def setup(self):
super(SliceTrackerTargetTablePlugin, self).setup()
self.targetTable = qt.QTableView()
self.targetTableModel = CustomTargetTableModel(self.logic)
# self.targetTableModel.addEventObserver(vtk.vtkCommand.ModifiedEvent, self.updateNeedleModel)
self.targetTable.setModel(self.targetTableModel)
self.targetTable.setSelectionBehavior(qt.QTableView.SelectItems)
self.setTargetTableSizeConstraints()
self.targetTable.verticalHeader().hide()
self.targetTable.minimumHeight = 150
self.targetTable.setStyleSheet("QTableView::item:selected{background-color: #ff7f7f; color: black};")
self.layout().addWidget(self.targetTable)
def setup(self):
super(TargetsDefinitionTable, self).setup()
self.targetTable = qt.QTableView()
self.targetTableModel = CustomTargetTableModel(self.session)
self.targetTable.setModel(self.targetTableModel)
self.displayCol = self.targetTableModel.getColunmNumForHeaderName(self.targetTableModel.COLUMN_DISPLAY)
self.needleTypeCol = self.targetTableModel.getColunmNumForHeaderName(self.targetTableModel.COLUMN_NEEDLETYPE)
self.targetTable.setItemDelegateForColumn(self.displayCol, CheckBoxDelegate(self, self.session))
self.targetTable.setItemDelegateForColumn(self.needleTypeCol, ComBoxDelegate(self, self.session))
self.setTargetTableSizeConstraints()
self.targetTable.verticalHeader().hide()
self.targetTable.minimumHeight = 150
self.targetTable.setStyleSheet("QTableView::item:selected{background-color: #ff7f7f; color: black};")
self.layout().addWidget(self.targetTable)
def __init__(self, columnNames):
super().__init__()
self.addButton = qt.QPushButton('+')
self.addButton.clicked.connect(self.onAddButton)
self.removeButton = qt.QPushButton('-')
self.removeButton.clicked.connect(self.onRemoveButton)
self.linkStagesPushButton = qt.QPushButton('Link Across Stages')
self.linkStagesPushButton.toolTip = 'When checked, settings will be the same for all stages.'
self.linkStagesPushButton.checkable = True
self.buttonsFrame = qt.QFrame()
self.buttonsFrame.setSizePolicy(qt.QSizePolicy.Preferred,
qt.QSizePolicy.Minimum)
self.buttonsFrame.setLayout(qt.QHBoxLayout())
self.buttonsFrame.layout().addWidget(self.addButton)
self.buttonsFrame.layout().addWidget(self.removeButton)
self.buttonsFrame.layout().addWidget(self.linkStagesPushButton)
self.model = qt.QStandardItemModel(1, len(columnNames))
for i, columnName in enumerate(columnNames):
self.model.setHeaderData(i, qt.Qt.Horizontal, columnName)
self.view = qt.QTableView()
self.view.setEditTriggers(self.view.CurrentChanged +
self.view.DoubleClicked +
self.view.SelectedClicked)
self.view.setSelectionMode(self.view.SingleSelection)
self.view.setSelectionBehavior(self.view.SelectRows)
self.view.horizontalHeader().setStretchLastSection(True)
self.view.setHorizontalScrollMode(self.view.ScrollPerPixel)
self.view.verticalHeader().setMaximumSectionSize(self.RowHeight)
self.view.verticalHeader().setMinimumSectionSize(self.RowHeight)
self.view.verticalHeader().setDefaultSectionSize(self.RowHeight)
self.view.setFixedHeight(65)
self.view.setModel(self.model)
self.view.setCurrentIndex(self.model.index(0, 0))
self.view.selectionModel().selectionChanged.connect(
self.onSelectionChanged)
layout = qt.QVBoxLayout(self)
layout.addWidget(self.buttonsFrame)
layout.addWidget(self.view)
return layout
def setupSegmentationSelector(self, Layout, parent):
self.segmentationSelector = slicer.qMRMLNodeComboBox()
self.segmentationSelector.nodeTypes = ["vtkMRMLSegmentationNode"]
self.segmentationSelector.addEnabled = False
self.segmentationSelector.removeEnabled = True
self.segmentationSelector.renameEnabled = True
self.segmentationSelector.setMRMLScene(slicer.mrmlScene)
self.segmentationSelector.setToolTip(
"Pick the segmentation to compute statistics for")
Layout.addRow("Segmentation:", self.segmentationSelector)
self.scalarSelector = slicer.qMRMLNodeComboBox()
self.scalarSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.scalarSelector.addEnabled = False
self.scalarSelector.removeEnabled = True
self.scalarSelector.renameEnabled = True
self.scalarSelector.noneEnabled = True
self.scalarSelector.showChildNodeTypes = False
self.scalarSelector.setMRMLScene(slicer.mrmlScene)
self.scalarSelector.setToolTip(
"Select the scalar volume that you want to get the statistics")
Layout.addRow("Scalar Volume 1:", self.scalarSelector)
self.scalarSelector2 = slicer.qMRMLNodeComboBox()
self.scalarSelector2.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.scalarSelector2.addEnabled = False
self.scalarSelector2.removeEnabled = True
self.scalarSelector2.renameEnabled = True
self.scalarSelector2.noneEnabled = True
