def setupLayers(self):
layers = []
fromDiskSlot = self.topLevelOperatorView.ImageOnDisk
if fromDiskSlot.ready():
exportLayer = ColortableLayer(createDataSource(fromDiskSlot),
colorTable=self.ct)
exportLayer.name = "Selected Output - Exported"
exportLayer.visible = True
layers.append(exportLayer)
previewSlot = self.topLevelOperatorView.ImageToExport
if previewSlot.ready():
previewLayer = ColortableLayer(createDataSource(previewSlot),
colorTable=self.ct)
previewLayer.name = "Selected Output - Preview"
previewLayer.visible = False
layers.append(previewLayer)
rawSlot = self.topLevelOperatorView.RawData
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot(rawSlot)
rawLayer.name = "Raw Data"
rawLayer.opacity = 1.0
layers.append(rawLayer)
return layers
def setupLayers(self):
layers = []
predictionSlot = self.topLevelOperatorView.PredictionImage
if predictionSlot.ready():
predictLayer = ColortableLayer(createDataSource(predictionSlot),
colorTable=self._colorTable16)
predictLayer.name = "Blockwise prediction"
predictLayer.visible = False
layers.append(predictLayer)
binarySlot = self.topLevelOperatorView.BinaryImage
if binarySlot.ready():
ct_binary = [
QColor(0, 0, 0, 0).rgba(),
QColor(255, 255, 255, 255).rgba()
]
binaryLayer = ColortableLayer(createDataSource(binarySlot),
ct_binary)
binaryLayer.name = "Binary Image"
layers.append(binaryLayer)
rawSlot = self.topLevelOperatorView.RawImage
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot(rawSlot)
rawLayer.name = "Raw data"
layers.append(rawLayer)
return layers
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
binct = [QColor(Qt.black), QColor(Qt.white)]
# binct[0] = 0
ct = create_default_16bit()
# associate label 0 with black/transparent?
ct[0] = 0
# Show the cached output, since it goes through a blocked cache
if op.CachedOutput.ready():
outputSrc = createDataSource(op.CachedOutput)
outputLayer = ColortableLayer(outputSrc, ct)
outputLayer.name = "Connected Components"
outputLayer.visible = False
outputLayer.opacity = 1.0
outputLayer.setToolTip("Results of connected component analysis")
layers.append(outputLayer)
if op.Input.ready():
rawSrc = createDataSource(op.Input)
rawLayer = ColortableLayer(outputSrc, binct)
# rawLayer = self.createStandardLayerFromSlot(op.Input)
rawLayer.name = "Raw data"
rawLayer.visible = True
rawLayer.opacity = 1.0
layers.append(rawLayer)
return layers
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
# Superpixels
if op.Superpixels.ready():
layer = ColortableLayer( createDataSource(op.Superpixels), self._sp_colortable )
layer.colortableIsRandom = True
layer.name = "Superpixels"
layer.visible = True
layer.opacity = 0.5
layers.append(layer)
del layer
# Debug layers
if op.debug_results:
for name, compressed_array in list(op.debug_results.items()):
axiskeys = op.Superpixels.meta.getAxisKeys()[:-1] # debug images don't have a channel axis
permutation = [axiskeys.index(key) if key in axiskeys else None for key in 'txyzc']
arraysource = ArraySource( TransposedView(compressed_array, permutation) )
if compressed_array.dtype == np.uint32:
layer = ColortableLayer(arraysource, self._sp_colortable)
else:
layer = GrayscaleLayer(arraysource)
