def makePyramidWidgets(self):
self.pyramidTab = qt.QWidget()
self.parametersTabWidget.addTab(self.pyramidTab, 'Pyramid levels')
self.pyramidLayout = qt.QGridLayout(self.pyramidTab)
self.pyramidHighestSpinBox = qt.QSpinBox()
self.pyramidHighestSpinBox.value = 3
self.pyramidHighestSpinBox.setAlignment(qt.Qt.AlignCenter)
self.pyramidHighestSpinBox.valueChanged.connect(
self.onPyramidLevelsChanged)
self.pyramidHighestLabel = qt.QLabel()
self.pyramidHighestLabel.setAlignment(qt.Qt.AlignCenter)
self.pyramidLayout.addWidget(qt.QLabel('Highest:'), 0, 0)
self.pyramidLayout.addWidget(self.pyramidHighestSpinBox, 0, 1)
self.pyramidLayout.addWidget(self.pyramidHighestLabel, 0, 2)
self.pyramidLowestSpinBox = qt.QSpinBox()
self.pyramidLowestSpinBox.value = 2
self.pyramidLowestSpinBox.setAlignment(qt.Qt.AlignCenter)
self.pyramidLowestSpinBox.valueChanged.connect(
self.onPyramidLevelsChanged)
self.pyramidLowestLabel = qt.QLabel()
self.pyramidLowestLabel.setAlignment(qt.Qt.AlignCenter)
self.pyramidLayout.addWidget(qt.QLabel('Lowest:'), 1, 0)
self.pyramidLayout.addWidget(self.pyramidLowestSpinBox, 1, 1)
self.pyramidLayout.addWidget(self.pyramidLowestLabel, 1, 2)
self.pyramidGaussianFilteringCheckBox = qt.QCheckBox()
self.pyramidLayout.addWidget(qt.QLabel('Gaussian filtering:'), 2, 0)
self.pyramidLayout.addWidget(self.pyramidGaussianFilteringCheckBox, 2,
1)
def setupOptionsFrame(self):
# input volume selector
self.inputVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputVolumeSelector.selectNodeUponCreation = True
self.inputVolumeSelector.addEnabled = True
self.inputVolumeSelector.removeEnabled = True
self.inputVolumeSelector.noneEnabled = True
self.inputVolumeSelector.noneDisplay = "(Master volume)"
self.inputVolumeSelector.showHidden = False
self.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeSelector.setToolTip(
"Volume to split. Default is current master volume node.")
self.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.updateMRMLFromGUI)
inputLayout = qt.QHBoxLayout()
inputLayout.addWidget(self.inputVolumeSelector)
self.scriptedEffect.addLabeledOptionsWidget("Input Volume: ",
inputLayout)
# Pad size
self.padEdit = qt.QSpinBox()
self.padEdit.setToolTip(
"Choose the number of voxels used to pad the image in each dimension"
)
self.padEdit.minimum = 0
self.padEdit.maximum = 1000
self.padEdit.connect("valueChanged(int)", self.updateMRMLFromGUI)
self.padLabel = qt.QLabel("Pad voxels: ")
# Fill value layouts
# addWidget(*Widget, row, column, rowspan, colspan)
padValueLayout = qt.QFormLayout()
padValueLayout.addRow(self.padLabel, self.padEdit)
self.scriptedEffect.addOptionsWidget(padValueLayout)
self.fillValueEdit = qt.QSpinBox()
self.fillValueEdit.setToolTip(
"Choose the voxel intensity that will be used to pad the output volumes."
)
self.fillValueEdit.minimum = -32768
self.fillValueEdit.maximum = 65535
self.fillValueEdit.value = 0
self.fillValueEdit.connect("valueChanged(int)", self.updateMRMLFromGUI)
self.fillValueLabel = qt.QLabel("Fill value: ")
fillValueLayout = qt.QFormLayout()
fillValueLayout.addRow(self.fillValueLabel, self.fillValueEdit)
self.scriptedEffect.addOptionsWidget(fillValueLayout)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip(
"Generate a volume for each visible segment")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
def SetupDoubleSliderControl(self,
WidgetName='Set Threshold',
SpinBoxStep=5):
self.Slider = ctk.ctkDoubleRangeSlider()
self.Label = qt.QLabel(WidgetName)
self.Slider.orientation = 1
self.SpinBoxL = qt.QSpinBox()
self.SpinBoxL.prefix = 'Min: '
self.SpinBoxL.setSingleStep(SpinBoxStep)
self.SpinBoxR = qt.QSpinBox()
self.SpinBoxR.prefix = 'Max: '
self.SpinBoxR.setSingleStep(SpinBoxStep)
ControlHBox = qt.QHBoxLayout()
ControlHBox.addWidget(self.Label)
ControlHBox.addWidget(self.SpinBoxL)
ControlHBox.addWidget(self.Slider)
ControlHBox.addWidget(self.SpinBoxR)
self.DisplayLayout.addRow(ControlHBox)
self.Slider.minimum = 0
self.SpinBoxL.setRange(0, 0)
self.Slider.maximum = 0
self.SpinBoxR.setRange(0, 0)
def __init__(self):
columnNames = ['Convergence', 'Smoothing Sigmas', 'Shrink Factors']
layout = CustomTable.__init__(self, columnNames)
self.view.setItemDelegateForColumn(0, SpinBoxDelegate(self.model))
self.view.setItemDelegateForColumn(1, SpinBoxDelegate(self.model))
self.view.setItemDelegateForColumn(2, SpinBoxDelegate(self.model))
self.smoothingSigmasUnitComboBox = qt.QComboBox()
self.smoothingSigmasUnitComboBox.addItems(['vox', 'mm'])
self.convergenceThresholdSpinBox = qt.QSpinBox()
self.convergenceWindowSizeSpinBox = qt.QSpinBox()
levelsSettingsFrame = qt.QFrame()
levelsSettingsFrame.setLayout(qt.QFormLayout())
levelsSettingsFrame.layout().addRow('Smoothing Sigmas Unit: ',
self.smoothingSigmasUnitComboBox)
levelsSettingsFrame.layout().addRow('Convergence Threshold (1e-N): ',
self.convergenceThresholdSpinBox)
levelsSettingsFrame.layout().addRow('Convergence Window Size: ',