self.scalarSelector2.showChildNodeTypes = False
self.scalarSelector2.setMRMLScene(slicer.mrmlScene)
self.scalarSelector2.setToolTip(
"Select the scalar volume that you want to get the statistics")
Layout.addRow("Scalar Volume 2:", self.scalarSelector2)
self.SButton = qt.QPushButton("Get Statistics")
self.SButton.toolTip = "Get the statistics for the segmentation selected"
self.SButton.enabled = False
Layout.addRow(self.SButton)
self.table = qt.QTableView()
self.table.sortingEnabled = True
parent.addWidget(self.table)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# the inps volume selector
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "IO Volumes"
self.parent.layout().addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
parametersFormLayout.setVerticalSpacing(5)
self.CTSelector = slicer.qMRMLNodeComboBox()
self.CTSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.CTSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.CTSelector.selectNodeUponCreation = False
self.CTSelector.addEnabled = False
self.CTSelector.removeEnabled = False
self.CTSelector.noneEnabled = True
self.CTSelector.showHidden = False
self.CTSelector.showChildNodeTypes = False
self.CTSelector.setMRMLScene(slicer.mrmlScene)
self.CTSelector.setToolTip("Pick the CT image to work on.")
parametersFormLayout.addRow("Input CT Volume: ", self.CTSelector)
#
# the label map volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
# self.labelSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
# self.labelSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 1 )
self.labelSelector.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.labelSelector.selectNodeUponCreation = True
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to the algorithm.")
parametersFormLayout.addRow("Label Map Volume: ", self.labelSelector)
# Image filtering section
self.preProcessingWidget = PreProcessingWidget(
self.moduleName, parentWidget=self.parent)
self.preProcessingWidget.setup()
#
# self.splitRadioButton = qt.QRadioButton()
# self.splitRadioButton.setText('Split Label Map')
# self.splitRadioButton.setChecked(0)
# self.parent.layout().addWidget(self.splitRadioButton, 0, 3)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Parenchyma Phenotypes."
self.applyButton.enabled = False
self.applyButton.setFixedSize(300, 30)
self.parent.layout().addWidget(self.applyButton, 0, 4)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# model and view for EXP stats table
"""self.viewexp = qt.QTableView()
self.viewexp.sortingEnabled = True
self.parent.layout().addWidget(self.viewexp)"""
# Histogram Selection
self.HistSection = qt.QFrame()
self.HistSection.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.HistSection)
self.HistSection.setObjectName('HistSection')
self.HistSection.setStyleSheet(
'#HistSection {border: 0.5px solid lightGray; }')
HistSectionTitle = qt.QLabel()
HistSectionTitle.setText('Histogram Section')
# HistSectionTitle.setStyleSheet('border: 1px solid white; color: black')
self.HistSection.layout().addWidget(HistSectionTitle)
self.histogramCheckBoxes = []
self.histFrame = qt.QFrame()
# self.histFrame.setStyleSheet('border: 1px solid white')
self.histFrame.setLayout(qt.QHBoxLayout())
self.GlobalHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.GlobalHistCheckBox)
self.histFrame.layout().addWidget(self.GlobalHistCheckBox)
self.RightHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RightHistCheckBox)
self.histFrame.layout().addWidget(self.RightHistCheckBox)
self.LeftHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LeftHistCheckBox)
self.histFrame.layout().addWidget(self.LeftHistCheckBox)
self.RULHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RULHistCheckBox)
self.histFrame.layout().addWidget(self.RULHistCheckBox)
self.RLLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RLLHistCheckBox)
self.histFrame.layout().addWidget(self.RLLHistCheckBox)
self.RMLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RMLHistCheckBox)
self.histFrame.layout().addWidget(self.RMLHistCheckBox)
self.LULHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LULHistCheckBox)
self.histFrame.layout().addWidget(self.LULHistCheckBox)
self.LLLHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LLLHistCheckBox)
self.histFrame.layout().addWidget(self.LLLHistCheckBox)
self.LUTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LUTHistCheckBox)
self.histFrame.layout().addWidget(self.LUTHistCheckBox)
self.LMTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LMTHistCheckBox)
self.histFrame.layout().addWidget(self.LMTHistCheckBox)
self.LLTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.LLTHistCheckBox)
