def calculatePValue(self, images):
"""
Calculate the P-value
"""
coloctest = vtkbxd.vtkImageColocalizationTest()
self.eventDesc = "Calculating P-Value"
method = 2
if self.parameters["Costes"]: method = 1
if self.parameters["Fay"]: method = 0
coloctest.SetMethod(method)
Logging.info("Calculating P-value, method = %d"%method)
if self.parameters["PSF"]:
Logging.info("Using manual PSF size %d"%int(self.parameters["PSF"]))
coloctest.SetManualPSFSize(int(self.parameters["PSF"]))
coloctest.SetNumIterations(self.parameters["Iterations"])
images[0].SetUpdateExtent(images[0].GetWholeExtent())
images[1].SetUpdateExtent(images[1].GetWholeExtent())
images[0].Update()
images[1].Update()
for data in images:
coloctest.AddInput(data)
coloctest.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(coloctest, "ProgressEvent", self.updateProgress)
coloctest.Update()
for i in ["PValue", "RObserved", "RRandMean", "RRandSD",
"NumIterations", "ColocCount", "Method"]:
val = eval("coloctest.Get%s()" % i)
self.setResultVariable(i, val)
lib.messenger.send(None, "update_progress", 100, "Done.")
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 calculatePValue(self, images):
"""
Calculate the P-value
"""
coloctest = vtkbxd.vtkImageColocalizationTest()
self.eventDesc = "Calculating P-Value"
method = 2
if self.parameters["Costes"]: method = 1
if self.parameters["Fay"]: method = 0
coloctest.SetMethod(method)
Logging.info("Calculating P-value, method = %d" % method)
if self.parameters["PSF"]:
Logging.info("Using manual PSF size %d" %
int(self.parameters["PSF"]))
coloctest.SetManualPSFSize(int(self.parameters["PSF"]))
coloctest.SetNumIterations(self.parameters["Iterations"])
images[0].SetUpdateExtent(images[0].GetWholeExtent())
images[1].SetUpdateExtent(images[1].GetWholeExtent())
images[0].Update()
images[1].Update()
for data in images:
coloctest.AddInput(data)
coloctest.AddObserver('ProgressEvent', lib.messenger.send)
lib.messenger.connect(coloctest, "ProgressEvent", self.updateProgress)
coloctest.Update()
for i in [
"PValue", "RObserved", "RRandMean", "RRandSD", "NumIterations",
"ColocCount", "Method"
]:
val = eval("coloctest.Get%s()" % i)
self.setResultVariable(i, val)
lib.messenger.send(None, "update_progress", 100, "Done.")