def _addMissingPreopDataAnnotation(self, widget):
self._removeMissingPreopDataAnnotation()
self.noPreopSegmentationAnnotation = SliceAnnotation(
widget,
constants.MISSING_PREOP_ANNOTATION_TEXT,
opacity=0.7,
color=(1, 0, 0))
def addSideBySideSliceAnnotations(self):
self.removeSliceAnnotations()
kwargs = {"yPos":55 if ModuleWidgetMixin.isQtVersionOlder() else 80, "size":30}
self.sliceAnnotations.append(SliceAnnotation(self.redWidget, constants.LEFT_VIEWER_SLICE_ANNOTATION_TEXT, **kwargs))
self.sliceAnnotations.append(SliceAnnotation(self.yellowWidget, constants.RIGHT_VIEWER_SLICE_ANNOTATION_TEXT, **kwargs))
self.addNewImageAnnotation(self.yellowWidget, constants.RIGHT_VIEWER_SLICE_NEEDLE_IMAGE_ANNOTATION_TEXT)
self.addOldImageAnnotation(self.yellowWidget, constants.RIGHT_VIEWER_SLICE_TRANSFORMED_ANNOTATION_TEXT)
self.addRegistrationResultStatusAnnotation(self.yellowWidget)
def addZFrameInstructions(self, step=1):
self.removeZFrameInstructionAnnotation()
self.zFrameStep = step
text = ProstateAblationConstants.ZFrame_INSTRUCTION_STEPS[self.zFrameStep]
self.zFrameInstructionAnnotation = SliceAnnotation(self.redWidget, text, yPos=55, horizontalAlign="center",
opacity=0.6, color=(0,0.6,0))
self.zFrameClickObserver = self.redSliceViewInteractor.AddObserver(vtk.vtkCommand.LeftButtonReleaseEvent,
self.onZFrameStepAccomplished)
def addFourUpSliceAnnotations(self):
self.removeSliceAnnotations()
if not (self.currentResult.skipped or (self.session.seriesTypeManager.isCoverProstate(self.currentResult.name) and
not self.session.data.usePreopData)):
self.sliceAnnotations.append(SliceAnnotation(self.redWidget, constants.RIGHT_VIEWER_SLICE_ANNOTATION_TEXT,
yPos=50 if ModuleWidgetMixin.isQtVersionOlder() else 75, size=20))
self.addNewImageAnnotation(self.redWidget, constants.RIGHT_VIEWER_SLICE_NEEDLE_IMAGE_ANNOTATION_TEXT, size=15)
self.addOldImageAnnotation(self.redWidget, constants.RIGHT_VIEWER_SLICE_TRANSFORMED_ANNOTATION_TEXT, size=15)
self.addRegistrationResultStatusAnnotation(self.redWidget)
def addRegistrationResultStatusAnnotation(self, widget):
annotationText = None
if self.currentResult.approved:
annotationText = constants.APPROVED_RESULT_TEXT_ANNOTATION
elif self.currentResult.rejected:
annotationText = constants.REJECTED_RESULT_TEXT_ANNOTATION
elif self.currentResult.skipped:
annotationText = constants.SKIPPED_RESULT_TEXT_ANNOTATION
if annotationText:
self.sliceAnnotations.append(SliceAnnotation(widget, annotationText, yPos=20, size=15))
def addSliceAnnotations(self):
self.removeSliceAnnotations()
widgets = [self.yellowWidget] if self.layoutManager.layout == constants.LAYOUT_SIDE_BY_SIDE else \
[self.redWidget, self.yellowWidget, self.greenWidget]
for widget in widgets:
self.sliceAnnotations.append(
SliceAnnotation(widget,
"Targeting Mode",
opacity=0.5,
verticalAlign="top",
horizontalAlign="center"))
def enableTargetMovingMode(self):
self.clearTargetMovementObserverAndAnnotations()
targetName = self.targetTableModel.targetList.GetNthFiducialLabel(self.currentlyMovedTargetModelIndex.row())
widgets = [self.yellowWidget] if self.layoutManager.layout == constants.LAYOUT_SIDE_BY_SIDE else \
[self.redWidget, self.yellowWidget, self.greenWidget]
for widget in widgets:
sliceView = widget.sliceView()
interactor = sliceView.interactorStyle().GetInteractor()
observer = interactor.AddObserver(vtk.vtkCommand.LeftButtonReleaseEvent, self.onViewerClickEvent)
sliceView.setCursor(qt.Qt.CrossCursor)
annotation = SliceAnnotation(widget, "Target Movement Mode (%s)" % targetName, opacity=0.5,
verticalAlign="top", horizontalAlign="center")
self.mouseReleaseEventObservers[widget] = (observer, annotation)
self.moveTargetMode = True
class SliceTrackerZFrameRegistrationStep(SliceTrackerStep):
