def setup(self):
self.tableAreaWidget = qt.QWidget()
self.layout.addWidget(self.tableAreaWidget)
self.tableLayout = qt.QVBoxLayout(self.tableAreaWidget)
label = qt.QLabel('Clinical Data')
#self.tableLayout.addWidget(label)
self.clinicalDataTableWidget = qt.QTableWidget()
self.tableLayout.addWidget(self.clinicalDataTableWidget)
verticalheader = self.clinicalDataTableWidget.verticalHeader()
verticalheader.setDefaultSectionSize(20)
self.buttonsWidget = qt.QWidget()
self.buttonsLayout = qt.QHBoxLayout(self.buttonsWidget)
self.layout.addWidget(self.buttonsWidget)
self.accessLabel = qt.QLabel('')
self.buttonsLayout.addWidget(self.accessLabel)
self.buttonsLayout.addStretch(1)
self.updateButton = qt.QPushButton('Update Cache')
self.updateButton.toolTip = 'Connect to cBioPortal and update the data'
self.buttonsLayout.addWidget(self.updateButton)
self.closeButton = qt.QPushButton('Close')
self.buttonsLayout.addWidget(self.closeButton)
# Connections
self.updateButton.connect('clicked(bool)', self.onUpdateButton)
self.closeButton.connect('clicked(bool)', self.onCloseButton)
def displaySearchResults( self, searchResults ): # look into highlighting query rows or another option to remove session numbers
# Add a table with all the search results
searchResultsTable = qt.QTableWidget()
searchResultsTable.setWindowTitle( "Sessions" )
searchResultsTable.resize( 6 * SEARCH_TABLE_ID_COLUMN_WIDTH, 4 * SEARCH_TABLE_ID_COLUMN_WIDTH )
searchResultsTable.setRowCount( len( searchResults ) )
searchResultsTable.setColumnCount( SEARCH_TABLE_NUMBER_OF_COLUMNS )
searchResultsTable.setHorizontalHeaderItem( 0, qt.QTableWidgetItem( "User ID" ) )
searchResultsTable.setColumnWidth( 0, SEARCH_TABLE_ID_COLUMN_WIDTH )
searchResultsTable.setHorizontalHeaderItem( 1, qt.QTableWidgetItem( "Study ID" ) )
searchResultsTable.setColumnWidth( 1, SEARCH_TABLE_ID_COLUMN_WIDTH )
searchResultsTable.setHorizontalHeaderItem( 2, qt.QTableWidgetItem( "Trial ID" ) )
searchResultsTable.setColumnWidth( 2, SEARCH_TABLE_ID_COLUMN_WIDTH )
searchResultsTable.setHorizontalHeaderItem( 3, qt.QTableWidgetItem( "Skill Level" ) )
searchResultsTable.setColumnWidth( 3, SEARCH_TABLE_ID_COLUMN_WIDTH )
searchResultsTable.setHorizontalHeaderItem( 4, qt.QTableWidgetItem( "Date" ) )
searchResultsTable.setColumnWidth( 4, 2 * SEARCH_TABLE_ID_COLUMN_WIDTH )
for row in range( len( searchResults ) ):
for col in range( SEARCH_TABLE_NUMBER_OF_COLUMNS ):
searchResultsTable.setItem( row, col, qt.QTableWidgetItem( searchResults[ row ][ col ] ) )
searchResultsTable.show()
searchResultsTable.connect( "cellDoubleClicked(int,int)", partial( self.onLoadSession, searchResultsTable, searchResults ) )
def addTableWidget(self):
self.tableWidgetBox = qt.QGroupBox()
layout = qt.QHBoxLayout()
self.tableWidgetBox.setLayout(layout)
self.tableWidgetBox.setStyleSheet('QGroupBox{border:0;}')
self.tableWidget = qt.QTableWidget()
self.tableWidget.setStyleSheet('QGroupBox{border:0;}')
self.tableWidget.horizontalScrollBar().setEnabled(True)
self.tableWidget.setHorizontalScrollBarPolicy(1)
self.tableWidget.setVerticalScrollBarPolicy(1)
#layout.setColumnMinimumWidth(0,340)
#layout.setRowMinimumHeight(0,100)
#layout.setGeometry (qt.QRect(0, 0, 340, 100))
layout.addWidget(self.tableWidget)
#self.tableWidget.setGeometry (qt.QRect(0, 0, 400, 200))
#self.tableWidget.setMinimumHeight(200)
#self.tableWidget.setMinimumWidth(300)
self.tableWidget.setObjectName('tableWidget')
self.tableWidget.setColumnCount(2)
self.tableWidget.setRowCount(2)
#self.tableWidget.resizeRowsToContents()
#self.tableWidget.resizeColumnsToContents()
self.tableWidget.setHorizontalHeaderLabels(
"Venous;Ventricle".split(";"))
self.tableWidget.setVerticalHeaderLabels("Serial1;Serial2".split(";"))
def setupTargetTable(self): self.table = qt.QTableWidget(0, 2) self.table.setSelectionBehavior(qt.QAbstractItemView.SelectRows) self.table.setSelectionMode(qt.QAbstractItemView.SingleSelection) self.table.setMaximumHeight(200) self.table.horizontalHeader().setStretchLastSection(True) self.resetTable() self.layout().addWidget(self.table)
def __init__(self,parent, width=350,height=100):
self.widget = qt.QTableWidget(parent)
self.widget.setMinimumHeight(height)
self.widget.setMinimumWidth(width)
self.width = width
self.height = height
self.items = []
self.loadables = {}
self.setLoadables([])
def build_process_setup(self):
self.processTable = qt.QTableWidget(0, 1)
self.processTable.setEditTriggers(qt.QAbstractItemView.NoEditTriggers)
self.processTable.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.processTable.horizontalHeader().hide()
self.processTable.horizontalHeader().setSectionResizeMode(
0, qt.QHeaderView.Stretch)
self.processTable.setSizePolicy(qt.QSizePolicy.Minimum,
qt.QSizePolicy.Minimum)
self.processTable.setMaximumHeight(70)
self.processTools = qt.QFrame()
box = qt.QHBoxLayout(self.processTools)
box.addWidget(
InterfaceTools.build_button(
'Add Custom Elastix', lambda: self.click_add_registration_step(
RegistrationType.CUSTOM_ELASTIX)))
box.addWidget(
InterfaceTools.build_button(
'Add Custom BRAINS',
lambda: self.click_add_registration_step(RegistrationType.
CUSTOM_BRAINS),
tooltip='transformType : Rigid' + '\n' +
'samplingPercentage : 1.0' + '\n' +
'initialTransformMode : off' + '\n' +
'maskProcessingMode : NOMASK' + '\n' +
'costMetric : NC' + '\n' +
'numberOfIterations : 1000' + '\n' +
'minimumStepLength : 0.0000001' + '\n' +
'maximumStepLength : 0.001' + '\n' +
'skewScale : 1.0' + '\n' +
'reproportionScale : 1.0' + '\n' +
'relaxationFactor : 0.5' + '\n' +
'translationScale : 1.0'))
b = InterfaceTools.build_button('Clear',
self.click_clear_registration_step)
b.setFixedWidth(73)
box.addWidget(b)
box.setContentsMargins(0, 0, 0, 0)
layout = qt.QFormLayout()
layout.addRow("Registration Steps:", self.processTable)
layout.addWidget(self.processTools)
layout.setMargin(10)
return layout
def build_volume_pair_table(self):
self.volumeTable = qt.QTableWidget(0, 3)
self.volumeTable.setEditTriggers(qt.QAbstractItemView.NoEditTriggers)
self.volumeTable.setHorizontalHeaderLabels(
["Fixed Volume", "Moving Volume", "Status"])
self.volumeTable.verticalHeader().setFixedWidth(30)
self.volumeTable.verticalHeader().setSectionResizeMode(
qt.QHeaderView.Fixed)
self.volumeTable.horizontalHeader().setSectionResizeMode(
0, qt.QHeaderView.Stretch)
self.volumeTable.horizontalHeader().setSectionResizeMode(
1, qt.QHeaderView.Stretch)
self.volumeTable.setColumnWidth(2, 70)
self.volumeTable.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.volumeTable.connect('itemSelectionChanged()',
self.update_selection)
layout = qt.QVBoxLayout()
layout.addWidget(self.volumeTable)
layout.setMargin(10)
return layout
def setup(self):
