def refreshWaveForm(self, widget=None, data=None):
self.builder.get_object("WaveFormImage").set_from_stock(gtk.STOCK_REFRESH, gtk.ICON_SIZE_LARGE_TOOLBAR)
self.clearEvents()
tmpname = tempfile.mkstemp()
starttime = float(self.builder.get_object("txtStart").get_text())
endtime = float(self.builder.get_object("txtEnd").get_text())
msmode = True
if self.cbTimeAxis.get_active() == 0:
starttime = starttime / 1000.0
endtime = endtime / 1000.0
msmode = False
gle = GLE()
if data == None or data["type"] == "preview":
gle.format = 'png'
pid = gle.waveform(tmpname[1], self.wavfile, self.framerate, msmode=msmode, minX=starttime, maxX=endtime)
watch = child_watch_add(pid, self.updateWaveFormImage, data=tmpname[1])
self.clearEvents()
def createVariables(self):
self.filename = ''
self.clean_filename = StringVar()
self.clean_filename.set('No File Loaded')
self.cellID = StringVar()
self.frequency = StringVar()
self.amplitude = StringVar()
self.rasterOffset = StringVar()
self.rasterOffset.set('0')
self.rasterStart = StringVar()
self.rasterStart.set('-0.5')
self.rasterEnd = StringVar()
self.rasterEnd.set('')
self.rasterYAxisChannel = IntVar()
self.rasterYAxisType = IntVar()
self.stimFilterA = StringVar()
self.stimFilterB = StringVar()
self.binWindow = StringVar()
self.binWindow.set('20')
self.GLE = GLE()
class Application(Frame):
def __init__(self, master=None):
Frame.__init__(self, master)
self.settings = Settings()
self.grid()
self.createVariables()
self.createWidgets()
self.bind("<Destroy>", self.windowdestroy)
def windowdestroy(self, event):
self.quit()
def quit(self):
self.GLE.cleantmp()
Frame.quit(self)
def createVariables(self):
self.filename = ''
self.clean_filename = StringVar()
self.clean_filename.set('No File Loaded')
self.cellID = StringVar()
self.frequency = StringVar()
self.amplitude = StringVar()
self.rasterOffset = StringVar()
self.rasterOffset.set('0')
self.rasterStart = StringVar()
self.rasterStart.set('-0.5')
self.rasterEnd = StringVar()
self.rasterEnd.set('')
self.rasterYAxisChannel = IntVar()
self.rasterYAxisType = IntVar()
self.stimFilterA = StringVar()
self.stimFilterB = StringVar()
self.binWindow = StringVar()
self.binWindow.set('20')
self.GLE = GLE()
def stimuliFilter(self):
s = []
for stim in range(len(self.stimuli)):
if stim+1 >= int(self.stimFilterA.get()) and stim+1 <= int(self.stimFilterB.get()):
s.append(self.stimuli[stim])
return s
def spikesFilter(self):
s = []
for spike in self.spikes:
if spike.stim >= int(self.stimFilterA.get()) and spike.stim <= int(self.stimFilterB.get()):
newSpike = Spikes()
newSpike.stim = spike.stim - int(self.stimFilterA.get())+1
newSpike.spikes = spike.spikes
s.append(newSpike)
return s
def setupPlot(self):
G = self.GLE
G.scale = 4
G.rasterStart = float(self.rasterStart.get())
G.rasterEnd = float(self.rasterEnd.get())
G.rasterOffset = float(self.rasterOffset.get())
G.format = 'png' # Used for previewing
G.stimuli = self.stimuli
G.spikes = self.spikes
G.stimFilterA = int(self.stimFilterA.get())
G.stimFilterB = int(self.stimFilterB.get())
G.Channel = self.rasterYAxisChannel.get()
G.VariableType = self.rasterYAxisType.get()
G.binWindow = float(self.binWindow.get())
def previewSpikeRaster(self):
tmpname = tempfile.mkstemp()
notes = ''
self.setupPlot()
self.GLE.spikeraster(tmpname[1], notes)
image = Image.open(tmpname[1]+'.'+self.GLE.format)
self.previewImage = ImageTk.PhotoImage(image)
self.previewLabel.config(image=self.previewImage)
def previewMeanSpikes(self):
