def setupOptionsFrame(self):
# Autoscroll range slider
self.autoscrollRangeSlider = slicer.qMRMLSliderWidget()
self.autoscrollRangeSlider.setMRMLScene(slicer.mrmlScene)
self.autoscrollRangeSlider.minimum = 0
self.autoscrollRangeSlider.maximum = 10
self.autoscrollRangeSlider.value = 5
self.autoscrollRangeSlider.setToolTip(
'How many slices you would like to autoscroll up and down')
self.scriptedEffect.addLabeledOptionsWidget("Slice range:",
self.autoscrollRangeSlider)
# Autoscroll speed slider
self.autoscrollSpeedSlider = slicer.qMRMLSliderWidget()
self.autoscrollSpeedSlider.setMRMLScene(slicer.mrmlScene)
self.autoscrollSpeedSlider.minimum = 1
self.autoscrollSpeedSlider.maximum = 100
self.autoscrollSpeedSlider.value = 20
self.autoscrollSpeedSlider.setToolTip(
'How many slices you want to autoscroll per second')
self.scriptedEffect.addLabeledOptionsWidget("Slice speed:",
self.autoscrollSpeedSlider)
# Input view selector
self.sliceNodeSelector = qt.QComboBox()
self.sliceNodeSelector.setToolTip(
"This slice will be excluded during autoscrolling.")
self.scriptedEffect.addLabeledOptionsWidget("Exclude view:",
self.sliceNodeSelector)
# Start button
self.applyButton = qt.QPushButton("Start")
self.applyButton.objectName = self.__class__.__name__ + 'Start'
self.applyButton.setToolTip("Start/Stop autoscrolling (Alt+C)")
self.scriptedEffect.addOptionsWidget(self.applyButton)
# Set Hotkeys
self.hotkey = qt.QShortcut(qt.QKeySequence("Alt+C"),
slicer.util.mainWindow())
self.hotkey2 = qt.QShortcut(qt.QKeySequence("Ctrl+Alt+C"),
slicer.util.mainWindow())
# Connections
self.applyButton.connect('clicked()', self.onApply)
self.sliceNodeSelector.connect("currentIndexChanged(int)",
self.updateGUIFromMRML)
self.hotkey.connect('activated()', self.autoscrollHotkey)
self.hotkey2.connect('activated()', self.openSettings)
# Initialize variables
self.setupVariables()
def setup(self):
self.coefficientsSlider = slicer.qMRMLSliderWidget()
self.coefficientsSlider.singleStep = 0.01
self.coefficientsSlider.maximum = 2
self.coefficientsSlider.value = self.getDefaultValue('coefficients')
self.layout.addRow('Coefficients: ', self.coefficientsSlider)
self.orderSpinBox = qt.QSpinBox()
self.orderSpinBox.maximum = 6
self.orderSpinBox.value = self.getDefaultValue('order')
self.layout.addRow('Polynomial order: ', self.orderSpinBox)
def setup(self):
self.numSpikesSpinBox = qt.QSpinBox()
self.numSpikesSpinBox.maximum = 10
self.numSpikesSpinBox.value = self.getDefaultValue('num_spikes')
self.layout.addRow('Spikes: ', self.numSpikesSpinBox)
self.intensitySlider = slicer.qMRMLSliderWidget()
self.intensitySlider.singleStep = 0.01
self.intensitySlider.maximum = 5
self.intensitySlider.value = np.mean(self.getDefaultValue('intensity'))
self.layout.addRow('Intensity: ', self.intensitySlider)
def setup(self):
self.numGhostsSpinBox = qt.QSpinBox()
self.numGhostsSpinBox.maximum = 50
default = int(np.mean(self.getDefaultValue('num_ghosts')))
self.numGhostsSpinBox.value = default
self.layout.addRow('Ghosts: ', self.numGhostsSpinBox)
self.axesLayout, self.axesDict = self.makeAxesLayout()
self.layout.addRow('Axes: ', self.axesLayout)
self.intensitySlider = slicer.qMRMLSliderWidget()
self.intensitySlider.singleStep = 0.01
self.intensitySlider.maximum = 1
self.intensitySlider.value = np.mean(self.getDefaultValue('intensity'))
self.layout.addRow('Intensity: ', self.intensitySlider)
def setupOptionsFrame(self):
AbstractScriptedSegmentEditorAutoCompleteEffect.setupOptionsFrame(self)
# Object scale slider
self.objectScaleMmSlider = slicer.qMRMLSliderWidget()
self.objectScaleMmSlider.setMRMLScene(slicer.mrmlScene)
self.objectScaleMmSlider.quantity = "length" # get unit, precision, etc. from MRML unit node
self.objectScaleMmSlider.minimum = 0
self.objectScaleMmSlider.maximum = 10
self.objectScaleMmSlider.value = 2.0
self.objectScaleMmSlider.setToolTip(
'Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection.'
