def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnSelectFeatures = TabButton('Select Features', ilastikIcons.Select)
self.btnStartLive = TabButton('Start Live Prediction', ilastikIcons.Play)
self.btnStartLive.setCheckable(True)
self.btnTrainPredict = TabButton('Train and Predict', ilastikIcons.System)
self.btnExportClassifier = TabButton('Export Classifier', ilastikIcons.Select)
self.btnClassifierOptions = TabButton('Classifier Options', ilastikIcons.Select)
self.btnSelectFeatures.setToolTip('Select and compute features')
self.btnStartLive.setToolTip('Toggle interactive prediction of the current image while labeling')
self.btnTrainPredict.setToolTip('Train and predict all images offline; this step is necessary for automation')
self.btnExportClassifier.setToolTip('Save current classifier and its feature settings')
self.btnClassifierOptions.setToolTip('Select a classifier and change its settings')
self.on_otherProject()
tl.addWidget(self.btnSelectFeatures)
tl.addWidget(self.btnStartLive)
tl.addWidget(self.btnTrainPredict)
tl.addStretch()
tl.addWidget(self.btnExportClassifier)
tl.addWidget(self.btnClassifierOptions)
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseOverlay = TabButton('Select overlay', ilastikIcons.Select)
self.btn3D = TabButton('3D', ilastikIcons.Play)
self.btnReport = TabButton('Generate report', ilastikIcons.Play)
self.btnSelectAll = TabButton('Select all', ilastikIcons.Select)
self.btnClearAll = TabButton('Clear all', ilastikIcons.Select)
self.btnChooseOverlay.setToolTip('Choose the overlay with objects')
self.btn3D.setToolTip('Display the currently selected objects in 3D')
self.btnReport.setToolTip('Generate a report for all currently selected objects')
self.btnSelectAll.setToolTip('Select all the objects')
self.btnClearAll.setToolTip('Clear selection')
tl.addWidget(self.btnChooseOverlay)
tl.addWidget(self.btn3D)
tl.addWidget(self.btnReport)
tl.addStretch()
tl.addWidget(self.btnSelectAll)
tl.addWidget(self.btnClearAll)
self.setLayout(tl)
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)
class HelpTab(IlastikTabBase, QtGui.QWidget):
name = 'Help'
position = 101
moduleName = "Help"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
def on_activation(self):
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())
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
overlayWidget.setVisible(False)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnShortcuts = TabButton('Shortcuts', ilastikIcons.Help)
self.btnAbout = TabButton('About', ilastikIcons.Ilastik)
self.btnShortcuts.setToolTip('Show a list of ilastik shortcuts')
tl.addWidget(self.btnShortcuts)
tl.addWidget(self.btnAbout)
tl.addStretch()
self.setLayout(tl)
#self.shortcutManager = shortcutManager()
def _initConnects(self):
self.connect(self.btnShortcuts, QtCore.SIGNAL('clicked()'), self.on_btnShortcuts_clicked)
self.connect(self.btnAbout, QtCore.SIGNAL('clicked()'), self.on_btnAbout_clicked)
def on_btnShortcuts_clicked(self):
shortcutManager.showDialog(self.ilastik)
def on_btnAbout_clicked(self):
about = About(self.ilastik)
about.show()
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnBatchProcess = TabButton('Batch Process', ilastikIcons.Play)
self.btnBatchProcess.setToolTip(
'Select and batch predict files with the currently trained classifier'
)
tl.addWidget(self.btnBatchProcess)
tl.addStretch()
self.setLayout(tl)
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.btnCCOptions = TabButton('Options', ilastikIcons.System)
self.btnInputOverlay.setToolTip('Select an overlay for connected components search')
self.btnCC.setToolTip('Run connected componets on the selected overlay')
self.btnCCBack.setToolTip('Run connected components with background')
self.btnCCOptions.setToolTip('Set options')
self.btnInputOverlay.setEnabled(True)
self.btnCC.setEnabled(False)
self.btnCCBack.setEnabled(False)
self.btnCCOptions.setEnabled(True)
tl.addWidget(self.btnInputOverlay)
tl.addWidget(self.btnCC)
tl.addWidget(self.btnCCBack)
tl.addStretch()
tl.addWidget(self.btnCCOptions)
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Border Probability Overlay', ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnChooseWeights.setToolTip('Choose the input overlay that contains border probabilities')
self.btnSegment.setToolTip('Segment the image')
tl.addWidget(self.btnChooseWeights)
tl.addWidget(self.btnSegment)
tl.addStretch()
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnNew = TabButton('New', ilastikIcons.New, 'Create new project')
self.btnOpen = TabButton('Open', ilastikIcons.Open,
'Open existing project')
self.btnSave = TabButton('Save', ilastikIcons.Save,
'Save current project to file')
self.btnEdit = TabButton('Edit', ilastikIcons.Edit,
'Edit current project')
self.btnOptions = TabButton('Options', ilastikIcons.Edit,
'Edit ilastik options')
tl.addWidget(self.btnNew)
tl.addWidget(self.btnOpen)
tl.addWidget(self.btnSave)
tl.addWidget(self.btnEdit)
tl.addStretch()
tl.addWidget(self.btnOptions)
self.btnSave.setEnabled(False)
self.btnEdit.setEnabled(False)
self.btnOptions.setEnabled(False)
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnShortcuts = TabButton('Shortcuts', ilastikIcons.Help)
self.btnAbout = TabButton('About', ilastikIcons.Ilastik)
self.btnShortcuts.setToolTip('Show a list of ilastik shortcuts')
tl.addWidget(self.btnShortcuts)
tl.addWidget(self.btnAbout)
tl.addStretch()
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Border Probability Overlay',
ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnChooseWeights.setToolTip(
'Choose the input overlay that contains border probabilities')
self.btnSegment.setToolTip('Segment the image')
tl.addWidget(self.btnChooseWeights)
tl.addWidget(self.btnSegment)
tl.addStretch()
self.setLayout(tl)
class AutomateTab(IlastikTabBase, QtGui.QWidget):
name = 'Automate'
