def __init__(self, anglePlanes, id, pointlocatordictionary):
qt.QFrame.__init__(self)
self.id = id
self.setLayout(qt.QFormLayout())
self.pointLocatorDictionary = pointlocatordictionary
landmarkLayout = qt.QHBoxLayout()
planeLabel = qt.QLabel('Plane ' + str(id) + ":")
landmarkLayout.addWidget(planeLabel)
self.logic = AnglePlanesLogic(id)
label1 = qt.QLabel(' L1:')
self.landmark1ComboBox = qt.QComboBox()
landmark1ComboBox = self.landmark1ComboBox
landmark1ComboBox.addItem("Select")
landmark1ComboBox.connect('currentIndexChanged(QString)',
self.placePlaneClicked)
landmarkLayout.addWidget(label1)
landmarkLayout.addWidget(landmark1ComboBox)
label2 = qt.QLabel(' L2:')
self.landmark2ComboBox = qt.QComboBox()
landmark2ComboBox = self.landmark2ComboBox
landmark2ComboBox.addItem("Select")
landmark2ComboBox.connect('currentIndexChanged(QString)',
self.placePlaneClicked)
landmarkLayout.addWidget(label2)
landmarkLayout.addWidget(landmark2ComboBox)
label3 = qt.QLabel(' L3:')
self.landmark3ComboBox = qt.QComboBox()
landmark3ComboBox = self.landmark3ComboBox
landmark3ComboBox.addItem("Select")
landmark3ComboBox.connect('currentIndexChanged(QString)',
self.placePlaneClicked)
landmarkLayout.addWidget(label3)
landmarkLayout.addWidget(landmark3ComboBox)
addFiducialLabel = qt.QLabel('Add')
addFiducialButton = qt.QPushButton(
qt.QIcon(":/Icons/MarkupsAddFiducial.png"), " ")
addFiducialButton.setFixedSize(50, 25)
addFiducialButton.connect('clicked()', self.addLandMarkClicked)
addFiducialButton.setEnabled(True)
landmarkLayout.addWidget(addFiducialLabel)
landmarkLayout.addWidget(addFiducialButton)
#fiducial list for the plane
fidNode = self.logic.getFiducialList()
for i in range(0, fidNode.GetNumberOfFiducials()):
label = fidNode.GetNthFiducialLabel(i)
landmark1ComboBox.addItem(label)
landmark2ComboBox.addItem(label)
landmark3ComboBox.addItem(label)
anglePlanes.landmarkComboBox1MidPoint.addItem(label)
anglePlanes.landmarkComboBox2MidPoint.addItem(label)
anglePlanes.midPointFiducialDictionaryID[
label] = fidNode.GetNthMarkupID(i)
fidNode.AddObserver(fidNode.MarkupAddedEvent, self.onFiducialAdded)
fidNode.AddObserver(fidNode.MarkupRemovedEvent, self.onFiducialRemoved)
self.setPointModifiedEventId = fidNode.AddObserver(
fidNode.PointModifiedEvent, self.onPointModifiedEvent)
# This observers are in AnglePlaneWidgets, they listen to any fiducial being added
#
fidNode.AddObserver(fidNode.MarkupAddedEvent,
anglePlanes.onFiducialAddedMidPoint)
fidNode.AddObserver(fidNode.MarkupRemovedEvent,
anglePlanes.onFiducialRemovedMidPoint)
self.layout().addRow(landmarkLayout)
self.slider = ctk.ctkSliderWidget()
slider = self.slider
slider.singleStep = 0.1
slider.minimum = 0.1
slider.maximum = 10
slider.value = 1.0
slider.toolTip = "Set the size of your plane."
self.slideOpacity = ctk.ctkSliderWidget()
slideOpacity = self.slideOpacity
slideOpacity.singleStep = 0.1
slideOpacity.minimum = 0.1
slideOpacity.maximum = 1
slideOpacity.value = 1.0
slideOpacity.toolTip = "Set the opacity of your plane."
slider.connect('valueChanged(double)', self.placePlaneClicked)
slideOpacity.connect('valueChanged(double)', self.placePlaneClicked)
landmarkSliderLayout = qt.QHBoxLayout()
label = qt.QLabel(' Size:')
label2 = qt.QLabel(' Opacity:')
landmarkSliderLayout.addWidget(label)
landmarkSliderLayout.addWidget(self.slider)
landmarkSliderLayout.addWidget(label2)
landmarkSliderLayout.addWidget(self.slideOpacity)
self.surfaceDeplacementCheckBox = qt.QCheckBox("On Surface")
self.surfaceDeplacementCheckBox.setChecked(True)
self.surfaceDeplacementCheckBox.connect(
'stateChanged(int)', self.onSurfaceDeplacementStateChanged)
landmarkSliderLayout.addWidget(self.surfaceDeplacementCheckBox)
self.layout().addRow(landmarkSliderLayout)
def loadFromMRML(self, mrmlNode=None):
'''
'''
if not self.__updating:
self.__updating = 1
self.resetPanel()
if mrmlNode:
# adjust the panel to the given mrmlNode
vtkId = self.mrmlManager().MapMRMLNodeIDToVTKNodeID(
mrmlNode.GetID())
# number of volumes
numberOfVolumes = self.mrmlManager(
).GetTargetNumberOfSelectedVolumes()
# re-enable the widgets
self.resetPanel(True)
self.__classLabel2.setText("Class: " + mrmlNode.GetName())
self.setupManualSampleTable(mrmlNode)
for c in range(numberOfVolumes):
value = self.mrmlManager(
).GetTreeNodeDistributionMeanWithCorrection(vtkId, c)
for r in range(numberOfVolumes):
for c in range(numberOfVolumes):
value = self.mrmlManager(
).GetTreeNodeDistributionLogCovarianceWithCorrection(
vtkId, r, c)
#
# overview panel
#
# first, clear it all
for i in self.__classWeights:
self.__overviewBoxLayout.removeWidget(i)
i.deleteLater()
i.setParent(None)
i = None
self.__classWeights = []
self.__classWeightLayouts = []
self.__classWeightLabels = []
self.__classWeightSpinBoxes = []
self.__classWeightCheckBoxes = []
# fill it again
if vtkId != self.mrmlManager().GetTreeRootNodeID():
# other node than root selected
parent = self.mrmlManager().GetTreeNodeParentNodeID(vtkId)
numberOfChildren = self.mrmlManager(
).GetTreeNodeNumberOfChildren(parent)
for i in range(numberOfChildren):
child = self.mrmlManager().GetTreeNodeChildNodeID(
parent, i)
name = self.mrmlManager().GetTreeNodeName(child)
probability = self.mrmlManager(
).GetTreeNodeClassProbability(child)
label = qt.QLabel(name + ":")
spinBox = qt.QDoubleSpinBox()
spinBox.minimum = 0
spinBox.maximum = 1
spinBox.singleStep = 0.01
spinBox.value = probability
checkBox = qt.QCheckBox(" ")
checkBox.toolTip = 'Toggle for auto-update when changing other weights.'
self.__classWeightLabels.append(label)
self.__classWeightSpinBoxes.append(spinBox)
self.__classWeightCheckBoxes.append(checkBox)
self.__classWeightSpinBoxes[-1].connect(
'valueChanged(double)', self.updateClassWeights)
self.__classWeightCheckBoxes[-1].connect(
'stateChanged(int)', self.updateClassWeights)
weightRow = qt.QWidget()
weightRowLayout = qt.QHBoxLayout(weightRow)
weightRowLayout.addWidget(self.__classWeightLabels[-1])
weightRowLayout.addWidget(
self.__classWeightSpinBoxes[-1])
weightRowLayout.addWidget(
self.__classWeightCheckBoxes[-1])
self.__classWeights.append(weightRow)
self.__classWeightLayouts.append(weightRowLayout)
self.__overviewBoxLayout.addWidget(
self.__classWeights[-1], 0, 2)
self.__updating = 0
def createUserInterface(self):
'''
'''
self.__layout = super(EMSegmentQuickStep3, self).createUserInterface()
self.__top = qt.QWidget()
self.__topLayout = qt.QHBoxLayout(self.__top)
# the anatomical tree
anatomicalTreeGroupBox = qt.QGroupBox()
anatomicalTreeGroupBox.setTitle('Anatomical Tree')
self.__topLayout.addWidget(anatomicalTreeGroupBox)
anatomicalTreeGroupBoxLayout = qt.QFormLayout(anatomicalTreeGroupBox)
self.__anatomicalTree = slicer.modulewidget.qSlicerEMSegmentAnatomicalTreeWidget(
)
self.__anatomicalTree.structureNameEditable = False
self.__anatomicalTree.labelColumnVisible = False
self.__anatomicalTree.probabilityMapColumnVisible = False
self.__anatomicalTree.classWeightColumnVisible = False
self.__anatomicalTree.updateClassWeightColumnVisible = False
self.__anatomicalTree.atlasWeightColumnVisible = False
self.__anatomicalTree.alphaColumnVisible = False
self.__anatomicalTree.displayAlphaCheckBoxVisible = False
self.__anatomicalTree.setMinimumHeight(200)
self.__anatomicalTree.toolTip = 'Select a structure to configure the intensity distribution.'
self.__anatomicalTree.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.MinimumExpanding)
self.__anatomicalTree.connect('currentTreeNodeChanged(vtkMRMLNode*)',
self.onTreeSelectionChanged)
anatomicalTreeGroupBoxLayout.addWidget(self.__anatomicalTree)
#
# overview of class weights panel
#
self.__overviewBox = qt.QGroupBox()
self.__overviewBox.title = 'Guesses of Probability'
self.__overviewBox.toolTip = 'These are your guesses of probability relations between structures. Which structure takes how much percentage of the volume?'