)
self.scriptedEffect.addLabeledOptionsWidget("Object scale:",
self.objectScaleMmSlider)
self.objectScaleMmSlider.connect('valueChanged(double)',
self.updateAlgorithmParameterFromGUI)
def setupOptionsFrame(self):
# Object scale slider
self.objectScaleMmSlider = slicer.qMRMLSliderWidget()
self.objectScaleMmSlider.setMRMLScene(slicer.mrmlScene)
self.objectScaleMmSlider.quantity = "length" # get unit, precision, etc. from MRML unit node
self.objectScaleMmSlider.minimum = 0
self.objectScaleMmSlider.maximum = 10
self.objectScaleMmSlider.value = 2.0
self.objectScaleMmSlider.setToolTip('Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection.')
self.scriptedEffect.addLabeledOptionsWidget("Object scale:", self.objectScaleMmSlider)
self.objectScaleMmSlider.connect('valueChanged(double)', self.updateMRMLFromGUI)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Accept previewed result")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
def setupOptionsFrame(self):
# Object scale slider
self.objectScaleMmSlider = slicer.qMRMLSliderWidget()
self.objectScaleMmSlider.setMRMLScene(slicer.mrmlScene)
self.objectScaleMmSlider.quantity = "length" # get unit, precision, etc. from MRML unit node
self.objectScaleMmSlider.minimum = 0
self.objectScaleMmSlider.maximum = 10
self.objectScaleMmSlider.value = 2.0
self.objectScaleMmSlider.setToolTip('Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection.')
self.scriptedEffect.addLabeledOptionsWidget("Object scale:", self.objectScaleMmSlider)
self.objectScaleMmSlider.connect('valueChanged(double)', self.updateMRMLFromGUI)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Accept previewed result")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
def setupOptionsFrame(self):
AbstractScriptedSegmentEditorAutoCompleteEffect.setupOptionsFrame(self)
# Object scale slider
self.seedLocalityFactorSlider = slicer.qMRMLSliderWidget()
self.seedLocalityFactorSlider.setMRMLScene(slicer.mrmlScene)
self.seedLocalityFactorSlider.minimum = 0
self.seedLocalityFactorSlider.maximum = 10
self.seedLocalityFactorSlider.value = 0.0
self.seedLocalityFactorSlider.decimals = 1
self.seedLocalityFactorSlider.singleStep = 0.1
self.seedLocalityFactorSlider.pageStep = 1.0
self.seedLocalityFactorSlider.setToolTip(
'Increasing this value makes the effect of seeds more localized,'
' thereby reducing leaks, but requires seed regions to be more evenly distributed in the image.'
' The value is specified as an additional "intensity level difference" per "unit distance."'
)
self.scriptedEffect.addLabeledOptionsWidget(
"Seed locality:", self.seedLocalityFactorSlider)
self.seedLocalityFactorSlider.connect(
'valueChanged(double)', self.updateAlgorithmParameterFromGUI)
def setup(self):
# this is the function that implements all GUI
ScriptedLoadableModuleWidget.setup(self)
# This sets the view being used to the red view only
slicer.app.layoutManager().setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#Section 3.2.1: Ultrasound connection ang widgets
#the following code provides a GUI to connect to an external ultrasound scanner throught the PlusServer
#this section also provides examples of other widgets that can be used
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
##################################################################################################################
#This section creates all the widgets
#This is where you will create the type of widget and what it will say
##################################################################################################################
#This code block creates a collapsible button
#This defines which type of button you are using
self.usButton = ctk.ctkCollapsibleButton()
#This is what the button will say
self.usButton.text = "Ultrasound Connection"
#This actually creates that button
#This descirbes the type of widget
self.inputIPLineEdit = qt.QLineEdit()
#This sets a placehoder example of what should be inputted to the line edit
self.inputIPLineEdit.setPlaceholderText("127.0.0.1")
#This is the help tooltip
self.inputIPLineEdit.toolTip = "Put the IP address of your ultrasound device here"
#This code block is the exact same as the one above only it asks for the server port
self.inputPortLineEdit = qt.QLineEdit()
self.inputPortLineEdit.setPlaceholderText("18944")
self.inputPortLineEdit.setValidator(qt.QIntValidator())
self.inputPortLineEdit.toolTip = "Put the port ID of the OpenIGTLink here (18944)"
#This is a push button
self.connectButton = qt.QPushButton()
self.connectButton.setDefault(False)
#This button says connect
self.connectButton.text = "Connect"
#help tooltip that explains the funciton
self.connectButton.toolTip = "Connects to Ultrasound"
#adds the widget to the layout
self.freezeButton = qt.QPushButton()
self.freezeButton.text = "Freeze"
self.freezeButton.toolTip = "Freeze the ultrasound image for fiducial placement"
# Combobox for image selection
self.imageSelector = slicer.qMRMLNodeComboBox()
self.imageSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.imageSelector.selectNodeUponCreation = True
self.imageSelector.addEnabled = False
self.imageSelector.removeEnabled = False
self.imageSelector.noneEnabled = True
self.imageSelector.showHidden = False
self.imageSelector.showChildNodeTypes = False
self.imageSelector.setMRMLScene(slicer.mrmlScene)
self.imageSelector.setToolTip("Pick the image to be used.")