position = 100
moduleName = "Classification"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
def on_activation(self):
overlayWidget = OverlayWidget(self.ilastik.labelWidget,
self.ilastik.project.dataMgr)
overlayWidget.setVisible(False)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnBatchProcess = TabButton('Batch Process', ilastikIcons.Play)
self.btnBatchProcess.setToolTip(
'Select and batch predict files with the currently trained classifier'
)
tl.addWidget(self.btnBatchProcess)
tl.addStretch()
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnBatchProcess, QtCore.SIGNAL('clicked()'),
self.on_btnBatchProcess_clicked)
def on_btnBatchProcess_clicked(self):
dialog = BatchProcess(self.parent)
dialog.exec_()
class AutomateTab(IlastikTabBase, QtGui.QWidget):
name = 'Automate'
position = 100
moduleName = "Classification"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
def on_activation(self):
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
overlayWidget.setVisible(False)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnBatchProcess = TabButton('Batch Process', ilastikIcons.Play)
self.btnBatchProcess.setToolTip('Select and batch predict files with the currently trained classifier')
tl.addWidget(self.btnBatchProcess)
tl.addStretch()
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnBatchProcess, QtCore.SIGNAL('clicked()'), self.on_btnBatchProcess_clicked)
def on_btnBatchProcess_clicked(self):
dialog = BatchProcess(self.parent)
dialog.exec_()
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnBatchProcess = TabButton('Batch Process', ilastikIcons.Play)
self.btnBatchProcess.setToolTip('Select and batch predict files with the currently trained classifier')
tl.addWidget(self.btnBatchProcess)
tl.addStretch()
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnSelectFeatures = TabButton('Select Features',
ilastikIcons.Select)
self.btnStartLive = TabButton('Start Live Prediction',
ilastikIcons.Play)
self.btnStartLive.setCheckable(True)
self.btnTrainPredict = TabButton('Train and Predict',
ilastikIcons.System)
self.btnExportClassifier = TabButton('Export Classifier',
ilastikIcons.Select)
self.btnClassifierOptions = TabButton('Classifier Options',
ilastikIcons.Select)
self.btnSelectFeatures.setToolTip('Select and compute features')
self.btnStartLive.setToolTip(
'Toggle interactive prediction of the current image while labeling'
)
self.btnTrainPredict.setToolTip(
'Train and predict all images offline; this step is necessary for automation'
)
self.btnExportClassifier.setToolTip(
'Save current classifier and its feature settings')
self.btnClassifierOptions.setToolTip(
'Select a classifier and change its settings')
self.on_otherProject()
tl.addWidget(self.btnSelectFeatures)
tl.addWidget(self.btnStartLive)
tl.addWidget(self.btnTrainPredict)
tl.addStretch()
tl.addWidget(self.btnExportClassifier)
tl.addWidget(self.btnClassifierOptions)
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnShortcuts = TabButton('Shortcuts', ilastikIcons.Help)
self.btnAbout = TabButton('About', ilastikIcons.Ilastik)
self.btnShortcuts.setToolTip('Show a list of ilastik shortcuts')
tl.addWidget(self.btnShortcuts)
tl.addWidget(self.btnAbout)
tl.addStretch()
self.setLayout(tl)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseOverlays = TabButton('Select Overlay', ilastikIcons.Select)
self.btnDecompose = TabButton('decompose', ilastikIcons.Play)
self.btnUnsupervisedOptions = TabButton('Unsupervised Decomposition Options', ilastikIcons.System)
self.btnDecompose.setEnabled(False)
self.btnUnsupervisedOptions.setEnabled(False)
self.btnChooseOverlays.setToolTip('Choose the overlays for unsupervised decomposition')
self.btnDecompose.setToolTip('perform unsupervised decomposition')
self.btnUnsupervisedOptions.setToolTip('select an unsupervised decomposition plugin and change settings')
tl.addWidget(self.btnChooseOverlays)
tl.addWidget(self.btnDecompose)
tl.addStretch()
tl.addWidget(self.btnUnsupervisedOptions)
self.setLayout(tl)
class ClassificationTab(IlastikTabBase, QtGui.QWidget):
name = 'Classification'
position = 1
moduleName = "Classification"
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
if self.ilastik._activeImage.module[self.name] is None:
self.ilastik._activeImage.module[self.name] = PropertyMgr(
self.ilastik._activeImage)
ovs = self.ilastik._activeImage.module[self.name].getOverlayRefs()
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
overlayWidget = OverlayWidget(self.ilastik.labelWidget,
self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
ov = self.ilastik._activeImage.overlayMgr["Classification/Labels"]
overlayWidget.addOverlayRef(ov.getRef())
overlayWidget.addOverlayRef(raw.getRef())
self.ilastik.labelWidget.setLabelWidget(
LabelListWidget(
self.ilastik.project.dataMgr.module["Classification"].labelMgr,
self.ilastik.project.dataMgr.module["Classification"]
["labelDescriptions"], self.ilastik.labelWidget, ov))
def on_deActivation(self):
if self.ilastik.project is None:
return
if hasattr(self.parent, "classificationInteractive"):
self.btnStartLive.click()
if self.ilastik.labelWidget is not None and self.ilastik.labelWidget._history != self.ilastik._activeImage.module[
"Classification"]["labelHistory"]:
self.ilastik._activeImage.module["Classification"][
"labelHistory"] = self.ilastik.labelWidget._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnSelectFeatures = TabButton('Select Features',
ilastikIcons.Select)
self.btnStartLive = TabButton('Start Live Prediction',
ilastikIcons.Play)
self.btnStartLive.setCheckable(True)
self.btnTrainPredict = TabButton('Train and Predict',
ilastikIcons.System)
self.btnExportClassifier = TabButton('Export Classifier',
ilastikIcons.Select)
self.btnClassifierOptions = TabButton('Classifier Options',
ilastikIcons.Select)
self.btnSelectFeatures.setToolTip('Select and compute features')