self.__overviewBoxLayout = qt.QVBoxLayout(self.__overviewBox)
self.__topLayout.addWidget(self.__overviewBox)
self.__layout.addWidget(self.__top)
self.__tabWidget = qt.QTabWidget()
self.__layout.addWidget(self.__tabWidget)
#
# manualSamplingPage
#
manualSamplingPage = qt.QWidget()
manualSamplingPageLayout = qt.QFormLayout(manualSamplingPage)
self.__classLabel2 = qt.QLabel("Class: XX")
manualSamplingPageLayout.addWidget(self.__classLabel2)
self.__infoLabel = qt.QLabel(
"left mouse Click in a slice window to pick a sample")
manualSamplingPageLayout.addWidget(self.__infoLabel)
self.__manualSampleTable = qt.QTableWidget()
manualSamplingPageLayout.addWidget(self.__manualSampleTable)
self.__tabWidget.addTab(manualSamplingPage, "Manual Sampling")
self.__plotDistributionButton = qt.QPushButton()
self.__plotDistributionButton.text = "Plot Distribution"
self.__plotDistributionButton.toolTip = 'Click to plot the intensity distributions for all structures.'
self.__layout.addRow(self.__plotDistributionButton)
self.__plotDistributionButton.connect('clicked()',
self.plotDistribution)
def setup(self):
self.developerMode = False
ScriptedLoadableModuleWidget.setup(self)
annotationsCollapsibleButton = ctk.ctkCollapsibleButton()
annotationsCollapsibleButton.text = "Astro Annotations"
self.layout.addWidget(annotationsCollapsibleButton)
# Layout within the dummy collapsible button
annotationsFormLayout = qt.QVBoxLayout(annotationsCollapsibleButton)
# Color
horizontalLayout_1 = qt.QHBoxLayout()
horizontalLayout_1.setObjectName("horizontalLayout_1")
self.colorLabel = qt.QLabel()
self.colorLabel.setText("Annotations color:")
self.colorLabel.setFixedSize(qt.QSize(120, 30))
horizontalLayout_1.addWidget(self.colorLabel)
self.colorSelector = ctk.ctkColorPickerButton()
self.colorSelector.setObjectName("ColorPickerButton")
sizePolicy = qt.QSizePolicy()
sizePolicy.setHorizontalPolicy(qt.QSizePolicy.Expanding)
sizePolicy.setVerticalPolicy(qt.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(
self.colorSelector.sizePolicy.hasHeightForWidth())
self.colorSelector.setSizePolicy(sizePolicy)
self.colorSelector.setMinimumSize(qt.QSize(0, 30))
self.colorSelector.setIconSize(qt.QSize(32, 32))
self.colorSelector.setColor(qt.QColor(255, 187, 20))
self.colorSelector.setDisplayColorName(0)
horizontalLayout_1.addWidget(self.colorSelector)
annotationsFormLayout.addLayout(horizontalLayout_1)
# Font Style
horizontalLayout_2 = qt.QHBoxLayout()
horizontalLayout_2.setObjectName("horizontalLayout_2")
self.fontStyleLabel = qt.QLabel()
self.fontStyleLabel.setText("Font style:")
self.fontStyleLabel.setFixedSize(qt.QSize(120, 30))
horizontalLayout_2.addWidget(self.fontStyleLabel)
self.styleComboBox = qt.QComboBox()
self.styleComboBox.addItem("Arial")
self.styleComboBox.addItem("Courier")
self.styleComboBox.addItem("Times")
sizePolicy.setHeightForWidth(
self.styleComboBox.sizePolicy.hasHeightForWidth())
self.styleComboBox.setMinimumSize(qt.QSize(0, 30))
horizontalLayout_2.addWidget(self.styleComboBox)
annotationsFormLayout.addLayout(horizontalLayout_2)
# Font size
horizontalLayout_3 = qt.QHBoxLayout()
horizontalLayout_3.setObjectName("horizontalLayout_3")
self.fontSizeLabel = qt.QLabel()
self.fontSizeLabel.setText("Font size:")
self.fontSizeLabel.setFixedSize(qt.QSize(120, 30))
horizontalLayout_3.addWidget(self.fontSizeLabel)
self.sizeSpinBox = qt.QSpinBox()
sizePolicy.setHeightForWidth(
self.sizeSpinBox.sizePolicy.hasHeightForWidth())
self.sizeSpinBox.setMinimumSize(qt.QSize(0, 30))
self.sizeSpinBox.minimum = 1
self.sizeSpinBox.maximum = 30
self.sizeSpinBox.setValue(12)
self.sizeSpinBox.setToolTip(
"This value is multiplied for 1.5 if the ruler is set to thick.")
horizontalLayout_3.addWidget(self.sizeSpinBox)
annotationsFormLayout.addLayout(horizontalLayout_3)
verticalSpacer = qt.QSpacerItem(200, 200, qt.QSizePolicy.Minimum,
qt.QSizePolicy.Expanding)
self.layout.addItem(verticalSpacer)
# Connections
self.colorSelector.connect('colorChanged(QColor)',
self.onAnnotationsColorChanged)
self.styleComboBox.connect('currentTextChanged(QString)',
self.onAnnotationsFontStyleChanged)
self.sizeSpinBox.connect('valueChanged(int)',
self.onAnnotationsFontSizeChanged)
def create(self):
super(PaintEffectOptions, self).create()
labelVolume = self.editUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
dimensions = labelVolume.GetImageData().GetDimensions()
self.minimumRadius = 0.5 * min(spacing)
bounds = [a * b for a, b in zip(spacing, dimensions)]
self.maximumRadius = 0.5 * max(bounds)
else:
self.minimumRadius = 0.01
self.maximumRadius = 100
self.radiusFrame = qt.QFrame(self.frame)
self.radiusFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.radiusFrame)
self.widgets.append(self.radiusFrame)
self.radiusLabel = qt.QLabel("Radius:", self.radiusFrame)
self.radiusLabel.setToolTip(
"Set the radius of the paint brush in millimeters")
self.radiusFrame.layout().addWidget(self.radiusLabel)
self.widgets.append(self.radiusLabel)
self.radiusSpinBox = qt.QDoubleSpinBox(self.radiusFrame)
self.radiusSpinBox.setToolTip(
"Set the radius of the paint brush in millimeters")
self.radiusSpinBox.minimum = self.minimumRadius
self.radiusSpinBox.maximum = self.maximumRadius
self.radiusSpinBox.suffix = "mm"
from math import log, floor
decimals = floor(log(self.minimumRadius, 10))
if decimals < 0:
self.radiusSpinBox.decimals = -decimals + 2
self.radiusFrame.layout().addWidget(self.radiusSpinBox)
self.widgets.append(self.radiusSpinBox)
self.radiusUnitsToggle = qt.QPushButton("px:")
self.radiusUnitsToggle.setToolTip(
"Toggle radius quick set buttons between mm and label volume pixel size units"
)
self.radiusUnitsToggle.setFixedWidth(35)
self.radiusFrame.layout().addWidget(self.radiusUnitsToggle)
self.radiusUnitsToggle.connect('clicked()', self.onRadiusUnitsToggle)
self.radiusQuickies = {}
quickies = ((2, self.onQuickie2Clicked), (3, self.onQuickie3Clicked),
(4, self.onQuickie4Clicked), (5, self.onQuickie5Clicked),
(10, self.onQuickie10Clicked), (20,
self.onQuickie20Clicked))
for rad, callback in quickies:
self.radiusQuickies[rad] = qt.QPushButton(str(rad))
self.radiusFrame.layout().addWidget(self.radiusQuickies[rad])
self.radiusQuickies[rad].setFixedWidth(25)
self.radiusQuickies[rad].connect('clicked()', callback)
self.radiusQuickies[rad].setToolTip(
"Set radius based on mm or label voxel size units depending on toggle value"
)
self.radius = ctk.ctkDoubleSlider(self.frame)
self.radius.minimum = self.minimumRadius
self.radius.maximum = self.maximumRadius
self.radius.orientation = 1
self.radius.singleStep = self.minimumRadius
self.frame.layout().addWidget(self.radius)
self.widgets.append(self.radius)
self.smudge = qt.QCheckBox("Smudge", self.frame)
self.smudge.setToolTip(
"Set the label number automatically by sampling the pixel location where the brush stroke starts."
)
self.frame.layout().addWidget(self.smudge)
self.widgets.append(self.smudge)
EditorLib.HelpButton(
self.frame,
"Use this tool to paint with a round brush of the selected radius")
self.connections.append(
(self.smudge, 'clicked()', self.updateMRMLFromGUI))
self.connections.append(
(self.radius, 'valueChanged(double)', self.onRadiusValueChanged))
self.connections.append((self.radiusSpinBox, 'valueChanged(double)',
self.onRadiusSpinBoxChanged))
# Add vertical spacer
self.frame.layout().addStretch(1)
# set the node parameters that are dependent on the input data
self.parameterNode.SetParameter("PaintEffect,radius",
str(self.minimumRadius * 10))
def setup(self):
# Instantiate and connect widgets ...
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "QuantitativeIndicesTool Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
self.reloadAndTestButton.setEnabled(False)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# grayscale volume selector
#
self.grayscaleSelector = slicer.qMRMLNodeComboBox()
self.grayscaleSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.grayscaleSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", 0)
self.grayscaleSelector.selectNodeUponCreation = True
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = True
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene(slicer.mrmlScene)
self.grayscaleSelector.setToolTip("Input grayscale volume.")
parametersFormLayout.addRow("Input Volume: ", self.grayscaleSelector)
self.grayscaleNode = None
#
# label map volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.labelSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
1)
self.labelSelector.selectNodeUponCreation = True
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Input label map volume.")
parametersFormLayout.addRow("Label Map: ", self.labelSelector)
self.labelNode = None
#
# CLI node name and set button
#
self.parameterFrame = qt.QFrame(self.parent)
self.parameterFrame.setLayout(qt.QHBoxLayout())
parametersFormLayout.addRow("Parameter Set: ", self.parameterFrame)
self.parameterFrameLabel = qt.QLabel(" (none generated) ",
self.parameterFrame)
self.parameterFrameLabel.setToolTip(
"Nodes for storing parameter flags and output.")
self.parameterFrame.layout().addWidget(self.parameterFrameLabel)
self.parameterName = qt.QLabel("", self.parameterFrame)
self.parameterName.setToolTip(
"Nodes for storing parameter flags and output.")
self.parameterFrame.layout().addWidget(self.parameterName)
self.parameterSetButton = qt.QPushButton("Generate",
self.parameterFrame)
self.parameterSetButton.setToolTip(
"Generate a set of parameter nodes to store with the scene")
self.parameterSetButton.setEnabled(False)
self.parameterFrame.layout().addWidget(self.parameterSetButton)
self.cliNodes = None
self.changeVolumesButton = qt.QPushButton("Change Volumes",
self.parameterFrame)
self.changeVolumesButton.setToolTip(
"Change the grayscale volume and/or the label map. Previous calculations from the scene will be deleted."
