def doOperation(self):
"""
Does color merging for the dataset
"""
t1 = time.time()
datasets = []
alphas = []
processed = []
imagelen = len(self.images)
if not imagelen:
return None
self.shift = 0
self.scale = 0.333
self.scale /= imagelen
luminance = 0
self.shift = 0
self.scale = 1
self.merge = vtkbxd.vtkImageColorMerge()
self.merge.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.merge, 'ProgressEvent', self.updateProgress)
if self.doAlpha:
self.merge.BuildAlphaOn()
if self.alphaMode[0] == 0:
Logging.info("Alpha mode = maximum", kw="processing")
self.merge.MaximumModeOn()
elif self.alphaMode[0] == 1:
Logging.info("Alpha mode = average, threshold = ",
self.alphaMode[1],
kw="processing")
self.merge.AverageModeOn()
self.merge.SetAverageThreshold(self.alphaMode[1])
elif self.alphaMode[0] == 2:
self.merge.LuminanceModeOn()
Logging.info("Alpha mode = luminance", kw="processing")
else:
self.merge.BuildAlphaOff()
else:
self.merge.BuildAlphaOff()
images = lib.ImageOperations.castImagesToLargestDataType(self.images)
for i, image in enumerate(images):
self.merge.AddInput(image)
self.merge.AddLookupTable(self.ctfs[i])
if self.intensityTransferFunctions[i] != None:
self.merge.AddIntensityTransferFunction(
self.intensityTransferFunctions[i])
#data = self.getLimitedOutput(self.merge)
data = self.merge.GetOutput()
t3 = time.time()
Logging.info("Merging took %.4f seconds" % (t3 - t1), kw="processing")
#lib.messenger.send(None, "update_progress", 100, "Done.")
#data.GlobalReleaseDataFlagOn()
return data
def doOperation(self):
"""
Does color merging for the dataset
"""
t1 = time.time()
datasets = []
alphas = []
processed = []
imagelen = len(self.images)
if not imagelen:
return None
self.shift = 0
self.scale = 0.333
self.scale /= imagelen
luminance = 0
self.shift = 0
self.scale = 1
self.merge = vtkbxd.vtkImageColorMerge()
self.merge.AddObserver("ProgressEvent", lib.messenger.send)
lib.messenger.connect(self.merge, "ProgressEvent", self.updateProgress)
if self.doAlpha:
self.merge.BuildAlphaOn()
if self.alphaMode[0] == 0:
Logging.info("Alpha mode = maximum", kw="processing")
self.merge.MaximumModeOn()
elif self.alphaMode[0] == 1:
Logging.info("Alpha mode = average, threshold = ", self.alphaMode[1], kw="processing")
self.merge.AverageModeOn()
self.merge.SetAverageThreshold(self.alphaMode[1])
elif self.alphaMode[0] == 2:
self.merge.LuminanceModeOn()
Logging.info("Alpha mode = luminance", kw="processing")
else:
self.merge.BuildAlphaOff()
else:
self.merge.BuildAlphaOff()
images = lib.ImageOperations.castImagesToLargestDataType(self.images)
for i, image in enumerate(images):
self.merge.AddInput(image)
self.merge.AddLookupTable(self.ctfs[i])
if self.intensityTransferFunctions[i] != None:
self.merge.AddIntensityTransferFunction(self.intensityTransferFunctions[i])
# data = self.getLimitedOutput(self.merge)
data = self.merge.GetOutput()
t3 = time.time()
Logging.info("Merging took %.4f seconds" % (t3 - t1), kw="processing")