NAME = "ZFrame Registration"
LogicClass = SliceTrackerZFrameRegistrationStepLogic
LayoutClass = qt.QVBoxLayout
def __init__(self):
self.annotationLogic = slicer.modules.annotations.logic()
self.zFrameRegistrationClass = getattr(
sys.modules[__name__],
self.getSetting("ZFrame_Registration_Class_Name"))
self.roiObserverTag = None
self.coverTemplateROI = None
self.zFrameCroppedVolume = None
self.zFrameLabelVolume = None
self.zFrameMaskedVolume = None
self.zFrameClickObserver = None
self.zFrameInstructionAnnotation = None
super(SliceTrackerZFrameRegistrationStep, self).__init__()
self.logic.templateVolume = None
def setupIcons(self):
self.zFrameIcon = self.createIcon('icon-zframe.png')
self.needleIcon = self.createIcon('icon-needle.png')
self.templateIcon = self.createIcon('icon-template.png')
def setup(self):
super(SliceTrackerZFrameRegistrationStep, self).setup()
self.setupManualIndexesGroupBox()
self.setupActionButtons()
self.layout().addWidget(self.zFrameRegistrationManualIndexesGroupBox)
self.layout().addWidget(
self.createHLayout([
self.runZFrameRegistrationButton,
self.retryZFrameRegistrationButton,
self.approveZFrameRegistrationButton
]))
self.layout().addStretch(1)
def setupManualIndexesGroupBox(self):
self.zFrameRegistrationManualIndexesGroupBox = qt.QGroupBox(
"Use manual start/end indexes")
self.zFrameRegistrationManualIndexesGroupBox.setCheckable(True)
self.zFrameRegistrationManualIndexesGroupBoxLayout = qt.QGridLayout()
self.zFrameRegistrationManualIndexesGroupBox.setLayout(
self.zFrameRegistrationManualIndexesGroupBoxLayout)
self.zFrameRegistrationManualIndexesGroupBox.checked = False
self.zFrameRegistrationStartIndex = qt.QSpinBox()
self.zFrameRegistrationEndIndex = qt.QSpinBox()
hBox = self.createHLayout([
qt.QLabel("start"), self.zFrameRegistrationStartIndex,
qt.QLabel("end"), self.zFrameRegistrationEndIndex
])
self.zFrameRegistrationManualIndexesGroupBoxLayout.addWidget(
hBox, 1, 1, qt.Qt.AlignRight)
def setupActionButtons(self):
iconSize = qt.QSize(36, 36)
self.runZFrameRegistrationButton = self.createButton(
"",
icon=Icons.start,
iconSize=iconSize,
enabled=False,
toolTip="Run ZFrame Registration")
self.approveZFrameRegistrationButton = self.createButton(
"",
icon=Icons.apply,
iconSize=iconSize,
enabled=self.zFrameRegistrationClass is LineMarkerRegistration,
toolTip="Confirm registration accuracy",
)
self.retryZFrameRegistrationButton = self.createButton(
"",
icon=Icons.retry,
iconSize=iconSize,
enabled=False,
visible=self.zFrameRegistrationClass is
OpenSourceZFrameRegistration,
toolTip="Reset")
def setupAdditionalViewSettingButtons(self):
iconSize = qt.QSize(24, 24)
self.showZFrameModelButton = self.createButton(
"",
icon=self.zFrameIcon,
iconSize=iconSize,
checkable=True,
toolTip="Display zFrame model")
self.showTemplateButton = self.createButton("",
icon=self.templateIcon,
iconSize=iconSize,
checkable=True,
toolTip="Display template")
# self.showNeedlePathButton = self.createButton("", icon=self.needleIcon, iconSize=iconSize, checkable=True, toolTip="Display needle path")
self.showTemplatePathButton = self.createButton(
"",
icon=self.templateIcon,
iconSize=iconSize,
checkable=True,
toolTip="Display template paths")
self.viewSettingButtons = [
self.showZFrameModelButton, self.showTemplateButton
]
def setupConnections(self):
self.retryZFrameRegistrationButton.clicked.connect(
self.onRetryZFrameRegistrationButtonClicked)
self.approveZFrameRegistrationButton.clicked.connect(
self.onApproveZFrameRegistrationButtonClicked)
self.runZFrameRegistrationButton.clicked.connect(
self.onApplyZFrameRegistrationButtonClicked)
self.showZFrameModelButton.connect('toggled(bool)',
self.onShowZFrameModelToggled)
self.showTemplateButton.connect('toggled(bool)',
