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(LazyflowSource(watershedSlot), colortable)
watershedLayer.name = "Watershed"
watershedLayer.visible = False
watershedLayer.opacity = 1.0
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 )
inputSlot = opLane.InputData
if inputSlot.ready():
inputLayer = self.createStandardLayerFromSlot( inputSlot )
inputLayer.name = "Input Data"
inputLayer.visible = True
inputLayer.opacity = 1.0
layers.append( inputLayer )
''' FIXME: disabled for 0.6 release
rawSlot = opLane.RawData
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot( rawSlot )
rawLayer.name = "Raw Data"
rawLayer.visible = True
rawLayer.opacity = 1.0
layers.append( rawLayer )
'''
return layers
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)
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(LazyflowSource(watershedSlot), colortable)
watershedLayer.name = "Watershed"
watershedLayer.visible = False
watershedLayer.opacity = 1.0
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 )
inputSlot = opLane.InputData
if inputSlot.ready():
inputLayer = self.createStandardLayerFromSlot( inputSlot )
inputLayer.name = "Input Data"
inputLayer.visible = True
inputLayer.opacity = 1.0
layers.append( inputLayer )
''' FIXME: disabled for 0.6 release
rawSlot = opLane.RawData
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot( rawSlot )
rawLayer.name = "Raw Data"
rawLayer.visible = True
rawLayer.opacity = 1.0
layers.append( rawLayer )
'''
return layers
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)
def setUp(self):
if 'TRAVIS' in os.environ:
# Colortable requests require vigra, which is not installed on our Travis-CI build.
# Skip this test on Travis-CI.
import nose
raise nose.SkipTest
super(ColortableImageSourceTest2, self).setUp()
self.seg = numpy.zeros((6, 7), dtype=numpy.uint32)
self.seg = numpy.ma.masked_array(self.seg,
mask=numpy.zeros(self.seg.shape,
dtype=bool),
shrink=False)
self.seg[0:2, :] = 0
self.seg[1, :] = numpy.ma.masked
self.seg[2:4, :] = 1
self.seg[3, :] = numpy.ma.masked
self.seg[4:6, :] = 2
self.seg[5, :] = numpy.ma.masked
self.ars = _ArraySource2d(self.seg)
self.ctable = [
QColor(255, 0, 0).rgba(),
QColor(0, 255, 0).rgba(),
QColor(0, 0, 255).rgba()
]
self.layer = ColortableLayer(self.ars, self.ctable)
self.ims = ColortableImageSource(self.ars, self.layer)
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 _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 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)
def setupLayers( self ):
layers = []
self.translationsrc = self.mainOperator.TranslationVectorsDisplay
translationLayer = self.createStandardLayerFromSlot( self.translationsrc )
translationLayer.name = "Translation Vector"
translationLayer.opacity = 0.8
translationLayer.visible = False
layers.append(translationLayer)
ct = colortables.create_default_8bit()
ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
ct[1] = QColor(0,255,0,255).rgba() # foreground is green
self.warpedSrc = LazyflowSource( self.mainOperator.WarpedImage )
warpedLayer = ColortableLayer( self.warpedSrc, ct )
warpedLayer.name = "Translation Corrected Binary Image"
warpedLayer.visible = False
warpedLayer.opacity = 0.4
layers.append(warpedLayer)
ct = colortables.create_default_8bit()
ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
ct[1] = QColor(255,0,0,255).rgba() # foreground is read
self.binarySrc = LazyflowSource( self.mainOperator.BinaryImage )
binaryLayer = ColortableLayer( self.binarySrc, ct )
binaryLayer.name = "Binary Image"
binaryLayer.visible = True
binaryLayer.opacity = 0.8
layers.append(binaryLayer)
## raw data layer
self.rawsrc = LazyflowSource( self.mainOperator.RawImage )
rawLayer = GrayscaleLayer( self.rawsrc )
rawLayer.name = "Raw Image"
layers.insert( len(layers), rawLayer )
if self.topLevelOperatorView.TranslationVectors.meta.shape:
self.editor.dataShape = self.topLevelOperatorView.TranslationVectors.meta.shape
self.topLevelOperatorView.RawImage.notifyReady( self._onReady )
self.topLevelOperatorView.RawImage.notifyMetaChanged( self._onMetaChanged )
self._onParametersChanged()
self._drawer.methodBox.currentIndexChanged.connect(self._onMethodChanged)
self._drawer.templateSizeBox.valueChanged.connect(self._onMethodChanged)
self._drawer.maxTranslationBox.valueChanged.connect(self._onMethodChanged)
self._drawer.maxDiffValsBox.valueChanged.connect(self._onMethodChanged)
return layers
def setUp(self):
self.seg = numpy.zeros((6, 7), dtype=numpy.uint32)
self.seg[0:2, :] = 0
self.seg[2:4, :] = 1
self.seg[4:6, :] = 2
self.ars = _ArraySource2d(self.seg)
self.ctable = [
QColor(255, 0, 0).rgba(),
QColor(0, 255, 0).rgba(),
QColor(0, 0, 255).rgba()
]
self.layer = ColortableLayer(self.ars, self.ctable)
self.ims = ColortableImageSource(self.ars, self.layer)
def add_layer_from_datasource(self,
source,
name=None,
colortable=None,
direct=False):
if colortable is None:
colortable = self._randomColors()
self._overlay_layer = ColortableLayer(source,
colortable,
direct=direct)
if name:
self._overlay_layer.name = name
self.layerstack.append(self._overlay_layer)
return self._overlay_layer
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 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(LazyflowSource(watershedSlot), colortable)
watershedLayer.name = "Watershed"
watershedLayer.visible = False
watershedLayer.opacity = 1.0
layers.append(watershedLayer)
filteredSlot = opLane.FilteredImage
if filteredSlot.ready():
filteredLayer = self.createStandardLayerFromSlot( filteredSlot )
filteredLayer.name = "Filtered Data"
filteredLayer.visible = False
filteredLayer.opacity = 1.0
layers.append( filteredLayer )
# Raw data
rawSlot = opLane.RawData
if rawSlot.ready():
rawLayer = self.createStandardLayerFromSlot( rawSlot )
rawLayer.name = "Raw Data"
rawLayer.visible = True
rawLayer.opacity = 1.0
layers.append( rawLayer )
return layers
def setUp(self):
if "TRAVIS" in os.environ:
