def on_doneOverlaysAvailable(self):
s = self.ilastik._activeImage.Interactive_Segmentation
bluetable = [QtGui.qRgb(0, 0, 255) for i in range(256)]
bluetable[0] = long(0) #transparency
randomColorTable = [QtGui.qRgb(random.randint(0,255),random.randint(0,255),random.randint(0,255)) for i in range(256)]
randomColorTable[0] = long(0) #transparency
self.doneBinaryOverlay = OverlayItem(s.done, color = 0, colorTable=bluetable, alpha = 0.5, autoAdd = True, autoVisible = True, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Done"] = self.doneBinaryOverlay
self.doneObjectsOverlay = OverlayItem(s.done, color=0, colorTable=randomColorTable, alpha=0.7, autoAdd=False, autoVisible=False, min = 0, max = 255)
self.ilastik._activeImage.overlayMgr["Segmentation/Objects"] = self.doneObjectsOverlay
self.overlayWidget.addOverlayRef(self.doneBinaryOverlay.getRef())
def on_overlaysChanged(self):
if type(self.parent.labelWidget.labelWidget) is DummyLabelWidget: return
s = self.ilastik._activeImage.Interactive_Segmentation
if s.segmentation is None:
#the segmentation has been cleared, remove overlay
self.activeImage.overlayMgr.remove("Segmentation/Segmentation")
self.segmentationOverlay = None
elif self.activeImage.overlayMgr["Segmentation/Segmentation"] is None:
#ensure that we have a 'Segmentation' overlay which will display the result of the segmentation algorithm
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay = OverlayItem(self.localMgr.segmentation, color = 0, alpha = 1.0, colorTable = origColorTable, autoAdd = True, autoVisible = True, linkColorTable = True)
#this overlay can be shown in 3D
#the label 0 never occurs, label 1 is assigned to the background class
self.segmentationOverlay.displayable3D = True
self.segmentationOverlay.backgroundClasses = set([1])
self.activeImage.overlayMgr["Segmentation/Segmentation"] = self.segmentationOverlay
if s.segmentation is not None:
#create Overlay for segmentation:
res = self.localMgr.segmentation
self.segmentationOverlay._data = DataAccessor(res)
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
origColorTable[1] = 255
self.segmentationOverlay.colorTable = origColorTable
if self.localMgr.potentials is not None:
origColorTable = copy.deepcopy(self.parent.labelWidget.labelWidget.colorTab)
ov = OverlayItem(self.localMgr.potentials,color = origColorTable[1], alpha = 1.0, autoAdd = True, autoVisible = True, min = 0.0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Potentials"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Potentials")
if self.localMgr.borders is not None:
#colorTab = []
#for i in range(256):
# color = QtGui.QColor(random.randint(0,255),random.randint(0,255),random.randint(0,255)).rgba()
# colorTab.append(color)
ov = OverlayItem(self.localMgr.borders, color = QtGui.QColor(), alpha = 1.0, autoAdd = True, autoVisible = False, min = 0, max = 1.0)
self.activeImage.overlayMgr["Segmentation/Supervoxels"] = ov
else:
self.activeImage.overlayMgr.remove("Segmentation/Supervoxels")
self.parent.labelWidget.repaint()
def importOverlay(dataItem, filename, prefix="File Overlays/", attrs=None):
theDataItem = DataImpex.importDataItem(filename, None)
if theDataItem is None:
print "could not load", filename
return None
data = theDataItem[:, :, :, :, :]
if attrs == None:
attrs = OverlayAttributes(filename)
if attrs.min is None:
attrs.min = numpy.min(data)
if attrs.max is None:
attrs.max = numpy.max(data)
if data.shape[0:-1] == dataItem.shape[0:-1]:
ov = OverlayItem(data,
color=attrs.color,
alpha=attrs.alpha,
colorTable=attrs.colorTable,
autoAdd=attrs.autoAdd,
autoVisible=attrs.autoVisible,
min=attrs.min,
max=attrs.max)
ov.key = attrs.key
if len(prefix) > 0:
if prefix[-1] != "/":
prefix = prefix + "/"
