def setupLayers(self):
layers = []
op = self.topLevelOperatorView
ravelerLabelsSlot = op.RavelerLabels
if ravelerLabelsSlot.ready():
colortable = []
for _ in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
ravelerLabelLayer = ColortableLayer(LazyflowSource(ravelerLabelsSlot), colortable, direct=True)
ravelerLabelLayer.name = "Raveler Labels"
ravelerLabelLayer.visible = False
ravelerLabelLayer.opacity = 0.4
layers.append(ravelerLabelLayer)
supervoxelsSlot = op.Supervoxels
if supervoxelsSlot.ready():
colortable = []
for i in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
supervoxelsLayer = ColortableLayer(LazyflowSource(supervoxelsSlot), colortable)
supervoxelsLayer.name = "Input Supervoxels"
supervoxelsLayer.visible = False
supervoxelsLayer.opacity = 1.0
layers.append(supervoxelsLayer)
def addFragmentSegmentationLayers(mslot, name):
if mslot.ready():
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
colortable = []
for i in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
colortable[0] = QColor(0,0,0,0).rgba()
fragSegLayer = ColortableLayer(LazyflowSource(slot), colortable, direct=True)
fragSegLayer.name = "{} #{} ({})".format( name, index, raveler_label )
fragSegLayer.visible = False
fragSegLayer.opacity = 1.0
layers.append(fragSegLayer)
addFragmentSegmentationLayers( op.MaskedSupervoxels, "Masked Supervoxels" )
addFragmentSegmentationLayers( op.FilteredMaskedSupervoxels, "Filtered Masked Supervoxels" )
addFragmentSegmentationLayers( op.HoleFilledSupervoxels, "Hole Filled Supervoxels" )
addFragmentSegmentationLayers( op.RelabeledSupervoxels, "Relabeled Supervoxels" )
mslot = op.EditedRavelerBodies
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
# 0=Black, 1=Transparent
colortable = [QColor(0, 0, 0).rgba(), QColor(0, 0, 0, 0).rgba()]
bodyMaskLayer = ColortableLayer(LazyflowSource(slot), colortable, direct=True)
bodyMaskLayer.name = "Raveler Body Mask #{} ({})".format( index, raveler_label )
bodyMaskLayer.visible = False
bodyMaskLayer.opacity = 1.0
layers.append(bodyMaskLayer)
finalSegSlot = op.FinalSupervoxels
if finalSegSlot.ready():
colortable = []
for _ in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
finalLayer = ColortableLayer(LazyflowSource(finalSegSlot), colortable)
finalLayer.name = "Final Supervoxels"
finalLayer.visible = False
finalLayer.opacity = 0.4
layers.append(finalLayer)
inputSlot = op.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot) )
layer.name = "WS Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#raw data
rawSlot = self.topLevelOperatorView.RawData
if rawSlot.ready():
raw5D = self.topLevelOperatorView.RawData.value
layer = GrayscaleLayer(ArraySource(raw5D), direct=True)
#layer = GrayscaleLayer( LazyflowSource(rawSlot) )
layer.name = "raw"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
return layers
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
ravelerLabelsSlot = op.RavelerLabels
if ravelerLabelsSlot.ready():
colortable = []
for _ in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
ravelerLabelLayer = ColortableLayer(LazyflowSource(ravelerLabelsSlot), colortable, direct=True)
ravelerLabelLayer.name = "Raveler Labels"
ravelerLabelLayer.visible = False
ravelerLabelLayer.opacity = 0.4
layers.append(ravelerLabelLayer)
def addFragmentSegmentationLayers(mslot, name):
if mslot.ready():
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
colortable = map(QColor.rgba, self._fragmentColors)
fragSegLayer = ColortableLayer(LazyflowSource(slot), colortable, direct=True)
fragSegLayer.name = "{} #{} ({})".format( name, index, raveler_label )
fragSegLayer.visible = False
fragSegLayer.opacity = 1.0
layers.append(fragSegLayer)
addFragmentSegmentationLayers( op.FragmentedBodies, "Saved Fragments" )
addFragmentSegmentationLayers( op.RelabeledFragments, "Relabeled Fragments" )
addFragmentSegmentationLayers( op.FilteredFragmentedBodies, "CC-Filtered Fragments" )
addFragmentSegmentationLayers( op.WatershedFilledBodies, "Watershed-filled Fragments" )
mslot = op.EditedRavelerBodies
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
# 0=Black, 1=Transparent
colortable = [QColor(0, 0, 0).rgba(), QColor(0, 0, 0, 0).rgba()]
bodyMaskLayer = ColortableLayer(LazyflowSource(slot), colortable, direct=True)
