def __init__(self, SettingsFile):
""" Init function.
"""
#--------------------
# Call parent init.
#--------------------
qt.QFrame.__init__(self)
#--------------------
# Track all widgets.
#--------------------
self.collapsibles = {}
self.metadataWidgets = {}
self.defaultMetadataEditors = {}
self.customMetadataEditors = {}
self.buttons = {}
self.labels = {}
self.collapsibleLayouts = {}
self.editCustomButtons = {}
self.currItemType = ''
self.Events = MokaUtils.Events(self.EVENT_TYPES)
#--------------------
# The mainLayout eventually becomes
# the layout of the MetadataEditorSet via
# the '.setLayout' function
#--------------------
self.mainLayout = qt.QVBoxLayout()
#--------------------
# The Edit Button group.
#
# NOTE: A button group is created because
# normal qt.QPushButton.connect events do not
# send the button 'name' to the even method. A
# button group allows you to send the actual
# button to the vent method.
#--------------------
self.editCustomButtonGroup = qt.QButtonGroup()
self.editCustomButtonGroup.connect('buttonClicked(QAbstractButton*)', \
self.editCustomClicked)
self.editButtonsVisible = True
#--------------------
# Construct the manager
#--------------------
self.construct()
#--------------------
# Set the default states of the
# collapsibles.
#--------------------
for key, collapsible in self.collapsibles.items():
collapsible.suspendAnim(True)
collapsible.show()
collapsible.setChecked(True)
collapsible.suspendAnim(False)
def createCheckbox(parent, options, exclusive=False):
'''group.buttons()[0].checked -- whether first item checked
'''
optionWidgets = [qt.QCheckBox(i) for i in options]
group = qt.QButtonGroup(parent)
group.setExclusive(exclusive)
[group.addButton(i) for i in optionWidgets]
[parent.layout().addWidget(i) for i in optionWidgets]
return group
def create(self):
super(WindowLevelEffectOptions,self).create()
#self.thresholdPaint.hide()
#self.paintOver.hide()
#self.threshold.hide()
#self.thresholdLabel.hide()
# add the selection whether it should work as regular w/l control,
# or as a rectangle
self.normalMode = qt.QRadioButton('Normal mode')
self.rectangleMode = qt.QRadioButton('Rectangle mode')
self.rectangleMode.setChecked(1)
label = qt.QLabel('Mode of operation:')
self.frame.layout().addWidget(label)
self.viewGroup = qt.QButtonGroup()
self.viewGroup.addButton(self.normalMode,1)
self.viewGroup.addButton(self.rectangleMode,2)
self.frame.layout().addWidget(self.normalMode)
self.frame.layout().addWidget(self.rectangleMode)
self.viewGroup.connect('buttonClicked(int)',self.updateMRMLFromGUI)
label = qt.QLabel('Layers affected:')
self.bgSelector = qt.QCheckBox('Background')
self.fgSelector = qt.QCheckBox('Foreground')
self.bgSelector.checked = 1
self.fgSelector.checked = 1
self.frame.layout().addWidget(label)
self.frame.layout().addWidget(self.bgSelector)
self.frame.layout().addWidget(self.fgSelector)
self.bgSelector.connect('stateChanged(int)',self.updateMRMLFromGUI)
self.fgSelector.connect('stateChanged(int)',self.updateMRMLFromGUI)
EditorLib.HelpButton(self.frame, "Use this tool to change window/level of background/foreground volumes based on the intensity range of the selected rectangle.\n\nNormal mode: use primary mouse button to adjust window level. Depending on the selection, Foreground, Background or both layers are affected.\n\nRectangle mode: Left Click and Drag: sweep out an outline that will draw when the button is released. The outline will define the rectangle for calculating the new window/level settings for the selected layers.\n\n")
# step4Layout.addRow(self.normalMode, rectangleMode)
# Add vertical spacer
self.frame.layout().addStretch(1)
# set effect-specific parameters
if self.parameterNode.GetParameter('WindowLevelEffect,wlmode') == '':
self.parameterNode.SetParameter('WindowLevelEffect,wlmode', 'Rectangle')
if self.parameterNode.GetParameter('WindowLevelEffect,changeBg') == '':
self.parameterNode.SetParameter('WindowLevelEffect,changeBg','1')
if self.parameterNode.GetParameter('WindowLevelEffect,changeFg') == '':
self.parameterNode.SetParameter('WindowLevelEffect,changeFg','1')
if self.parameterNode.GetParameter('Effect,scope') == '':
self.parameterNode.SetParameter('Effect,scope','')
def setupUi( self ):
self.loadUi('InitialStep.ui')
moduleName = 'Workflow'
scriptedModulesPath = eval('slicer.modules.%s.path' % moduleName.lower())
scriptedModulesPath = os.path.dirname(scriptedModulesPath)
iconsPath = os.path.join(scriptedModulesPath, 'Widgets', 'Resources', 'Icons')
buttonGroup = qt.QButtonGroup(self.get('InitialCollapsibleGroupBox'))
logic = slicer.modules.workflow.logic()
resourceDir = qt.QDir(logic.GetModuleShareDirectory() + '/Resources')
for dir in resourceDir.entryList(resourceDir.Dirs | resourceDir.NoDotAndDotDot):
pushButton = qt.QPushButton(self.get('InitialCollapsibleGroupBox'))
buttonGroup.addButton(pushButton)
pushButton.text = dir.replace('_', ' ')
pushButton.setProperty('Path', resourceDir.absolutePath() + '/' + dir)
pushButton.checkable = True
pushButton.connect('clicked()', self.onPresetSelected)
pushButton.setIcon(qt.QIcon(os.path.join(iconsPath, dir)))
pushButton.setIconSize(qt.QSize(75, 75))
self.PresetButtons.append(pushButton)
self.get('InitialCollapsibleGroupBox').layout().addWidget(pushButton)
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.values():
self.contextComboBox.addItem(context)
## Operation
self.operationLabel = qt.QLabel("Optimization")
self.operationComboBox = qt.QComboBox()
for operation in self.operations.values():
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.values():
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.values():
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.values()):
slicer.connect('valueChanged(int)',
self.__onNumberOfSlicesChanged__)
self.crosshairCheckbox.connect("stateChanged(int)",
self.__onCrosshairCheckChanged__)
self.centerButton.connect("clicked()", self.__onCenterButtonClicked__)
def setupCollapsibleButtonGroup(self):
"""" Making sure only one collapsible button is open at a time."""
self.collapsibleButtonsGroup = qt.QButtonGroup()
self.collapsibleButtonsGroup.addButton(self.valvesCollapsibleButton)
self.collapsibleButtonsGroup.addButton(self.fieldsCollapsibleButton)
self.collapsibleButtonsGroup.addButton(self.outputCollapsibleButton)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.logic = NeedleTrackingLogic(None)
self.logic.setWidget(self)
#--------------------------------------------------
# For debugging
#
# Reload and Test area
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
reloadCollapsibleButton.collapsed = True
# 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 = "Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
#
#--------------------------------------------------
self.nCath = 1 # Number of catheters
#--------------------------------------------------
# GUI components
#
# Connection Area
#
connectionCollapsibleButton = ctk.ctkCollapsibleButton()
connectionCollapsibleButton.text = "Connection (OpenIGTLink)"
self.layout.addWidget(connectionCollapsibleButton)
# Layout within the dummy collapsible button
connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
#--------------------------------------------------
# Connector Selector
#--------------------------------------------------
self.igtlConnector1 = NeedleTrackingIGTLConnector("Connector 1")
self.igtlConnector1.port = 18944
self.igtlConnector1.buildGUI(connectionFormLayout)
#--------------------------------------------------
# Catheter
#--------------------------------------------------
catheterCollapsibleButton = ctk.ctkCollapsibleButton()
catheterCollapsibleButton.text = "Tracking Node"
self.layout.addWidget(catheterCollapsibleButton)
catheterFormLayout = qt.QFormLayout(catheterCollapsibleButton)
#--------------------------------------------------
# Tracking node selector
trackingNodeGroupBox = ctk.ctkCollapsibleGroupBox()
trackingNodeGroupBox.title = "Tracking Node"
catheterFormLayout.addWidget(trackingNodeGroupBox)
trackingNodeFormLayout = qt.QFormLayout(trackingNodeGroupBox)
self.trackingDataSelector = slicer.qMRMLNodeComboBox()
self.trackingDataSelector.nodeTypes = ((
"vtkMRMLIGTLTrackingDataBundleNode"), "")
self.trackingDataSelector.selectNodeUponCreation = True
self.trackingDataSelector.addEnabled = True
self.trackingDataSelector.removeEnabled = False
self.trackingDataSelector.noneEnabled = False
self.trackingDataSelector.showHidden = True
self.trackingDataSelector.showChildNodeTypes = False
self.trackingDataSelector.setMRMLScene(slicer.mrmlScene)
self.trackingDataSelector.setToolTip("Incoming tracking data")
trackingNodeFormLayout.addRow("TrackingData: ",
self.trackingDataSelector)
#
# check box to trigger transform conversion
#
self.activeTrackingCheckBox = qt.QCheckBox()
self.activeTrackingCheckBox.checked = 0
self.activeTrackingCheckBox.enabled = 1
self.activeTrackingCheckBox.setToolTip("Activate Tracking")
trackingNodeFormLayout.addRow("Active: ", self.activeTrackingCheckBox)
#--------------------------------------------------
# Catheter Configuration
configGroupBox = ctk.ctkCollapsibleGroupBox()
configGroupBox.title = "Catheter Configuration"
configGroupBox.collapsed = True
catheterFormLayout.addWidget(configGroupBox)
configFormLayout = qt.QFormLayout(configGroupBox)
self.tipLengthSliderWidget = [None] * self.nCath
self.catheterDiameterSliderWidget = [None] * self.nCath
self.catheterOpacitySliderWidget = [None] * self.nCath
for cath in range(self.nCath):
#
# Tip Length (legnth between the catheter tip and the first coil)
#
self.tipLengthSliderWidget[cath] = ctk.ctkSliderWidget()
self.tipLengthSliderWidget[cath].singleStep = 0.5
self.tipLengthSliderWidget[cath].minimum = 0.0
self.tipLengthSliderWidget[cath].maximum = 100.0
self.tipLengthSliderWidget[cath].value = 10.0
self.tipLengthSliderWidget[cath].setToolTip(
"Set the length of the catheter tip.")
