def setupLayers(self):
layers = []
op = self.__topLevelOperatorView
mc_edge_layer = self.create_multicut_edge_layer()
if mc_edge_layer:
layers.append(mc_edge_layer)
# Superpixels -- Edge Probabilities
# We use the RAG's superpixels, which may have different IDs
self.superpixel_edge_layer = None
if op.Superpixels.ready() and op.EdgeProbabilitiesDict.ready():
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels))
layer.name = "Superpixel Edge Probabilities"
layer.visible = True
layer.opacity = 1.0
self.superpixel_edge_layer = layer
self.__update_probability_edges() # Initialize
layers.append(layer)
del layer
# Superpixels -- Edges
if op.Superpixels.ready():
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.yellow)
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels),
default_pen)
layer.name = "Superpixel Edges"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
mc_seg_layer = self.create_multicut_segmentation_layer()
if mc_seg_layer:
layers.append(mc_seg_layer)
# Superpixels
if op.Superpixels.ready():
layer = self.createStandardLayerFromSlot(op.Superpixels)
layer.name = "Superpixels"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot(op.RawData)
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
del layer
return layers
def setupLayers(self):
layers = []
op = self.__topLevelOperatorView
mc_edge_layer = self.create_multicut_edge_layer()
if mc_edge_layer:
layers.append(mc_edge_layer)
# Superpixels -- Edge Probabilities
# We use the RAG's superpixels, which may have different IDs
self.superpixel_edge_layer = None
if op.Superpixels.ready() and op.EdgeProbabilitiesDict.ready():
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels))
layer.name = "Superpixel Edge Probabilities"
layer.visible = True
layer.opacity = 1.0
self.superpixel_edge_layer = layer
self.__update_probability_edges() # Initialize
layers.append(layer)
del layer
# Superpixels -- Edges
if op.Superpixels.ready():
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.yellow)
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels), default_pen)
layer.name = "Superpixel Edges"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
mc_seg_layer = self.create_multicut_segmentation_layer()
if mc_seg_layer:
layers.append(mc_seg_layer)
# Superpixels
if op.Superpixels.ready():
layer = self.createStandardLayerFromSlot(op.Superpixels)
layer.name = "Superpixels"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot(op.RawData)
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
del layer
return layers
def create_multicut_edge_layer(self):
ActionInfo = ShortcutManager.ActionInfo
op = self.__topLevelOperatorView
if not op.Output.ready():
return None
# Final segmentation -- Edges
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.blue)
layer = SegmentationEdgesLayer(LazyflowSource(op.Output), default_pen)
layer.name = "Multicut Edges"
layer.visible = False # Off by default...
layer.opacity = 1.0
layer.shortcutRegistration = (
"m",
ActionInfo(
"Multicut",
"MulticutEdgesVisibility",
"Show/Hide Multicut Edges",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
return layer
def create_multicut_edge_layer(self):
ActionInfo = ShortcutManager.ActionInfo
op = self.__topLevelOperatorView
if not op.Output.ready():
return None
# Final segmentation -- Edges
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.blue)
layer = SegmentationEdgesLayer(createDataSource(op.Output),
default_pen)
layer.name = "Multicut Edges"
layer.visible = False # Off by default...
layer.opacity = 1.0
layer.shortcutRegistration = (
"m",
ActionInfo(
"Multicut",
"MulticutEdgesVisibility",
"Show/Hide Multicut Edges",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
return layer
def create_multicut_disagreement_layer(self):
ActionInfo = ShortcutManager.ActionInfo
op = self.__topLevelOperatorView
if not op.Output.ready():
return None
# Final segmentation -- Edges
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.transparent)
layer = SegmentationEdgesLayer(createDataSource(op.Superpixels),
default_pen)
layer.name = "Multicut Disagreements"
layer.visible = False # Off by default...
layer.opacity = 1.0
self.disagreement_layer = layer
self.__update_disagreement_edges() # Initialize
layer.shortcutRegistration = (
"d",
ActionInfo(
"Multicut",
"MulticutDisagrementVisibility",
"Show/Hide Multicut Disagreement Edges",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
return layer
def create_multicut_disagreement_layer(self):
ActionInfo = ShortcutManager.ActionInfo
op = self.__topLevelOperatorView
if not op.Output.ready():
return None
# Final segmentation -- Edges
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.transparent)
layer = SegmentationEdgesLayer( LazyflowSource(op.Superpixels), default_pen )
layer.name = "Multicut Disagreements"
layer.visible = False # Off by default...