# Instantiate and connect widgets ...
ScriptedLoadableModuleWidget.setup(self)
#self.logic = CIP_CalciumScoringLogic()
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# target volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
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("Target Volume: ", self.inputSelector)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onVolumeChanged)
self.volumeNode = self.inputSelector.currentNode()
#
# calcification type
#
# self.calcificationTypeBox = qt.QComboBox()
# self.calcificationTypeBox.addItem("Heart")
# self.calcificationTypeBox.addItem("Aorta")
# parametersFormLayout.addRow("Region", self.calcificationTypeBox)
# self.calcificationTypeBox.connect("currentIndexChanged(int)", self.onTypeChanged)
self.ThresholdRange = ctk.ctkRangeWidget()
self.ThresholdRange.minimum = 0
self.ThresholdRange.maximum = 2000
self.ThresholdRange.setMinimumValue(self.ThresholdMin)
self.ThresholdRange.setMaximumValue(self.ThresholdMax)
self.ThresholdRange.connect("minimumValueChanged(double)", self.onThresholdMinChanged)
self.ThresholdRange.connect("maximumValueChanged(double)", self.onThresholdMaxChanged)
parametersFormLayout.addRow("Threshold Value", self.ThresholdRange)
self.ThresholdRange.setMinimumValue(self.ThresholdMin)
self.ThresholdRange.setMaximumValue(self.ThresholdMax)
self.LesionSizeRange= ctk.ctkRangeWidget()
self.LesionSizeRange.minimum = 0.5
self.LesionSizeRange.maximum = 1000
self.LesionSizeRange.setMinimumValue(self.MinimumLesionSize)
self.LesionSizeRange.setMaximumValue(self.MaximumLesionSize)
self.LesionSizeRange.connect("minimumValueChanged(double)", self.onMinSizeChanged)
self.LesionSizeRange.connect("maximumValueChanged(double)", self.onMaxSizeChanged)
parametersFormLayout.addRow("Lesion Size (mm^3)", self.LesionSizeRange)
self.LesionSizeRange.setMinimumValue(self.MinimumLesionSize)
self.LesionSizeRange.setMaximumValue(self.MaximumLesionSize)
self.scoreField=dict()
for sr in self.summary_reports:
self.scoreField[sr] = qt.QLineEdit()
self.scoreField[sr].setText(0)
parametersFormLayout.addRow("Total "+sr, self.scoreField[sr])
#
# Update button and Select Table
#
self.updateButton = qt.QPushButton("Update")
self.updateButton.toolTip = "Update calcium score computation"
self.updateButton.enabled = True
self.updateButton.setFixedSize(100, 50)
#parametersFormLayout.addRow("", self.updateButton)
self.updateButton.connect('clicked()', self.onUpdate)
#
# Select table
#
self.selectLabels = qt.QTableWidget()
#self.selectLabels.horizontalHeader().hide()
self.selectLabels.verticalHeader().hide()
self.selectLabels.setColumnCount(6)
self.selectLabels.itemClicked.connect(self.handleItemClicked)
#Add row with columns name
col_names=["","Agatston Score","Mass Score","Volume (mm^3)","Mean HU","Max HU"]
self.selectLabels.setHorizontalHeaderLabels(col_names)
parametersFormLayout.addRow(self.updateButton, self.selectLabels)
#
# Save Widget Area
#
#self.saveCollapsibleButton = ctk.ctkCollapsibleButton()
#self.saveCollapsibleButton.text = "Saving"
#self.layout.addWidget(self.saveCollapsibleButton)
self.reportsWidget = CaseReportsWidget(self.moduleName, self.columnsDict, parentWidget=self.parent)
self.reportsWidget.setup()
self.reportsWidget.showPrintButton(False)
self.reportsWidget.addObservable(self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
#
# ROI Area
#
self.roiCollapsibleButton = ctk.ctkCollapsibleButton()
self.roiCollapsibleButton.text = "ROI"
self.roiCollapsibleButton.setChecked(False)
self.layout.addWidget(self.roiCollapsibleButton)
# Layout within the dummy collapsible button
roiFormLayout = qt.QFormLayout(self.roiCollapsibleButton)
#
# ROI
#
self.ROIWidget = slicer.qMRMLAnnotationROIWidget()
self.roiNode = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(self.roiNode)
self.ROIWidget.setMRMLAnnotationROINode(self.roiNode)
roiFormLayout.addRow("", self.ROIWidget)
#self.roiNode.AddObserver("ModifiedEvent", self.onROIChangedEvent, 1)
# Add vertical spacer
self.layout.addStretch(1)
# Add temp nodes
self.croppedNode=slicer.vtkMRMLScalarVolumeNode()
self.croppedNode.SetHideFromEditors(1)
slicer.mrmlScene.AddNode(self.croppedNode)
self.labelsNode=slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(self.labelsNode)
if self.inputSelector.currentNode():
self.onVolumeChanged(self.inputSelector.currentNode())
def __init__(self,parent): self.widget = qt.QTableWidget(parent,width=350,height=300) self.items = [] self.setHeader(None)
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)
l = slicer.modules.createmodels.logic()
self.needleModel = l.CreateNeedle(150, 0.4, 0, False)
#This code block creates a collapsible button
#This defines which type of button you are using
self.usContainer = ctk.ctkCollapsibleButton()
#This is what the button will say
self.usContainer.text = "Ultrasound Information"
#Thiss actually creates that button
self.layout.addWidget(self.usContainer)
#This creates a variable that describes layout within this collapsible button
self.usLayout = qt.QFormLayout(self.usContainer)
#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 is the text that is input inot the line
self.IPLabel = qt.QLabel("Server IP:")
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.usLayout.addRow(self.IPLabel, self.inputIPLineEdit)
#This code block is the exact same as the one above only it asks for the server port
self.layout.addWidget(self.usContainer)
self.inputPortLineEdit = qt.QLineEdit()
self.inputPortLineEdit.setPlaceholderText("18944")
self.inputPortLineEdit.setValidator(qt.QIntValidator())
self.inputPortLineEdit.toolTip = "Put the Port of your ultrasound device here"
self.portLabel = qt.QLabel("Sever Port:")
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.usLayout.addRow(self.portLabel, self.inputPortLineEdit)
#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
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.usLayout.addWidget(self.connectButton)
# 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.usLayout.addRow("US Volume: ", self.imageSelector)
#add combo box for linear transform node
self.TransformSelector = slicer.qMRMLNodeComboBox()
self.TransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.TransformSelector.selectNodeUponCreation = True
self.TransformSelector.addEnabled = False
self.TransformSelector.removeEnabled = False
self.TransformSelector.noneEnabled = True
self.TransformSelector.showHidden = False
self.TransformSelector.showChildNodeTypes = False
self.TransformSelector.setMRMLScene( slicer.mrmlScene )
self.TransformSelector.setToolTip( "Pick the transform representing the straw line." )
self.usLayout.addRow("Tip to Probe: ", self.TransformSelector)
self.calibrationContainer = ctk.ctkCollapsibleButton()
#This is what the button will say
self.calibrationContainer.text = "Calibration Parameters"
#Thiss actually creates that button
self.layout.addWidget(self.calibrationContainer)
#This creates a variable that describes layout within this collapsible button
self.calibrationLayout = qt.QFormLayout(self.calibrationContainer)
self.segLabel = qt.QLabel()
self.calibrationLayout.addRow(qt.QLabel("Type of segmentation:"), self.segLabel)
self.recordContainer = ctk.ctkCollapsibleButton()
#This is what the button will say
self.recordContainer.text = "Recording Options"
#Thiss actually creates that button
#This creates a variable that describes layout within this collapsible button
self.recordLayout = qt.QFormLayout(self.recordContainer)
self.RecordButton = qt.QPushButton()
self.RecordButton.text = "Start Recording"
self.recordLayout.addWidget(self.RecordButton)
self.StopRecordButton = qt.QPushButton()
self.StopRecordButton.text = "Stop Recording"
self.recordLayout.addWidget(self.StopRecordButton)
self.pathInput = qt.QLineEdit()
self.pathInput.setPlaceholderText("Enter the path to save files to")
self.pathText = qt.QLabel("File Path:")
self.recordLayout.addRow(self.pathText, self.pathInput)
self.SaveRecordButton = qt.QPushButton()
self.SaveRecordButton.text = "Save Recording"