self.onShowZFrameTemplateToggled)
self.showTemplatePathButton.connect('toggled(bool)',
self.onShowTemplatePathToggled)
# self.showNeedlePathButton.connect('toggled(bool)', self.onShowNeedlePathToggled)
def addSessionObservers(self):
super(SliceTrackerZFrameRegistrationStep, self).addSessionObservers()
self.session.addEventObserver(
self.session.InitiateZFrameCalibrationEvent,
self.onInitiateZFrameCalibration)
def removeSessionEventObservers(self):
super(SliceTrackerZFrameRegistrationStep,
self).removeSessionEventObservers()
self.session.removeEventObserver(
self.session.InitiateZFrameCalibrationEvent,
self.onInitiateZFrameCalibration)
def onShowZFrameModelToggled(self, checked):
self.logic.setZFrameVisibility(checked)
def onShowZFrameTemplateToggled(self, checked):
self.logic.setTemplateVisibility(checked)
self.logic.setTemplatePathVisibility(checked)
def onShowTemplatePathToggled(self, checked):
self.logic.setTemplatePathVisibility(checked)
def onShowNeedlePathToggled(self, checked):
self.logic.setNeedlePathVisibility(checked)
def resetViewSettingButtons(self):
self.showTemplateButton.enabled = self.logic.templateSuccessfulLoaded
self.showTemplatePathButton.enabled = self.logic.templateSuccessfulLoaded
self.showZFrameModelButton.enabled = self.logic.zFrameSuccessfulLoaded
def onInitiateZFrameCalibration(self, caller, event):
self.logic.templateVolume = self.session.currentSeriesVolume
self.active = True
@vtk.calldata_type(vtk.VTK_STRING)
def onNewImageSeriesReceived(self, caller, event, callData):
# TODO: control here to automatically activate the step
if not self.active:
return
newImageSeries = ast.literal_eval(callData)
for series in reversed(newImageSeries):
if self.session.seriesTypeManager.isCoverTemplate(series):
if self.logic.templateVolume and series != self.logic.templateVolume.GetName(
):
if not slicer.util.confirmYesNoDisplay(
"Another %s was received. Do you want to use this one for "
"calibration?" %
self.getSetting("COVER_TEMPLATE_PATTERN")):
return
self.session.currentSeries = series
self.removeZFrameInstructionAnnotation()
self.logic.templateVolume = self.session.currentSeriesVolume
self.initiateZFrameRegistrationStep()
return
def onLoadingMetadataSuccessful(self, caller, event):
if self.session.zFrameRegistrationSuccessful:
self.applyZFrameTransform()
def onActivation(self):
super(SliceTrackerZFrameRegistrationStep, self).onActivation()
self.layoutManager.setLayout(SliceTrackerConstants.LAYOUT_FOUR_UP)
self.showZFrameModelButton.checked = True
self.showTemplateButton.checked = True
self.showTemplatePathButton.checked = True
self.zFrameRegistrationManualIndexesGroupBox.checked = False
if self.logic.templateVolume:
self.initiateZFrameRegistrationStep()
def onDeactivation(self):
super(SliceTrackerZFrameRegistrationStep, self).onDeactivation()
self.showZFrameModelButton.checked = False
self.showTemplateButton.checked = False
self.showTemplatePathButton.checked = False
self.logic.templateVolume = None
def initiateZFrameRegistrationStep(self):
self.resetZFrameRegistration()
self.setupFourUpView(self.logic.templateVolume)
self.redSliceNode.SetSliceVisible(True)
if self.zFrameRegistrationClass is OpenSourceZFrameRegistration:
self.addROIObserver()
self.activateCreateROIMode()
self.addZFrameInstructions()
def resetZFrameRegistration(self):
self.runZFrameRegistrationButton.enabled = False
self.approveZFrameRegistrationButton.enabled = False
self.retryZFrameRegistrationButton.enabled = False
self.removeNodeFromMRMLScene(self.coverTemplateROI)
self.removeNodeFromMRMLScene(self.zFrameCroppedVolume)
self.removeNodeFromMRMLScene(self.zFrameLabelVolume)
self.removeNodeFromMRMLScene(self.zFrameMaskedVolume)
if self.session.data.zFrameRegistrationResult:
self.removeNodeFromMRMLScene(
