def createLabelLayer(self, direct=False):
"""
Return a colortable layer that displays the label slot data, along with its associated label source.
direct: whether this layer is drawn synchronously by volumina
"""
labelOutput = self._labelingSlots.labelOutput
if not labelOutput.ready():
return (None, None)
else:
# Add the layer to draw the labels, but don't add any labels
labelsrc = LazyflowSinkSource(self._labelingSlots.labelOutput,
self._labelingSlots.labelInput)
labellayer = ColortableLayer(labelsrc,
colorTable=self._colorTable16,
direct=direct)
labellayer.name = "Labels"
labellayer.ref_object = None
labellayer.contexts.append(
QAction("Import...",
None,
triggered=partial(import_labeling_layer, labellayer,
self._labelingSlots, self)))
labellayer.shortcutRegistration = ("0",
ShortcutManager.ActionInfo(
"Labeling",
"LabelVisibility",
"Show/Hide Labels",
labellayer.toggleVisible,
self.viewerControlWidget(),
labellayer))
return labellayer, labelsrc
def setupLayers(self):
"""
Sets up the label layer for display by our base class (LayerViewerGui).
If our subclass overrides this function to add his own layers,
he **must** call this function explicitly.
"""
layers = []
# Labels
labellayer, labelsrc = self.createLabelLayer()
if labellayer is not None:
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
# Side effect 1: We want to guarantee that the label list
# is up-to-date before our subclass adds his layers
self._updateLabelList()
# Raw Input Layer
if self._rawInputSlot is not None and self._rawInputSlot.ready():
layer = self.createStandardLayerFromSlot(self._rawInputSlot)
layer.name = "Raw Input"
layer.visible = True
layer.opacity = 1.0
# the flag window_leveling is used to determine if the contrast
# of the layer is adjustable
if isinstance(layer, GrayscaleLayer):
layer.window_leveling = True
else:
layer.window_leveling = False
layers.append(layer)
# The thresholding button can only be used if the data is displayed as grayscale.
if layer.window_leveling:
self.labelingDrawerUi.thresToolButton.show()
else:
self.labelingDrawerUi.thresToolButton.hide()
def toggleTopToBottom():
index = self.layerstack.layerIndex(layer)
self.layerstack.selectRow(index)
if index == 0:
self.layerstack.moveSelectedToBottom()
else:
self.layerstack.moveSelectedToTop()
layer.shortcutRegistration = ("i",
ShortcutManager.ActionInfo(
"Prediction Layers",
"Bring Input To Top/Bottom",
"Bring Input To Top/Bottom",
toggleTopToBottom,
self.viewerControlWidget(),
layer))
return layers
def setupLayers(self):
"""
Sets up the label layer for display by our base class (LayerViewerGui).
If our subclass overrides this function to add his own layers,
he **must** call this function explicitly.
"""
layers = []
# Labels
labellayer, labelsrc = self.createLabelLayer()
if labellayer is not None:
layers.append(labellayer)
# Side effect 1: We want to guarantee that the label list
# is up-to-date before our subclass adds his layers
self._updateLabelList()
# Raw Input Layer
if self._rawInputSlot is not None and self._rawInputSlot.ready():
layer = self.createStandardLayerFromSlot(self._rawInputSlot,
name="Raw Input")
layers.append(layer)
if isinstance(layer, GrayscaleLayer):
self.labelingDrawerUi.thresToolButton.show()
else:
self.labelingDrawerUi.thresToolButton.hide()
def toggleTopToBottom():
index = self.layerstack.layerIndex(layer)
self.layerstack.selectRow(index)
if index == 0:
self.layerstack.moveSelectedToBottom()
else:
self.layerstack.moveSelectedToTop()
layer.shortcutRegistration = (
"i",
ShortcutManager.ActionInfo(
"Prediction Layers",
"Bring Input To Top/Bottom",
"Bring Input To Top/Bottom",
toggleTopToBottom,
self.viewerControlWidget(),
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