self.histFrame.layout().addWidget(self.LLTHistCheckBox)
self.RUTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RUTHistCheckBox)
self.histFrame.layout().addWidget(self.RUTHistCheckBox)
self.RMTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RMTHistCheckBox)
self.histFrame.layout().addWidget(self.RMTHistCheckBox)
self.RLTHistCheckBox = qt.QCheckBox()
self.histogramCheckBoxes.append(self.RLTHistCheckBox)
self.histFrame.layout().addWidget(self.RLTHistCheckBox)
for i in xrange(len(self.histogramCheckBoxes)):
self.histogramCheckBoxes[i].setText(self.rTags[i])
self.histogramCheckBoxes[i].hide()
self.HistSection.layout().addWidget(self.histFrame)
self.HistSection.enabled = False
# Chart button
self.chartBox = qt.QFrame()
self.chartBox.setObjectName("chartBox")
self.chartBox.setStyleSheet(
'#chartBox {border: 0.5px solid lightGray;}')
self.chartBox.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.chartBox)
chartSectionTitle = qt.QLabel()
chartSectionTitle.setText('Chart Section')
self.chartBox.layout().addWidget(chartSectionTitle)
chartFrame = qt.QFrame()
chartFrame.setLayout(qt.QHBoxLayout())
self.chartBox.layout().addWidget(chartFrame)
self.chartButton = qt.QPushButton("Chart")
self.chartButton.toolTip = "Make a chart from the current statistics."
chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox()
self.chartOption.addItems(self.chartOptions)
chartFrame.layout().addWidget(self.chartOption)
self.chartBox.enabled = False
self.reportsWidget = CaseReportsWidget(self.moduleName,
self.columnsDict,
parentWidget=self.parent)
self.reportsWidget.setup()
self.reportsWidget.showPrintButton(True)
# self.reportsWidget.saveButton.enabled = False
# self.reportsWidget.openButton.enabled = False
# self.reportsWidget.exportButton.enabled = False
# self.reportsWidget.removeButton.enabled = False
# By default, the Print button is hidden
# self.reportsWidget.showPrintButton.enabled = False
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_PRINT_BUTTON_CLICKED, self.onPrintReport)
self.CTSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onCTSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
self.GlobalHistCheckBox.connect('clicked()', self.onHistogram)
self.RightHistCheckBox.connect('clicked()', self.onHistogram)
self.LeftHistCheckBox.connect('clicked()', self.onHistogram)
self.RULHistCheckBox.connect('clicked()', self.onHistogram)
self.RLLHistCheckBox.connect('clicked()', self.onHistogram)
self.RMLHistCheckBox.connect('clicked()', self.onHistogram)
self.LULHistCheckBox.connect('clicked()', self.onHistogram)
self.LLLHistCheckBox.connect('clicked()', self.onHistogram)
self.LUTHistCheckBox.connect('clicked()', self.onHistogram)
self.LMTHistCheckBox.connect('clicked()', self.onHistogram)
self.LLTHistCheckBox.connect('clicked()', self.onHistogram)
self.RUTHistCheckBox.connect('clicked()', self.onHistogram)
self.RMTHistCheckBox.connect('clicked()', self.onHistogram)
self.RLTHistCheckBox.connect('clicked()', self.onHistogram)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
### Parameters Area
inputCollapsibleButton = ctk.ctkCollapsibleButton()
inputCollapsibleButton.text = "Input"
self.layout.addWidget(inputCollapsibleButton)
# Layout within the dummy collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
# fixed landmarks (mrml input)
self.fixedLandmarks = slicer.qMRMLNodeComboBox()
self.fixedLandmarks.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.fixedLandmarks.selectNodeUponCreation = True
self.fixedLandmarks.addEnabled = False
self.fixedLandmarks.removeEnabled = False
self.fixedLandmarks.noneEnabled = True
self.fixedLandmarks.showHidden = False
self.fixedLandmarks.renameEnabled = True
self.fixedLandmarks.setMRMLScene(slicer.mrmlScene)
self.fixedLandmarks.setToolTip("Landmarks on fixed image.")
inputFormLayout.addRow("Fixed landmarks: ", self.fixedLandmarks)
# fixed landmarks (directory input)
self.fixedLandmarksDirectory = ctk.ctkDirectoryButton()
self.fixedLandmarksDirectory.directory = qt.QDir.homePath()
inputFormLayout.addRow("", self.fixedLandmarksDirectory)
# moving landmarks (mrml input)
self.movingLandmarks = slicer.qMRMLNodeComboBox()
self.movingLandmarks.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.movingLandmarks.selectNodeUponCreation = True
self.movingLandmarks.addEnabled = False
self.movingLandmarks.removeEnabled = False
self.movingLandmarks.noneEnabled = True
self.movingLandmarks.showHidden = False
self.movingLandmarks.showChildNodeTypes = False
self.movingLandmarks.setMRMLScene(slicer.mrmlScene)
self.movingLandmarks.setToolTip("Landmarks on moving image.")