self.session.data.zFrameRegistrationResult.transform)
self.session.data.zFrameRegistrationResult = None
def addROIObserver(self):
@vtk.calldata_type(vtk.VTK_OBJECT)
def onNodeAdded(caller, event, calldata):
node = calldata
if isinstance(node, slicer.vtkMRMLAnnotationROINode):
self.removeROIObserver()
self.coverTemplateROI = node
self.runZFrameRegistrationButton.enabled = self.isRegistrationPossible(
)
if self.roiObserverTag:
self.removeROIObserver()
self.roiObserverTag = slicer.mrmlScene.AddObserver(
slicer.vtkMRMLScene.NodeAddedEvent, onNodeAdded)
def isRegistrationPossible(self):
return self.coverTemplateROI is not None
def removeROIObserver(self):
if self.roiObserverTag:
self.roiObserverTag = slicer.mrmlScene.RemoveObserver(
self.roiObserverTag)
def activateCreateROIMode(self):
mrmlScene = self.annotationLogic.GetMRMLScene()
selectionNode = mrmlScene.GetNthNodeByClass(0, "vtkMRMLSelectionNode")
selectionNode.SetReferenceActivePlaceNodeClassName(
"vtkMRMLAnnotationROINode")
# self.annotationLogic.StopPlaceMode(False) # BUG: http://na-mic.org/Mantis/view.php?id=4355
self.annotationLogic.StartPlaceMode(False)
def addZFrameInstructions(self, step=1):
self.removeZFrameInstructionAnnotation()
self.zFrameStep = step
text = SliceTrackerConstants.ZFrame_INSTRUCTION_STEPS[self.zFrameStep]
self.zFrameInstructionAnnotation = SliceAnnotation(
self.redWidget,
text,
yPos=55,
horizontalAlign="center",
opacity=0.6,
color=(0, 0.6, 0))
self.zFrameClickObserver = self.redSliceViewInteractor.AddObserver(
vtk.vtkCommand.LeftButtonReleaseEvent,
self.onZFrameStepAccomplished)
# TODO
# self.onShowAnnotationsToggled(self.showAnnotationsButton.checked)
def onZFrameStepAccomplished(self, observee, event):
self.removeZFrameInstructionAnnotation()
nextStep = self.zFrameStep + 1
if nextStep in SliceTrackerConstants.ZFrame_INSTRUCTION_STEPS.keys():
self.addZFrameInstructions(nextStep)
def removeZFrameInstructionAnnotation(self):
if hasattr(self, "zFrameInstructionAnnotation"
) and self.zFrameInstructionAnnotation:
self.zFrameInstructionAnnotation.remove()
self.zFrameInstructionAnnotation = None
if self.zFrameClickObserver:
self.redSliceViewInteractor.RemoveObserver(
self.zFrameClickObserver)
self.zFrameClickObserver = None
def onApplyZFrameRegistrationButtonClicked(self):
zFrameTemplateVolume = self.logic.templateVolume
try:
if self.zFrameRegistrationClass is OpenSourceZFrameRegistration:
self.annotationLogic.SetAnnotationLockedUnlocked(
self.coverTemplateROI.GetID())
self.zFrameCroppedVolume = self.logic.createCroppedVolume(
zFrameTemplateVolume, self.coverTemplateROI)
self.zFrameLabelVolume = self.logic.createLabelMapFromCroppedVolume(
self.zFrameCroppedVolume, "labelmap")
self.zFrameMaskedVolume = self.logic.createMaskedVolume(
zFrameTemplateVolume,
self.zFrameLabelVolume,
outputVolumeName="maskedTemplateVolume")
self.zFrameMaskedVolume.SetName(
zFrameTemplateVolume.GetName() + "-label")
if not self.zFrameRegistrationManualIndexesGroupBox.checked:
start, center, end = self.logic.getROIMinCenterMaxSliceNumbers(
self.coverTemplateROI)
otsuOutputVolume = self.logic.applyOtsuFilter(
self.zFrameMaskedVolume)
self.logic.dilateMask(otsuOutputVolume)
start, end = self.logic.getStartEndWithConnectedComponents(
otsuOutputVolume, center)
self.zFrameRegistrationStartIndex.value = start
self.zFrameRegistrationEndIndex.value = end
else:
start = self.zFrameRegistrationStartIndex.value
end = self.zFrameRegistrationEndIndex.value
self.logic.runZFrameRegistration(self.zFrameMaskedVolume,
self.zFrameRegistrationClass,
startSlice=start,
endSlice=end)
else:
self.logic.runZFrameRegistration(zFrameTemplateVolume,
self.zFrameRegistrationClass)
self.applyZFrameTransform()
except AttributeError as exc:
slicer.util.errorDisplay(
"An error occurred. For further information click 'Show Details...'",
windowTitle=self.__class__.__name__,
detailedText=str(exc.message))
else:
self.setBackgroundToVolumeID(zFrameTemplateVolume)
self.approveZFrameRegistrationButton.enabled = True
self.retryZFrameRegistrationButton.enabled = True
def applyZFrameTransform(self):
for node in [
node for node in [
self.logic.pathModelNode, self.logic.tempModelNode,
self.logic.zFrameModelNode, self.logic.needleModelNode
] if node
]:
node.SetAndObserveTransformNodeID(
self.session.data.zFrameRegistrationResult.transform.GetID())
def onApproveZFrameRegistrationButtonClicked(self):
self.redSliceNode.SetSliceVisible(False)
if self.zFrameRegistrationClass is OpenSourceZFrameRegistration:
self.annotationLogic.SetAnnotationVisibility(
self.coverTemplateROI.GetID())
self.session.approvedCoverTemplate = self.logic.templateVolume
def onRetryZFrameRegistrationButtonClicked(self):
self.removeZFrameInstructionAnnotation()
self.annotationLogic.SetAnnotationVisibility(
self.coverTemplateROI.GetID())
self.initiateZFrameRegistrationStep()
class SliceTrackerSegmentationStep(SliceTrackerStep):
NAME = "Segmentation"
LogicClass = SliceTrackerSegmentationStepLogic
LayoutClass = qt.QVBoxLayout
def __init__(self):
super(SliceTrackerSegmentationStep, self).__init__()
self.session.retryMode = False
self.segmentationData = None
def setup(self):
super(SliceTrackerSegmentationStep, self).setup()
self._setupTargetingPlugin()
self._setupManualSegmentationPlugin()
self._setupAutomaticSegmentationPlugin()
self._setupNavigationButtons()
self.layout().addWidget(self.manualSegmentationPlugin)
self.layout().addWidget(
self.createHLayout([self.backButton, self.finishStepButton]))
self.layout().addWidget(self.targetingPlugin)
self.layout().addStretch(1)
def _setupTargetingPlugin(self):
self.targetingPlugin = SliceTrackerTargetingPlugin()
self.targetingPlugin.addEventObserver(
self.targetingPlugin.TargetingStartedEvent,
self._onTargetingStarted)
self.targetingPlugin.addEventObserver(
self.targetingPlugin.TargetingFinishedEvent,
self._onTargetingFinished)
self.addPlugin(self.targetingPlugin)
def _setupManualSegmentationPlugin(self):
self.manualSegmentationPlugin = SliceTrackerManualSegmentationPlugin()
self.manualSegmentationPlugin.addEventObserver(
self.manualSegmentationPlugin.SegmentationStartedEvent,
self._onSegmentationStarted)
self.manualSegmentationPlugin.addEventObserver(
self.manualSegmentationPlugin.SegmentationCanceledEvent,
self._onSegmentationCanceled)
self.manualSegmentationPlugin.addEventObserver(
self.manualSegmentationPlugin.SegmentationFinishedEvent,
self._onManualSegmentationFinished)
self.manualSegmentationPlugin.surfaceCutToLabelWidget.segmentEditorButtonVisible = False
self.addPlugin(self.manualSegmentationPlugin)
def _setupAutomaticSegmentationPlugin(self):
self.automaticSegmentationPlugin = SliceTrackerAutomaticSegmentationPlugin(
)
self.automaticSegmentationPlugin.addEventObserver(
self.automaticSegmentationPlugin.SegmentationStartedEvent,
self._onAutomaticSegmentationStarted)
self.automaticSegmentationPlugin.addEventObserver(
self.automaticSegmentationPlugin.SegmentationFailedEvent,
self._onSegmentationFailed)
self.automaticSegmentationPlugin.addEventObserver(
self.automaticSegmentationPlugin.SegmentationFinishedEvent,
self._onAutomaticSegmentationFinished)
self.addPlugin(self.automaticSegmentationPlugin)
def _setupNavigationButtons(self):
iconSize = qt.QSize(36, 36)
self.backButton = self.createButton("",
icon=Icons.back,
iconSize=iconSize,
toolTip="Return to last step")
self.finishStepButton = self.createButton(
"",
icon=Icons.start,
iconSize=iconSize,
toolTip="Run Registration/Finish Step")
def setupConnections(self):