)
self.changeVolumesButton.setEnabled(False)
self.parameterFrame.layout().addWidget(self.changeVolumesButton)
#
# label map value spin box
#
self.labelValueSelector = qt.QSpinBox()
self.labelValueSelector.setEnabled(False)
self.labelValueSelector.setMinimum(0)
self.labelValueSelector.setValue(1)
self.labelValueSelector.setToolTip("Label value to calculate features")
parametersFormLayout.addRow("Label Value: ", self.labelValueSelector)
self.totalLabels = 0
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = False
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
#parametersFormLayout.addRow("Enable Screenshots", self.enableScreenshotsFlagCheckBox)
#
# scale factor for screen shots
#
self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
self.screenshotScaleFactorSliderWidget.singleStep = 1.0
self.screenshotScaleFactorSliderWidget.minimum = 1.0
self.screenshotScaleFactorSliderWidget.maximum = 50.0
self.screenshotScaleFactorSliderWidget.value = 1.0
self.screenshotScaleFactorSliderWidget.setToolTip(
"Set scale factor for the screen shots.")
#parametersFormLayout.addRow("Screenshot scale factor", self.screenshotScaleFactorSliderWidget)
#
# Create large list of quantitative features
#
self.featuresCollapsibleButton = ctk.ctkCollapsibleButton()
self.featuresCollapsibleButton.text = "Features to Calculate"
self.layout.addWidget(self.featuresCollapsibleButton)
self.featuresFormLayout = qt.QFormLayout(
self.featuresCollapsibleButton)
self.QIFrame1 = qt.QFrame(self.parent)
self.QIFrame1.setLayout(qt.QHBoxLayout())
self.QIFrame1.layout().setSpacing(0)
self.QIFrame1.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame1)
self.MeanCheckBox = qt.QCheckBox("Mean", self.QIFrame1)
self.QIFrame1.layout().addWidget(self.MeanCheckBox)
self.MeanCheckBox.checked = False
self.VarianceCheckBox = qt.QCheckBox("Variance", self.QIFrame1)
self.QIFrame1.layout().addWidget(self.VarianceCheckBox)
self.VarianceCheckBox.checked = False
self.MinCheckBox = qt.QCheckBox("Minimum", self.QIFrame1)
self.QIFrame1.layout().addWidget(self.MinCheckBox)
self.MinCheckBox.checked = False
self.MaxCheckBox = qt.QCheckBox("Maximum", self.QIFrame1)
self.QIFrame1.layout().addWidget(self.MaxCheckBox)
self.MaxCheckBox.checked = False
self.QIFrame2 = qt.QFrame(self.parent)
self.QIFrame2.setLayout(qt.QHBoxLayout())
self.QIFrame2.layout().setSpacing(0)
self.QIFrame2.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame2)
self.Quart1CheckBox = qt.QCheckBox("1st Quartile", self.QIFrame2)
self.QIFrame2.layout().addWidget(self.Quart1CheckBox)
self.Quart1CheckBox.checked = False
self.MedianCheckBox = qt.QCheckBox("Median", self.QIFrame2)
self.QIFrame2.layout().addWidget(self.MedianCheckBox)
self.MedianCheckBox.checked = False
self.Quart3CheckBox = qt.QCheckBox("3rd Quartile", self.QIFrame2)
self.QIFrame2.layout().addWidget(self.Quart3CheckBox)
self.Quart3CheckBox.checked = False
self.UpperAdjacentCheckBox = qt.QCheckBox("Upper Adjacent",
self.QIFrame2)
self.QIFrame2.layout().addWidget(self.UpperAdjacentCheckBox)
self.UpperAdjacentCheckBox.checked = False
self.QIFrame3 = qt.QFrame(self.parent)
self.QIFrame3.setLayout(qt.QHBoxLayout())
self.QIFrame3.layout().setSpacing(0)
self.QIFrame3.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame3)
self.Q1CheckBox = qt.QCheckBox("Q1 Distribution", self.QIFrame3)
self.QIFrame3.layout().addWidget(self.Q1CheckBox)
self.Q1CheckBox.checked = False
self.Q2CheckBox = qt.QCheckBox("Q2 Distribution", self.QIFrame3)
self.QIFrame3.layout().addWidget(self.Q2CheckBox)
self.Q2CheckBox.checked = False
self.Q3CheckBox = qt.QCheckBox("Q3 Distribution", self.QIFrame3)
self.QIFrame3.layout().addWidget(self.Q3CheckBox)
self.Q3CheckBox.checked = False
self.Q4CheckBox = qt.QCheckBox("Q4 Distribution", self.QIFrame3)
self.QIFrame3.layout().addWidget(self.Q4CheckBox)
self.Q4CheckBox.checked = False
self.QIFrame4 = qt.QFrame(self.parent)
self.QIFrame4.setLayout(qt.QHBoxLayout())
self.QIFrame4.layout().setSpacing(0)
self.QIFrame4.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame4)
self.Gly1CheckBox = qt.QCheckBox("Glycolysis Q1", self.QIFrame4)
self.QIFrame4.layout().addWidget(self.Gly1CheckBox)
self.Gly1CheckBox.checked = False
self.Gly2CheckBox = qt.QCheckBox("Glycolysis Q2", self.QIFrame4)
self.QIFrame4.layout().addWidget(self.Gly2CheckBox)
self.Gly2CheckBox.checked = False
self.Gly3CheckBox = qt.QCheckBox("Glycolysis Q3", self.QIFrame4)
self.QIFrame4.layout().addWidget(self.Gly3CheckBox)
self.Gly3CheckBox.checked = False
self.Gly4CheckBox = qt.QCheckBox("Glycolysis Q4", self.QIFrame4)
self.QIFrame4.layout().addWidget(self.Gly4CheckBox)
self.Gly4CheckBox.checked = False
self.QIFrame5 = qt.QFrame(self.parent)
self.QIFrame5.setLayout(qt.QHBoxLayout())
self.QIFrame5.layout().setSpacing(0)
self.QIFrame5.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame5)
self.TLGCheckBox = qt.QCheckBox("TLG", self.QIFrame5)
self.QIFrame5.layout().addWidget(self.TLGCheckBox)
self.TLGCheckBox.checked = False
self.SAMCheckBox = qt.QCheckBox("SAM", self.QIFrame5)
self.QIFrame5.layout().addWidget(self.SAMCheckBox)
self.SAMCheckBox.checked = False
self.SAMBGCheckBox = qt.QCheckBox("SAM Background", self.QIFrame5)
self.QIFrame5.layout().addWidget(self.SAMBGCheckBox)
self.SAMBGCheckBox.checked = False
self.RMSCheckBox = qt.QCheckBox("RMS", self.QIFrame5)
self.QIFrame5.layout().addWidget(self.RMSCheckBox)
self.RMSCheckBox.checked = False
self.QIFrame6 = qt.QFrame(self.parent)
self.QIFrame6.setLayout(qt.QHBoxLayout())
self.QIFrame6.layout().setSpacing(0)
self.QIFrame6.layout().setMargin(0)
self.featuresFormLayout.addRow("", self.QIFrame6)
self.PeakCheckBox = qt.QCheckBox("Peak", self.QIFrame6)
self.QIFrame6.layout().addWidget(self.PeakCheckBox)
self.PeakCheckBox.checked = False
self.VolumeCheckBox = qt.QCheckBox("Volume", self.QIFrame6)
self.QIFrame6.layout().addWidget(self.VolumeCheckBox)
self.VolumeCheckBox.checked = False
self.selectAllButton = qt.QPushButton("Select All")
self.selectAllButton.toolTip = "Select all quantitative features."
self.QIFrame6.layout().addWidget(self.selectAllButton)
self.deselectAllButton = qt.QPushButton("Deselect All")
self.deselectAllButton.toolTip = "Deselect all quantitative features."
self.QIFrame6.layout().addWidget(self.deselectAllButton)
#
# Calculate Button
#
self.calculateButton = qt.QPushButton("Calculate")
self.calculateButton.toolTip = "Calculate quantitative features."