layer.opacity = 1.0
self.disagreement_layer = layer
self.__update_disagreement_edges() # Initialize
layer.shortcutRegistration = ( "d",
ActionInfo( "Multicut",
"MulticutDisagrementVisibility",
"Show/Hide Multicut Disagreement Edges",
layer.toggleVisible,
self.viewerControlWidget(),
layer ) )
return layer
def setupLayers(self):
layers = []
op = self.__topLevelOperatorView
mc_disagreement_layer = self.create_multicut_disagreement_layer()
if mc_disagreement_layer:
layers.append(mc_disagreement_layer)
mc_edge_layer = self.create_multicut_edge_layer()
if mc_edge_layer:
layers.append(mc_edge_layer)
# Superpixels -- Edge Probabilities
# We use the RAG's superpixels, which may have different IDs
self.superpixel_edge_layer = None
if op.Superpixels.ready() and op.EdgeProbabilitiesDict.ready():
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels))
layer.name = "Superpixel Edge Probabilities"
layer.visible = True
layer.opacity = 1.0
self.superpixel_edge_layer = layer
self.__update_probability_edges() # Initialize
layers.append(layer)
del layer
# Superpixels -- Edges
if op.Superpixels.ready():
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.yellow)
layer = SegmentationEdgesLayer(LazyflowSource(op.Superpixels),
default_pen)
layer.name = "Superpixel Edges"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
mc_seg_layer = self.create_multicut_segmentation_layer()
if mc_seg_layer:
layers.append(mc_seg_layer)
# Superpixels
if op.Superpixels.ready():
layer = self.createStandardLayerFromSlot(op.Superpixels)
layer.name = "Superpixels"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot(op.RawData)
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
layer.shortcutRegistration = ("i",
ActionInfo(
"Multicut"
"Hide all but Raw",
"Hide all but Raw",
partial(self.toggle_show_raw,
"Raw Data"),
self.viewerControlWidget(),
layer))
del layer
return layers
def setupLayers(self):
layers = []
op = self.__topLevelOperatorView
mc_disagreement_layer = self.create_multicut_disagreement_layer()
if mc_disagreement_layer:
layers.append(mc_disagreement_layer)
mc_edge_layer = self.create_multicut_edge_layer()
if mc_edge_layer:
layers.append(mc_edge_layer)
# Superpixels -- Edge Probabilities
# We use the RAG's superpixels, which may have different IDs
self.superpixel_edge_layer = None
if op.Superpixels.ready() and op.EdgeProbabilitiesDict.ready():
layer = SegmentationEdgesLayer( LazyflowSource(op.Superpixels) )
layer.name = "Superpixel Edge Probabilities"
layer.visible = True
layer.opacity = 1.0
self.superpixel_edge_layer = layer
self.__update_probability_edges() # Initialize
layers.append(layer)
del layer
# Superpixels -- Edges
if op.Superpixels.ready():
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.yellow)
layer = SegmentationEdgesLayer( LazyflowSource(op.Superpixels), default_pen )
layer.name = "Superpixel Edges"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
mc_seg_layer = self.create_multicut_segmentation_layer()
if mc_seg_layer:
layers.append(mc_seg_layer)
# Superpixels
if op.Superpixels.ready():
layer = self.createStandardLayerFromSlot( op.Superpixels )
layer.name = "Superpixels"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot( op.RawData )
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
layer.shortcutRegistration = ( "i", ActionInfo( "Multicut"
"Hide all but Raw",
"Hide all but Raw",
partial(self.toggle_show_raw, "Raw Data"),
self.viewerControlWidget(),
layer ) )
del layer
return layers
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
ActionInfo = ShortcutManager.ActionInfo
superpixels_ready = op.Superpixels.ready()
with_training = op.TrainRandomForest.value
# Superpixels -- Edge Probabilities
if superpixels_ready and op.EdgeProbabilitiesDict.ready(
) and with_training:
layer = SegmentationEdgesLayer(createDataSource(op.Superpixels),
isHoverable=True)
layer.name = "Edge Probabilities" # Name is hard-coded in multiple places: grep before changing.
