def loadBXDLutFromString(lut, ctf):
"""
Load a BXD format lut from a given string
"""
lut = lut[6:]
start, end = struct.unpack("ff", lut[0:8])
lut = lut[8:]
Logging.info("The palette is in range %d-%d" % (start, end), kw="ctf")
j = 0
# start = int(start)
# end = int(end)
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.SetInputString(lut, len(lut))
handle.LoadColorTransferFunctionFromString(ctf, start, end)
# k = ( len(lut) / 3 ) - 1
# reds = lut[0: k + 1]
# greens = lut[k + 1: 2 * k + 2]
# blues = lut[(2 * k) + 2: 3 * k + 3]
# j = 0
# for i in range(start, end + 1):
# red = ord(reds[j])
# green = ord(greens[j])
# blue = ord(blues[j])
# red /= 255.0
# green /= 255.0
# blue /= 255.0
# ctf.AddRGBPoint(i, red, green, blue)
# j += 1
return
def lutToString(ctf, luttype="ImageJ"):
"""
Write a lut to a string
"""
stringOfLUT = ""
if ctf is None:
return stringOfLUT
minval, maxval = ctf.GetRange()
if luttype == "ImageJ":
perColor = maxval / 255
else:
perColor = 1
if luttype == "BioImageXD":
stringOfLUT = "BXDLUT"
Logging.info("Adding to BXDLUT structure the minval=%f, maxval=%f" %
(minval, maxval),
kw="ctf")
stringOfLUT += struct.pack("f", minval)
stringOfLUT += struct.pack("f", maxval)
size = maxval - minval + 1
if size < ctf.GetSize():
size = ctf.GetSize()
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.ColorTransferFunctionToString(ctf, int(perColor), int(size))
ctfstr = handle.GetOutputString()
for i in xrange(0, ctfstr.GetNumberOfTuples()):
stringOfLUT += chr(ctfstr.GetValue(i))
#for col in range(0, 3):
# for i in range(0, int(maxval) + 1, int(perColor)):
# val = [0, 0, 0]
# ctf.GetColor(i, val)
# red, green, blue = val
# red *= 255
# green *= 255
# blue *= 255
# red = int(red)
# green = int(green)
# blue = int(blue)
# if red < 0:
# red = 0
# if blue < 0:
# blue = 0
# if green < 0:
# green = 0
# if red >= 255:
# red = 255
# if green >= 255:
# green = 255
# if blue >= 255:
# blue = 255
# color = [red, green, blue]
# stringOfLUT += chr(color[col])
return stringOfLUT
def loadBXDLutFromString(lut, ctf):
"""
Load a BXD format lut from a given string
"""
lut = lut[6:]
start, end = struct.unpack("ff", lut[0:8])
lut = lut[8:]
Logging.info("The palette is in range %d-%d" % (start, end), kw="ctf")
j = 0
#start = int(start)
#end = int(end)
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.SetInputString(lut, len(lut))
handle.LoadColorTransferFunctionFromString(ctf, start, end)
#k = ( len(lut) / 3 ) - 1
#reds = lut[0: k + 1]
#greens = lut[k + 1: 2 * k + 2]
#blues = lut[(2 * k) + 2: 3 * k + 3]
#j = 0
#for i in range(start, end + 1):
# red = ord(reds[j])
# green = ord(greens[j])
# blue = ord(blues[j])
# red /= 255.0
# green /= 255.0
# blue /= 255.0
# ctf.AddRGBPoint(i, red, green, blue)
# j += 1
return
def lutToString(ctf, luttype="ImageJ"):
"""
Write a lut to a string
"""
stringOfLUT = ""
if ctf is None:
return stringOfLUT
minval, maxval = ctf.GetRange()
if luttype == "ImageJ":
perColor = maxval / 255
else:
perColor = 1
if luttype == "BioImageXD":
stringOfLUT = "BXDLUT"
Logging.info("Adding to BXDLUT structure the minval=%f, maxval=%f" % (minval, maxval), kw="ctf")
stringOfLUT += struct.pack("f", minval)
stringOfLUT += struct.pack("f", maxval)
size = maxval - minval + 1
if size < ctf.GetSize():
size = ctf.GetSize()
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.ColorTransferFunctionToString(ctf, int(perColor), int(size))
ctfstr = handle.GetOutputString()
for i in xrange(0, ctfstr.GetNumberOfTuples()):
stringOfLUT += chr(ctfstr.GetValue(i))
# for col in range(0, 3):
# for i in range(0, int(maxval) + 1, int(perColor)):
# val = [0, 0, 0]
# ctf.GetColor(i, val)
# red, green, blue = val
# red *= 255
# green *= 255
# blue *= 255
# red = int(red)
# green = int(green)
# blue = int(blue)
# if red < 0:
# red = 0
# if blue < 0:
# blue = 0
# if green < 0:
# green = 0
# if red >= 255:
# red = 255
# if green >= 255:
# green = 255
# if blue >= 255:
# blue = 255
# color = [red, green, blue]
# stringOfLUT += chr(color[col])
return stringOfLUT
def execute(self, inputs, update=0, last=0):
"""
Execute the filter with given inputs and return the output
"""
if not lib.ProcessingFilter.ProcessingFilter.execute(self, inputs):
return None
bitDepth = 8
minVal = 0.0
maxVal = 255.0
image = self.getInput(1)
self.vtkfilter.SetInput(image)
self.vtkfilter.SetClampOverflow(self.parameters["ClampOverflow"])
output = self.vtkfilter.GetOutput()
for param in [
"Float", "Double", "Int", "UnsignedInt", "Long",
"UnsignedLong", "Short", "UnsignedShort", "Char",
"UnsignedChar"
]:
if self.parameters[param]:
eval("self.vtkfilter.SetOutputScalarTypeTo%s()" % param)
output.Update()
minVal, maxVal = output.GetScalarRange()
self.eventDesc = "Casting the image to datatype %s" % param
if param in ["Short", "UnsignedShort"]:
bitDepth = 16
if param in ["Int", "UnsignedInt", "Float"]:
bitDepth = 32
if param in ["Double", "Long", "UnsignedLong"]:
bitDepth = 64
settings = self.dataUnit.getSettings()
settings.set("BitDepth", bitDepth)
if self.parameters["RescaleCTF"]:
ctf = settings.get("ColorTransferFunction")
scaledCtf = vtk.vtkColorTransferFunction()
handleCtf = vtkbxd.vtkHandleColorTransferFunction()
handleCtf.ScaleColorTransferFunction(ctf, scaledCtf, minVal,
maxVal)
settings.set("ColorTransferFunction", scaledCtf)
#if update:
self.vtkfilter.Update()
return self.vtkfilter.GetOutput()
def watershedPalette(ctfLowerBound,
ctfUpperBound,
ignoreColors=2,
filename=""):
"""
Returns a randomly created CTF.