# lib.messenger.send(None, "update_progress", 100, "Done.")
# data.GlobalReleaseDataFlagOn()
return data
r1 = vtkbxd.vtkLSMReader() r1.SetFileName(D) r1.SetUpdateChannel(0) d1 = r1.GetOutput() itf1 = vtkbxd.vtkIntensityTransferFunction() itf1.SetBrightness(50.0) ctf1 = vtkbxd.vtkColorTransferFunction() ctf1.AddRGBPoint(0, 0, 0, 0) ctf1.AddRGBPoint(255.0, 0, 1.0, 0) print "Feeding channels to merge ", elapsed() merge = vtkbxd.vtkImageColorMerge() #merge.SetNumberOfThreads(5) merge.AddInput(d1) merge.AddLookupTable(ctf1) merge.AddIntensityTransferFunction(itf1) itfmap = vtkbxd.vtkImageMapToIntensities() itfmap.SetInput(d1) itfmap.SetIntensityTransferFunction(itf1) maptocolor = vtk.vtkImageMapToColors() maptocolor.SetOutputFormatToRGB() maptocolor.SetInput(itfmap.GetOutput()) maptocolor.SetLookupTable(ctf1) mip = vtkbxd.vtkImageSimpleMIP()
def doPreview(self, depth, renew, timePoint=0):
"""
Makes a two-dimensional preview using the class-specific combination function
Parameters: depth The preview depth
renew Flag indicating, whether the preview should be
regenerated or if a stored image can be reused
timePoint The timepoint from which to generate the preview
Defaults to 0
"""
Logging.info("Creating preview", kw="dataunit")
preview = None
if timePoint > self.getNumberOfTimepoints():
timepoint = self.getNumberOfTimepoints() - 1
self.oldAlphaStatus = scripting.wantAlphaChannel
if depth == scripting.WHOLE_DATASET_NO_ALPHA:
scripting.wantAlphaChannel = 0
# If the previously requested preview was a "show original" preview
# then we can just restore the preview before that without any
# processing
showOrig = self.settings.get("ShowOriginal")
# If the requested output channels have been specified,
# then we map those through their corresponding ctf's
# to be merged to the output
n = len(self.sourceunits)
merged = []
if self.outputChannels:
for i, unit in enumerate(self.sourceunits):
if i in self.outputChannels and self.outputChannels[i]:
data = unit.getTimepoint(timePoint)
merged.append((data, unit.getColorTransferFunction()))
if n not in self.outputChannels:
self.outputChannels[n] = 0
# If either no output channels have been specified (in which case
# we return just the normal preview) or the combined result
# (n = last chl+1) has been requested
if self.merging or not self.outputChannels or (
n in self.outputChannels and self.outputChannels[n]):
# If the renew flag is true, we need to regenerate the preview
if renew:
Logging.info("Renewing preview", kw="dataunit")
# We then tell the module to reset itself and
# initialize it again
self.module.reset()
# Go through all the source datasets for the module
self.module.setSettings(self.settings)
self.module.setTimepoint(timePoint)
images = []
for dataunit in self.sourceunits:
Logging.info("Adding source image data from %d dataunits" %
len(self.sourceunits),
kw="dataunit")
image = dataunit.getTimepoint(timePoint)
x, y, z = image.GetDimensions()
# If a whole volume is requested, but the data is acquired with an update
# extent selecting only a single slice, then reset the update extent
if depth < 0 and z <= 1:
image.SetUpdateExtent(image.GetWholeExtent())
image.Update()
elif depth >= 0 and not (x or y):
# If a dataset has not been updated yet, then set the appropriate
# update extent
ex0, ex1, ey0, ey1, ez0, ez1 = image.GetWholeExtent()
image.SetUpdateExtent(ex0, ex1, ey0, ey1, depth, depth)
image.Update()
self.module.addInput(dataunit, image)
Logging.info("Getting preview from module %s" % str(self.module),
kw="dataunit")
preview = self.module.getPreview(depth)
if type(preview) == types.TupleType:
preview = preview[0]
if preview is not None:
isMultiComponent = preview.GetNumberOfScalarComponents(
) > 1 # doesn't work when preview isn't updated
else:
isMultiComponent = False
if not isMultiComponent:
for unit in self.sourceunits:
isMultiComponent = unit.getBitDepth(
) > unit.getSingleComponentBitDepth()
if isMultiComponent:
break
if not self.merging and self.outputChannels:
if preview:
merged.append((preview, self.getColorTransferFunction()))
if len(merged) > 1:
Logging.info("Merging the output channels", kw="dataunit")
if not self.merge:
self.merge = vtkbxd.vtkImageColorMerge()
else:
self.merge.RemoveAllInputs()
self.merge.RemoveLookupTables()
images = [x[0] for x in merged]
images = lib.ImageOperations.castImagesToLargestDataType(
images)
for i, (data, ctf) in enumerate(merged):
image = images[i]
self.merge.AddInput(image)
self.merge.AddLookupTable(ctf)
preview = self.merge.GetOutput()
elif len(merged
) == 1 and scripting.preferRGB and not isMultiComponent:
Logging.info("Mapping the output to color", kw="dataunit")
data, ctf = merged[0]
if not self.maptocolor:
self.maptocolor = vtk.vtkImageMapToColors()
self.maptocolor.SetNumberOfThreads(1)
self.maptocolor.SetOutputFormatToRGB()
else:
self.maptocolor.RemoveAllInputs()
self.maptocolor.SetInput(data)
self.maptocolor.SetLookupTable(ctf)
preview = self.maptocolor.GetOutput()
scripting.wantAlphaChannel = self.oldAlphaStatus