layer.visible = False
layer.opacity = 1.0
self.update_probability_edges() # Initialize
layer.contexts.append(
self.create_prefetch_menu("Edge Probabilities"))
layer.shortcutRegistration = (
"p",
ActionInfo(
"Edge Training Layers",
"EdgePredictionsVisibility",
"Show/Hide Edge Predictions",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
layers.append(layer)
del layer
# Superpixels -- Edge Labels
if superpixels_ready and op.EdgeLabelsDict.ready() and with_training:
edge_labels = op.EdgeLabelsDict.value
layer = LabelableSegmentationEdgesLayer(
createDataSource(op.Superpixels), self.edge_label_pen_table,
edge_labels)
layer.name = "Edge Labels"
layer.visible = True
layer.opacity = 1.0
self.update_labeled_edges() # Initialize
layer.labelsChanged.connect(self._handle_edge_label_clicked)
layer.contexts.append(self.create_prefetch_menu("Edge Labels"))
layer.shortcutRegistration = (
"0",
ActionInfo(
"Edge Training Layers",
"LabelVisibility",
"Show/Hide Edge Labels",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
layers.append(layer)
del layer
# Superpixels -- Edges
if superpixels_ready:
layer = SegmentationEdgesLayer(createDataSource(op.Superpixels),
default_pen=self.DEFAULT_PEN,
isHoverable=with_training)
layer.name = "Superpixel Edges"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
del layer
# Naive Segmentation
if op.NaiveSegmentation.ready():
layer = self.createStandardLayerFromSlot(op.NaiveSegmentation)
layer.name = "Naive Segmentation"
layer.visible = False
layer.opacity = 0.5
layer.shortcutRegistration = (
"n",
ActionInfo(
"Edge Training Layers",
"NaiveSegmentationVisibility",
"Show/Hide Naive Segmentation (shows output if classifier output is respected verbatim)",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
layers.append(layer)
del layer
# Groundtruth
if op.GroundtruthSegmentation.ready():
layer = self.createStandardLayerFromSlot(
op.GroundtruthSegmentation)
layer.name = "Groundtruth"
layer.visible = False
layer.opacity = 0.5
layer.shortcutRegistration = (
"g",
ActionInfo(
"Edge Training Layers",
"GroundtruthVisibility",
"Show/Hide Groundtruth",
layer.toggleVisible,
self.viewerControlWidget(),
layer,
),
)
layers.append(layer)
del layer
# Voxel data
if op.VoxelData.ready():
layer = self._create_grayscale_layer_from_slot(
op.VoxelData,
op.VoxelData.meta.getTaggedShape()["c"])
layer.name = "Voxel Data"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot(op.RawData)
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
layer.shortcutRegistration = (
"i",
ActionInfo(
"Edge Training Layers",
"Hide all but Raw",
"Hide all but Raw",
partial(self.toggle_show_raw, "Raw Data"),
self.viewerControlWidget(),
layer,
),
)
del layer
return layers
def setupLayers(self):
layers = []
op = self.__topLevelOperatorView
mc_disagreement_layer = self.create_multicut_disagreement_layer()
if mc_disagreement_layer:
layers.append(mc_disagreement_layer)
mc_edge_layer = self.create_multicut_edge_layer()
if mc_edge_layer:
layers.append(mc_edge_layer)
# Superpixels -- Edge Probabilities
# We use the RAG's superpixels, which may have different IDs
self.superpixel_edge_layer = None
if op.Superpixels.ready() and op.EdgeProbabilitiesDict.ready():
layer = SegmentationEdgesLayer( LazyflowSource(op.Superpixels) )
layer.name = "Superpixel Edge Probabilities"
layer.visible = True
layer.opacity = 1.0
self.superpixel_edge_layer = layer
self.__update_probability_edges() # Initialize
layers.append(layer)
del layer
# Superpixels -- Edges
if op.Superpixels.ready():
default_pen = QPen(SegmentationEdgesLayer.DEFAULT_PEN)
default_pen.setColor(Qt.yellow)
layer = SegmentationEdgesLayer( LazyflowSource(op.Superpixels), default_pen )
layer.name = "Superpixel Edges"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
mc_seg_layer = self.create_multicut_segmentation_layer()
if mc_seg_layer:
layers.append(mc_seg_layer)
# Superpixels
if op.Superpixels.ready():
layer = self.createStandardLayerFromSlot( op.Superpixels )
layer.name = "Superpixels"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.RawData.ready():
layer = self.createStandardLayerFromSlot( op.RawData )
layer.name = "Raw Data"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
raw_layer = layer
def toggleTopToBottom():
index = self.layerstack.layerIndex( raw_layer )
self.layerstack.selectRow( index )
if index == 0:
self.layerstack.moveSelectedToBottom()
else:
self.layerstack.moveSelectedToTop()
layer.shortcutRegistration = ( "i", ActionInfo( "Multicut"
"Bring Input To Top/Bottom",
"Bring Input To Top/Bottom",
toggleTopToBottom,
self.viewerControlWidget(),
raw_layer ) )
del layer
return layers