self.recordLayout.addWidget(self.SaveRecordButton)
# This creates another collapsible button
self.fiducialContainer = ctk.ctkCollapsibleButton()
self.fiducialContainer.text = "Registration"
self.fiducialLayout = qt.QFormLayout(self.fiducialContainer)
#This is the exact same as the code block below but it freezes the US to capture a screenshot
self.freezeButton = qt.QPushButton()
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.freezeButton.text = "Freeze"
else:
self.freezeButton.text = "Place Fiducial"
self.freezeButton.toolTip = "Freeze the ultrasound image for fiducial placement"
self.fiducialLayout.addRow(self.freezeButton)
self.shortcut = qt.QShortcut(qt.QKeySequence('f'), slicer.util.mainWindow())
self.numFidLabel = qt.QLabel()
self.fiducialLayout.addRow(qt.QLabel("Fiducials collected:"), self.numFidLabel)
self.transformTable = qt.QTableWidget()
self.transTableItem = qt.QTableWidgetItem()
self.fidError = qt.QLabel()
self.transformTable.setRowCount(4)
self.transformTable.setColumnCount(4)
self.transformTable.horizontalHeader().hide()
self.transformTable.verticalHeader().hide()
self.transformTable.setItem(0,0, qt.QTableWidgetItem("1"))
self.transformTable.setItem(0,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,1, qt.QTableWidgetItem("1"))
self.transformTable.setItem(1,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,2, qt.QTableWidgetItem("1"))
self.transformTable.setItem(2,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,3, qt.QTableWidgetItem("1"))
self.transformTable.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.MinimumExpanding)
self.copyIcon =qt.QIcon(":Icons/Medium/SlicerEditCopy.png")
self.copyButton = qt.QPushButton()
self.copyButton.setIcon(self.copyIcon)
self.copyButton.toolTip = "Copy"
self.copyButton.setMaximumWidth(64)
self.copyHbox = qt.QHBoxLayout()
self.copyHbox.addWidget(self.copyButton)
self.copyButton.enabled = False
if self.numFidLabel >= 2:
self.copyButton.enabled = True
self.fiducialLayout.addRow(qt.QLabel("Image to probe transform:"))
self.fiducialLayout.addRow(self.transformTable)
# Add vertical spacer
self.layout.addStretch(1)
# Add vertical spacer
self.layout.addStretch(1)
self.fiducialLayout.addRow("Copy:", self.copyHbox)
self.validationContainer = ctk.ctkCollapsibleButton()
self.validationContainer.text = "Validation"
self.validationLayout = qt.QFormLayout(self.validationContainer)
self.visualizeButton = qt.QPushButton('Show 3D Scene')
self.visualizeButton.toolTip = "This button enables the 3D view for visual validation"
self.validationLayout.addRow(self.visualizeButton)
self.visualizeButton.connect('clicked(bool)', self.onVisualizeButtonClicked)
self.resetButton = qt.QPushButton('Reset')
self.resetButton.setDefault(False)
self.resetButton.toolTip = "This Button Resets the Module"
self.validationLayout.addRow(self.resetButton)
# Add the containers to the parent
self.layout.addWidget(self.usContainer)
self.layout.addWidget(self.calibrationContainer)
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.layout.addWidget(self.recordContainer)
self.layout.addWidget(self.fiducialContainer)
#self.layout.addWidget(self.transformContainer)
self.layout.addWidget(self.validationContainer)
# Add vertical spacer
self.layout.addStretch(1)
# Connections
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.connectButton.connect('clicked(bool)', self.onConnectButtonClicked)
self.freezeButton.connect('clicked(bool)', self.onConnectButtonClicked)
self.shortcut.connect('activated()', self.onConnectButtonClicked)
else:
self.shortcut.connect('activated()', self.onFiducialClicked)
self.freezeButton.connect('clicked(bool)', self.onFiducialClicked)
self.RecordButton.connect('clicked(bool)', self.onRecordButtonClicked)
self.StopRecordButton.connect('clicked(bool)', self.onStopRecordButtonClicked)
self.SaveRecordButton.connect('clicked(bool)', self.onSaveRecordButtonClicked)
self.copyButton.connect('clicked(bool)', self.onCopyButtonClicked)
self.inputIPLineEdit.connect('textChanged(QString)', self.onInputChanged)
self.inputPortLineEdit.connect('textChanged(QString)', self.onInputChanged)
self.imageSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onImageChanged)
self.TransformSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onTransformChanged)
self.resetButton.connect('clicked(bool)', self.onResetButtonClicked)
# Disable buttons until conditions are met
self.connectButton.setEnabled(True)
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.freezeButton.setEnabled(False)
self.StopRecordButton.setEnabled(False)
self.sceneObserverTag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, self.onNodeAdded)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = CNN_Image_ClassifierLogic()
self.moduleDir = os.path.dirname(
slicer.modules.collect_training_images.path)
# 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)
self.modelSelector = qt.QComboBox()
self.modelSelector.addItems(["Select model"])
modelDirectoryContents = os.listdir(
os.path.join(self.moduleDir, os.pardir, "Models/retrainContainer"))
modelNames = [
dir for dir in modelDirectoryContents
if dir.find(".") == -1 and dir != "Dockerfile"
]
self.modelSelector.addItems(["Create new model"])
self.modelSelector.addItems(modelNames)
parametersFormLayout.addRow(self.modelSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Start")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# Object table
#
self.objectTable = qt.QTableWidget()
self.objectTable.setColumnCount(3)
self.objectTable.setHorizontalHeaderLabels(
["Name", "Found", "Confidence"])
parametersFormLayout.addRow(self.objectTable)
#
# Adjust Confidence Thresholds
#
confidenceThresholdsCollapsibleButton = ctk.ctkCollapsibleButton()
confidenceThresholdsCollapsibleButton.text = "Confidence Thresholds"
self.layout.addWidget(confidenceThresholdsCollapsibleButton)
confidenceFormLayout = qt.QFormLayout(
confidenceThresholdsCollapsibleButton)
self.confidenceSlider = qt.QSlider(0x1) #horizontal slider
self.confidenceSlider.setRange(0, 100)
self.confidenceSlider.setTickInterval(5)
self.confidenceSlider.setTickPosition(2) #Ticks appear below slider
self.confidenceSlider.setSliderPosition(80)
self.confidenceSlider.setToolTip(
"Set the minimum degree of confidence that must be met for an object to be considered found"
)
confidenceFormLayout.addRow("Confidence: ", self.confidenceSlider)
self.confidenceLabel = qt.QLabel("80%")
confidenceFormLayout.addRow(self.confidenceLabel)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.modelSelector.connect('currentIndexChanged(int)',
self.onModelSelected)
self.confidenceSlider.connect('sliderMoved(int)',
self.onConfidenceChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
self.webcamReference = slicer.util.getNode('Webcam_Reference')
if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
####################
# For debugging
#
# Reload and Test area
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
reloadCollapsibleButton.collapsed = True
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "PathCollisionAnalysis Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
#
####################
#
# Main area
#
mainCollapsibleButton = ctk.ctkCollapsibleButton()
mainCollapsibleButton.text = "Collision Analysis"
mainCollapsibleButton.collapsed = False
self.layout.addWidget(mainCollapsibleButton)
mainFormLayout = qt.QFormLayout(mainCollapsibleButton)
# - input fiducials (trajectory) selector
self.inputFiducialSelector = slicer.qMRMLNodeComboBox()
self.inputFiducialSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.inputFiducialSelector.selectNodeUponCreation = True
self.inputFiducialSelector.addEnabled = True
self.inputFiducialSelector.removeEnabled = True
self.inputFiducialSelector.noneEnabled = False
self.inputFiducialSelector.showHidden = False
self.inputFiducialSelector.showChildNodeTypes = False
self.inputFiducialSelector.setMRMLScene(slicer.mrmlScene)
self.inputFiducialSelector.setToolTip("Pick the trajectory.")