self.btnStartLive.setToolTip(
'Toggle interactive prediction of the current image while labeling'
)
self.btnTrainPredict.setToolTip(
'Train and predict all images offline; this step is necessary for automation'
)
self.btnExportClassifier.setToolTip(
'Save current classifier and its feature settings')
self.btnClassifierOptions.setToolTip(
'Select a classifier and change its settings')
self.on_otherProject()
tl.addWidget(self.btnSelectFeatures)
tl.addWidget(self.btnStartLive)
tl.addWidget(self.btnTrainPredict)
tl.addStretch()
tl.addWidget(self.btnExportClassifier)
tl.addWidget(self.btnClassifierOptions)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnSelectFeatures, QtCore.SIGNAL('clicked()'),
self.on_btnSelectFeatures_clicked)
self.connect(self.btnStartLive, QtCore.SIGNAL('toggled(bool)'),
self.on_btnStartLive_clicked)
self.connect(self.btnTrainPredict, QtCore.SIGNAL('clicked()'),
self.on_btnTrainPredict_clicked)
self.connect(self.btnExportClassifier, QtCore.SIGNAL('clicked()'),
self.on_btnExportClassifier_clicked)
self.connect(self.btnClassifierOptions, QtCore.SIGNAL('clicked()'),
self.on_btnClassifierOptions_clicked)
def on_otherProject(self):
self.btnSelectFeatures.setEnabled(True)
self.btnStartLive.setEnabled(False)
self.btnTrainPredict.setEnabled(False)
self.btnExportClassifier.setEnabled(False)
self.btnClassifierOptions.setEnabled(True)
def on_btnSelectFeatures_clicked(self):
preview = self.parent.project.dataMgr[0]._dataVol._data[0, 0, :, :,
0:3]
newFeatureDlg = FeatureDlg(self.ilastik, preview)
answer = newFeatureDlg.exec_()
if answer == QtGui.QDialog.Accepted:
self.featureComputation = FeatureComputation(self.ilastik)
newFeatureDlg.close()
newFeatureDlg.deleteLater()
del newFeatureDlg
gc.collect()
def on_btnStartLive_clicked(self, state):
if state:
self.ilastik.ribbon.getTab('Classification').btnStartLive.setText(
'Stop Live Prediction')
self.classificationInteractive = ClassificationInteractive(
self.ilastik)
else:
self.classificationInteractive.stop()
self.ilastik.ribbon.getTab('Classification').btnStartLive.setText(
'Start Live Prediction')
def on_btnTrainPredict_clicked(self):
self.classificationTrain = ClassificationTrain(self.ilastik)
self.connect(self.classificationTrain,
QtCore.SIGNAL("trainingFinished()"),
self.on_trainingFinished)
def on_trainingFinished(self):
print "Training finished"
self.classificationPredict = ClassificationPredict(self.ilastik)
def on_btnExportClassifier_clicked(self):
fileName = QtGui.QFileDialog.getSaveFileName(
self, "Export Classifier", filter="HDF5 Files (*.h5)")
try:
self.ilastik.project.dataMgr.Classification.exportClassifiers(
fileName)
except (RuntimeError, AttributeError, IOError) as e:
QtGui.QMessageBox.warning(self, 'Error', str(e),
QtGui.QMessageBox.Ok)
return
try:
self.ilastik.project.dataMgr.Classification.featureMgr.exportFeatureItems(
fileName)
except RuntimeError as e:
QtGui.QMessageBox.warning(self, 'Error', str(e),
QtGui.QMessageBox.Ok)
return
QtGui.QMessageBox.information(
self, 'Success',
"The classifier and the feature information have been saved successfully to:\n %s"
% str(fileName), QtGui.QMessageBox.Ok)
def on_btnClassifierOptions_clicked(self):
dialog = ClassifierSelectionDlg(self.parent)
self.parent.project.dataMgr.module[
"Classification"].classifier = dialog.exec_()
class ObjectsTab(IlastikTabBase, QtGui.QWidget):
name = 'Objects'
moduleName = "Object_Picking"
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.objectLabels = ObjectListWidget(
self.ilastik._activeImage.Object_Picking,
self.ilastik._activeImage.Object_Picking.objects,
self.ilastik.labelWidget)
self.ilastik.labelWidget.setLabelWidget(self.objectLabels)
#create ObjectsOverlay
ov = ObjectOverlayItem(
self.objectLabels,
self.ilastik._activeImage.Object_Picking.objects._data,
color=0,
alpha=1.0,
autoAdd=True,
autoVisible=True,
linkColorTable=True)
self.ilastik._activeImage.overlayMgr["Objects/Selection"] = ov
ov = self.ilastik._activeImage.overlayMgr["Objects/Selection"]
self.ilastik.labelWidget.setLabelWidget(self.objectLabels)
def on_deActivation(self):
if self.ilastik.project is None:
return
self.ilastik._activeImage.Object_Picking.objects._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Object_Picking.objects._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Object_Picking.objects._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseOverlay = TabButton('Select overlay',
ilastikIcons.Select)
self.btn3D = TabButton('3D', ilastikIcons.Play)
self.btnReport = TabButton('Generate report', ilastikIcons.Play)
self.btnSelectAll = TabButton('Select all', ilastikIcons.Select)
self.btnClearAll = TabButton('Clear all', ilastikIcons.Select)
self.btnChooseOverlay.setToolTip('Choose the overlay with objects')
self.btn3D.setToolTip('Display the currently selected objects in 3D')
self.btnReport.setToolTip(
'Generate a report for all currently selected objects')
self.btnSelectAll.setToolTip('Select all the objects')
self.btnClearAll.setToolTip('Clear selection')
tl.addWidget(self.btnChooseOverlay)
tl.addWidget(self.btn3D)
tl.addWidget(self.btnReport)
tl.addStretch()
tl.addWidget(self.btnSelectAll)
tl.addWidget(self.btnClearAll)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnChooseOverlay, QtCore.SIGNAL('clicked()'),
self.on_btnChooseOverlay_clicked)
self.connect(self.btn3D, QtCore.SIGNAL('clicked()'),
self.on_btn3D_clicked)
self.connect(self.btnReport, QtCore.SIGNAL('clicked()'),
self.on_btnReport_clicked)
self.connect(self.btnSelectAll, QtCore.SIGNAL('clicked()'),
self.on_btnSelectAll_clicked)
self.connect(self.btnClearAll, QtCore.SIGNAL('clicked()'),
self.on_btnClearAll_clicked)
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_btn3D_clicked(self):
pass
def on_btnSelectAll_clicked(self):
self.parent.project.dataMgr[
self.parent.project.dataMgr.
