def createOptionsFrame(self):
"""
Creates a frame that contains the various widgets
used to control the colocalization settings
"""
TaskPanel.createOptionsFrame(self)
self.paletteLbl = wx.StaticText(self, -1, "Channel palette:")
self.commonSettingsSizer.Add(self.paletteLbl, (1, 0))
self.colorBtn = CTFButton(self)
self.commonSettingsSizer.Add(self.colorBtn, (2, 0))
self.Layout()
def createOptionsFrame(self):
"""
Creates a frame that contains the various widgets
used to control the colocalization settings
"""
TaskPanel.createOptionsFrame(self)
self.paletteLbl = wx.StaticText(self, -1, "Channel palette:")
self.commonSettingsSizer.Add(self.paletteLbl, (1, 0))
self.colorBtn = CTFButton(self)
self.commonSettingsSizer.Add(self.colorBtn, (2, 0))
self.Layout()
class AdjustPanel(TaskPanel):
"""
Description: A window for processing a single dataunit
"""
def __init__(self, parent, tb):
"""
Initialization
Parameters:
root Is the parent widget of this window
"""
self.operationName = "Adjust"
self.lbls = []
self.btns = []
self.entries = []
self.timePoint = 0
TaskPanel.__init__(self, parent, tb)
# Preview has to be generated heregoto
# self.colorChooser=None
self.createIntensityTransferPage()
lib.messenger.connect(None, "timepoint_changed", self.updateTimepoint)
self.Show()
self.mainsizer.Fit(self)
self.mainsizer.Layout()
def createIntensityInterpolationPanel(self):
"""
Creates a frame holding the entries for configuring
interpolation
"""
self.interpolationPanel = wx.Panel(self.settingsNotebook)
# self.interpolationPanel=wx.Panel(self.iTFEditor)
self.interpolationSizer = wx.GridBagSizer()
lbl = wx.StaticText(self.interpolationPanel, -1, "Interpolate intensities:")
self.interpolationSizer.Add(lbl, (0, 0))
lbl = wx.StaticText(self.interpolationPanel, -1, "from timepoint")
self.lbls.append(lbl)
self.numOfPoints = 5
for i in range(self.numOfPoints - 2):
lbl = wx.StaticText(self.interpolationPanel, -1, "thru")
self.lbls.append(lbl)
lbl = wx.StaticText(self.interpolationPanel, -1, "to timepoint")
self.lbls.append(lbl)
for i in range(self.numOfPoints):
btn = wx.Button(self.interpolationPanel, -1, "goto")
btn.Bind(wx.EVT_BUTTON, lambda event, x=i: self.gotoInterpolationTimePoint(x))
entry = wx.TextCtrl(self.interpolationPanel, size=(50, -1))
self.btns.append(btn)
self.entries.append(entry)
for entry in self.entries:
entry.Bind(wx.EVT_TEXT, self.setInterpolationTimePoints)
last = 0
for i in range(self.numOfPoints):
lbl, entry, btn = self.lbls[i], self.entries[i], self.btns[i]
self.interpolationSizer.Add(lbl, (i + 1, 0))
self.interpolationSizer.Add(entry, (i + 1, 1))
self.interpolationSizer.Add(btn, (i + 1, 2))
last = i + 1
# self.editIntensitySizer.Add(self.interpolationPanel,(0,1))
self.interpolationPanel.SetSizer(self.interpolationSizer)
self.interpolationPanel.SetAutoLayout(1)
self.interpolationSizer.SetSizeHints(self.interpolationPanel)
self.settingsNotebook.AddPage(self.interpolationPanel, "Interpolation")
self.interpolationBox = wx.BoxSizer(wx.HORIZONTAL)
self.reset2Btn = wx.Button(self.interpolationPanel, -1, "Reset all timepoints")
self.reset2Btn.Bind(wx.EVT_BUTTON, self.resetTransferFunctions)
self.interpolationBox.Add(self.reset2Btn)
self.interpolateBtn = wx.Button(self.interpolationPanel, -1, "Interpolate")
self.interpolateBtn.Bind(wx.EVT_BUTTON, self.startInterpolation)
self.interpolationBox.Add(self.interpolateBtn)
self.interpolationSizer.Add(self.interpolationBox, (last + 1, 0))
# self.mainsizer.Add(self.interpolationPanel,(1,0))
# self.panel.Layout()
# self.mainsizer.Fit(self.panel)
def createIntensityTransferPage(self):
"""
Creates a frame holding the entries for configuring
intensity
"""
self.editIntensityPanel = wx.Panel(self.settingsNotebook, -1)
self.editIntensitySizer = wx.GridBagSizer()
self.iTFEditor = IntensityTransferEditor(self.editIntensityPanel)
self.editIntensitySizer.Add(self.iTFEditor, (0, 0)) # ,span=(1,2))
self.box = wx.BoxSizer(wx.HORIZONTAL)
self.editIntensitySizer.Add(self.box, (2, 0))
self.createIntensityInterpolationPanel()
self.restoreBtn = wx.Button(self.editIntensityPanel, -1, "Reset current timepoint")
self.restoreBtn.Bind(wx.EVT_BUTTON, self.iTFEditor.restoreDefaults)
self.box.Add(self.restoreBtn)
self.resetBtn = wx.Button(self.editIntensityPanel, -1, "Reset all timepoints")
self.resetBtn.Bind(wx.EVT_BUTTON, self.resetTransferFunctions)
self.box.Add(self.resetBtn)
self.copyiTFBtn = wx.Button(self.editIntensityPanel, -1, "Copy to all timepoints")
self.copyiTFBtn.Bind(wx.EVT_BUTTON, self.copyTransferFunctionToAll)
self.box.Add(self.copyiTFBtn)
self.editIntensityPanel.SetSizer(self.editIntensitySizer)
self.editIntensityPanel.SetAutoLayout(1)
self.settingsNotebook.InsertPage(0, self.editIntensityPanel, "Transfer Function")
self.settingsNotebook.SetSelection(0)
self.updateSettings()
def setInterpolationTimePoints(self, event):
"""
A callback that is called when a timepoint entry for
intensity interpolation changes. Updates the list of
timepoints between which the interpolation is carried out
by the dataunit
"""
lst = []
for i in self.entries:
val = i.GetValue()
try:
n = int(val)
# n -= 1
lst.append(n)
except:
# For entries that have no value, add -1 as a place holder
lst.append(-1)
# self.dataUnit.setInterpolationTimePoints(lst)
self.settings.set("InterpolationTimepoints", lst)
def gotoInterpolationTimePoint(self, entrynum):
"""
The previewed timepoint is set to timepoint specified in
self.entries[entrynum]
"""
try:
tp = int(self.entries[entrynum].GetValue())
except:
pass
else:
tp -= 1
Logging.info("Previewing timepoint ", tp, "(will send change event)", kw="task")
lib.messenger.send(None, "timepoint_changed", tp)
# self.updateTimepoint(evt)
def createButtonBox(self):
"""
Creates a button box containing the buttons Render,
Preview and Close
"""
TaskPanel.createButtonBox(self)
# self.processButton.SetLabel("Process Dataset Series")
# self.processButton.Bind(wx.EVT_BUTTON,self.doProcessingCallback)
lib.messenger.connect(None, "process_dataset", self.doProcessingCallback)
def createOptionsFrame(self):
"""
Creates a frame that contains the various widgets
used to control the colocalization settings
"""
TaskPanel.createOptionsFrame(self)
self.paletteLbl = wx.StaticText(self, -1, "Channel palette:")
self.commonSettingsSizer.Add(self.paletteLbl, (1, 0))
self.colorBtn = CTFButton(self)
self.commonSettingsSizer.Add(self.colorBtn, (2, 0))
self.Layout()
def updateTimepoint(self, obj, evt, timePoint):
"""
A callback function called when the timepoint is changed
"""
# timePoint=event.getValue()
Logging.info("Now configuring timepoint", timePoint, kw="task")
itf = self.settings.getCounted("IntensityTransferFunctions", timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
self.timePoint = timePoint
def copyTransferFunctionToAll(self, event=None):
"""
A method to copy this transfer function to all timepooints
"""
itf = self.settings.getCounted("IntensityTransferFunctions", self.timePoint)
l = self.dataUnit.getNumberOfTimepoints()
for i in range(l):
if i != self.timePoint:
self.settings.setCounted("IntensityTransferFunctions", i, itf)
def resetTransferFunctions(self, event=None):
"""
A method to reset all the intensity transfer functions
"""
l = self.dataUnit.getNumberOfTimepoints()
sources = self.dataUnit.getSourceDataUnits()
for i in range(l):
minval = min([a.getScalarRange()[0] for a in sources])
maxval = max([a.getScalarRange()[1] for a in sources])
bitdepth = sources[0].getBitDepth()
minval = min(0, minval)
maxval = max(2 ** bitdepth - 1, maxval)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.settings.setCounted("IntensityTransferFunctions", i, itf)
itf = self.settings.getCounted("IntensityTransferFunctions", self.timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
def startInterpolation(self, evt):
"""
A callback to interpolate intensity transfer functions
between the specified timepoints
"""
self.dataUnit.interpolateIntensities()
# self.doPreviewCallback()
def updateSettings(self, force=0):
"""
A method used to set the GUI widgets to their proper values
"""
if self.dataUnit:
self.iTFEditor.setIntensityTransferFunction(
self.settings.getCounted("IntensityTransferFunctions", self.timePoint)
)
tps = self.settings.get("InterpolationTimepoints")
if not tps:
tps = []
for i in range(len(tps)):
n = tps[i]
# If there was nothing in the entry at this position, the
# value is -1 in that case, we leave the entry empty
if n != -1:
self.entries[i].SetValue(str(n))
ctf = self.settings.get("ColorTransferFunction")
if ctf and self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
self.colorBtn.Refresh()
def doProcessingCallback(self, *args):
"""
A callback for the button "Process Dataset Series"
"""
TaskPanel.doOperation(self)
def setCombinedDataUnit(self, dataUnit):
"""
Sets the processed dataunit that is to be processed.