mainFormLayout.addRow("Trajectory: ", self.inputFiducialSelector)
# - Model selector
self.inputModelHierarchySelector = slicer.qMRMLNodeComboBox()
self.inputModelHierarchySelector.nodeTypes = [
"vtkMRMLModelHierarchyNode"
]
self.inputModelHierarchySelector.selectNodeUponCreation = True
self.inputModelHierarchySelector.addEnabled = True
self.inputModelHierarchySelector.removeEnabled = True
self.inputModelHierarchySelector.noneEnabled = False
self.inputModelHierarchySelector.showHidden = False
self.inputModelHierarchySelector.showChildNodeTypes = False
self.inputModelHierarchySelector.setMRMLScene(slicer.mrmlScene)
self.inputModelHierarchySelector.setToolTip("Select a 3D Model")
mainFormLayout.addRow("Model:", self.inputModelHierarchySelector)
self.modelNode = None
#self.inputModelHierarchySelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onModelSelected)
self.intersectionTable = qt.QTableWidget(1, 6)
self.intersectionTable.setSelectionBehavior(
qt.QAbstractItemView.SelectRows)
self.intersectionTable.setSelectionMode(
qt.QAbstractItemView.SingleSelection)
self.intersectionTableHeader = [
"Model", "Entry 1", "Entry 2", "Length", "Curvature 1",
"Curvature 2"
]
self.intersectionTable.setHorizontalHeaderLabels(
self.intersectionTableHeader)
self.intersectionTable.horizontalHeader().setStretchLastSection(True)
mainFormLayout.addWidget(self.intersectionTable)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
mainFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputModelHierarchySelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
# variables
self.objectIDs = None
self.objectNames = None
self.normalVectors = None
self.entryAngles = None
self.totalLengthInObject = None
self.curvatures = None
self.radiusNormals = None
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)
#
# Spawn table view for common DICOM tags and their values
#
self.taglist = {
"Patient ID" : "N/A",
"Patient Name" : "N/A",
"Patient Birth Date" : "N/A",
"Patient Sex" : "N/A",
"Study ID" : "N/A",
"Study Date" : "N/A",
"Study Description" : "N/A",
"Study Instance UID" : "N/A",
"Series Number" : "N/A",
"Modality" : "N/A",
"Series Date" : "N/A",
"Series Description" : "N/A",
"Protocol Name" : "N/A",
"Body Part Examined" : "N/A",
"Patient Position" : "N/A",
"Columns" : "N/A",
"Rows" : "N/A",
"Number of Slices" : "N/A",
"Pixel Spacing" : "N/A",
"Slice Thickness" : "N/A",
"Spacing Between Slices" : "N/A",
"Voxel Size" : "N/A",
"Field of View" : "N/A",
"Series Instance UID" : "N/A",
}
self.table = qt.QTableWidget(parametersCollapsibleButton)
self.table.setColumnCount(2)
#self.table.setRowCount(24)
self.table.setRowCount(len(self.taglist))
self.table.setHorizontalHeaderLabels(["Attribute", "Value"]) # This must follow table resize
i = 0
for key, value in self.taglist.iteritems():
self.table.setItem(i, 0, qt.QTableWidgetItem(key))
self.table.setItem(i, 1, qt.QTableWidgetItem(value))
i = i + 1
#for i in range(25):
# self.table.setItem(i, 1, qt.QTableWidgetItem("N/A"))
self.table.resizeColumnsToContents()
self.table.resizeRowsToContents()
self.table.setAlternatingRowColors(True)
self.table.setShowGrid(False)
self.table.verticalHeader().hide()
parametersFormLayout.addRow("Volume Info:", self.table)
# connections
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Table view state
self.onSelect(self.inputSelector.currentNode())
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.pbucLogic = PointerBasedUSCalibrationLogic() # Have reference to an instance of the logic
#
# Tracked ultrasound playback toolbox
#
self.playToolBox = qt.QToolBox()
self.layout.addWidget( self.playToolBox )
#
# Real-time playback
#
self.realTimeFrame = qt.QFrame( self.playToolBox )
self.realTimeLayout = qt.QVBoxLayout( self.realTimeFrame )
self.connectorNodeSelector = slicer.qMRMLNodeComboBox()
self.connectorNodeSelector.nodeTypes = [ "vtkMRMLIGTLConnectorNode" ]
self.connectorNodeSelector.addEnabled = False
self.connectorNodeSelector.removeEnabled = False
self.connectorNodeSelector.noneEnabled = False
self.connectorNodeSelector.showHidden = False
self.connectorNodeSelector.showChildNodeTypes = False
self.connectorNodeSelector.setMRMLScene( slicer.mrmlScene )
self.connectorNodeSelector.setToolTip( "Select the connector node for playback." )
self.realTimeLayout.addWidget( self.connectorNodeSelector )
self.freezeButton = qt.QPushButton( "Freeze" )
self.freezeButton.setToolTip( "Freeze the connection." )
self.realTimeLayout.addWidget( self.freezeButton )
#
# Recorded sequence playback
#
self.sequenceFrame = qt.QFrame( self.playToolBox )
self.sequenceLayout = qt.QVBoxLayout( self.sequenceFrame )
self.sequenceBrowserNodeSelector = slicer.qMRMLNodeComboBox()
self.sequenceBrowserNodeSelector.nodeTypes = [ "vtkMRMLSequenceBrowserNode" ]
self.sequenceBrowserNodeSelector.addEnabled = False
self.sequenceBrowserNodeSelector.removeEnabled = False
self.sequenceBrowserNodeSelector.noneEnabled = False
self.sequenceBrowserNodeSelector.showHidden = False
self.sequenceBrowserNodeSelector.showChildNodeTypes = False
self.sequenceBrowserNodeSelector.setMRMLScene( slicer.mrmlScene )
self.sequenceBrowserNodeSelector.setToolTip( "Select the sequence browser node for playback." )
self.sequenceLayout.addWidget( self.sequenceBrowserNodeSelector )
self.sequenceBrowserPlayWidget = slicer.qMRMLSequenceBrowserPlayWidget() # TODO: Somehow disable the recording button without changing sequences' recording states
self.sequenceBrowserPlayWidget.setMRMLSequenceBrowserNode( self.sequenceBrowserNodeSelector.currentNode() )
self.sequenceLayout.addWidget( self.sequenceBrowserPlayWidget )
self.sequenceBrowserSeekWidget = slicer.qMRMLSequenceBrowserSeekWidget()
self.sequenceBrowserSeekWidget.setMRMLSequenceBrowserNode( self.sequenceBrowserNodeSelector.currentNode() )
self.sequenceLayout.addWidget( self.sequenceBrowserSeekWidget )
# Add the playback modes to the tool box
self.playToolBox.addItem( self.realTimeFrame, "Real-time" )
self.playToolBox.addItem( self.sequenceFrame, "Sequence" )
#
# Points group box
#
self.pointGroupBox = qt.QGroupBox()
self.pointGroupBox.setTitle( "Points" )
self.layout.addWidget( self.pointGroupBox )
# Layout within the group box
self.pointGroupBoxLayout = qt.QHBoxLayout( self.pointGroupBox )
# Mark point
self.markPointButton = qt.QPushButton( "Mark Point" )
self.markPointButton.setIcon( qt.QIcon( ":/Icons/MarkupsMouseModePlace.png" ) )
self.markPointButton.setToolTip( "Start placing a point on the ultrasound image." )
self.pointGroupBoxLayout.addWidget( self.markPointButton )
# Undo
self.undoPointsButton = qt.QPushButton( "" )
self.undoPointsButton.setIcon( qt.QIcon( ":/Icons/Small/SlicerUndo.png" ) )
self.undoPointsButton.setSizePolicy( qt.QSizePolicy.Fixed, qt.QSizePolicy.Fixed )
self.undoPointsButton.setToolTip( "Remove the most recently placed point." )
self.pointGroupBoxLayout.addWidget( self.undoPointsButton )
# Reset
self.resetPointsButton = qt.QPushButton( "" )
self.resetPointsButton.setIcon( qt.QApplication.style().standardIcon( qt.QStyle.SP_DialogResetButton ) )
self.resetPointsButton.setSizePolicy( qt.QSizePolicy.Fixed, qt.QSizePolicy.Fixed )
self.resetPointsButton.setToolTip( "Clear all points." )
self.pointGroupBoxLayout.addWidget( self.resetPointsButton )
#
# Result label
#
self.calibrationResultLabel = qt.QLabel()
self.calibrationResultLabel.setText( "No calibration parameters selected." )
self.calibrationResultLabel.setToolTip( "Output from the calibration." )
self.layout.addWidget( self.calibrationResultLabel )
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.setText( "Advanced" )
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget( self.advancedCollapsibleButton )
# Layout within the collapsible button
self.advancedLayout = qt.QFormLayout( self.advancedCollapsibleButton )
# Mark point
self.applyButton = qt.QPushButton( "Apply" )
self.applyButton.setToolTip( "Apply the ImageToProbe transform to the ultrasound image." )