inputFormLayout.addRow("Moving landmarks: ", self.movingLandmarks)
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# moving landmarks (directory input)
self.movingLandmarksDirectory = ctk.ctkDirectoryButton()
self.movingLandmarksDirectory.directory = qt.QDir.homePath()
inputFormLayout.addRow("", self.movingLandmarksDirectory)
# Apply Button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
self.layout.addWidget(self.applyButton)
### Output Area
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output statistics"
self.layout.addWidget(outputCollapsibleButton)
# Layout within the dummy collapsible button
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
# output statistics
buttonLayout = qt.QHBoxLayout()
self.averageError = qt.QLineEdit()
self.averageErrorValue = 1
self.averageError.setToolTip("Average landmark separation")
buttonLayout.addWidget(self.averageError)
outputFormLayout.addRow("Average error:", buttonLayout)
buttonLayout = qt.QHBoxLayout()
self.Variance = qt.QLineEdit()
self.VarianceValue = 1
self.Variance.setToolTip("Variance")
buttonLayout.addWidget(self.Variance)
outputFormLayout.addRow("Variance:", buttonLayout)
buttonLayout = qt.QHBoxLayout()
self.stDev = qt.QLineEdit()
self.stDevValue = 1
self.stDev.setToolTip("Standard deviation")
buttonLayout.addWidget(self.stDev)
outputFormLayout.addRow("Standard deviation:", buttonLayout)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# connections
self.fixedLandmarks.connect("currentNodeChanged(vtkMRMLNode*)",
self.onFixedLandmarksSelect)
self.movingLandmarks.connect("currentNodeChanged(vtkMRMLNode*)",
self.onMovingLandmarksSelect)
self.applyButton.connect('clicked(bool)', self.onMismatchErrorApply)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Input/Export Area
#
IOCollapsibleButton = ctk.ctkCollapsibleButton()
IOCollapsibleButton.text = "Input and Export"
self.layout.addWidget(IOCollapsibleButton)
# Layout within the dummy collapsible button
#IOFormLayout = qt.QFormLayout(IOCollapsibleButton)
IOFormLayout = qt.QFormLayout(IOCollapsibleButton)
#
# Username input
#
self.userNameInput = qt.QLineEdit()
self.userNameInput.setText(slicer.userNameDefault)
self.userNameInput.setToolTip("Input MorphoSource account username")
IOFormLayout.addRow("MorphSource Username: "******"Input MorphoSource account password")
IOFormLayout.addRow("MorphSource Password: "******"Log in")
self.loginButton.toolTip = "Log into the Morphosource database"
self.loginButton.enabled = False
IOFormLayout.addRow(self.loginButton)
#
# Query parameter area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Query parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Username input
#
self.orderInput = qt.QLineEdit()
self.orderInput.setToolTip(
"Input the the specimen order, eg: 'Euprimates' ")
parametersFormLayout.addRow("Query order: ", self.orderInput)
#
# Username input
#
self.elementInput = qt.QLineEdit()
self.elementInput.setToolTip(
"Input the speciment element, eg: 'Cranuim' ")
parametersFormLayout.addRow("Query element: ", self.elementInput)
#
# Submit query Button
#
self.submitQueryButton = qt.QPushButton("Submit query")
self.submitQueryButton.toolTip = "Query the MorphoSource database for 3D models. This may take a few minutes."
self.submitQueryButton.enabled = False
parametersFormLayout.addRow(self.submitQueryButton)
#
# Query results area
#
resultsCollapsibleButton = ctk.ctkCollapsibleButton()
resultsCollapsibleButton.text = "Query results:"
resultsCollapsibleButton.collapsed = False
self.layout.addWidget(resultsCollapsibleButton)
resultsFormLayout = qt.QFormLayout(resultsCollapsibleButton)
self.resultsModel = qt.QStandardItemModel()
self.resultsTable = qt.QTableView()
self.resultsTable.horizontalHeader().stretchLastSection = True
self.resultsTable.horizontalHeader().visible = False
self.resultsTable.verticalHeader().visible = False
self.resultsTable.setSelectionBehavior(
qt.QAbstractItemView().SelectRows)
self.resultsTable.setModel(self.resultsModel)
resultsFormLayout.addRow(self.resultsTable)
self.loadResultsButton = qt.QPushButton("Load selected models")
self.loadResultsButton.toolTip = "Load the selected models into the scene."