self.convergenceWindowSizeSpinBox)
layout.addWidget(levelsSettingsFrame)
def setupManualIndexesGroupBox(self):
self.zFrameRegistrationManualIndexesGroupBox = qt.QGroupBox("Use manual start/end indexes")
self.zFrameRegistrationManualIndexesGroupBox.setCheckable(True)
self.zFrameRegistrationManualIndexesGroupBoxLayout = qt.QGridLayout()
self.zFrameRegistrationManualIndexesGroupBox.setLayout(self.zFrameRegistrationManualIndexesGroupBoxLayout)
self.zFrameRegistrationManualIndexesGroupBox.checked = False
self.zFrameRegistrationStartIndex = qt.QSpinBox()
self.zFrameRegistrationEndIndex = qt.QSpinBox()
hBox = self.createHLayout([qt.QLabel("start"), self.zFrameRegistrationStartIndex,
qt.QLabel("end"), self.zFrameRegistrationEndIndex])
self.zFrameRegistrationManualIndexesGroupBoxLayout.addWidget(hBox, 1, 1, qt.Qt.AlignRight)
def setupGUIAndConnections(self):
iconSize = qt.QSize(36, 36)
self.inputVolumeGroupBox = qt.QGroupBox()
self.inputVolumeGroupBoxLayout = qt.QFormLayout()
self.inputVolumeGroupBox.setLayout(self.inputVolumeGroupBoxLayout)
self.inputVolumeGroupBox.setFlat(True)
self.zFrameTemplateVolumeSelector = self.createComboBox(
nodeTypes=["vtkMRMLScalarVolumeNode", ""])
self.inputVolumeGroupBoxLayout.addRow(
"ZFrame template volume: ", self.zFrameTemplateVolumeSelector)
self.layout.addWidget(self.inputVolumeGroupBox)
self.layout.addStretch()
self.zFrameRegistrationManualIndexesGroupBox = qt.QGroupBox(
"Use manual start/end indexes")
self.zFrameRegistrationManualIndexesGroupBox.setCheckable(True)
self.zFrameRegistrationManualIndexesGroupBoxLayout = qt.QGridLayout()
self.zFrameRegistrationManualIndexesGroupBox.setLayout(
self.zFrameRegistrationManualIndexesGroupBoxLayout)
self.zFrameRegistrationManualIndexesGroupBox.checked = False
self.zFrameRegistrationStartIndex = qt.QSpinBox()
self.zFrameRegistrationEndIndex = qt.QSpinBox()
hBox = qt.QWidget()
hBox.setLayout(qt.QHBoxLayout())
hBox.layout().addWidget(qt.QLabel("start"))
hBox.layout().addWidget(self.zFrameRegistrationStartIndex)
hBox.layout().addWidget(qt.QLabel("end"))
hBox.layout().addWidget(self.zFrameRegistrationEndIndex)
self.zFrameRegistrationManualIndexesGroupBoxLayout.addWidget(
hBox, 1, 1, qt.Qt.AlignRight)
self.runZFrameRegistrationButton = self.createButton(
"",
enabled=False,
icon=Icons.apply,
iconSize=iconSize,
toolTip="Run ZFrame Registration")
self.retryZFrameRegistrationButton = self.createButton(
"",
enabled=False,
icon=Icons.retry,
iconSize=iconSize,
toolTip="Reset")
self.layout.addWidget(self.zFrameRegistrationManualIndexesGroupBox)
widget = qt.QWidget()
widget.setLayout(qt.QHBoxLayout())
widget.layout().addWidget(self.runZFrameRegistrationButton)
widget.layout().addWidget(self.retryZFrameRegistrationButton)
self.layout.addWidget(widget)
self.layout.addStretch(1)
self.zFrameTemplateVolumeSelector.connect(
'currentNodeChanged(bool)', self.loadVolumeAndEnableEditor)
self.retryZFrameRegistrationButton.clicked.connect(
self.onRetryZFrameRegistrationButtonClicked)
self.runZFrameRegistrationButton.clicked.connect(
self.onApplyZFrameRegistrationButtonClicked)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Parameters Area
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parametros"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
mainFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# label(mask) value
self.labelROISpin = qt.QSpinBox()
self.labelROISpin.setMinimum(0)
self.labelROISpin.setMaximum(2048)
self.labelROISpin.setToolTip("Valor do Label (cor) para o ROI.")
mainFormLayout.addRow("ROI Label Value", self.labelROISpin)
# label(mask) value
self.labelCortSpin = qt.QSpinBox()
self.labelCortSpin.setMinimum(0)
self.labelCortSpin.setMaximum(2048)
self.labelCortSpin.setToolTip("valor do Label (cor) para o Osso Cortical")
mainFormLayout.addRow("Osso Cortical Label Value", self.labelCortSpin)
# Apply Button
self.applyButton = qt.QPushButton("Iniciar")
self.applyButton.toolTip = "Inicie o processamento."
#self.applyButton.enabled = False
mainFormLayout.addRow(self.applyButton)
# Progress Bar
self.progressBar = qt.QProgressBar()
self.progressBar.setMinimum(0)
self.progressBar.setMaximum(100)
self.progressBar.setVisible(False)
mainFormLayout.addRow(self.progressBar)
self.resultButton = qt.QPushButton("Salvar imagens")
#self.resultButton.enabled = False
mainFormLayout.addRow(self.resultButton)
# Add vertical spacer
self.layout.addStretch(1)
# Conexoes
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.resultButton.connect('clicked(bool)', self.onResultButton)
# Refresh Apply button state
self.onSelect()
def setupUI(self):
self.setWindowTitle("Case Number Selection")
self.spinbox = qt.QSpinBox()
self.spinbox.setRange(self.minimum, int("9" * self.CASE_NUMBER_OF_DIGITS))
self.hideInvisibleUnneededComponents()
self.textLabel = qt.QLabel("Please select a case number for the new case.")