configFormLayout.addRow("Cath %d Tip Length (mm): " % cath,
self.tipLengthSliderWidget[cath])
#
# Catheter #1 Catheter diameter
#
self.catheterDiameterSliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterDiameterSliderWidget[cath].singleStep = 0.1
self.catheterDiameterSliderWidget[cath].minimum = 0.1
self.catheterDiameterSliderWidget[cath].maximum = 10.0
self.catheterDiameterSliderWidget[cath].value = 1.0
self.catheterDiameterSliderWidget[cath].setToolTip(
"Set the diameter of the catheter")
configFormLayout.addRow("Cath %d Diameter (mm): " % cath,
self.catheterDiameterSliderWidget[cath])
#
# Catheter #1 Catheter opacity
#
self.catheterOpacitySliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterOpacitySliderWidget[cath].singleStep = 0.1
self.catheterOpacitySliderWidget[cath].minimum = 0.0
self.catheterOpacitySliderWidget[cath].maximum = 1.0
self.catheterOpacitySliderWidget[cath].value = 1.0
self.catheterOpacitySliderWidget[cath].setToolTip(
"Set the opacity of the catheter")
configFormLayout.addRow("Cath %d Opacity: " % cath,
self.catheterOpacitySliderWidget[cath])
#
# Check box to show/hide coil labels
#
self.showCoilLabelCheckBox = qt.QCheckBox()
self.showCoilLabelCheckBox.checked = 0
self.showCoilLabelCheckBox.setToolTip("Show/hide coil labels")
configFormLayout.addRow("Show Coil Labels: ",
self.showCoilLabelCheckBox)
#--------------------------------------------------
# Coordinate System
#
coordinateGroupBox = ctk.ctkCollapsibleGroupBox()
coordinateGroupBox.title = "Coordinate System"
coordinateGroupBox.collapsed = True
catheterFormLayout.addWidget(coordinateGroupBox)
coordinateLayout = qt.QFormLayout(coordinateGroupBox)
self.coordinateRPlusRadioButton = qt.QRadioButton("+X")
self.coordinateRMinusRadioButton = qt.QRadioButton("-X")
self.coordinateRPlusRadioButton.checked = 1
self.coordinateRBoxLayout = qt.QHBoxLayout()
self.coordinateRBoxLayout.addWidget(self.coordinateRPlusRadioButton)
self.coordinateRBoxLayout.addWidget(self.coordinateRMinusRadioButton)
self.coordinateRGroup = qt.QButtonGroup()
self.coordinateRGroup.addButton(self.coordinateRPlusRadioButton)
self.coordinateRGroup.addButton(self.coordinateRMinusRadioButton)
coordinateLayout.addRow("Right:", self.coordinateRBoxLayout)
self.coordinateAPlusRadioButton = qt.QRadioButton("+Y")
self.coordinateAMinusRadioButton = qt.QRadioButton("-Y")
self.coordinateAPlusRadioButton.checked = 1
self.coordinateABoxLayout = qt.QHBoxLayout()
self.coordinateABoxLayout.addWidget(self.coordinateAPlusRadioButton)
self.coordinateABoxLayout.addWidget(self.coordinateAMinusRadioButton)
self.coordinateAGroup = qt.QButtonGroup()
self.coordinateAGroup.addButton(self.coordinateAPlusRadioButton)
self.coordinateAGroup.addButton(self.coordinateAMinusRadioButton)
coordinateLayout.addRow("Anterior:", self.coordinateABoxLayout)
self.coordinateSPlusRadioButton = qt.QRadioButton("+Z")
self.coordinateSMinusRadioButton = qt.QRadioButton("-Z")
self.coordinateSPlusRadioButton.checked = 1
self.coordinateSBoxLayout = qt.QHBoxLayout()
self.coordinateSBoxLayout.addWidget(self.coordinateSPlusRadioButton)
self.coordinateSBoxLayout.addWidget(self.coordinateSMinusRadioButton)
self.coordinateSGroup = qt.QButtonGroup()
self.coordinateSGroup.addButton(self.coordinateSPlusRadioButton)
self.coordinateSGroup.addButton(self.coordinateSMinusRadioButton)
coordinateLayout.addRow("Superior:", self.coordinateSBoxLayout)
#--------------------------------------------------
# Reslice
#
resliceCollapsibleButton = ctk.ctkCollapsibleButton()
resliceCollapsibleButton.text = "Image Reslice"
self.layout.addWidget(resliceCollapsibleButton)
#resliceLayout = qt.QFormLayout(resliceCollapsibleButton)
self.reslice = NeedleTrackingReslice("Image Reslice")
self.reslice.nCath = self.nCath
self.reslice.buildGUI(resliceCollapsibleButton)
#--------------------------------------------------
# Connections
#--------------------------------------------------
self.trackingDataSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onTrackingDataSelected)
self.activeTrackingCheckBox.connect('toggled(bool)',
self.onActiveTracking)
for cath in range(self.nCath):
self.tipLengthSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onTipLengthChanged, cath))
self.catheterDiameterSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterDiameterChanged, cath))
self.catheterOpacitySliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterOpacityChanged, cath))
self.showCoilLabelCheckBox.connect('toggled(bool)',
self.onCoilLabelChecked)
self.coordinateRPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateRMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
"""Init the widget """
self.modulePath = SlicerUtil.getModuleFolder("CIP_GetImage")
self.resourcesPath = os.path.join(self.modulePath,
"CIP_GetImage_Resources")
self.StudyId = ""
self.logic = CIP_GetImageLogic(self.modulePath)
# Widget to load cases faster
self.loadSaveDatabuttonsWidget = CIPUI.LoadSaveDataWidget(
parentWidget=self.parent)
self.loadSaveDatabuttonsWidget.setup(moduleName="CIP_GetImage")
#
# Obligatory parameters area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Image data"
self.layout.addWidget(parametersCollapsibleButton)
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# Study radio buttons
label = qt.QLabel()
label.text = "Select the study:"
parametersFormLayout.addRow(label)
self.rbgStudy = qt.QButtonGroup()
for key in self.studyIds:
rbStudyid = qt.QRadioButton(key)
self.rbgStudy.addButton(rbStudyid)
parametersFormLayout.addWidget(rbStudyid)
self.txtOtherStudy = qt.QLineEdit()
self.txtOtherStudy.hide()
parametersFormLayout.addWidget(self.txtOtherStudy)
# Case id
self.txtCaseId = qt.QLineEdit()
parametersFormLayout.addRow("Case ID ", self.txtCaseId)
# Image types
label = qt.QLabel()
label.text = "Select the images that you want to load:"
parametersFormLayout.addRow(label)
self.cbsImageTypes = []
for key in self.imageTypes:
check = qt.QCheckBox()
check.checked = True
check.setText(key)
parametersFormLayout.addWidget(check)
self.cbsImageTypes.append(check)
# Label maps
label = qt.QLabel()
label.text = "Select the label maps that you want to load:"
parametersFormLayout.addRow(label)
# Labelmap types checkboxes
self.cbsLabelMapTypes = []
for key in self.labelMapTypes:
check = qt.QCheckBox()
check.setText(key)
check.checked = self.labelMapTypes[key][0]
parametersFormLayout.addWidget(check)
self.cbsLabelMapTypes.append(check)
# Load image Button
self.downloadButton = qt.QPushButton("Download")
self.downloadButton.toolTip = "Load the image"
#self.downloadButton.enabled = False
self.downloadButton.setStyleSheet(
"background-color: green; font-weight:bold; color:white")
parametersFormLayout.addRow(self.downloadButton)
self.downloadButton.connect('clicked (bool)', self.onDownloadButton)
# Information message
self.lblDownloading = qt.QLabel()
self.lblDownloading.text = "Downloading images. Please wait..."
self.lblDownloading.hide()
parametersFormLayout.addRow(self.lblDownloading)
#
# Optional Parameters
#
optionalParametersCollapsibleButton = ctk.ctkCollapsibleButton()
optionalParametersCollapsibleButton.text = "Optional parameters"
self.layout.addWidget(optionalParametersCollapsibleButton)
optionalParametersFormLayout = qt.QFormLayout(
optionalParametersCollapsibleButton)
# Local storage (Slicer temporary path)
self.localStoragePath = "{0}/CIP".format(slicer.app.temporaryPath)
if not os.path.exists(self.localStoragePath):
os.makedirs(self.localStoragePath)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(self.localStoragePath, 0o777)
self.storagePathButton = ctk.ctkDirectoryButton()
self.storagePathButton.directory = self.localStoragePath
optionalParametersFormLayout.addRow("Local directory: ",
self.storagePathButton)
# Connection type (SSH, "normal")
label = qt.QLabel()
label.text = "Connection type:"
optionalParametersFormLayout.addRow(label)
self.rbgConnectionType = qt.QButtonGroup()
self.rbSSH = qt.QRadioButton("SSH (secure connection)")
self.rbSSH.setChecked(True)
self.rbgConnectionType.addButton(self.rbSSH)
optionalParametersFormLayout.addWidget(self.rbSSH)
self.rbCP = qt.QRadioButton("Common")
self.rbgConnectionType.addButton(self.rbCP)
optionalParametersFormLayout.addWidget(self.rbCP)
# SSH Server login
self.txtServer = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault(
"CIP_GetImage", "server",
"This is your ssh user and server. Example: [email protected]")
self.txtServer.text = s # This is your ssh user and server. Example: [email protected]"
optionalParametersFormLayout.addRow("Server:", self.txtServer)
# Server root path
self.txtServerpath = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault(
"CIP_GetImage", "serverRootPath",
"This is your root path to search for files. Ex: /Cases/Processed")
self.txtServerpath.text = s # This is your root path to search for files. Ex: /Cases/Processed
optionalParametersFormLayout.addRow("Server root path:",
self.txtServerpath)
# SSH Private key
self.txtPrivateKeySSH = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault("CIP_GetImage", "sshKey", "")
self.txtPrivateKeySSH.text = s # this is the full path to your ssh key if you need it. Be aware of Unix/Windows comaptibility (hint: use os.path.join)
# Please notice that you won't need a SSH key if your computer already has one locally installed"
optionalParametersFormLayout.addRow(
"SSH private key (leave blank for computer's default): ",
self.txtPrivateKeySSH)
# Cache mode
self.cbCacheMode = qt.QCheckBox("Cache mode activated")
self.cbCacheMode.setChecked(True) # Cache mode is activated by default
optionalParametersFormLayout.addRow("", self.cbCacheMode)
# Clean cache Button
self.cleanCacheButton = qt.QPushButton("Clean cache")
self.cleanCacheButton.toolTip = "Remove all the local cached files"
optionalParametersFormLayout.addRow(self.cleanCacheButton)
optionalParametersCollapsibleButton.collapsed = True
if SlicerUtil.IsDevelopment:
# reload button
self.reloadButton = qt.QPushButton("Reload (just development)")
self.reloadButton.toolTip = "Reload this module (for development purposes)."