# Colortable requests require vigra, which is not installed on our Travis-CI build.
# Skip this test on Travis-CI.
import nose
raise nose.SkipTest
super(ColortableImageSourceTest, self).setUp()
self.seg = numpy.zeros((6, 7), dtype=numpy.uint32)
self.seg[0:2, :] = 0
self.seg[2:4, :] = 1
self.seg[4:6, :] = 2
self.ars = _ArraySource2d(self.seg)
self.ctable = [QColor(255, 0, 0).rgba(), QColor(0, 255, 0).rgba(), QColor(0, 0, 255).rgba()]
self.layer = ColortableLayer(self.ars, self.ctable)
self.ims = ColortableImageSource(self.ars, self.layer)
def setUp(self):
super(ColortableImageSourceTest2, self).setUp()
self.seg = numpy.zeros((6, 7), dtype=numpy.uint32)
self.seg = numpy.ma.masked_array(self.seg,
mask=numpy.zeros(self.seg.shape,
dtype=bool),
shrink=False)
self.seg[0:2, :] = 0
self.seg[1, :] = numpy.ma.masked
self.seg[2:4, :] = 1
self.seg[3, :] = numpy.ma.masked
self.seg[4:6, :] = 2
self.seg[5, :] = numpy.ma.masked
self.ars = _ArraySource2d(self.seg)
self.ctable = [
QColor(255, 0, 0).rgba(),
QColor(0, 255, 0).rgba(),
QColor(0, 0, 255).rgba()
]
self.layer = ColortableLayer(self.ars, self.ctable)
self.ims = ColortableImageSource(self.ars, self.layer)
def setupLayers( self ):
logger.debug( "setupLayers" )
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
labellayer._allowToggleVisible = False
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#uncertainty
#if self._showUncertaintyLayer:
# uncert = self.topLevelOperatorView.Uncertainty
# if uncert.ready():
# colortable = []
# for i in range(256-len(colortable)):
# r,g,b,a = i,0,0,i
# colortable.append(QColor(r,g,b,a).rgba())
# layer = ColortableLayer(LazyflowSource(uncert), colortable, direct=True)
# layer.name = "Uncertainty"
# layer.visible = True
# layer.opacity = 0.3
# layers.append(layer)
#segmentation
seg = self.topLevelOperatorView.Segmentation
#seg = self.topLevelOperatorView.MST.value.segmentation
#temp = self._done_lut[self.MST.value.supervoxelUint32[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
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())
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "Segmentation"
layer.setToolTip("This layer displays the <i>current</i> segmentation. Simply add foreground and background " \
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self.topLevelOperatorView.DoneObjects
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
#have to use lazyflow because it provides dirty signals
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip("In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b> in one color (<b>blue</b>). " \
"The reason for only one color is that for finding out which " \
"objects to label next, the identity of already completed objects is unimportant " \
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
#done seg
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip("<html>In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b>, each with a random color.</html>")
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
#supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.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())
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "Supervoxels"
layer.setToolTip("<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving " \
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an " \
"object. Sometimes, supervoxels are too large and straddle two distinct objects " \
"(undersegmentation). In this case, it will be impossible to achieve the desired " \
"segmentation. This layer helps you to understand these cases.</html>")
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
# Visual overlay (just for easier labeling)
overlaySlot = self.topLevelOperatorView.OverlayData
if overlaySlot.ready():
overlay5D = self.topLevelOperatorView.OverlayData.value
layer = GrayscaleLayer(ArraySource(overlay5D), direct=True)
layer.visible = True
layer.name = 'Overlay'
layer.opacity = 1.0
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot), direct=True )
layer.name = "Input Data"
layer.setToolTip("<html>The data originally loaded into ilastik (unprocessed).</html>")
#layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
# Window leveling is already active on the Overlay,
# but if no overlay was provided, then activate window_leveling on the raw data instead.
if not overlaySlot.ready():
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer( LazyflowSource(filteredSlot) )
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
def setupLayers(self):
def findLayer(f, layerlist):
for l in layerlist:
if f(l):
return l
return None
layers = []
baseCarvingLayers = super(SplitBodyCarvingGui, self).setupLayers()
crosshairSlot = self.topLevelOperatorView.AnnotationCrosshairs
if crosshairSlot.ready():
# 0=Transparent, 1=pink
colortable = [
QColor(0, 0, 0, 0).rgba(),
QColor(236, 184, 201).rgba()
]
crosshairLayer = ColortableLayer(LazyflowSource(crosshairSlot),
colortable,
direct=True)
crosshairLayer.name = "Annotation Points"
crosshairLayer.visible = True
crosshairLayer.opacity = 1.0
layers.append(crosshairLayer)
highlightedObjectSlot = self.topLevelOperatorView.CurrentRavelerObject
if highlightedObjectSlot.ready():
# 0=Transparent, 1=blue
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(0, 0, 255).rgba()]
highlightedObjectLayer = ColortableLayer(
LazyflowSource(highlightedObjectSlot), colortable, direct=True)
highlightedObjectLayer.name = "Current Raveler Object"
highlightedObjectLayer.visible = False
highlightedObjectLayer.opacity = 0.25
layers.append(highlightedObjectLayer)
remainingRavelerObjectSlot = self.topLevelOperatorView.CurrentRavelerObjectRemainder
if remainingRavelerObjectSlot.ready():
# 0=Transparent, 1=blue
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(255, 0, 0).rgba()]
remainingObjectLayer = ColortableLayer(
LazyflowSource(remainingRavelerObjectSlot),
colortable,
direct=True)
remainingObjectLayer.name = "Remaining Raveler Object"
remainingObjectLayer.visible = True
remainingObjectLayer.opacity = 0.25
layers.append(remainingObjectLayer)
fragmentSegSlot = self.topLevelOperatorView.CurrentFragmentSegmentation
if fragmentSegSlot.ready():
colortable = map(QColor.rgba, self._fragmentColors)
fragSegLayer = ColortableLayer(LazyflowSource(fragmentSegSlot),
colortable,
direct=True)
fragSegLayer.name = "Saved Fragments"
fragSegLayer.visible = True
fragSegLayer.opacity = 0.25
layers.append(fragSegLayer)
ravelerLabelsSlot = self.topLevelOperatorView.RavelerLabels
if ravelerLabelsSlot.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())
ravelerLabelLayer = ColortableLayer(
LazyflowSource(ravelerLabelsSlot), colortable, direct=True)
ravelerLabelLayer.name = "Raveler Labels"
ravelerLabelLayer.visible = False
ravelerLabelLayer.opacity = 0.4
layers.append(ravelerLabelLayer)
maskedSegSlot = self.topLevelOperatorView.MaskedSegmentation
if maskedSegSlot.ready():
colortable = [
QColor(0, 0, 0, 0).rgba(),
QColor(0, 0, 0, 0).rgba(),
QColor(0, 255, 0).rgba()
]
maskedSegLayer = ColortableLayer(LazyflowSource(maskedSegSlot),
colortable,
direct=True)
maskedSegLayer.name = "Masked Segmentation"
maskedSegLayer.visible = True
maskedSegLayer.opacity = 0.3
layers.append(maskedSegLayer)
# Hide the original carving segmentation.
# TODO: Remove it from the list altogether?
carvingSeg = findLayer(lambda l: l.name == "segmentation",
baseCarvingLayers)
if carvingSeg is not None:
carvingSeg.visible = False
def removeBaseLayer(layerName):
layer = findLayer(lambda l: l.name == layerName, baseCarvingLayers)
if layer:
baseCarvingLayers.remove(layer)
# Don't show carving layers that aren't relevant to the split-body workflow
removeBaseLayer("Uncertainty")
removeBaseLayer("Segmentation")
removeBaseLayer("Completed segments (unicolor)")
#removeBaseLayer( "pmap" )
#removeBaseLayer( "hints" )
#removeBaseLayer( "done" )
#removeBaseLayer( "done" )
ActionInfo = ShortcutManager.ActionInfo
# Attach a shortcut to the raw data layer
if self.topLevelOperatorView.RawData.ready():
rawLayer = findLayer(lambda l: l.name == "Raw Data",
baseCarvingLayers)
assert rawLayer is not None, "Couldn't find the raw data layer. Did it's name change?"
rawLayer.shortcutRegistration = (
"f",
ActionInfo("Carving", "Raw Data to Top", "Raw Data to Top",
partial(self._toggleRawDataPosition, rawLayer),
self.viewerControlWidget(), rawLayer))
layers += baseCarvingLayers
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
data_arr = (255 * numpy.random.random(SHAPE)).astype(numpy.uint8)
label_arr = numpy.zeros(SHAPE, dtype=numpy.uint8)
##-----
app = QApplication(sys.argv)
v = Viewer()
data_src = ArraySource(data_arr)
data_layer = GrayscaleLayer(data_src)
data_layer.name = "Raw"
data_layer.numberOfChannels = 1
label_src = ArraySinkSource(label_arr)
label_layer = ColortableLayer(label_src,
colorTable=default16_new,
direct=False)
label_layer.name = "Labels"
label_layer.ref_object = None
assert SHAPE == label_arr.shape == data_arr.shape
v.dataShape = SHAPE
v.layerstack.append(data_layer)
v.layerstack.append(label_layer)
v.editor.setLabelSink(label_src)
v.editor.setInteractionMode("brushing")
v.setWindowTitle("labeling")
v.showMaximized()
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):
def findLayer(f, layerlist):
for l in layerlist:
if f(l):
return l
return None
layers = []
baseCarvingLayers = super(SplitBodyCarvingGui, self).setupLayers()
crosshairSlot = self.topLevelOperatorView.AnnotationCrosshairs
if crosshairSlot.ready():
# 0=Transparent, 1=pink
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(236, 184, 201).rgba()]