if not showOrig and not self.doOrig:
self.origPreview = preview
elif showOrig:
self.doOrig = 1
return preview
r1.SetFileName(D) r1.SetUpdateChannel(0) d1=r1.GetOutput() itf1=vtkbxd.vtkIntensityTransferFunction() itf1.SetBrightness(50.0) ctf1=vtkbxd.vtkColorTransferFunction() ctf1.AddRGBPoint(0,0,0,0) ctf1.AddRGBPoint(255.0,0,1.0,0) print "Feeding channels to merge ",elapsed() merge = vtkbxd.vtkImageColorMerge() #merge.SetNumberOfThreads(5) merge.AddInput(d1) merge.AddLookupTable(ctf1) merge.AddIntensityTransferFunction(itf1) itfmap = vtkbxd.vtkImageMapToIntensities() itfmap.SetInput(d1) itfmap.SetIntensityTransferFunction(itf1) maptocolor=vtk.vtkImageMapToColors() maptocolor.SetOutputFormatToRGB() maptocolor.SetInput(itfmap.GetOutput()) maptocolor.SetLookupTable(ctf1)
def doPreview(self, depth, renew, timePoint = 0):
"""
Makes a two-dimensional preview using the class-specific combination function
Parameters: depth The preview depth
renew Flag indicating, whether the preview should be
regenerated or if a stored image can be reused
timePoint The timepoint from which to generate the preview
Defaults to 0
"""
Logging.info("Creating preview",kw="dataunit")
preview = None
if timePoint > self.getNumberOfTimepoints():
timepoint = self.getNumberOfTimepoints() - 1
self.oldAlphaStatus = scripting.wantAlphaChannel
if depth == scripting.WHOLE_DATASET_NO_ALPHA:
scripting.wantAlphaChannel = 0
# If the previously requested preview was a "show original" preview
# then we can just restore the preview before that without any
# processing
showOrig = self.settings.get("ShowOriginal")
# If the requested output channels have been specified,
# then we map those through their corresponding ctf's
# to be merged to the output
n = len(self.sourceunits)
merged = []
if self.outputChannels:
for i, unit in enumerate(self.sourceunits):
if i in self.outputChannels and self.outputChannels[i]:
data = unit.getTimepoint(timePoint)
merged.append((data, unit.getColorTransferFunction()))
if n not in self.outputChannels:
self.outputChannels[n] = 0
# If either no output channels have been specified (in which case
# we return just the normal preview) or the combined result
# (n = last chl+1) has been requested
if self.merging or not self.outputChannels or (n in self.outputChannels and self.outputChannels[n]):
# If the renew flag is true, we need to regenerate the preview
if renew:
Logging.info("Renewing preview", kw="dataunit")
# We then tell the module to reset itself and
# initialize it again
self.module.reset()
# Go through all the source datasets for the module
self.module.setSettings(self.settings)
self.module.setTimepoint(timePoint)
images = []
for dataunit in self.sourceunits:
Logging.info("Adding source image data from %d dataunits"%len(self.sourceunits), kw = "dataunit")
image = dataunit.getTimepoint(timePoint)
x, y, z = image.GetDimensions()
# If a whole volume is requested, but the data is acquired with an update
# extent selecting only a single slice, then reset the update extent
if depth < 0 and z <= 1:
image.SetUpdateExtent(image.GetWholeExtent())
image.Update()
elif depth >= 0 and not (x or y):
# If a dataset has not been updated yet, then set the appropriate
# update extent
ex0, ex1, ey0, ey1, ez0, ez1 = image.GetWholeExtent()
image.SetUpdateExtent(ex0, ex1, ey0, ey1, depth, depth)
image.Update()
self.module.addInput(dataunit, image)
Logging.info("Getting preview from module %s"%str(self.module), kw="dataunit")
preview = self.module.getPreview(depth)
if type(preview) == types.TupleType:
preview = preview[0]
if preview is not None:
isMultiComponent = preview.GetNumberOfScalarComponents() > 1 # doesn't work when preview isn't updated
else:
isMultiComponent = False
if not isMultiComponent:
for unit in self.sourceunits:
isMultiComponent = unit.getBitDepth() > unit.getSingleComponentBitDepth()
if isMultiComponent:
break
if not self.merging and self.outputChannels:
if preview:
merged.append((preview, self.getColorTransferFunction()))
if len(merged) > 1:
Logging.info("Merging the output channels", kw="dataunit")
if not self.merge:
self.merge = vtkbxd.vtkImageColorMerge()
else:
self.merge.RemoveAllInputs()
self.merge.RemoveLookupTables()
images = [x[0] for x in merged]
images = lib.ImageOperations.castImagesToLargestDataType(images)
for i, (data, ctf) in enumerate(merged):
image = images[i]
self.merge.AddInput(image)
self.merge.AddLookupTable(ctf)
preview = self.merge.GetOutput()
elif len(merged) == 1 and scripting.preferRGB and not isMultiComponent:
Logging.info("Mapping the output to color",kw="dataunit")
data, ctf = merged[0]
if not self.maptocolor:
self.maptocolor = vtk.vtkImageMapToColors()
self.maptocolor.SetNumberOfThreads(1)
self.maptocolor.SetOutputFormatToRGB()
else:
self.maptocolor.RemoveAllInputs()
self.maptocolor.SetInput(data)
self.maptocolor.SetLookupTable(ctf)
preview = self.maptocolor.GetOutput()
scripting.wantAlphaChannel = self.oldAlphaStatus
if not showOrig and not self.doOrig:
self.origPreview = preview
elif showOrig:
self.doOrig = 1
return preview