# TODO: Normalize? Maybe the drange should be included with the debug image.
layer.name = name
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
del layer
# Threshold
if op.ThresholdedInput.ready():
layer = ColortableLayer( createDataSource(op.ThresholdedInput), self._threshold_colortable )
layer.name = "Thresholded Input"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
del layer
# Raw Data (grayscale)
if op.Input.ready():
layer = self._create_grayscale_layer_from_slot( op.Input, op.Input.meta.getTaggedShape()['c'] )
layer.name = "Probability Map"
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)
del layer
return layers
def _create_rgba_layer_from_slot(cls, slot, numChannels, lastChannelIsAlpha):
bindex = aindex = None
rindex, gindex = 0,1
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
bindex = 2
if lastChannelIsAlpha:
aindex = numChannels-1
if numChannels>=2:
gindex = 1
if numChannels>=3:
bindex = 2
if numChannels>=4:
aindex = numChannels-1
redSource = None
if rindex is not None:
redProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
redProvider.Input.connect(slot)
redProvider.Index.setValue( rindex )
redSource = createDataSource( redProvider.Output )
redSource.additional_owned_ops.append( redProvider )
greenSource = None
if gindex is not None:
greenProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue( gindex )
greenSource = createDataSource( greenProvider.Output )
greenSource.additional_owned_ops.append( greenProvider )
blueSource = None
if bindex is not None:
blueProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue( bindex )
blueSource = createDataSource( blueProvider.Output )
blueSource.additional_owned_ops.append( blueProvider )
alphaSource = None
if aindex is not None:
alphaProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue( aindex )
alphaSource = createDataSource( alphaProvider.Output )
alphaSource.additional_owned_ops.append( alphaProvider )
layer = RGBALayer( red=redSource, green=greenSource, blue=blueSource, alpha=alphaSource)
normalize = cls._should_normalize_display(slot)
for i in range(4):
if [redSource,greenSource,blueSource,alphaSource][i]:
layer.set_range(i, slot.meta.drange)
layer.set_normalize(i, normalize)
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 _initPredictionLayers(self, predictionSlot):
layers = []
opLane = self.topLevelOperatorView
# Use a slicer to provide a separate slot for each channel layer
opSlicer = OpMultiArraySlicer2(parent=opLane.viewed_operator().parent)
opSlicer.Input.connect(predictionSlot)
opSlicer.AxisFlag.setValue("c")
for channel, channelSlot in enumerate(opSlicer.Slices):
if channelSlot.ready():
drange = channelSlot.meta.drange or (0.0, 1.0)
predictsrc = createDataSource(channelSlot)
predictLayer = AlphaModulatedLayer(
predictsrc,
tintColor=QColor.fromRgba(self._colorTable16[channel + 1]),
# FIXME: This is weird. Why are range and normalize both set to the same thing?
range=drange,
normalize=drange,
)
predictLayer.opacity = 1.0
predictLayer.visible = True
predictLayer.name = "Probability Channel #{}".format(channel +
1)
layers.append(predictLayer)
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(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 _add_color_layer(self, data, name=None, visible=False):
'''
adds a color layer to the layerstack
:param data: numpy array (2D, c) containing the data (c is color)
:param name: name of layer
:param visible: bool determining whether this layer should be set to visible
:return:
'''
assert len(data.shape) == 3
data_sources = []
for i in range(data.shape[2]):
a, data_shape = createDataSource(data[:,:,i], True)
data_sources.append(a)
self.editor.dataShape = list(data_shape)
if data.shape[2] == 2:
new_layer = RGBALayer(data_sources[0], data_sources[1])
elif data.shape[2] == 3:
new_layer = RGBALayer(data_sources[0], data_sources[1], data_sources[2])
elif data.shape[2] == 4:
new_layer = RGBALayer(data_sources[0], data_sources[1], data_sources[2], data_sources[3])
else:
raise Exception("Unexpected number of colors")
new_layer.visible = visible
if name is not None:
new_layer.name = name
self.layerstack.append(new_layer)
def setupLayers(self):
layers = [self.createStandardLayerFromSlot(self.topLevelOperatorView.Input)]
layers[0].opacity = 1.0
superVoxelBoundarySlot = self.topLevelOperatorView.BoundariesOutput
if superVoxelBoundarySlot.ready():
layer = AlphaModulatedLayer(
LazyflowSource(superVoxelBoundarySlot),
tintColor=QColor(Qt.blue),
range=(0.0, 1.0),
normalize=(0.0, 1.0),
)
layer.name = "Supervoxel Boundaries"
layer.visible = True
layer.opacity = 1.0
layers.insert(0, layer)
superVoxelSlot = self.topLevelOperatorView.Output
if superVoxelSlot.ready():
colortable = generateRandomColors(M=256, clamp={"v": 1.0, "s": 0.5}, zeroIsTransparent=False)
layer = ColortableLayer(createDataSource(superVoxelSlot), colortable)
layer.colortableIsRandom = True
layer.name = "SLIC Superpixels"
layer.visible = True
layer.opacity = 1.0
layers.insert(0, layer)
return layers
def _onReady(self, slot):
if slot is self.topLevelOperatorView.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = createDataSource(
self.topLevelOperatorView.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw data"
self.layerstack.append(layerraw)
def _create_grayscale_layer_from_slot(cls, slot, n_channels):
