def on_btnChooseOverlay_clicked(self):
dlg = OverlaySelectionDialog(self.parent, singleSelection=True)
answer = dlg.exec_()
if len(answer) > 0:
import ilastik.core.overlays.selectionOverlay
if self.parent.project.dataMgr[
self.parent._activeImageNumber].overlayMgr[
"Objects/Selection Result"] is None:
ov = ilastik.core.overlays.selectionOverlay.SelectionOverlay(
answer[0]._data,
color=long(QtGui.QColor(0, 255, 255).rgba()))
ov.displayable3D = True
ov.backgroundClasses = set([0])
ov.smooth3D = True
self.parent.project.dataMgr[
self.parent._activeImageNumber].overlayMgr[
"Objects/Selection Result"] = ov
ov = self.parent.project.dataMgr[
self.parent.
_activeImageNumber].overlayMgr["Objects/Selection Result"]
ref = answer[0].getRef()
ref.setAlpha(0.4)
self.parent.labelWidget.overlayWidget.addOverlayRef(ref)
self.parent.project.dataMgr[
self.parent.project.dataMgr.
_activeImageNumber].Object_Picking.setInputData(
answer[0]._data)
self.parent.labelWidget.repaint()
def on_btnChooseWeights_clicked(self):
#First question: Which overlay?
dlg = OverlaySelectionDialog(self.ilastik, singleSelection = True)
answer = dlg.exec_()
if len(answer) == 0: return #dialog was dismissed
s = self.ilastik._activeImage.Interactive_Segmentation
overlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(overlay.getRef())
volume = overlay._data[0,:,:,:,0]
#Second question: Which border indicator?
borderIndicator = QtGui.QInputDialog.getItem(self.ilastik, \
"Select Border Indicator", "Indicator", \
["Brightness", "Darkness", "Gradient Magnitude"], \
editable = False)
if not borderIndicator[1]: return #Dialog was dismissed
borderIndicator = str(borderIndicator[0])
#Write the choice of weights to a file so that they can be reproduced
if s.outputPath:
f = open(s.outputPath+'/'+'config.txt', 'w')
f.write("overlay=%s\n" % (dlg.selectedOverlayPaths[0]))
f.write("borderIndicator=%s" % (borderIndicator))
f.close()
#calculate the weights
#this will call on_setupWeights via a signal/slot connection
s.calculateWeights(volume, borderIndicator)
def on_btnChooseWeights_clicked(self):
dlg = OverlaySelectionDialog(self.ilastik, singleSelection=True)
answer = dlg.exec_()
if len(answer) > 0:
overlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(
overlay.getRef())
volume = overlay._data[0, :, :, :, 0]
borderIndicator = QtGui.QInputDialog.getItem(
self.ilastik,
"Select border indicator type",
"Select the border probability type : \n (Normal: bright pixels mean high border probability, Inverted: dark pixels mean high border probability) ",
["Normal", "Inverted"],
editable=False)
borderIndicator = str(borderIndicator[0])
if borderIndicator == "Normal":
weights = volume[:, :, :]
elif borderIndicator == "Inverted":
weights = self.parent.project.dataMgr.Automatic_Segmentation.invertPotential(
volume)
weights = self.parent.project.dataMgr.Automatic_Segmentation.normalizePotential(
weights)
self.weights = weights
def on_btnInputOverlay_clicked(self):
dlg = OverlaySelectionDialog(self.ilastik, singleSelection = True)
answer = dlg.exec_()
if len(answer) > 0:
overlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(overlay.getRef())
print overlay.key
self.parent.project.dataMgr.connCompBackgroundKey = overlay.key
self.btnCC.setEnabled(True)
self.btnCCBack.setEnabled(True)
def on_btnInputOverlay_clicked(self):
dlg = OverlaySelectionDialog(self.ilastik, singleSelection = True)
answer = dlg.exec_()
if len(answer) > 0:
ref = answer[0].getRef()
ref.setAlpha(0.4)
self.inputOverlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(ref)
self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.setInputData(answer[0]._data)
self.parent.labelWidget.repaint()
self.btnCC.setEnabled(True)
self.btnCCBack.setEnabled(True)
def on_btnInputOverlay_clicked(self):
dlg = OverlaySelectionDialog(self.ilastik, singleSelection=True)
answer = dlg.exec_()
if len(answer) > 0:
ref = answer[0].getRef()
ref.setAlpha(0.4)
self.inputOverlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(ref)
self.parent.project.dataMgr[
self.parent.project.dataMgr.
_activeImageNumber].Connected_Components.setInputData(
answer[0]._data)
self.parent.labelWidget.repaint()
self.btnCC.setEnabled(True)
self.btnCCBack.setEnabled(True)
def on_btnChooseOverlays_clicked(self):
dlg = OverlaySelectionDialog(self.parent, singleSelection = False)
overlays = dlg.exec_()
if len(overlays) > 0:
self.overlays = overlays
# add all overlays
for overlay in overlays:
ref = overlay.getRef()
ref.setAlpha(0.4)
self.parent.labelWidget.overlayWidget.addOverlayRef(ref)
self.parent.labelWidget.repaint()
self.btnDecompose.setEnabled(True)
else:
self.btnDecompose.setEnabled(False)
def on_btnChooseWeights_clicked(self):
dlg = OverlaySelectionDialog(self.ilastik, singleSelection = True)
answer = dlg.exec_()
if len(answer) > 0:
overlay = answer[0]
self.parent.labelWidget.overlayWidget.addOverlayRef(overlay.getRef())
volume = overlay._data[0,:,:,:,0]
borderIndicator = QtGui.QInputDialog.getItem(self.ilastik, "Select border indicator type", "Select the border probability type : \n (Normal: bright pixels mean high border probability, Inverted: dark pixels mean high border probability) ", ["Normal", "Inverted"], editable = False)
borderIndicator = str(borderIndicator[0])
if borderIndicator == "Normal":
weights = volume[:,:,:]
elif borderIndicator == "Inverted":
weights = self.parent.project.dataMgr.Automatic_Segmentation.invertPotential(volume)
weights = self.parent.project.dataMgr.Automatic_Segmentation.normalizePotential(weights)
self.weights = weights
def on_btnChooseOverlay_clicked(self):
dlg = OverlaySelectionDialog(self.parent, singleSelection = True)
answer = dlg.exec_()
if len(answer) > 0:
import ilastik.core.overlays.selectionOverlay
if self.parent.project.dataMgr[self.parent._activeImageNumber].overlayMgr["Objects/Selection Result"] is None:
ov = ilastik.core.overlays.selectionOverlay.SelectionOverlay(answer[0]._data, color = long(QtGui.QColor(0,255,255).rgba()))
ov.displayable3D = True
ov.backgroundClasses = set([0])
ov.smooth3D = True
self.parent.project.dataMgr[self.parent._activeImageNumber].overlayMgr["Objects/Selection Result"] = ov
ov = self.parent.project.dataMgr[self.parent._activeImageNumber].overlayMgr["Objects/Selection Result"]
ref = answer[0].getRef()
ref.setAlpha(0.4)
self.parent.labelWidget.overlayWidget.addOverlayRef(ref)
self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Object_Picking.setInputData(answer[0]._data)
self.parent.labelWidget.repaint()