It is then used to get the names of all the source data
units and they are added to the menu.
This is overwritten from TaskPanel since we only process
one dataunit here, not multiple source data units
"""
TaskPanel.setCombinedDataUnit(self, dataUnit)
ctf = self.settings.get("ColorTransferFunction")
if ctf and self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
# We register a callback to be notified when the timepoint changes
# We do it here because the timePointChanged() code requires the dataunit
# self.Bind(EVT_TIMEPOINT_CHANGED,self.timePointChanged,id=ID_TIMEPOINT)
tf = self.settings.getCounted("IntensityTransferFunctions", self.timePoint)
self.iTFEditor.setIntensityTransferFunction(tf)
self.iTFEditor.updateCallback = self.doPreviewCallback
self.restoreFromCache()
self.updateSettings()
class ColocalizationPanel(TaskPanel):
"""
The GUI for colocalization task
"""
def __init__(self, parent, tb):
self.scatterPlot = None
self.createItemSelection = 0
self.timePoint = 0
TaskPanel.__init__(self, parent, tb, wantNotebook = 0)
self.operationName = "Colocalization"
self.voxelSize = None
self.mainsizer.Layout()
self.mainsizer.Fit(self)
lib.messenger.connect(None, "timepoint_changed", self.updateTimepoint)
lib.messenger.connect(None, "zslice_changed", self.updateZSlice)
lib.messenger.connect(None, "threshold_changed", self.updateSettings)
lib.messenger.connect(None, bxdevents.DATA_DIMENSIONS_CHANGED, self.onDataChanged)
def deregister(self):
"""
Removes all listeners
"""
TaskPanel.deregister(self)
try:
lib.messenger.disconnect(None, "timepoint_changed", self.updateTimepoint)
lib.messenger.disconnect(None, "zslice_changed", self.updateZSlice)
lib.messenger.disconnect(None, "threshold_changed", self.updateSettings)
lib.messenger.disconnect(None, "data_changed", self.onDataChanged)
except:
pass
def autoThreshold(self):
"""
Use vtkAutoThresholdColocalization to determine thresholds
for colocalization and calculate statistics
"""
self.clearVariables()
self.dataUnit.getSourceDataUnits()[0].getSettings().set("CalculateThresholds", 1)
self.eventDesc = "Calculating thresholds"
self.doPreviewCallback(None)
self.dataUnit.getSourceDataUnits()[0].getSettings().set("CalculateThresholds", 0)
lib.messenger.send(None, "threshold_changed")
def getAutoThreshold(self, event = None):
"""
Calculate the automatic threshold for colocalization
"""
do_cmd = """scripting.mainWindow.tasks['Colocalization'].autoThreshold()"""
cmd = lib.Command.Command(lib.Command.GUI_CMD, None, None, do_cmd, "", \
desc = "Calculate automatic threshold")
cmd.run()
def statistics(self):
"""
Calculate the statistics
"""
self.dataUnit.getSourceDataUnits()[0].getSettings().set("CalculateThresholds", 2)
self.eventDesc = "Calculating statistics"
self.doPreviewCallback(None)
self.dataUnit.getSourceDataUnits()[0].getSettings().set("CalculateThresholds", 0)
def getStatistics(self, event = None):
"""
Method: getStatistics
Use vtkAutoThresholdColocalization to determine thresholds
for colocalization and calculate statistics
"""
do_cmd = """scripting.mainWindow.tasks['Colocalization'].statistics()"""
cmd = lib.Command.Command(lib.Command.GUI_CMD, None, None, do_cmd, "", \
desc = "Calculate colocalization statistics")
cmd.run()
pos = self.radiobox.GetSelection()
if pos:
map = [1, 0, 2]
method = map[pos - 1]
smethod = ""
if method == 0:
smethod = "Fay"
if method == 1:
smethod = "Costes"
if method == 2:
smethod = "van Steensel"
try:
n = int(self.iterations.GetValue())
iterations = ", iterations = %d" % n
except:
pass
if method != 1:
iterations = ""
do_cmd = "scripting.mainWindow.tasks['Colocalization'].getPValue('%s'%s)" % (smethod, iterations)
cmd = lib.Command.Command(lib.Command.GUI_CMD, None, None, do_cmd, "", \
desc = "Calculate P-Value of colocalization")
cmd.run()
def getPValue(self, method = 1, iterations = 100):
"""
Method: getPValue
Get the P value for colocalization
"""
try:
n = int(self.iterations.GetValue())
if n != iterations:
self.iterations.SetValue("%d" % iterations)
except:
pass
coloctest = vtkbxd.vtkImageColocalizationTest()
#coloctest.SetRandomizeZ(1)
sources = self.dataUnit.getSourceDataUnits()
self.eventDesc = "Calculating P-Value"
methods = ["Fay", "Costes", "van Steensel"]
if type(method) == types.StringType:
method = methods.index(method)
Logging.info("Using %s method (%d)" % (methods[method], method), kw = "processing")
t = time.time()
coloctest.SetMethod(method)
try:
n = float(self.fixedPSF.GetValue())
except:
lib.messenger.send(None, "show_error", "Bad PSF width", \
"The given width for point spread function is invalid.")
return
print "Setting PSF width", int(n)
coloctest.SetManualPSFSize(int(n))
coloctest.SetNumIterations(iterations)
for i in sources:
data = i.getTimepoint(self.timePoint)
coloctest.AddInput(data)
coloctest.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(coloctest, "ProgressEvent", self.updateProgress)
coloctest.Update()
print "It took ", time.time() - t, "seconds to calculate p-value"
set = sources[0].getSettings().set
for i in ["PValue", "RObserved", "RRandMean", "RRandSD",
"NumIterations", "ColocCount", "Method"]:
val = eval("coloctest.Get%s()" % i)
set(i, val)
lib.messenger.send(None, "update_progress", 100, "Done.")