self.textLabel.setStyleSheet("font-weight: bold;")
self.previewLabel = qt.QLabel("New case directory:")
self.preview = qt.QLabel()
self.notice = qt.QLabel()
self.notice.setStyleSheet("color:red;")
self.okButton = self.addButton(self.Ok)
self.okButton.enabled = False
self.cancelButton = self.addButton(self.Cancel)
self.setDefaultButton(self.okButton)
self.groupBox = qt.QGroupBox()
self.groupBox.setLayout(qt.QGridLayout())
self.groupBox.layout().addWidget(self.textLabel, 0, 0, 1, 2)
self.groupBox.layout().addWidget(qt.QLabel("Proposed Case Number"), 1, 0)
self.groupBox.layout().addWidget(self.spinbox, 1, 1)
self.groupBox.layout().addWidget(self.previewLabel, 2, 0, 1, 2)
self.groupBox.layout().addWidget(self.preview, 3, 0, 1, 2)
self.groupBox.layout().addWidget(self.notice, 4, 0, 1, 2)
self.groupBox.layout().addWidget(self.okButton, 5, 0)
self.groupBox.layout().addWidget(self.cancelButton, 5, 1)
self.layout().addWidget(self.groupBox, 1, 1)
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the parameters collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# fiber
self.fiberSelector = slicer.qMRMLNodeComboBox(
parametersCollapsibleButton)
self.fiberSelector.nodeTypes = ["vtkMRMLFiberBundleNode"]
self.fiberSelector.selectNodeUponCreation = False
self.fiberSelector.addEnabled = False
self.fiberSelector.removeEnabled = False
self.fiberSelector.noneEnabled = True
self.fiberSelector.showHidden = False
self.fiberSelector.showChildNodeTypes = False
self.fiberSelector.setMRMLScene(slicer.mrmlScene)
self.fiberSelector.setToolTip("Pick the fiber bundle to be converted.")
parametersFormLayout.addRow("Fiber Bundle", self.fiberSelector)
# label map
self.labelSelector = slicer.qMRMLNodeComboBox(
parametersCollapsibleButton)
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip(
"Pick the target label volume. Must already exists in order to define sampling grid. If needed, create one in the Editor module based on template volume."
)
parametersFormLayout.addRow("Target LabelMap", self.labelSelector)
# label value
self.labelValue = qt.QSpinBox(parametersCollapsibleButton)
self.labelValue.setToolTip(
"The numerical value for the rasterized fiber label.")
self.labelValue.setValue(1)
parametersFormLayout.addRow("Label Value", self.labelValue)
# apply
self.applyButton = qt.QPushButton(parametersCollapsibleButton)
self.applyButton.text = "Apply"
parametersFormLayout.addWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
# Add vertical spacer
self.layout.addStretch(1)
def __init__(self, parent=None):
self._window = qt.QDialog(parent)
self._window.setIcon(getPixmap("smart"))
self._window.setCaption(_("New Package Priority"))
self._window.setModal(True)
#self._window.setMinimumSize(600, 400)
vbox = qt.QVBox(self._window)
vbox.setMargin(10)
vbox.setSpacing(10)
vbox.show()
table = qt.QGrid(2, vbox)
table.setSpacing(10)
table.show()
label = qt.QLabel(_("Package Name:"), table)
self._name = qt.QLineEdit(table)
self._name.show()
label = qt.QLabel(_("Channel Alias:"), table)
self._alias = qt.QLineEdit(table)
self._alias.setText("*")
self._alias.show()
label = qt.QLabel(_("Priority:"), table)
self._priority = qt.QSpinBox(table)
self._priority.setSteps(1, 10)
self._priority.setRange(-100000,+100000)
self._priority.show()
sep = qt.QFrame(vbox)
sep.setFrameShape(qt.QFrame.HLine)
sep.setFrameShadow(qt.QFrame.Sunken)
sep.show()
bbox = qt.QHBox(vbox)
bbox.setSpacing(10)
bbox.layout().addStretch(1)
bbox.show()
button = qt.QPushButton(_("Cancel"), bbox)
qt.QObject.connect(button, qt.SIGNAL("clicked()"), self._window, qt.SLOT("reject()"))
button = qt.QPushButton(_("OK"), bbox)
qt.QObject.connect(button, qt.SIGNAL("clicked()"), self._window, qt.SLOT("accept()"))
button.setDefault(True)
vbox.adjustSize()
self._window.adjustSize()
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 _setupColorFrame(self):
self.colorGroupBox = qt.QGroupBox("Color")
self.colorGroupBoxLayout = qt.QHBoxLayout()
self.colorGroupBox.setLayout(self.colorGroupBoxLayout)
self.colorSpin = qt.QSpinBox()
self.colorSpin.objectName = 'ColorSpinBox'
self.colorSpin.setMaximum(64000) # TODO: should be detected from colorNode maximum value
self.colorSpin.setToolTip( "Click colored patch at right to bring up color selection pop up window." )
self.colorGroupBoxLayout.addWidget(self.colorSpin)
self.colorPatch = self.createButton("", objectName="ColorPatchButton")
self.colorGroupBoxLayout.addWidget(self.colorPatch)
self.layout.addWidget(self.colorGroupBox)
def setupUI(self):
self.setWindowTitle("Case Number Selection")
self.setText("Please select a case number for the new case.")
self.setIcon(qt.QMessageBox.Question)
self.spinbox = qt.QSpinBox()
self.spinbox.setRange(self.minimum, int("9"*self.CASE_NUMBER_DIGITS))
self.preview = qt.QLabel()
self.notice = qt.QLabel()
self.layout().addWidget(self.createVLayout([self.createHLayout([qt.QLabel("Proposed Case Number"), self.spinbox]),
self.preview, self.notice]), 2, 1)
self.okButton = self.addButton(self.Ok)
self.okButton.enabled = False
self.cancelButton = self.addButton(self.Cancel)
self.setDefaultButton(self.okButton)
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 addField(self,
key,
label,
value,
ftype,
editable=True,
tip=None,
needed=False):
if ftype is bool:
spacer = qt.QWidget(self._table)
spacer.show()
widget = qt.QCheckBox(label, self._table)
widget.setChecked(value)
else:
_label = qt.QLabel("%s:" % label, self._table)
_label.show()
if tip:
qt.QToolTip.add(_label, tip)
if ftype is int:
widget = qt.QSpinBox(self._table)
widget.setSteps(1, 10)
widget.setRange(-100000, +100000)
widget.setValue(value)
elif ftype is str:
widget = qt.QLineEdit(self._table)
widget.setText(value)
if key in ("alias", "type"):
#widget.setMaxLength(20)
pass # "usually enough for about 15 to 20 characters"
else:
widget.resize(
qt.QSize(widget.sizeHint().width() * 2,
widget.sizeHint().height()))
else:
raise Error, _("Don't know how to handle %s fields") % ftype
widget.show()
widget.setEnabled(bool(editable))
if tip:
qt.QToolTip.add(widget, tip)
self._fields[key] = widget
self._fieldn += 1
def create(self):
self.frame = qt.QFrame(self.parent)
self.frame.objectName = 'EditColorFrame'
self.frame.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.frame)
self.colorFrame = qt.QFrame(self.frame)
self.colorFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.colorFrame)
self.label = qt.QLabel(self.colorFrame)
self.label.setText("Label: ")
self.colorFrame.layout().addWidget(self.label)
self.labelName = qt.QLabel(self.colorFrame)
self.labelName.setText("")
self.colorFrame.layout().addWidget(self.labelName)
self.colorSpin = qt.QSpinBox(self.colorFrame)
self.colorSpin.objectName = 'ColorSpinBox'
self.colorSpin.setMaximum(64000)
self.colorSpin.setValue(EditUtil.getLabel())
self.colorSpin.setToolTip(
"Click colored patch at right to bring up color selection pop up window. Use the 'c' key to bring up color popup menu."