self.reloadButton.name = "Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Add vertical spacer
self.layout.addStretch(1)
# Connections
self.rbgStudy.connect("buttonClicked (QAbstractButton*)",
self.onRbStudyClicked)
self.txtOtherStudy.connect("textEdited (QString)",
self.onTxtOtherStudyEdited)
self.rbgConnectionType.connect("buttonClicked (QAbstractButton*)",
self.onRbgConnectionType)
self.storagePathButton.connect("directorySelected(QString)",
self.onTmpDirChanged)
self.cleanCacheButton.connect('clicked (bool)',
self.onCleanCacheButtonClicked)
def setup(self):
# Tags are used to manage event ovservers
self.tagSourceNode = None
self.tagDestinationNode = None
#Set up area for creating curves
createCurveBttn = ctk.ctkCollapsibleButton()
createCurveBttn.text = "Create Curve"
self.layout.addWidget(createCurveBttn)
layout = qt.QFormLayout(createCurveBttn)
#Selecting source points from fiducials
self.SourceSelector = slicer.qMRMLNodeComboBox()
self.SourceSelector.nodeTypes = (("vtkMRMLMarkupsFiducialNode"), "")
self.SourceSelector.addEnabled = True
self.SourceSelector.removeEnabled = True
self.SourceSelector.noneEnabled = True
self.SourceSelector.renameEnabled = True
self.SourceSelector.setMRMLScene(slicer.mrmlScene)
self.SourceSelector.setToolTip(
"Select source of points or create a new list")
layout.addRow("Source points: ", self.SourceSelector)
#Selecting destination for new curve
self.DestinationSelector = slicer.qMRMLNodeComboBox()
self.DestinationSelector.nodeTypes = (("vtkMRMLModelNode"), "")
self.DestinationSelector.addEnabled = True
self.DestinationSelector.removeEnabled = True
self.DestinationSelector.noneEnabled = True
self.DestinationSelector.renameEnabled = True
self.DestinationSelector.selectNodeUponCreation = True
self.DestinationSelector.setMRMLScene(slicer.mrmlScene)
self.DestinationSelector.setToolTip(
"Select existing curve model or create a new one")
layout.addRow("Curve model: ", self.DestinationSelector)
#x, y, z inputs for new fiducial
self.validator = qt.QDoubleValidator()
self.AddFiducialLayout = qt.QHBoxLayout()
self.AddX = qt.QLineEdit("X")
self.AddX.setValidator(self.validator)
self.AddY = qt.QLineEdit("Y")
self.AddY.setValidator(self.validator)
self.AddZ = qt.QLineEdit("Z")
self.AddZ.setValidator(self.validator)
self.AddFiducialLayout.addWidget(self.AddX)
self.AddFiducialLayout.addWidget(self.AddY)
self.AddFiducialLayout.addWidget(self.AddZ)
layout.addRow("X, Y, Z coordinates for new fiducial: ",
self.AddFiducialLayout)
#Add fiducial button
self.AddFiducialButton = qt.QPushButton("Add Fiducial")
self.AddFiducialButton.toolTip = "Adds fiducial using given x, y, z coordinates"
self.AddFiducialButton.enabled = True
layout.addRow("", self.AddFiducialButton)
#Current fiducials table
self.FiducialTable = qt.QTableWidget(1, 4)
self.FiducialTableHeaders = ["Name", "X (mm)", "Y (mm)", "Z (mm)"]
self.FiducialTable.setHorizontalHeaderLabels(self.FiducialTableHeaders)
layout.addWidget(self.FiducialTable)
#Radius of curve
self.RadiusSliderWidget = ctk.ctkSliderWidget()
self.RadiusSliderWidget.singleStep = 0.5
self.RadiusSliderWidget.minimum = 0.5
self.RadiusSliderWidget.maximum = 20.0
self.RadiusSliderWidget.value = 3.0
self.RadiusSliderWidget.setToolTip(
"Determines the thickness of the curve")
layout.addRow("Thickness: ", self.RadiusSliderWidget)
#Select the method of interpolation
self.InterpolationLayout = qt.QHBoxLayout()
self.InterpolationLinear = qt.QRadioButton("Linear")
self.InterpolationLinear.setToolTip(
"Straight lines from point to point")
self.InterpolationSpline = qt.QRadioButton("Spline")
self.InterpolationSpline.setToolTip(
"Cardinal spline will create curvature between points")
self.InterpolationLayout.addWidget(self.InterpolationLinear)
self.InterpolationLayout.addWidget(self.InterpolationSpline)
self.InterpolationGroup = qt.QButtonGroup()
self.InterpolationGroup.addButton(self.InterpolationLinear)
self.InterpolationGroup.addButton(self.InterpolationSpline)
layout.addRow("Interpolation: ", self.InterpolationLayout)
#Button for generating specified curve
self.GenerateButton = qt.QPushButton("Generate/Update Curve")
self.GenerateButton.toolTip = "Creates or updates curve specified"
self.GenerateButton.enabled = True
layout.addRow("", self.GenerateButton)
#Linking buttons to methods
self.InterpolationLinear.connect('clicked(bool)',
self.onSelectInterpolationLinear)
self.InterpolationSpline.connect('clicked(bool)',
self.onSelectInterpolationSpline)
self.SourceSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSourceSelected)
self.DestinationSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onDestinationSelected)
self.AddX.textChanged.connect(
lambda inputSelection: self.checkInputState('x'))
self.AddX.textChanged.emit(self.AddX.text)
self.AddY.textChanged.connect(
lambda inputSelection: self.checkInputState('y'))
self.AddY.textChanged.emit(self.AddY.text)
self.AddZ.textChanged.connect(
lambda inputSelection: self.checkInputState('z'))
self.AddZ.textChanged.emit(self.AddZ.text)
self.AddFiducialButton.connect('clicked(bool)', self.addFiducial)
self.RadiusSliderWidget.connect("valueChanged(double)",
self.onThicknessUpdated)
self.GenerateButton.connect('clicked(bool)', self.generateCurve)
#Default checkboxes
self.InterpolationSpline.setChecked(True)
self.onSelectInterpolationSpline(True)
self.layout.addStretch(1)
def setup(self):
# intialize variables
# Data of current loaded patient
self.IDcurrPatient = {}
self.imageNodes = {} # List of currently loaded image nodes
self.labelNodes = {} # List of currently loaded label nodes
self.ModelNodes = {}
# Data of database
self.mainPatientdir = self.outputDir = self.datafile = {}
#---------------------------------------------------------
# 2D Slice Snapshots
self.IMGSliceExtractCollapsibleButton = ctk.ctkCollapsibleButton()
self.IMGSliceExtractCollapsibleButton.text = "2D Slice and Model Image Capture"
self.layout.addWidget(self.IMGSliceExtractCollapsibleButton)
self.IMGSliceExtractCollapsibleButton.collapsed = False
self.IMGSliceExtractFormLayout = qt.QFormLayout(
self.IMGSliceExtractCollapsibleButton)
# Input 1: Input Directory selector
self.input6Frame = qt.QFrame(self.IMGSliceExtractCollapsibleButton)
self.input6Frame.setLayout(qt.QHBoxLayout())
self.IMGSliceExtractFormLayout.addWidget(self.input6Frame)
self.input6Selector = qt.QLabel("Input Directory (DICOM): ",
self.input6Frame)
self.input6Frame.layout().addWidget(self.input6Selector)
self.input6Button = qt.QPushButton("Select main directory DICOM files")
self.input6Button.toolTip = "Select main directory with DICOM files (folder names are patient names)"
self.input6Button.enabled = True
self.input6Frame.layout().addWidget(self.input6Button)
# Input 2: Output Directory selector
self.input7Frame = qt.QFrame(self.IMGSliceExtractCollapsibleButton)
self.input7Frame.setLayout(qt.QHBoxLayout())
self.IMGSliceExtractFormLayout.addWidget(self.input7Frame)
self.input7Selector = qt.QLabel("Output Directory: ",
self.input7Frame)
self.input7Frame.layout().addWidget(self.input7Selector)
self.input7Button = qt.QPushButton(
"Select main directory output NRRD or NFITI files")
self.input7Button.toolTip = "Select main directory for output NRRD or NIFTI files (folder names are patient names)"
self.input7Button.enabled = True
self.input7Frame.layout().addWidget(self.input7Button)
# Keywords Collapsible Button
self.KeywordsCollapsibleButton = ctk.ctkCollapsibleButton(
self.IMGSliceExtractCollapsibleButton)
self.KeywordsCollapsibleButton.text = "Keyword Matching"
self.KeywordsCollapsibleButtonLayout = qt.QHBoxLayout()
self.KeywordsCollapsibleButton.setLayout(
self.KeywordsCollapsibleButtonLayout)
self.IMGSliceExtractFormLayout.addWidget(
self.KeywordsCollapsibleButton)
self.KeywordsCollapsibleButton.collapsed = False
self.keywordsFrame = qt.QFrame(self.KeywordsCollapsibleButton)
self.keywordsFrame.setLayout(qt.QFormLayout())
self.KeywordsCollapsibleButtonLayout.addWidget(self.keywordsFrame)
# Radio Buttons Frame
self.radioButtonFrame = qt.QFrame(self.keywordsFrame)
self.radioButtonFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.radioButtonFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.radioButtonFrame.layout().addRow(self.nrrdButton,
self.niftiButton)
self.keywordsHeader = qt.QLabel("Keyword Matching:",
self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.keywordsHeader)
# Keywords Frame
self.inputMaskHeader = qt.QLabel("Input Image File Type:",
self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputMaskHeader,
self.radioButtonFrame)
self.inputImageKeywords = qt.QLabel("Input Image Keywords:",
self.keywordsFrame)
self.inputImageKeywordsField = qt.QLineEdit("", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageKeywords,
self.inputImageKeywordsField)
self.inputImageExclusionKeywords = qt.QLabel(
"Input Image Exclusion Keywords:", self.keywordsFrame)
self.inputImageExclusionKeywordsField = qt.QLineEdit(
"", self.keywordsFrame)
self.keywordsFrame.layout().addRow(
self.inputImageExclusionKeywords,
self.inputImageExclusionKeywordsField)
self.inputLabelKeywords = qt.QLabel("Input Label Keywords:",
self.keywordsFrame)
self.inputLabelKeywordsField = qt.QLineEdit("", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelKeywords,
self.inputLabelKeywordsField)
self.inputLabelExclusionKeywords = qt.QLabel(
"Input Label Exclusion Keywords:", self.keywordsFrame)
self.inputLabelExclusionKeywordsField = qt.QLineEdit(
"", self.keywordsFrame)
self.keywordsFrame.layout().addRow(
self.inputLabelExclusionKeywords,
self.inputLabelExclusionKeywordsField)
# IMG Slice Extract Button
self.IMGSliceExtractButton = qt.QPushButton("Extract Images")
self.IMGSliceExtractFormLayout.addWidget(self.IMGSliceExtractButton)
#---------------------------------------------------------
# Connections
self.input6Button.connect('clicked(bool)', self.onInput6Button)
self.input7Button.connect('clicked(bool)', self.onInput7Button)