tmpname = tempfile.mkstemp()
notes = ''
self.setupPlot()
self.GLE.meanspikespertrial(tmpname[1], 'spike', notes)
image = Image.open(tmpname[1]+'.'+self.GLE.format)
self.previewImage = ImageTk.PhotoImage(image)
self.previewLabel.config(image=self.previewImage)
def previewMeanFSL(self):
tmpname = tempfile.mkstemp()
notes = ''
self.setupPlot()
self.GLE.meanspikespertrial(tmpname[1], 'fsl', notes)
image = Image.open(tmpname[1]+'.'+self.GLE.format)
self.previewImage = ImageTk.PhotoImage(image)
self.previewLabel.config(image=self.previewImage)
def previewMeanLSL(self):
tmpname = tempfile.mkstemp()
notes = ''
self.setupPlot()
self.GLE.meanspikespertrial(tmpname[1], 'lsl', notes)
image = Image.open(tmpname[1]+'.'+self.GLE.format)
self.previewImage = ImageTk.PhotoImage(image)
self.previewLabel.config(image=self.previewImage)
def previewSpikeRatio(self):
tmpname = tempfile.mkstemp()
notes = ''
self.setupPlot()
self.GLE.meanspikespertrial(tmpname[1], 'ratio', notes)
image = Image.open(tmpname[1]+'.'+self.GLE.format)
self.previewImage = ImageTk.PhotoImage(image)
self.previewLabel.config(image=self.previewImage)
def createWidgets(self):
# Setup the menu
menubar = Menu(self.master)
self.master.config(menu=menubar)
fileMenu = Menu(menubar, tearoff=0)
fileMenu.add_command(label='Quit', command=self.quit)
menubar.add_cascade(label='File', underline=0, menu=fileMenu)
# Setup the main frames
self.settingsFrame = LabelFrame(self, text='General Settings')
self.settingsFrame.grid(column=0, row=0, sticky=N+S+E+W)
self.graphFrame = LabelFrame(self, text='Generated Graph')
self.graphFrame.grid(column=1, row=0, sticky=N+S, rowspan=4)
self.spikeSettingsFrame = LabelFrame(self, text='Data Filters')
self.spikeSettingsFrame.grid(column = 0, row = 1, sticky=E+W)
self.graphButtonFrame = LabelFrame(self, text='Generate Graphs')
self.graphButtonFrame.grid(column=0, row=2, sticky=N+S+E+W)
self.saveGraphButtonFrame = LabelFrame(self, text='Save Graphs')
self.saveGraphButtonFrame.grid(column=0, row=3, sticky=N+S+E+W)
# Settings frame widgets
self.fileLabel = Label(self.settingsFrame, textvariable=self.clean_filename)
self.fileLabel.grid(column=0, row=0)
self.fileOpen = Button(self.settingsFrame, text='Open Spike File', command=self.openSpikeFile)
self.fileOpen.grid(column=1, row=0)
self.cellIDLabel = Label(self.settingsFrame, text='Cell ID')
self.cellIDLabel.grid(column=0, row=1, sticky=E)
self.cellIDEntry = Entry(self.settingsFrame, textvariable=self.cellID, width=12, state=DISABLED)
self.cellIDEntry.grid(column=1, row=1, sticky=W)
self.frequencyLabel = Label(self.settingsFrame, text='Frequency')
self.frequencyLabel.grid(column=0, row=2, sticky=E)
self.frequencyEntry = Entry(self.settingsFrame, textvariable=self.frequency, width=12, state=DISABLED)
self.frequencyEntry.grid(column=1, row=2, sticky=W)
self.amplitudeLabel = Label(self.settingsFrame, text='Amplitude')
self.amplitudeLabel.grid(column=0, row=3, sticky=E)
self.amplitudeEntry = Entry(self.settingsFrame, textvariable=self.amplitude, width=20, state=DISABLED)
self.amplitudeEntry.grid(column=1, row=3, sticky=W)
self.spikeOffsetLabel = Label(self.spikeSettingsFrame, text='Zero Time At')
self.spikeOffsetLabel.grid(column=0, row=0, sticky=E)
self.spikeOffsetEntry = Entry(self.spikeSettingsFrame, textvariable=self.rasterOffset, width=5, state=DISABLED)
self.spikeOffsetEntry.grid(column=1, row=0, sticky=W)
self.timeOffsetLabel = Label(self.spikeSettingsFrame, text='Time Start')