)
self.colorFrame.layout().addWidget(self.colorSpin)
self.colorPatch = qt.QPushButton(self.colorFrame)
self.colorPatch.setObjectName('ColorPatchButton')
self.colorFrame.layout().addWidget(self.colorPatch)
self.updateParameterNode(slicer.mrmlScene,
vtk.vtkCommand.ModifiedEvent)
self.updateGUIFromMRML(self.parameterNode,
vtk.vtkCommand.ModifiedEvent)
self.frame.connect('destroyed()', self.cleanup)
self.colorSpin.connect('valueChanged(int)', self.updateMRMLFromGUI)
self.colorPatch.connect('clicked()', self.showColorBox)
# TODO: change this to look for specfic events (added, removed...)
# but this requires being able to access events by number from wrapped code
self.addObserver(slicer.mrmlScene, vtk.vtkCommand.ModifiedEvent,
self.updateParameterNode)
def buildGUI(self, parent):
connectorGroupBox = ctk.ctkCollapsibleGroupBox()
connectorGroupBox.title = self.cname
parent.addWidget(connectorGroupBox)
connectorFormLayout = qt.QFormLayout(connectorGroupBox)
if self.connectorSelector == None:
self.connectorSelector = slicer.qMRMLNodeComboBox()
self.connectorSelector.nodeTypes = ( ("vtkMRMLIGTLConnectorNode"), "" )
self.connectorSelector.selectNodeUponCreation = True
self.connectorSelector.addEnabled = True
self.connectorSelector.removeEnabled = False
self.connectorSelector.noneEnabled = False
self.connectorSelector.showHidden = False
self.connectorSelector.showChildNodeTypes = False
self.connectorSelector.setMRMLScene( slicer.mrmlScene )
self.connectorSelector.setToolTip( "Establish a connection with the server" )
connectorFormLayout.addRow("Connector: ", self.connectorSelector)
if self.portSpinBox == None:
self.portSpinBox = qt.QSpinBox()
self.portSpinBox.objectName = 'PortSpinBox'
self.portSpinBox.setMaximum(64000)
self.portSpinBox.setValue(self.port)
self.portSpinBox.setToolTip("Port number of the server")
connectorFormLayout.addRow("Port: ", self.portSpinBox)
# check box to trigger transform conversion
if self.activeConnectionCheckBox == None:
self.activeConnectionCheckBox = qt.QCheckBox()
self.activeConnectionCheckBox.checked = 0
self.activeConnectionCheckBox.enabled = 0
self.activeConnectionCheckBox.setToolTip("Activate OpenIGTLink connection")
connectorFormLayout.addRow("Active: ", self.activeConnectionCheckBox)
#--------------------------------------------------
# Connections
#--------------------------------------------------
self.connectorSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onConnectorSelected)
self.activeConnectionCheckBox.connect('toggled(bool)', self.onActiveConnection)
def setup(self):
degrees = self.getDefaultValue('degrees')
self.degreesSlider = self.makeRangeWidget(-180, -degrees, degrees, 180,
1, 'degrees')
self.layout.addRow('Degrees: ', self.degreesSlider)
translation = self.getDefaultValue('translation')
self.translationSlider = self.makeRangeWidget(-50, -translation,
translation, 50, 1,
'translation')
self.layout.addRow('Translation: ', self.translationSlider)
self.numTransformsSpinBox = qt.QSpinBox()
self.numTransformsSpinBox.maximum = 10
self.numTransformsSpinBox.value = self.getDefaultValue(
'num_transforms')
self.layout.addRow('Number of motions: ', self.numTransformsSpinBox)
self.interpolationComboBox = self.makeInterpolationComboBox()
self.layout.addRow('Interpolation: ', self.interpolationComboBox)
def setupOptionsFrame(self):
# mask inside/outside the surface checkbox
self.maskOutsideSurfaceCheckBox = qt.QCheckBox()
self.maskOutsideSurfaceCheckBox.checked = False
self.maskOutsideSurfaceCheckBox.setToolTip(
"If checked, voxel values will be filled outside the segment.")
self.scriptedEffect.addLabeledOptionsWidget(
"Mask outside: ", self.maskOutsideSurfaceCheckBox)
# outside fill value
self.fillValueEdit = qt.QSpinBox()
self.fillValueEdit.setToolTip(
"Choose the voxel intensity that will be used to fill the masked region."
)
self.fillValueEdit.minimum = -32768
self.fillValueEdit.maximum = 65535
self.scriptedEffect.addLabeledOptionsWidget("Fill value: ",
self.fillValueEdit)
# output volume selector
self.outputVolumeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.outputVolumeSelector.selectNodeUponCreation = True
self.outputVolumeSelector.addEnabled = True
self.outputVolumeSelector.removeEnabled = True
self.outputVolumeSelector.noneEnabled = False
self.outputVolumeSelector.showHidden = False
self.outputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeSelector.setToolTip(
"Masked output volume. It may be the same as the input volume for cumulative masking."
