def setEraseEffectEnabled(enabled):
with NodeModify(EditUtil.getParameterNode()):
if enabled and not EditUtil.isEraseEffectEnabled():
EditUtil.backupLabel()
EditUtil.setLabel(0)
elif not enabled and EditUtil.isEraseEffectEnabled():
EditUtil.restoreLabel()
def setEraseEffectEnabled(self, enabled):
with NodeModify(self.getParameterNode()):
if enabled and not self.isEraseEffectEnabled():
self.backupLabel()
self.setLabel(0)
elif not enabled and self.isEraseEffectEnabled():
self.restoreLabel()
def setSlicesZoom(factor):
for sliceLogic in slicer.app.applicationLogic().GetSliceLogics():
sliceNode = sliceLogic.GetSliceNode()
with NodeModify(sliceNode):
sliceLogic.FitSliceToAll()
fov = sliceNode.GetFieldOfView()
sliceNode.SetFieldOfView(fov[0] * factor, fov[1] * factor,
fov[2])
def setWindowLevelPreset(self, presetName):
for volumeNode in slicer.util.getNodesByClass(
"vtkMRMLScalarVolumeNode"):
volumeDisplayNode = volumeNode.GetDisplayNode()
with NodeModify(volumeDisplayNode):
volumeDisplayNode.SetAutoWindowLevel(0)
volumeDisplayNode.SetWindowLevel(
*self.WINDOW_LEVEL_PRESETS[presetName])
def setSlicesZoomOneToOne(volumeNode):
"""1:1 means image 1 image pixel to 1 screen pixel.
This means 512 by 512 image occupies 512 by 512 screen pixels.
"""
for sliceLogic in slicer.app.applicationLogic().GetSliceLogics():
sliceNode = sliceLogic.GetSliceNode()
with NodeModify(sliceNode):
QReadsLogic.setSliceZoomOneToOne(sliceLogic, volumeNode)
QReadsLogic.centerSlice(sliceLogic, volumeNode)
sliceLogic.SnapSliceOffsetToIJK()
def setUserStatisticsTableNode(self, node):
parameterNode = self.getParameterNode()
if parameterNode is None:
return
with NodeModify(parameterNode):
tableNode = parameterNode.GetNodeReference(self.USER_STATISTICS_TABLE_REFERENCE_ROLE)
if node is tableNode:
return
nodeID = ""
if node:
nodeID = node.GetID()
parameterNode.SetNodeReferenceID(self.USER_STATISTICS_TABLE_REFERENCE_ROLE, nodeID)
def updateWindowLevel(windowStep=None, levelStep=None):
for volumeNode in slicer.util.getNodesByClass(
"vtkMRMLScalarVolumeNode"):
volumeDisplayNode = volumeNode.GetDisplayNode()
with NodeModify(volumeDisplayNode):
window = volumeDisplayNode.GetWindow()
if windowStep is not None:
window = window + windowStep
level = volumeDisplayNode.GetLevel()
if levelStep is not None:
level = level + levelStep
volumeDisplayNode.SetAutoWindowLevel(0)
volumeDisplayNode.SetWindowLevel(window, level)
def updateParameterNodeFromGui(self):
self.updateButtonStates()
if self._parameterNode is None:
return
with NodeModify(self._parameterNode):
self._parameterNode.SetParameter("InputVectorVolume",
getNodeID(self.inputVolumeNode()))
self._parameterNode.SetParameter(
"OutputScalarVolume", getNodeID(self.outputVolumeNode()))
self._parameterNode.SetParameter(
"ConversionMethod",
self.conversionMethodWidget.conversionMethod())
self._parameterNode.SetParameter(
"ComponentToExtract",
str(self.conversionMethodWidget.componentToExtract()))
def updateMRMLFromGUI(self):
with NodeModify(self.parameterNode):
super().updateMRMLFromGUI()
self.scope = self.availableScopeOptions[
self.scopeComboBox.currentIndex]
self.parameterNode.SetParameter("Effect,scope", str(self.scope))
def setup(self):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer).