self.listctrl.updateListCtrl(self.getVariables())
def updateProgress(self, obj, evt, *args):
"""
Method: updateProgress
Sends a update_progress event and yields time for the GUI
"""
wx.GetApp().Yield(1)
progress = obj.GetProgress()
txt = obj.GetProgressText()
if not txt:
txt = self.eventDesc
lib.messenger.send(None, "update_progress", progress, txt)
def createButtonBox(self):
"""
Creates a button box containing the buttons Render,
Preview and Close
"""
TaskPanel.createButtonBox(self)
lib.messenger.connect(None, "process_dataset", self.doColocalizationCallback)
def createOptionsFrame(self):
"""
Creates a frame that contains the various widgets
used to control the colocalization settings
"""
#TaskPanel.createOptionsFrame(self)
# self.colocalizationPanel=wx.Panel(self.settingsNotebook,-1)
self.colocalizationPanel = wx.Panel(self, -1)
self.colocalizationSizer = wx.GridBagSizer()
n = 0
self.lowerThresholdLbl1 = wx.StaticText(self.colocalizationPanel, -1, "Ch1 lower threshold:")
self.upperThresholdLbl1 = wx.StaticText(self.colocalizationPanel, -1, "Ch1 upper threshold:")
self.lowerThresholdLbl2 = wx.StaticText(self.colocalizationPanel, -1, "Ch2 lower threshold:")
self.upperThresholdLbl2 = wx.StaticText(self.colocalizationPanel, -1, "Ch2 upper threshold:")
self.lowerthreshold1 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \
maxValue = 255, size = (300, -1),
style = wx.SL_HORIZONTAL | wx.SL_LABELS)
self.lowerthreshold1.Bind(wx.EVT_SCROLL, self.updateThreshold)
self.upperthreshold1 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \
maxValue = 255, size = (300, -1),
style = wx.SL_HORIZONTAL | wx.SL_LABELS)
self.upperthreshold1.Bind(wx.EVT_SCROLL, self.updateThreshold)
self.lowerthreshold2 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \
maxValue = 255, size = (300, -1),
style = wx.SL_HORIZONTAL | wx.SL_LABELS)
self.lowerthreshold2.Bind(wx.EVT_SCROLL, self.updateThreshold)
self.upperthreshold2 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \
maxValue = 255, size = (300, -1),
style = wx.SL_HORIZONTAL | wx.SL_LABELS)
self.upperthreshold2.Bind(wx.EVT_SCROLL, self.updateThreshold)
self.colocalizationSizer.Add(self.lowerThresholdLbl1, (n, 0))
n += 1
self.colocalizationSizer.Add(self.lowerthreshold1, (n, 0))
n += 1
self.colocalizationSizer.Add(self.upperThresholdLbl1, (n, 0))
n += 1
self.colocalizationSizer.Add(self.upperthreshold1, (n, 0))
n += 1
self.colocalizationSizer.Add(self.lowerThresholdLbl2, (n, 0))
n += 1
self.colocalizationSizer.Add(self.lowerthreshold2, (n, 0))
n += 1
self.colocalizationSizer.Add(self.upperThresholdLbl2, (n, 0))
n += 1
self.colocalizationSizer.Add(self.upperthreshold2, (n, 0))
n += 1
sbox = wx.StaticBox(self.colocalizationPanel, -1, "2D histogram (right-click for more options)")
box = wx.StaticBoxSizer(sbox, wx.VERTICAL)
self.scatterPlot = Scatterplot(self.colocalizationPanel, drawLegend = 1)
lib.messenger.connect(self.scatterPlot, "scatterplot_thresholds", self.onUpdateScatterplotThresholds)
box.Add(self.scatterPlot)
self.colocalizationSizer.Add(box, (n, 0))
n += 1
sbox = wx.StaticBox(self.colocalizationPanel, -1, "Colocalization quantification")
box = wx.StaticBoxSizer(sbox, wx.VERTICAL)
self.automaticThresholdStaticBox = sbox
self.automaticThresholdSizer = box
#self.pvaluebox = wx.StaticBox(self.colocalizationPanel, -1, "Calculate P-Value")
self.radiobox = wx.RadioBox(self.colocalizationPanel, -1, "Calculate P-Value",
choices = ["None", "Costes", "Fay", "van Steensel"], majorDimension = 2,
style = wx.RA_SPECIFY_COLS
)
self.radiobox.Bind(wx.EVT_RADIOBOX, self.onSetTestMethod)
#self.pvalueNone = wx.RadioButton(self.colocalizationPanel, -1, "None", name="pvalue")
#self.pvalueNone.SetValue(True)
#self.pvalueNone.Bind(wx.EVT_RADIOBUTTON, self.onSetNone)
#self.pvalueCostes = wx.RadioButton(self.colocalizationPanel, -1, "Costes", name="pvalue")
#self.pvalueCostes.SetValue(False)
#self.pvalueCostes
#self.pvalueFay = wx.RadioButton(self.colocalizationPanel, -1, "Fay", name="pvalue")
#self.pvalueFay.SetValue(False)
#self.pvaluevanSteensel = wx.RadioButton(self.colocalizationPanel, -1, "van Steensel", name="pvalue")
#self.pvaluevanSteensel.SetValue(False)
box.Add(self.radiobox)
self.iterLbl = wx.StaticText(self.colocalizationPanel, -1, "Iterations:")
self.iterations = wx.SpinCtrl(self.colocalizationPanel, -1, "100", min = 2, \
max = 999, initial = 100)
self.iterations.Bind(wx.EVT_SPINCTRL, self.onSetIterations)
fixedPSFLbl = wx.StaticText(self.colocalizationPanel, -1, "PSF radius (px):")
self.fixedPSF = wx.TextCtrl(self.colocalizationPanel, -1, "")
costesgrid = wx.GridBagSizer()
#sboxsizer.Add(costesgrid)
costesgrid.Add(self.iterLbl, (0, 0))
costesgrid.Add(self.iterations, (0, 1))
costesgrid.Add(fixedPSFLbl, (1, 0))
costesgrid.Add(self.fixedPSF, (1, 1))
NALbl = wx.StaticText(self.colocalizationPanel, -1, "Numerical Aperture:")
self.NA = wx.TextCtrl(self.colocalizationPanel, -1, "1.4")
costesgrid.Add(NALbl, (2, 0))
costesgrid.Add(self.NA, (2, 1))
Ch2LambdaLbl = wx.StaticText(self.colocalizationPanel, -1, u"Ch2 \u03BB (nm):")
self.Ch2Lambda = wx.TextCtrl(self.colocalizationPanel, -1, "520")
costesgrid.Add(Ch2LambdaLbl, (3, 0))
costesgrid.Add(self.Ch2Lambda, (3, 1))
#pvaluebox.Add(costesgrid)
self.NA.Bind(wx.EVT_TEXT, self.onUpdatePSF)
self.Ch2Lambda.Bind(wx.EVT_TEXT, self.onUpdatePSF)
self.iterations.Enable(0)
self.NA.Enable(0)
self.Ch2Lambda.Enable(0)
self.fixedPSF.Enable(0)
box.Add(costesgrid)
box2 = wx.BoxSizer(wx.HORIZONTAL)
self.statsButton = wx.Button(self.colocalizationPanel, -1, "Calculate statistics")
self.statsButton.Bind(wx.EVT_BUTTON, self.getStatistics)
box2.Add(self.statsButton)
self.thresholdButton = wx.Button(self.colocalizationPanel, -1, "Calculate thresholds")
self.thresholdButton.Bind(wx.EVT_BUTTON, self.getAutoThreshold)
box2.Add(self.thresholdButton)
self.statsButtonSizer = box2
box.Add(box2)
self.colocalizationSizer.Add(box, (n, 0), flag = wx.EXPAND | wx.LEFT | wx.RIGHT)
n += 1
sbox = wx.StaticBox(self.colocalizationPanel, -1, "Coloc Volume Statistics")
box = wx.StaticBoxSizer(sbox, wx.VERTICAL)
self.colocStatsStaticBox = sbox
