def __init__(self, ilastik, instance=None):
QtGui.QDialog.__init__(self, ilastik)
self.setWindowTitle("Multi-variate Thresholding")
self.ilastik = ilastik
if instance != None:
self.overlayItem = instance
else:
ovm = self.ilastik.project.dataMgr[
self.ilastik._activeImageNumber].overlayMgr
k = ovm.keys()[0]
ov = ovm[k]
self.overlayItem = ThresholdOverlay([ov], [])
self.volumeEditor = ilastik.labelWidget
self.project = ilastik.project
self.mainlayout = QtGui.QVBoxLayout()
self.setLayout(self.mainlayout)
self.mainwidget = QtGui.QWidget()
self.mainlayout.addWidget(self.mainwidget)
self.hbox = None
self.buildDialog()
self.acceptButton = QtGui.QPushButton("Ok")
self.connect(self.acceptButton, QtCore.SIGNAL('clicked()'),
self.okClicked)
self.mainlayout.addWidget(self.acceptButton)
def __init__(self, ilastik, instance = None):
QtGui.QDialog.__init__(self, ilastik)
self.setWindowTitle("Multi-variate Thresholding")
self.ilastik = ilastik
if instance != None:
self.overlayItem = instance
else:
ovm = self.ilastik.project.dataMgr[self.ilastik._activeImageNumber].overlayMgr
k = ovm.keys()[0]
ov = ovm[k]
self.overlayItem = ThresholdOverlay([ov], [])
self.volumeEditor = ilastik.labelWidget
self.project = ilastik.project
self.mainlayout = QtGui.QVBoxLayout()
self.setLayout(self.mainlayout)
self.mainwidget = QtGui.QWidget()
self.mainlayout.addWidget(self.mainwidget)
self.hbox = None
self.buildDialog()
self.acceptButton = QtGui.QPushButton("Ok")
self.connect(self.acceptButton, QtCore.SIGNAL('clicked()'), self.okClicked)
self.mainlayout.addWidget(self.acceptButton)
class MultivariateThresholdDialog(overlayDialogBase.OverlayDialogBase,
QtGui.QDialog):
configuresClass = "ilastik.core.overlays.thresholdOverlay.ThresholdOverlay"
name = "Thresholding Overlay"
author = "C. N. S."
homepage = "hci"
description = "lazy evaluation thresholding"
def __init__(self, ilastik, instance=None):
QtGui.QDialog.__init__(self, ilastik)
self.setWindowTitle("Multi-variate Thresholding")
self.ilastik = ilastik
if instance != None:
self.overlayItem = instance
else:
ovm = self.ilastik.project.dataMgr[
self.ilastik._activeImageNumber].overlayMgr
k = ovm.keys()[0]
ov = ovm[k]
self.overlayItem = ThresholdOverlay([ov], [])
self.volumeEditor = ilastik.labelWidget
self.project = ilastik.project
self.mainlayout = QtGui.QVBoxLayout()
self.setLayout(self.mainlayout)
self.mainwidget = QtGui.QWidget()
self.mainlayout.addWidget(self.mainwidget)
self.hbox = None
self.buildDialog()
self.acceptButton = QtGui.QPushButton("Ok")
self.connect(self.acceptButton, QtCore.SIGNAL('clicked()'),
self.okClicked)
self.mainlayout.addWidget(self.acceptButton)
def buildDialog(self):
self.mainwidget.hide()
self.mainlayout.removeWidget(self.mainwidget)
self.mainwidget.close()
del self.mainwidget
self.mainwidget = QtGui.QWidget()
self.mainlayout.insertWidget(0, self.mainwidget)
self.hbox = QtGui.QHBoxLayout()
self.mainwidget.setLayout(self.hbox)
self.sliders = []
self.sliderReceivers = []
self.previousValues = []
self.totalValue = 0
for index, t in enumerate(self.overlayItem.foregrounds):
l = QtGui.QVBoxLayout()
#print t.name
#print len(self.overlayItem.thresholds)
#print index
self.sliderReceivers.append(
SliderReceiver(self, index,
self.overlayItem.thresholds[index] * 1000))
w = QtGui.QSlider(QtCore.Qt.Vertical)
#*******************************************************************************
# p r o b a b i l i t y *
#*******************************************************************************
w.setToolTip(
"Change the threshold for " + str(t.name) +
"\n a low threshold compared to the other thresholds means a high class probability"
)
w.setRange(0, 999)
w.setSingleStep(1)
w.setValue(self.overlayItem.thresholds[index] * 1000)
l.addWidget(w)
label = QtGui.QLabel(t.name)
l.addWidget(label)
self.sliderReceivers[-1].connect(
w, QtCore.SIGNAL('sliderMoved(int)'),
self.sliderReceivers[-1].sliderMoved)
self.sliders.append(w)
self.hbox.addLayout(l)
if len(self.overlayItem.backgrounds) > 0:
l = QtGui.QVBoxLayout()
self.sliderReceivers.append(
SliderReceiver(self, len(self.sliders),
self.overlayItem.thresholds[-1] * 1000))
w = QtGui.QSlider(QtCore.Qt.Vertical)
w.setRange(0, 1000)
w.setSingleStep(1)
w.setValue(self.overlayItem.thresholds[-1] * 1000)
l.addWidget(w)
label = QtGui.QLabel('Background')
l.addWidget(label)
self.sliderReceivers[-1].connect(
w, QtCore.SIGNAL('sliderMoved(int)'),
self.sliderReceivers[-1].sliderMoved)
self.sliders.append(w)
self.hbox.addLayout(l)
l = QtGui.QVBoxLayout()
w = QtGui.QPushButton("Select Foreground")
self.connect(w, QtCore.SIGNAL("clicked()"), self.selectForegrounds)
l.addWidget(w)
w = QtGui.QPushButton("Select Background")
self.connect(w, QtCore.SIGNAL("clicked()"), self.selectBackgrounds)
l.addWidget(w)
l2 = QtGui.QHBoxLayout()
self.smoothing = QtGui.QCheckBox("Smooth")
self.smoothing.setToolTip(
"Smooth the input overlays with the specified pixel sigma using a gaussian\n Smoothing may take a while depending on the size of the data..."