super(SliceTrackerSegmentationStep, self).setupConnections()
self.backButton.clicked.connect(self._onBackButtonClicked)
self.finishStepButton.clicked.connect(self._onFinishStepButtonClicked)
def addSessionObservers(self):
super(SliceTrackerSegmentationStep, self).addSessionObservers()
self.session.addEventObserver(self.session.InitiateSegmentationEvent,
self.onInitiateSegmentation)
def removeSessionEventObservers(self):
super(SliceTrackerSegmentationStep, self).removeSessionEventObservers()
self.session.removeEventObserver(
self.session.InitiateSegmentationEvent,
self.onInitiateSegmentation)
def onActivation(self):
self.segmentationData = None
self.finishStepButton.enabled = False
self.session.fixedVolume = self.session.currentSeriesVolume
if not self.session.fixedVolume:
return
self._updateAvailableLayouts()
super(SliceTrackerSegmentationStep, self).onActivation()
def onDeactivation(self):
super(SliceTrackerSegmentationStep, self).onDeactivation()
self._removeMissingPreopDataAnnotation()
@onModuleSelected(SliceTrackerStep.MODULE_NAME)
def onLayoutChanged(self, layout=None):
if self.layoutManager.layout == constants.LAYOUT_SIDE_BY_SIDE:
self._setupSideBySideSegmentationView()
elif self.layoutManager.layout in [
constants.LAYOUT_FOUR_UP, constants.LAYOUT_RED_SLICE_ONLY
]:
self._removeMissingPreopDataAnnotation()
self.setBackgroundToVolumeID(self.session.currentSeriesVolume,
clearLabels=False)
@vtk.calldata_type(vtk.VTK_STRING)
def onInitiateSegmentation(self, caller, event, callData):
self._initiateSegmentation(ast.literal_eval(callData))
def _initiateSegmentation(self, retryMode=False):
self.session.retryMode = retryMode
self.finishStepButton.setEnabled(
True if self.logic.inputsAreSet() else False)
if self.session.seriesTypeManager.isCoverProstate(
self.session.currentSeries):
self.initializeCoverProstate()
else:
self._loadLatestCoverProstateResultData()
self.active = True
def initializeCoverProstate(self):
if self.session.data.usePreopData:
if self.session.retryMode:
if not self._loadLatestCoverProstateResultData():
self.logic.loadInitialData()
else:
self.logic.loadInitialData()
else:
self.session.movingVolume = self.session.currentSeriesVolume
def _loadLatestCoverProstateResultData(self):
coverProstate = self.session.data.getMostRecentApprovedCoverProstateRegistration(
)
if coverProstate:
self.session.movingVolume = coverProstate.volumes.fixed
self.session.movingLabel = coverProstate.labels.fixed
self.session.movingTargets = coverProstate.targets.approved
return True
return False
def _updateAvailableLayouts(self):
layouts = [constants.LAYOUT_RED_SLICE_ONLY, constants.LAYOUT_FOUR_UP]
if self.session.data.usePreopData or self.session.retryMode:
layouts.append(constants.LAYOUT_SIDE_BY_SIDE)
self.setAvailableLayouts(layouts)
def _setupSideBySideSegmentationView(self):
# TODO: red slice view should not be possible to set target
coverProstate = self.session.data.getMostRecentApprovedCoverProstateRegistration(
)
redVolume = coverProstate.volumes.fixed if coverProstate and self.session.retryMode else self.session.data.initialVolume
redLabel = coverProstate.labels.fixed if coverProstate and self.session.retryMode else self.session.data.initialLabel
if redVolume and redLabel:
self.redCompositeNode.SetBackgroundVolumeID(redVolume.GetID())
self.redCompositeNode.SetLabelVolumeID(redLabel.GetID())
self.redCompositeNode.SetLabelOpacity(1)
else:
self.redCompositeNode.SetBackgroundVolumeID(None)
self.redCompositeNode.SetLabelVolumeID(None)
self._addMissingPreopDataAnnotation(self.redWidget)
self.yellowCompositeNode.SetBackgroundVolumeID(
self.session.currentSeriesVolume.GetID())
self.setAxialOrientation()
if redVolume and redLabel:
self.redSliceNode.SetUseLabelOutline(True)