self.advancedLayout.addWidget( self.applyButton )
#
# Results area
#
self.resultsCollapsibleButton = ctk.ctkCollapsibleButton()
self.resultsCollapsibleButton.setText( "Results" )
self.resultsCollapsibleButton.collapsed = True
self.advancedLayout.addWidget( self.resultsCollapsibleButton )
# Layout within the collapsible button
self.resultsLayout = qt.QFormLayout( self.resultsCollapsibleButton )
# Results table
self.resultsTable = qt.QTableWidget( self.resultsCollapsibleButton )
self.resultsTable.setColumnCount( self.RESULTS_NUM_INDICES )
self.resultsTable.setHorizontalHeaderLabels( [ "Image Points", "Probe Points", "Error", "Delete" ] )
self.resultsTable.horizontalHeader().setResizeMode( qt.QHeaderView.Stretch )
self.resultsTable.horizontalHeader().setResizeMode( self.RESULTS_DELETE_INDEX, qt.QHeaderView.Fixed )
self.resultsLayout.addRow( self.resultsTable )
#
# Parameters area
#
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.setText( "Parameters" )
self.parametersCollapsibleButton.collapsed = True
self.advancedLayout.addWidget( self.parametersCollapsibleButton )
# Layout within the collapsible button
self.parametersLayout = qt.QVBoxLayout( self.parametersCollapsibleButton )
# Parameters node
self.frwNodeSelector = slicer.qMRMLNodeComboBox()
self.frwNodeSelector.nodeTypes = [ "vtkMRMLFiducialRegistrationWizardNode" ]
self.frwNodeSelector.addEnabled = True
self.frwNodeSelector.removeEnabled = True
self.frwNodeSelector.noneEnabled = False
self.frwNodeSelector.showHidden = False
self.frwNodeSelector.showChildNodeTypes = False
self.frwNodeSelector.baseName = "UltrasoundCalibration"
self.frwNodeSelector.setMRMLScene( slicer.mrmlScene )
self.frwNodeSelector.setToolTip( "Select the ultrasound calibration parameters node." )
self.parametersLayout.addWidget( self.frwNodeSelector )
#
# Input group box
#
self.inputGroupBox = qt.QGroupBox( self.parametersCollapsibleButton )
self.inputGroupBox.setTitle( "Input" )
self.parametersLayout.addWidget( self.inputGroupBox )
# Layout within the group box
self.inputGroupBoxLayout = qt.QFormLayout( self.inputGroupBox )
# US image selector
self.usImageNodeSelector = slicer.qMRMLNodeComboBox()
self.usImageNodeSelector.nodeTypes = [ "vtkMRMLVolumeNode" ]
self.usImageNodeSelector.addEnabled = False
self.usImageNodeSelector.removeEnabled = False
self.usImageNodeSelector.noneEnabled = True
self.usImageNodeSelector.showHidden = False
self.usImageNodeSelector.showChildNodeTypes = True
self.usImageNodeSelector.setMRMLScene( slicer.mrmlScene )
self.usImageNodeSelector.setToolTip( "Select the ultrasound image node." )
self.inputGroupBoxLayout.addRow( "Ultrasound image ", self.usImageNodeSelector )
# StylusTipToProbe selector
self.stylusTipToProbeNodeSelector = slicer.qMRMLNodeComboBox()
self.stylusTipToProbeNodeSelector.nodeTypes = [ "vtkMRMLLinearTransformNode" ]
self.stylusTipToProbeNodeSelector.addEnabled = False
self.stylusTipToProbeNodeSelector.removeEnabled = False
self.stylusTipToProbeNodeSelector.noneEnabled = True
self.stylusTipToProbeNodeSelector.showHidden = False
self.stylusTipToProbeNodeSelector.showChildNodeTypes = True
self.stylusTipToProbeNodeSelector.setMRMLScene( slicer.mrmlScene )
self.stylusTipToProbeNodeSelector.setToolTip( "Select the StylusTipToProbe node (parent transforms will be applied)." )
self.inputGroupBoxLayout.addRow( "StylusTipToProbe ", self.stylusTipToProbeNodeSelector )
#
# Output group box
#
self.outputGroupBox = qt.QGroupBox( self.parametersCollapsibleButton )
self.outputGroupBox.setTitle( "Output" )
self.parametersLayout.addWidget( self.outputGroupBox )
# Layout within the group box
self.outputGroupBoxLayout = qt.QFormLayout( self.outputGroupBox )
# ImageToProbe selector
self.imageToProbeNodeSelector = slicer.qMRMLNodeComboBox()
self.imageToProbeNodeSelector.nodeTypes = [ "vtkMRMLLinearTransformNode" ]
self.imageToProbeNodeSelector.addEnabled = True
self.imageToProbeNodeSelector.removeEnabled = False
self.imageToProbeNodeSelector.noneEnabled = True
self.imageToProbeNodeSelector.renameEnabled = True
self.imageToProbeNodeSelector.showHidden = False
self.imageToProbeNodeSelector.showChildNodeTypes = True
self.imageToProbeNodeSelector.setMRMLScene( slicer.mrmlScene )
self.imageToProbeNodeSelector.setToolTip( "Select the ImageToProbe output node (stores the result of the calibration)." )
self.outputGroupBoxLayout.addRow( "ImageToProbe ", self.imageToProbeNodeSelector )
#
# Set up connections
#
self.freezeButton.connect( "clicked(bool)", self.onFreezeButtonClicked )
self.sequenceBrowserNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onSequenceBrowserNodeChanged )
self.frwNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onCalibrationNodeChanged )
self.usImageNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onUSImageNodeChanged )
self.stylusTipToProbeNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onStylusTipToProbeNodeChanged )
self.markPointButton.connect( "clicked(bool)", self.onMarkPointButtonClicked )
self.undoPointsButton.connect( "clicked(bool)", self.onUndoPointsButtonClicked )
self.resetPointsButton.connect( "clicked(bool)", self.onResetPointsButtonClicked )
self.imageToProbeNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onImageToProbeNodeChanged )
self.applyButton.connect( "clicked(bool)", self.onApplyOutputTransformToImageClicked )
#
# Create a parameters node by default
#
defaultFRWNode = slicer.vtkMRMLFiducialRegistrationWizardNode()
defaultFRWNode.SetName( "UltrasoundCalibration" )
defaultFRWNode.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( defaultFRWNode )
self.frwNodeSelector.setCurrentNodeID( defaultFRWNode.GetID() )
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = VisualizationLogic()
self.watchDog = None
self.trackedToolTipTransform = None
# Instantiate and connect widgets ...
#
# Parameters Area
#
# watch dog stuff
watchDogCollapsibleButton = ctk.ctkCollapsibleButton()
watchDogCollapsibleButton.text = "Tracked Instruments"
watchDogCollapsibleButton.collapsed = True
self.layout.addWidget(watchDogCollapsibleButton)
watchDogCollapsibleButton.connect("clicked(bool)",
self.onWatchDogCollapsibleButton)
watchDogFormLayout = qt.QFormLayout(watchDogCollapsibleButton)
self.table = qt.QTableWidget()
self.table.setColumnCount(2)
header = ['Name', 'Status']
self.table.setHorizontalHeaderLabels(header)
watchDogFormLayout.addWidget(self.table)
visualizationCollapsibleButton = ctk.ctkCollapsibleButton()
visualizationCollapsibleButton.text = "Visualization Tools"
visualizationCollapsibleButton.collapsed = True
self.layout.addWidget(visualizationCollapsibleButton)
visualizationFormLayout = qt.QFormLayout(
visualizationCollapsibleButton)
# input tool model selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLModelNode"]
self.inputSelector.selectNodeUponCreation = False
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = True
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.renameEnabled = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("The currently navigated tool")
visualizationFormLayout.addRow("Tracking Tool: ", self.inputSelector)
# connection
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onToolNavigated)
self.toolViewCheckBox = qt.QCheckBox()
self.toolViewCheckBox.checked = 0
self.toolViewCheckBox.setToolTip(
"If checked, the views will track the tip of the tool selected")
self.toolViewCheckBox.connect('stateChanged(int)',
self.onToolViewCheckBox)
visualizationFormLayout.addRow("Attach views to tool tip",
self.toolViewCheckBox)
self.toolErrorCheckBox = qt.QCheckBox()
self.toolErrorCheckBox.checked = 0
self.toolErrorCheckBox.setToolTip("If checked, the show error cone")
self.toolErrorCheckBox.connect('stateChanged(int)',
self.onToolErrorCheckBox)
visualizationFormLayout.addRow("Show the Error cone",
self.toolErrorCheckBox)
#
self.screenShotButton = qt.QPushButton("Take Screenshot")
self.screenShotButton.toolTip = "Takes screenshot of the procedure display and saves the image in the ?? folder."