self.IMGSliceExtractButton.connect('clicked(bool)',
self.onIMGSliceExtract)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# fixed image selector
#
self.fixedImageSelector = slicer.qMRMLNodeComboBox()
self.fixedImageSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.fixedImageSelector.selectNodeUponCreation = True
self.fixedImageSelector.addEnabled = False
self.fixedImageSelector.removeEnabled = False
self.fixedImageSelector.noneEnabled = True
self.fixedImageSelector.showHidden = False
self.fixedImageSelector.showChildNodeTypes = False
self.fixedImageSelector.setMRMLScene(slicer.mrmlScene)
self.fixedImageSelector.setToolTip("Fixed image (optional)")
parametersFormLayout.addRow("Fixed Image: ", self.fixedImageSelector)
#
# fixed image label selector
#
self.fixedImageLabelSelector = slicer.qMRMLNodeComboBox()
self.fixedImageLabelSelector.nodeTypes = ((
"vtkMRMLLabelMapVolumeNode"), "")
self.fixedImageLabelSelector.selectNodeUponCreation = True
self.fixedImageLabelSelector.addEnabled = False
self.fixedImageLabelSelector.removeEnabled = False
self.fixedImageLabelSelector.noneEnabled = False
self.fixedImageLabelSelector.showHidden = False
self.fixedImageLabelSelector.showChildNodeTypes = False
self.fixedImageLabelSelector.setMRMLScene(slicer.mrmlScene)
self.fixedImageLabelSelector.setToolTip(
"Segmentation of the fixed image")
parametersFormLayout.addRow("Segmentation of the fixed Image: ",
self.fixedImageLabelSelector)
#
# moving image selector
#
self.movingImageSelector = slicer.qMRMLNodeComboBox()
self.movingImageSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.movingImageSelector.selectNodeUponCreation = True
self.movingImageSelector.addEnabled = False
self.movingImageSelector.removeEnabled = False
self.movingImageSelector.noneEnabled = True
self.movingImageSelector.showHidden = False
self.movingImageSelector.showChildNodeTypes = False
self.movingImageSelector.setMRMLScene(slicer.mrmlScene)
self.movingImageSelector.setToolTip("Moving image (optional)")
parametersFormLayout.addRow("Moving Image: ", self.movingImageSelector)
#
# moving image label selector
#
self.movingImageLabelSelector = slicer.qMRMLNodeComboBox()
self.movingImageLabelSelector.nodeTypes = ((
"vtkMRMLLabelMapVolumeNode"), "")
self.movingImageLabelSelector.selectNodeUponCreation = True
self.movingImageLabelSelector.addEnabled = False
self.movingImageLabelSelector.removeEnabled = False
self.movingImageLabelSelector.noneEnabled = False
self.movingImageLabelSelector.showHidden = False
self.movingImageLabelSelector.showChildNodeTypes = False
self.movingImageLabelSelector.setMRMLScene(slicer.mrmlScene)
self.movingImageLabelSelector.setToolTip(
"Segmentation of the moving image")
parametersFormLayout.addRow("Segmentation of the moving Image: ",
self.movingImageLabelSelector)
#
# Affine output transform selector
#
self.affineTransformSelector = slicer.qMRMLNodeComboBox()
self.affineTransformSelector.nodeTypes = (("vtkMRMLTransformNode"), "")
self.affineTransformSelector.selectNodeUponCreation = True
self.affineTransformSelector.addEnabled = True
self.affineTransformSelector.removeEnabled = False
self.affineTransformSelector.noneEnabled = False
self.affineTransformSelector.showHidden = False
self.affineTransformSelector.showChildNodeTypes = False
self.affineTransformSelector.baseName = 'Affine Transform'
self.affineTransformSelector.setMRMLScene(slicer.mrmlScene)
self.affineTransformSelector.setToolTip(
"Registration affine transform")
parametersFormLayout.addRow("Registration affine transform: ",
self.affineTransformSelector)
#
# B-spline output transform selector
#
self.bsplineTransformSelector = slicer.qMRMLNodeComboBox()
self.bsplineTransformSelector.nodeTypes = (("vtkMRMLTransformNode"),
"")
self.bsplineTransformSelector.selectNodeUponCreation = True
self.bsplineTransformSelector.addEnabled = True
self.bsplineTransformSelector.removeEnabled = False
self.bsplineTransformSelector.noneEnabled = False
self.bsplineTransformSelector.showHidden = False
self.bsplineTransformSelector.showChildNodeTypes = False
self.bsplineTransformSelector.baseName = 'Deformable Transform'
self.bsplineTransformSelector.setMRMLScene(slicer.mrmlScene)
self.bsplineTransformSelector.setToolTip(
"Registration b-spline transform")
parametersFormLayout.addRow("Registration B-spline Transform: ",
self.bsplineTransformSelector)
#
# registered volume selector
#
'''
self.outputImageSelector = slicer.qMRMLNodeComboBox()
self.outputImageSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
# self.outputImageSelector.nodeTypes = ( ("vtkMRMLLabelMapVolumeNode"), "" )
self.outputImageSelector.selectNodeUponCreation = True
self.outputImageSelector.addEnabled = True
self.outputImageSelector.removeEnabled = True
self.outputImageSelector.noneEnabled = True
self.outputImageSelector.showHidden = False
self.outputImageSelector.showChildNodeTypes = False
self.outputImageSelector.baseName = 'Registered Volume'
self.outputImageSelector.setMRMLScene( slicer.mrmlScene )
self.outputImageSelector.setToolTip( "Registered volume (will be generated only if the moving image was provided)" )
parametersFormLayout.addRow("Registered Volume: ", self.outputImageSelector)
'''
#
# To be added later: advanced parameters
# registration modes (rigid/affine/bspline), save rigid/affine transforms,
# crop box margin, number of samples, ...
#
# Add parameter node to facilitate registration from other modules and
# command line
#
self.registrationModeGroup = qt.QButtonGroup()
self.noRegistrationRadio = qt.QRadioButton('Before registration')
self.linearRegistrationRadio = qt.QRadioButton(
'After linear registration')
self.deformableRegistrationRadio = qt.QRadioButton(
'After deformable registration')
self.noRegistrationRadio.setChecked(1)
self.registrationModeGroup.addButton(self.noRegistrationRadio, 1)
self.registrationModeGroup.addButton(self.linearRegistrationRadio, 2)
self.registrationModeGroup.addButton(self.deformableRegistrationRadio,
3)
parametersFormLayout.addRow(qt.QLabel("Visualization"))
parametersFormLayout.addRow("", self.noRegistrationRadio)
parametersFormLayout.addRow("", self.linearRegistrationRadio)
parametersFormLayout.addRow("", self.deformableRegistrationRadio)
self.registrationModeGroup.connect('buttonClicked(int)',
self.onVisualizationModeClicked)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
#self.onSelect()
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
'''
def __init__(self, parent, *args, **kwargs):
""" Init function.
"""
super(FingerTabWidget, self).__init__(parent)
#--------------------
# Define sizing parameters.
#--------------------
self.marginVal = 5
self.currentIndex = 0
self.tabWidth = 120
#--------------------
# Make and style 'tabColumn', which is a qFrame.
#--------------------
self.tabColumn = qt.QFrame(self)
self.tabColumn.setFixedWidth(self.tabWidth)
self.tabColumn.setObjectName('tabColumn')
self.tabColumn.setStyleSheet('#tabColumn {background:#E8E8E8 ; height: 4000px;' +
'border-right-width: 1px; border-right-color: gray;' +
'border-right-style: solid; margin-top: 5px;' +
'margin-left: 5px; margin-bottom: 5px}')
#--------------------
# Define the layout of the 'tabColumn' qFrame,
# set the layout to the 'tabColumn' qFrame.
#--------------------
self.tabColumnLayout = qt.QVBoxLayout()
self.tabColumnLayout.setContentsMargins(0,0,0,0)
self.tabColumnLayout.setSpacing(0)
self.tabColumnLayout.addStretch()
self.tabColumn.setLayout(self.tabColumnLayout)
#--------------------
# Define the 'innerWindowLayout'.
#--------------------
self.innerWindowLayout = qt.QStackedLayout()
self.innerWindowLayout.setStackingMode(1)
self.innerWindowLayout.setSpacing(0)
self.innerWindowLayout.setContentsMargins(0,0,0,0)
#--------------------
# Define the 'widgetStack' object, which takes
# the whole span of the window.
#--------------------
self.widgetStack = qt.QWidget(self)
self.widgetStack.setObjectName("widgetStack")
self.widgetStack.setStyleSheet("#widgetStack{ border: none; background: transparent}")
#--------------------
# The layout for the 'widgetStack' is
# 'widgetStackLayout', which is an HBoxLayout. We set
# a left spacing the length of the tabs-1 to accomodate for the border
# and tabs of the widget.
#--------------------
self.widgetStackLayout = qt.QHBoxLayout()
self.widgetStackLayout.setContentsMargins(0,self.marginVal,self.marginVal,self.marginVal)
self.widgetStackLayout.addSpacing(self.tabWidth - 1)
self.widgetStack.setLayout(self.widgetStackLayout)
#--------------------
# Define the 'tabPageStack', add to the widgetStackLayout.
#
# NOTE: The 'tabPageStack' is the stacked layout were all
# of the tab pages reside.
#--------------------
self.tabPageStack = qt.QStackedLayout()
self.widgetStackLayout.addLayout(self.tabPageStack)
#--------------------
# Define the tabButtons as part of a
# button group, for easier event listening.
#
# Set their styles as well.
#--------------------
self.buttonGroup = qt.QButtonGroup(self)
self.buttonGroup.connect('buttonClicked(QAbstractButton*)', self.onTabClicked)
self.tabButtons = []
self.tabWidgets = []
self.tabObjectName = 'fingerTab'
self.tabToggledStyle = '#fingerTab {border: 1px solid gray; border-right-width: 1px; border-right-color: white; background-color: white;}'
self.tabUntoggledStyle ='#fingerTab {border: 1px solid #D0D0D0; border-right-width: 1px; border-right-color: gray; background-color: #C0C0C0;}'
self.tabToggledFont = qt.QFont('Arial', 12, 100, False)
self.tabUntoggledFont = qt.QFont('Arial', 12, 25, False)
#--------------------
# Add 'tabColumn' and 'widgetStack' to 'innerWindowLayout'. Set the current
# index of the widgetStack (this will allow for the black
# borders between the tabs and the windows to connect).
#--------------------
self.innerWindowLayout.addWidget(self.tabColumn)
self.innerWindowLayout.addWidget(self.widgetStack)
self.innerWindowLayout.setCurrentIndex(1)