dataItem.overlayMgr[prefix + ov.key] = ov
return ov
def on_activation(self):
if self.ilastik.project is None: return
self._initContent()
self._initConnects()
self.interactionLog = []
self.defaultSegmentor = False
#initially add 'Raw Data' overlay
ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs()
if "Raw Data" in self.ilastik._activeImage.overlayMgr.keys():
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None: ovs.append(raw.getRef())
self.ilastik.labelWidget.interactionLog = self.interactionLog
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
self.overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(self.overlayWidget)
if self.parent.project.dataMgr.Interactive_Segmentation.segmentor is None:
segmentors = self.parent.project.dataMgr.Interactive_Segmentation.segmentorClasses
for i, seg in enumerate(segmentors):
if seg.name == "Supervoxel Segmentation":
self.parent.project.dataMgr.Interactive_Segmentation.segmentor = seg()
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget, view='default')
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = True
break
#Finally, initialize the core module
s = self.ilastik._activeImage.Interactive_Segmentation
self.connect(s, QtCore.SIGNAL('overlaysChanged()'), self.on_overlaysChanged)
self.connect(s, QtCore.SIGNAL('doneOverlaysAvailable()'), self.on_doneOverlaysAvailable)
self.connect(s, QtCore.SIGNAL('weightsSetup()'), self.on_setupWeights)
self.connect(s, QtCore.SIGNAL('newSegmentation()'), self.on_newSegmentation)
self.connect(s, QtCore.SIGNAL('numColorsNeeded(int)'), self.on_numColorsNeeded)
self.connect(s, QtCore.SIGNAL('saveAsPossible(bool)'), lambda b: self.btnSaveAs.setEnabled(b))
self.connect(s, QtCore.SIGNAL('savePossible(bool)'), lambda b: self.btnSave.setEnabled(b))
self.connect(s, QtCore.SIGNAL('seedsAvailable(bool)'), lambda b: self.btnSegment.setEnabled(b))
s.init()
#add 'Seeds' overlay
self.seedOverlay = OverlayItem(s.seedLabelsVolume._data, color = 0, alpha = 1.0, colorTable = s.seedLabelsVolume.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Segmentation/Seeds"] = self.seedOverlay
self.seedWidget = SeedListWidget(self.ilastik.project.dataMgr.Interactive_Segmentation.seedMgr, s.seedLabelsVolume, self.ilastik.labelWidget, self.seedOverlay)
self.ilastik.labelWidget.setLabelWidget(self.seedWidget)
self.seedOverlay.displayable3D = True
self.seedOverlay.backgroundClasses = set([0])
self.seedOverlay.smooth3D = False
def finalizeResults(self):
colortable = OverlayItem.createDefaultColorTable('RGB', 256)
#create Overlay for segmentation:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"] is None:
ov = OverlayItem(self.res,
color=0,
alpha=1.0,
colorTable=colortable,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Auto Segmentation/Segmentation"]._data = DataAccessor(
self.res)
def finalizeResults(self):
#create Overlay for connected components:
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"] is None:
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0)
ov = OverlayItem(self.ccThread.result,
color=myColor,
alpha=1.0,
colorTable=colortab,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"]._data = DataAccessor(
self.ccThread.result)
def on_activation(self):
if self.ilastik.project is None:
return
ovs = self.ilastik._activeImage._dataVol.backgroundOverlays
if len(ovs) == 0:
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None:
ovs.append(raw.getRef())
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
#create background overlay
ov = OverlayItem(self.ilastik._activeImage._dataVol.background._data, color=0, alpha=1.0, colorTable = self.ilastik._activeImage._dataVol.background.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Connected Components/Background"] = ov