self.calculateButton.enabled = False
self.featuresFormLayout.addRow(self.calculateButton)
#
# Results Frame
#
self.resultsCollapsibleButton = ctk.ctkCollapsibleButton()
self.resultsCollapsibleButton.text = "Results"
self.layout.addWidget(self.resultsCollapsibleButton)
self.resultsFormLayout = qt.QFormLayout(self.resultsCollapsibleButton)
self.resultsFrame = qt.QFrame(self.resultsCollapsibleButton)
self.resultsFrame.setLayout(qt.QHBoxLayout())
self.resultsFrame.layout().setSpacing(0)
self.resultsFrame.layout().setMargin(0)
self.resultsFormLayout.addWidget(self.resultsFrame)
self.resultsFrameLabel = qt.QLabel('', self.resultsFrame)
self.resultsFrame.layout().addWidget(self.resultsFrameLabel)
# Add vertical spacer
self.layout.addStretch(1)
# connections
self.calculateButton.connect('clicked(bool)', self.onCalculateButton)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
self.parameterSetButton.connect('clicked(bool)',
self.onParameterSetButton)
self.changeVolumesButton.connect('clicked(bool)',
self.onChangeVolumesButton)
self.labelValueSelector.connect('valueChanged(int)',
self.onLabelValueSelect)
self.selectAllButton.connect('clicked(bool)', self.onSelectAllButton)
self.deselectAllButton.connect('clicked(bool)',
self.onDeselectAllButton)
def setup(self):
"""This is called one time when the module GUI is initialized
"""
# Declare ALL the GUI components (depending on the context we will add different ones to the layout)
self.widgetMainFrame = qt.QFrame()
self.widgetMainLayout = qt.QGridLayout()
self.widgetMainFrame.setLayout(self.widgetMainLayout)
self.layout.addWidget(self.widgetMainFrame)
## Context
self.contextLabel = qt.QLabel("Context")
self.contextComboBox = qt.QComboBox()
for context in self.contexts.itervalues():
self.contextComboBox.addItem(context)
## Operation
self.operationLabel = qt.QLabel("Optimization")
self.operationComboBox = qt.QComboBox()
for operation in self.operations.itervalues():
if operation != self.OPERATION_NONE:
self.operationComboBox.addItem(operation)
## Plane
self.planeLabel = qt.QLabel("Plane")
# Buttons group
self.planesButtonGroup = qt.QButtonGroup()
# Axial
self.axialButton = qt.QPushButton()
self.axialButton.setCheckable(True)
self.axialButton.toolTip = "Axial plane"
self.axialButton.setFixedSize(40, 40)
self.axialButton.setIcon(SlicerUtil.getIcon("axial.png"))
self.planesButtonGroup.addButton(self.axialButton, self.PLANE_AXIAL)
# Sagittal
self.sagittalButton = qt.QPushButton()
self.sagittalButton.setCheckable(True)
self.sagittalButton.toolTip = "Sagittal plane"
self.sagittalButton.setFixedSize(40, 40)
self.sagittalButton.setIcon(SlicerUtil.getIcon("sagittal.png"))
self.widgetMainLayout.addWidget(self.sagittalButton, 2, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.planesButtonGroup.addButton(self.sagittalButton,
self.PLANE_SAGITTAL)
# Coronal
self.coronalButton = qt.QPushButton()
self.coronalButton.setCheckable(True)
self.coronalButton.toolTip = "coronal plane"
self.coronalButton.setFixedSize(40, 40)
self.coronalButton.setIcon(SlicerUtil.getIcon("coronal.png"))
self.planesButtonGroup.addButton(self.coronalButton,
self.PLANE_CORONAL)
# Null button (to uncheck all)
self.nullPlaneButton = qt.QPushButton()
self.nullPlaneButton.setCheckable(True)
self.planesButtonGroup.addButton(self.nullPlaneButton, -1)
# Buttons labels
self.axialButtonLabel = qt.QLabel("Axial")
self.axialButtonLabel.setStyleSheet("margin-bottom: 10px")
self.sagittalButtonLabel = qt.QLabel("Sagittal")
self.sagittalButtonLabel.setStyleSheet("margin-bottom: 10px")
self.coronalButtonLabel = qt.QLabel("Coronal")
self.coronalButtonLabel.setStyleSheet("margin-bottom: 10px")
## Layout
self.layoutLabel = qt.QLabel("Layout")
# Buttons group
self.layoutsButtonGroup = qt.QButtonGroup()
# Single slice Button
self.singleSlideViewButton = qt.QPushButton()
self.singleSlideViewButton.setCheckable(True)
self.singleSlideViewButton.toolTip = "Single slice view"
self.singleSlideViewButton.setFixedSize(40, 40)
self.singleSlideViewButton.setIcon(
qt.QIcon(":/Icons/LayoutOneUpRedSliceView.png"))
self.layoutsButtonGroup.addButton(self.singleSlideViewButton,
self.LAYOUT_RED_ONLY)
# Side by side Button
self.sideBySideViewButton = qt.QPushButton()
self.sideBySideViewButton.setCheckable(True)
self.sideBySideViewButton.toolTip = "Side by side view"
self.sideBySideViewButton.setFixedSize(40, 40)
self.sideBySideViewButton.setIcon(
qt.QIcon(":/Icons/LayoutSideBySideView.png"))
self.layoutsButtonGroup.addButton(self.sideBySideViewButton,
self.LAYOUT_SIDE_BY_SIDE)
# Three over three button
self.threeOverThreeViewButton = qt.QPushButton()
self.threeOverThreeViewButton.setCheckable(True)
self.threeOverThreeViewButton.toolTip = "Compare 2 images in their 3 planes"
self.threeOverThreeViewButton.setFixedSize(40, 40)
self.threeOverThreeViewButton.setIcon(
qt.QIcon(":/Icons/LayoutThreeOverThreeView.png"))
self.layoutsButtonGroup.addButton(self.threeOverThreeViewButton,
self.LAYOUT_THREE_OVER_THREE)
# Comparative MIP-MinIP button
self.maxMinCompareViewButton = qt.QPushButton()
self.maxMinCompareViewButton.setCheckable(True)
self.maxMinCompareViewButton.toolTip = "MIP and MinIP comparison"
self.maxMinCompareViewButton.setFixedSize(40, 40)
self.maxMinCompareViewButton.setIcon(
qt.QIcon(":/Icons/LayoutFourUpView.png"))
self.layoutsButtonGroup.addButton(self.maxMinCompareViewButton,
self.LAYOUT_COMPARE)
# Null button (to uncheck all)
self.nullLayoutButton = qt.QPushButton()
self.nullLayoutButton.setCheckable(True)
self.layoutsButtonGroup.addButton(self.nullLayoutButton, -2)
# Reset Button
self.resetViewButton = qt.QPushButton()
self.resetViewButton.toolTip = "Go back to the original layout"
self.resetViewButton.setFixedSize(40, 40)
# self.resetViewButton.setIconSize(qt.QSize(24, 24))
self.resetViewButton.setIcon(
qt.QIcon(os.path.join(SlicerUtil.CIP_ICON_DIR, "Reload.png")))
# Buttons labels
self.singleSlideButtonLabel = qt.QLabel("Single")
self.sideBySideButtonLabel = qt.QLabel("Side by side")
self.threeOverThreeButtonLabel = qt.QLabel("3x3")
self.maxMinCompareButtonLabel = qt.QLabel("MIP+MinIP")
self.resetLabel = qt.QLabel("Reset")
self.resetLabel.setStyleSheet("font-weight: bold")
# Number of slices (different for each operation). The size of the slider also changes
self.spacingSliderItems = OrderedDict()
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MIP])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 1000
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MIP] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MIP, 20)
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MinIP])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 200
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MinIP] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MinIP, 5)
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MEAN])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 200
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MEAN] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MEAN, 20)
# Crosshair
self.crosshairCheckbox = qt.QCheckBox()
self.crosshairCheckbox.setText("Crosshair cursor")
self.crosshairCheckbox.toolTip = "Activate/Desactivate the crosshair cursor for a better visualization"
self.crosshairCheckbox.setStyleSheet("margin-top:10px")
# Center button
self.centerButton = qt.QPushButton()
self.centerButton.setText("Center volumes")
self.centerButton.setFixedSize(100, 40)
self.centerButton.setStyleSheet("margin-top:10px")
if self.fullModeOn:
###### FULL MODE
# Context
self.widgetMainLayout.addWidget(self.contextLabel, 0, 0)
self.widgetMainLayout.addWidget(self.contextComboBox, 0, 1, 1, 3)
# Operation
self.widgetMainLayout.addWidget(self.operationLabel, 1, 0)
self.widgetMainLayout.addWidget(self.operationComboBox, 1, 1, 1, 3)
# Plane
self.widgetMainLayout.addWidget(self.planeLabel, 2, 0)
self.widgetMainLayout.addWidget(
self.axialButton, 2, 1, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButton, 2, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.axialButtonLabel, 3, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButtonLabel, 3, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButtonLabel, 3, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Layout
self.widgetMainLayout.addWidget(self.layoutLabel, 4, 0)
self.widgetMainLayout.addWidget(
self.singleSlideViewButton, 4, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sideBySideViewButton, 4, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeViewButton, 4, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.maxMinCompareViewButton, 4, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.resetViewButton, 4, 5,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.singleSlideButtonLabel, 5, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sideBySideButtonLabel, 5, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeButtonLabel, 5, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.maxMinCompareButtonLabel, 5, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.resetLabel, 5, 5, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Number of slices
row = 6
for structure in self.spacingSliderItems.itervalues():
self.widgetMainLayout.addWidget(structure[0], row, 0, 1, 2)
self.widgetMainLayout.addWidget(structure[1], row, 2, 1, 3)
self.widgetMainLayout.addWidget(structure[2], row, 5)
row += 1
self.widgetMainLayout.addWidget(self.crosshairCheckbox, row, 0, 1,
2)
self.crosshairCheckbox.setChecked(True)
self.widgetMainLayout.addWidget(self.centerButton, row, 2, 1, 2)
else:
##### COLLAPSED MODE
# Plane
self.widgetMainLayout.addWidget(self.planeLabel, 0, 0)
self.widgetMainLayout.addWidget(
self.axialButton, 0, 1, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButton, 0, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButton, 0, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeViewButton, 0, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.axialButtonLabel, 1, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButtonLabel, 1, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButtonLabel, 1, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeButtonLabel, 1, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Number of slices
row = 2
for structure in self.spacingSliderItems.itervalues():
self.widgetMainLayout.addWidget(structure[0], row, 0)
self.widgetMainLayout.addWidget(structure[1], row, 1, 1, 3)
self.widgetMainLayout.addWidget(structure[2], row, 4)
row += 1
self.widgetMainLayout.addWidget(self.crosshairCheckbox, row, 0)
self.widgetMainLayout.addWidget(self.centerButton, row, 1, 1, 2)
self.layout.addStretch(1)
self.__refreshUI__()
# Connections
self.contextComboBox.connect("currentIndexChanged (int)",
self.__onContextIndexChanged__)
self.operationComboBox.connect("currentIndexChanged (int)",
self.__onOperationIndexChanged__)
self.planesButtonGroup.connect("buttonClicked(int)",
self.__onPlaneButtonClicked__)
self.singleSlideViewButton.connect("clicked()",
self.__onSingleSlideButtonClicked__)
self.sideBySideViewButton.connect("clicked()",
self.__onSideBySideButtonClicked__)
self.threeOverThreeViewButton.connect(
"clicked()", self.__onThreeOverThreeViewButtonClicked__)
self.maxMinCompareViewButton.connect(
"clicked()", self.__onMaxMinCompareViewButtonClicked__)
self.resetViewButton.connect("clicked()",
self.__onResetViewButtonClicked__)
for slicer in (item[1]
for item in self.spacingSliderItems.itervalues()):
slicer.connect('valueChanged(int)',
self.__onNumberOfSlicesChanged__)
self.crosshairCheckbox.connect("stateChanged(int)",
self.__onCrosshairCheckChanged__)
self.centerButton.connect("clicked()", self.__onCenterButtonClicked__)
def construct(self):
""" Constructs the MetadataEditorSet widget.