#--------------------
# Set 'mainWidgetLayout' to hold the 'innerWindowLayout'.
# The 'mainWidgetLayout' exists because subclasses of
# 'FingerTabWidget' and others that use it can add
# further rows to the window (such as 'Done' and 'Cancel'
# buttons).
#--------------------
self.mainWidgetLayout = qt.QVBoxLayout()
self.mainWidgetLayout.setContentsMargins(5,5,5,5)
self.mainWidgetLayout.addLayout(self.innerWindowLayout)
#--------------------
# Set the primary layout to the 'mainWidgetLayout'
#--------------------
self.setLayout(self.mainWidgetLayout)
def setup(self):
#
# 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 = "Radiomics 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)
reloadCollapsibleButton.collapsed = True
#---------------------------------------------------------
#
# Compute Radiomics area
#
self.computeRadiomicsCollapsibleButton = ctk.ctkCollapsibleButton()
self.computeRadiomicsCollapsibleButton.text = "Slicer Radiomics Platform"
self.layout.addWidget(self.computeRadiomicsCollapsibleButton)
self.computeRadiomicsFormLayout = qt.QFormLayout(
self.computeRadiomicsCollapsibleButton)
#
# Universal Advanced Settings Collapsible Button
#
self.AdvancedSettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.AdvancedSettingsCollapsibleButton.text = "Advanced Settings"
self.AdvancedSettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.AdvancedSettingsCollapsibleButton.setLayout(qt.QHBoxLayout())
self.computeRadiomicsFormLayout.addWidget(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsCollapsibleButton.collapsed = True
self.AdvancedSettingsFrame = qt.QFrame(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsFrameLayout = qt.QFormLayout()
self.AdvancedSettingsFrame.setLayout(self.AdvancedSettingsFrameLayout)
self.AdvancedSettingsCollapsibleButton.layout().addWidget(
self.AdvancedSettingsFrame)
# Label Values
self.inputLabelValues = qt.QLabel("Label Values:",
self.AdvancedSettingsFrame)
self.inputLabelValuesField = qt.QLineEdit("1",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputLabelValues,
self.inputLabelValuesField)
# Interpolation Settings
self.settingsRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.settingsRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.interpolationsGroup = qt.QButtonGroup(
self.settingsRadioButtonFrame)
self.ipRawButton = qt.QRadioButton("Raw")
self.ip1x1x1Button = qt.QRadioButton("(1,1,1)")
self.ip2x2x2Button = qt.QRadioButton("(2,2,2)")
self.ip3x3x3Button = qt.QRadioButton("(3,3,3)")
self.ipRawButton.checked = True
self.interpolationsGroup.addButton(self.ipRawButton)
self.interpolationsGroup.addButton(self.ip1x1x1Button)
self.interpolationsGroup.addButton(self.ip2x2x2Button)
self.interpolationsGroup.addButton(self.ip3x3x3Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ipRawButton)
self.settingsRadioButtonFrame.layout().addWidget(self.ip1x1x1Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip2x2x2Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip3x3x3Button)
self.interpHeader = qt.QLabel("Interpolation:")
self.AdvancedSettingsFrameLayout.addRow(self.interpHeader,
self.settingsRadioButtonFrame)
# Bin Width
self.inputBinWidth = qt.QLabel("Bin Width:",
self.AdvancedSettingsFrame)
self.inputBinWidthField = qt.QLineEdit("25",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputBinWidth,
self.inputBinWidthField)
# Modality Radio Buttons Frame
self.ModalityRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.ModalityRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.ModalityFileFormatGroup = qt.QButtonGroup(
self.ModalityRadioButtonFrame)
self.CTButton = qt.QRadioButton("CT")
self.CTButton.checked = True
self.MRIButton = qt.QRadioButton("MRI")
self.PETButton = qt.QRadioButton("PET")
self.ModalityFileFormatGroup.addButton(self.CTButton)
self.ModalityFileFormatGroup.addButton(self.MRIButton)
self.ModalityFileFormatGroup.addButton(self.PETButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.CTButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.MRIButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.PETButton)
self.ModalityInputLabel = qt.QLabel("Image Modality:",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.ModalityInputLabel,
self.ModalityRadioButtonFrame)
#
# End Universal Advanced Settings Collapsible Button
#
# Parent Tab Widget
self.computeRadiomicsTabWidget = qt.QTabWidget()
self.computeRadiomicsFormLayout.addWidget(
self.computeRadiomicsTabWidget)
# Radiomics Current Mode
self.tabComputeRadiomicsCurr = qt.QWidget()
self.singleCaseInputFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsCurr.setLayout(self.singleCaseInputFormLayout)
self.tabComputeRadiomicsCurrName = "Single Case Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsCurr,
self.tabComputeRadiomicsCurrName)
# Input 1: Input Image
self.input1Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input1Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input1Frame)
self.input1Selector = qt.QLabel("Input Image: ", self.input1Frame)
self.input1Frame.layout().addWidget(self.input1Selector)
self.input1Selector = slicer.qMRMLNodeComboBox(self.input1Frame)
self.input1Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input1Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.input1Selector.addEnabled = False
self.input1Selector.removeEnabled = False
self.input1Selector.setMRMLScene(slicer.mrmlScene)
self.input1Frame.layout().addWidget(self.input1Selector)
# Input 2: Input Segmentation
self.input2Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input2Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input2Frame)
self.input2Selector = qt.QLabel("Input Label: ", self.input2Frame)
self.input2Frame.layout().addWidget(self.input2Selector)
self.input2Selector = slicer.qMRMLNodeComboBox(self.input2Frame)
self.input2Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input2Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
1)
self.input2Selector.addEnabled = False
self.input2Selector.removeEnabled = False
self.input2Selector.setMRMLScene(slicer.mrmlScene)
self.input2Frame.layout().addWidget(self.input2Selector)
# Settings Collapsible Button
self.SettingsCollapsibleButtonCurr = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButtonCurr.text = "Settings"
self.SettingsCollapsibleButtonCurrLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButtonCurr.setLayout(
self.SettingsCollapsibleButtonCurrLayout)
self.singleCaseInputFormLayout.addWidget(
self.SettingsCollapsibleButtonCurr)
self.SettingsCollapsibleButtonCurr.collapsed = False
self.SettingsFrameCurr = qt.QFrame(self.SettingsCollapsibleButtonCurr)
self.SettingsFrameCurr.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonCurrLayout.addWidget(
self.SettingsFrameCurr)
# Settings
self.para2curr = qt.QCheckBox("Use MatlabBridge",
self.tabComputeRadiomicsCurr)
self.para2curr.toolTip = "When checked: Matlab features extracted"
self.para2curr.checked = False
self.SettingsFrameCurr.layout().addRow(self.para2curr)
# Apply Radiomics button
self.RadiomicCurrButtonsFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicCurrButtonsFrame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton = qt.QPushButton(
"Compute Radiomics Features (Single Case)",
self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton.enabled = True
self.radiomicsCurrButton.toolTip = "Run the feature extraction for a single case."
self.RadiomicCurrButtonsFrame.layout().addWidget(
self.radiomicsCurrButton)
# Chart
self.RadiomicsTableFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicsTableFrameLayout = qt.QHBoxLayout()
self.RadiomicsTableFrame.setLayout(self.RadiomicsTableFrameLayout)
self.singleCaseInputFormLayout.addWidget(self.RadiomicsTableFrame)
self.RadiomicsTableView = qt.QTableView(self.RadiomicsTableFrame)
self.RadiomicsTableView.sortingEnabled = True
self.RadiomicsTableView.minimumHeight = 175
self.RadiomicsTableView.verticalHeader().visible = False
self.RadiomicsTableView.setColumnWidth(0, 30)
self.RadiomicsTableFrameLayout.addWidget(self.RadiomicsTableView)
self.RadiomicsTableModel = qt.QStandardItemModel()
# Save Table Button
self.saveButton = qt.QPushButton("Save Table to CSV File",
self.RadiomicCurrButtonsFrame)
self.saveButton.toolTip = "Save Radiomics Feature from table to CSV file"
self.saveButton.enabled = False
self.singleCaseInputFormLayout.layout().addWidget(self.saveButton)
"""
#
# The interface we use for batch mode (not part of this module)
#
#---------------------------------------------------------
# Radiomics Batch
self.tabComputeRadiomicsBatch = qt.QWidget()
self.RadiomicsFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsBatch.setLayout(self.RadiomicsFormLayout)
self.tabComputeRadiomicsBatchName = "Batch Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsBatch, self.tabComputeRadiomicsBatchName)
# Input 3: Database selection
self.input3Frame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.input3Frame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.input3Frame)
self.DatabaseButton = qt.QPushButton("Set Root Patient Directory")
self.DatabaseButton.toolTip = "Set the main Patient Data location"
self.DatabaseButton.enabled = True
self.input3Frame.layout().addWidget(self.DatabaseButton)
self.PatientSelector = qt.QComboBox()
self.PatientSelector.enabled = False
self.input3Frame.layout().addWidget(self.PatientSelector)
# Settings Collapsible Button
self.SettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButton.text = "Settings"
self.SettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButton.setLayout(self.SettingsCollapsibleButtonLayout)
self.RadiomicsFormLayout.addWidget(self.SettingsCollapsibleButton)
self.SettingsCollapsibleButton.collapsed = False
self.SettingsFrame = qt.QFrame(self.SettingsCollapsibleButton)
self.SettingsFrame.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonLayout.addWidget(self.SettingsFrame)
# Settings
self.para2 = qt.QCheckBox("Use MatlabBridge", self.SettingsFrame)
self.para2.toolTip = "When checked: Matlab features extracted"
self.para2.checked = True
self.SettingsFrame.layout().addRow(self.para2)
self.para3 = qt.QCheckBox("Clear Database", self.SettingsFrame)
self.para3.toolTip = "When checked: old database is cleared"
self.para3.checked = True
self.SettingsFrame.layout().addRow(self.para3)
# Keywords Collapsible Button
self.KeywordsCollapsibleButton = ctk.ctkCollapsibleButton()
self.KeywordsCollapsibleButton.text = "Keyword Matching"
self.KeywordsCollapsibleButtonLayout = qt.QHBoxLayout()
self.KeywordsCollapsibleButton.setLayout(self.KeywordsCollapsibleButtonLayout)
self.SettingsFrame.layout().addRow(self.KeywordsCollapsibleButton)
self.KeywordsCollapsibleButton.collapsed = True
self.keywordsFrame = qt.QFrame(self.KeywordsCollapsibleButton)
self.keywordsFrame.setLayout(qt.QFormLayout())
self.KeywordsCollapsibleButtonLayout.addWidget(self.keywordsFrame)
self.keywordsHeader = qt.QLabel("Keyword Matching:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.keywordsHeader)
# File Type Radio Buttons Frame
self.radioButtonFrame = qt.QFrame(self.keywordsFrame)
self.radioButtonFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.radioButtonFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.radioButtonFrame.layout().addRow(self.nrrdButton, self.niftiButton)
self.inputMaskHeader = qt.QLabel("Input Image File Type:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputMaskHeader, self.radioButtonFrame)
# Keywords Frame
self.inputImageKeywords = qt.QLabel("Input Image Keywords:", self.keywordsFrame)
self.inputImageKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageKeywords, self.inputImageKeywordsField )
self.inputImageExclusionKeywords = qt.QLabel("Input Image Exclusion Keywords:", self.keywordsFrame)
self.inputImageExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageExclusionKeywords, self.inputImageExclusionKeywordsField )
self.inputLabelKeywords = qt.QLabel("Input Label Keywords:", self.keywordsFrame)
self.inputLabelKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelKeywords, self.inputLabelKeywordsField )
self.inputLabelExclusionKeywords = qt.QLabel("Input Label Exclusion Keywords:", self.keywordsFrame)
self.inputLabelExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelExclusionKeywords, self.inputLabelExclusionKeywordsField )
# Radiomic Mode Buttons
self.RadiomicButtonsFrame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.RadiomicButtonsFrame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.RadiomicButtonsFrame)
self.radiomicsBatchButton = qt.QPushButton("Compute Radiomics Features (Batch Mode)")
self.radiomicsBatchButton.toolTip = "Run the feature extraction for database batch."