crosshairLayer = ColortableLayer(LazyflowSource(crosshairSlot), colortable, direct=True)
crosshairLayer.name = "Annotation Points"
crosshairLayer.visible = True
crosshairLayer.opacity = 1.0
layers.append(crosshairLayer)
highlightedObjectSlot = self.topLevelOperatorView.CurrentRavelerObject
if highlightedObjectSlot.ready():
# 0=Transparent, 1=blue
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(0, 0, 255).rgba()]
highlightedObjectLayer = ColortableLayer(LazyflowSource(highlightedObjectSlot), colortable, direct=True)
highlightedObjectLayer.name = "Current Raveler Object"
highlightedObjectLayer.visible = False
highlightedObjectLayer.opacity = 0.25
layers.append(highlightedObjectLayer)
remainingRavelerObjectSlot = self.topLevelOperatorView.CurrentRavelerObjectRemainder
if remainingRavelerObjectSlot.ready():
# 0=Transparent, 1=blue
colortable = [QColor(0, 0, 0, 0).rgba(), QColor(255, 0, 0).rgba()]
remainingObjectLayer = ColortableLayer(LazyflowSource(remainingRavelerObjectSlot), colortable, direct=True)
remainingObjectLayer.name = "Remaining Raveler Object"
remainingObjectLayer.visible = True
remainingObjectLayer.opacity = 0.25
layers.append(remainingObjectLayer)
fragmentSegSlot = self.topLevelOperatorView.CurrentFragmentSegmentation
if fragmentSegSlot.ready():
colortable = map(QColor.rgba, self._fragmentColors)
fragSegLayer = ColortableLayer(LazyflowSource(fragmentSegSlot), colortable, direct=True)
fragSegLayer.name = "Saved Fragments"
fragSegLayer.visible = True
fragSegLayer.opacity = 0.25
layers.append(fragSegLayer)
ravelerLabelsSlot = self.topLevelOperatorView.RavelerLabels
if ravelerLabelsSlot.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())
ravelerLabelLayer = ColortableLayer(LazyflowSource(ravelerLabelsSlot), colortable, direct=True)
ravelerLabelLayer.name = "Raveler Labels"
ravelerLabelLayer.visible = False
ravelerLabelLayer.opacity = 0.4
layers.append(ravelerLabelLayer)
maskedSegSlot = self.topLevelOperatorView.MaskedSegmentation
if maskedSegSlot.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
maskedSegLayer = ColortableLayer(LazyflowSource(maskedSegSlot), colortable, direct=True)
maskedSegLayer.name = "Masked Segmentation"
maskedSegLayer.visible = True
maskedSegLayer.opacity = 0.3
layers.append(maskedSegLayer)
# Hide the original carving segmentation.
# TODO: Remove it from the list altogether?
carvingSeg = findLayer( lambda l: l.name == "segmentation", baseCarvingLayers )
if carvingSeg is not None:
carvingSeg.visible = False
def removeBaseLayer(layerName):
layer = findLayer(lambda l: l.name == layerName, baseCarvingLayers)
if layer:
baseCarvingLayers.remove(layer)
# Don't show carving layers that aren't relevant to the split-body workflow
removeBaseLayer( "uncertainty" )
removeBaseLayer( "done seg" )
removeBaseLayer( "pmap" )
removeBaseLayer( "hints" )
removeBaseLayer( "done" )
removeBaseLayer( "done" )
# Attach a shortcut to the raw data layer
if self.topLevelOperatorView.RawData.ready():
rawLayer = findLayer(lambda l: l.name == "raw", baseCarvingLayers)
assert rawLayer is not None, "Couldn't find the raw data layer. Did it's name change?"
rawLayer.shortcutRegistration = ( "Carving",
"Raw Data to Top",
QShortcut( QKeySequence("f"),
self.viewerControlWidget(),
partial(self._toggleRawDataPosition, rawLayer) ),
rawLayer )
layers += baseCarvingLayers
return layers
def setupLayers( self, currentImageIndex ):
layers = []
def onButtonsEnabled(slot, roi):
currObj = self._carvingApplet.topLevelOperator.opCarving[currentImageIndex].CurrentObjectName.value
hasSeg = self._carvingApplet.topLevelOperator.opCarving[currentImageIndex].HasSegmentation.value
nzLB = self._carvingApplet.topLevelOperator.opLabeling.NonzeroLabelBlocks[currentImageIndex][:].wait()[0]
self.labelingDrawerUi.currentObjectLabel.setText("current object: %s" % currObj)
self.labelingDrawerUi.save.setEnabled(currObj != "" and hasSeg)
self.labelingDrawerUi.saveAs.setEnabled(currObj == "" and hasSeg)
#rethink this
#self.labelingDrawerUi.segment.setEnabled(len(nzLB) > 0)
#self.labelingDrawerUi.clear.setEnabled(len(nzLB) > 0)
self._carvingApplet.topLevelOperator.opCarving[currentImageIndex].CurrentObjectName.notifyDirty(onButtonsEnabled)
self._carvingApplet.topLevelOperator.opCarving[currentImageIndex].HasSegmentation.notifyDirty(onButtonsEnabled)
self._carvingApplet.topLevelOperator.opLabeling.NonzeroLabelBlocks[currentImageIndex].notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(currentImageIndex, direct=True)
if labellayer is not None:
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#segmentation
seg = self._carvingApplet.topLevelOperator.opCarving.Segmentation[currentImageIndex]
#seg = self._carvingApplet.topLevelOperator.opCarving[0]._mst.segmentation
#temp = self._done_lut[self._mst.regionVol[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
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())
#layer = DirectColorTableLayer(seg, colortable, lazyflow=True)
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "segmentation"
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self._carvingApplet.topLevelOperator.opCarving.DoneObjects[currentImageIndex]
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
for i in range(254-len(colortable)):
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())
#have to use lazyflow because it provides dirty signals