self.timeOffsetLabel.grid(column=0, row=1, sticky=E)
self.timeOffsetEntry = Entry(self.spikeSettingsFrame, textvariable=self.rasterStart, width=5, state=DISABLED)
self.timeOffsetEntry.grid(column=1, row=1, sticky=W)
self.maxTimeLabel = Label(self.spikeSettingsFrame, text='Time End')
self.maxTimeLabel.grid(column=0, row=2, sticky=E)
self.maxTimeEntry = Entry(self.spikeSettingsFrame, textvariable=self.rasterEnd, width=5, state=DISABLED)
self.maxTimeEntry.grid(column=1, row=2, sticky=W)
self.binWindowLabel = Label(self.spikeSettingsFrame, text='Classifier Window')
self.binWindowLabel.grid(column=0,row=3,sticky=E)
self.binWindowEntry = Entry(self.spikeSettingsFrame, textvariable=self.binWindow, width=5, state=DISABLED)
self.binWindowEntry.grid(column=1,row=3,sticky=W)
self.stimFilterLabel = Label(self.spikeSettingsFrame, text='Stimuli')
self.stimFilterLabel.grid(column=0, row=4)
self.stimFilterAEntry = Entry(self.spikeSettingsFrame, textvariable=self.stimFilterA, width=2, state=DISABLED)
self.stimFilterAEntry.grid(column=1, row=4,stick=W)
self.stimFilterBEntry = Entry(self.spikeSettingsFrame, textvariable=self.stimFilterB, width=2, state=DISABLED)
self.stimFilterBEntry.grid(column=1, row=4, sticky=E)
# Graph Generators
self.genRasterButton = Button(self.graphButtonFrame, text='Spike Raster', command=self.previewSpikeRaster, state=DISABLED)
self.genRasterButton.grid(column=0, row=0)
self.genMeansButton = Button(self.graphButtonFrame, text='Spikes per Trial', command=self.previewMeanSpikes, state=DISABLED)
self.genMeansButton.grid(column=1, row=0)
self.genMeanFSL = Button(self.graphButtonFrame, text='Mean FSL', command=self.previewMeanFSL, state=DISABLED)
self.genMeanFSL.grid(column=0, row=1)
self.genMeanLSL = Button(self.graphButtonFrame, text='Mean LSL', command=self.previewMeanLSL, state=DISABLED)
self.genMeanLSL.grid(column=1, row=1)
self.genSpikeRatio = Button(self.graphButtonFrame, text='Spike Ratio', command=self.previewSpikeRatio, state=DISABLED)
self.genSpikeRatio.grid(column=0, row=2)
self.rasterYAxisChannelRadio1 = Radiobutton(self.graphButtonFrame, text="Channel 1", variable=self.rasterYAxisChannel, value=0, state=DISABLED)
self.rasterYAxisChannelRadio1.grid(column=0, row=3)
self.rasterYAxisChannelRadio2 = Radiobutton(self.graphButtonFrame, text="Channel 2", variable=self.rasterYAxisChannel, value=1, state=DISABLED)
self.rasterYAxisChannelRadio2.grid(column=1, row=3)
self.rasterYAxisDurationRadio = Radiobutton(self.graphButtonFrame, text="Duration", variable=self.rasterYAxisType, value=0, state=DISABLED)
self.rasterYAxisDurationRadio.grid(column=0,row=4)
self.rasterYAxisDelayRadio = Radiobutton(self.graphButtonFrame, text="Delay", variable=self.rasterYAxisType, value=1, state=DISABLED)
self.rasterYAxisDelayRadio.grid(column=1,row=4)
self.qgleButton = Button(self.saveGraphButtonFrame, text='Launch QGLE', command=self.launchQGLE, state=DISABLED)
self.qgleButton.grid(column=0, row=0)
self.saveButton = Button(self.saveGraphButtonFrame, text='Save GLE Script', command=self.saveGLE, state=DISABLED)
self.saveButton.grid(column=1, row=0)
# Graph frame widgets
self.previewImage = PhotoImage()
self.previewLabel = Label(self.graphFrame, image=self.previewImage)
self.previewLabel.grid()
def launchQGLE(self):
self.GLE.launchQGLE()
def saveGLE(self):
folder = askdirectory(mustexist=True, title='Select Folder to Save To')
if folder != ():
self.GLE.save(folder,self.clean_filename.get().split('.')[0].replace('_','.'))