self.screenShotButton.enabled = True
visualizationFormLayout.addRow(self.screenShotButton)
# connections
self.screenShotButton.connect('clicked(bool)', self.onScreenShotButton)
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "RFA Generator Parameters"
parametersCollapsibleButton.collapsed = True
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input time
self.rfaTime = qt.QSpinBox()
self.rfaTime.minimum = 0
self.rfaTime.maximum = 900
self.rfaTime.suffix = 's'
self.rfaTime.setValue(900)
parametersFormLayout.addRow("Input Ablation Time: ", self.rfaTime)
#
# output volume selector
#
self.rfaPower = qt.QSpinBox()
self.rfaPower.minimum = -1
self.rfaPower.maximum = 15
self.rfaPower.suffix = 'W'
self.rfaPower.setValue(5)
parametersFormLayout.addRow("RFA Power: ", self.rfaPower)
self.ablationButton = qt.QPushButton("Start Ablation")
self.ablationButton.toolTip = "Ablation timer countdown"
self.ablationButton.enabled = True
parametersFormLayout.addRow(self.ablationButton)
# connections
self.ablationButton.connect('clicked(bool)', self.onStartAblation)
self.qLabel = qt.QLabel('')
self.layout.addWidget(self.qLabel)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
ScriptedLoadableModuleWidget.setup(self)
#self.logic = CIP_CalciumScoringLogic()
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# target volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
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("Target Volume: ", self.inputSelector)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onVolumeChanged)
self.volumeNode = self.inputSelector.currentNode()
#
# Calcination type
#
self.calcinationTypeBox = qt.QComboBox()
self.calcinationTypeBox.addItem("Heart")
self.calcinationTypeBox.addItem("Aorta")
parametersFormLayout.addRow("Calcination Region", self.calcinationTypeBox)
self.calcinationTypeBox.connect("currentIndexChanged(int)", self.onTypeChanged)
self.ThresholdRange = ctk.ctkRangeWidget()
self.ThresholdRange.minimum = 0
self.ThresholdRange.maximum = 3000
self.ThresholdRange.setMinimumValue(self.ThresholdMin)
self.ThresholdRange.setMaximumValue(self.ThresholdMax)
self.ThresholdRange.connect("minimumValueChanged(double)", self.onThresholdMinChanged)
self.ThresholdRange.connect("maximumValueChanged(double)", self.onThresholdMaxChanged)
parametersFormLayout.addRow("Threshold Value", self.ThresholdRange)
self.ThresholdRange.setMinimumValue(self.ThresholdMin)
self.ThresholdRange.setMaximumValue(self.ThresholdMax)
self.LesionSizeRange= ctk.ctkRangeWidget()
self.LesionSizeRange.minimum = 1
self.LesionSizeRange.maximum = 1000
self.LesionSizeRange.setMinimumValue(self.MinimumLesionSize)
self.LesionSizeRange.setMaximumValue(self.MaximumLesionSize)
self.LesionSizeRange.connect("minimumValueChanged(double)", self.onMinSizeChanged)
self.LesionSizeRange.connect("maximumValueChanged(double)", self.onMaxSizeChanged)
parametersFormLayout.addRow("Lesion Size (mm^3)", self.LesionSizeRange)
self.LesionSizeRange.setMinimumValue(self.MinimumLesionSize)
self.LesionSizeRange.setMaximumValue(self.MaximumLesionSize)
self.scoreField = qt.QLineEdit()
self.scoreField.setText(self.totalScore)
parametersFormLayout.addRow("Total Score", self.scoreField)
#
# Select table
#
self.selectLabels = qt.QTableWidget()
self.selectLabels.horizontalHeader().hide()
self.selectLabels.verticalHeader().hide()
self.selectLabels.setColumnCount(2)
self.selectLabels.itemClicked.connect(self.handleItemClicked)
parametersFormLayout.addRow("", self.selectLabels)
#
# ROI Area
#
self.roiCollapsibleButton = ctk.ctkCollapsibleButton()
self.roiCollapsibleButton.text = "Heart ROI"
self.roiCollapsibleButton.setChecked(False)
self.layout.addWidget(self.roiCollapsibleButton)
# Layout within the dummy collapsible button
roiFormLayout = qt.QFormLayout(self.roiCollapsibleButton)
#
# ROI
#
self.ROIWidget = slicer.qMRMLAnnotationROIWidget()
self.roiNode = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(self.roiNode)
self.ROIWidget.setMRMLAnnotationROINode(self.roiNode)
roiFormLayout.addRow("", self.ROIWidget)
self.roiNode.AddObserver("ModifiedEvent", self.onROIChangedEvent, 1)
# Add vertical spacer
self.layout.addStretch(1)
# Add temp nodes
self.croppedNode=slicer.vtkMRMLScalarVolumeNode()
self.croppedNode.SetHideFromEditors(1)
slicer.mrmlScene.AddNode(self.croppedNode)
self.labelsNode=slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(self.labelsNode)
if self.inputSelector.currentNode():
self.onVolumeChanged(self.inputSelector.currentNode())
self.createModels()
def __init__(self, logic, applyButton, buttonsList):
super(ILSVisualizationWidget, self).__init__()
self.logic = logic
self.applyButton = applyButton
self.fiducialButtonsList = buttonsList
self.widget = qt.QWidget()
self.layout = qt.QFormLayout(self.widget)
self.boxHolder = qt.QWidget()
self.boxHolder.setLayout(qt.QVBoxLayout())
self.layout.addRow(self.boxHolder)
self.groupBox = qt.QFrame()
self.groupBox.setLayout(qt.QHBoxLayout())
self.fiducialsCollapsibleButton = ctk.ctkCollapsibleButton()
self.fiducialsCollapsibleButton.text = "Show Fiducials"
self.fiducialsCollapsibleButton.hide()
self.fiducialsFormLayout = qt.QFormLayout(
self.fiducialsCollapsibleButton)
# Table Widget Definition
self.tableWidget = qt.QTableWidget()
self.tableWidget.sortingEnabled = False
self.tableWidget.hide()
self.tableWidget.setColumnCount(3)
self.tableWidget.setColumnWidth(0, 190)
self.tableWidget.setColumnWidth(1, 190)
self.tableWidget.setColumnWidth(2, 190)
self.tableWidget.setMaximumWidth(590)
horizontalBar = self.tableWidget.horizontalScrollBar()
horizontalBar.setDisabled(True)
horizontalBar.hide()
self.tableWidget.setHorizontalHeaderLabels([
"Left Oblique Fiducials", "Right Oblique Fiducials",
"Right Horizontal Fiducials"
])
behavior = qt.QAbstractItemView()
self.tableWidget.setSelectionBehavior(behavior.SelectItems)
self.tableWidget.setSelectionMode(behavior.SingleSelection)
self.tableWidget.setContextMenuPolicy(3)
self.tableWidget.customContextMenuRequested.connect(self.onRightClick)
self.groupBox.layout().addWidget(self.tableWidget)
self.fiducialsFormLayout.addWidget(self.groupBox)
self.boxHolder.layout().addWidget(self.fiducialsCollapsibleButton)
self.pendingUpdate = False
self.updatingFiducials = False
self.observerTags = []
self.leftRow = 0
self.rightObliqueRow = 0
self.rightHorizontalRow = 0
self.tableItems = []
self.deletionGroupBox = qt.QFrame()
self.deletionGroupBox.setLayout(qt.QHBoxLayout())
self.fiducialsFormLayout.addWidget(self.deletionGroupBox)
#
# Delete Selected Fiducials Button
#
self.deleteButton = qt.QPushButton("Delete Selected Fiducial")
self.deleteButton.toolTip = "Select a fiducial from the table and push this button to delete the selected fiducial from the scene."
self.deleteButton.enabled = True
selectedIcon = qt.QIcon(":/Icons/MarkupsDelete.png")
self.deleteButton.setIcon(selectedIcon)
self.deleteButton.setFixedSize(220, 30)
self.deletionGroupBox.layout().addWidget(self.deleteButton)
self.deleteButton.connect('clicked(bool)',
self.onDeleteOneFiducialButton)
#
# Delete All Fiducials Button
#
self.deleteAllButton = qt.QPushButton("Delete All Fiducials")
self.deleteAllButton.toolTip = "Delete all fiducials in the scene."
self.deleteAllButton.enabled = True
allIcon = qt.QIcon(":/Icons/MarkupsDeleteAllRows.png")
self.deleteAllButton.setIcon(allIcon)
self.deleteAllButton.setFixedSize(220, 30)
self.deletionGroupBox.layout().addWidget(self.deleteAllButton)
# self.fiducialsFormLayout.addRow(self.deleteAllButton)
self.deleteAllButton.connect('clicked(bool)', self.dialogBoxFunction)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# layoutLogic = slicer.app.layoutManager.layoutLogic()
slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutSideBySideView)
l = slicer.modules.createmodels.logic()
self.needleModel = l.CreateNeedle(150, 0.4, 0, False)
self.redWidget = slicer.app.layoutManager().sliceWidget('Red')
self.yellowWidget = slicer.app.layoutManager().sliceWidget('Yellow')
self.usContainer = ctk.ctkCollapsibleButton()
#This is what the button will say
self.usContainer.text = "Connection Information"
#Thiss actually creates that button
#This creates a variable that describes layout within this collapsible button
self.usLayout = qt.QFormLayout(self.usContainer)
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
#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.usLayout.addWidget(self.connectButton)
# self.normalImageButton = qt.QCheckBox()
# self.normalImageButton.text = "Select if performing a 2D Calibration"
# self.usLayout.addRow(self.normalImageButton)
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.usLayout.addRow("Left view volume: ", self.imageSelector)
self.imageSelector2 = slicer.qMRMLNodeComboBox()
self.imageSelector2.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.imageSelector2.selectNodeUponCreation = True
self.imageSelector2.addEnabled = False
self.imageSelector2.removeEnabled = False