_activeImageNumber].Object_Picking.selectAll()
def on_btnClearAll_clicked(self):
self.parent.project.dataMgr[
self.parent.project.dataMgr.
_activeImageNumber].Object_Picking.clearAll()
def on_btnReport_clicked(self):
fileName = QtGui.QFileDialog.getSaveFileName(
self, "Save Report", ilastik.gui.LAST_DIRECTORY,
"Reports (*.html)")
fn = str(QtCore.QDir.convertSeparators(fileName))
ilastik.gui.LAST_DIRECTORY = QtCore.QFileInfo(fn).path()
self.parent.project.dataMgr[
self.parent.project.dataMgr.
_activeImageNumber].Object_Picking.generateReport(fn)
class AutoSegmentationTab(IlastikTabBase, QtGui.QWidget):
name = 'Auto Segmentation'
position = 2
moduleName = "Automatic_Segmentation"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
self.weights = None
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.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Border Probability Overlay',
ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnChooseWeights.setToolTip(
'Choose the input overlay that contains border probabilities')
self.btnSegment.setToolTip('Segment the image')
tl.addWidget(self.btnChooseWeights)
tl.addWidget(self.btnSegment)
tl.addStretch()
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnChooseWeights, QtCore.SIGNAL('clicked()'),
self.on_btnChooseWeights_clicked)
self.connect(self.btnSegment, QtCore.SIGNAL('clicked()'),
self.on_btnSegment_clicked)
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_btnSegment_clicked(self):
if self.weights is not None:
self.parent.project.dataMgr.Automatic_Segmentation.computeResults(
self.weights)
self.parent.project.dataMgr.Automatic_Segmentation.finalizeResults(
)
self.parent.labelWidget.repaint()
def on_btnSegmentorsOptions_clicked(self):
pass
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 _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Weights', ilastikIcons.Select)
self.btnChooseDimensions = TabButton('Using 3D', ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnSaveAs = TabButton('Save As', ilastikIcons.SaveAs)
self.btnSave = TabButton('Save', ilastikIcons.Save)
self.btnSegmentorsOptions = TabButton('Change Segmentor', ilastikIcons.System)
self.inlineSettings = InlineSettingsWidget(self)
self.only2D = False
self.btnChooseWeights.setToolTip('Choose the edge weights for the segmentation task')
self.btnSegment.setToolTip('Segment the image into foreground/background')
self.btnChooseDimensions.setToolTip('Switch between slice based 2D segmentation and full 3D segmentation\n This is mainly useful for 3D Date with very weak border indicators, where seeds placed in one slice can bleed out badly to other regions')
self.btnSegmentorsOptions.setToolTip('Select a segmentation plugin and change settings')
tl.addWidget(self.btnChooseWeights)
#tl.addWidget(self.btnChooseDimensions)
tl.addWidget(self.btnSegment)
tl.addWidget(self.inlineSettings)
tl.addWidget(self.btnSave)
tl.addWidget(self.btnSaveAs)
tl.addStretch()
tl.addWidget(self.btnSegmentorsOptions)
self.btnSegment.setEnabled(False)
self.btnSaveAs.setEnabled(False)
self.btnSave.setEnabled(False)
self.btnChooseDimensions.setEnabled(False)
self.btnSegmentorsOptions.setEnabled(False)
self.setLayout(tl)
class ProjectTab(IlastikTabBase, QtGui.QWidget):
name = 'Project'
position = 0
moduleName = "Project"
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:
self.ilastik.setTabBusy(True)
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)
overlayWidget.setVisible(False)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnNew = TabButton('New', ilastikIcons.New, 'Create new project')
self.btnOpen = TabButton('Open', ilastikIcons.Open,
'Open existing project')
self.btnSave = TabButton('Save', ilastikIcons.Save,
'Save current project to file')
self.btnEdit = TabButton('Edit', ilastikIcons.Edit,
'Edit current project')
self.btnOptions = TabButton('Options', ilastikIcons.Edit,
'Edit ilastik options')
tl.addWidget(self.btnNew)
tl.addWidget(self.btnOpen)
tl.addWidget(self.btnSave)
tl.addWidget(self.btnEdit)
tl.addStretch()
tl.addWidget(self.btnOptions)
self.btnSave.setEnabled(False)
self.btnEdit.setEnabled(False)
self.btnOptions.setEnabled(False)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnNew, QtCore.SIGNAL('clicked()'),
self.on_btnNew_clicked)
self.connect(self.btnOpen, QtCore.SIGNAL('clicked()'),
self.on_btnOpen_clicked)
self.connect(self.btnSave, QtCore.SIGNAL('clicked()'),
self.on_btnSave_clicked)
self.connect(self.btnEdit, QtCore.SIGNAL('clicked()'),
self.on_btnEdit_clicked)
self.connect(self.btnOptions, QtCore.SIGNAL('clicked()'),
self.on_btnOptions_clicked)
# Custom Callbacks
def on_btnNew_clicked(self):
self.parent.projectDlg = ProjectDlg(self.parent)
if self.parent.projectDlg.exec_() == QtGui.QDialog.Accepted:
self.btnSave.setEnabled(True)
self.btnEdit.setEnabled(True)
self.btnOptions.setEnabled(True)
self.parent.updateFileSelector()
self.parent._activeImageNumber = 0
self.ilastik.setTabBusy(False)