)
self.smoothing.setCheckState(self.overlayItem.smoothing * 2)
self.connect(self.smoothing, QtCore.SIGNAL("stateChanged(int)"),
self.smoothingChanged)
self.sigma = QtGui.QLineEdit(str(self.overlayItem.sigma))
self.sigma.setToolTip("sigma in pixels")
l2.addWidget(self.smoothing)
l2.addWidget(self.sigma)
l.addLayout(l2)
self.hbox.addLayout(l)
self.setMinimumHeight(300)
def smoothingChanged(self, state):
sigma = self.overlayItem.sigma
try:
sigma = float(self.sigma.text())
except:
pass
self.overlayItem.sigma = sigma
if state == QtCore.Qt.Checked:
self.overlayItem.smoothing = True
else:
self.overlayItem.smoothing = False
self.overlayItem.setForegrounds(self.overlayItem.foregrounds)
thresholds = []
for i, s in enumerate(self.sliders):
if s.value() > 0:
thresholds.append(s.value() / 1000.0)
else:
thresholds.append(-1 / 1000.0)
self.overlayItem.setThresholds(thresholds)
self.volumeEditor.repaint()
def selectForegrounds(self):
d = ilastik.gui.overlaySelectionDlg.OverlaySelectionDialog(
self.ilastik, singleSelection=False)
o = d.exec_()
if len(o) > 0:
self.overlayItem.setForegrounds(o)
self.buildDialog()
def selectBackgrounds(self):
d = ilastik.gui.overlaySelectionDlg.OverlaySelectionDialog(
self.ilastik, singleSelection=False)
o = d.exec_()
self.overlayItem.setBackgrounds(o)
self.buildDialog()
def sliderMoved(self, index, value, oldValue):
self.sliders[index].setValue(value)
thresholds = []
for i, s in enumerate(self.sliders):
if s.value() > 0:
thresholds.append(s.value() / 1000.0)
else:
thresholds.append(-1 / 1000.0)
self.overlayItem.setThresholds(thresholds)
self.volumeEditor.repaint()
def okClicked(self):
if len(self.overlayItem.dsets) >= 2:
self.accept()
else:
QtGui.QMessageBox.warning(
self, "Error",
"Please select more than one Overlay for thresholding - either more than one foreground overlays, or one foreground and one background overlay !"
)
def exec_(self):
if QtGui.QDialog.exec_(self) == QtGui.QDialog.Accepted:
return self.overlayItem
else:
return None
class MultivariateThresholdDialog(overlayDialogBase.OverlayDialogBase, QtGui.QDialog):
configuresClass = "ilastik.core.overlays.thresholdOverlay.ThresholdOverlay"
name = "Thresholding Overlay"
author = "C. N. S."