self.checkBox = qt.QCheckBox()
self.checkBox.text = "This is a check box"
self.checkBox.toolTip = "This an example check box"
#### EXAMPLE: to access the functionality of a check box you can use an if statement
#### if self.checkBox.isChecked() == True:
self.radioButton = qt.QRadioButton()
self.radioButton.text = "This is an example radio button"
self.radioButton.toolTip = "This an example radio button"
self.sliderWidget = slicer.qMRMLSliderWidget()
self.sliderWidget.minimum = 0.00
self.sliderWidget.maximum = 100.00
self.resetButton = qt.QPushButton('Reset')
self.resetButton.setDefault(False)
self.resetButton.toolTip = "This Button Resets the Module"
##################################################################################################################
#This section adds the containers to the parent widget
##################################################################################################################
self.layout.addWidget(self.usButton)
#This creates a variable that describes layout within this collapsible button
self.usLayout = qt.QFormLayout(self.usButton)
self.usLayout.addRow("Server IP:", self.inputIPLineEdit)
self.usLayout.addRow("Server Port:", self.inputPortLineEdit)
self.usLayout.addWidget(self.connectButton)
self.usLayout.addRow("US Volume: ", self.imageSelector)
self.usLayout.addRow(self.freezeButton)
self.shortcut = qt.QShortcut(qt.QKeySequence('f'),
slicer.util.mainWindow())
self.usLayout.addRow(self.checkBox)
self.usLayout.addRow(self.radioButton)
self.usLayout.addRow(self.sliderWidget)
# Add vertical spacer
self.layout.addStretch(1)
##################################################################################################################
#This section connects the widgets to functions
##################################################################################################################
self.connectButton.connect('clicked(bool)',
self.onConnectButtonClicked)
self.freezeButton.connect('clicked(bool)', self.onConnectButtonClicked)
self.inputIPLineEdit.connect('textChanged(QString)',
self.onInputChanged)
self.inputPortLineEdit.connect('textChanged(QString)',
self.onInputChanged)
self.imageSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onImageChanged)
# Disable buttons until conditions are met
self.connectButton.setEnabled(False)
self.freezeButton.setEnabled(False)
def createSliderWidget(self, minimum, maximum):
slider = slicer.qMRMLSliderWidget()
slider.minimum = minimum
slider.maximum = maximum
return slider
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
# Input file
# Text + Button invoking QFileDialog
self.inputFileLayout = qt.QHBoxLayout()
self.inputFileLabelHeader = qt.QLabel()
self.inputFileLabelHeader.text = "Input File: "
self.inputFileLabelFile = qt.QLabel()
self.inputFileLabelFile.text = "Input header.xml or .m3d"
self.inputFileButton = qt.QPushButton()
self.inputFileButton.text = "Browse"
self.inputFileLayout.addWidget(self.inputFileLabelHeader)
self.inputFileLayout.addWidget(self.inputFileLabelFile)
self.inputFileLayout.addWidget(self.inputFileButton)
self.layout.addLayout(self.inputFileLayout)
#
# Parameters Area
#
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.collapsed = True
self.parametersCollapsibleButton.text = "Parameters for legacy m3d format"
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(self.parametersCollapsibleButton)
# set distance of fold curve from interior points
self.distSlider = slicer.qMRMLSliderWidget()
self.distSlider.setProperty('maximum', 0.6)
self.distSlider.setProperty('minimum', 0.0)
self.distSlider.setProperty('singleStep', 0.01)
self.distSlider.setToolTip(
"Parameter used in transformation from legacy s-rep to new s-rep")
parametersFormLayout.addRow("Set distance to expand fold curve",
self.distSlider)
self.outputFolderLayout = qt.QHBoxLayout()
self.outputFolderLabelHeader = qt.QLabel()
self.outputFolderLabelHeader.text = "Output folder: "
self.outputFolderLabelFile = qt.QLabel()
self.outputFolderLabelFile.text = "Folder to save the new xml format"
self.outputFolderButton = qt.QPushButton()
self.outputFolderButton.text = "Browse"
self.outputFolderLayout.addWidget(self.outputFolderLabelHeader)
self.outputFolderLayout.addWidget(self.outputFolderLabelFile)
self.outputFolderLayout.addWidget(self.outputFolderButton)
parametersFormLayout.addRow(self.outputFolderLayout)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Visualize s-rep file")
self.applyButton.toolTip = "Parse and visualize s-rep."