def on_btnSave_clicked(self):
self.parent.saveProject()
def openProject(self, fileName):
labelWidget = None
self.parent.project = projectClass.Project.loadFromDisk(
str(fileName), self.parent.featureCache)
self.btnSave.setEnabled(True)
self.btnEdit.setEnabled(True)
self.btnOptions.setEnabled(True)
self.parent.updateFileSelector()
self.parent.on_otherProject()
self.ilastik.setTabBusy(False)
ilastik.gui.LAST_DIRECTORY = QtCore.QFileInfo(fileName).path()
gc.collect()
if labelWidget is not None:
if labelWidget() is not None:
refs = gc.get_referrers(labelWidget())
for i, r in enumerate(refs):
print type(r)
print "##################################################################"
print r
def on_btnOpen_clicked(self):
fileName = QtGui.QFileDialog.getOpenFileName(
self, "Open Project", ilastik.gui.LAST_DIRECTORY,
"Project Files (*.ilp)")
if str(fileName) != "":
self.openProject(fileName)
def on_btnEdit_clicked(self):
self.parent.projectDlg = ProjectDlg(self.parent, False)
self.parent.projectDlg.updateDlg(self.parent.project)
self.parent.projectModified()
def on_btnOptions_clicked(self):
tmp = ProjectSettingsDlg(self.ilastik, self.ilastik.project)
tmp.exec_()
class ObjectsTab(IlastikTabBase, QtGui.QWidget):
name = 'Objects'
moduleName = "Object_Picking"
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.objectLabels = ObjectListWidget(self.ilastik._activeImage.Object_Picking, self.ilastik._activeImage.Object_Picking.objects, self.ilastik.labelWidget)
self.ilastik.labelWidget.setLabelWidget(self.objectLabels)
#create ObjectsOverlay
ov = ObjectOverlayItem(self.objectLabels, self.ilastik._activeImage.Object_Picking.objects._data, color = 0, alpha = 1.0, autoAdd = True, autoVisible = True, linkColorTable = True)
self.ilastik._activeImage.overlayMgr["Objects/Selection"] = ov
ov = self.ilastik._activeImage.overlayMgr["Objects/Selection"]
self.ilastik.labelWidget.setLabelWidget(self.objectLabels)
def on_deActivation(self):
if self.ilastik.project is None:
return
self.ilastik._activeImage.Object_Picking.objects._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Object_Picking.objects._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Object_Picking.objects._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseOverlay = TabButton('Select overlay', ilastikIcons.Select)
self.btn3D = TabButton('3D', ilastikIcons.Play)
self.btnReport = TabButton('Generate report', ilastikIcons.Play)
self.btnSelectAll = TabButton('Select all', ilastikIcons.Select)
self.btnClearAll = TabButton('Clear all', ilastikIcons.Select)
self.btnChooseOverlay.setToolTip('Choose the overlay with objects')
self.btn3D.setToolTip('Display the currently selected objects in 3D')
self.btnReport.setToolTip('Generate a report for all currently selected objects')
self.btnSelectAll.setToolTip('Select all the objects')
self.btnClearAll.setToolTip('Clear selection')
tl.addWidget(self.btnChooseOverlay)
tl.addWidget(self.btn3D)
tl.addWidget(self.btnReport)
tl.addStretch()
tl.addWidget(self.btnSelectAll)
tl.addWidget(self.btnClearAll)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnChooseOverlay, QtCore.SIGNAL('clicked()'), self.on_btnChooseOverlay_clicked)
self.connect(self.btn3D, QtCore.SIGNAL('clicked()'), self.on_btn3D_clicked)
self.connect(self.btnReport, QtCore.SIGNAL('clicked()'), self.on_btnReport_clicked)
self.connect(self.btnSelectAll, QtCore.SIGNAL('clicked()'), self.on_btnSelectAll_clicked)
self.connect(self.btnClearAll, QtCore.SIGNAL('clicked()'), self.on_btnClearAll_clicked)
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_btn3D_clicked(self):
pass
def on_btnSelectAll_clicked(self):
self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Object_Picking.selectAll()
def on_btnClearAll_clicked(self):
self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Object_Picking.clearAll()
def on_btnReport_clicked(self):
fileName = QtGui.QFileDialog.getSaveFileName(self, "Save Report", ilastik.gui.LAST_DIRECTORY, "Reports (*.html)")
fn = str(QtCore.QDir.convertSeparators(fileName))
ilastik.gui.LAST_DIRECTORY = QtCore.QFileInfo(fn).path()
self.parent.project.dataMgr[self.parent.project.dataMgr._activeImageNumber].Object_Picking.generateReport(fn)
class ConnectedComponentsTab(IlastikTabBase, QtGui.QWidget):
name = "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._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 on_deActivation(self):
if self.ilastik.project is None:
return
self.ilastik._activeImage._dataVol.background._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage._dataVol.background._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage._dataVol.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.btnCCOptions = TabButton('Options', ilastikIcons.System)
self.btnInputOverlay.setToolTip('Select an overlay for connected components search')
self.btnCC.setToolTip('Run connected componets on the selected overlay')
self.btnCCBack.setToolTip('Run connected components with background')