# FIXME: move all of this stuff into the class constructor. Same for all
# _create_*layer_from_slot methods.
source = createDataSource(slot)
layer = GrayscaleLayer(source, window_leveling=True)
layer.numberOfChannels = n_channels
layer.set_normalize(0, (slot.meta.normalizeDisplay and slot.meta.drange) or None)
return layer
def _create_binary_mask_layer_from_slot(cls, slot):
# 0: black, 1-255: transparent
# This works perfectly for uint8.
# For uint32, etc., values of 256,512, etc. will be appear 'off'.
# But why would you use uint32 for a binary mask anyway?
colortable = [QColor(0, 0, 0, 255).rgba()]
colortable += 255 * [QColor(0, 0, 0, 0).rgba()]
layer = ColortableLayer(createDataSource(slot), colortable)
return layer
def setupLayers(self):
layers = []
opLane = self.topLevelOperatorView
selection_names = opLane.SelectionNames.value
selection = selection_names[opLane.InputSelection.value]
# This code is written to handle the specific output cases we know about.
# If those change, update this function!
assert selection in [
"Object Predictions",
"Object Probabilities",
"Blockwise Object Predictions",
"Blockwise Object Probabilities",
"Object Identities",
"Pixel Probabilities",
]
if selection in ("Object Predictions", "Blockwise Object Predictions"):
previewSlot = self.topLevelOperatorView.ImageToExport
if previewSlot.ready():
previewLayer = ColortableLayer(createDataSource(previewSlot),
colorTable=self._colorTable16)
previewLayer.name = "Prediction - Preview"
previewLayer.visible = False
layers.append(previewLayer)
elif selection in ("Object Probabilities",
"Blockwise Object Probabilities"):
previewLayers = self._initPredictionLayers(opLane.ImageToExport)
for layer in previewLayers:
layer.visible = False
layer.name = layer.name + "- Preview"
layers += previewLayers
elif selection == "Pixel Probabilities":
previewLayers = self._initPredictionLayers(opLane.ImageToExport)
for layer in previewLayers:
layer.visible = False
layer.name = layer.name + "- Preview"
layers += previewLayers
elif selection == "Object Identities":
previewSlot = self.topLevelOperatorView.ImageToExport
layer = self._initColortableLayer(previewSlot)
layers.append(layer)
else:
assert False, "Unknown selection."