homepage = "hci"
description = "lazy evaluation thresholding"
def __init__(self, ilastik, instance = None):
QtGui.QDialog.__init__(self, ilastik)
self.setWindowTitle("Multi-variate Thresholding")
self.ilastik = ilastik
if instance != None:
self.overlayItem = instance
else:
ovm = self.ilastik.project.dataMgr[self.ilastik._activeImageNumber].overlayMgr
k = ovm.keys()[0]
ov = ovm[k]
self.overlayItem = ThresholdOverlay([ov], [])
self.volumeEditor = ilastik.labelWidget
self.project = ilastik.project
self.mainlayout = QtGui.QVBoxLayout()
self.setLayout(self.mainlayout)
self.mainwidget = QtGui.QWidget()
self.mainlayout.addWidget(self.mainwidget)
self.hbox = None
self.buildDialog()
self.acceptButton = QtGui.QPushButton("Ok")
self.connect(self.acceptButton, QtCore.SIGNAL('clicked()'), self.okClicked)
self.mainlayout.addWidget(self.acceptButton)
def buildDialog(self):
self.mainwidget.hide()
self.mainlayout.removeWidget(self.mainwidget)
self.mainwidget.close()
del self.mainwidget
self.mainwidget = QtGui.QWidget()
self.mainlayout.insertWidget(0, self.mainwidget)
self.hbox = QtGui.QHBoxLayout()
self.mainwidget.setLayout(self.hbox)
self.sliders = []
self.sliderReceivers = []
self.previousValues = []
self.totalValue = 0
for index, t in enumerate(self.overlayItem.foregrounds):
l = QtGui.QVBoxLayout()
#print t.name
#print len(self.overlayItem.thresholds)
#print index
self.sliderReceivers.append(SliderReceiver(self,index,self.overlayItem.thresholds[index] * 1000))
w = QtGui.QSlider(QtCore.Qt.Vertical)
#*******************************************************************************
# p r o b a b i l i t y *
#*******************************************************************************
w.setToolTip("Change the threshold for " + str(t.name) + "\n a low threshold compared to the other thresholds means a high class probability")
w.setRange(0,999)
w.setSingleStep(1)
w.setValue(self.overlayItem.thresholds[index] * 1000)
l.addWidget(w)
label = QtGui.QLabel(t.name)
l.addWidget(label)
self.sliderReceivers[-1].connect(w, QtCore.SIGNAL('sliderMoved(int)'), self.sliderReceivers[-1].sliderMoved)
self.sliders.append(w)
self.hbox.addLayout(l)
if len(self.overlayItem.backgrounds) > 0:
l = QtGui.QVBoxLayout()
self.sliderReceivers.append(SliderReceiver(self,len(self.sliders),self.overlayItem.thresholds[-1] * 1000))
w = QtGui.QSlider(QtCore.Qt.Vertical)
w.setRange(0,1000)
w.setSingleStep(1)
w.setValue(self.overlayItem.thresholds[-1] * 1000)
l.addWidget(w)
label = QtGui.QLabel('Background')
l.addWidget(label)
self.sliderReceivers[-1].connect(w, QtCore.SIGNAL('sliderMoved(int)'), self.sliderReceivers[-1].sliderMoved)
self.sliders.append(w)
self.hbox.addLayout(l)
l = QtGui.QVBoxLayout()
w = QtGui.QPushButton("Select Foreground")
self.connect(w, QtCore.SIGNAL("clicked()"), self.selectForegrounds)
l.addWidget(w)
w = QtGui.QPushButton("Select Background")
self.connect(w, QtCore.SIGNAL("clicked()"), self.selectBackgrounds)
l.addWidget(w)
l2 = QtGui.QHBoxLayout()
self.smoothing = QtGui.QCheckBox("Smooth")
self.smoothing.setToolTip("Smooth the input overlays with the specified pixel sigma using a gaussian\n Smoothing may take a while depending on the size of the data...")
self.smoothing.setCheckState(self.overlayItem.smoothing * 2)
self.connect(self.smoothing, QtCore.SIGNAL("stateChanged(int)"), self.smoothingChanged)
self.sigma = QtGui.QLineEdit(str(self.overlayItem.sigma))
self.sigma.setToolTip("sigma in pixels")
l2.addWidget(self.smoothing)
l2.addWidget(self.sigma)
l.addLayout(l2)
self.hbox.addLayout(l)
self.setMinimumHeight(300)
def smoothingChanged(self, state):
sigma = self.overlayItem.sigma
try:
sigma = float(self.sigma.text())
except:
pass
self.overlayItem.sigma = sigma
if state == QtCore.Qt.Checked:
self.overlayItem.smoothing = True
else:
self.overlayItem.smoothing = False
self.overlayItem.setForegrounds(self.overlayItem.foregrounds)
thresholds = []
for i,s in enumerate(self.sliders):
if s.value() > 0:
thresholds.append(s.value() / 1000.0)
else:
thresholds.append(-1 / 1000.0)
self.overlayItem.setThresholds(thresholds)
self.volumeEditor.repaint()
def selectForegrounds(self):
d = ilastik.gui.overlaySelectionDlg.OverlaySelectionDialog(self.ilastik, singleSelection = False)
o = d.exec_()
if len(o) > 0:
self.overlayItem.setForegrounds(o)
self.buildDialog()
def selectBackgrounds(self):
d = ilastik.gui.overlaySelectionDlg.OverlaySelectionDialog(self.ilastik, singleSelection = False)
o = d.exec_()
self.overlayItem.setBackgrounds(o)
self.buildDialog()
def sliderMoved(self, index, value, oldValue):
self.sliders[index].setValue(value)
thresholds = []
for i,s in enumerate(self.sliders):
if s.value() > 0:
thresholds.append(s.value() / 1000.0)
else:
thresholds.append(-1 / 1000.0)
self.overlayItem.setThresholds(thresholds)
self.volumeEditor.repaint()
def okClicked(self):
if len(self.overlayItem.dsets) >= 2:
self.accept()
else:
QtGui.QMessageBox.warning(self, "Error", "Please select more than one Overlay for thresholding - either more than one foreground overlays, or one foreground and one background overlay !")
def exec_(self):
if QtGui.QDialog.exec_(self) == QtGui.QDialog.Accepted:
return self.overlayItem
else:
return None