"""
try:
ctf = vtk.vtkColorTransferFunction()
if filename:
loadLUT(filename, ctf)
except:
ctf = vtk.vtkColorTransferFunction()
ctfFileSize = ctf.GetSize()
if ctfFileSize > 0:
for i in range(0, ignoreColors):
color = ctf.GetColor(i)
ctf.AddRGBPoint(ctf.GetSize(), color[0], color[1], color[2])
for i in range(0, ignoreColors):
ctf.AddRGBPoint(i, 0, 0, 0)
if ctfLowerBound < 1:
ctfLowerBound = 1
if ctfFileSize > 0 and ctf.GetSize() > ctfLowerBound:
ctfLowerBound = ctf.GetSize()
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.CreateRandomColorTransferFunction(ctf, ctfLowerBound, ctfUpperBound,
1.5)
#for i in range(int(ctfLowerBound), int(ctfUpperBound)):
# red = 0
# green = 0
# blue = 0
# while red + green + blue < 1.5:
# red = random.random()
# green = random.random()
# blue = random.random()
# ctf.AddRGBPoint(float(i), float(red), float(green), float(blue))
if ctf.GetSize() > ctfUpperBound:
for i in xrange(ctfUpperBound, ctf.GetSize() - 1):
ctf.RemovePoint(i)
return ctf
def watershedPalette(ctfLowerBound, ctfUpperBound, ignoreColors=2, filename=""):
"""
Returns a randomly created CTF.
"""
try:
ctf = vtk.vtkColorTransferFunction()
if filename:
loadLUT(filename, ctf)
except:
ctf = vtk.vtkColorTransferFunction()
ctfFileSize = ctf.GetSize()
if ctfFileSize > 0:
for i in range(0, ignoreColors):
color = ctf.GetColor(i)
ctf.AddRGBPoint(ctf.GetSize(), color[0], color[1], color[2])
for i in range(0, ignoreColors):
ctf.AddRGBPoint(i, 0, 0, 0)
if ctfLowerBound < 1:
ctfLowerBound = 1
if ctfFileSize > 0 and ctf.GetSize() > ctfLowerBound:
ctfLowerBound = ctf.GetSize()
handle = vtkbxd.vtkHandleColorTransferFunction()
handle.CreateRandomColorTransferFunction(ctf, ctfLowerBound, ctfUpperBound, 1.5)
# for i in range(int(ctfLowerBound), int(ctfUpperBound)):
# red = 0
# green = 0
# blue = 0
# while red + green + blue < 1.5:
# red = random.random()
# green = random.random()
# blue = random.random()
# ctf.AddRGBPoint(float(i), float(red), float(green), float(blue))
if ctf.GetSize() > ctfUpperBound:
for i in xrange(ctfUpperBound, ctf.GetSize() - 1):
ctf.RemovePoint(i)
return ctf
def execute(self, inputs, update = 0, last = 0):
"""
Execute the filter with given inputs and return the output
"""
if not lib.ProcessingFilter.ProcessingFilter.execute(self, inputs):
return None
bitDepth = 8
minVal = 0.0
maxVal = 255.0
image = self.getInput(1)
self.vtkfilter.SetInput(image)
self.vtkfilter.SetClampOverflow(self.parameters["ClampOverflow"])
output = self.vtkfilter.GetOutput()
for param in ["Float","Double","Int","UnsignedInt","Long","UnsignedLong","Short","UnsignedShort","Char","UnsignedChar"]:
if self.parameters[param]:
eval("self.vtkfilter.SetOutputScalarTypeTo%s()"%param)
output.Update()
minVal,maxVal = output.GetScalarRange()
self.eventDesc = "Casting the image to datatype %s"%param
if param in ["Short", "UnsignedShort"]:
bitDepth = 16
if param in ["Int", "UnsignedInt", "Float"]:
bitDepth = 32
if param in ["Double", "Long", "UnsignedLong"]:
bitDepth = 64
settings = self.dataUnit.getSettings()
settings.set("BitDepth", bitDepth)
if self.parameters["RescaleCTF"]:
ctf = settings.get("ColorTransferFunction")
scaledCtf = vtk.vtkColorTransferFunction()
handleCtf = vtkbxd.vtkHandleColorTransferFunction()
handleCtf.ScaleColorTransferFunction(ctf,scaledCtf,minVal,maxVal)
settings.set("ColorTransferFunction",scaledCtf)
#if update:
self.vtkfilter.Update()
return self.vtkfilter.GetOutput()