self.radiomicsBatchButton.enabled = True
self.RadiomicButtonsFrame.layout().addWidget(self.radiomicsBatchButton)
self.RadiomicButtonsFrame.enabled = True
"""
#---------------------------------------------------------
# Connections
#self.DatabaseButton.connect('clicked(bool)', self.onDatabaseButton)
self.radiomicsCurrButton.connect('clicked(bool)', self.onRadiomicsCurr)
#self.radiomicsBatchButton.connect('clicked(bool)', self.onRadiomicsBatch)
self.saveButton.connect('clicked()', self.onSave)
self.layout.addStretch(1) # Add vertical spacer
def setup(self):
#---------------------------------------------------------
# Batch Covert DICOM to NRRD
self.BatchConvertCollapsibleButton = ctk.ctkCollapsibleButton()
self.BatchConvertCollapsibleButton.text = "Batch convert DICOM to NRRD or NIFTI"
self.layout.addWidget(self.BatchConvertCollapsibleButton)
self.BatchConvertCollapsibleButton.collapsed = False
self.BatchConvertFormLayout = qt.QFormLayout(
self.BatchConvertCollapsibleButton)
# Input 1: Input Directory selector
self.input1Selector = qt.QLabel("Input Directory (DICOM): ",
self.BatchConvertCollapsibleButton)
self.input1Button = qt.QPushButton(
"Select Main Input Directory of DICOM files")
self.input1Button.toolTip = "Select main directory with DICOM files (folder names are patient names)"
self.input1Button.enabled = True
self.BatchConvertFormLayout.addRow(self.input1Selector,
self.input1Button)
# Input 2: Output Directory selector
self.input2Selector = qt.QLabel("Output Directory: ",
self.BatchConvertCollapsibleButton)
self.input2Button = qt.QPushButton("Select Main Output Directory")
self.input2Button.toolTip = "Select main directory for output NRRD or NIFTI files (folder names are patient names)"
self.input2Button.enabled = True
self.BatchConvertFormLayout.addRow(self.input2Selector,
self.input2Button)
# RTStruct Conversion
self.contourConvertLabel = qt.QLabel(
"Convert DICOM-RT Contours: ", self.BatchConvertCollapsibleButton)
self.contourConvertSelectFrame = qt.QFrame(
self.BatchConvertCollapsibleButton)
self.contourConvertSelectFrame.setLayout(qt.QHBoxLayout())
self.contourConvertGroup = qt.QButtonGroup(
self.contourConvertSelectFrame)
self.noConvertButton = qt.QRadioButton("None")
self.noConvertButton.checked = True
self.allConvertButton = qt.QRadioButton("All")
self.selectConvertButton = qt.QRadioButton("Select")
self.contourConvertGroup.addButton(self.noConvertButton)
self.contourConvertGroup.addButton(self.allConvertButton)
self.contourConvertGroup.addButton(self.selectConvertButton)
self.contourConvertSelectFrame.layout().addWidget(self.noConvertButton)
self.contourConvertSelectFrame.layout().addWidget(
self.allConvertButton)
self.contourConvertSelectFrame.layout().addWidget(
self.selectConvertButton)
self.BatchConvertFormLayout.layout().addRow(
self.contourConvertLabel, self.contourConvertSelectFrame)
self.contourConvertCollapsibleButton = ctk.ctkCollapsibleButton(
self.BatchConvertCollapsibleButton)
self.contourConvertCollapsibleButton.text = "Select Contours to Convert"
self.BatchConvertFormLayout.addRow(
self.contourConvertCollapsibleButton)
self.contourConvertCollapsibleButton.enabled = False
self.contourConvertCollapsibleButton.collapsed = True
self.contourConvertFormLayout = qt.QFormLayout(
self.contourConvertCollapsibleButton)
# Keywords to catch RTStruct Structures
self.contoursFrame = qt.QFrame(self.contourConvertCollapsibleButton)
self.contoursFrame.setLayout(qt.QVBoxLayout())
self.contoursFrame.setFrameStyle(2)
self.contourConvertFormLayout.addWidget(self.contoursFrame)
self.addContourButton = qt.QPushButton(
"Add Contour to convert from RTStruct (separate keywords by comma)",
self.contoursFrame)
self.keywordsScrollWidget = qt.QWidget()
self.keywordsScrollWidget.setLayout(qt.QFormLayout())
self.keywordsScroll = qt.QScrollArea()
self.keywordsScroll.setWidgetResizable(True)
self.keywordsScroll.setWidget(self.keywordsScrollWidget)
self.contoursFrame.layout().addWidget(self.keywordsScroll)
self.contoursFrame.layout().addWidget(self.addContourButton)
# Settings Collapsible Button
self.settingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.settingsCollapsibleButton.text = "Settings"
self.settingsCollapsibleButton.setLayout(qt.QFormLayout())
self.layout.addWidget(self.settingsCollapsibleButton)
# NRRD or NIFTI Radio Buttons
self.fileFormatLabel = qt.QLabel("Output File Format: ",
self.settingsCollapsibleButton)
self.fileFormatSelectFrame = qt.QFrame(self.settingsCollapsibleButton)
self.fileFormatSelectFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.fileFormatSelectFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.fileFormatSelectFrame.layout().addRow(self.nrrdButton,
self.niftiButton)
self.settingsCollapsibleButton.layout().addRow(
self.fileFormatLabel, self.fileFormatSelectFrame)
# Use input DICOM Patient Directory names as PatientID or infer from DICOM Metadata
self.patientIDLabel = qt.QLabel("Infer Patient IDs from: ",
self.settingsCollapsibleButton)
self.patientIDLabel.toolTip = "Use input DICOM Patient Directory names as PatientID or infer from DICOM Metadata"
self.patientIDSelectFrame = qt.QFrame(self.settingsCollapsibleButton)
self.patientIDSelectFrame.setLayout(qt.QFormLayout())
self.patientIDGroup = qt.QButtonGroup(self.patientIDSelectFrame)
self.metadataButton = qt.QRadioButton("Series DICOM Metadata")
self.metadataButton.checked = True
self.inputDirButton = qt.QRadioButton("Input Patient Subdirectories")
self.patientIDGroup.addButton(self.metadataButton)
self.patientIDGroup.addButton(self.inputDirButton)
self.patientIDSelectFrame.layout().addRow(self.metadataButton,
self.inputDirButton)
self.settingsCollapsibleButton.layout().addRow(
self.patientIDLabel, self.patientIDSelectFrame)
# Center Images option
self.centerImagesLabel = qt.QLabel("Center Images: ",
self.settingsCollapsibleButton)
self.centerImagesSelectFrame = qt.QFrame(
self.settingsCollapsibleButton)
self.centerImagesSelectFrame.setLayout(qt.QFormLayout())
self.centerImagesGroup = qt.QButtonGroup(self.centerImagesSelectFrame)
self.centerImagesButton = qt.QRadioButton("Yes")
self.noCenterImagesButton = qt.QRadioButton("No")
self.noCenterImagesButton.checked = True
self.centerImagesGroup.addButton(self.centerImagesButton)
self.centerImagesGroup.addButton(self.noCenterImagesButton)
self.centerImagesSelectFrame.layout().addRow(self.centerImagesButton,
self.noCenterImagesButton)
self.settingsCollapsibleButton.layout().addRow(
self.centerImagesLabel, self.centerImagesSelectFrame)
# Center Labels option
self.centerLabelsLabel = qt.QLabel("Center Labels: ",
self.settingsCollapsibleButton)
self.centerLabelsSelectFrame = qt.QFrame(
self.settingsCollapsibleButton)
self.centerLabelsSelectFrame.setLayout(qt.QFormLayout())
self.centerLabelsGroup = qt.QButtonGroup(self.centerLabelsSelectFrame)
self.centerLabelsButton = qt.QRadioButton("Yes")
self.noCenterLabelsButton = qt.QRadioButton("No")
self.noCenterLabelsButton.checked = True
self.centerLabelsGroup.addButton(self.centerLabelsButton)
self.centerLabelsGroup.addButton(self.noCenterLabelsButton)
self.centerLabelsSelectFrame.layout().addRow(self.centerLabelsButton,
self.noCenterLabelsButton)
self.settingsCollapsibleButton.layout().addRow(
self.centerLabelsLabel, self.centerLabelsSelectFrame)
# Parse and Save DICOM Metadata to CSV
self.metadataExtractLabel = qt.QLabel("DICOM Metadata Extraction",
self.settingsCollapsibleButton)
self.metadataExtractLabel.toolTip = "Extract and Save all DICOM Metadata to a CSV file"
self.metadataExtractSelectFrame = qt.QFrame(
self.settingsCollapsibleButton)
self.metadataExtractSelectFrame.setLayout(qt.QFormLayout())
self.metadataExtractGroup = qt.QButtonGroup(
self.metadataExtractSelectFrame)
self.extractCSVButton = qt.QRadioButton("CSV")
self.extractCSVButton.checked = True
#self.extractJSONButton = qt.QRadioButton("JSON")
self.doNotExtractButton = qt.QRadioButton("None")
self.metadataExtractGroup.addButton(self.extractCSVButton)
self.metadataExtractGroup.addButton(self.doNotExtractButton)
self.metadataExtractSelectFrame.layout().addRow(
self.extractCSVButton, self.doNotExtractButton)
self.settingsCollapsibleButton.layout().addRow(
self.metadataExtractLabel, self.metadataExtractSelectFrame)
# Apply Batch Convert button
self.applyBatchButton = qt.QPushButton("Apply Batch Convert")
self.applyBatchButton.toolTip = "Batch convert DICOM to NRRD or NIFTI files"
self.layout.addWidget(self.applyBatchButton)
self.applyBatchButton.enabled = False
#---------------------------------------------------------
# Connections
self.input1Button.connect('clicked(bool)', self.onInput1Button)
self.input2Button.connect('clicked(bool)', self.onInput2Button)
self.selectConvertButton.toggled.connect(self.selectConvert)
self.addContourButton.connect('clicked(bool)',
self.addContourFilterWidget)
self.applyBatchButton.connect('clicked(bool)', self.onBatchApply)
def setup(self):
# Instantiate and connect widgets ...
self.RingOff = None
self.RingOn = None
# Tags to manage event observers
self.tagSourceNode = None
self.tagDestinationNode = None
#####################
## For debugging
##
## 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 = "CurveMaker Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
##
#####################
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Source points (vtkMRMLMarkupsFiducialNode)
#
self.SourceSelector = slicer.qMRMLNodeComboBox()
self.SourceSelector.nodeTypes = (("vtkMRMLMarkupsFiducialNode"), "")
self.SourceSelector.addEnabled = True
self.SourceSelector.removeEnabled = False
self.SourceSelector.noneEnabled = True
self.SourceSelector.showHidden = False
self.SourceSelector.renameEnabled = True
self.SourceSelector.showChildNodeTypes = False
self.SourceSelector.setMRMLScene(slicer.mrmlScene)
self.SourceSelector.setToolTip(
"Pick up a Markups node listing fiducials.")
parametersFormLayout.addRow("Source points: ", self.SourceSelector)
#
# Target point (vtkMRMLMarkupsFiducialNode)
#
self.DestinationSelector = slicer.qMRMLNodeComboBox()
self.DestinationSelector.nodeTypes = (("vtkMRMLModelNode"), "")
self.DestinationSelector.addEnabled = True
self.DestinationSelector.removeEnabled = False
self.DestinationSelector.noneEnabled = True
self.DestinationSelector.showHidden = False
self.DestinationSelector.renameEnabled = True
self.DestinationSelector.selectNodeUponCreation = True
self.DestinationSelector.showChildNodeTypes = False
self.DestinationSelector.setMRMLScene(slicer.mrmlScene)
self.DestinationSelector.setToolTip("Pick up or create a Model node.")
parametersFormLayout.addRow("Curve model: ", self.DestinationSelector)
#
# Radius for the tube
#
self.RadiusSliderWidget = ctk.ctkSliderWidget()
self.RadiusSliderWidget.singleStep = 1.0
self.RadiusSliderWidget.minimum = 1.0
self.RadiusSliderWidget.maximum = 50.0
self.RadiusSliderWidget.value = 5.0
self.RadiusSliderWidget.setToolTip("Set the raidus of the tube.")
parametersFormLayout.addRow("Radius (mm): ", self.RadiusSliderWidget)
#
# Radio button to select interpolation method
#
self.InterpolationLayout = qt.QHBoxLayout()
self.InterpolationNone = qt.QRadioButton("None")
self.InterpolationCardinalSpline = qt.QRadioButton("Cardinal Spline")
self.InterpolationHermiteSpline = qt.QRadioButton(
"Hermite Spline (for Endoscopy)")
self.InterpolationLayout.addWidget(self.InterpolationNone)
self.InterpolationLayout.addWidget(self.InterpolationCardinalSpline)
self.InterpolationLayout.addWidget(self.InterpolationHermiteSpline)
self.InterpolationGroup = qt.QButtonGroup()
self.InterpolationGroup.addButton(self.InterpolationNone)
self.InterpolationGroup.addButton(self.InterpolationCardinalSpline)
self.InterpolationGroup.addButton(self.InterpolationHermiteSpline)
parametersFormLayout.addRow("Interpolation: ",
self.InterpolationLayout)
#
# Interpolation Resolution
#
self.InterpResolutionSliderWidget = ctk.ctkSliderWidget()
self.InterpResolutionSliderWidget.singleStep = 1.0
self.InterpResolutionSliderWidget.minimum = 3.0
self.InterpResolutionSliderWidget.maximum = 50.0
self.InterpResolutionSliderWidget.value = 25.0
self.InterpResolutionSliderWidget.setToolTip(
"Number of interpolation points between control points. Default is 25."