self.loadResultsButton.enabled = False
resultsFormLayout.addRow(self.loadResultsButton)
# connections
self.loginButton.connect('clicked(bool)', self.onLogin)
self.userNameInput.connect('textChanged(const QString &)',
self.onLoginStringChanged)
self.passwordInput.connect('textChanged(const QString &)',
self.onLoginStringChanged)
self.orderInput.connect('textChanged(const QString &)',
self.onQueryStringChanged)
self.elementInput.connect('textChanged(const QString &)',
self.onQueryStringChanged)
self.submitQueryButton.connect('clicked(bool)', self.onSubmitQuery)
self.loadResultsButton.connect('clicked(bool)', self.onLoadResults)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onLoginStringChanged()
self.onQueryStringChanged()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
self.fileModel = qt.QStandardItemModel()
self.fileTable = qt.QTableView()
self.fileTable.horizontalHeader().stretchLastSection = True
self.fileTable.horizontalHeader().visible = False
self.fileTable.setModel(self.fileModel)
filesFormLayout.addRow(self.fileTable)
buttonLayout = qt.QHBoxLayout()
self.addByBrowsingButton = qt.QPushButton("Browse for files")
self.clearFilesButton = qt.QPushButton("Clear files")
buttonLayout.addWidget(self.addByBrowsingButton)
buttonLayout.addWidget(self.clearFilesButton)
filesFormLayout.addRow(buttonLayout)
#
# output area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
outputCollapsibleButton.collapsed = False
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
#
# output volume selector
#
#self.outputSelector = slicer.qMRMLSubjectHierarchyComboBox()
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode",]
#self.outputSelector.setNodeTypes(["vtkMRMLScalarVolumeNode",]) ; TODO: make nodeTypes property for SH box
"""
TODO: which are supported and needed for SubjectHierarchy combo box.
TODO: can we delete/rename/create as with SH
self.outputSelector.defaultText = "Create new volume." ; # TODO any way to reset value?
"""
self.outputSelector.showChildNodeTypes = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.selectNodeUponCreation = False
self.outputSelector.noneEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.renameEnabled = True
self.outputSelector.addEnabled = True
self.outputSelector.setMRMLScene( slicer.mrmlScene )
self.outputSelector.setToolTip( "Pick the output volume to populate or None to autogenerate." )
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
self.spacing = ctk.ctkCoordinatesWidget()
self.spacing.coordinates = "1,1,1"
self.spacing.toolTip = "Set the colunm, row, slice spacing in mm"
outputFormLayout.addRow("Spacing: ", self.spacing)
self.loadButton = qt.QPushButton("Load files")
outputFormLayout.addRow(self.loadButton)
#
# Add by name area
#
addByNameCollapsibleButton = ctk.ctkCollapsibleButton()
addByNameCollapsibleButton.text = "Add files by name"
addByNameCollapsibleButton.collapsed = True
addByNameFormLayout = qt.QFormLayout(addByNameCollapsibleButton)
# Don't enable Add by name for now - let's see if it's actually needed
# self.layout.addWidget(addByNameCollapsibleButton)
forExample = """
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
pathFormat = '%s/1326__rec%04d.png'
start, end = (50, 621)
"""
self.archetypePathEdit = ctk.ctkPathLineEdit()
addByNameFormLayout.addRow("Archetype file", self.archetypePathEdit)
self.archetypeFormat = qt.QLineEdit()
addByNameFormLayout.addRow("Name format", self.archetypeFormat)
self.indexRange = ctk.ctkRangeWidget()
self.indexRange.decimals = 0
self.indexRange.maximum = 0
addByNameFormLayout.addRow("Index range", self.indexRange)
self.generateNamesButton = qt.QPushButton("Apply")
self.generateNamesButton.toolTip = "Run the algorithm."