self.colocStatsSizer = box
self.listctrl = GUI.ColocListView.ColocListView(self.colocalizationPanel, -1, size = (350, 300))
box.Add(self.listctrl)
self.statsButton = wx.Button(self.colocalizationPanel, -1, "Export")
self.statsButton.Bind(wx.EVT_BUTTON, self.onExportStatistics)
box.Add(self.statsButton)
self.listctrl.updateListCtrl(self.getVariables())
self.colocalizationSizer.Add(box, (n, 0))
n += 1
sbox = wx.StaticBox(self.colocalizationPanel, -1, "Colocalization color")
sboxsizer = wx.StaticBoxSizer(sbox, wx.VERTICAL)
self.colocColorBox = sbox
self.colocColorSizer = sboxsizer
self.colorBtn = CTFButton(self.colocalizationPanel)
sboxsizer.Add(self.colorBtn)
val = AcceptedValidator
self.constColocCheckbox = wx.CheckBox(self.colocalizationPanel, -1, \
"Use single (1-bit) value for colocalization")
self.constColocValue = wx.TextCtrl(self.colocalizationPanel, -1, "255",
validator = val(string.digits, below = 255))
self.constColocValue.Enable(0)
self.constColocValue.Bind(wx.EVT_TEXT, self.onSetColocValue)
self.constColocCheckbox.Bind(wx.EVT_CHECKBOX, self.onSetColocCheckbox)
sboxsizer.Add(self.constColocCheckbox)
sboxsizer.Add(self.constColocValue)
self.colocalizationSizer.Add(sboxsizer, (n, 0))
n += 1
self.colocalizationPanel.SetSizer(self.colocalizationSizer)
self.colocalizationPanel.SetAutoLayout(1)
self.settingsSizer.Add(self.colocalizationPanel, (1, 0), flag = wx.EXPAND | wx.ALL)
# self.settingsNotebook.AddPage(self.colocalizationPanel,"Colocalization")
def onUpdateScatterplotThresholds(self, scatterplot, event, ch1thresholds, ch2thresholds):
"""
Updates the colocalization thresholds based on user's scatterplot drawing
"""
ch1lower, ch1upper = ch1thresholds
ch2lower, ch2upper = ch2thresholds
sources = self.dataUnit.getSourceDataUnits()
print "Setting thresholds to",ch1lower, ch1upper, ch2lower, ch2upper
sources[0].getSettings().set("ColocalizationLowerThreshold", ch1lower)
sources[0].getSettings().set("ColocalizationUpperThreshold", ch1upper)
sources[1].getSettings().set("ColocalizationLowerThreshold", ch2lower)
sources[1].getSettings().set("ColocalizationUpperThreshold", ch2upper)
lib.messenger.send(None, "threshold_changed", (ch1lower, ch1upper), (ch2lower, ch2upper))
lib.messenger.send(None, "data_changed", True)
def onUpdatePSF(self, event):
"""
Update the PSF based on the given NA and lambda
"""
if event:
event.Skip()
if not self.voxelSize:
sources = self.dataUnit.getSourceDataUnits()
if sources:
self.voxelSize = sources[0].getVoxelSize()
else:
return
vx, vy, vz = self.voxelSize
try:
l = float(self.Ch2Lambda.GetValue())
na = float(self.NA.GetValue())
self.settings.set("Ch2Lambda", l)
self.settings.set("NumericalAperture", na)
except:
return
if na == 0:
na = 1.00
psf = (0.61 * l) / na
# psf is now in nanometers
psf /= (vx * 1000 * 1000000)
self.fixedPSF.SetValue("%.4f" % float(psf))
self.settings.set("PSF", psf)
def onSetIterations(self, event):
"""
Set number of iterations
"""
value = self.iterations.GetValue()
self.settings.set("NumIterations", value)
def onSetTestMethod(self, event):
"""
Set the method used for colocalisation test
"""
n = self.radiobox.GetSelection()
flag = (n == 1)
self.iterations.Enable(flag)
self.NA.Enable(flag)
self.Ch2Lambda.Enable(flag)
self.fixedPSF.Enable(flag)
self.settings.set("Method", n)
def onSetColocCheckbox(self, event):
"""
Set coloc value checkbox
"""
checked = self.constColocCheckbox.IsChecked()
self.constColocValue.Enable(checked)
self.settings.set("ColocalizationDepth", checked)
def onSetColocValue(self, event):
"""
Set coloc value
"""
value = self.constColocValue.GetValue()
self.settings.set("OutputScalar", float(value))
def onExportStatistics(self, event):
"""
Export colocalization statistics to file
"""
name = self.dataUnit.getName()
filename = GUI.Dialogs.askSaveAsFileName(self, "Save colocalization statistics as", \
"%s.csv" % name, "CSV File (*.csv)|*.csv")
if filename:
filename = filename.replace("\\", "\\\\")
do_cmd = "scripting.mainWindow.tasks['Colocalization'].exportStatistics('%s')" % filename
cmd = lib.Command.Command(lib.Command.GUI_CMD, None, None, do_cmd, "", \
desc = "Export colocalization statistics")
cmd.run()
def decode(self, d):
"""
Replace any unicode characeters with their ascii counterparts
"""
d = d.replace(u"\u00B1", "+-")
return d
def exportStatistics(self, filename):
"""
Export the colocalization stats
"""
name = self.dataUnit.getName()
sources = self.dataUnit.getSourceDataUnits()
names = []
names2 = []
names = [x.getName() for x in sources]
names2 = [os.path.basename(x.getFileName()) for x in sources]
names3 = names2[:]
namestr = " and ".join(names)
leadstr = "From file "
if len(names3) > 1:
leadstr = "From files "
namestr2 = leadstr + " and ".join(names3)
if not filename:
Logging.info("Got no name for coloc statistics", kw = "processing")
return
f = codecs.open(filename, "wb", "latin-1")
w = csv.writer(f, dialect = "excel", delimiter = ";")
get1 = sources[0].getSettings().get
get2 = sources[1].getSettings().get
w.writerow(["Statistics for colocalization of channels %s" % namestr])
w.writerow([namestr2])
w.writerow(["Timepoint", self.timePoint])
w.writerow([time.ctime()])
for item in self.listctrl.headervals:
header, val1, val2, col = item
header = self.decode(header)
if type(val1) == types.UnicodeType:
val1 = self.decode(val1)
if val2:
if type(val2) == types.UnicodeType:
val2 = self.decode(val2)
w.writerow([header, val1, val2])
else:
w.writerow([header, val1])
f.close()
del w
del f
def updateZSlice(self, obj, event, zslice):
"""
A callback function called when the zslice is changed
"""
if self.scatterPlot:
self.scatterPlot.setZSlice(zslice)
self.scatterPlot.updatePreview()
self.listctrl.updateListCtrl(self.getVariables())
def updateTimepoint(self, obj, event, timePoint):
"""
A callback function called when the timepoint is changed
"""
self.timePoint = timePoint
if self.scatterPlot:
self.scatterPlot.setTimepoint(self.timePoint)
self.scatterPlot.updatePreview()
def updateThreshold(self, event):
"""
A callback function called when the threshold is configured via the slider
"""