self.btnCCOptions.setToolTip('Set options')
self.btnInputOverlay.setEnabled(True)
self.btnCC.setEnabled(False)
self.btnCCBack.setEnabled(False)
self.btnCCOptions.setEnabled(True)
tl.addWidget(self.btnInputOverlay)
tl.addWidget(self.btnCC)
tl.addWidget(self.btnCCBack)
tl.addStretch()
tl.addWidget(self.btnCCOptions)
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.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:
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_btnCC_clicked(self):
self.parent.on_connectComponents(background = False)
def on_btnCCBack_clicked(self):
self.parent.on_connectComponents(background = True)
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()
class AutoSegmentationTab(IlastikTabBase, QtGui.QWidget):
name = 'Auto Segmentation'
position = 2
moduleName = "Automatic_Segmentation"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
self.weights = None
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.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_deActivation(self):
pass
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Border Probability Overlay', ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnChooseWeights.setToolTip('Choose the input overlay that contains border probabilities')
self.btnSegment.setToolTip('Segment the image')
tl.addWidget(self.btnChooseWeights)
tl.addWidget(self.btnSegment)
tl.addStretch()
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnChooseWeights, QtCore.SIGNAL('clicked()'), self.on_btnChooseWeights_clicked)
self.connect(self.btnSegment, QtCore.SIGNAL('clicked()'), self.on_btnSegment_clicked)
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_btnSegment_clicked(self):
if self.weights is not None:
self.parent.project.dataMgr.Automatic_Segmentation.computeResults(self.weights)
self.parent.project.dataMgr.Automatic_Segmentation.finalizeResults()
self.parent.labelWidget.repaint()
def on_btnSegmentorsOptions_clicked(self):
pass
class ClassificationTab(IlastikTabBase, QtGui.QWidget):
name = 'Classification'
position = 1
moduleName = "Classification"
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
if self.ilastik._activeImage.module[self.name] is None:
self.ilastik._activeImage.module[self.name] = PropertyMgr(self.ilastik._activeImage)
ovs = self.ilastik._activeImage.module[self.name].getOverlayRefs()
raw = self.ilastik._activeImage.overlayMgr["Raw Data"]
self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget
overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr)
self.ilastik.labelWidget.setOverlayWidget(overlayWidget)
ov = self.ilastik._activeImage.overlayMgr["Classification/Labels"]
overlayWidget.addOverlayRef(ov.getRef())
overlayWidget.addOverlayRef(raw.getRef())
self.ilastik.labelWidget.setLabelWidget(LabelListWidget(self.ilastik.project.dataMgr.module["Classification"].labelMgr, self.ilastik.project.dataMgr.module["Classification"]["labelDescriptions"], self.ilastik.labelWidget, ov))
def on_deActivation(self):
if self.ilastik.project is None:
return
if hasattr(self.parent, "classificationInteractive"):
self.btnStartLive.click()
if self.ilastik.labelWidget is not None and self.ilastik.labelWidget._history != self.ilastik._activeImage.module["Classification"]["labelHistory"]:
self.ilastik._activeImage.module["Classification"]["labelHistory"] = self.ilastik.labelWidget._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnSelectFeatures = TabButton('Select Features', ilastikIcons.Select)
self.btnStartLive = TabButton('Start Live Prediction', ilastikIcons.Play)
self.btnStartLive.setCheckable(True)
self.btnTrainPredict = TabButton('Train and Predict', ilastikIcons.System)
self.btnExportClassifier = TabButton('Export Classifier', ilastikIcons.Select)
self.btnClassifierOptions = TabButton('Classifier Options', ilastikIcons.Select)
self.btnSelectFeatures.setToolTip('Select and compute features')
self.btnStartLive.setToolTip('Toggle interactive prediction of the current image while labeling')
self.btnTrainPredict.setToolTip('Train and predict all images offline; this step is necessary for automation')
self.btnExportClassifier.setToolTip('Save current classifier and its feature settings')
self.btnClassifierOptions.setToolTip('Select a classifier and change its settings')
self.on_otherProject()
tl.addWidget(self.btnSelectFeatures)
tl.addWidget(self.btnStartLive)
tl.addWidget(self.btnTrainPredict)
tl.addStretch()
tl.addWidget(self.btnExportClassifier)
tl.addWidget(self.btnClassifierOptions)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnSelectFeatures, QtCore.SIGNAL('clicked()'), self.on_btnSelectFeatures_clicked)
self.connect(self.btnStartLive, QtCore.SIGNAL('toggled(bool)'), self.on_btnStartLive_clicked)
self.connect(self.btnTrainPredict, QtCore.SIGNAL('clicked()'), self.on_btnTrainPredict_clicked)
self.connect(self.btnExportClassifier, QtCore.SIGNAL('clicked()'), self.on_btnExportClassifier_clicked)
