class ConnectedComponentsTab(IlastikTabBase, QtGui.QWidget):
name = 'Connected Components'
position = 2
moduleName = "Connected_Components"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
def on_activation(self):
if self.ilastik.project is None:
return
ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs()
if len(ovs) == 0:
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None:
ovs.append(raw.getRef())
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.backgroundLabels = BackgroundWidget(self.ilastik._activeImage.Connected_Components, self.ilastik._activeImage.Connected_Components.background, self.ilastik.labelWidget)
self.ilastik.labelWidget.setLabelWidget(self.backgroundLabels)
#create ObjectsOverlay
ov = BackgroundOverlayItem(self.backgroundLabels, self.ilastik._activeImage.Connected_Components.background._data, color = 0, alpha = 1.0, 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(self.backgroundLabels)
def on_deActivation(self):
if self.ilastik.project is None:
return
self.ilastik._activeImage.Connected_Components.background._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Connected_Components.background._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Connected_Components.background._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnInputOverlay = TabButton('Select Overlay', ilastikIcons.Select)
self.btnCC = TabButton('CC', ilastikIcons.System)
self.btnCCBack = TabButton('CC with background', ilastikIcons.System)
self.btnFilter = TabButton('Filter synapses', ilastikIcons.System)
self.btnInputOverlay.setToolTip('Select an overlay for connected components search')
self.btnCC.setToolTip('Run connected components on the selected overlay')
self.btnCCBack.setToolTip('Run connected components with background')
self.btnFilter.setToolTip('Perform synapse filtering and dilation')
self.btnInputOverlay.setEnabled(True)
self.btnCC.setEnabled(False)
self.btnCCBack.setEnabled(False)
self.btnFilter.setEnabled(True)
tl.addWidget(self.btnInputOverlay)
tl.addWidget(self.btnCC)
tl.addWidget(self.btnCCBack)
tl.addStretch()
tl.addWidget(self.btnFilter)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnInputOverlay, QtCore.SIGNAL('clicked()'), self.on_btnInputOverlay_clicked)
self.connect(self.btnCC, QtCore.SIGNAL('clicked()'), self.on_btnCC_clicked)
self.connect(self.btnCCBack, QtCore.SIGNAL('clicked()'), self.on_btnCCBack_clicked)
self.connect(self.btnFilter, QtCore.SIGNAL('clicked()'), self.on_btnFilter_clicked)
#self.connect(self.btnCCOptions, QtCore.SIGNAL('clicked()'), self.on_btnCCOptions_clicked)
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_btnCC_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(None)
#self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connect(background = False)
def on_btnCCBack_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connCompBackgroundClasses)
self.btnFilter.setEnabled(True)
#self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connect(background = True)
def on_btnFilter_clicked(self):
descriptions = self.parent.project.dataMgr.module["Classification"]["labelDescriptions"]
desc_names = []
for i, d in enumerate(descriptions):
tempstr = str(i)+" "+d.name
desc_names.append(tempstr)
dlg = LabelSelectionForm(self.ilastik, desc_names)
label, minsize, maxsize = dlg.exec_()
print label, minsize, maxsize
# call core function
self.parent.project.dataMgr.Connected_Components.filterSynapses(self.inputOverlay, label, minsize, maxsize)
self.ilastik.labelWidget.repaint()
def on_btnCCBack_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connCompBackgroundClasses)
self.btnFilter.setEnabled(True)
def on_btnCC_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(None)
class ConnectedComponentsTab(IlastikTabBase, QtGui.QWidget):
name = 'Connected Components'
position = 2
moduleName = "Connected_Components"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
def on_activation(self):
if self.ilastik.project is None:
return
ovs = self.ilastik._activeImage.module[
self.__class__.moduleName].getOverlayRefs()
if len(ovs) == 0:
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
if raw is not None:
ovs.append(raw.getRef())
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
overlayWidget = OverlayWidget(self.ilastik.labelWidget,
self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.backgroundLabels = BackgroundWidget(
self.ilastik._activeImage.Connected_Components,
self.ilastik._activeImage.Connected_Components.background,
self.ilastik.labelWidget)
self.ilastik.labelWidget.setLabelWidget(self.backgroundLabels)
#create ObjectsOverlay
ov = BackgroundOverlayItem(
self.backgroundLabels,
self.ilastik._activeImage.Connected_Components.background._data,
color=0,
alpha=1.0,
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(self.backgroundLabels)
def on_deActivation(self):
if self.ilastik.project is None:
return
self.ilastik._activeImage.Connected_Components.background._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Connected_Components.background._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Connected_Components.background._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnInputOverlay = TabButton('Select Overlay', ilastikIcons.Select)
self.btnCC = TabButton('CC', ilastikIcons.System)
self.btnCCBack = TabButton('CC with background', ilastikIcons.System)
self.btnFilter = TabButton('Filter synapses', ilastikIcons.System)
self.btnInputOverlay.setToolTip(
'Select an overlay for connected components search')
self.btnCC.setToolTip(
'Run connected components on the selected overlay')
self.btnCCBack.setToolTip('Run connected components with background')
self.btnFilter.setToolTip('Perform synapse filtering and dilation')
self.btnInputOverlay.setEnabled(True)
self.btnCC.setEnabled(False)
self.btnCCBack.setEnabled(False)
self.btnFilter.setEnabled(True)
tl.addWidget(self.btnInputOverlay)
tl.addWidget(self.btnCC)
tl.addWidget(self.btnCCBack)
tl.addStretch()
tl.addWidget(self.btnFilter)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnInputOverlay, QtCore.SIGNAL('clicked()'),
self.on_btnInputOverlay_clicked)
self.connect(self.btnCC, QtCore.SIGNAL('clicked()'),
self.on_btnCC_clicked)
self.connect(self.btnCCBack, QtCore.SIGNAL('clicked()'),
self.on_btnCCBack_clicked)
self.connect(self.btnFilter, QtCore.SIGNAL('clicked()'),
self.on_btnFilter_clicked)
#self.connect(self.btnCCOptions, QtCore.SIGNAL('clicked()'), self.on_btnCCOptions_clicked)
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_btnCC_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(None)
#self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connect(background = False)
def on_btnCCBack_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(self.parent.project.dataMgr[
self.parent.project.dataMgr._activeImageNumber].
Connected_Components.connCompBackgroundClasses)
self.btnFilter.setEnabled(True)
#self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Connected_Components.connect(background = True)
def on_btnFilter_clicked(self):
descriptions = self.parent.project.dataMgr.module["Classification"][
"labelDescriptions"]
desc_names = []
for i, d in enumerate(descriptions):
tempstr = str(i) + " " + d.name
desc_names.append(tempstr)
dlg = LabelSelectionForm(self.ilastik, desc_names)
label, minsize, maxsize = dlg.exec_()
print label, minsize, maxsize
# call core function
self.parent.project.dataMgr.Connected_Components.filterSynapses(
self.inputOverlay, label, minsize, maxsize)
self.ilastik.labelWidget.repaint()
def on_btnCCBack_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(self.parent.project.dataMgr[
self.parent.project.dataMgr._activeImageNumber].
Connected_Components.connCompBackgroundClasses)
self.btnFilter.setEnabled(True)
def on_btnCC_clicked(self):
self.connComp = CC(self.ilastik)
self.connComp.start(None)