# We might get called before any channel has been selected.
# In that case, do nothing
if self.settings:
self.clearVariables()
oldlthreshold1 = self.settings.getCounted("ColocalizationLowerThreshold", 0)
olduthreshold1 = self.settings.getCounted("ColocalizationUpperThreshold", 0)
newlthreshold1 = int(self.lowerthreshold1.GetValue())
newuthreshold1 = int(self.upperthreshold1.GetValue())
self.settings.setCounted("ColocalizationLowerThreshold", 0, newlthreshold1)
self.settings.setCounted("ColocalizationUpperThreshold", 0, newuthreshold1)
oldlthreshold2 = self.settings.getCounted("ColocalizationLowerThreshold", 1)
olduthreshold2 = self.settings.getCounted("ColocalizationUpperThreshold", 1)
newlthreshold2 = int(self.lowerthreshold2.GetValue())
newuthreshold2 = int(self.upperthreshold2.GetValue())
self.settings.setCounted("ColocalizationLowerThreshold", 1, newlthreshold2)
self.settings.setCounted("ColocalizationUpperThreshold", 1, newuthreshold2)
if (oldlthreshold1 != newlthreshold1) or (olduthreshold1 != newuthreshold1) or (oldlthreshold2 != newlthreshold2) or (olduthreshold2 != newuthreshold2):
lib.messenger.send(None, "threshold_changed")
self.doPreviewCallback()
def updateSettings(self, force = 0, *args):
"""
A method used to set the GUI widgets to their proper values
based on the selected channel, the settings of which are
stored in the instance variable self.settings
"""
Logging.info("Updating coloc settings", kw="processing")
if self.settings:
format = self.settings.get("ColocalizationDepth")
scalar = self.settings.get("OutputScalar")
self.constColocCheckbox.SetValue(format == 1)
self.constColocValue.SetValue("%d" %int(scalar))
self.constColocValue.Enable(format == 1)
th = self.settings.getCounted("ColocalizationLowerThreshold", 0)
if th != None:
self.lowerthreshold1.SetValue(th)
th = self.settings.getCounted("ColocalizationUpperThreshold", 0)
if th != None:
self.upperthreshold1.SetValue(th)
th = self.settings.getCounted("ColocalizationLowerThreshold", 1)
if th != None:
self.lowerthreshold2.SetValue(th)
th = self.settings.getCounted("ColocalizationUpperThreshold", 1)
if th != None:
self.upperthreshold2.SetValue(th)
method = self.settings.get("Method")
if method is not None:
self.radiobox.SetSelection(int(method))
flag = (int(method) == 1)
self.iterations.Enable(flag)
self.NA.Enable(flag)
self.Ch2Lambda.Enable(flag)
self.fixedPSF.Enable(flag)
psf = self.settings.get("PSF")
if psf is not None:
self.fixedPSF.SetValue("%.4f"%float(psf))
iterations = self.settings.get("NumIterations")
if iterations is not None:
self.iterations.SetValue(int(iterations))
na = self.settings.get("NumericalAperture")
if na is not None:
self.NA.SetValue("%.4f"%float(na))
ch2lambda = self.settings.get("Ch2Lambda")
if ch2lambda is not None:
self.Ch2Lambda.SetValue("%d"%int(ch2lambda))
# If the scatterplot exists, update it's thresholds
if self.scatterPlot:
sources = self.dataUnit.getSourceDataUnits()
ch1 = sources[0].getSettings()
ch2 = sources[1].getSettings()
ch1lower, ch1upper = ch1.get("ColocalizationLowerThreshold"), ch1.get("ColocalizationUpperThreshold")
ch2lower, ch2upper = ch2.get("ColocalizationLowerThreshold"), ch2.get("ColocalizationUpperThreshold")
self.scatterPlot.setThresholds(ch1lower, ch1upper, ch2lower, ch2upper)
if self.dataUnit and self.settings:
ctf = self.dataUnit.getSettings().get("ColorTransferFunction")
if ctf and self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
self.colorBtn.Refresh()
def doColocalizationCallback(self, *args):
"""
A callback for the button "Do colocalization"
"""
self.updateBitDepth()
TaskPanel.doOperation(self)
def updateBitDepth(self, event = None):
"""
Updates the preview to be done at the selected depth
"""
if self.settings:
#depth=self.depthMenu.GetSelection()
#table=[1,8,32]
#self.settings.set("ColocalizationDepth",table[depth])
if self.constColocCheckbox.GetValue():
self.settings.set("ColocalizationDepth", 1)
colocval = self.constColocValue.GetValue()
colocval = int(colocval)
self.settings.set("OutputScalar", colocval)
else:
self.settings.set("ColocalizationDepth", 8)
def doPreviewCallback(self, event = None, *args):
"""
A callback for the button "Preview" and other events
that wish to update the preview
"""
self.updateBitDepth()
TaskPanel.doPreviewCallback(self, event)
if self.scatterPlot:
self.scatterPlot.setSlope(self.dataUnit.getSettings().get("Slope"))
self.scatterPlot.setIntercept(self.dataUnit.getSettings().get("Intercept"))
self.scatterPlot.setZSlice(0)
self.scatterPlot.setTimepoint(self.timePoint)
self.scatterPlot.setDataUnit(self.dataUnit)
ctf = self.dataUnit.getSettings().get("ColorTransferFunction")
self.dataUnit.getSettings().set("ColocalizationColorTransferFunction", ctf)
self.listctrl.updateListCtrl(self.getVariables())
def getVariables(self):
"""
Return the colocalization variables in a dictionary
"""
variables = {}
if not self.dataUnit: return {}
sources = self.dataUnit.getSourceDataUnits()
variables["LowerThresholdCh1"] = sources[0].getSettings().get("ColocalizationLowerThreshold")
variables["LowerThresholdCh2"] = sources[1].getSettings().get("ColocalizationLowerThreshold")
variables["UpperThresholdCh1"] = sources[0].getSettings().get("ColocalizationUpperThreshold")
variables["UpperThresholdCh2"] = sources[1].getSettings().get("ColocalizationUpperThreshold")
for var in ["Ch1ThresholdMax", "Ch2ThresholdMax", "PearsonImageAbove",
"PearsonImageBelow", "PearsonWholeImage", "M1", "M2",
"K1", "K2", "DiffStainIntCh1", "DiffStainIntCh2",
"DiffStainVoxelsCh1", "DiffStainVoxelsCh2",
"ThresholdM1", "ThresholdM2",
"ColocAmount", "ColocPercent", "PercentageVolumeCh1",
"PercentageTotalCh1", "PercentageTotalCh2",
"PercentageVolumeCh2", "PercentageMaterialCh1", "PercentageMaterialCh2",
"SumOverThresholdCh1", "SumOverThresholdCh2", "SumCh1", "SumCh2",
"NonZeroCh1", "NonZeroCh2", "OverThresholdCh2", "OverThresholdCh1",
"PValue", "RObserved", "RRandMean", "RRandSD",
"NumIterations", "ColocCount", "Method"]:
variables[var] = sources[0].getSettings().get(var)
return variables
def clearVariables(self):
"""
Clear colocalization statistics
"""
sources = self.dataUnit.getSourceDataUnits()
settings = sources[0].getSettings()
for var in ["Ch1ThresholdMax", "Ch2ThresholdMax", "PearsonImageAbove",
"PearsonImageBelow", "PearsonWholeImage", "M1", "M2",
"K1", "K2", "DiffStainIntCh1", "DiffStainIntCh2",
"DiffStainVoxelsCh1", "DiffStainVoxelsCh2",
"ThresholdM1", "ThresholdM2",
"ColocAmount", "ColocPercent", "PercentageVolumeCh1",
"PercentageTotalCh1", "PercentageTotalCh2",
"PercentageVolumeCh2", "PercentageMaterialCh1", "PercentageMaterialCh2",
"SumOverThresholdCh1", "SumOverThresholdCh2", "SumCh1", "SumCh2",
"NonZeroCh1", "NonZeroCh2", "OverThresholdCh2", "OverThresholdCh1"]:
settings.set(var,0)
def setCombinedDataUnit(self, dataUnit):
"""
Set the dataunit used for the colocalization
"""
TaskPanel.setCombinedDataUnit(self, dataUnit)