#layer = DirectColorTableLayer(done, colortable, lazyflow=True)
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "done"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
doneSeg = self._carvingApplet.topLevelOperator.opCarving.DoneSegmentation[currentImageIndex]
if doneSeg.ready():
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "done seg"
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
#supervoxel
sv = self._carvingApplet.topLevelOperator.opCarving.Supervoxels[currentImageIndex]
if sv.ready():
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())
#layer = DirectColorTableLayer(sv, colortable, lazyflow=True)
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "supervoxels"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#
# load additional layer: features / probability map
#
import h5py
f = h5py.File("pmap.h5")
pmap = f["data"].value
#
# here we load the actual raw data from an ArraySource rather than from a LazyflowSource for speed reasons
#
raw = self._carvingApplet.topLevelOperator.opCarving[0]._mst.raw
raw5D = numpy.zeros((1,)+raw.shape+(1,), dtype=raw.dtype)
raw5D[0,:,:,:,0] = raw[:,:,:]
#layer = DirectGrayscaleLayer(raw5D)
layer = GrayscaleLayer(ArraySource(raw5D), direct=True)
layer.name = "raw"
layer.visible = True
layer.opacity = 1.0
#layers.insert(1, layer)
layers.append(layer)
return layers
def setupLayers(self):
logger.debug("setupLayers")
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(
onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(
onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
labellayer._allowToggleVisible = False
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
# uncertainty
# if self._showUncertaintyLayer:
# uncert = self.topLevelOperatorView.Uncertainty
# if uncert.ready():
# colortable = []
# for i in range(256-len(colortable)):
# r,g,b,a = i,0,0,i
# colortable.append(QColor(r,g,b,a).rgba())
# layer = ColortableLayer(createDataSource(uncert), colortable, direct=True)
# layer.name = "Uncertainty"
# layer.visible = True
# layer.opacity = 0.3
# layers.append(layer)
# segmentation
seg = self.topLevelOperatorView.Segmentation
# seg = self.topLevelOperatorView.MST.value.segmentation
# temp = self._done_lut[self.MST.value.supervoxelUint32[sl[1:4]]]
if seg.ready():
# source = RelabelingArraySource(seg)
# source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
# assign to the object label color, 0 is transparent, 1 is background
colortable = [
QColor(0, 0, 0, 0).rgba(),
QColor(0, 0, 0, 0).rgba(), labellayer._colorTable[2]
]
for i in range(256 - len(colortable)):
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())
layer = ColortableLayer(createDataSource(seg),
colortable,
direct=True)
layer.name = "Segmentation"
layer.setToolTip(
"This layer displays the <i>current</i> segmentation. Simply add foreground and background "
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
# done
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
# FIXME: if the user segments more than 255 objects, those with indices that divide by 255 will be shown as transparent
# both here and in the _doneSegmentationColortable
colortable = 254 * [QColor(230, 25, 75).rgba()]
colortable.insert(0, QColor(0, 0, 0, 0).rgba())
# have to use lazyflow because it provides dirty signals
layer = ColortableLayer(createDataSource(doneSeg),
colortable,
direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip(
"In order to keep track of which objects you have already completed, this layer "
"shows <b>all completed object</b> in one color (<b>blue</b>). "
"The reason for only one color is that for finding out which "
"objects to label next, the identity of already completed objects is unimportant "
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
layer = ColortableLayer(createDataSource(doneSeg),
self._doneSegmentationColortable,
direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip(
"<html>In order to keep track of which objects you have already completed, this layer "
"shows <b>all completed object</b>, each with a random color.</html>"
)
layer.visible = False
layer.opacity = 0.5
layer.colortableIsRandom = True
self._doneSegmentationLayer = layer
layers.append(layer)
# supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.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())
layer = ColortableLayer(createDataSource(sv),
colortable,
direct=True)
layer.name = "Supervoxels"
layer.setToolTip(
"<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving "
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an "
"object. Sometimes, supervoxels are too large and straddle two distinct objects "
"(undersegmentation). In this case, it will be impossible to achieve the desired "
"segmentation. This layer helps you to understand these cases.</html>"
)
layer.visible = False
layer.colortableIsRandom = True
layer.opacity = 0.5
layers.append(layer)
# Visual overlay (just for easier labeling)
overlaySlot = self.topLevelOperatorView.OverlayData
if overlaySlot.ready():
overlay5D = self.topLevelOperatorView.OverlayData.value
layer = GrayscaleLayer(ArraySource(overlay5D), direct=True)
layer.visible = True
layer.name = "Overlay"
layer.opacity = 1.0
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer(createDataSource(inputSlot), direct=True)
layer.name = "Input Data"
layer.setToolTip(
"<html>The data originally loaded into ilastik (unprocessed).</html>"
)
# layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
# Window leveling is already active on the Overlay,
# but if no overlay was provided, then activate window_leveling on the raw data instead.
if not overlaySlot.ready():
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
self.labelingDrawerUi.thresToolButton.show()
layers.append(layer)
del layer
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer(createDataSource(filteredSlot))
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
def showStuff(raw_name,
pred_viewer1,
pred_viewer2,
cutout_name,
one_extra=None):
# display the raw and annotations for cremi challenge data
raw = vigra.impex.readHDF5(indir + datasets[raw_name], "data", order='C')
# raw_old = vigra.readHDF5(indir+datasets["raw_bad"], "data", order = 'C')
defect_prediction_128 = vigra.impex.readHDF5(indir +
datasets[pred_viewer2],
"data",
order='C')
defect_prediction_150 = vigra.impex.readHDF5(indir +
datasets[pred_viewer1],
"data",
order='C')
cutout_from_150_pred = vigra.impex.readHDF5(indir + datasets[cutout_name],
"data",
order='C')
####################################################################################################################
# only used for fast testing stuff
#change_one = vigra.readHDF5(indir+datasets["segmentation_on_equalized_image"], "data", order = 'C')
#pdb.set_trace()
#defect_prediction_150[1,:,:] = change_one[0,:,:,0]
####################################################################################################################
# defect_prediction_150 = gt[..., 0]
cutout = numpy.asarray(cutout_from_150_pred)
rawdata = numpy.asarray(raw)
# rawdata_old = numpy.asarray(raw_old)
# op5ify
# shape5d = rawdata.shape
shape5d = (1, ) + rawdata.shape + (1, )
print shape5d, rawdata.shape, rawdata.dtype
app = QApplication([])
v = Viewer()
direct = False
# layer for raw data
rawdata = numpy.reshape(rawdata, shape5d)
rawsource = ArraySource(rawdata)
v.dataShape = shape5d
lraw = GrayscaleLayer(rawsource, direct=direct)
lraw.visible = True
lraw.name = "raw"
v.layerstack.append(lraw)
# layer for cutout regions from raw data
cutout = numpy.reshape(cutout, shape5d)
cutoutsource = ArraySource(cutout)
lcutout = GrayscaleLayer(cutoutsource, direct=direct)
lcutout.visible = False
lcutout.name = "cut_out"
v.layerstack.append(lcutout)
# layer for first prediction result
defect_prediction_128 = numpy.reshape(defect_prediction_128, shape5d)
synsource = ArraySource(defect_prediction_128)
ct = create_random_16bit()
ct[0] = 0
lsyn = ColortableLayer(synsource, ct)
lsyn.name = pred_viewer2
lsyn.visible = False
v.layerstack.append(lsyn)
# layer for second prediction result
segm = numpy.reshape(defect_prediction_150, shape5d)
segsource = ArraySource(segm)
ct = create_random_16bit()
ct[0] = 0
lseg = ColortableLayer(segsource, ct)
lseg.name = pred_viewer1
lseg.visible = False
v.layerstack.append(lseg)
if one_extra is None:
v.showMaximized()
app.exec_()
if one_extra is not None:
# layer for third prediction result
extra_prediction = vigra.readHDF5(indir + datasets[one_extra],
"data",
order='C')
extra_pred_reshaped = numpy.reshape(extra_prediction, shape5d)
segsource = ArraySource(extra_pred_reshaped)
ct = create_random_16bit()
ct[0] = 0
# ct = create_default_16bit()
lseg = ColortableLayer(segsource, ct)
lseg.name = one_extra
lseg.visible = False
v.layerstack.append(lseg)
v.showMaximized()
app.exec_()
def setupLayers(self):
layers = []
op = self.topLevelOperatorView
# Superpixels
if op.Superpixels.ready():
layer = ColortableLayer(LazyflowSource(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 op.debug_results.items():
axiskeys = op.Superpixels.meta.getAxisKeys(
)[:-1] # debug images don't have a channel axis
permutation = map(
lambda key: axiskeys.index(key)
if key in axiskeys else None, '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(LazyflowSource(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 = "Input"
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 setupLayers(self):
layers = []
op = self.topLevelOperatorView
# Superpixels
if op.Superpixels.ready():
layer = ColortableLayer( LazyflowSource(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 op.debug_results.items():
axiskeys = op.Superpixels.meta.getAxisKeys()[:-1] # debug images don't have a channel axis
permutation = map(lambda key: axiskeys.index(key) if key in axiskeys else None, '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( LazyflowSource(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 = "Input"
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 setupLayers( self ):
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.opCarving.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.opCarving.HasSegmentation.value
nzLB = self.topLevelOperatorView.opCarving.opLabeling.NonzeroLabelBlocks[:].wait()[0]
self.labelingDrawerUi.currentObjectLabel.setText("current object: %s" % currObj)
self.labelingDrawerUi.save.setEnabled(currObj != "" and hasSeg)
self.labelingDrawerUi.saveAs.setEnabled(currObj == "" and hasSeg)
#rethink this
#self.labelingDrawerUi.segment.setEnabled(len(nzLB) > 0)
#self.labelingDrawerUi.clear.setEnabled(len(nzLB) > 0)
self.topLevelOperatorView.opCarving.CurrentObjectName.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opCarving.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opCarving.opLabeling.NonzeroLabelBlocks.notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#uncertainty
uncert = self.topLevelOperatorView.opCarving.Uncertainty
if uncert.ready():
colortable = []
for i in range(256-len(colortable)):
r,g,b,a = i,0,0,i
colortable.append(QColor(r,g,b,a).rgba())
layer = ColortableLayer(LazyflowSource(uncert), colortable, direct=True)
layer.name = "uncertainty"
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#segmentation
seg = self.topLevelOperatorView.opCarving.Segmentation
#seg = self.topLevelOperatorView.opCarving.MST.value.segmentation
#temp = self._done_lut[self.MST.value.regionVol[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
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())
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "segmentation"
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self.topLevelOperatorView.opCarving.DoneObjects
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
for i in range(254-len(colortable)):
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())
#have to use lazyflow because it provides dirty signals
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "done"
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
#hints
useLazyflow = True
ctable = [QColor(0,0,0,0).rgba(), QColor(255,0,0).rgba()]