"""
#--------------------
# Loop through all folders as per
# Xnat.path.DEFAULT_LEVELS. We create an AnimatedCollapsible
# for every folder, one MetadataEditor_Custom and one
# MetadataEditor_Default, along with the relevant buttons for
# very folder in XNAT_LEVELS.
#--------------------
for xnatLevel in Xnat.path.DEFAULT_LEVELS:
#
# Set DEFAULT label per xnat level.
#
self.labels[xnatLevel] = []
self.labels[xnatLevel].append(qt.QLabel('<b>DEFAULT<b>'))
self.labels[xnatLevel][0].setFont(
XnatSlicerGlobals.LABEL_FONT_BOLD)
#
# Set the collapsible's internal layout
# (a qt.QGridLayout) per folder.
#
self.collapsibleLayouts[xnatLevel] = qt.QGridLayout()
self.collapsibleLayouts[xnatLevel].\
addWidget(self.labels[xnatLevel][0], 0, 0)
#
# Set the MetadataEditor_Default,
# add to layout.
#
self.defaultMetadataEditors[xnatLevel] = \
MetadataEditor_Default(xnatLevel)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.defaultMetadataEditors[xnatLevel], 1, 0)
#
# Set the MetadataEditor_Custom,
# add to layout.
#
self.customMetadataEditors[xnatLevel] = \
MetadataEditor_Custom(xnatLevel)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.customMetadataEditors[xnatLevel], 1, 1, 1, 2)
#
# Set DEFAULT label per xnat level.
#
self.labels[xnatLevel].append(qt.QLabel('<b>CUSTOM<b>'))
self.labels[xnatLevel][1].setFont(
XnatSlicerGlobals.LABEL_FONT_BOLD)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.labels[xnatLevel][1], 0, 1)
#
# Add the 'editCustom' button.
#
# NOTE: The user can choose to hide/show these buttons,
# based on what's needed. For isntance, the Settings['METADATA']
# class hides these buttons as they are not necessary for
# its workflow.
#
self.editCustomButtons[xnatLevel] = \
XnatSlicerUtils.generateButton(iconOrLabel = \
"Edit custom tags for '%s'"%(xnatLevel),
toolTip = "Adds a custom metadata tag to display in the" +
" 'Info' column.",
font = XnatSlicerGlobals.LABEL_FONT,
size = qt.QSize(180, 20),
enabled = True)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.editCustomButtons[xnatLevel], 0, 2)
self.editCustomButtonGroup.\
addButton(self.editCustomButtons[xnatLevel])
#
# Put all of the widgets into first, a contentsWidget.
# Then set the widget of the AnimatedCollapsible to the
# contentsWidget.
#
self.collapsibles[xnatLevel] = AnimatedCollapsible(self, \
xnatLevel.title())
self.collapsibles[xnatLevel].setMaxExpandedHeight(250)
self.collapsibles[xnatLevel].setMinExpandedHeight(250)
contentsWidget = qt.QWidget()
contentsWidget.setLayout(self.collapsibleLayouts[xnatLevel])
self.collapsibles[xnatLevel].setContents(contentsWidget)
self.collapsibles[xnatLevel].setFixedWidth(550)
#
# Add collapsible to self.mainLayout.
#
self.mainLayout.addWidget(self.collapsibles[xnatLevel])
self.mainLayout.addSpacing(10)
#--------------------
# Set callback to Update XNATSlicer's
# layout when animating.
#--------------------
for key, collapsible in self.collapsibles.iteritems():
collapsible.onEvent('animate', self.updateLayout)
#--------------------
# Set mainLayout to the master layout.
#--------------------
self.mainLayout.addStretch()
self.setLayout(self.mainLayout)
#--------------------
# Set the current item tyype to label.
# The user can change it to 'checkbox'
# later.
#--------------------
self.setItemType('label')
def setup(self):
print("=======================================================")
print(" VisSim Cervical Spine Tools ")
print("=======================================================")
ScriptedLoadableModuleWidget.setup(self)
# to access logic class functions and setup global variables
self.logic = CervicalSpineToolsLogic()
self.vsc = VisSimCommon.VisSimCommonLogic()
#------------------------------------------------------------
# Create the GUI interface
#------------------------------------------------------------
# Create main collapsible Button
self.mainCollapsibleBtn = ctk.ctkCollapsibleButton()
self.mainCollapsibleBtn.setStyleSheet(
"ctkCollapsibleButton { background-color: DarkSeaGreen }")
self.mainCollapsibleBtn.text = "VisSim Cervical Spine Tools"
self.layout.addWidget(self.mainCollapsibleBtn)
self.mainFormLayout = qt.QFormLayout(self.mainCollapsibleBtn)
# Create input Volume Selector
self.inputSelectorCoBx = slicer.qMRMLNodeComboBox()
self.inputSelectorCoBx.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelectorCoBx.setFixedWidth(200)
self.inputSelectorCoBx.selectNodeUponCreation = True
self.inputSelectorCoBx.addEnabled = False
self.inputSelectorCoBx.removeEnabled = False
self.inputSelectorCoBx.noneEnabled = False
self.inputSelectorCoBx.showHidden = False
self.inputSelectorCoBx.showChildNodeTypes = False
self.inputSelectorCoBx.setMRMLScene(slicer.mrmlScene)
self.inputSelectorCoBx.setToolTip("select the input image")
self.mainFormLayout.addRow("Input image: ", self.inputSelectorCoBx)
# use qtcombobox
self.vILbl = qt.QLabel()
self.vILbl.setText("Which Vertebra? 1-7")
self.vILbl.setFixedHeight(20)
self.vILbl.setFixedWidth(150)
#TODO: include head and shoulders
self.vtIDCoBx = qt.QComboBox()
self.vtIDCoBx.addItems(["C1", "C2", "C3", "C4", "C5", "C6", "C7"])
self.vtIDCoBx.setCurrentIndex(2)
self.vtIDCoBx.setFixedHeight(20)
self.vtIDCoBx.setFixedWidth(100)
#self.vtIDCoBx.setReadOnly(False) # The point can only be edited by placing a new Fiducial
# if changed , the default value will change
self.vtIDCoBx.connect("currentIndexChanged(int)",
self.onVtIDCoBxChange)
#self.mainFormLayout.addRow( self.vILbl, self.vtIDCoBx )
# Create a textbox for vertebra location
# TODO activate input IJK values as well
self.inputPointEdt = qt.QLineEdit()
self.inputPointEdt.setFixedHeight(20)
self.inputPointEdt.setFixedWidth(100)
self.inputPointEdt.setText("[0,0,0]")
self.inputPointEdt.connect("textChanged(QString)",
self.onInputPointEdtChanged)
#self.inputPointEdt.connect("textEdited(str)", self.onInputPointEdtEdited)
self.mainFormLayout.addRow(self.inputPointEdt, self.vtIDCoBx)
# Add check box for extracting ligaments points
self.ligPtsChkBx = qt.QCheckBox("Ligaments points")
self.ligPtsChkBx.checked = True
self.ligPtsChkBx.stateChanged.connect(self.onLigPtsChkBxChange)
self.mainFormLayout.addRow(self.ligPtsChkBx)
# Create a time label
self.timeLbl = qt.QLabel(" Time: 00:00")
self.timeLbl.setFixedWidth(500)
self.tmLbl = self.timeLbl
# Create a button to run segmentation
self.applyBtn = qt.QPushButton("Run")
self.applyBtn.setFixedHeight(50)
self.applyBtn.setFixedWidth(150)
self.applyBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.applyBtn.toolTip = (
'How to use:'
' Load an images into Slicer. Pick vertebra locations using the buttons and the Slicer Fiducial tool '
)
self.applyBtn.connect('clicked(bool)', self.onApplyBtnClick)
self.mainFormLayout.addRow(self.applyBtn, self.timeLbl)
self.runBtn = self.applyBtn
# Create a button to display result folder
self.openResultFolderBtn = qt.QPushButton("open output folder")
self.openResultFolderBtn.setFixedHeight(20)
self.openResultFolderBtn.setFixedWidth(150)
self.openResultFolderBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.openResultFolderBtn.toolTip = (
'Scale model and points to 1 mm and translate them to the model center of mass '
)
self.openResultFolderBtn.connect('clicked(bool)',
self.onOpenResultFolderBtnClick)
self.mainFormLayout.addRow(self.openResultFolderBtn)
self.layout.addStretch(
1
) # Collapsible button is held in place when collapsing/expanding.