self.generateNamesButton.enabled = False
addByNameFormLayout.addRow(self.generateNamesButton)
# connections
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.clearFilesButton.connect('clicked()', self.fileTable.model().clear)
self.archetypePathEdit.connect('currentPathChanged(QString)', self.validateInput)
self.archetypePathEdit.connect('currentPathChanged(QString)', self.updateGUIFromArchetype)
self.archetypeFormat.connect('textChanged(QString)', self.validateInput)
self.generateNamesButton.connect('clicked()', self.onGenerateNames)
# self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.validateInput) # TODO - this is missing
self.loadButton.connect('clicked()', self.onLoadButton)
# refill last selection
self.archetypePathEdit.currentPath = slicer.util.settingsValue("ImageStacks/lastArchetypePath", "")
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.validateInput()
def __init__(self):
columnNames = ["Include", "Name", "Radius"]
self.model = firstColumnCheckableModel(1, len(columnNames))
self.model.updateSelectedFuntion = self.updateSelected
for i, columnName in enumerate(columnNames):
self.model.setHeaderData(i, qt.Qt.Horizontal, columnName)
self.view = qt.QTableView()
self.view.setEditTriggers(self.view.DoubleClicked)
self.view.setSelectionMode(self.view.SingleSelection)
self.view.setSelectionBehavior(self.view.SelectRows)
self.view.horizontalHeader().setStretchLastSection(True)
self.view.verticalHeader().setDefaultSectionSize(
self.view.verticalHeader().defaultSectionSize * 3 / 4)
self.view.setHorizontalScrollMode(self.view.ScrollPerPixel)
self.view.setModel(self.model)
self.view.clicked.connect(self.onSelectionChanged)
self.view.setItemDelegateForColumn(
1, TextEditDelegate(self.model, self.renameControlPoints))
self.view.setItemDelegateForColumn(
2, SpinBoxDelegate(self.model, self.updateRadius))
super().__init__()
effectPixmap = qt.QPixmap(
os.path.join(
os.path.split(WarpDrive.__file__)[0], 'Resources', 'Icons',
'SlicerVisible.png'))
effectIcon = qt.QIcon(effectPixmap)
self.sourceVisibleButton = qt.QToolButton()
self.sourceVisibleButton.setToolButtonStyle(
qt.Qt.ToolButtonTextUnderIcon)
self.sourceVisibleButton.setIcon(effectIcon)
self.sourceVisibleButton.setIconSize(effectPixmap.rect().size())
self.sourceVisibleButton.setText('Source')
self.sourceVisibleButton.setToolTip(
'Toggle source fiducials visibility')
self.sourceVisibleButton.setCheckable(True)
self.sourceVisibleButton.setChecked(False)
self.sourceVisibleButton.setEnabled(True)
self.sourceVisibleButton.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Maximum)
self.sourceVisibleButton.toggled.connect(self.onSourceVisibleToggled)
effectPixmap = qt.QPixmap(
os.path.join(
os.path.split(WarpDrive.__file__)[0], 'Resources', 'Icons',
'SlicerVisible.png'))
effectIcon = qt.QIcon(effectPixmap)
self.targetVisibleButton = qt.QToolButton()
self.targetVisibleButton.setToolButtonStyle(
qt.Qt.ToolButtonTextUnderIcon)
self.targetVisibleButton.setIcon(effectIcon)
self.targetVisibleButton.setIconSize(effectPixmap.rect().size())
self.targetVisibleButton.setText('Target')
self.targetVisibleButton.setToolTip(
'Toggle target fiducials visibility')
self.targetVisibleButton.setCheckable(True)
self.targetVisibleButton.setChecked(False)
self.targetVisibleButton.setEnabled(True)
self.targetVisibleButton.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Maximum)
self.targetVisibleButton.toggled.connect(self.onTargetVisibleToggled)
self.buttonsFrame.layout().addWidget(self.sourceVisibleButton, 1)
self.buttonsFrame.layout().addWidget(self.targetVisibleButton, 1)
self.addButton.setText('Fixed point')
self.addButton.setToolTip('Add fixed point')
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.chartOptions = ("Count", "Volume mm^3", "Volume cc", "Min", "Max", "Mean", "StdDev")
self.logic = None
self.grayscaleNode = None
self.labelNode = None
self.fileName = None
self.fileDialog = None
# Instantiate and connect widgets ...
#
# the grayscale volume selector
#
self.grayscaleSelectorFrame = qt.QFrame(self.parent)
self.grayscaleSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel = qt.QLabel("Grayscale Volume: ", self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel.setToolTip( "Select the grayscale volume (background grayscale scalar volume node) for statistics calculations")
self.grayscaleSelectorFrame.layout().addWidget(self.grayscaleSelectorLabel)
self.grayscaleSelector = slicer.qMRMLNodeComboBox(self.grayscaleSelectorFrame)
self.grayscaleSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.grayscaleSelector.selectNodeUponCreation = False
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = True
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene( slicer.mrmlScene )
# TODO: need to add a QLabel
# self.grayscaleSelector.SetLabelText( "Master Volume:" )
self.grayscaleSelectorFrame.layout().addWidget(self.grayscaleSelector)
#
# the label volume selector
#
self.labelSelectorFrame = qt.QFrame()
self.labelSelectorFrame.setLayout( qt.QHBoxLayout() )
self.parent.layout().addWidget( self.labelSelectorFrame )
self.labelSelectorLabel = qt.QLabel()
self.labelSelectorLabel.setText( "Label Map: " )
self.labelSelectorFrame.layout().addWidget( self.labelSelectorLabel )
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
# todo addAttribute
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.removeEnabled = False
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = True
self.labelSelector.setMRMLScene( slicer.mrmlScene )
self.labelSelector.setToolTip( "Pick the label map to edit" )
self.labelSelectorFrame.layout().addWidget( self.labelSelector )
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Statistics."