)
parametersFormLayout.addRow("Resolution: ",
self.InterpResolutionSliderWidget)
#
# Radio button for ring mode
#
self.RingLayout = qt.QHBoxLayout()
self.RingOff = qt.QRadioButton("Off")
self.RingOn = qt.QRadioButton("On")
self.RingLayout.addWidget(self.RingOff)
self.RingLayout.addWidget(self.RingOn)
self.RingGroup = qt.QButtonGroup()
self.RingGroup.addButton(self.RingOff)
self.RingGroup.addButton(self.RingOn)
parametersFormLayout.addRow("Ring mode: ", self.RingLayout)
#
# Check box to start curve visualization
#
self.EnableAutoUpdateCheckBox = qt.QCheckBox()
self.EnableAutoUpdateCheckBox.checked = 0
self.EnableAutoUpdateCheckBox.setToolTip(
"If checked, the CurveMaker module keeps updating the model as the points are updated."
)
parametersFormLayout.addRow("Auto update:",
self.EnableAutoUpdateCheckBox)
#
# Button to generate a curve
#
self.GenerateButton = qt.QPushButton("Generate Curve")
self.GenerateButton.toolTip = "Generate Curve"
self.GenerateButton.enabled = True
parametersFormLayout.addRow("", self.GenerateButton)
# Connections
self.InterpolationNone.connect('clicked(bool)',
self.onSelectInterpolationNone)
self.InterpolationCardinalSpline.connect(
'clicked(bool)', self.onSelectInterpolationCardinalSpline)
self.InterpolationHermiteSpline.connect(
'clicked(bool)', self.onSelectInterpolationHermiteSpline)
self.RingOff.connect('clicked(bool)', self.onRingOff)
self.RingOn.connect('clicked(bool)', self.onRingOn)
self.EnableAutoUpdateCheckBox.connect('toggled(bool)',
self.onEnableAutoUpdate)
self.SourceSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSourceSelected)
self.DestinationSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onDestinationSelected)
self.RadiusSliderWidget.connect("valueChanged(double)",
self.onTubeUpdated)
self.InterpResolutionSliderWidget.connect(
"valueChanged(double)", self.onInterpResolutionUpdated)
self.GenerateButton.connect('clicked(bool)', self.onGenerateCurve)
# Set default
## default interpolation method
self.InterpolationCardinalSpline.setChecked(True)
self.onSelectInterpolationCardinalSpline(True)
## default ring mode
self.RingOff.setChecked(True)
self.onRingOff(True)
#
# Curve Length area
#
lengthCollapsibleButton = ctk.ctkCollapsibleButton()
lengthCollapsibleButton.text = "Length"
self.layout.addWidget(lengthCollapsibleButton)
lengthFormLayout = qt.QFormLayout(lengthCollapsibleButton)
lengthCollapsibleButton.collapsed = True
#-- Curve length
self.lengthLineEdit = qt.QLineEdit()
self.lengthLineEdit.text = '--'
self.lengthLineEdit.readOnly = True
self.lengthLineEdit.frame = True
self.lengthLineEdit.styleSheet = "QLineEdit { background:transparent; }"
self.lengthLineEdit.cursor = qt.QCursor(qt.Qt.IBeamCursor)
lengthFormLayout.addRow("Curve Length (mm):", self.lengthLineEdit)
#
# Distance Area
#
distanceCollapsibleButton = ctk.ctkCollapsibleButton()
distanceCollapsibleButton.text = "Distance"
distanceCollapsibleButton.collapsed = True
self.layout.addWidget(distanceCollapsibleButton)
distanceFormLayout = qt.QFormLayout(distanceCollapsibleButton)
#-- Point-to-curve distance
# - Markups selector for input points
distanceLayout = qt.QVBoxLayout()
self.targetFiducialsSelector = slicer.qMRMLNodeComboBox()
self.targetFiducialsSelector.nodeTypes = ((
"vtkMRMLMarkupsFiducialNode"), "")
self.targetFiducialsSelector.selectNodeUponCreation = True
self.targetFiducialsSelector.addEnabled = True
self.targetFiducialsSelector.removeEnabled = True
self.targetFiducialsSelector.noneEnabled = True
self.targetFiducialsSelector.showHidden = False
self.targetFiducialsSelector.showChildNodeTypes = False
self.targetFiducialsSelector.setMRMLScene(slicer.mrmlScene)
self.targetFiducialsSelector.setToolTip("Select Markups for targets")
distanceLayout.addWidget(self.targetFiducialsSelector)
self.targetFiducialsNode = None
self.tagDestinationDispNode = None
self.targetFiducialsSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onTargetFiducialsSelected)
self.fiducialsTable = qt.QTableWidget(1, 3)
self.fiducialsTable.setSelectionBehavior(
qt.QAbstractItemView.SelectRows)
self.fiducialsTable.setSelectionMode(
qt.QAbstractItemView.SingleSelection)
self.fiducialsTableHeaders = ["Name", "Position (mm)", "Distance (mm)"]
self.fiducialsTable.setHorizontalHeaderLabels(
self.fiducialsTableHeaders)
self.fiducialsTable.horizontalHeader().setStretchLastSection(True)
distanceLayout.addWidget(self.fiducialsTable)
self.extrapolateCheckBox = qt.QCheckBox()
self.extrapolateCheckBox.checked = 0
self.extrapolateCheckBox.setToolTip(
"Extrapolate the first and last segment to calculate the distance")
self.extrapolateCheckBox.connect('toggled(bool)',
self.updateTargetFiducialsTable)
self.extrapolateCheckBox.text = 'Extrapolate curves to measure the distances'
self.showErrorVectorCheckBox = qt.QCheckBox()
self.showErrorVectorCheckBox.checked = 0
self.showErrorVectorCheckBox.setToolTip(
"Show error vectors, which is defined by the target point and the closest point on the curve. The vector is perpendicular to the curve, unless the closest point is one end of the curve."
)
self.showErrorVectorCheckBox.connect('toggled(bool)',
self.updateTargetFiducialsTable)
self.showErrorVectorCheckBox.text = 'Show error vectors'
distanceLayout.addWidget(self.extrapolateCheckBox)
distanceLayout.addWidget(self.showErrorVectorCheckBox)
distanceFormLayout.addRow("Distance from:", distanceLayout)
#
# Curvature Area
#
curvatureCollapsibleButton = ctk.ctkCollapsibleButton()
curvatureCollapsibleButton.text = "Curvature"
curvatureCollapsibleButton.collapsed = True
self.layout.addWidget(curvatureCollapsibleButton)
curvatureFormLayout = qt.QFormLayout(curvatureCollapsibleButton)
#-- Curvature
self.curvatureLayout = qt.QHBoxLayout()
self.curvatureOff = qt.QRadioButton("Off")
self.curvatureOff.connect('clicked(bool)', self.onCurvatureOff)
self.curvatureOn = qt.QRadioButton("On")
self.curvatureOn.connect('clicked(bool)', self.onCurvatureOn)
self.curvatureLayout.addWidget(self.curvatureOff)
self.curvatureLayout.addWidget(self.curvatureOn)
self.curvatureGroup = qt.QButtonGroup()
self.curvatureGroup.addButton(self.curvatureOff)
self.curvatureGroup.addButton(self.curvatureOn)
curvatureFormLayout.addRow("Curvature mode:", self.curvatureLayout)
autoCurvatureRangeFormLayout = qt.QFormLayout(
curvatureCollapsibleButton)
self.autoCurvatureRangeLayout = qt.QHBoxLayout()
self.autoCurvatureRangeOff = qt.QRadioButton("Manual")
self.autoCurvatureRangeOff.connect('clicked(bool)',
self.onAutoCurvatureRangeOff)
self.autoCurvatureRangeOn = qt.QRadioButton("Auto")
self.autoCurvatureRangeOn.connect('clicked(bool)',
self.onAutoCurvatureRangeOn)
self.autoCurvatureRangeLayout.addWidget(self.autoCurvatureRangeOff)
self.autoCurvatureRangeLayout.addWidget(self.autoCurvatureRangeOn)
self.autoCurvatureRangeGroup = qt.QButtonGroup()
self.autoCurvatureRangeGroup.addButton(self.autoCurvatureRangeOff)
self.autoCurvatureRangeGroup.addButton(self.autoCurvatureRangeOn)
curvatureFormLayout.addRow("Color range:",
self.autoCurvatureRangeLayout)
#-- Color range
self.curvatureColorRangeWidget = ctk.ctkRangeWidget()
self.curvatureColorRangeWidget.setToolTip("Set color range")
self.curvatureColorRangeWidget.setDecimals(3)
self.curvatureColorRangeWidget.singleStep = 0.001
self.curvatureColorRangeWidget.minimumValue = 0.0
self.curvatureColorRangeWidget.maximumValue = 0.5
self.curvatureColorRangeWidget.minimum = 0.0
self.curvatureColorRangeWidget.maximum = 1.0
curvatureFormLayout.addRow("Color range: ",
self.curvatureColorRangeWidget)
self.curvatureColorRangeWidget.connect(
'valuesChanged(double, double)', self.onUpdateCurvatureColorRange)
#-- Curvature data
self.meanCurvatureLineEdit = qt.QLineEdit()
self.meanCurvatureLineEdit.text = '--'
self.meanCurvatureLineEdit.readOnly = True
self.meanCurvatureLineEdit.frame = True
self.meanCurvatureLineEdit.styleSheet = "QLineEdit { background:transparent; }"
self.meanCurvatureLineEdit.cursor = qt.QCursor(qt.Qt.IBeamCursor)
self.meanCurvatureLineEdit.enabled = False
curvatureFormLayout.addRow("Mean (mm^-1):", self.meanCurvatureLineEdit)
self.minCurvatureLineEdit = qt.QLineEdit()
self.minCurvatureLineEdit.text = '--'
self.minCurvatureLineEdit.readOnly = True
self.minCurvatureLineEdit.frame = True
self.minCurvatureLineEdit.styleSheet = "QLineEdit { background:transparent; }"
self.minCurvatureLineEdit.cursor = qt.QCursor(qt.Qt.IBeamCursor)
self.minCurvatureLineEdit.enabled = False
curvatureFormLayout.addRow("Minimum (mm^-1):",
self.minCurvatureLineEdit)
self.maxCurvatureLineEdit = qt.QLineEdit()
self.maxCurvatureLineEdit.text = '--'
self.maxCurvatureLineEdit.readOnly = True
self.maxCurvatureLineEdit.frame = True
self.maxCurvatureLineEdit.styleSheet = "QLineEdit { background:transparent; }"
self.maxCurvatureLineEdit.cursor = qt.QCursor(qt.Qt.IBeamCursor)
self.maxCurvatureLineEdit.enabled = False
curvatureFormLayout.addRow("Maximum (mm^-1):",
self.maxCurvatureLineEdit)
## Create a scale for curvature
self.scalarBarWidget = vtk.vtkScalarBarWidget()
actor = self.scalarBarWidget.GetScalarBarActor()
actor.SetOrientationToVertical()
actor.SetNumberOfLabels(11)
actor.SetTitle("Curvature (mm^-1)")
actor.SetLabelFormat(" %#8.3f")
actor.SetPosition(0.1, 0.1)
actor.SetWidth(0.1)
actor.SetHeight(0.8)
self.scalarBarWidget.SetEnabled(0)
layout = slicer.app.layoutManager()
view = layout.threeDWidget(0).threeDView()
renderer = layout.activeThreeDRenderer()
self.scalarBarWidget.SetInteractor(
renderer.GetRenderWindow().GetInteractor())
self.lookupTable = vtk.vtkLookupTable()
self.lookupTable.SetRange(0.0, 100.0)
self.scalarBarWidget.GetScalarBarActor().SetLookupTable(
self.lookupTable)
## default curvature mode: off
self.curvatureOff.setChecked(True)