lm = slicer.app.layoutManager()
lm.setLayout(2)
def setupAdvancedPanel(self):
logging.debug('setupAdvancedPanel')
self.advancedCollapsibleButton.setProperty('collapsedHeight', 20)
self.advancedCollapsibleButton.text = "Settings"
self.sliceletPanelLayout.addWidget(self.advancedCollapsibleButton)
self.advancedLayout = qt.QFormLayout(self.advancedCollapsibleButton)
self.advancedLayout.setContentsMargins(12, 4, 4, 4)
self.advancedLayout.setSpacing(4)
# Layout selection combo box
self.viewSelectorComboBox = qt.QComboBox(self.advancedCollapsibleButton)
self.advancedLayout.addRow("Layout: ", self.viewSelectorComboBox)
self.registerDefaultGuideletLayouts()
self.selectView(self.VIEW_ULTRASOUND_3D)
# OpenIGTLink connector node selection
self.linkInputSelector = slicer.qMRMLNodeComboBox()
self.linkInputSelector.nodeTypes = ("vtkMRMLIGTLConnectorNode", "")
self.linkInputSelector.selectNodeUponCreation = True
self.linkInputSelector.addEnabled = False
self.linkInputSelector.removeEnabled = True
self.linkInputSelector.noneEnabled = False
self.linkInputSelector.showHidden = False
self.linkInputSelector.showChildNodeTypes = False
self.linkInputSelector.setMRMLScene( slicer.mrmlScene )
self.linkInputSelector.setToolTip( "Select connector node" )
self.advancedLayout.addRow("OpenIGTLink connector: ", self.linkInputSelector)
self.showFullSlicerInterfaceButton = qt.QPushButton()
self.showFullSlicerInterfaceButton.setText("Show 3D Slicer user interface")
self.advancedLayout.addRow(self.showFullSlicerInterfaceButton)
self.showGuideletFullscreenButton = qt.QPushButton()
self.showGuideletFullscreenButton.setText("Show Guidelet in full screen")
self.advancedLayout.addRow(self.showGuideletFullscreenButton)
self.saveSceneButton = qt.QPushButton()
self.saveSceneButton.setText("Save Guidelet scene")
self.advancedLayout.addRow(self.saveSceneButton)
self.saveDirectoryLineEdit = ctk.ctkPathLineEdit()
node = self.logic.getParameterNode()
sceneSaveDirectory = node.GetParameter('SavedScenesDirectory')
self.saveDirectoryLineEdit.currentPath = sceneSaveDirectory
self.saveDirectoryLineEdit.filters = ctk.ctkPathLineEdit.Dirs
self.saveDirectoryLineEdit.options = ctk.ctkPathLineEdit.DontUseSheet
self.saveDirectoryLineEdit.options = ctk.ctkPathLineEdit.ShowDirsOnly
self.saveDirectoryLineEdit.showHistoryButton = False
self.saveDirectoryLineEdit.setMinimumWidth(100)
self.saveDirectoryLineEdit.setMaximumWidth(500)
saveLabel = qt.QLabel()
saveLabel.setText("Save scene directory:")
hbox = qt.QHBoxLayout()
hbox.addWidget(saveLabel)
hbox.addWidget(self.saveDirectoryLineEdit)
self.advancedLayout.addRow(hbox)
self.exitButton = qt.QPushButton()
self.exitButton.setText("Exit")
self.advancedLayout.addRow(self.exitButton)
def setup(self):
# check if the SlicerVmtk4 module is installed properly
#self.__vmtkInstalled = SlicerVmtk4CommonLib.Helper.CheckIfVmtkIsInstalled()
#Helper.Debug("VMTK found: " + self.__vmtkInstalled)
#
# the I/O panel
#
ioCollapsibleButton = ctk.ctkCollapsibleButton()
ioCollapsibleButton.text = "Input/Output"
self.layout.addWidget(ioCollapsibleButton)
ioFormLayout = qt.QFormLayout(ioCollapsibleButton)
# inputVolume selector
self.__inputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__inputVolumeNodeSelector.objectName = 'inputVolumeNodeSelector'
self.__inputVolumeNodeSelector.toolTip = "Select the input volume. This should always be the original image and not a vesselness image, if possible."
self.__inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__inputVolumeNodeSelector.noneEnabled = False
self.__inputVolumeNodeSelector.addEnabled = False
self.__inputVolumeNodeSelector.removeEnabled = False
self.__inputVolumeNodeSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", "0")
ioFormLayout.addRow("Input Volume:", self.__inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__inputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__inputVolumeNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.onInputVolumeChanged)
self.__inputVolumeNodeSelector.connect('nodeActivated(vtkMRMLNode*)',
self.onInputVolumeChanged)
# seed selector
self.__seedFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.__seedFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Seeds."
self.__seedFiducialsNodeSelector.nodeTypes = [
'vtkMRMLAnnotationHierarchyNode'
]
self.__seedFiducialsNodeSelector.baseName = "Seeds"
self.__seedFiducialsNodeSelector.noneEnabled = False
self.__seedFiducialsNodeSelector.addEnabled = False
self.__seedFiducialsNodeSelector.removeEnabled = False
ioFormLayout.addRow("Seeds:", self.__seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__seedFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__ioAdvancedToggle = qt.QCheckBox("Show Advanced I/O Properties")
self.__ioAdvancedToggle.setChecked(False)
ioFormLayout.addRow(self.__ioAdvancedToggle)
#
# I/O advanced panel
#
self.__ioAdvancedPanel = qt.QFrame(ioCollapsibleButton)
self.__ioAdvancedPanel.hide()
self.__ioAdvancedPanel.setFrameStyle(6)
ioFormLayout.addRow(self.__ioAdvancedPanel)
self.__ioAdvancedToggle.connect("clicked()", self.onIOAdvancedToggle)
ioAdvancedFormLayout = qt.QFormLayout(self.__ioAdvancedPanel)
# inputVolume selector
self.__vesselnessVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__vesselnessVolumeNodeSelector.objectName = 'vesselnessVolumeNodeSelector'
self.__vesselnessVolumeNodeSelector.toolTip = "Select the input vesselness volume. This is optional input."
self.__vesselnessVolumeNodeSelector.nodeTypes = [
'vtkMRMLScalarVolumeNode'
]
self.__vesselnessVolumeNodeSelector.noneEnabled = True
self.__vesselnessVolumeNodeSelector.addEnabled = False
self.__vesselnessVolumeNodeSelector.removeEnabled = False
self.__vesselnessVolumeNodeSelector.addAttribute(
"vtkMRMLScalarVolumeNode", "LabelMap", "0")
ioAdvancedFormLayout.addRow("Vesselness Volume:",
self.__vesselnessVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__vesselnessVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__vesselnessVolumeNodeSelector.setCurrentNode(None)
# stopper selector
self.__stopperFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__stopperFiducialsNodeSelector.objectName = 'stopperFiducialsNodeSelector'
self.__stopperFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Stoppers. Whenever one stopper is reached, the segmentation stops."
self.__stopperFiducialsNodeSelector.nodeTypes = [
'vtkMRMLAnnotationHierarchyNode'
]
self.__stopperFiducialsNodeSelector.baseName = "Stoppers"
self.__stopperFiducialsNodeSelector.noneEnabled = False
self.__stopperFiducialsNodeSelector.addEnabled = True
self.__stopperFiducialsNodeSelector.removeEnabled = False
ioAdvancedFormLayout.addRow("Stoppers:",
self.__stopperFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__stopperFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputVolume selector
self.__outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.__outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__outputVolumeNodeSelector.baseName = "LevelSetSegmentation"
self.__outputVolumeNodeSelector.noneEnabled = False
self.__outputVolumeNodeSelector.addEnabled = True
self.__outputVolumeNodeSelector.selectNodeUponCreation = True
self.__outputVolumeNodeSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", "1")
self.__outputVolumeNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow("Output Labelmap:",
self.__outputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__outputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputModel selector
self.__outputModelNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputModelNodeSelector.objectName = 'outputModelNodeSelector'
self.__outputModelNodeSelector.toolTip = "Select the output model."
self.__outputModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.__outputModelNodeSelector.baseName = "LevelSetSegmentationModel"
self.__outputModelNodeSelector.hideChildNodeTypes = [
'vtkMRMLAnnotationNode'
] # hide all annotation nodes
self.__outputModelNodeSelector.noneEnabled = False
self.__outputModelNodeSelector.addEnabled = True
self.__outputModelNodeSelector.selectNodeUponCreation = True
self.__outputModelNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow("Output Model:",
self.__outputModelNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__outputModelNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
#
# the segmentation panel
#
segmentationCollapsibleButton = ctk.ctkCollapsibleButton()
segmentationCollapsibleButton.text = "Segmentation"
self.layout.addWidget(segmentationCollapsibleButton)
segmentationFormLayout = qt.QFormLayout(segmentationCollapsibleButton)
# Threshold slider
thresholdLabel = qt.QLabel()
thresholdLabel.text = "Thresholding" + SlicerVmtk4CommonLib.Helper.CreateSpace(
7)
thresholdLabel.toolTip = "Choose the intensity range to segment."
thresholdLabel.setAlignment(4)
segmentationFormLayout.addRow(thresholdLabel)
self.__thresholdSlider = slicer.qMRMLRangeWidget()
segmentationFormLayout.addRow(self.__thresholdSlider)
self.__thresholdSlider.connect('valuesChanged(double,double)',
self.onThresholdSliderChanged)
self.__segmentationAdvancedToggle = qt.QCheckBox(
"Show Advanced Segmentation Properties")
self.__segmentationAdvancedToggle.setChecked(False)
segmentationFormLayout.addRow(self.__segmentationAdvancedToggle)
#
# segmentation advanced panel
#
self.__segmentationAdvancedPanel = qt.QFrame(
segmentationCollapsibleButton)
self.__segmentationAdvancedPanel.hide()
self.__segmentationAdvancedPanel.setFrameStyle(6)
segmentationFormLayout.addRow(self.__segmentationAdvancedPanel)
self.__segmentationAdvancedToggle.connect(
"clicked()", self.onSegmentationAdvancedToggle)
segmentationAdvancedFormLayout = qt.QFormLayout(
self.__segmentationAdvancedPanel)
# inflation slider
inflationLabel = qt.QLabel()
inflationLabel.text = "less inflation <-> more inflation" + SlicerVmtk4CommonLib.Helper.CreateSpace(
14)
inflationLabel.setAlignment(4)
inflationLabel.toolTip = "Define how fast the segmentation expands."
segmentationAdvancedFormLayout.addRow(inflationLabel)
self.__inflationSlider = ctk.ctkSliderWidget()
self.__inflationSlider.decimals = 0
self.__inflationSlider.minimum = -100
self.__inflationSlider.maximum = 100
self.__inflationSlider.singleStep = 10
self.__inflationSlider.toolTip = inflationLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__inflationSlider)
# curvature slider
curvatureLabel = qt.QLabel()
curvatureLabel.text = "less curvature <-> more curvature" + SlicerVmtk4CommonLib.Helper.CreateSpace(
14)
curvatureLabel.setAlignment(4)
curvatureLabel.toolTip = "Choose a high curvature to generate a smooth segmentation."