self.layout.addWidget(self.applyButton)
# Unused
# self.boundarySurfaceRendering = qt.QCheckBox()
# self.boundarySurfaceRendering.checked = 0
# self.boundarySurfaceRendering.setToolTip("If checked, set the visibility of the boundary mesh")
# self.layout.addWidget(self.boundarySurfaceRendering)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputFileButton.connect('clicked(bool)',
self.onInputFileButtonClicked)
self.outputFolderButton.connect('clicked(bool)',
self.onOutputFolderButtonClicked)
# Add vertical spacer
self.layout.addStretch(1)
def createSliderWidget(self, minimum, maximum): slider = slicer.qMRMLSliderWidget() slider.minimum = minimum slider.maximum = maximum return slider
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)
#
# input volume selector
#
# self.inputSelector = slicer.qMRMLNodeComboBox()
# self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
# self.inputSelector.selectNodeUponCreation = True
# self.inputSelector.addEnabled = False
# self.inputSelector.removeEnabled = False
# self.inputSelector.noneEnabled = False
# self.inputSelector.showHidden = False
# self.inputSelector.showChildNodeTypes = False
# self.inputSelector.setMRMLScene(slicer.mrmlScene)
# self.inputSelector.setToolTip("Pick the input to the algorithm.")
# parametersFormLayout.addRow("Input Volume: ", self.inputSelector)
# set distance of fold curve from interior points
self.distSlider = slicer.qMRMLSliderWidget()
# self.distSlider.setMaximum(0.6)
# self.distSlider.setMinimum(0.0)
self.distSlider.setProperty('maximum', 0.6)
self.distSlider.setProperty('minimum', 0.0)
self.distSlider.setProperty('singleStep', 0.01)
# self.distSlider.setValue(0.02)
self.distSlider.setToolTip(
"Parameter used in transformation from legacy s-rep to new s-rep")
parametersFormLayout.addRow("Set distance to expand fold curve",
self.distSlider)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Select s-rep file")
self.applyButton.toolTip = "Run the algorithm."
parametersFormLayout.addRow(self.applyButton)
self.boundarySurfaceRendering = qt.QCheckBox()
self.boundarySurfaceRendering.checked = 0
self.boundarySurfaceRendering.setToolTip(
"If checked, set the visibility of the boundary mesh")
parametersFormLayout.addRow("Show Boundary Mesh",
self.boundarySurfaceRendering)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.setupViewSettingsArea()
# Setup a logger for the extension log messages
self.logger = logging.getLogger('SlicerCaseIterator')
self.logic = None
# These variables hold connections to other parts of Slicer, such as registered keyboard shortcuts and
# Event observers
self.shortcuts = []
self.observers = []