bodyMaskLayer.name = "Raveler Body Mask #{} ({})".format( index, raveler_label )
bodyMaskLayer.visible = False
bodyMaskLayer.opacity = 1.0
layers.append(bodyMaskLayer)
finalSegSlot = op.FinalSegmentation
if finalSegSlot.ready():
colortable = []
for _ in range(256):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
colortable.append(QColor(r,g,b).rgba())
finalLayer = ColortableLayer(LazyflowSource(finalSegSlot), colortable, direct=True)
finalLayer.name = "Final Segmentation"
finalLayer.visible = False
finalLayer.opacity = 0.4
layers.append(finalLayer)
inputSlot = op.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot) )
layer.name = "WS Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#raw data
rawSlot = self.topLevelOperatorView.RawData
rawLayer = None
if rawSlot.ready():
raw5D = self.topLevelOperatorView.RawData.value
rawLayer = GrayscaleLayer(ArraySource(raw5D), direct=True)
#rawLayer = GrayscaleLayer( LazyflowSource(rawSlot) )
rawLayer.name = "raw"
rawLayer.visible = True
rawLayer.opacity = 1.0
rawLayer.shortcutRegistration = ( "g", ShortcutManager.ActionInfo(
"Postprocessing",
"Raw Data to Top",
"Raw Data to Top",
partial(self._toggleRawDataPosition, rawLayer),
self.viewerControlWidget(),
rawLayer ) )
layers.append(rawLayer)
return layers
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
ravelerLabelsSlot = op.RavelerLabels
if ravelerLabelsSlot.ready():
colortable = []
for _ in range(256):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
ravelerLabelLayer = ColortableLayer(
LazyflowSource(ravelerLabelsSlot), colortable, direct=True)
ravelerLabelLayer.name = "Raveler Labels"
ravelerLabelLayer.visible = False
ravelerLabelLayer.opacity = 0.4
layers.append(ravelerLabelLayer)
supervoxelsSlot = op.Supervoxels
if supervoxelsSlot.ready():
colortable = []
for i in range(256):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
supervoxelsLayer = ColortableLayer(LazyflowSource(supervoxelsSlot),
colortable)
supervoxelsLayer.name = "Input Supervoxels"
supervoxelsLayer.visible = False
supervoxelsLayer.opacity = 1.0
layers.append(supervoxelsLayer)
def addFragmentSegmentationLayers(mslot, name):
if mslot.ready():
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
colortable = []
for i in range(256):
r, g, b = numpy.random.randint(
0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
colortable[0] = QColor(0, 0, 0, 0).rgba()
fragSegLayer = ColortableLayer(LazyflowSource(slot),
colortable,
direct=True)
fragSegLayer.name = "{} #{} ({})".format(
name, index, raveler_label)
fragSegLayer.visible = False
fragSegLayer.opacity = 1.0
layers.append(fragSegLayer)
addFragmentSegmentationLayers(op.MaskedSupervoxels,
"Masked Supervoxels")
addFragmentSegmentationLayers(op.FilteredMaskedSupervoxels,
"Filtered Masked Supervoxels")
addFragmentSegmentationLayers(op.HoleFilledSupervoxels,
"Hole Filled Supervoxels")
addFragmentSegmentationLayers(op.RelabeledSupervoxels,
"Relabeled Supervoxels")
mslot = op.EditedRavelerBodies
for index, slot in enumerate(mslot):
if slot.ready():
raveler_label = slot.meta.selected_label
# 0=Black, 1=Transparent
colortable = [
QColor(0, 0, 0).rgba(),
QColor(0, 0, 0, 0).rgba()
]
bodyMaskLayer = ColortableLayer(LazyflowSource(slot),
colortable,
direct=True)
bodyMaskLayer.name = "Raveler Body Mask #{} ({})".format(
index, raveler_label)
bodyMaskLayer.visible = False
bodyMaskLayer.opacity = 1.0
layers.append(bodyMaskLayer)
finalSegSlot = op.FinalSupervoxels
if finalSegSlot.ready():
colortable = []
for _ in range(256):
r, g, b = numpy.random.randint(0, 255), numpy.random.randint(
0, 255), numpy.random.randint(0, 255)
colortable.append(QColor(r, g, b).rgba())
finalLayer = ColortableLayer(LazyflowSource(finalSegSlot),
colortable)
finalLayer.name = "Final Supervoxels"
finalLayer.visible = False
finalLayer.opacity = 0.4
layers.append(finalLayer)
inputSlot = op.InputData
if inputSlot.ready():
layer = GrayscaleLayer(LazyflowSource(inputSlot))
layer.name = "WS Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#raw data
rawSlot = self.topLevelOperatorView.RawData
if rawSlot.ready():
raw5D = self.topLevelOperatorView.RawData.value
layer = GrayscaleLayer(ArraySource(raw5D), direct=True)
#layer = GrayscaleLayer( LazyflowSource(rawSlot) )
layer.name = "raw"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
return layers