rawSlot = self.topLevelOperatorView.RawData
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot(rawSlot)
rawLayer.name = "Raw Data"
rawLayer.opacity = 1.0
layers.append(rawLayer)
return layers
def setupLayers(self):
layers = []
opLane = self.topLevelOperatorView
# Supervoxels
watershedSlot = opLane.WatershedImage
if watershedSlot.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())
watershedLayer = ColortableLayer(createDataSource(watershedSlot),
colortable)
watershedLayer.name = "Watershed"
watershedLayer.visible = False
watershedLayer.opacity = 0.5
watershedLayer.colortableIsRandom = True
layers.append(watershedLayer)
""" FIXME: disabled for 0.6 release
wsSourceSlot = opLane.WatershedSourceImage
if wsSourceSlot.ready():
wsSourceLayer = self.createStandardLayerFromSlot( wsSourceSlot )
wsSourceLayer.name = "Watershed Source"
wsSourceLayer.visible = False
wsSourceLayer.opacity = 1.0
layers.append( wsSourceLayer )
"""
filteredSlot = opLane.FilteredImage
if filteredSlot.ready():
filteredLayer = self.createStandardLayerFromSlot(filteredSlot)
filteredLayer.name = "Filtered Data"
filteredLayer.visible = False
filteredLayer.opacity = 1.0
layers.append(filteredLayer)
overlaySlot = opLane.OverlayData
if overlaySlot.ready():
inputLayer = self.createStandardLayerFromSlot(overlaySlot)
inputLayer.name = "Overlay Image"
inputLayer.visible = False
inputLayer.opacity = 1.0
layers.append(inputLayer)
inputSlot = opLane.InputData
if inputSlot.ready():
inputLayer = self.createStandardLayerFromSlot(inputSlot)
inputLayer.name = "Input Data"
inputLayer.visible = True
inputLayer.opacity = 1.0
layers.append(inputLayer)
return layers
def _create_random_colortable_layer_from_slot(cls, slot, num_colors=256):
colortable = generateRandomColors(num_colors,
clamp={
"v": 1.0,
"s": 0.5
},
zeroIsTransparent=True)
layer = ColortableLayer(createDataSource(slot), colortable)
layer.colortableIsRandom = True
return layer
def _initColortableLayer(self, labelSlot):
objectssrc = createDataSource(labelSlot)
objectssrc.setObjectName("LabelImage LazyflowSrc")
ct = colortables.create_default_16bit()
ct[0] = QColor(0, 0, 0, 0).rgba() # make 0 transparent
layer = ColortableLayer(objectssrc, ct)
layer.name = "Object Identities - Preview"
layer.setToolTip("Segmented objects, shown in different colors")
layer.visible = False
layer.opacity = 0.5
layer.colortableIsRandom = True
return layer
def _onMetaChanged(self, slot):
# FiXME: why do we need that?
if slot is self.topLevelOperatorView.BinaryImage:
if slot.meta.shape:
self.editor.dataShape = slot.meta.shape
if slot is self.topLevelOperatorView.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = createDataSource(
self.topLevelOperatorView.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw data"
self.layerstack.append(layerraw)
def setupLayers(self):
"""
which layers will be shown in the layerviewergui.
Triggers the prediciton by setting the layer on visible
"""
inputSlot = self.topLevelOperator.InputImage
layers = []
for channel, predictionSlot in enumerate(
self.topLevelOperator.PredictionProbabilityChannels):
if predictionSlot.ready():
predictsrc = createDataSource(predictionSlot)
predictionLayer = AlphaModulatedLayer(predictsrc,
range=(0.0, 1.0),
normalize=(0.0, 1.0))
predictionLayer.visible = self.drawer.liveUpdateButton.isChecked(
)
predictionLayer.opacity = 0.25
predictionLayer.visibleChanged.connect(
self.updateShowPredictionCheckbox)
def setPredLayerName(n,
predictLayer_=predictionLayer,
initializing=False):
"""
function for setting the names for every Channel
"""
if not initializing and predictLayer_ not in self.layerstack:
# This layer has been removed from the layerstack already.
# Don't touch it.
return
newName = "Prediction for %s" % n
predictLayer_.name = newName
setPredLayerName(channel, initializing=True)
layers.append(predictionLayer)
# always as last layer
if inputSlot.ready():
rawLayer = self.createStandardLayerFromSlot(inputSlot)
rawLayer.visible = True
rawLayer.opacity = 1.0
rawLayer.name = "Raw Data (display only)"
layers.append(rawLayer)
return layers
def _initColortablelayer(self, segSlot):
"""
Used to export both segmentation and labels
"""
if not segSlot.ready():
return None
opLane = self.topLevelOperatorView
colors = opLane.PmapColors.value
colortable = []
colortable.append(QColor(0, 0, 0, 0).rgba()) # transparent
for color in colors:
colortable.append(QColor(*color).rgba())
segsrc = createDataSource(segSlot)
seglayer = ColortableLayer(segsrc, colortable)
return seglayer
def _add_grayscale_layer(self, data, name=None, visible=False):
'''
adds a grayscale layer to the layerstack
:param data: numpy array (2D) containing the data
:param name: name of layer
:param visible: bool determining whether this layer should be set to visible
:return:
'''
#assert len(data.shape) == 2
a, data_shape = createDataSource(data, True)
self.editor.dataShape = list(data_shape)
new_layer = GrayscaleLayer(a)
new_layer.visible = visible
if name is not None:
new_layer.name = name
self.layerstack.append(new_layer)
def _initPredictionLayers(self, predictionSlot):
opLane = self.topLevelOperatorView
if not opLane.LabelNames.ready() or not opLane.PmapColors.ready():
return []
layers = []
colors = opLane.PmapColors.value
names = opLane.LabelNames.value
if predictionSlot.ready():
if 'c' in predictionSlot.meta.getAxisKeys():
num_channels = predictionSlot.meta.getTaggedShape()['c']
else:
num_channels = 1
if num_channels != len(names) or num_channels != len(colors):
names = [
"Label {}".format(n) for n in range(1, num_channels + 1)
]
colors = num_channels * [
(0, 0, 0)
] # it doesn't matter, if the pmaps color is not known,
# we are either initializing and it will be rewritten or
# something is very wrong elsewhere
# Use a slicer to provide a separate slot for each channel layer
opSlicer = OpMultiArraySlicer2(parent=opLane.viewed_operator().parent)
opSlicer.Input.connect(predictionSlot)
opSlicer.AxisFlag.setValue('c')
for channel, channelSlot in enumerate(opSlicer.Slices):
if channelSlot.ready(
) and channel < len(colors) and channel < len(names):
drange = channelSlot.meta.drange or (0.0, 1.0)
predictsrc = createDataSource(channelSlot)
predictLayer = AlphaModulatedLayer(
predictsrc,
tintColor=QColor(*colors[channel]),
# FIXME: This is weird. Why are range and normalize both set to the same thing?
range=drange,
normalize=drange)
predictLayer.opacity = 0.25
predictLayer.visible = True
predictLayer.name = names[channel]
layers.append(predictLayer)
return layers
def _add_segmentation_layer(self, data, name=None, visible=False):
'''
adds a segementation layer to the layerstack
:param data: numpy array (2D) containing the data
:param name: name of layer
:param visible: bool determining whether this layer should be set to visible