self.imageSelector2.noneEnabled = True
self.imageSelector2.showHidden = False
self.imageSelector2.showChildNodeTypes = False
self.imageSelector2.setMRMLScene( slicer.mrmlScene )
self.imageSelector2.setToolTip( "Pick the image to be used." )
self.usLayout.addRow("Right view volume: ", self.imageSelector2)
#add combo box for linear transform node
self.TransformSelector = slicer.qMRMLNodeComboBox()
self.TransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.TransformSelector.selectNodeUponCreation = True
self.TransformSelector.addEnabled = False
self.TransformSelector.removeEnabled = False
self.TransformSelector.noneEnabled = True
self.TransformSelector.showHidden = False
self.TransformSelector.showChildNodeTypes = False
self.TransformSelector.setMRMLScene( slicer.mrmlScene )
self.TransformSelector.setToolTip( "Pick the transform representing the straw line." )
self.usLayout.addRow("Tip to Probe: ", self.TransformSelector)
self.recordContainer = ctk.ctkCollapsibleButton()
#This is what the button will say
self.recordContainer.text = "Recording Options"
#Thiss actually creates that button
#This creates a variable that describes layout within this collapsible button
self.recordLayout = qt.QFormLayout(self.recordContainer)
self.RecordButton = qt.QPushButton()
self.RecordButton.text = "Start Recording"
self.recordLayout.addWidget(self.RecordButton)
self.StopRecordButton = qt.QPushButton()
self.StopRecordButton.text = "Stop Recording"
self.recordLayout.addWidget(self.StopRecordButton)
self.pathInput = qt.QLineEdit()
self.pathInput.setPlaceholderText("Enter the path to save files to")
self.pathText = qt.QLabel("File Path:")
self.recordLayout.addRow(self.pathText, self.pathInput)
self.SaveRecordButton = qt.QPushButton()
self.SaveRecordButton.text = "Save Recording"
self.recordLayout.addWidget(self.SaveRecordButton)
# This creates another collapsible button
self.fiducialContainer = ctk.ctkCollapsibleButton()
self.fiducialContainer.text = "Registration"
self.fiducialLayout = qt.QFormLayout(self.fiducialContainer)
self.freezeButton = qt.QPushButton()
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.freezeButton.text = "Freeze"
else:
self.freezeButton.text = "Place Fiducial"
self.freezeButton.toolTip = "Freeze the ultrasound image for fiducial placement"
self.fiducialLayout.addRow(self.freezeButton)
self.shortcut = qt.QShortcut(qt.QKeySequence('f'), slicer.util.mainWindow())
self.numFidLabel = qt.QLabel()
self.fiducialLayout.addRow(qt.QLabel("Fiducials collected:"), self.numFidLabel)
self.transformTable = qt.QTableWidget()
self.transTableItem = qt.QTableWidgetItem()
self.fidError = qt.QLabel()
self.transformTable.setRowCount(4)
self.transformTable.setColumnCount(4)
self.transformTable.horizontalHeader().hide()
self.transformTable.verticalHeader().hide()
self.transformTable.setItem(0,0, qt.QTableWidgetItem("1"))
self.transformTable.setItem(0,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,1, qt.QTableWidgetItem("1"))
self.transformTable.setItem(1,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2,2, qt.QTableWidgetItem("1"))
self.transformTable.setItem(2,3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3,3, qt.QTableWidgetItem("1"))
self.transformTable.setSizePolicy(qt.QSizePolicy.Minimum, qt.QSizePolicy.MinimumExpanding)
self.copyIcon =qt.QIcon(":Icons/Medium/SlicerEditCopy.png")
self.copyButton = qt.QPushButton()
self.copyButton.setIcon(self.copyIcon)
self.copyButton.setMaximumWidth(64)
self.copyButton.enabled = False
if self.numFidLabel >= 2:
self.copyButton.enabled = True
self.fiducialLayout.addRow(qt.QLabel("Image to probe transform:"))
self.fiducialLayout.addRow(self.transformTable)
self.fiducialLayout.addRow("Copy:", self.copyButton)
self.validationContainer = ctk.ctkCollapsibleButton()
self.validationContainer.text = "Validation"
self.validationLayout = qt.QFormLayout(self.validationContainer)
self.visualizeButton = qt.QPushButton('Show 3D Scene')
self.visualizeButton.toolTip = "This button enables the 3D view for visual validation"
self.validationLayout.addRow(self.visualizeButton)
self.visualizeButton.connect('clicked(bool)', self.onVisualizeButtonClicked)
self.layout.addWidget(self.usContainer)
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.layout.addWidget(self.recordContainer)
self.layout.addWidget(self.fiducialContainer)
self.layout.addWidget(self.validationContainer)
if slicer.mrmlScene.GetNodesByClass("vtkMRMLSequenceNode").GetNumberOfItems() == 0:
self.connectButton.connect('clicked(bool)', self.onConnectButtonClicked)
self.freezeButton.connect('clicked(bool)', self.onConnectButtonClicked)
self.shortcut.connect('activated()', self.onConnectButtonClicked)
self.RecordButton.connect('clicked(bool)', self.onRecordButtonClicked)
self.StopRecordButton.connect('clicked(bool)', self.onStopButtonClicked)
self.SaveRecordButton.connect('clicked(bool)', self.onSaveButtonClicked)
else:
self.shortcut.connect('activated()', self.onFiducialClicked)
self.freezeButton.connect('clicked(bool)', self.onFiducialClicked)
self.imageSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onImageChanged)
self.imageSelector2.connect('currentNodeChanged(vtkMRMLNode*)', self.onImageChanged2)
self.TransformSelector.connect('currentNodeChanged(vtkMRMLNode*)',self.onTransformChanged)
self.copyButton.connect('clicked(bool)', self.onCopyButtonClicked)
self.layout.addStretch(1)
self.sceneObserverTag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeAddedEvent, self.onNodeAdded)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Ultrasonic motors Area
#
ultrasonicMotorsCollapsibleButton = ctk.ctkCollapsibleButton()
ultrasonicMotorsCollapsibleButton.text = "Shinsei motors"
self.layout.addWidget(ultrasonicMotorsCollapsibleButton)
ultrasonicFormLayout = qt.QFormLayout(
ultrasonicMotorsCollapsibleButton)
# Apply Button
self.applyButton = qt.QPushButton("Homing Shinsei")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
ultrasonicFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
#
# Piezo motors Area
#
piezoMotorsCollapsibleButton = ctk.ctkCollapsibleButton()
piezoMotorsCollapsibleButton.text = "Piezo motors"
self.layout.addWidget(piezoMotorsCollapsibleButton)
piezoFormLayout = qt.QFormLayout(piezoMotorsCollapsibleButton)
#
# Add target table
#
self.positionTable = qt.QTableWidget()
self.positionTable.setRowCount(3)
self.positionTable.setColumnCount(3)
self.positionTable.setHorizontalHeaderLabels(['1', '2', '3'])
self.cbh = qt.QComboBox()
self.cbh.addItem("Left")
self.cbh.addItem("Center")
self.cbh.addItem("Right")
self.cbh.currentIndexChanged.connect(self.onSelectionChange)
piezoFormLayout.addRow("Horizontal:", self.cbh)
self.cbv = qt.QComboBox()
self.cbv.addItems([str('Top'), str('Center'), str('Bottom')])
self.cbv.currentIndexChanged.connect(self.onSelectionChange)
piezoFormLayout.addRow("Vertical:", self.cbv)
self.label = qt.QLabel()
pixmap = qt.QPixmap('/Resources/CB.png')
self.label.setPixmap(pixmap)
piezoFormLayout.addRow(self.label)
# Apply Button
self.piezoHomingButton = qt.QPushButton("Homing Piezo")
self.piezoHomingButton.toolTip = "Run the algorithm."
self.piezoHomingButton.enabled = True
piezoFormLayout.addRow(self.piezoHomingButton)
# connections
self.piezoHomingButton.connect('clicked(bool)',
self.onPiezoHomingButton)
# Add vertical spacer
# Apply Button
self.doneHomingButton = qt.QPushButton("Done Homing")
self.doneHomingButton.toolTip = "Run the algorithm."
self.doneHomingButton.enabled = True
piezoFormLayout.addRow(self.doneHomingButton)
# connections
self.doneHomingButton.connect('clicked(bool)', self.onDoneHoming)
def setupWindow(self):
self.setWindowTitle("lapdMouse Data Archive Browser")
self.resize(1000, 600)
if 'lapdMouseDBBrowser' in slicer.util.moduleNames():
self.modulePath = slicer.modules.lapdmousedbbrowser.path.replace(
"lapdMouseDBBrowser.py", "")
else:
self.modulePath = '.'
self.downloadIcon = qt.QIcon(
os.path.join(self.modulePath, 'Resources', 'Icons',
'download.png'))
self.storedIcon = qt.QIcon(
os.path.join(self.modulePath, 'Resources', 'Icons', 'stored.png'))
self.logo = qt.QPixmap(
os.path.join(self.modulePath, 'Resources', 'Icons',
'lapdMouseDBBrowser.png'))
self.banner = qt.QFrame()
self.banner.setLayout(qt.QGridLayout())
logo = qt.QLabel()
logo.setPixmap(self.logo)
self.banner.layout().addWidget(logo, 0, 0)
self.bannerTextBrowser = qt.QTextBrowser()
self.bannerTextBrowser.setOpenExternalLinks(True)
self.bannerTextBrowser.setMaximumHeight(120)
text = "<h1>lapdMouse Data Archive Browser</h1>"
text += "The lapdMouse data archive contains anatomically derived lung models and aerosol deposition measurements of mice for modeling and computational toxicology in mice."
text += " For more details about available datasets, data representation, other software, and support, please visit the <a href=\"https://doi.org/10.25820/9arg-9w56\">lapdMouse archive</a>"
text += "<br />This work was supported in part by NIH project R01ES023863."