self.connect(self.btnClassifierOptions, QtCore.SIGNAL('clicked()'), self.on_btnClassifierOptions_clicked)
def on_otherProject(self):
self.btnSelectFeatures.setEnabled(True)
self.btnStartLive.setEnabled(False)
self.btnTrainPredict.setEnabled(False)
self.btnExportClassifier.setEnabled(False)
self.btnClassifierOptions.setEnabled(True)
def on_btnSelectFeatures_clicked(self):
preview = self.parent.project.dataMgr[0]._dataVol._data[0,0,:,:,0:3]
newFeatureDlg = FeatureDlg(self.ilastik, preview)
answer = newFeatureDlg.exec_()
if answer == QtGui.QDialog.Accepted:
self.featureComputation = FeatureComputation(self.ilastik)
newFeatureDlg.close()
newFeatureDlg.deleteLater()
del newFeatureDlg
gc.collect()
def on_btnStartLive_clicked(self, state):
if state:
self.ilastik.ribbon.getTab('Classification').btnStartLive.setText('Stop Live Prediction')
self.classificationInteractive = ClassificationInteractive(self.ilastik)
else:
self.classificationInteractive.stop()
self.ilastik.ribbon.getTab('Classification').btnStartLive.setText('Start Live Prediction')
def on_btnTrainPredict_clicked(self):
self.classificationTrain = ClassificationTrain(self.ilastik)
self.connect(self.classificationTrain, QtCore.SIGNAL("trainingFinished()"), self.on_trainingFinished)
def on_trainingFinished(self):
print "Training finished"
self.classificationPredict = ClassificationPredict(self.ilastik)
def on_btnExportClassifier_clicked(self):
fileName = QtGui.QFileDialog.getSaveFileName(self, "Export Classifier", filter = "HDF5 Files (*.h5)")
try:
self.ilastik.project.dataMgr.Classification.exportClassifiers(fileName)
except (RuntimeError, AttributeError, IOError) as e:
QtGui.QMessageBox.warning(self, 'Error', str(e), QtGui.QMessageBox.Ok)
return
try:
self.ilastik.project.dataMgr.Classification.featureMgr.exportFeatureItems(fileName)
except RuntimeError as e:
QtGui.QMessageBox.warning(self, 'Error', str(e), QtGui.QMessageBox.Ok)
return
QtGui.QMessageBox.information(self, 'Success', "The classifier and the feature information have been saved successfully to:\n %s" % str(fileName), QtGui.QMessageBox.Ok)
def on_btnClassifierOptions_clicked(self):
dialog = ClassifierSelectionDlg(self.parent)
self.parent.project.dataMgr.module["Classification"].classifier = dialog.exec_()
class UnsupervisedTab(IlastikTabBase, QtGui.QWidget):
name = 'Unsupervised Decomposition'
position = 2
moduleName = "Unsupervised_Decomposition"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self._initContent()
self._initConnects()
self.overlays = None
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.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
self.btnUnsupervisedOptions.setEnabled(True)
def on_deActivation(self):
self.btnDecompose.setEnabled(False)
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseOverlays = TabButton('Select Overlay', ilastikIcons.Select)
self.btnDecompose = TabButton('decompose', ilastikIcons.Play)
self.btnUnsupervisedOptions = TabButton('Unsupervised Decomposition Options', ilastikIcons.System)
self.btnDecompose.setEnabled(False)
self.btnUnsupervisedOptions.setEnabled(False)
self.btnChooseOverlays.setToolTip('Choose the overlays for unsupervised decomposition')
self.btnDecompose.setToolTip('perform unsupervised decomposition')
self.btnUnsupervisedOptions.setToolTip('select an unsupervised decomposition plugin and change settings')
tl.addWidget(self.btnChooseOverlays)
tl.addWidget(self.btnDecompose)
tl.addStretch()
tl.addWidget(self.btnUnsupervisedOptions)
self.setLayout(tl)
def _initConnects(self):
self.connect(self.btnChooseOverlays, QtCore.SIGNAL('clicked()'), self.on_btnChooseOverlays_clicked)
self.connect(self.btnDecompose, QtCore.SIGNAL('clicked()'), self.on_btnDecompose_clicked)
self.connect(self.btnUnsupervisedOptions, QtCore.SIGNAL('clicked()'), self.on_btnUnsupervisedOptions_clicked)
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_btnDecompose_clicked(self):
self.unsDec = UnsupervisedDecomposition(self.ilastik)
self.unsDec.start(self.overlays)
def on_btnUnsupervisedOptions_clicked(self):
dialog = UnsupervisedSelectionDlg(self.parent)
answer = dialog.exec_()
if answer != None:
self.parent.project.dataMgr.module["Unsupervised_Decomposition"].unsupervisedMethod = answer
class InteractiveSegmentationTab(IlastikTabBase, QtGui.QWidget):
name = 'Interactive Segmentation'
position = 3
moduleName = "Interactive_Segmentation"
def __init__(self, parent=None):
IlastikTabBase.__init__(self, parent)
QtGui.QWidget.__init__(self, parent)
self.outputPath = os.path.expanduser("~/test-segmentation/")
self.mapping = dict()
self.doneBinaryOverlay = None
self.doneObjectsOverlay = None
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_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 on_numColorsNeeded(self, numColors):
"""make sure that there are enough label colors.
numColors refers to the _total_ number of colors,
including the background. Note that the background label color
is always present."""