:return:
'''
assert len(data.shape) == 2
a, data_shape = createDataSource(data, True)
self.editor.dataShape = list(data_shape)
new_layer = ColortableLayer(a, self.colortable)
new_layer.visible = visible
new_layer.opacity = 0.5
if name is not None:
new_layer.name = name
self.layerstack.append(new_layer)
def initUic(self):
self.g = g = Graph()
#get the absolute path of the 'ilastik' module
uic.loadUi("designerElements/MainWindow.ui", self)
self.actionQuit.triggered.connect(qApp.quit)
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
self.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.layerstack = LayerStackModel()
readerNew = op.OpH5ReaderBigDataset(g)
readerNew.inputs["Filenames"].setValue([
"scripts/CB_compressed_XY.h5", "scripts/CB_compressed_XZ.h5",
"scripts/CB_compressed_YZ.h5"
])
readerNew.inputs["hdf5Path"].setValue("volume/data")
datasrc = createDataSource(readerNew.outputs["Output"])
layer1 = GrayscaleLayer(datasrc)
layer1.name = "Big Data"
self.layerstack.append(layer1)
shape = readerNew.outputs["Output"].meta.shape
print(shape)
self.editor = VolumeEditor(shape, self.layerstack)
#self.editor.setDrawingEnabled(False)
self.volumeEditorWidget.init(self.editor)
model = self.editor.layerStack
self.layerWidget.init(model)
self.UpButton.clicked.connect(model.moveSelectedUp)
model.canMoveSelectedUp.connect(self.UpButton.setEnabled)
self.DownButton.clicked.connect(model.moveSelectedDown)
model.canMoveSelectedDown.connect(self.DownButton.setEnabled)
self.DeleteButton.clicked.connect(model.deleteSelected)
model.canDeleteSelected.connect(self.DeleteButton.setEnabled)
def _initPredictionLayers(self, predictionSlot):
layers = []
colors = []
names = []
opLane = self.topLevelOperatorView
if opLane.PmapColors.ready():
colors = opLane.PmapColors.value
if opLane.LabelNames.ready():
names = opLane.LabelNames.value
# Use a slicer to provide a separate slot for each channel layer
opSlicer = OpMultiArraySlicer2(parent=opLane.viewed_operator().parent)
opSlicer.Input.connect(predictionSlot)
opSlicer.AxisFlag.setValue("c")
colors = [QColor(*c) for c in colors]
for channel in range(len(colors), len(opSlicer.Slices)):
colors.append(PredictionViewerGui.DefaultColors[channel])
for channel in range(len(names), len(opSlicer.Slices)):
names.append("Class {}".format(channel + 1))
for channel, channelSlot in enumerate(opSlicer.Slices):
if channelSlot.ready(
) and channel < len(colors) and channel < len(names):
predictsrc = createDataSource(channelSlot)
predictLayer = AlphaModulatedLayer(predictsrc,
tintColor=colors[channel],
range=(0.0, 1.0),
normalize=(0.0, 1.0))
predictLayer.opacity = 0.25
predictLayer.visible = True
predictLayer.name = names[channel]
layers.append(predictLayer)
return layers
return colors
def _initPredictionLayers(self, predictionSlot):
layers = []
opLane = self.topLevelOperatorView
if predictionSlot.ready(
) and self.topLevelOperatorView.UpperBound.ready():
upperBound = self.topLevelOperatorView.UpperBound.value
layer = ColortableLayer(createDataSource(predictionSlot),
colorTable=countingColorTable,
normalize=(0, upperBound))
layer.name = "Density"
layers.append(layer)