ov = self.ilastik._activeImage.overlayMgr["Connected Components/Background"]
self.ilastik.labelWidget.setLabelWidget(BackgroundWidget(self.ilastik.project.backgroundMgr, self.ilastik._activeImage._dataVol.background, self.ilastik.labelWidget, ov))
def __init__(self, labelMgr, volumeLabels, volumeEditor):
QtGui.QGroupBox.__init__(self, "Object Picker")
BaseLabelWidget.__init__(self, None)
self.setLayout(QtGui.QVBoxLayout())
self.layout().setMargin(5)
self.listWidget = QtGui.QListWidget(self)
self.layout().addWidget(self.listWidget)
self.volumeEditor = volumeEditor
self.labelMgr = labelMgr
self.listWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.listWidget.connect(
self.listWidget,
QtCore.SIGNAL("customContextMenuRequested(QPoint)"),
self.onContext)
self.volumeLabels = volumeLabels
self.colorTab = []
self.items = []
self.volumeEditor = volumeEditor
self.labelColorTable = [
QtGui.QColor(QtCore.Qt.red),
QtGui.QColor(QtCore.Qt.green),
QtGui.QColor(QtCore.Qt.yellow),
QtGui.QColor(QtCore.Qt.blue),
QtGui.QColor(QtCore.Qt.magenta),
QtGui.QColor(QtCore.Qt.darkYellow),
QtGui.QColor(QtCore.Qt.lightGray)
]
#self.connect(self, QtCore.SIGNAL("currentTextChanged(QString)"), self.changeText)
self.labelPropertiesChanged_callback = None
self.listWidget.setSelectionMode(
QtGui.QAbstractItemView.SingleSelection)
self.initFromVolumeLabels(volumeLabels)
if self.listWidget.model().rowCount() == 0:
self.addLabel("Picker", 1, QtGui.QColor(0, 0, 255))
self.overlayItem = OverlayItem(self.labelMgr.objects._data)
def filterSynapses(self, inputOverlay, label, minsize, maxsize):
#This is a special function to filter synapses. It assumes that the input overlay
#is a threhsold overlay and computes it for equal probabilities, and then dilates the
#the current connected components to the size of their counterparts in the equal
#probability connected components. The resulting objects are filtered to be between minsize
#and maxsize pixels in volume.
#FIXME: This function is very specific and is only put here until ilastik 0.6 allows
#to make it into a special workflow. Remove as soon as possible!
parts = label.split(" ")
labelnum = int(parts[0])
#labelname = parts[1]
thres = self.dataMgr[
self.dataMgr._activeImageNumber].Connected_Components.inputData
cc = self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Results"]
if thres is None:
print "no threshold overlay"
return
if not isinstance(thres._data, MultivariateThresholdAccessor):
print "no threshold overlay used for connected components"
return
if cc is None:
print "No connected components overlay"
return
sfad = SynapseFilterAndSegmentor(self.dataMgr, labelnum, minsize,
maxsize, cc, inputOverlay)
objs_user = sfad.computeUserThreshObjects()
objs_ref = sfad.computeReferenceObjects()
#goodsizes = [s for s in goodsizes if s>100]
#mingoodsize = min(goodsizes)
#maxgoodsize = max(goodsizes)
objs_final = sfad.filterObjects(objs_user, objs_ref)
#create a new, filtered overlay:
result = numpy.zeros(cc.shape, dtype='int32')
objcounter = 1
for iobj in objs_final:
for i in range(len(iobj[0])):
result[0, iobj[0][i], iobj[1][i], iobj[2][i],
0] = int(objcounter)
objcounter = objcounter + 1
if self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"] is None:
#colortab = [QtGui.qRgb(i, i, i) for i in range(256)]
colortab = OverlayItem.createDefault16ColorColorTable()
myColor = OverlayItem.qrgb(255, 0, 0) #QtGui.QColor(255, 0, 0)
ov = OverlayItem(result,
color=myColor,
alpha=1.0,
colorTable=colortab,
autoAdd=True,
autoVisible=True)
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"] = ov
else:
self.dataMgr[self.dataMgr._activeImageNumber].overlayMgr[
"Connected Components/CC Filtered"]._data = DataAccessor(
result)