# Instantiate and connect widgets ...
#
# ComboBox for mode selection
#
self.modeGroup = qt.QGroupBox("Mode Selection")
self.modeGroup.setLayout(qt.QFormLayout())
self.layout.addWidget(self.modeGroup)
modes = IteratorFactory.getImplementationNames()
self.modeComboBox = qt.QComboBox()
self.modeComboBox.addItems([""] + modes)
self.modeGroup.layout().addWidget(self.modeComboBox)
#
# Select and Load input data section
#
self.inputDataCollapsibleButton = ctk.ctkCollapsibleButton()
self.inputDataCollapsibleButton.text = 'Select and Load case data'
self.layout.addWidget(self.inputDataCollapsibleButton)
#
# Parameters Area
#
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = 'Case iteration parameters'
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(self.parametersCollapsibleButton)
#
# Reader Name
#
self.txtReaderName = qt.QLineEdit()
self.txtReaderName.text = ''
self.txtReaderName.toolTip = 'Name of the current reader; if not empty, this name will be added to the filename ' \
'of saved masks'
parametersFormLayout.addRow('Reader name', self.txtReaderName)
#
# Start position
#
self.npStart = qt.QSpinBox()
self.npStart.minimum = 1
self.npStart.maximum = 999999
self.npStart.value = 1
self.npStart.toolTip = 'Start position in the CSV file (1 = first patient)'
parametersFormLayout.addRow('Start position', self.npStart)
#
# Visualization Properties
#
self.visualizationPropertiesCollapsibleButton = ctk.ctkCollapsibleButton(
)
self.visualizationPropertiesCollapsibleButton.text = 'Visualization properties'
self.layout.addWidget(self.visualizationPropertiesCollapsibleButton)
visualizationPropertiesFormLayout = qt.QVBoxLayout(
self.visualizationPropertiesCollapsibleButton)
#
# Mask Groupbox
#
self.maskGroup = qt.QGroupBox("Mask")
self.maskGroup.setLayout(qt.QFormLayout())
visualizationPropertiesFormLayout.addWidget(self.maskGroup)
self.sliceFill2DSlider = slicer.qMRMLSliderWidget()
self.sliceFill2DSlider.minimum = 0.0
self.sliceFill2DSlider.maximum = 1.0
self.sliceFill2DSlider.singleStep = 0.1
self.maskGroup.layout().addRow("Slice 2D fill:",
self.sliceFill2DSlider)
self.sliceOutline2DSlider = slicer.qMRMLSliderWidget()
self.sliceOutline2DSlider.minimum = 0.0
self.sliceOutline2DSlider.maximum = 1.0
self.sliceOutline2DSlider.singleStep = 0.1
self.sliceOutline2DSlider.value = 1.0
self.maskGroup.layout().addRow("Slice 2D outline:",
self.sliceOutline2DSlider)
#
# Progressbar
#
self.progressBar = qt.QProgressBar()
self.progressBar.setFormat("%v/%m")
self.progressBar.visible = False
self.layout.addWidget(self.progressBar)
#
# Case Button Row
#
self.caseButtonWidget = qt.QWidget()
self.caseButtonWidget.setLayout(qt.QHBoxLayout())
self.layout.addWidget(self.caseButtonWidget)
#
# Reset
#
self.resetButton = qt.QPushButton('Start Batch')
self.resetButton.enabled = False
self.caseButtonWidget.layout().addWidget(self.resetButton)
#
# Previous Case
#
self.previousButton = qt.QPushButton('Previous Case')
self.previousButton.enabled = False
self.previousButton.toolTip = '(Ctrl+P) Press this button to go to the previous case, previous new masks are not reloaded'
self.caseButtonWidget.layout().addWidget(self.previousButton)
#
# Load CSV / Next Case
#
self.nextButton = qt.QPushButton('Next Case')
self.nextButton.enabled = False
self.nextButton.toolTip = '(Ctrl+N) Press this button to go to the next case'
self.caseButtonWidget.layout().addWidget(self.nextButton)
#
# Collapsible Button group for enabling only one at a time
#
self.collapsibleButtonGroup = qt.QButtonGroup()
self.collapsibleButtonGroup.setExclusive(True)
self.collapsibleButtonGroup.addButton(self.inputDataCollapsibleButton)
self.collapsibleButtonGroup.addButton(self.parametersCollapsibleButton)
self.collapsibleButtonGroup.addButton(
self.visualizationPropertiesCollapsibleButton)
self.layout.addStretch(1)
#
# Connect buttons to functions
#
self.modeComboBox.currentTextChanged.connect(self.onModeSelected)
self.previousButton.connect('clicked(bool)', self.onPrevious)
self.nextButton.connect('clicked(bool)', self.onNext)
self.resetButton.connect('clicked(bool)', self.onReset)
self.sliceFill2DSlider.valueChanged.connect(
lambda value: self.updateSegmentationProperties())
self.sliceOutline2DSlider.valueChanged.connect(
lambda value: self.updateSegmentationProperties())
if len(modes) == 1:
self.modeComboBox.hide()
self.onModeSelected(modes[1])
self._setGUIstate(csv_loaded=False)
