def __init__(self, *args, **kwargs):
super(_OpThresholdTwoLevels, self).__init__(*args, **kwargs)
self._opLowThresholder = OpPixelOperator(parent=self)
self._opLowThresholder.Input.connect(self.InputImage)
self._opHighThresholder = OpPixelOperator(parent=self)
self._opHighThresholder.Input.connect(self.InputImage)
self._opLowLabeler = OpLabelVolume(parent=self)
self._opLowLabeler.Method.setValue(_labeling_impl)
self._opLowLabeler.Input.connect(self._opLowThresholder.Output)
self._opHighLabeler = OpLabelVolume(parent=self)
self._opHighLabeler.Method.setValue(_labeling_impl)
self._opHighLabeler.Input.connect(self._opHighThresholder.Output)
self._opHighLabelSizeFilter = OpFilterLabels(parent=self)
self._opHighLabelSizeFilter.Input.connect(self._opHighLabeler.Output)
self._opHighLabelSizeFilter.MinLabelSize.connect(self.MinSize)
self._opHighLabelSizeFilter.MaxLabelSize.connect(self.MaxSize)
self._opHighLabelSizeFilter.BinaryOut.setValue(
False) # we do the binarization in opSelectLabels
# this way, we get to display pretty colors
self._opSelectLabels = OpSelectLabels(parent=self)
self._opSelectLabels.BigLabels.connect(self._opLowLabeler.Output)
self._opSelectLabels.SmallLabels.connect(
self._opHighLabelSizeFilter.Output)
# remove the remaining very large objects -
# they might still be present in case a big object
# was split into many small ones for the higher threshold
# and they got reconnected again at lower threshold
self._opFinalLabelSizeFilter = OpFilterLabels(parent=self)
self._opFinalLabelSizeFilter.Input.connect(self._opSelectLabels.Output)
self._opFinalLabelSizeFilter.MinLabelSize.connect(self.MinSize)
self._opFinalLabelSizeFilter.MaxLabelSize.connect(self.MaxSize)
self._opFinalLabelSizeFilter.BinaryOut.setValue(False)
self._opCache = OpCompressedCache(parent=self)
self._opCache.name = "_OpThresholdTwoLevels._opCache"
self._opCache.InputHdf5.connect(self.InputHdf5)
self._opCache.Input.connect(self._opFinalLabelSizeFilter.Output)
# Connect our own outputs
self.Output.connect(self._opFinalLabelSizeFilter.Output)
self.CachedOutput.connect(self._opCache.Output)
# Serialization outputs
self.CleanBlocks.connect(self._opCache.CleanBlocks)
self.OutputHdf5.connect(self._opCache.OutputHdf5)
#self.InputChannel.connect( self._opChannelSelector.Output )
# More debug outputs. These all go through their own caches
self._opBigRegionCache = OpCompressedCache(parent=self)
self._opBigRegionCache.name = "_OpThresholdTwoLevels._opBigRegionCache"
self._opBigRegionCache.Input.connect(self._opLowThresholder.Output)
self.BigRegions.connect(self._opBigRegionCache.Output)
self._opSmallRegionCache = OpCompressedCache(parent=self)
self._opSmallRegionCache.name = "_OpThresholdTwoLevels._opSmallRegionCache"
self._opSmallRegionCache.Input.connect(self._opHighThresholder.Output)
self.SmallRegions.connect(self._opSmallRegionCache.Output)
self._opFilteredSmallLabelsCache = OpCompressedCache(parent=self)
self._opFilteredSmallLabelsCache.name = "_OpThresholdTwoLevels._opFilteredSmallLabelsCache"
self._opFilteredSmallLabelsCache.Input.connect(
self._opHighLabelSizeFilter.Output)
self._opColorizeSmallLabels = OpColorizeLabels(parent=self)
self._opColorizeSmallLabels.Input.connect(
self._opFilteredSmallLabelsCache.Output)
self.FilteredSmallLabels.connect(self._opColorizeSmallLabels.Output)
def __init__(self, *args, **kwargs):
super(OpVigraWatershedViewer, self).__init__(*args, **kwargs)
self._seedThreshold = None
# Overview Schematic
# Example here uses input channels 0,2,5
# InputChannelIndexes=[0,2,5] ----
# \
# InputImage --> opChannelSlicer .Slices[0] ---\
# .Slices[1] ----> opAverage -------------------------------------------------> opWatershed --> opWatershedCache --> opColorizer --> GUI
# .Slices[2] ---/ \ /
# \ MinSeedSize /
# \ \ /
# SeedThresholdValue ----------> opThreshold --> opSeedLabeler --> opSeedFilter --> opSeedCache --> opSeedColorizer --> GUI
# Create operators
self.opChannelSlicer = OpMultiArraySlicer2(parent=self)
self.opAverage = OpMultiArrayMerger(parent=self)
self.opWatershed = OpVigraWatershed(parent=self)
self.opWatershedCache = OpSlicedBlockedArrayCache(parent=self)
self.opColorizer = OpColorizeLabels(parent=self)
self.opThreshold = OpPixelOperator(parent=self)
self.opSeedLabeler = OpVigraLabelVolume(parent=self)
self.opSeedFilter = OpFilterLabels(parent=self)
self.opSeedCache = OpSlicedBlockedArrayCache(parent=self)
self.opSeedColorizer = OpColorizeLabels(parent=self)
# Select specific input channels
self.opChannelSlicer.Input.connect(self.InputImage)
self.opChannelSlicer.SliceIndexes.connect(self.InputChannelIndexes)
self.opChannelSlicer.AxisFlag.setValue('c')
# Average selected channels
def average(arrays):
if len(arrays) == 0:
return 0
else:
return sum(arrays) / float(len(arrays))
self.opAverage.MergingFunction.setValue(average)
self.opAverage.Inputs.connect(self.opChannelSlicer.Slices)
# Threshold for seeds
self.opThreshold.Input.connect(self.opAverage.Output)
# Label seeds
self.opSeedLabeler.Input.connect(self.opThreshold.Output)
# Filter seeds
self.opSeedFilter.MinLabelSize.connect(self.MinSeedSize)
self.opSeedFilter.Input.connect(self.opSeedLabeler.Output)
# Cache seeds
self.opSeedCache.fixAtCurrent.connect(self.FreezeCache)
self.opSeedCache.Input.connect(self.opSeedFilter.Output)
# Color seeds for RBG display
self.opSeedColorizer.Input.connect(self.opSeedCache.Output)
self.opSeedColorizer.OverrideColors.setValue({0: (0, 0, 0, 0)})
# Compute watershed labels (possibly with seeds, see setupOutputs)
self.opWatershed.InputImage.connect(self.opAverage.Output)
self.opWatershed.PaddingWidth.connect(self.WatershedPadding)
# Cache the watershed output
self.opWatershedCache.fixAtCurrent.connect(self.FreezeCache)
self.opWatershedCache.Input.connect(self.opWatershed.Output)
# Colorize the watershed labels for RGB display
self.opColorizer.Input.connect(self.opWatershedCache.Output)
self.opColorizer.OverrideColors.connect(self.OverrideLabels)
# Connnect external outputs the operators that provide them
self.Seeds.connect(self.opSeedCache.Output)
self.ColoredPixels.connect(self.opColorizer.Output)
self.SelectedInputChannels.connect(self.opChannelSlicer.Slices)
self.SummedInput.connect(self.opAverage.Output)
self.ColoredSeeds.connect(self.opSeedColorizer.Output)