segmentationAdvancedFormLayout.addRow(curvatureLabel)
self.__curvatureSlider = ctk.ctkSliderWidget()
self.__curvatureSlider.decimals = 0
self.__curvatureSlider.minimum = -100
self.__curvatureSlider.maximum = 100
self.__curvatureSlider.singleStep = 10
self.__curvatureSlider.toolTip = curvatureLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__curvatureSlider)
# attraction slider
attractionLabel = qt.QLabel()
attractionLabel.text = "less attraction to gradient <-> more attraction to gradient" + SlicerVmtk4CommonLib.Helper.CreateSpace(
14)
attractionLabel.setAlignment(4)
attractionLabel.toolTip = "Configure how the segmentation travels towards gradient ridges (vessel lumen wall)."
segmentationAdvancedFormLayout.addRow(attractionLabel)
self.__attractionSlider = ctk.ctkSliderWidget()
self.__attractionSlider.decimals = 0
self.__attractionSlider.minimum = -100
self.__attractionSlider.maximum = 100
self.__attractionSlider.singleStep = 10
self.__attractionSlider.toolTip = attractionLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__attractionSlider)
# iteration spinbox
self.__iterationSpinBox = qt.QSpinBox()
self.__iterationSpinBox.minimum = 0
self.__iterationSpinBox.maximum = 5000
self.__iterationSpinBox.singleStep = 10
self.__iterationSpinBox.toolTip = "Choose the number of evolution iterations."
segmentationAdvancedFormLayout.addRow(
SlicerVmtk4CommonLib.Helper.CreateSpace(100) + "Iterations:",
self.__iterationSpinBox)
#
# Reset, preview and apply buttons
#
self.__buttonBox = qt.QDialogButtonBox()
self.__resetButton = self.__buttonBox.addButton(
self.__buttonBox.RestoreDefaults)
self.__resetButton.toolTip = "Click to reset all input elements to default."
self.__previewButton = self.__buttonBox.addButton(
self.__buttonBox.Discard)
self.__previewButton.setIcon(qt.QIcon())
self.__previewButton.text = "Preview.."
self.__previewButton.toolTip = "Click to refresh the preview."
self.__startButton = self.__buttonBox.addButton(self.__buttonBox.Apply)
self.__startButton.setIcon(qt.QIcon())
self.__startButton.text = "Start!"
self.__startButton.enabled = False
self.__startButton.toolTip = "Click to start the filtering."
self.layout.addWidget(self.__buttonBox)
self.__resetButton.connect("clicked()", self.restoreDefaults)
self.__previewButton.connect("clicked()", self.onRefreshButtonClicked)
self.__startButton.connect("clicked()", self.onStartButtonClicked)
# be ready for events
self.__updating = 0
# set default values
self.restoreDefaults()
# compress the layout
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
# reload button
# (use this during development, but remove it when delivering
# your module to users)
# Collapsible button
dummyCollapsibleButton = ctk.ctkCollapsibleButton()
dummyCollapsibleButton.text = "Parameters"
self.layout.addWidget(dummyCollapsibleButton)
# Layout within the dummy collapsible button
dummyFormLayout = qt.QFormLayout(dummyCollapsibleButton)
#LABEL VOLUME SELECTOR
self.labelSelectorFrame = qt.QFrame()
self.labelSelectorFrame.setLayout(qt.QHBoxLayout())
dummyFormLayout.addWidget(self.labelSelectorFrame)
self.labelSelectorLabel = qt.QLabel()
self.labelSelectorLabel.setText("Label Map: ")
dummyFormLayout.addWidget(self.labelSelectorLabel)
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.labelSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
"1")
# todo addAttribute
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.removeEnabled = False
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to edit")
dummyFormLayout.addWidget(self.labelSelector)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
# the grayscale volume selector
#
self.grayscaleSelectorFrame = qt.QFrame(self.parent)
self.grayscaleSelectorFrame.setLayout(qt.QHBoxLayout())
dummyFormLayout.addWidget(self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel = qt.QLabel("Grayscale Volume: ",
self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel.setToolTip(
"Select the grayscale volume (background grayscale scalar volume node) for statistics calculations"
)
dummyFormLayout.addWidget(self.grayscaleSelectorLabel)
self.grayscaleSelector = slicer.qMRMLNodeComboBox(
self.grayscaleSelectorFrame)
self.grayscaleSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.grayscaleSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", 0)
self.grayscaleSelector.selectNodeUponCreation = False
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = True
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.grayscaleSelector.SetLabelText( "Master Volume:" )
dummyFormLayout.addWidget(self.grayscaleSelector)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "diagnosis Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Calculate button
self.calcButton = qt.QPushButton("Calculates")
self.calcButton.toolTip = "Calculates the level of stenosis on the most patological slice"
dummyFormLayout.addWidget(self.calcButton)
self.calcButton.enabled = False
self.calcButton.connect('clicked(bool)', self.onCalcButtonClicked)
# Botton temporal para llenar tabla ***************************************
self.fillTable = qt.QPushButton("Fill")
self.fillTable.toolTip = "Testing"
dummyFormLayout.addWidget(self.fillTable)
self.fillTable.enabled = True
self.fillTable.connect('clicked(bool)', self.onFillButtonClicked)
# Add Vertical Spacer
self.layout.addStretch(1)
# Parametros tabla
self.vista = qt.QTableView()
self.vista.sortingEnabled = False
self.vista.visible = False
self.vista.verticalHeader().visible = False
self.vista.horizontalHeader().visible = False
self.vista.setAlternatingRowColors(True)
dummyFormLayout.addWidget(self.vista)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "MarginCalculator Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# Collapsible button
self.marginCalculationCollapsibleButton = ctk.ctkCollapsibleButton()
self.marginCalculationCollapsibleButton.text = "Margin Calculation"
self.layout.addWidget(self.marginCalculationCollapsibleButton)
# Layout within the collapsible button
self.marginCalculationFormLayout = qt.QFormLayout(self.marginCalculationCollapsibleButton)
# Input Dose Volume selector
self.inputDoseVolumeSelectorLabel = qt.QLabel('Input Dose Volume:')
self.inputDoseVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputDoseVolumeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputDoseVolumeSelector.noneEnabled = False
self.inputDoseVolumeSelector.addEnabled = False
self.inputDoseVolumeSelector.removeEnabled = False
self.inputDoseVolumeSelector.setMRMLScene( slicer.mrmlScene )
self.inputDoseVolumeSelector.setToolTip( "Set the input Dose volume" )
self.marginCalculationFormLayout.addRow(self.inputDoseVolumeSelectorLabel, self.inputDoseVolumeSelector)
# Reference Dose Volume selector
self.referenceDoseVolumeSelectorLabel = qt.QLabel()
self.referenceDoseVolumeSelectorLabel.setText( "Reference Dose Volume: " )
self.referenceDoseVolumeSelector = slicer.qMRMLNodeComboBox()
self.referenceDoseVolumeSelector.nodeTypes = ( "vtkMRMLScalarVolumeNode", "" )
self.referenceDoseVolumeSelector.noneEnabled = False
self.referenceDoseVolumeSelector.addEnabled = False
self.referenceDoseVolumeSelector.removeEnabled = False
self.referenceDoseVolumeSelector.setMRMLScene( slicer.mrmlScene )
self.referenceDoseVolumeSelector.setToolTip( "Set the Reference dose volume" )
self.marginCalculationFormLayout.addRow(self.referenceDoseVolumeSelectorLabel, self.referenceDoseVolumeSelector)
# Input Contour selector
self.inputContourSelectorLabel = qt.QLabel('Input Contour Labelmap:')
self.inputContourSelector = slicer.qMRMLNodeComboBox()
self.inputContourSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputContourSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1 )
self.inputContourSelector.noneEnabled = False
self.inputContourSelector.addEnabled = False
self.inputContourSelector.removeEnabled = False
self.inputContourSelector.setMRMLScene( slicer.mrmlScene )
self.inputContourSelector.setToolTip( "Set the input Contour" )
self.marginCalculationFormLayout.addRow(self.inputContourSelectorLabel, self.inputContourSelector)
# Number of simulations
self.numberOfSimulationsSlider = ctk.ctkSliderWidget()
self.numberOfSimulationsSlider.decimals = 0
self.numberOfSimulationsSlider.minimum = 0
self.numberOfSimulationsSlider.maximum = 2000
self.numberOfSimulationsSlider.singleStep = 1
self.numberOfSimulationsSlider.pageStep = 100
self.numberOfSimulationsSlider.value = 100
self.marginCalculationFormLayout.addRow("Number of Simulations: ", self.numberOfSimulationsSlider)
# Number of fractions
self.numberOfFractionsSlider = ctk.ctkSliderWidget()
self.numberOfFractionsSlider.decimals = 0
self.numberOfFractionsSlider.minimum = 0
self.numberOfFractionsSlider.maximum = 10
self.numberOfFractionsSlider.singleStep = 1
self.numberOfFractionsSlider.pageStep = 5
self.numberOfFractionsSlider.value = 1
self.marginCalculationFormLayout.addRow("Number of Fractions: ", self.numberOfFractionsSlider)
# Systematic error slider
self.systematicErrorRangeSlider = ctk.ctkSliderWidget()
self.systematicErrorRangeSlider.decimals = 1
self.systematicErrorRangeSlider.minimum = 0
self.systematicErrorRangeSlider.maximum = 5
self.systematicErrorRangeSlider.singleStep = 0.1
self.systematicErrorRangeSlider.pageStep = 1.0