# See if the dataunit has a stored colocalizationctf
# then use that.
sources = self.dataUnit.getSourceDataUnits()
self.updateNames()
minval, maxval = sources[0].getScalarRange()
minval2, maxval2 = sources[1].getScalarRange()
minval = min(minval, minval2)
bitmax1 = (2**sources[0].getSingleComponentBitDepth())-1
bitmax2 = (2**sources[0].getSingleComponentBitDepth())-1
maxval = max(maxval, maxval2, bitmax1, bitmax2)
self.lowerthreshold1.SetRange(minval, maxval)
self.lowerthreshold1.SetValue((maxval - minval + 1) / 2)
self.upperthreshold1.SetRange(minval, maxval)
self.upperthreshold1.SetValue(maxval)
self.lowerthreshold2.SetRange(minval, maxval)
self.lowerthreshold2.SetValue((maxval - minval + 1) / 2)
self.upperthreshold2.SetRange(minval, maxval)
self.upperthreshold2.SetValue(maxval)
self.updateThreshold(None)
na = sources[1].getNumericalAperture()
emission = sources[1].getEmissionWavelength()
if na:
self.NA.SetValue("%.4f" % na)
if emission:
self.Ch2Lambda.SetValue("%d" % emission)
self.onUpdatePSF(None)
ctf = self.dataUnit.getSettings().get("ColocalizationColorTransferFunction")
if not ctf:
ctf = self.dataUnit.getSettings().get("ColorTransferFunction")
else:
Logging.info("Using ColocalizationColorTransferFunction", kw = "task")
if self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
self.scatterPlot.setDataUnit(dataUnit)
if self.scatterPlot:
#self.scatterPlot.setZSlice(self.preview.z)
self.scatterPlot.setZSlice(0)
self.scatterPlot.setTimepoint(self.timePoint)
self.scatterPlot.updatePreview()
self.colocalizationPanel.Layout()
def createItemToolbar(self):
"""
Method to create a toolbar for the window that allows use to select processed channel
"""
n = TaskPanel.createItemToolbar(self)
coloc = vtkbxd.vtkImageColocalizationFilter()
coloc.SetOutputDepth(8)
i = 0
for data in self.itemMips:
coloc.AddInput(data)
coloc.SetColocalizationLowerThreshold(i, 100)
coloc.SetColocalizationUpperThreshold(i, 255)
i = i + 1
coloc.Update()
ctf = vtk.vtkColorTransferFunction()
ctf.AddRGBPoint(0, 0, 0, 0)
ctf.AddRGBPoint(255, 1, 1, 1)
maptocolor = vtk.vtkImageMapToColors()
maptocolor.SetInput(coloc.GetOutput())
maptocolor.SetLookupTable(ctf)
maptocolor.SetOutputFormatToRGB()
maptocolor.Update()
imagedata = maptocolor.GetOutput()
bmp = ImageOperations.vtkImageDataToWxImage(imagedata).ConvertToBitmap()
bmp = self.getChannelItemBitmap(bmp, (255, 255, 0))
toolid = wx.NewId()
name = "Colocalization"
self.toolMgr.addChannelItem(name, bmp, toolid, lambda e, x = n, s = self:s.setPreviewedData(e, x))
for i, tid in enumerate(self.toolIds):
self.dataUnit.setOutputChannel(i, 0)
self.toolMgr.toggleTool(tid, 0)
self.dataUnit.setOutputChannel(len(self.toolIds), 1)
self.toolIds.append(toolid)
self.toolMgr.toggleTool(toolid, 1)
self.restoreFromCache()
def updateNames(self):
"""
Updates names of channels
"""
sources = self.dataUnit.getSourceDataUnits()
n1 = sources[0].getName()
n2 = sources[1].getName()
self.listctrl.setChannelNames(n1,n2)
self.lowerThresholdLbl1.SetLabel("%s lower threshold:"%(n1))
self.lowerThresholdLbl2.SetLabel("%s lower threshold:"%(n2))
self.upperThresholdLbl1.SetLabel("%s upper threshold:"%(n1))
self.upperThresholdLbl2.SetLabel("%s upper threshold:"%(n2))
def onDataChanged(self, obj, event):
"""
Handler of data changed event
"""
if self.scatterPlot:
self.scatterPlot.setSlope(self.dataUnit.getSettings().get("Slope"))
self.scatterPlot.setIntercept(self.dataUnit.getSettings().get("Intercept"))
self.scatterPlot.setZSlice(0)
self.scatterPlot.setTimepoint(self.timePoint)
self.scatterPlot.setDataUnit(self.dataUnit)
del self.scatterPlot.verticalLegend
self.scatterPlot.verticalLegend = None
del self.scatterPlot.horizontalLegend
self.scatterPlot.horizontalLegend = None
ctf = self.dataUnit.getSettings().get("ColorTransferFunction")
self.dataUnit.getSettings().set("ColocalizationColorTransferFunction", ctf)
self.clearVariables()
self.listctrl.ClearAll()
self.listctrl.populateListCtrl()
self.updateNames()
def createOptionsFrame(self): """ Creates a frame that contains the various widgets used to control the colocalization settings """ #TaskPanel.createOptionsFrame(self) # self.colocalizationPanel=wx.Panel(self.settingsNotebook,-1) self.colocalizationPanel = wx.Panel(self, -1) self.colocalizationSizer = wx.GridBagSizer() n = 0 self.lowerThresholdLbl1 = wx.StaticText(self.colocalizationPanel, -1, "Ch1 lower threshold:") self.upperThresholdLbl1 = wx.StaticText(self.colocalizationPanel, -1, "Ch1 upper threshold:") self.lowerThresholdLbl2 = wx.StaticText(self.colocalizationPanel, -1, "Ch2 lower threshold:") self.upperThresholdLbl2 = wx.StaticText(self.colocalizationPanel, -1, "Ch2 upper threshold:") self.lowerthreshold1 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \ maxValue = 255, size = (300, -1), style = wx.SL_HORIZONTAL | wx.SL_LABELS) self.lowerthreshold1.Bind(wx.EVT_SCROLL, self.updateThreshold) self.upperthreshold1 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \ maxValue = 255, size = (300, -1), style = wx.SL_HORIZONTAL | wx.SL_LABELS) self.upperthreshold1.Bind(wx.EVT_SCROLL, self.updateThreshold) self.lowerthreshold2 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \ maxValue = 255, size = (300, -1), style = wx.SL_HORIZONTAL | wx.SL_LABELS) self.lowerthreshold2.Bind(wx.EVT_SCROLL, self.updateThreshold) self.upperthreshold2 = wx.Slider(self.colocalizationPanel, value = 128, minValue = 1, \ maxValue = 255, size = (300, -1), style = wx.SL_HORIZONTAL | wx.SL_LABELS) self.upperthreshold2.Bind(wx.EVT_SCROLL, self.updateThreshold) self.colocalizationSizer.Add(self.lowerThresholdLbl1, (n, 0)) n += 1 self.colocalizationSizer.Add(self.lowerthreshold1, (n, 0)) n += 1 self.colocalizationSizer.Add(self.upperThresholdLbl1, (n, 0)) n += 1 self.colocalizationSizer.Add(self.upperthreshold1, (n, 0)) n += 1 self.colocalizationSizer.Add(self.lowerThresholdLbl2, (n, 0)) n += 1 self.colocalizationSizer.Add(self.lowerthreshold2, (n, 0)) n += 1 self.colocalizationSizer.Add(self.upperThresholdLbl2, (n, 0)) n += 1 self.colocalizationSizer.Add(self.upperthreshold2, (n, 0)) n += 1 sbox = wx.StaticBox(self.colocalizationPanel, -1, "2D histogram (right-click for more options)") box = wx.StaticBoxSizer(sbox, wx.VERTICAL) self.scatterPlot = Scatterplot(self.colocalizationPanel, drawLegend = 1) lib.messenger.connect(self.scatterPlot, "scatterplot_thresholds", self.onUpdateScatterplotThresholds) box.Add(self.scatterPlot) self.colocalizationSizer.Add(box, (n, 0)) n += 1 sbox = wx.StaticBox(self.colocalizationPanel, -1, "Colocalization quantification") box = wx.StaticBoxSizer(sbox, wx.VERTICAL) self.automaticThresholdStaticBox = sbox self.automaticThresholdSizer = box #self.pvaluebox = wx.StaticBox(self.colocalizationPanel, -1, "Calculate P-Value") self.radiobox = wx.RadioBox(self.colocalizationPanel, -1, "Calculate P-Value", choices = ["None", "Costes", "Fay", "van Steensel"], majorDimension = 2, style = wx.RA_SPECIFY_COLS ) self.radiobox.Bind(wx.EVT_RADIOBOX, self.onSetTestMethod) #self.pvalueNone = wx.RadioButton(self.colocalizationPanel, -1, "None", name="pvalue") #self.pvalueNone.SetValue(True) #self.pvalueNone.Bind(wx.EVT_RADIOBUTTON, self.onSetNone) #self.pvalueCostes = wx.RadioButton(self.colocalizationPanel, -1, "Costes", name="pvalue") #self.pvalueCostes.SetValue(False) #self.pvalueCostes #self.pvalueFay = wx.RadioButton(self.colocalizationPanel, -1, "Fay", name="pvalue") #self.pvalueFay.SetValue(False) #self.pvaluevanSteensel = wx.RadioButton(self.colocalizationPanel, -1, "van Steensel", name="pvalue") #self.pvaluevanSteensel.SetValue(False) box.Add(self.radiobox) self.iterLbl = wx.StaticText(self.colocalizationPanel, -1, "Iterations:") self.iterations = wx.SpinCtrl(self.colocalizationPanel, -1, "100", min = 2, \ max = 999, initial = 100) self.iterations.Bind(wx.EVT_SPINCTRL, self.onSetIterations) fixedPSFLbl = wx.StaticText(self.colocalizationPanel, -1, "PSF radius (px):") self.fixedPSF = wx.TextCtrl(self.colocalizationPanel, -1, "") costesgrid = wx.GridBagSizer() #sboxsizer.Add(costesgrid) costesgrid.Add(self.iterLbl, (0, 0)) costesgrid.Add(self.iterations, (0, 1)) costesgrid.Add(fixedPSFLbl, (1, 0)) costesgrid.Add(self.fixedPSF, (1, 1)) NALbl = wx.StaticText(self.colocalizationPanel, -1, "Numerical Aperture:") self.NA = wx.TextCtrl(self.colocalizationPanel, -1, "1.4") costesgrid.Add(NALbl, (2, 0)) costesgrid.Add(self.NA, (2, 1)) Ch2LambdaLbl = wx.StaticText(self.colocalizationPanel, -1, u"Ch2 \u03BB (nm):") self.Ch2Lambda = wx.TextCtrl(self.colocalizationPanel, -1, "520") costesgrid.Add(Ch2LambdaLbl, (3, 0)) costesgrid.Add(self.Ch2Lambda, (3, 1)) #pvaluebox.Add(costesgrid) self.NA.Bind(wx.EVT_TEXT, self.onUpdatePSF) self.Ch2Lambda.Bind(wx.EVT_TEXT, self.onUpdatePSF) self.iterations.Enable(0) self.NA.Enable(0) self.Ch2Lambda.Enable(0) self.fixedPSF.Enable(0) box.Add(costesgrid) box2 = wx.BoxSizer(wx.HORIZONTAL) self.statsButton = wx.Button(self.colocalizationPanel, -1, "Calculate statistics") self.statsButton.Bind(wx.EVT_BUTTON, self.getStatistics) box2.Add(self.statsButton) self.thresholdButton = wx.Button(self.colocalizationPanel, -1, "Calculate thresholds") self.thresholdButton.Bind(wx.EVT_BUTTON, self.getAutoThreshold) box2.Add(self.thresholdButton) self.statsButtonSizer = box2 box.Add(box2) self.colocalizationSizer.Add(box, (n, 0), flag = wx.EXPAND | wx.LEFT | wx.RIGHT) n += 1 sbox = wx.StaticBox(self.colocalizationPanel, -1, "Coloc Volume Statistics") box = wx.StaticBoxSizer(sbox, wx.VERTICAL) self.colocStatsStaticBox = sbox self.colocStatsSizer = box self.listctrl = GUI.ColocListView.ColocListView(self.colocalizationPanel, -1, size = (350, 300)) box.Add(self.listctrl) self.statsButton = wx.Button(self.colocalizationPanel, -1, "Export") self.statsButton.Bind(wx.EVT_BUTTON, self.onExportStatistics) box.Add(self.statsButton) self.listctrl.updateListCtrl(self.getVariables()) self.colocalizationSizer.Add(box, (n, 0)) n += 1 sbox = wx.StaticBox(self.colocalizationPanel, -1, "Colocalization color") sboxsizer = wx.StaticBoxSizer(sbox, wx.VERTICAL) self.colocColorBox = sbox self.colocColorSizer = sboxsizer self.colorBtn = CTFButton(self.colocalizationPanel) sboxsizer.Add(self.colorBtn) val = AcceptedValidator self.constColocCheckbox = wx.CheckBox(self.colocalizationPanel, -1, \ "Use single (1-bit) value for colocalization") self.constColocValue = wx.TextCtrl(self.colocalizationPanel, -1, "255", validator = val(string.digits, below = 255)) self.constColocValue.Enable(0) self.constColocValue.Bind(wx.EVT_TEXT, self.onSetColocValue) self.constColocCheckbox.Bind(wx.EVT_CHECKBOX, self.onSetColocCheckbox) sboxsizer.Add(self.constColocCheckbox) sboxsizer.Add(self.constColocValue) self.colocalizationSizer.Add(sboxsizer, (n, 0)) n += 1 self.colocalizationPanel.SetSizer(self.colocalizationSizer) self.colocalizationPanel.SetAutoLayout(1) self.settingsSizer.Add(self.colocalizationPanel, (1, 0), flag = wx.EXPAND | wx.ALL)
class AdjustPanel(TaskPanel):
"""
Description: A window for processing a single dataunit
"""
def __init__(self, parent, tb):
"""
Initialization
Parameters:
root Is the parent widget of this window
"""
self.operationName = "Adjust"
self.lbls = []
self.btns = []
self.entries = []
self.timePoint = 0
TaskPanel.__init__(self, parent, tb)
# Preview has to be generated heregoto
# self.colorChooser=None
self.createIntensityTransferPage()
lib.messenger.connect(None, "timepoint_changed", self.updateTimepoint)
self.Show()
self.mainsizer.Fit(self)
self.mainsizer.Layout()
def createIntensityInterpolationPanel(self):
"""
Creates a frame holding the entries for configuring
interpolation
"""
self.interpolationPanel = wx.Panel(self.settingsNotebook)
#self.interpolationPanel=wx.Panel(self.iTFEditor)
self.interpolationSizer = wx.GridBagSizer()
lbl = wx.StaticText(self.interpolationPanel, -1,
"Interpolate intensities:")
self.interpolationSizer.Add(lbl, (0, 0))
lbl = wx.StaticText(self.interpolationPanel, -1, "from timepoint")
self.lbls.append(lbl)
self.numOfPoints = 5
for i in range(self.numOfPoints - 2):
lbl = wx.StaticText(self.interpolationPanel, -1, "thru")
self.lbls.append(lbl)
lbl = wx.StaticText(self.interpolationPanel, -1, "to timepoint")
self.lbls.append(lbl)
for i in range(self.numOfPoints):
btn = wx.Button(self.interpolationPanel, -1, "goto")
btn.Bind(wx.EVT_BUTTON,
lambda event, x=i: self.gotoInterpolationTimePoint(x))
entry = wx.TextCtrl(self.interpolationPanel, size=(50, -1))
self.btns.append(btn)
self.entries.append(entry)
for entry in self.entries:
entry.Bind(wx.EVT_TEXT, self.setInterpolationTimePoints)
last = 0
for i in range(self.numOfPoints):
lbl, entry, btn = self.lbls[i], self.entries[i], self.btns[i]
self.interpolationSizer.Add(lbl, (i + 1, 0))
self.interpolationSizer.Add(entry, (i + 1, 1))
self.interpolationSizer.Add(btn, (i + 1, 2))
last = i + 1
#self.editIntensitySizer.Add(self.interpolationPanel,(0,1))
self.interpolationPanel.SetSizer(self.interpolationSizer)
self.interpolationPanel.SetAutoLayout(1)
self.interpolationSizer.SetSizeHints(self.interpolationPanel)
self.settingsNotebook.AddPage(self.interpolationPanel, "Interpolation")
self.interpolationBox = wx.BoxSizer(wx.HORIZONTAL)
self.reset2Btn = wx.Button(self.interpolationPanel, -1,