ctable.extend( [QColor(255*random.random(), 255*random.random(), 255*random.random()) for x in range(254)] )
if useLazyflow:
hints = self.topLevelOperatorView.opCarving.HintOverlay
layer = ColortableLayer(LazyflowSource(hints), ctable, direct=True)
else:
hints = self.topLevelOperatorView.opCarving._hints
layer = ColortableLayer(ArraySource(hints), ctable, direct=True)
if not useLazyflow or hints.ready():
layer.name = "hints"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#pmaps
useLazyflow = True
pmaps = self.topLevelOperatorView.opCarving._pmap
if pmaps is not None:
layer = GrayscaleLayer(ArraySource(pmaps), direct=True)
layer.name = "pmap"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#done seg
doneSeg = self.topLevelOperatorView.opCarving.DoneSegmentation
if doneSeg.ready():
if self._doneSegmentationLayer is None:
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "done seg"
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
else:
layers.append(self._doneSegmentationLayer)
#supervoxel
sv = self.topLevelOperatorView.opCarving.Supervoxels
if sv.ready():
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())
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "supervoxels"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
#raw data
#(here we load the actual raw data from an ArraySource rather than from a LazyflowSource for speed reasons)
raw5D = self.topLevelOperatorView.RawData.value
layer = GrayscaleLayer(ArraySource(raw5D), direct=True)
layer.name = "raw"
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
return layers
def setupLayers( self ):
logger.debug( "setupLayers" )
layers = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
labellayer._allowToggleVisible = False
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#uncertainty
if self._showUncertaintyLayer:
uncert = self.topLevelOperatorView.Uncertainty
if uncert.ready():
colortable = []
for i in range(256-len(colortable)):
r,g,b,a = i,0,0,i
colortable.append(QColor(r,g,b,a).rgba())
layer = ColortableLayer(LazyflowSource(uncert), colortable, direct=True)
layer.name = "Uncertainty"
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#segmentation
seg = self.topLevelOperatorView.Segmentation
#seg = self.topLevelOperatorView.MST.value.segmentation
#temp = self._done_lut[self.MST.value.regionVol[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
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())
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "Segmentation"
layer.setToolTip("This layer displays the <i>current</i> segmentation. Simply add foreground and background " \
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self.topLevelOperatorView.DoneObjects
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
#have to use lazyflow because it provides dirty signals
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip("In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b> in one color (<b>blue</b>). " \
"The reason for only one color is that for finding out which " \
"objects to label next, the identity of already completed objects is unimportant " \
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
#done seg
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip("<html>In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b>, each with a random color.</html>")
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
#supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.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())
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "Supervoxels"
layer.setToolTip("<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving " \
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an " \
"object. Sometimes, supervoxels are too large and straddle two distinct objects " \
"(undersegmentation). In this case, it will be impossible to achieve the desired " \
"segmentation. This layer helps you to understand these cases.</html>")
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.visible = True
layer.name = 'Raw Data'
layer.opacity = 1.0
layers.append(layer)
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot), direct=True )
layer.name = "Input Data"
layer.setToolTip("<html>The data originally loaded into ilastik (unprocessed).</html>")
#layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
# if the flag window_leveling is set the contrast
# of the layer is adjustable
layer.window_leveling = True
layers.append(layer)
if layer.window_leveling:
self.labelingDrawerUi.thresToolButton.show()
else:
self.labelingDrawerUi.thresToolButton.hide()
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer( LazyflowSource(filteredSlot) )
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
# 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()
def showStuff(raw_name, pred_viewer1, pred_viewer2, cutout_name, one_extra = None):
# display the raw and annotations for cremi challenge data
raw = vigra.impex.readHDF5(indir+datasets[raw_name], "data", order = 'C')
# raw_old = vigra.readHDF5(indir+datasets["raw_bad"], "data", order = 'C')
defect_prediction_128 = vigra.impex.readHDF5(indir+datasets[pred_viewer2], "data", order = 'C')
defect_prediction_150 = vigra.impex.readHDF5(indir+datasets[pred_viewer1], "data", order = 'C')
cutout_from_150_pred = vigra.impex.readHDF5(indir+datasets[cutout_name], "data", order = 'C')
####################################################################################################################
# only used for fast testing stuff
#change_one = vigra.readHDF5(indir+datasets["segmentation_on_equalized_image"], "data", order = 'C')
#pdb.set_trace()
#defect_prediction_150[1,:,:] = change_one[0,:,:,0]
####################################################################################################################
# defect_prediction_150 = gt[..., 0]
cutout = numpy.asarray(cutout_from_150_pred)
rawdata = numpy.asarray(raw)
# rawdata_old = numpy.asarray(raw_old)
# op5ify
# shape5d = rawdata.shape
shape5d = (1,)+rawdata.shape+(1,)
print shape5d, rawdata.shape, rawdata.dtype
app = QApplication([])
v = Viewer()
direct = False
# layer for raw data
rawdata = numpy.reshape(rawdata, shape5d)
rawsource = ArraySource(rawdata)
v.dataShape = shape5d
lraw = GrayscaleLayer(rawsource, direct=direct)
lraw.visible = True
lraw.name = "raw"
v.layerstack.append(lraw)
# layer for cutout regions from raw data
cutout = numpy.reshape(cutout, shape5d)
cutoutsource = ArraySource(cutout)
lcutout = GrayscaleLayer(cutoutsource, direct = direct)
lcutout.visible = False
lcutout.name = "cut_out"
v.layerstack.append(lcutout)