)
self.scriptedEffect.addLabeledOptionsWidget("Output Volume: ",
self.outputVolumeSelector)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Apply segment as volume mask")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
def __init__( self, parent = None ):
qt.QFrame.__init__( self )
self.parameterNode = None
#
# Parameters area
#
self.parametersLayout = qt.QFormLayout( self )
self.setLayout( self.parametersLayout )
#
# Polynomial regression order spin box
#
self.regressionOrderSpinBox = qt.QSpinBox()
self.regressionOrderSpinBox.setRange( 1, 10 )
self.regressionOrderSpinBox.setSingleStep( 1 )
self.regressionOrderSpinBox.setToolTip( "Choose the order of polynomial fit for the regression model." )
self.parametersLayout.addRow( "Order ", self.regressionOrderSpinBox )
# connections
self.regressionOrderSpinBox.connect( 'valueChanged(int)', self.onRegressionOrderChanged )
def setup(self):
self.setLayout(qt.QGridLayout())
settingNames = self.getSettingNames()
for index, setting in enumerate(settingNames):
label = self.createLabel(setting)
value = self.getSetting(setting)
if value.lower() in ["true", "false"]:
element = qt.QCheckBox()
element.checked = value.lower() == "true"
elif value.isdigit():
element = qt.QSpinBox()
element.value = int(value)
elif os.path.exists(value):
element = ctk.ctkPathLineEdit()
if os.path.isdir(value):
element.filters = ctk.ctkPathLineEdit.Dirs
else:
element.filters = ctk.ctkPathLineEdit.Files
element.currentPath = value
else:
element = self.createLineEdit(value)
element.minimumWidth = self.getMinimumTextWidth(
element.text) + 10
self.layout().addWidget(label, index, 0)
self.layout().addWidget(element, index, 1, 1,
qt.QSizePolicy.ExpandFlag)
self.keyElementPairs.append((label.text, element))
self.okButton = self.createButton("OK")
self.cancelButton = self.createButton("Cancel")
self.addButton(self.okButton, qt.QMessageBox.AcceptRole)
self.addButton(self.cancelButton, qt.QMessageBox.NoRole)
self.layout().addWidget(
self.createHLayout([self.okButton, self.cancelButton]),
len(settingNames), 1)
self.okButton.clicked.connect(self.onOkButtonClicked)
def __init__(self, parent=None):
qt.QFrame.__init__(self)
self.parameterNode = None
#
# Parameters area
#
self.parametersLayout = qt.QFormLayout(self)
self.setLayout(self.parametersLayout)
#
# Combination method combo box
#
self.neighborWeightComboBox = qt.QComboBox()
self.neighborWeightComboBox.addItem(NEIGHBOR_WEIGHT_EQUAL)
self.neighborWeightComboBox.addItem(NEIGHBOR_WEIGHT_DISTANCE)
self.neighborWeightComboBox.addItem(NEIGHBOR_WEIGHT_RANK)
self.neighborWeightComboBox.setToolTip(
"Choose the weighting scheme for neighbors.")
self.parametersLayout.addRow("Weighting ", self.neighborWeightComboBox)
#
# Number of neighbors
#
self.numberOfNeighborsSpinBox = qt.QSpinBox()
self.numberOfNeighborsSpinBox.setRange(1, 100)
self.numberOfNeighborsSpinBox.setSingleStep(1)
self.numberOfNeighborsSpinBox.setToolTip(
"Choose the number of neighbors (k).")
self.parametersLayout.addRow("Neighbors ",
self.numberOfNeighborsSpinBox)
# connections
self.neighborWeightComboBox.connect('currentIndexChanged(QString)',
self.onNeighborWeightChanged)
self.numberOfNeighborsSpinBox.connect('valueChanged(int)',
self.onNumberOfNeighborsChanged)
def setup(self):
self.controlPointsWidget = CoordinatesWidget(
decimals=0,
coordinates=self.getDefaultValue('num_control_points'),
)
self.layout.addRow('Control points: ', self.controlPointsWidget.widget)
self.maxDisplacementWidget = CoordinatesWidget(
decimals=2,
coordinates=self.getDefaultValue('max_displacement'),
step=0.1,
)
self.layout.addRow('Maximum displacement: ',
self.maxDisplacementWidget.widget)
self.lockedBordersSpinBox = qt.QSpinBox()
self.lockedBordersSpinBox.maximum = 2
self.lockedBordersSpinBox.value = self.getDefaultValue(
'locked_borders')
self.layout.addRow('Locked borders: ', self.lockedBordersSpinBox)
self.interpolationComboBox = self.makeInterpolationComboBox()
self.layout.addRow('Interpolation: ', self.interpolationComboBox)
def onInputShapesDirectoryChanged(self):
inputShapesDirectory = self.shapeInputDirectory.directory.encode(
'utf-8')
row = 0
for file in sorted(os.listdir(inputShapesDirectory)):
if file.endswith(".vtk"):
self.tableWidget_inputShapeParameters.setRowCount(row + 1)
# Column 0:
rootname = os.path.basename(file).split(".")[0]
labelVTKFile = qt.QLabel(rootname)
labelVTKFile.setAlignment(0x84)
self.tableWidget_inputShapeParameters.setCellWidget(
row, 0, labelVTKFile)
# Column 1-2-3-4:
for column in range(1, 5):
widget = qt.QWidget()
layout = qt.QHBoxLayout(widget)
if not column == 2:
spinBox = qt.QSpinBox()
if column == 1:
spinBox.connect('valueChanged(int)',
self.onDefaultTimePointRange)
if column == 4:
spinBox.value = 1
else:
spinBox = qt.QDoubleSpinBox()
spinBox.setMinimum(0)
layout.addWidget(spinBox)
layout.setAlignment(0x84)
layout.setContentsMargins(0, 0, 0, 0)
widget.setLayout(layout)
self.tableWidget_inputShapeParameters.setCellWidget(
row, column, widget)
row = row + 1
def onSelectInputModels(self):
InputModelsDirectory = self.GroupsInputModelsDirectory.directory.encode(
'utf-8')
self.InputModelsDirectory = InputModelsDirectory
self.PropertiesNames = []
listMesh = os.listdir(InputModelsDirectory)
if listMesh.count(".DS_Store"):
listMesh.remove(".DS_Store")
#VTKfilepath = os.path.join( modelsDir, listMesh[0])
VTKfilepath = InputModelsDirectory + '/' + listMesh[0]
if os.path.exists(VTKfilepath):
reader = vtk.vtkPolyDataReader()
reader.SetFileName(VTKfilepath)
reader.Update()
polydata = reader.GetOutput()
for i in range(polydata.GetPointData().GetNumberOfArrays()):
self.PropertiesNames.append(
polydata.GetPointData().GetArrayName(i))
row = 0
for PropertyName in self.PropertiesNames:
self.GroupsProperties.setRowCount(row + 1)
# Column 0:
labelPropertyName = qt.QLabel(PropertyName)
labelPropertyName.setAlignment(0x84)
self.GroupsProperties.setCellWidget(row, 0, labelPropertyName)
# Column 1:
widget = qt.QWidget()
layout = qt.QHBoxLayout(widget)
spinBox = qt.QSpinBox()
spinBox.setMinimum(0)
layout.addWidget(spinBox)
layout.setAlignment(0x84)
layout.setContentsMargins(0, 0, 0, 0)
widget.setLayout(layout)
self.GroupsProperties.setCellWidget(row, 1, widget)
row = row + 1
def create(self):
super(IslandEffectOptions, self).create()
self.fullyConnected = qt.QCheckBox("Fully Connected", self.frame)
self.fullyConnected.setToolTip(
"When set, only pixels that share faces (not corners or edges) are considered connected."