self.systematicErrorRangeSlider.value = 0.5
self.marginCalculationFormLayout.addRow("Systematic Error Range (mm): ", self.systematicErrorRangeSlider)
# Random error slider
self.randomErrorRangeSlider = ctk.ctkSliderWidget()
self.randomErrorRangeSlider.decimals = 1
self.randomErrorRangeSlider.minimum = 0
self.randomErrorRangeSlider.maximum = 5
self.randomErrorRangeSlider.singleStep = 0.1
self.randomErrorRangeSlider.pageStep = 1.0
self.randomErrorRangeSlider.value = 0.5
self.marginCalculationFormLayout.addRow("Random Error Range (mm): ", self.randomErrorRangeSlider)
self.doseGrowingOptions = ("Dilation","Scaling")
#
#Initialization
#
self.groupBoxDoseGrow = qt.QGroupBox("Dose Growing Technique")
self.groupBoxLayout = qt.QHBoxLayout(self.groupBoxDoseGrow)
self.marginCalculationFormLayout.addRow(self.groupBoxDoseGrow)
#
# layout selection
#
for doseGrowingOption in self.doseGrowingOptions:
doseGrowingOptionButton = qt.QRadioButton(doseGrowingOption)
doseGrowingOptionButton.connect('clicked()', lambda dgo=doseGrowingOption: self.selectDoseGrowingOption(dgo))
self.groupBoxLayout.addWidget(doseGrowingOptionButton)
if doseGrowingOption == "Dilation":
doseGrowingOptionButton.checked = True
self.doseGrowingOption = "Dilation"
#self.groupBoxLayout.addRow("Layout", layoutHolder)
# Dose growing range slider
self.doseGrowRangeSlider = ctk.ctkSliderWidget()
self.doseGrowRangeSlider.decimals = 1
self.doseGrowRangeSlider.minimum = 0
self.doseGrowRangeSlider.maximum = 10
self.doseGrowRangeSlider.singleStep = 0.2
self.doseGrowRangeSlider.pageStep = 1.0
self.doseGrowRangeSlider.value = 5
self.marginCalculationFormLayout.addRow("Dose grow Range (mm): ", self.doseGrowRangeSlider)
# ROI radius x slider
self.ROIRadiusXSlider = ctk.ctkSliderWidget()
self.ROIRadiusXSlider.decimals = 1
self.ROIRadiusXSlider.minimum = 2
self.ROIRadiusXSlider.maximum = 30
self.ROIRadiusXSlider.singleStep = 0.1
self.ROIRadiusXSlider.pageStep = 2.0
self.ROIRadiusXSlider.value = 10
self.marginCalculationFormLayout.addRow("ROI Radius X(mm): ", self.ROIRadiusXSlider)
# ROI radius y slider
self.ROIRadiusYSlider = ctk.ctkSliderWidget()
self.ROIRadiusYSlider.decimals = 1
self.ROIRadiusYSlider.minimum = 2
self.ROIRadiusYSlider.maximum = 30
self.ROIRadiusYSlider.singleStep = 0.1
self.ROIRadiusYSlider.pageStep = 2.0
self.ROIRadiusYSlider.value = 10
self.marginCalculationFormLayout.addRow("ROI Radius Y(mm): ", self.ROIRadiusYSlider)
# ROI radius z slider
self.ROIRadiusZSlider = ctk.ctkSliderWidget()
self.ROIRadiusZSlider.decimals = 1
self.ROIRadiusZSlider.minimum = 2
self.ROIRadiusZSlider.maximum = 30
self.ROIRadiusZSlider.singleStep = 0.1
self.ROIRadiusZSlider.pageStep = 2.0
self.ROIRadiusZSlider.value = 10
self.marginCalculationFormLayout.addRow("ROI Radius Z(mm): ", self.ROIRadiusZSlider)
# Apply button
self.applyButton = qt.QPushButton("Calculate")
self.applyButton.toolTip = "Perform margin calculation"
self.marginCalculationFormLayout.addRow(self.applyButton)
self.UpdateApplyButtonState()
# model and view for stats table
self.tableWidget.sortingEnabled = False
self.tableWidget.setRowCount(0)
self.tableWidget.setColumnCount(5)
self.tableWidget.setHorizontalHeaderLabels(['Systematic','Random','P90','P95','P99'])
self.marginCalculationFormLayout.addRow(self.tableWidget)
# Save button
self.saveButton = qt.QPushButton("Save Result")
self.saveButton.toolTip = "Save result as csv."
self.saveButton.enabled = False
self.marginCalculationFormLayout.addRow(self.saveButton)
# Add vertical spacer
self.layout.addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.saveButton.connect('clicked()', self.onSave)
self.inputDoseVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onInputDoseVolumeSelect)
self.referenceDoseVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onReferenceDoseVolumeSelect)
self.inputContourSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onInputContourSelect)
self.numberOfSimulationsSlider.connect('valueChanged(double)', self.onNumberOfSimulationsChanged)
self.numberOfFractionsSlider.connect('valueChanged(double)', self.onNumberOfFractionsChanged)
self.systematicErrorRangeSlider.connect('valueChanged(double)', self.onSystematicErrorRangeChanged)
self.randomErrorRangeSlider.connect('valueChanged(double)', self.onRandomErrorRangeChanged)
self.doseGrowRangeSlider.connect('valueChanged(double)', self.onDoseGrowRangeChanged)
self.ROIRadiusXSlider.connect('valueChanged(double)', self.onROIRadiusXChanged)
self.ROIRadiusYSlider.connect('valueChanged(double)', self.onROIRadiusYChanged)
self.ROIRadiusZSlider.connect('valueChanged(double)', self.onROIRadiusZChanged)
def setup(self):
print(" ")
print("=======================================================")
print(" Automatic Cochlea Image Registration ")
print("=======================================================")
ScriptedLoadableModuleWidget.setup(self)
# to access logic class functions and setup global variables
self.logic = CochleaRegLogic()
# Set default VisSIm location in the user home
#TODO: add option user-defined path when installed first time
self.vsc = VisSimCommon.VisSimCommonLogic()
self.vsc.setGlobalVariables(0)
#-----------------------------------------------------------------
# Create the GUI interface
#-----------------------------------------------------------------
# Create collapsible Button for registration, transformix and invert transform
self.mainCollapsibleBtn = ctk.ctkCollapsibleButton()
self.mainCollapsibleBtn.setStyleSheet(
"ctkCollapsibleButton { background-color: DarkSeaGreen }")
self.mainCollapsibleBtn.text = "ACIR: Automatic Cochlea Image Registration"
self.layout.addWidget(self.mainCollapsibleBtn)
self.mainFormLayout = qt.QFormLayout(self.mainCollapsibleBtn)
# Create fixed Volume Selector
self.fixedSelectorCoBx = slicer.qMRMLNodeComboBox()
self.fixedSelectorCoBx.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.fixedSelectorCoBx.selectNodeUponCreation = True
self.fixedSelectorCoBx.addEnabled = False
self.fixedSelectorCoBx.removeEnabled = False
self.fixedSelectorCoBx.noneEnabled = False
self.fixedSelectorCoBx.showHidden = False
self.fixedSelectorCoBx.showChildNodeTypes = False
self.fixedSelectorCoBx.setMRMLScene(slicer.mrmlScene)
self.fixedSelectorCoBx.setToolTip("Pick the fixed volume")
self.mainFormLayout.addRow("Fixed Volume: ", self.fixedSelectorCoBx)
# Create moving Volume Selector
self.movingSelectorCoBx = slicer.qMRMLNodeComboBox()
self.movingSelectorCoBx.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.movingSelectorCoBx.selectNodeUponCreation = True
self.movingSelectorCoBx.addEnabled = False
self.movingSelectorCoBx.removeEnabled = False
self.movingSelectorCoBx.noneEnabled = False
self.movingSelectorCoBx.showHidden = False
self.movingSelectorCoBx.showChildNodeTypes = False
self.movingSelectorCoBx.setMRMLScene(slicer.mrmlScene)
self.movingSelectorCoBx.setToolTip("Pick the moving volume")
self.mainFormLayout.addRow("Moving Volume: ", self.movingSelectorCoBx)
# Create a time label
self.timeLbl = qt.QLabel(" Time: 00:00")
self.timeLbl.setFixedWidth(500)
self.tmLbl = self.timeLbl
# Create a textbox for cochlea location
# TODO activate input IJK values as well
self.fixedPointEdt = qt.QLineEdit()
self.fixedPointEdt.setFixedHeight(40)
self.fixedPointEdt.setText("[0,0,0]")
# Create a textbox for cochlea location
# TODO activate input IJK values as well
self.movingPointEdt = qt.QLineEdit()
self.movingPointEdt.setFixedHeight(40)
self.movingPointEdt.setText("[0,0,0]")
# Create a cochlea locator button
self.fixedFiducialBtn = qt.QPushButton(
"Pick cochlea location in fixed image ")
self.fixedFiducialBtn.setFixedHeight(40)
self.fixedFiducialBtn.setToolTip(
"Pick the fixed fiducial point that will be the center of the cropped image"
)
self.fixedFiducialBtn.connect(
'clicked(bool)', lambda: self.onInputFiducialBtnClick("F"))
self.mainFormLayout.addRow(self.fixedFiducialBtn, self.fixedPointEdt)
# Create a cochlea locator button
self.movingFiducialBtn = qt.QPushButton(
"Pick cochlea location in moving image ")
self.movingFiducialBtn.setFixedHeight(40)
self.movingFiducialBtn.setToolTip(
"Pick the moving fiducial point that will be the center of the cropped image"
)
self.movingFiducialBtn.connect(
'clicked(bool)', lambda: self.onInputFiducialBtnClick("M"))
self.mainFormLayout.addRow(self.movingFiducialBtn, self.movingPointEdt)
# Add check box for disabling colors in the result of the registration
self.colorsChkBox = qt.QCheckBox()
self.colorsChkBox.text = "Disable colors"
self.colorsChkBox.checked = False
self.colorsChkBox.stateChanged.connect(self.OnColorsChkBoxChange)
self.mainFormLayout.addRow(self.colorsChkBox)
# Create a button to run registration
self.applyBtn = qt.QPushButton("Run")
self.applyBtn.setFixedHeight(50)
self.applyBtn.setFixedWidth(250)
self.applyBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.applyBtn.toolTip = (
'How to use:'
' Load at least two images into Slicer. Pick cochlea locations using the buttons and the Slicer Fiducial tool '
)
self.applyBtn.connect('clicked(bool)', self.onApplyBtnClick)
self.mainFormLayout.addRow(self.applyBtn, self.timeLbl)
self.runBtn = self.applyBtn
self.layout.addStretch(
1
) # Collapsible button is held in place when collapsing/expanding.