# layer for first prediction result
defect_prediction_128 = numpy.reshape(defect_prediction_128, shape5d)
synsource = ArraySource(defect_prediction_128)
ct = create_random_16bit()
ct[0] = 0
lsyn = ColortableLayer(synsource, ct)
lsyn.name = pred_viewer2
lsyn.visible = False
v.layerstack.append(lsyn)
# layer for second prediction result
segm = numpy.reshape(defect_prediction_150, shape5d)
segsource = ArraySource(segm)
ct = create_random_16bit()
ct[0] = 0
lseg = ColortableLayer(segsource, ct)
lseg.name = pred_viewer1
lseg.visible = False
v.layerstack.append(lseg)
if one_extra is None:
v.showMaximized()
app.exec_()
if one_extra is not None:
# layer for third prediction result
extra_prediction = vigra.readHDF5(indir+datasets[one_extra], "data", order = 'C')
extra_pred_reshaped = numpy.reshape(extra_prediction, shape5d)
segsource = ArraySource(extra_pred_reshaped)
ct = create_random_16bit()
ct[0] = 0
# ct = create_default_16bit()
lseg = ColortableLayer(segsource, ct)
lseg.name = one_extra
lseg.visible = False
v.layerstack.append(lseg)
v.showMaximized()
app.exec_()
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 = []
def onButtonsEnabled(slot, roi):
currObj = self.topLevelOperatorView.CurrentObjectName.value
hasSeg = self.topLevelOperatorView.HasSegmentation.value
self.labelingDrawerUi.currentObjectLabel.setText(currObj)
self.labelingDrawerUi.save.setEnabled(hasSeg)
self.topLevelOperatorView.CurrentObjectName.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.HasSegmentation.notifyDirty(onButtonsEnabled)
self.topLevelOperatorView.opLabelArray.NonzeroBlocks.notifyDirty(onButtonsEnabled)
# Labels
labellayer, labelsrc = self.createLabelLayer(direct=True)
if labellayer is not None:
layers.append(labellayer)
# Tell the editor where to draw label data
self.editor.setLabelSink(labelsrc)
#uncertainty
if self._showUncertaintyLayer:
uncert = self.topLevelOperatorView.Uncertainty
if uncert.ready():
colortable = []
for i in range(256-len(colortable)):
r,g,b,a = i,0,0,i
colortable.append(QColor(r,g,b,a).rgba())
layer = ColortableLayer(LazyflowSource(uncert), colortable, direct=True)
layer.name = "Uncertainty"
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#segmentation
seg = self.topLevelOperatorView.Segmentation
#seg = self.topLevelOperatorView.MST.value.segmentation
#temp = self._done_lut[self.MST.value.regionVol[sl[1:4]]]
if seg.ready():
#source = RelabelingArraySource(seg)
#source.setRelabeling(numpy.arange(256, dtype=numpy.uint8))
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,0,0).rgba(), QColor(0,255,0).rgba()]
for i in range(256-len(colortable)):
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())
layer = ColortableLayer(LazyflowSource(seg), colortable, direct=True)
layer.name = "Segmentation"
layer.setToolTip("This layer displays the <i>current</i> segmentation. Simply add foreground and background " \
"labels, then press <i>Segment</i>.")
layer.visible = True
layer.opacity = 0.3
layers.append(layer)
#done
done = self.topLevelOperatorView.DoneObjects
if done.ready():
colortable = [QColor(0,0,0,0).rgba(), QColor(0,0,255).rgba()]
for i in range(254-len(colortable)):
r,g,b = numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255)
# ensure colors have sufficient distance to pure red and pure green
while (255 - r)+g+b<128 or r+(255-g)+b<128:
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())
#have to use lazyflow because it provides dirty signals
layer = ColortableLayer(LazyflowSource(done), colortable, direct=True)
layer.name = "Completed segments (unicolor)"
layer.setToolTip("In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b> in one color (<b>blue</b>). " \
"The reason for only one color is that for finding out which " \
"objects to label next, the identity of already completed objects is unimportant " \
"and destracting.")
layer.visible = False
layer.opacity = 0.5
layers.append(layer)
#hints
'''
useLazyflow = True
ctable = [QColor(0,0,0,0).rgba(), QColor(255,0,0).rgba()]
ctable.extend( [QColor(255*random.random(), 255*random.random(), 255*random.random()) for x in range(254)] )
if useLazyflow:
hints = self.topLevelOperatorView.HintOverlay
layer = ColortableLayer(LazyflowSource(hints), ctable, direct=True)
else:
hints = self.topLevelOperatorView._hints
layer = ColortableLayer(ArraySource(hints), ctable, direct=True)
if not useLazyflow or hints.ready():
layer.name = "hints"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
'''
'''
#pmaps
useLazyflow = True
pmaps = self.topLevelOperatorView._pmap
if pmaps is not None:
layer = GrayscaleLayer(ArraySource(pmaps), direct=True)
layer.name = "pmap"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
'''
#done seg
doneSeg = self.topLevelOperatorView.DoneSegmentation
if doneSeg.ready():
if self._doneSegmentationLayer is None:
layer = ColortableLayer(LazyflowSource(doneSeg), self._doneSegmentationColortable, direct=True)
layer.name = "Completed segments (one color per object)"
layer.setToolTip("<html>In order to keep track of which objects you have already completed, this layer " \
"shows <b>all completed object</b>, each with a random color.</html>")
layer.visible = False
layer.opacity = 0.5
self._doneSegmentationLayer = layer
layers.append(layer)
else:
layers.append(self._doneSegmentationLayer)
#supervoxel
sv = self.topLevelOperatorView.Supervoxels
if sv.ready():
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())
layer = ColortableLayer(LazyflowSource(sv), colortable, direct=True)
layer.name = "Supervoxels"
layer.setToolTip("<html>This layer shows the partitioning of the input image into <b>supervoxels</b>. The carving " \
"algorithm uses these tiny puzzle-piceces to piece together the segmentation of an " \
"object. Sometimes, supervoxels are too large and straddle two distinct objects " \
"(undersegmentation). In this case, it will be impossible to achieve the desired " \
"segmentation. This layer helps you to understand these cases.</html>")
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.visible = True
layer.name = 'raw'
layer.opacity = 1.0
layers.append(layer)
'''
inputSlot = self.topLevelOperatorView.InputData
if inputSlot.ready():
layer = GrayscaleLayer( LazyflowSource(inputSlot), direct=True )
layer.name = "Input Data"
layer.setToolTip("<html>The data originally loaded into ilastik (unprocessed).</html>")
#layer.visible = not rawSlot.ready()
layer.visible = True
layer.opacity = 1.0
layers.append(layer)
filteredSlot = self.topLevelOperatorView.FilteredInputData
if filteredSlot.ready():
layer = GrayscaleLayer( LazyflowSource(filteredSlot) )
layer.name = "Filtered Input"
layer.visible = False
layer.opacity = 1.0
layers.append(layer)
return layers