self.redSliceNode.RotateToVolumePlane(redVolume)
def _addMissingPreopDataAnnotation(self, widget):
self._removeMissingPreopDataAnnotation()
self.noPreopSegmentationAnnotation = SliceAnnotation(
widget,
constants.MISSING_PREOP_ANNOTATION_TEXT,
opacity=0.7,
color=(1, 0, 0))
def _removeMissingPreopDataAnnotation(self):
self.noPreopSegmentationAnnotation = getattr(
self, "noPreopSegmentationAnnotation", None)
if self.noPreopSegmentationAnnotation:
self.noPreopSegmentationAnnotation.remove()
self.noPreopSegmentationAnnotation = None
def _onBackButtonClicked(self):
if self.session.retryMode:
self.session.retryMode = False
if self.session.previousStep:
self.session.previousStep.active = True
def _onFinishStepButtonClicked(self):
self.session.data.segmentModelNode = self.manualSegmentationPlugin.segmentModelNode
self.session.data.inputMarkupNode = self.manualSegmentationPlugin.inputMarkupNode
if not self.session.data.usePreopData and not self.session.retryMode:
self._createCoverProstateRegistrationResultManually()
else:
self.session.onInvokeRegistration(
initial=True,
retryMode=self.session.retryMode,
segmentationData=self.segmentationData)
def _createCoverProstateRegistrationResultManually(self):
fixedVolume = self.session.currentSeriesVolume
result = self.session.generateNameAndCreateRegistrationResult(
fixedVolume)
approvedRegistrationType = "bSpline"
result.targets.original = self.session.movingTargets
targetName = str(
result.seriesNumber
) + '-TARGETS-' + approvedRegistrationType + result.suffix
clone = self.logic.cloneFiducials(self.session.movingTargets,
targetName)
self.session.applyDefaultTargetDisplayNode(clone)
result.setTargets(approvedRegistrationType, clone)
result.volumes.fixed = fixedVolume
result.labels.fixed = self.session.fixedLabel
result.receivedTime = self.session.seriesTimeStamps[
result.name.replace(result.suffix, "")]
result.segmentationData = self.segmentationData
if self.session.seriesTypeManager.isCoverProstate(self.session.currentResult.name) and \
self.session.data.getMostRecentApprovedCoverProstateRegistration() is not None:
self.session.data.getMostRecentApprovedCoverProstateRegistration(
).skip()
result.approve(approvedRegistrationType, consentedBy="Clinician")
def _onAutomaticSegmentationStarted(self, caller, event):
self.manualSegmentationPlugin.enabled = False
self._onSegmentationStarted(caller, event)
def _onSegmentationStarted(self, caller, event):
# self.setAvailableLayouts([constants.LAYOUT_RED_SLICE_ONLY, constants.LAYOUT_SIDE_BY_SIDE, constants.LAYOUT_FOUR_UP])
self.targetingPlugin.enabled = False
self.backButton.enabled = False
self.finishStepButton.enabled = False
def _onSegmentationCanceled(self, caller, event):
# self.setAvailableLayouts([constants.LAYOUT_FOUR_UP])
self.layoutManager.setLayout(constants.LAYOUT_FOUR_UP)
self.backButton.enabled = True
self.targetingPlugin.enabled = True
if self.logic.inputsAreSet():
self._displaySegmentationComparison()
self.finishStepButton.setEnabled(
1 if self.logic.inputsAreSet() else 0) # TODO: need to revise that
def _onSegmentationFailed(self, caller, event):
import logging
logging.debug("Segmentation failed")
self.setAvailableLayouts([constants.LAYOUT_FOUR_UP])
self.layoutManager.setLayout(constants.LAYOUT_FOUR_UP)
self.backButton.enabled = True
self.finishStepButton.setEnabled(False)
@vtk.calldata_type(vtk.VTK_STRING)
def onNewImageSeriesReceived(self, caller, event, callData):
if not self.active:
return
newImageSeries = ast.literal_eval(callData)
for series in reversed(newImageSeries):
if self.session.seriesTypeManager.isCoverProstate(series):
if series != self.session.currentSeries:
if slicer.util.confirmYesNoDisplay(
"Another %s was received. Do you want to use this one?"