if self.seedWidget.count() >= numColors: return
for i in range(numColors-self.seedWidget.count()):
self.seedWidget.createLabel()
def on_deActivation(self):
if self.ilastik.project is None:
return
self.interactionLog = self.ilastik.labelWidget.interactionLog
self.ilastik.labelWidget.interactionLog = None
if self.ilastik.labelWidget._history != self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history:
self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history = self.ilastik.labelWidget._history
if self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history is not None:
self.ilastik.labelWidget._history = self.ilastik._activeImage.Interactive_Segmentation.seedLabelsVolume._history
def _initContent(self):
tl = QtGui.QHBoxLayout()
tl.setMargin(0)
self.btnChooseWeights = TabButton('Choose Weights', ilastikIcons.Select)
self.btnChooseDimensions = TabButton('Using 3D', ilastikIcons.Select)
self.btnSegment = TabButton('Segment', ilastikIcons.Play)
self.btnSaveAs = TabButton('Save As', ilastikIcons.SaveAs)
self.btnSave = TabButton('Save', ilastikIcons.Save)
self.btnSegmentorsOptions = TabButton('Change Segmentor', ilastikIcons.System)
self.inlineSettings = InlineSettingsWidget(self)
self.only2D = False
self.btnChooseWeights.setToolTip('Choose the edge weights for the segmentation task')
self.btnSegment.setToolTip('Segment the image into foreground/background')
self.btnChooseDimensions.setToolTip('Switch between slice based 2D segmentation and full 3D segmentation\n This is mainly useful for 3D Date with very weak border indicators, where seeds placed in one slice can bleed out badly to other regions')
self.btnSegmentorsOptions.setToolTip('Select a segmentation plugin and change settings')
tl.addWidget(self.btnChooseWeights)
#tl.addWidget(self.btnChooseDimensions)
tl.addWidget(self.btnSegment)
tl.addWidget(self.inlineSettings)
tl.addWidget(self.btnSave)
tl.addWidget(self.btnSaveAs)
tl.addStretch()
tl.addWidget(self.btnSegmentorsOptions)
self.btnSegment.setEnabled(False)
self.btnSaveAs.setEnabled(False)
self.btnSave.setEnabled(False)
self.btnChooseDimensions.setEnabled(False)
self.btnSegmentorsOptions.setEnabled(False)
self.setLayout(tl)
def _initConnects(self):
s = self.ilastik._activeImage.Interactive_Segmentation
self.connect(self.btnChooseWeights, QtCore.SIGNAL('clicked()'), self.on_btnChooseWeights_clicked)
self.connect(self.btnSegment, QtCore.SIGNAL('clicked()'), s.segment)
self.connect(self.btnSaveAs, QtCore.SIGNAL('clicked()'), self.on_btnSaveAs_clicked)
self.connect(self.btnSave, QtCore.SIGNAL('clicked()'), self.on_btnSave_clicked)
self.connect(self.btnChooseDimensions, QtCore.SIGNAL('clicked()'), self.on_btnDimensions)
self.connect(self.btnSegmentorsOptions, QtCore.SIGNAL('clicked()'), self.on_btnSegmentorsOptions_clicked)
self.shortcutSegment = QtGui.QShortcut(QtGui.QKeySequence("s"), self, s.segment, s.segment)
#shortcutManager.register(self.shortcutNextLabel, "Labeling", "Go to next label (cyclic, forward)")
def on_btnDimensions(self):
self.only2D = not self.only2D
if self.only2D:
ov = self.parent.project.dataMgr[self.parent._activeImageNumber].overlayMgr["Segmentation/Segmentation"]
if ov is not None:
zerod = numpy.zeros(ov._data.shape, numpy.uint8)
ov._data = DataAccessor(zerod)
self.btnChooseDimensions.setText('Using 2D')
else:
self.btnChooseDimensions.setText('Using 3D')
self.setupWeights()
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_setupWeights(self, weights = None):
self.ilastik.labelWidget.interactionLog = []
self.btnSegmentorsOptions.setEnabled(True)
def clearSeeds(self):
self._seedL = None
self._seedIndices = None
def mouseReleaseEvent(self, event):
"""
mouse button release event
"""
button = event.button()
# select an item on which we clicked
def on_btnSave_clicked(self):
s = self.ilastik._activeImage.Interactive_Segmentation
s.saveCurrentSegment()
def on_btnSaveAs_clicked(self):
(segmentKey, accepted) = QtGui.QInputDialog.getText(self, "Finish object", "Enter object name:")
segmentKey = str(segmentKey) #convert to native python string
if not accepted: return #dialog was canceled
s = self.ilastik._activeImage.Interactive_Segmentation
#make sure the name is unique
if s.hasSegmentsKey(segmentKey):
msg = QtGui.QMessageBox.critical(self, "Finish object", \
"An object with name '%s' already exists. Please choose a different name" % (segmentKey))
return
s.saveCurrentSegmentsAs(segmentKey)
path = s.outputPath+'/'+str(segmentKey)
f = open(path + "/interactions.log", "w")
for l in self.ilastik.labelWidget.interactionLog:
f.write(l + "\n")
f.close()
self.ilastik.labelWidget.interactionLog = []
f = h5py.File(path + "/history.h5", 'w')
self.ilastik.labelWidget._history.serialize(f)
f.close()
self.ilastik.labelWidget.repaint()
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 on_newSegmentation(self):
if hasattr(self.ilastik.project.dataMgr.Interactive_Segmentation.segmentor, "bias"):
bias = self.ilastik.project.dataMgr.Interactive_Segmentation.segmentor.bias
s = "%f: segment(bias) %f" % (time.clock(),bias)
self.ilastik.labelWidget.interactionLog.append(s)
self.on_overlaysChanged()
def on_btnSegmentorsOptions_clicked(self):
dialog = SegmentorSelectionDlg(self.parent)
answer = dialog.exec_()
if answer != None:
self.parent.project.dataMgr.Interactive_Segmentation.segmentor = answer
self.setupWeights(self.parent.project.dataMgr[self.parent._activeImageNumber].Interactive_Segmentation._segmentationWeights)
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget)
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = False
elif self.defaultSegmentor is True:
ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget)
self.inlineSettings.changeWidget(ui)
self.defaultSegmentor = False