# Additional widgets can be instantiated manually and added to self.layout.
uiWidget = slicer.util.loadUI(self.resourcePath('UI/QReads.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
self.slabModeButtonGroup = qt.QButtonGroup()
self.slabModeButtonGroup.addButton(self.ui.SlabModeMaxRadioButton,
vtk.VTK_IMAGE_SLAB_MAX)
self.slabModeButtonGroup.addButton(self.ui.SlabModeMeanRadioButton,
vtk.VTK_IMAGE_SLAB_MEAN)
self.slabModeButtonGroup.addButton(self.ui.SlabModeMinRadioButton,
vtk.VTK_IMAGE_SLAB_MIN)
self.ui.ZoomComboBox.addItems(self.ZOOM_ACTIONS)
# Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
#uiWidget.setMRMLScene(slicer.mrmlScene)
# Create logic class. Logic implements all computations that should be possible to run
# in batch mode, without a graphical user interface.
self.logic = QReadsLogic()
# Connections
# These connections ensure that we update parameter node when scene is closed
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent,
self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent,
self.onSceneEndClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.NodeAddedEvent,
self.onNodeAdded)
# These connections ensure that whenever user changes some settings on the GUI, that is saved in the MRML scene
# (in the selected parameter node).
self.ui.ShowReferenceMarkersButton.connect(
"clicked()", self.updateParameterNodeFromGUI)
self.ui.ResetReferenceMarkersButton.connect(
"clicked()", QReadsLogic.resetReferenceMarkers)
self.ui.SlabButton.connect("clicked()",
self.updateParameterNodeFromGUI)
self.slabModeButtonGroup.connect("buttonClicked(int)",
self.updateParameterNodeFromGUI)
self.ui.SlabThicknessSliderWidget.connect(
"valueChanged(double)", self.updateParameterNodeFromGUI)
self.ui.InverseGrayButton.connect("clicked(bool)",
self.updateParameterNodeFromGUI)
# Increasing the level will make the image darker, whereas decreasing the level value will make the image brighter
self.ui.BrightnessUpButton.connect(
"clicked()",
lambda step=-self.BRIGHTNESS_STEP: QReadsLogic.updateWindowLevel(
levelStep=step))
self.ui.BrightnessDownButton.connect(
"clicked()",
lambda step=self.BRIGHTNESS_STEP: QReadsLogic.updateWindowLevel(
levelStep=step))
# Increasing window will reduce display contrast, whereas decreasing the window increases the brightness
self.ui.ContrastUpButton.connect(
"clicked()",
lambda step=-self.CONTRAST_STEP: QReadsLogic.updateWindowLevel(
windowStep=step))
self.ui.ContrastDownButton.connect(
"clicked()",
lambda step=self.CONTRAST_STEP: QReadsLogic.updateWindowLevel(
windowStep=step))
self.ui.CTBodySoftTissueWLPresetButton.connect(
"clicked()",
lambda presetName="CT-BodySoftTissue": self.logic.
setWindowLevelPreset(presetName))
self.ui.CTBoneWLPresetButton.connect(
"clicked()",
lambda presetName="CT-Bone": self.logic.setWindowLevelPreset(
presetName))
self.ui.CTBrainWLPresetButton.connect(
"clicked()",
lambda presetName="CT-Head": self.logic.setWindowLevelPreset(
presetName))
self.ui.CTLungWLPresetButton.connect(
"clicked()",
lambda presetName="CT-Lung": self.logic.setWindowLevelPreset(
presetName))
self.ui.ZoomComboBox.connect("currentTextChanged(QString)",
self.updateParameterNodeFromGUI)
self.ui.CloseApplicationPushButton.connect("clicked()",
slicer.util.quit)
# Make sure parameter node is initialized (needed for module reload)
self.initializeParameterNode()
# Hide main window components
slicer.util.setApplicationLogoVisible(False)
slicer.util.setMenuBarsVisible(False)
slicer.util.setModuleHelpSectionVisible(False)
slicer.util.setModulePanelTitleVisible(False)
slicer.util.setToolbarsVisible(False)
# Layout
slicer.app.layoutManager().setLayout(self.logic.registerCustomLayout())
for viewName, viewColor in QReadsLogic.SLICEVIEW_BACKGROUND_COLORS.items(
):
sliceWidget = slicer.app.layoutManager().sliceWidget(viewName)
sliceWidget.sliceView().setBackgroundColor(qt.QColor(viewColor))
sliceNode = sliceWidget.mrmlSliceNode()
sliceNode.SetOrientationMarkerType(
slicer.vtkMRMLAbstractViewNode.OrientationMarkerTypeAxes)
sliceNode.SetSliceVisible(True)
for viewName, viewColor in QReadsLogic.THREEDVIEW_BACKGROUND_COLORS.items(
):
with NodeModify(slicer.util.getNode("vtkMRMLViewNode%s" %
viewName)) as viewNode:
viewNode.SetBackgroundColor(0., 0., 0.)
viewNode.SetBackgroundColor2(0., 0., 0.)
viewNode.SetBoxVisible(False)
viewNode.SetAxisLabelsVisible(False)
viewNode.SetOrientationMarkerType(
slicer.vtkMRMLAbstractViewNode.OrientationMarkerTypeAxes)