% self.getSetting("COVER_PROSTATE_PATTERN")):
self.session.currentSeries = series
self.active = False
self._initiateSegmentation()
@vtk.calldata_type(vtk.VTK_OBJECT)
def _onAutomaticSegmentationFinished(self, caller, event, labelNode):
self.manualSegmentationPlugin.enabled = True
surfaceCutToLabelWidget = self.manualSegmentationPlugin.surfaceCutToLabelWidget
# segmentationsLogic = slicer.modules.segmentations.logic()
#
# segmentationNode = surfaceCutToLabelWidget.segmentationNode
# map(lambda x: segmentationNode.RemoveSegment(x), surfaceCutToLabelWidget.getSegmentIDs())
# segmentationsLogic.ImportLabelmapToSegmentationNode(labelNode, segmentationNode)
# surfaceCutToLabelWidget.configureSegmentVisibility()
# surfaceCutToLabelWidget.segmentEditorWidgetButton.enabled = True
surfaceCutToLabelWidget.imageVolume = self.session.currentSeriesVolume
surfaceCutToLabelWidget.labelVolume = labelNode
self.createSegmentationDataOrSetModified(
self.automaticSegmentationPlugin, labelNode)
self._onSegmentationFinished(caller, event, labelNode)
def createSegmentationDataOrSetModified(self, plugin, labelNode):
if not self.segmentationData or self.segmentationData.algorithm == "Manual":
self.segmentationData = SegmentationData(
segmentationType="Prostate",
algorithm=plugin.ALGORITHM_TYPE,
startTime=plugin.startTime,
endTime=plugin.endTime,
label=labelNode)
else:
self.segmentationData.setModified(startTime=plugin.startTime,
endTime=plugin.endTime,
label=labelNode)
@vtk.calldata_type(vtk.VTK_OBJECT)
def _onManualSegmentationFinished(self, caller, event, labelNode):
self.createSegmentationDataOrSetModified(self.manualSegmentationPlugin,
labelNode)
self._onSegmentationFinished(caller, event, labelNode)
@vtk.calldata_type(vtk.VTK_OBJECT)
def _onSegmentationFinished(self, caller, event, labelNode):
_, suffix = self.session.getRegistrationResultNameAndGeneratedSuffix(
self.session.currentSeries)
if labelNode.GetName(
).find(suffix) == -1 and not labelNode.GetName().endswith("_modified"):
labelNode.SetName(labelNode.GetName() + suffix)
self.session.fixedLabel = labelNode
self.finishStepButton.setEnabled(1 if self.logic.inputsAreSet() else 0)
self.backButton.enabled = True
self._displaySegmentationComparison()
def _displaySegmentationComparison(self):
self.setAvailableLayouts([constants.LAYOUT_SIDE_BY_SIDE])
if self.session.data.usePreopData or self.session.retryMode:
self.setAxialOrientation()
self._removeMissingPreopDataAnnotation()
self.targetingPlugin.enabled = True
if self.session.data.usePreopData or self.session.retryMode:
self.layoutManager.setLayout(constants.LAYOUT_SIDE_BY_SIDE)
self._setBackgroundAndLabel("red", self.session.movingVolume,
self.session.movingLabel)
self._setBackgroundAndLabel("yellow", self.session.fixedVolume,
self.session.fixedLabel)
self._centerLabelsOnVisibleSliceWidgets()
elif not self.session.movingTargets:
self.targetingPlugin.startTargeting()
else:
for compositeNode, sliceNode in zip(self._compositeNodes,
self._sliceNodes):
compositeNode.SetLabelVolumeID(self.session.fixedLabel.GetID())
compositeNode.SetLabelOpacity(1)
sliceNode.SetUseLabelOutline(True)
def _setBackgroundAndLabel(self, viewName, volume, label):
compositeNode = getattr(self, viewName + "CompositeNode")
compositeNode.SetReferenceBackgroundVolumeID(volume.GetID())
compositeNode.SetLabelVolumeID(label.GetID())
compositeNode.SetLabelOpacity(1)
sliceNode = getattr(self, viewName + "SliceNode")
sliceNode.SetOrientationToAxial()
sliceNode.RotateToVolumePlane(volume)
sliceNode.SetUseLabelOutline(True)
def _centerLabelsOnVisibleSliceWidgets(self):
for widget in self.getAllVisibleWidgets():
compositeNode = widget.mrmlSliceCompositeNode()
sliceNode = widget.sliceLogic().GetSliceNode()
labelID = compositeNode.GetLabelVolumeID()
if labelID:
label = slicer.mrmlScene.GetNodeByID(labelID)
centroid = self.logic.getCentroidForLabel(
label, self.session.segmentedLabelValue)
if centroid:
sliceNode.JumpSliceByCentering(centroid[0], centroid[1],
centroid[2])
def _onTargetingStarted(self, caller, event):
self.manualSegmentationPlugin.enabled = False
self.backButton.enabled = False
def _onTargetingFinished(self, caller, event):
self.finishStepButton.setEnabled(1 if self.logic.inputsAreSet() else 0)
self.manualSegmentationPlugin.enabled = True
self.backButton.enabled = True
def addOldImageAnnotation(self, widget, text, size=20):
self.oldImageAnnotation = SliceAnnotation(widget, text, yPos=35 if ModuleWidgetMixin.isQtVersionOlder() else 45,
size=size)
self.sliceAnnotations.append(self.oldImageAnnotation)
def addNewImageAnnotation(self, widget, text, size=20):
self.newImageAnnotation = SliceAnnotation(widget, text, yPos=35 if ModuleWidgetMixin.isQtVersionOlder() else 45,
opacity=0.0, color=(0, 0.5, 0), size=size)
self.sliceAnnotations.append(self.newImageAnnotation)