# def _initPredictionLayers(self, predictionSlot):
# layers = []
#
# opLane = self.topLevelOperatorView
# colors = opLane.PmapColors.value
# names = opLane.LabelNames.value
#
# # Use a slicer to provide a separate slot for each channel layer
# opSlicer = OpMultiArraySlicer2( parent=opLane.viewed_operator() )
# opSlicer.Input.connect( predictionSlot )
# opSlicer.AxisFlag.setValue('c')
#
# for channel, channelSlot in enumerate(opSlicer.Slices):
# if channelSlot.ready() and channel < len(colors) and channel < len(names):
# drange = channelSlot.meta.drange or (0.0, 1.0)
# predictsrc = createDataSource(channelSlot)
# predictLayer = AlphaModulatedLayer( predictsrc,
# tintColor=QColor(*colors[channel]),
# # FIXME: This is weird. Why are range and normalize both set to the same thing?
# range=drange,
# normalize=drange )
# predictLayer.opacity = 0.25
# predictLayer.visible = True
# predictLayer.name = names[channel]
# layers.append(predictLayer)
return layers
def setupLayers(self):
layers = []
opLane = self.topLevelOperatorView
labelSlot = opLane.LabelImage
if labelSlot.ready():
labelImageLayer = ColortableLayer(createDataSource(labelSlot),
colorTable=self._colorTable16)
labelImageLayer.name = "Label Image"
labelImageLayer.visible = True
layers.append(labelImageLayer)
# If available, also show the raw data layer
rawSlot = opLane.RawImage
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot(rawSlot)
rawLayer.name = "Raw Data"
rawLayer.visible = True
rawLayer.opacity = 1.0
layers.append(rawLayer)
return layers
def _initSegmentationLayers(self, segmentationSlot):
opLane = self.topLevelOperatorView
layers = []
# Use a slicer to provide a separate slot for each channel layer
opSlicer = OpMultiArraySlicer2(parent=opLane.viewed_operator().parent)
opSlicer.Input.connect(segmentationSlot)
opSlicer.AxisFlag.setValue("c")
for channel, segmentationSlot in enumerate(opSlicer.Slices):
if segmentationSlot.ready():
segmentationSrc = createDataSource(segmentationSlot)
segmentationLayer = AlphaModulatedLayer(segmentationSrc,
range=(0.0, 1.0),
normalize=(0.0, 1.0))
segmentationLayer.visible = (
channel == 1) # only show the channel with the foreground
segmentationLayer.opacity = 1
def setSegmentationLayerName(
n,
segmentationLayer_=segmentationLayer,
initializing=False):
"""
function for setting the names for every Channel
"""
if not initializing and segmentationLayer_ not in self.layerstack:
# This layer has been removed from the layerstack already.
# Don't touch it.
return
newName = "Segmentation of %s" % n
segmentationLayer_.name = newName
setSegmentationLayerName(channel, initializing=True)
layers.append(segmentationLayer)
return layers
def _initPredictionLayers(self, predictionSlot):
opLane = self.topLevelOperatorView
layers = []
# Use a slicer to provide a separate slot for each channel layer
opSlicer = OpMultiArraySlicer2(parent=opLane.viewed_operator().parent)
opSlicer.Input.connect(predictionSlot)
opSlicer.AxisFlag.setValue('c')
for channel, predictionSlot in enumerate(opSlicer.Slices):
if predictionSlot.ready():
predictsrc = createDataSource(predictionSlot)
predictLayer = AlphaModulatedLayer(predictsrc,
range=(0.0, 1.0),
normalize=(0.0, 1.0))
predictLayer.opacity = 0.25
predictLayer.visible = True
def setPredLayerName(n,
predictLayer_=predictLayer,
initializing=False):
"""
function for setting the names for every Channel
"""
if not initializing and predictLayer_ not in self.layerstack:
# This layer has been removed from the layerstack already.
# Don't touch it.
return
newName = "Prediction for %s" % n
predictLayer_.name = newName
setPredLayerName(channel, initializing=True)
layers.append(predictLayer)
return layers
def do():
# Generate
# array[:] = np.random.randint(0,255,500*500).reshape(shape).astype(np.uint8)
a = np.zeros(500 * 500).reshape(500, 500).astype(np.uint8)
ii = np.random.randint(0, 500, 1)
jj = np.random.randint(0, 500, 1)
a[ii, jj] = 1
a = vigra.filters.discDilation(a, radius=20)
array[:] = a.reshape(shape).view(np.ndarray) * 255
op.Input.setDirty()
do()
cron.timeout.connect(do)
ds = createDataSource(op.Output)
layer = ColortableLayer(ds, jet())
mainwin = Viewer()
mainwin.layerstack.append(layer)
mainwin.dataShape = (1, h, w, 1, 1)
print(mainwin.centralWidget())
BoxContr = BoxController(mainwin.editor, op.Output, boxListModel)
BoxInt = BoxInterpreter(mainwin.editor.navInterpret, mainwin.editor.posModel, BoxContr, mainwin.centralWidget())
mainwin.editor.setNavigationInterpreter(BoxInt)
# boxListModel.boxRemoved.connect(BoxContr.deleteItem)
LV.show()
mainwin.show()