self.applyButton.enabled = False
self.parent.layout().addWidget(self.applyButton)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# Chart button
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.chartFrame)
self.chartButton = qt.QPushButton("Chart")
self.chartButton.toolTip = "Make a chart from the current statistics."
self.chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox()
self.chartOption.addItems(self.chartOptions)
self.chartFrame.layout().addWidget(self.chartOption)
self.chartIgnoreZero = qt.QCheckBox()
self.chartIgnoreZero.setText('Ignore Zero')
self.chartIgnoreZero.checked = False
self.chartIgnoreZero.setToolTip('Do not include the zero index in the chart to avoid dwarfing other bars')
self.chartFrame.layout().addWidget(self.chartIgnoreZero)
self.chartFrame.enabled = False
# Save button
self.exportToTableButton = qt.QPushButton("Export to table")
self.exportToTableButton.toolTip = "Export statistics to table node"
self.exportToTableButton.enabled = False
self.parent.layout().addWidget(self.exportToTableButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.exportToTableButton.connect('clicked()', self.onExportToTable)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onLabelSelect)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
self.fileModel = qt.QStandardItemModel()
self.fileTable = qt.QTableView()
self.fileTable.horizontalHeader().stretchLastSection = True
self.fileTable.horizontalHeader().visible = False
self.fileTable.setModel(self.fileModel)
filesFormLayout.addRow(self.fileTable)
buttonLayout = qt.QHBoxLayout()
self.addByBrowsingButton = qt.QPushButton("Browse for files")
self.clearFilesButton = qt.QPushButton("Clear files")
buttonLayout.addWidget(self.addByBrowsingButton)
buttonLayout.addWidget(self.clearFilesButton)
filesFormLayout.addRow(buttonLayout)
self.propertiesLabel = qt.QLabel()
filesFormLayout.addRow(self.propertiesLabel)
#
# output area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
outputCollapsibleButton.collapsed = False
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = [
"vtkMRMLScalarVolumeNode",
]
self.outputSelector.showChildNodeTypes = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.noneEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.renameEnabled = True
self.outputSelector.addEnabled = True
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip(
"Pick the output volume to populate or None to autogenerate.")
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
self.spacing = ctk.ctkCoordinatesWidget()
self.spacing.decimals = 8
self.spacing.coordinates = "1,1,1"
self.spacing.toolTip = "Set the colunm, row, slice spacing in mm; original spacing not including downsample"
outputFormLayout.addRow("Spacing: ", self.spacing)
self.downsample = qt.QCheckBox()
self.downsample.toolTip = "Reduces data size by half in each dimension by skipping every other pixel and slice (uses about 1/8 memory)"
outputFormLayout.addRow("Downsample: ", self.downsample)
self.reverse = qt.QCheckBox()
self.reverse.toolTip = "Read the images in reverse order"
outputFormLayout.addRow("Reverse: ", self.reverse)
self.sliceSkip = ctk.ctkDoubleSpinBox()
self.sliceSkip.decimals = 0
self.sliceSkip.minimum = 0
self.sliceSkip.toolTip = "Skips the selected number of slices (use, for example, on long thin samples with more slices than in-plane resolution)"
outputFormLayout.addRow("Slice skip: ", self.sliceSkip)
self.loadButton = qt.QPushButton("Load files")
outputFormLayout.addRow(self.loadButton)
#
# Add by name area
#
addByNameCollapsibleButton = ctk.ctkCollapsibleButton()
addByNameCollapsibleButton.text = "Add files by name"
addByNameCollapsibleButton.collapsed = True
addByNameFormLayout = qt.QFormLayout(addByNameCollapsibleButton)
# Don't enable Add by name for now - let's see if it's actually needed
# self.layout.addWidget(addByNameCollapsibleButton)
forExample = """
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
pathFormat = '%s/1326__rec%04d.png'
start, end = (50, 621)
"""
self.archetypePathEdit = ctk.ctkPathLineEdit()
addByNameFormLayout.addRow("Archetype file", self.archetypePathEdit)
self.archetypeFormat = qt.QLineEdit()
addByNameFormLayout.addRow("Name format", self.archetypeFormat)
self.indexRange = ctk.ctkRangeWidget()
self.indexRange.decimals = 0
self.indexRange.maximum = 0
addByNameFormLayout.addRow("Index range", self.indexRange)
self.generateNamesButton = qt.QPushButton("Apply")
self.generateNamesButton.toolTip = "Run the algorithm."
