetId:
page = 'UserInterface/index.html'
documentation.showPage(page)
def onSendFeedback(self, event_):
dlg = FeedbackDialog()
if dlg.ShowModal() == wx.ID_OK:
queryDict = {
'pid': 10000,
'summary': dlg.summary(),
'description': dlg.description(),
'customfield_10000': dlg.contactEmail()
}
if platform.system() == 'Darwin':
environment = 'OS: Mac OS X ' + platform.mac_ver()[0] + '\n'
elif platform.system() == 'Windows':
release, version, csd, ptype = platform.win32_ver()
environment = 'OS: Windows ' + release + ' ' + version + ' ' + csd + ' ' + ptype + '\n'
else:
environment = 'OS: ' + platform.system(
) + ' ' + platform.version() + '\n'
environment += 'Python version: ' + platform.python_version(
) + '\n'
queryDict['environment'] = environment
if dlg.isBugReport():
queryDict['issuetype'] = 1
elif dlg.isFeatureRequest():
queryDict['issuetype'] = 2
# task = 3, improvement = 4
queryDict['versions'] = __version__.JIRA_version_id
url = 'http://www.neuroptikon.org/issues/secure/CreateIssueDetails.jspa?' + urllib.urlencode(
queryDict)
if not wx.LaunchDefaultBrowser(url):
message = gettext('The issue could not be created')
resolution = gettext(
'Please visit http://www.neuroptikon.org/issues/ to send your feedback.'
)
if platform.system() == 'Darwin':
wx.MessageBox(resolution, message)
else:
wx.MessageBox(gettext('Send Feedback'),
message + '\n\n' + resolution)
dlg.Destroy()
def onAboutNeuroptikon(self, event_):
info = wx.AboutDialogInfo()
info.SetName(gettext('Neuroptikon'))
info.SetVersion(__version__.version)
info.SetDescription(
gettext(
'Developed at the \nJanelia Farm Research Campus by:\n\nFrank Midgley\nVivek Jayaraman\nMitya Chklovskii\nDon Olbris'
))
info.SetCopyright(
gettext('Copyright \xa9 2010 - Howard Hughes Medical Institute'))
wx.AboutBox(info)
def showMessage(self, message, subMessage=None, isError=False):
"""
Display a message to the user.
"""
if platform.system() == 'Darwin':
wx.MessageBox(
subMessage,
message or '',
style=(wx.ICON_ERROR if isError else wx.ICON_INFORMATION)
| wx.OK)
else:
wx.MessageBox(
'Neuroptikon', (message + '\n\n' +
subMessage if message else subMessage or ''),
style=(wx.ICON_ERROR if isError else wx.ICON_INFORMATION)
| wx.OK)