def openSpikeFile(self):
initial_folder = self.settings.get("last_folder")
if initial_folder == "" or os.path.isdir(initial_folder) == False:
initial_folder = "."
filename = askopenfilename(filetypes=[("Spike Text Files","*.txt")], initialdir=initial_folder)
if filename:
self.filename = filename
clean_filename = filename.rsplit('/',1)
self.settings.set("last_folder", clean_filename[0])
if len(clean_filename) == 1:
clean_filename = clean_filename[0]
else:
clean_filename = clean_filename[1]
self.clean_filename.set(clean_filename)
# Guess that the filename is the cellID too
self.cellID.set(clean_filename.split('.')[0].replace('_','.'))
if self.parse():
self.genRasterButton.config(state=NORMAL)
self.genMeansButton.config(state=NORMAL)
self.genMeanFSL.config(state=NORMAL)
self.genMeanLSL.config(state=NORMAL)
self.frequencyEntry.config(state=NORMAL)
self.cellIDEntry.config(state=NORMAL)
self.amplitudeEntry.config(state=NORMAL)
self.spikeOffsetEntry.config(state=NORMAL)
self.timeOffsetEntry.config(state=NORMAL)
self.maxTimeEntry.config(state=NORMAL)
self.rasterYAxisChannelRadio1.config(state=NORMAL)
self.rasterYAxisDurationRadio.config(state=NORMAL)
self.rasterYAxisDelayRadio.config(state=NORMAL)
self.binWindowEntry.config(state=NORMAL)
self.qgleButton.config(state=NORMAL)
self.saveButton.config(state=NORMAL)
self.stimFilterAEntry.config(state=NORMAL)
self.stimFilterBEntry.config(state=NORMAL)
self.stimFilterA.set('1')
self.stimFilterB.set(str(len(self.stimuli)))
if len(self.stimuli) > 0 and len(self.stimuli[0].dur) > 1:
self.rasterYAxisChannelRadio2.config(state=NORMAL)
self.genSpikeRatio.config(state=NORMAL)
else:
self.rasterYAxisChannelRadio2.config(state=DISABLED)
self.genSpikeRatio.config(state=DISABLED)
self.previewSpikeRaster()
def parse(self):
FILE = open(self.filename, "r")
lines = FILE.readlines()
FILE.close()
found_stim = False
found_data = False
stimuli = []
data = []
curSweep = 0
minStim = 0
maxStim = 0
for l in lines:
if found_stim == True and l.strip() != 'n\tsweep\tX_value\tpass\tSpikeTimes':
temp = l.strip().split('\t')
if int(temp[0]) != curSweep:
if curSweep != 0:
stimuli.append(tmpStimulus)
tmpStimulus = Stimulus()
curSweep = int(temp[0])
if temp[3] != 'OFF':
tmpStimulus.delay.append(float(temp[4]))
tmpStimulus.dur.append(float(temp[5]))
if float(temp[4]) < minStim:
minStim = float(temp[4])
if float(temp[4])+float(temp[5]) > maxStim:
maxStim = float(temp[4])+float(temp[5])
if found_data == True:
data.append(l.strip().split('\t'))
if l.strip()[0:17] == 'Sweep\tTime_Offset':
found_stim = True
if l.strip() == 'n\tsweep\tX_value\tpass\tSpikeTimes':
found_data = True
found_stim = False
stimuli.append(tmpStimulus) # Add our last stimulus
# Record spike times
spikes = []
max_spike = -100
for d in data:
S = Spikes()
S.stim = int(d[1])
if len(d) > 4:
S.spikes = [float(i) for i in d[4].split(',')]
max_spike = max(max_spike, max(S.spikes))
spikes.append(S)
filename = self.filename
self.spikes = spikes
self.stimuli = stimuli
self.rasterStart.set(float(minStim-0.5))
self.rasterEnd.set(max([maxStim+minStim+1,int(round(max_spike/10+1)*10)]))
self.rasterOffset.set(0)
return found_data