self.generateNamesButton.enabled = False
addByNameFormLayout.addRow(self.generateNamesButton)
# connections
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.clearFilesButton.connect('clicked()', self.onClearFiles)
self.archetypePathEdit.connect('currentPathChanged(QString)',
self.validateInput)
self.archetypePathEdit.connect('currentPathChanged(QString)',
self.updateGUIFromArchetype)
self.archetypeFormat.connect('textChanged(QString)',
self.validateInput)
self.generateNamesButton.connect('clicked()', self.onGenerateNames)
# self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.validateInput) # TODO - this is missing
self.loadButton.connect('clicked()', self.onLoadButton)
# refill last selection
self.archetypePathEdit.currentPath = slicer.util.settingsValue(
"ImageStacks/lastArchetypePath", "")
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.validateInput()
def createSmall(self):
"""Make the internals of the widget to display in the
Data Probe frame (lower left of slicer main window by default)"""
# top row - things about the viewer itself
self.viewerFrame = qt.QFrame(self.frame)
self.viewerFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.viewerFrame)
self.viewerColor = qt.QLabel(self.viewerFrame)
self.viewerFrame.layout().addWidget(self.viewerColor)
self.viewerName = qt.QLabel(self.viewerFrame)
self.viewerFrame.layout().addWidget(self.viewerName)
self.viewerRAS = qt.QLabel()
self.viewerFrame.layout().addWidget(self.viewerRAS)
self.viewerOrient = qt.QLabel()
self.viewerFrame.layout().addWidget(self.viewerOrient)
self.viewerSpacing = qt.QLabel()
self.viewerFrame.layout().addWidget(self.viewerSpacing)
self.viewerFrame.layout().addStretch(1)
# the grid - things about the layers
if True:
# this method makes labels
self.layerGrid = qt.QFrame(self.frame)
self.layerGrid.setLayout(qt.QGridLayout())
self.frame.layout().addWidget(self.layerGrid)
layers = ('L', 'F', 'B')
self.layerNames = {}
self.layerIJKs = {}
self.layerValues = {}
row = 0
for layer in layers:
col = 0
self.layerGrid.layout().addWidget(qt.QLabel(layer), row, col)
col += 1
self.layerNames[layer] = qt.QLabel()
self.layerGrid.layout().addWidget(self.layerNames[layer], row,
col)
col += 1
self.layerIJKs[layer] = qt.QLabel()
self.layerGrid.layout().addWidget(self.layerIJKs[layer], row,
col)
col += 1
self.layerValues[layer] = qt.QLabel()
self.layerGrid.layout().addWidget(self.layerValues[layer], row,
col)
self.layerGrid.layout().setColumnStretch(col, 100)
col += 1
row += 1
else:
# this method use a model/view
self.layerView = qt.QTableView(self.frame)
self.layerView.verticalHeader().hide()
self.frame.layout().addWidget(self.layerView)
self.layerModel = qt.QStandardItemModel()
self.layerView.setModel(self.layerModel)
layers = ('L', 'F', 'B')
self.layerNames = {}
self.layerIJKs = {}
self.layerValues = {}
self.items = []
row = 0
for layer in layers:
col = 0
item = qt.QStandardItem()
item.setText(layer)
self.layerModel.setItem(row, col, item)
self.items.append(item)
col += 1
self.layerNames[layer] = qt.QStandardItem()
self.layerModel.setItem(row, col, self.layerNames[layer])
col += 1
self.layerIJKs[layer] = qt.QStandardItem()
self.layerModel.setItem(row, col, self.layerIJKs[layer])
col += 1
self.layerValues[layer] = qt.QStandardItem()
self.layerModel.setItem(row, col, self.layerValues[layer])
col += 1
row += 1
self.layerView.setColumnWidth(0, 15)
self.layerView.setColumnWidth(1, 80)
self.layerView.setColumnWidth(2, 65)
self.layerView.setColumnWidth(3, 55)
self.layerModel.setHeaderData(0, 1, "")
self.layerModel.setHeaderData(1, 1, "Volume")
self.layerModel.setHeaderData(2, 1, "IJK")
self.layerModel.setHeaderData(3, 1, "Value")
# goto module button
self.goToModule = qt.QPushButton('->', self.frame)
self.goToModule.setToolTip(
'Go to the DataProbe module for more information and options')
self.frame.layout().addWidget(self.goToModule)
self.goToModule.connect("clicked()", self.onGoToModule)
# hide this for now - there's not much to see in the module itself
self.goToModule.hide()