"Reset all timepoints")
self.reset2Btn.Bind(wx.EVT_BUTTON, self.resetTransferFunctions)
self.interpolationBox.Add(self.reset2Btn)
self.interpolateBtn = wx.Button(self.interpolationPanel, -1,
"Interpolate")
self.interpolateBtn.Bind(wx.EVT_BUTTON, self.startInterpolation)
self.interpolationBox.Add(self.interpolateBtn)
self.interpolationSizer.Add(self.interpolationBox, (last + 1, 0))
#self.mainsizer.Add(self.interpolationPanel,(1,0))
#self.panel.Layout()
#self.mainsizer.Fit(self.panel)
def createIntensityTransferPage(self):
"""
Creates a frame holding the entries for configuring
intensity
"""
self.editIntensityPanel = wx.Panel(self.settingsNotebook, -1)
self.editIntensitySizer = wx.GridBagSizer()
self.iTFEditor = IntensityTransferEditor(self.editIntensityPanel)
self.editIntensitySizer.Add(self.iTFEditor, (0, 0)) #,span=(1,2))
self.box = wx.BoxSizer(wx.HORIZONTAL)
self.editIntensitySizer.Add(self.box, (2, 0))
self.createIntensityInterpolationPanel()
self.restoreBtn = wx.Button(self.editIntensityPanel, -1,
"Reset current timepoint")
self.restoreBtn.Bind(wx.EVT_BUTTON, self.iTFEditor.restoreDefaults)
self.box.Add(self.restoreBtn)
self.resetBtn = wx.Button(self.editIntensityPanel, -1,
"Reset all timepoints")
self.resetBtn.Bind(wx.EVT_BUTTON, self.resetTransferFunctions)
self.box.Add(self.resetBtn)
self.copyiTFBtn = wx.Button(self.editIntensityPanel, -1,
"Copy to all timepoints")
self.copyiTFBtn.Bind(wx.EVT_BUTTON, self.copyTransferFunctionToAll)
self.box.Add(self.copyiTFBtn)
self.editIntensityPanel.SetSizer(self.editIntensitySizer)
self.editIntensityPanel.SetAutoLayout(1)
self.settingsNotebook.InsertPage(0, self.editIntensityPanel,
"Transfer Function")
self.settingsNotebook.SetSelection(0)
self.updateSettings()
def setInterpolationTimePoints(self, event):
"""
A callback that is called when a timepoint entry for
intensity interpolation changes. Updates the list of
timepoints between which the interpolation is carried out
by the dataunit
"""
lst = []
for i in self.entries:
val = i.GetValue()
try:
n = int(val)
#n -= 1
lst.append(n)
except:
# For entries that have no value, add -1 as a place holder
lst.append(-1)
#self.dataUnit.setInterpolationTimePoints(lst)
self.settings.set("InterpolationTimepoints", lst)
def gotoInterpolationTimePoint(self, entrynum):
"""
The previewed timepoint is set to timepoint specified in
self.entries[entrynum]
"""
try:
tp = int(self.entries[entrynum].GetValue())
except:
pass
else:
tp -= 1
Logging.info("Previewing timepoint ",
tp,
"(will send change event)",
kw="task")
lib.messenger.send(None, "timepoint_changed", tp)
#self.updateTimepoint(evt)
def createButtonBox(self):
"""
Creates a button box containing the buttons Render,
Preview and Close
"""
TaskPanel.createButtonBox(self)
#self.processButton.SetLabel("Process Dataset Series")
#self.processButton.Bind(wx.EVT_BUTTON,self.doProcessingCallback)
lib.messenger.connect(None, "process_dataset",
self.doProcessingCallback)
def createOptionsFrame(self):
"""
Creates a frame that contains the various widgets
used to control the colocalization settings
"""
TaskPanel.createOptionsFrame(self)
self.paletteLbl = wx.StaticText(self, -1, "Channel palette:")
self.commonSettingsSizer.Add(self.paletteLbl, (1, 0))
self.colorBtn = CTFButton(self)
self.commonSettingsSizer.Add(self.colorBtn, (2, 0))
self.Layout()
def updateTimepoint(self, obj, evt, timePoint):
"""
A callback function called when the timepoint is changed
"""
#timePoint=event.getValue()
Logging.info("Now configuring timepoint", timePoint, kw="task")
itf = self.settings.getCounted("IntensityTransferFunctions", timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
self.timePoint = timePoint
def copyTransferFunctionToAll(self, event=None):
"""
A method to copy this transfer function to all timepooints
"""
itf = self.settings.getCounted("IntensityTransferFunctions",
self.timePoint)
l = self.dataUnit.getNumberOfTimepoints()
for i in range(l):
if i != self.timePoint:
self.settings.setCounted("IntensityTransferFunctions", i, itf)
def resetTransferFunctions(self, event=None):
"""
A method to reset all the intensity transfer functions
"""
l = self.dataUnit.getNumberOfTimepoints()
sources = self.dataUnit.getSourceDataUnits()
for i in range(l):
minval = min([a.getScalarRange()[0] for a in sources])
maxval = max([a.getScalarRange()[1] for a in sources])
bitdepth = sources[0].getBitDepth()
minval = min(0, minval)
maxval = max(2**bitdepth - 1, maxval)
itf = vtkbxd.vtkIntensityTransferFunction()
itf.SetRangeMax(maxval)
self.settings.setCounted("IntensityTransferFunctions", i, itf)
itf = self.settings.getCounted("IntensityTransferFunctions",
self.timePoint)
self.iTFEditor.setIntensityTransferFunction(itf)
def startInterpolation(self, evt):
"""
A callback to interpolate intensity transfer functions
between the specified timepoints
"""
self.dataUnit.interpolateIntensities()
# self.doPreviewCallback()
def updateSettings(self, force=0):
"""
A method used to set the GUI widgets to their proper values
"""
if self.dataUnit:
self.iTFEditor.setIntensityTransferFunction(
self.settings.getCounted("IntensityTransferFunctions",
self.timePoint))
tps = self.settings.get("InterpolationTimepoints")
if not tps:
tps = []
for i in range(len(tps)):
n = tps[i]
# If there was nothing in the entry at this position, the
# value is -1 in that case, we leave the entry empty
if n != -1:
self.entries[i].SetValue(str(n))
ctf = self.settings.get("ColorTransferFunction")
if ctf and self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
self.colorBtn.Refresh()
def doProcessingCallback(self, *args):
"""
A callback for the button "Process Dataset Series"
"""
TaskPanel.doOperation(self)
def setCombinedDataUnit(self, dataUnit):
"""
Sets the processed dataunit that is to be processed.
It is then used to get the names of all the source data
units and they are added to the menu.
This is overwritten from TaskPanel since we only process
one dataunit here, not multiple source data units
"""
TaskPanel.setCombinedDataUnit(self, dataUnit)
ctf = self.settings.get("ColorTransferFunction")
if ctf and self.colorBtn:
self.colorBtn.setColorTransferFunction(ctf)
# We register a callback to be notified when the timepoint changes
# We do it here because the timePointChanged() code requires the dataunit
#self.Bind(EVT_TIMEPOINT_CHANGED,self.timePointChanged,id=ID_TIMEPOINT)
tf = self.settings.getCounted("IntensityTransferFunctions",
self.timePoint)
self.iTFEditor.setIntensityTransferFunction(tf)
self.iTFEditor.updateCallback = self.doPreviewCallback
self.restoreFromCache()
self.updateSettings()