)
self.frame.layout().addWidget(self.fullyConnected)
self.widgets.append(self.fullyConnected)
self.sizeLabel = qt.QLabel("Minimum Size", self.frame)
self.sizeLabel.setToolTip("Minimum size of islands to be considered.")
self.frame.layout().addWidget(self.sizeLabel)
self.widgets.append(self.sizeLabel)
self.minimumSize = qt.QSpinBox(self.frame)
self.minimumSize.minimum = 0
self.minimumSize.maximum = vtk.VTK_INT_MAX
self.minimumSize.value = 0
self.frame.layout().addWidget(self.minimumSize)
self.widgets.append(self.minimumSize)
self.connections.append(
(self.fullyConnected, "clicked()", self.updateMRMLFromGUI))
self.connections.append(
(self.minimumSize, "valueChanged(int)", self.updateMRMLFromGUI))
def setupOptionsFrame(self):
self.operationRadioButtons = []
# Fill operation buttons
self.fillInsideButton = qt.QRadioButton("Fill inside")
self.operationRadioButtons.append(self.fillInsideButton)
self.buttonToOperationNameMap[self.fillInsideButton] = 'FILL_INSIDE'
self.fillOutsideButton = qt.QRadioButton("Fill outside")
self.operationRadioButtons.append(self.fillOutsideButton)
self.buttonToOperationNameMap[self.fillOutsideButton] = 'FILL_OUTSIDE'
self.binaryMaskFillButton = qt.QRadioButton("Fill inside and outside")
self.binaryMaskFillButton.setToolTip("Create a labelmap volume with specified inside and outside fill values.")
self.operationRadioButtons.append(self.binaryMaskFillButton)
self.buttonToOperationNameMap[self.binaryMaskFillButton] = 'FILL_INSIDE_AND_OUTSIDE'
# Operation buttons layout
operationLayout = qt.QGridLayout()
operationLayout.addWidget(self.fillInsideButton, 0, 0)
operationLayout.addWidget(self.fillOutsideButton, 1, 0)
operationLayout.addWidget(self.binaryMaskFillButton, 0, 1)
self.scriptedEffect.addLabeledOptionsWidget("Operation:", operationLayout)
# fill value
self.fillValueEdit = qt.QSpinBox()
self.fillValueEdit.setToolTip("Choose the voxel intensity that will be used to fill the masked region.")
self.fillValueEdit.minimum = -32768
self.fillValueEdit.maximum = 65535
self.fillValueEdit.connect("valueChanged(int)", self.fillValueChanged)
self.fillValueLabel = qt.QLabel("Fill value: ")
# Binary mask fill outside value
self.binaryMaskFillOutsideEdit = qt.QSpinBox()
self.binaryMaskFillOutsideEdit.setToolTip("Choose the voxel intensity that will be used to fill outside the mask.")
self.binaryMaskFillOutsideEdit.minimum = -32768
self.binaryMaskFillOutsideEdit.maximum = 65535
self.binaryMaskFillOutsideEdit.connect("valueChanged(int)", self.fillValueChanged)
self.fillOutsideLabel = qt.QLabel("Outside fill value: ")
# Binary mask fill outside value
self.binaryMaskFillInsideEdit = qt.QSpinBox()
self.binaryMaskFillInsideEdit.setToolTip("Choose the voxel intensity that will be used to fill inside the mask.")
self.binaryMaskFillInsideEdit.minimum = -32768
self.binaryMaskFillInsideEdit.maximum = 65535
self.binaryMaskFillInsideEdit.connect("valueChanged(int)", self.fillValueChanged)
self.fillInsideLabel = qt.QLabel(" Inside fill value: ")
# Fill value layouts
fillValueLayout = qt.QFormLayout()
fillValueLayout.addRow(self.fillValueLabel, self.fillValueEdit)
fillOutsideLayout = qt.QFormLayout()
fillOutsideLayout.addRow(self.fillOutsideLabel, self.binaryMaskFillOutsideEdit)
fillInsideLayout = qt.QFormLayout()
fillInsideLayout.addRow(self.fillInsideLabel, self.binaryMaskFillInsideEdit)
binaryMaskFillLayout = qt.QHBoxLayout()
binaryMaskFillLayout.addLayout(fillOutsideLayout)
binaryMaskFillLayout.addLayout(fillInsideLayout)
fillValuesSpinBoxLayout = qt.QFormLayout()
fillValuesSpinBoxLayout.addRow(binaryMaskFillLayout)
fillValuesSpinBoxLayout.addRow(fillValueLayout)
self.scriptedEffect.addOptionsWidget(fillValuesSpinBoxLayout)
# input volume selector
self.inputVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputVolumeSelector.selectNodeUponCreation = True
self.inputVolumeSelector.addEnabled = True
self.inputVolumeSelector.removeEnabled = True
self.inputVolumeSelector.noneEnabled = True
self.inputVolumeSelector.noneDisplay = "(Master volume)"
self.inputVolumeSelector.showHidden = False
self.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeSelector.setToolTip("Volume to mask. Default is current master volume node.")
self.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputVolumeChanged)
self.inputVisibilityButton = qt.QToolButton()
self.inputVisibilityButton.setIcon(qt.QIcon(":/Icons/Small/SlicerInvisible.png"))
self.inputVisibilityButton.setAutoRaise(True)
self.inputVisibilityButton.setCheckable(True)
self.inputVisibilityButton.connect('clicked()', self.onInputVisibilityButtonClicked)
inputLayout = qt.QHBoxLayout()
inputLayout.addWidget(self.inputVisibilityButton)
inputLayout.addWidget(self.inputVolumeSelector)
self.scriptedEffect.addLabeledOptionsWidget("Input Volume: ", inputLayout)
# output volume selector
self.outputVolumeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode", "vtkMRMLLabelMapVolumeNode"]
self.outputVolumeSelector.selectNodeUponCreation = True
self.outputVolumeSelector.addEnabled = True
self.outputVolumeSelector.removeEnabled = True
self.outputVolumeSelector.renameEnabled = True
self.outputVolumeSelector.noneEnabled = True
self.outputVolumeSelector.noneDisplay = "(Create new Volume)"
self.outputVolumeSelector.showHidden = False
self.outputVolumeSelector.setMRMLScene( slicer.mrmlScene )
self.outputVolumeSelector.setToolTip("Masked output volume. It may be the same as the input volume for cumulative masking.")