self.onCurvatureOff(True)
self.autoCurvatureRangeOff.setChecked(True)
self.onAutoCurvatureRangeOff(True)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
plotFrameLayout.addWidget(self.plotSettingsFrame, 0, 1)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
label = qt.QLabel('Input secondary multivolume')
self.fgSelector = slicer.qMRMLNodeComboBox()
self.fgSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.fgSelector.setMRMLScene(slicer.mrmlScene)
self.fgSelector.addEnabled = 0
self.fgSelector.noneEnabled = 1
self.fgSelector.toolTip = "Secondary multivolume will be used for the secondary \
plot in interactive charting. As an example, this can be used to overlay the \
curve obtained by fitting a model to the data"
inputFrameLayout.addRow(label, self.fgSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
label = qt.QLabel('Current frame number')
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector, 1, 1, 1, 2)
ctrlFrameLayout.addWidget(self.extractButton, 2, 0, 1, 3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode', 'LabelMap',
'1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.chartButton = qt.QPushButton('Chart')
self.chartButton.checkable = False
self.chartButton.connect('clicked()', self.onChartRequested)
plotSettingsFrameLayout.addWidget(label, 0, 0)
plotSettingsFrameLayout.addWidget(self.__fSelector, 0, 1)
plotSettingsFrameLayout.addWidget(self.chartButton, 0, 2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotSettingsFrameLayout.addWidget(self.iCharting, 1, 0, 1, 3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
groupLabel = qt.QLabel('Interactive plotting mode:')
self.iChartingMode = qt.QButtonGroup()
self.iChartingIntensity = qt.QRadioButton('Signal intensity')
#self.iChartingIntensity.tooltip = 'Plot range adjusted dynamically to the range over the time course for the selected pixel'
self.iChartingIntensityFixedAxes = qt.QRadioButton(
'Fixed range intensity')
#self.iChartingIntensityFixedAxes.tooltip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.iChartingPercent = qt.QRadioButton('Percent change')
#self.iChartingPercent.tooltip = 'Percent change relative to the average of the first N frames (parameter set below)'
self.iChartingIntensity.setChecked(1)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(groupLabel)
self.groupLayout.addRow(self.iChartingIntensity)
self.groupLayout.addRow(self.iChartingIntensityFixedAxes)
self.groupLayout.addRow(self.iChartingPercent)
self.baselineFrames = qt.QSpinBox()
self.baselineFrames.minimum = 1
label = qt.QLabel('Number of frames for baseline calculation')
self.groupLayout.addRow(label, self.baselineFrames)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for X axis')
self.groupLayout.addRow(self.xLogScaleCheckBox, label)
self.xLogScaleCheckBox.connect('stateChanged(int)',
self.onXLogScaleRequested)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for Y axis')
self.groupLayout.addRow(self.yLogScaleCheckBox, label)
self.yLogScaleCheckBox.connect('stateChanged(int)',
self.onYLogScaleRequested)
plotSettingsFrameLayout.addWidget(self.groupWidget, 2, 0)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView, 3, 0, 1, 3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def setupFeaturePanelList(self):
featurePanelList = self.createFeaturePanels()
self.collapsibleButtonGroup = qt.QButtonGroup()
for panel in featurePanelList:
self.collapsibleButtonGroup.addButton(panel)
def setup(self):
"""This is called one time when the module GUI is initialized
"""
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self.logic = CIP_PAARatioLogic()
#
# Create all the widgets. Example Area
mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
mainAreaCollapsibleButton.text = "Main parameters"
self.layout.addWidget(mainAreaCollapsibleButton)
self.mainAreaLayout = qt.QGridLayout(mainAreaCollapsibleButton)
self.label = qt.QLabel("Select the volume")
self.label.setStyleSheet("margin:10px 0 20px 7px")
self.mainAreaLayout.addWidget(self.label, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
# DEPRECATED. Now there is a new vtkMRMLLabelMapNode
#self.volumeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "0" ) # No labelmaps
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = True
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setStyleSheet(
"margin:0px 0 0px 0; padding:2px 0 2px 5px")
self.mainAreaLayout.addWidget(self.volumeSelector, 0, 1)
# self.label2 = qt.QLabel("Select the slice")
# self.label2.setStyleSheet("margin:0px 0 20px 7px; padding-top:20px")
# self.mainAreaLayout.addWidget(self.label2, 1, 0)
self.placeDefaultRulersButton = ctk.ctkPushButton()
self.placeDefaultRulersButton.text = "Place default rulers"
# self.placeDefaultRulersSliceButton.toolTip = "Navigate to the best estimated slice to place the rulers"
self.placeDefaultRulersButton.setIcon(
qt.QIcon("{0}/next.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeDefaultRulersButton.setIconSize(qt.QSize(20, 20))
self.placeDefaultRulersButton.setStyleSheet("font-weight: bold;")
# self.placeDefaultRulersButton.setFixedWidth(140)
self.mainAreaLayout.addWidget(self.placeDefaultRulersButton, 1, 1)
### Structure Selector
self.structuresGroupbox = qt.QGroupBox("Select the structure")
self.groupboxLayout = qt.QVBoxLayout()
self.structuresGroupbox.setLayout(self.groupboxLayout)
self.mainAreaLayout.addWidget(self.structuresGroupbox, 2, 0)
self.structuresButtonGroup = qt.QButtonGroup()
# btn = qt.QRadioButton("None")
# btn.visible = False
# self.structuresButtonGroup.addButton(btn)
# self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Both")
btn.checked = True
self.structuresButtonGroup.addButton(btn, 0)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Pulmonary Arterial")
self.structuresButtonGroup.addButton(btn, 1)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Aorta")
self.structuresButtonGroup.addButton(btn, 2)
self.groupboxLayout.addWidget(btn)
### Buttons toolbox
self.buttonsToolboxFrame = qt.QFrame()
self.buttonsToolboxLayout = qt.QGridLayout()
self.buttonsToolboxFrame.setLayout(self.buttonsToolboxLayout)
self.mainAreaLayout.addWidget(self.buttonsToolboxFrame, 2, 1)
self.placeRulersButton = ctk.ctkPushButton()
self.placeRulersButton.text = "Place ruler/s"
self.placeRulersButton.toolTip = "Place the ruler/s for the selected structure/s in the current slice"
self.placeRulersButton.setIcon(
qt.QIcon("{0}/ruler.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeRulersButton.setIconSize(qt.QSize(20, 20))
self.placeRulersButton.setFixedWidth(105)
self.placeRulersButton.setStyleSheet("font-weight:bold")
self.buttonsToolboxLayout.addWidget(self.placeRulersButton, 0, 0)
self.moveUpButton = ctk.ctkPushButton()
self.moveUpButton.text = "Move up"
self.moveUpButton.toolTip = "Move the selected ruler/s one slice up"
self.moveUpButton.setIcon(
qt.QIcon("{0}/move_up.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveUpButton.setIconSize(qt.QSize(20, 20))
self.moveUpButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveUpButton, 0, 1)
self.moveDownButton = ctk.ctkPushButton()
self.moveDownButton.text = "Move down"
self.moveDownButton.toolTip = "Move the selected ruler/s one slice down"
self.moveDownButton.setIcon(
qt.QIcon("{0}/move_down.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveDownButton.setIconSize(qt.QSize(20, 20))
self.moveDownButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveDownButton, 0, 2)
self.removeButton = ctk.ctkPushButton()
self.removeButton.text = "Remove ALL rulers"
self.removeButton.toolTip = "Remove all the rulers for this volume"
self.removeButton.setIcon(
qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeButton.setIconSize(qt.QSize(20, 20))
self.buttonsToolboxLayout.addWidget(self.removeButton, 1, 1, 1, 2, 2)
### Textboxes
self.textboxesFrame = qt.QFrame()
self.textboxesLayout = qt.QFormLayout()
self.textboxesFrame.setLayout(self.textboxesLayout)
self.textboxesFrame.setFixedWidth(190)
self.mainAreaLayout.addWidget(self.textboxesFrame, 3, 0)
self.paTextBox = qt.QLineEdit()
self.paTextBox.setReadOnly(True)
self.textboxesLayout.addRow("PA (mm): ", self.paTextBox)
self.aortaTextBox = qt.QLineEdit()
self.aortaTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Aorta (mm): ", self.aortaTextBox)
self.ratioTextBox = qt.QLineEdit()
self.ratioTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Ratio PA/A: ", self.ratioTextBox)
# Save case data
self.reportsCollapsibleButton = ctk.ctkCollapsibleButton()
self.reportsCollapsibleButton.text = "Reporting"
self.layout.addWidget(self.reportsCollapsibleButton)
self.reportsLayout = qt.QHBoxLayout(self.reportsCollapsibleButton)
self.storedColumnNames = [
"caseId", "paDiameter_mm", "aortaDiameter_mm", "pa1r", "pa1a",
"pa1s", "pa2r", "pa2a", "pa2s", "a1r", "a1a", "a1s", "a2r", "a2a",
"a2s"
]
self.reportsWidget = CaseReportsWidget(
"CIP_PAARatio",
columnNames=self.storedColumnNames,
parentWidget=self.reportsCollapsibleButton)
self.reportsWidget.setup()
self.switchToRedView()
#####
# Case navigator
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
self.layout.addStretch()
# Connections
self.observers = []
self.__addSceneObservables__()
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onVolumeSelectorChanged)
self.placeDefaultRulersButton.connect('clicked()',
self.oPlaceDefaultRulersClicked)
self.placeRulersButton.connect('clicked()', self.onPlaceRulersClicked)
self.moveUpButton.connect('clicked()', self.onMoveUpRulerClicked)
self.moveDownButton.connect('clicked()', self.onMoveDownRulerClicked)
self.removeButton.connect('clicked()', self.onRemoveRulerClicked)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