self.outputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputVolumeChanged)
self.outputVisibilityButton = qt.QToolButton()
self.outputVisibilityButton.setIcon(qt.QIcon(":/Icons/Small/SlicerInvisible.png"))
self.outputVisibilityButton.setAutoRaise(True)
self.outputVisibilityButton.setCheckable(True)
self.outputVisibilityButton.connect('clicked()', self.onOutputVisibilityButtonClicked)
outputLayout = qt.QHBoxLayout()
outputLayout.addWidget(self.outputVisibilityButton)
outputLayout.addWidget(self.outputVolumeSelector)
self.scriptedEffect.addLabeledOptionsWidget("Output Volume: ", outputLayout)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Apply segment as volume mask. No undo operation available once applied.")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
for button in self.operationRadioButtons:
button.connect('toggled(bool)',
lambda toggle, widget=self.buttonToOperationNameMap[button]: self.onOperationSelectionChanged(widget, toggle))
def setupOptionsFrame(self):
self.operationRadioButtons = []
self.keepLargestOptionRadioButton = qt.QRadioButton(
"Keep largest island")
self.keepLargestOptionRadioButton.setToolTip(
"Keep only the largest island in selected segment, remove all other islands in the segment."
)
self.operationRadioButtons.append(self.keepLargestOptionRadioButton)
self.widgetToOperationNameMap[
self.keepLargestOptionRadioButton] = KEEP_LARGEST_ISLAND
self.keepSelectedOptionRadioButton = qt.QRadioButton(
"Keep selected island")
self.keepSelectedOptionRadioButton.setToolTip(
"Click on an island in a slice viewer to keep that island and remove all other islands in selected segment."
)
self.operationRadioButtons.append(self.keepSelectedOptionRadioButton)
self.widgetToOperationNameMap[
self.keepSelectedOptionRadioButton] = KEEP_SELECTED_ISLAND
self.removeSmallOptionRadioButton = qt.QRadioButton(
"Remove small islands")
self.removeSmallOptionRadioButton.setToolTip(
"Remove all islands from the selected segment that are smaller than the specified minimum size."
)
self.operationRadioButtons.append(self.removeSmallOptionRadioButton)
self.widgetToOperationNameMap[
self.removeSmallOptionRadioButton] = REMOVE_SMALL_ISLANDS
self.removeSelectedOptionRadioButton = qt.QRadioButton(
"Remove selected island")
self.removeSelectedOptionRadioButton.setToolTip(
"Click on an island to remove it from selected segment.")
self.operationRadioButtons.append(self.removeSelectedOptionRadioButton)
self.widgetToOperationNameMap[
self.removeSelectedOptionRadioButton] = REMOVE_SELECTED_ISLAND
self.addSelectedOptionRadioButton = qt.QRadioButton(
"Add selected island")
self.addSelectedOptionRadioButton.setToolTip(
"Click on a region to add it to selected segment.")
self.operationRadioButtons.append(self.addSelectedOptionRadioButton)
self.widgetToOperationNameMap[
self.addSelectedOptionRadioButton] = ADD_SELECTED_ISLAND
self.splitAllOptionRadioButton = qt.QRadioButton(
"Split islands to segments")
self.splitAllOptionRadioButton.setToolTip(
"Create a new segment for each island of selected segment. Islands smaller than minimum size will be removed. "
+ "Segments will be ordered by island size.")
self.operationRadioButtons.append(self.splitAllOptionRadioButton)
self.widgetToOperationNameMap[
self.splitAllOptionRadioButton] = SPLIT_ISLANDS_TO_SEGMENTS
operationLayout = qt.QGridLayout()
operationLayout.addWidget(self.keepLargestOptionRadioButton, 0, 0)
operationLayout.addWidget(self.removeSmallOptionRadioButton, 1, 0)
operationLayout.addWidget(self.splitAllOptionRadioButton, 2, 0)
operationLayout.addWidget(self.keepSelectedOptionRadioButton, 0, 1)
operationLayout.addWidget(self.removeSelectedOptionRadioButton, 1, 1)
operationLayout.addWidget(self.addSelectedOptionRadioButton, 2, 1)
self.operationRadioButtons[0].setChecked(True)
self.scriptedEffect.addOptionsWidget(operationLayout)
self.minimumSizeSpinBox = qt.QSpinBox()
self.minimumSizeSpinBox.setToolTip(
"Minimum size of islands to be considered.")
self.minimumSizeSpinBox.setMinimum(0)
self.minimumSizeSpinBox.setMaximum(vtk.VTK_INT_MAX)
self.minimumSizeSpinBox.setValue(1000)
self.minimumSizeLabel = self.scriptedEffect.addLabeledOptionsWidget(
"Minimum size:", self.minimumSizeSpinBox)
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.scriptedEffect.addOptionsWidget(self.applyButton)
for operationRadioButton in self.operationRadioButtons:
operationRadioButton.connect(
'toggled(bool)',
lambda toggle, widget=self.widgetToOperationNameMap[
operationRadioButton]: self.onOperationSelectionChanged(
widget, toggle))
self.minimumSizeSpinBox.connect('valueChanged(int)',
self.updateMRMLFromGUI)
self.applyButton.connect('clicked()', self.onApply)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
self.layout.addWidget(qt.QLabel("Failed to load VMTK libraries"))
return
#
# the I/O panel
#
ioCollapsibleButton = ctk.ctkCollapsibleButton()
ioCollapsibleButton.text = "Input/Output"
self.layout.addWidget(ioCollapsibleButton)
ioFormLayout = qt.QFormLayout(ioCollapsibleButton)
# inputVolume selector
self.inputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeNodeSelector.objectName = 'inputVolumeNodeSelector'
self.inputVolumeNodeSelector.toolTip = "Select the input volume."
self.inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputVolumeNodeSelector.noneEnabled = False
self.inputVolumeNodeSelector.addEnabled = False
self.inputVolumeNodeSelector.removeEnabled = False
ioFormLayout.addRow("Input Volume:", self.inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select a point in the largest vessel. Preview will be shown around this point. This is point is also used for determining maximum vessel diameter if automatic filtering parameters computation is enabled."
self.seedFiducialsNodeSelector.setNodeBaseName("DiameterSeed")
self.seedFiducialsNodeSelector.tableWidget().hide()
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(255, 0,
0) # red
self.seedFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = False
self.seedFiducialsNodeSelector.markupsPlaceWidget(
).placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
ioFormLayout.addRow("Seed point:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputVolume selector
self.outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.outputVolumeNodeSelector.baseName = "VesselnessFiltered"
self.outputVolumeNodeSelector.noneEnabled = True
self.outputVolumeNodeSelector.noneDisplay = "Create new volume"
self.outputVolumeNodeSelector.addEnabled = True
self.outputVolumeNodeSelector.selectNodeUponCreation = True
self.outputVolumeNodeSelector.removeEnabled = True
ioFormLayout.addRow("Output Volume:", self.outputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
# previewVolume selector
self.previewVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.previewVolumeNodeSelector.toolTip = "Select the preview volume."
self.previewVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.previewVolumeNodeSelector.baseName = "VesselnessPreview"
self.previewVolumeNodeSelector.noneEnabled = True
self.previewVolumeNodeSelector.noneDisplay = "Create new volume"
self.previewVolumeNodeSelector.addEnabled = True
self.previewVolumeNodeSelector.selectNodeUponCreation = True
self.previewVolumeNodeSelector.removeEnabled = True
advancedFormLayout.addRow("Preview volume:",
self.previewVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.previewVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.displayThresholdSlider = ctk.ctkSliderWidget()
self.displayThresholdSlider.decimals = 2
self.displayThresholdSlider.minimum = 0
self.displayThresholdSlider.maximum = 1.0
self.displayThresholdSlider.singleStep = 0.01
self.displayThresholdSlider.toolTip = "Voxels below this vesselness value will be hidden. It does not change the voxel values, only how the vesselness volume is displayed."
advancedFormLayout.addRow("Display threshold:",
self.displayThresholdSlider)
self.displayThresholdSlider.connect('valueChanged(double)',
self.onDisplayThresholdChanged)
self.previewVolumeDiameterVoxelSlider = ctk.ctkSliderWidget()
self.previewVolumeDiameterVoxelSlider.decimals = 0
self.previewVolumeDiameterVoxelSlider.minimum = 10
self.previewVolumeDiameterVoxelSlider.maximum = 200
self.previewVolumeDiameterVoxelSlider.singleStep = 5
self.previewVolumeDiameterVoxelSlider.suffix = " voxels"
self.previewVolumeDiameterVoxelSlider.toolTip = "Diameter of the preview area in voxels."
advancedFormLayout.addRow("Preview volume size:",
self.previewVolumeDiameterVoxelSlider)
# detect filterint parameters
self.detectPushButton = qt.QPushButton()
self.detectPushButton.text = "Compute vessel diameters and contrast from seed point"
self.detectPushButton.checkable = True
self.detectPushButton.checked = True
advancedFormLayout.addRow(self.detectPushButton)
self.detectPushButton.connect("clicked()", self.onNodeSelectionChanged)
self.minimumDiameterSpinBox = qt.QSpinBox()
self.minimumDiameterSpinBox.minimum = 1
self.minimumDiameterSpinBox.maximum = 1000
self.minimumDiameterSpinBox.singleStep = 1
self.minimumDiameterSpinBox.suffix = " voxels"
self.minimumDiameterSpinBox.enabled = False
self.minimumDiameterSpinBox.toolTip = "Tubular structures that have minimum this diameter will be enhanced."
advancedFormLayout.addRow("Minimum vessel diameter:",
self.minimumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)",
self.minimumDiameterSpinBox.setDisabled)
self.maximumDiameterSpinBox = qt.QSpinBox()
self.maximumDiameterSpinBox.minimum = 0
self.maximumDiameterSpinBox.maximum = 1000
self.maximumDiameterSpinBox.singleStep = 1
self.maximumDiameterSpinBox.suffix = " voxels"
self.maximumDiameterSpinBox.enabled = False
self.maximumDiameterSpinBox.toolTip = "Tubular structures that have maximum this diameter will be enhanced."
advancedFormLayout.addRow("Maximum vessel diameter:",
self.maximumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)",
self.maximumDiameterSpinBox.setDisabled)
self.contrastSlider = ctk.ctkSliderWidget()
self.contrastSlider.decimals = 0
self.contrastSlider.minimum = 0
self.contrastSlider.maximum = 500
self.contrastSlider.singleStep = 10
self.contrastSlider.enabled = False
self.contrastSlider.toolTip = "If the intensity contrast in the input image between vessel and background is high, choose a high value else choose a low value."
advancedFormLayout.addRow("Vessel contrast:", self.contrastSlider)
self.detectPushButton.connect("toggled(bool)",
self.contrastSlider.setDisabled)
self.suppressPlatesSlider = ctk.ctkSliderWidget()
self.suppressPlatesSlider.decimals = 0
self.suppressPlatesSlider.minimum = 0
self.suppressPlatesSlider.maximum = 100
self.suppressPlatesSlider.singleStep = 1
self.suppressPlatesSlider.suffix = " %"
self.suppressPlatesSlider.toolTip = "A higher value filters out more plate-like structures."
advancedFormLayout.addRow("Suppress plates:",
self.suppressPlatesSlider)
self.suppressBlobsSlider = ctk.ctkSliderWidget()
self.suppressBlobsSlider.decimals = 0
self.suppressBlobsSlider.minimum = 0
self.suppressBlobsSlider.maximum = 100
self.suppressBlobsSlider.singleStep = 1
self.suppressBlobsSlider.suffix = " %"
self.suppressBlobsSlider.toolTip = "A higher value filters out more blob-like structures."
advancedFormLayout.addRow("Suppress blobs:", self.suppressBlobsSlider)
#
# Reset, preview and apply buttons
#
self.buttonBox = qt.QDialogButtonBox()
self.resetButton = self.buttonBox.addButton(
self.buttonBox.RestoreDefaults)
self.resetButton.toolTip = "Click to reset all input elements to default."
self.previewButton = self.buttonBox.addButton(self.buttonBox.Discard)
self.previewButton.setIcon(qt.QIcon())
self.previewButton.text = "Preview"
self.startButton = self.buttonBox.addButton(self.buttonBox.Apply)
self.startButton.setIcon(qt.QIcon())
self.startButton.text = "Start"
self.startButton.enabled = False
self.layout.addWidget(self.buttonBox)
self.resetButton.connect("clicked()", self.restoreDefaults)
self.previewButton.connect("clicked()", self.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.previewVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeNodeSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.markupsSelectorComboBox().connect(
"currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.connect("updateFinished()",
self.onNodeSelectionChanged)
# set default values
self.restoreDefaults()
self.onNodeSelectionChanged()
# compress the layout
self.layout.addStretch(1)