self.bannerTextBrowser.html = text
self.banner.layout().addWidget(self.bannerTextBrowser, 0, 1)
self.table = qt.QTableWidget(self)
self.table.setRowCount(0)
self.table.setColumnCount(1)
self.table.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Expanding)
self.table.setHorizontalHeaderLabels(["Dataset name"
]) #,"Status","Comment"])
self.table.setSelectionBehavior(qt.QAbstractItemView.SelectRows)
self.table.setSelectionMode(qt.QAbstractItemView.SingleSelection)
self.table.horizontalHeader().setStretchLastSection(True)
self.table.connect("itemSelectionChanged()", self.onDatasetChanged)
self.customForm = qt.QFrame()
self.customForm.setLayout(qt.QFormLayout())
self.customFormName = qt.QLineEdit("", self.customForm)
self.customFormName.readOnly = True
self.customForm.layout().addRow("Name", self.customFormName)
self.customFormDatasetInfo = qt.QLabel('<a href=\"' + self.projectURL +
'\">info</a>')
self.customFormDatasetInfo.setTextFormat(1)
self.customFormDatasetInfo.setOpenExternalLinks(True)
self.customForm.layout().addRow("Info", self.customFormDatasetInfo)
self.customFormAction = qt.QFrame(self.customForm)
self.customFormAction.setLayout(qt.QHBoxLayout())
self.customFormAction.layout().setSpacing(0)
self.customFormAction.layout().setMargin(0)
self.customFormDownloadButton = qt.QPushButton(
"download standard file selection", self.customFormAction)
self.customFormAction.layout().addWidget(self.customFormDownloadButton)
self.customFormDownloadButton.connect("clicked()",
self.onDownloadDataset)
self.customFormLoadButton = qt.QPushButton(
"load standard file selection in Slicer", self.customFormAction)
self.customFormAction.layout().addWidget(self.customFormLoadButton)
self.customFormLoadButton.connect("clicked()", self.onLoadDataset)
self.customForm.layout().addRow("Quick actions", self.customFormAction)
self.customFormFiles = qt.QTableWidget(self.customForm)
self.customFormFiles.setRowCount(0)
self.customFormFiles.setColumnCount(3)
self.customFormFiles.setHorizontalHeaderLabels(
["Status", "Filename", "Size"])
self.customFormFiles.horizontalHeader().setSectionResizeMode(
1, qt.QHeaderView.Stretch)
self.customFormFiles.setSelectionBehavior(
qt.QAbstractItemView.SelectRows)
self.customFormFiles.setMinimumHeight(400)
self.customForm.layout().addRow("Files", self.customFormFiles)
self.customFormAction2 = qt.QFrame(self.customForm)
self.customFormAction2.setLayout(qt.QHBoxLayout())
self.customFormAction2.layout().setSpacing(0)
self.customFormAction2.layout().setMargin(0)
self.customFormDownloadButton2 = qt.QPushButton(
"download selected files", self.customFormAction2)
self.customFormAction2.layout().addWidget(
self.customFormDownloadButton2)
self.customFormDownloadButton2.connect("clicked()",
self.onDownloadSelectedDataset)
self.customFormDeleteButton2 = qt.QPushButton("delete selected files",
self.customFormAction2)
self.customFormAction2.layout().addWidget(self.customFormDeleteButton2)
self.customFormDeleteButton2.connect("clicked()",
self.onDeleteSelectedDataset)
self.customFormLoadButton2 = qt.QPushButton(
"load selected files in Slicer", self.customFormAction2)
self.customFormAction2.layout().addWidget(self.customFormLoadButton2)
self.customFormLoadButton2.connect("clicked()",
self.onLoadSelectedDataset)
self.customForm.layout().addRow("", self.customFormAction2)
splitView = qt.QSplitter(self)
splitView.addWidget(self.table)
splitView.addWidget(self.customForm)
splitView.setSizes([200, 800])
self.updateTable()
self.onDatasetChanged()
self.setMenuWidget(self.banner)
self.setCentralWidget(splitView)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
slicer.app.layoutManager().setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)
l = slicer.modules.createmodels.logic()
self.needleModel = l.CreateNeedle(150, 1, 2.5, False)
# self.array1 = np.array([29, 24.37, 160.992])
# self.array2 = np.array([28, 1.630, 69.785])
# self.array3 = np.array([29,-7.321, 33.884])
# self.array4 = np.array([-26, 24.129, 160.022])
# self.array5 = np.array([-28, 11.065, 107.626])
# self.array6 = np.array([-30.387, -7.394, 33.589])
self.jigArray = np.array([[29, 24.37, 160.992], [28, 1.630, 69.785],
[29, -7.321, 33.884], [-26, 24.129, 160.022],
[-28, 11.065, 107.626],
[-30.387, -7.394, 33.589]])
self.collectedArray = np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0],
[0, 0, 0], [0, 0, 0], [0, 0, 0]])
self.points = vtk.vtkPoints()
self.points.SetNumberOfPoints(6)
self.points.SetPoint(0, self.jigArray[0])
self.points.SetPoint(1, self.jigArray[1])
self.points.SetPoint(2, self.jigArray[2])
self.points.SetPoint(3, self.jigArray[3])
self.points.SetPoint(4, self.jigArray[4])
self.points.SetPoint(5, self.jigArray[5])
self.collectedPoints = vtk.vtkPoints()
self.collectedPoints.SetNumberOfPoints(6)
self.DN = self.markupsNode.GetDisplayNode()
self.DN.SetSelectedColor(0, 0, 1)
self.DN.SetTextScale(0)
self.markupsNode.AddFiducialFromArray(self.jigArray[0])
self.markupsNode.AddFiducialFromArray(self.jigArray[1])
self.markupsNode.AddFiducialFromArray(self.jigArray[2])
self.markupsNode.AddFiducialFromArray(self.jigArray[3])
self.markupsNode.AddFiducialFromArray(self.jigArray[4])
self.markupsNode.AddFiducialFromArray(self.jigArray[5])
slicer.app.layoutManager().setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(self.parametersCollapsibleButton)
self.parametersFormLayout = qt.QFormLayout(
self.parametersCollapsibleButton)
self.connectButton = qt.QPushButton()
self.connectButton.setDefault(False)
self.connectButton.text = "Connect"
self.parametersFormLayout.addWidget(self.connectButton)
self.TransformSelector = slicer.qMRMLNodeComboBox()
self.TransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.TransformSelector.selectNodeUponCreation = True
self.TransformSelector.addEnabled = False
self.TransformSelector.removeEnabled = False
self.TransformSelector.noneEnabled = True
self.TransformSelector.showHidden = False
self.TransformSelector.showChildNodeTypes = False
self.TransformSelector.setMRMLScene(slicer.mrmlScene)
self.TransformSelector.setToolTip(
"Pick the transform representing the straw line.")
self.parametersFormLayout.addRow("Tip to Probe: ",
self.TransformSelector)
self.collectButton = qt.QPushButton()
self.collectButton.setDefault(False)
self.collectButton.text = "Collect Fiducial"
self.parametersFormLayout.addWidget(self.collectButton)
self.shortcut = qt.QShortcut(qt.QKeySequence('c'),
slicer.util.mainWindow())
self.deleteButton = qt.QPushButton()
self.deleteButton.setDefault(False)
self.deleteButton.text = "Delete Last Fiducial"
self.parametersFormLayout.addWidget(self.deleteButton)
self.calculateButton = qt.QPushButton()
self.calculateButton.setDefault(False)
self.calculateButton.text = "Calculate Transformation Matrix"
self.parametersFormLayout.addWidget(self.calculateButton)
self.transformTable = qt.QTableWidget()
self.transTableItem = qt.QTableWidgetItem()
self.fidError = qt.QLabel()
self.transformTable.setRowCount(4)
self.transformTable.setColumnCount(4)
self.transformTable.horizontalHeader().hide()
self.transformTable.verticalHeader().hide()
self.transformTable.setItem(0, 0, qt.QTableWidgetItem("1"))
self.transformTable.setItem(0, 1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0, 2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(0, 3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1, 0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1, 1, qt.QTableWidgetItem("1"))
self.transformTable.setItem(1, 2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(1, 3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2, 0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2, 1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(2, 2, qt.QTableWidgetItem("1"))
self.transformTable.setItem(2, 3, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3, 0, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3, 1, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3, 2, qt.QTableWidgetItem("0"))
self.transformTable.setItem(3, 3, qt.QTableWidgetItem("1"))
self.transformTable.resizeColumnToContents(0)
self.transformTable.resizeColumnToContents(1)
self.transformTable.resizeColumnToContents(2)
self.transformTable.resizeColumnToContents(3)
self.transformTable.setSizePolicy(qt.QSizePolicy.Minimum,
qt.QSizePolicy.MinimumExpanding)
# self.copyIcon =qt.QIcon(":Icons/Medium/SlicerEditCopy.png")
# self.copyButton = qt.QPushButton()
# self.copyButton.setIcon(self.copyIcon)
# self.copyButton.toolTip = "Copy"
# self.copyButton.setMaximumWidth(64)
# self.copyHbox = qt.QHBoxLayout()
# self.copyHbox.addWidget(self.copyButton)
self.parametersFormLayout.addRow(qt.QLabel("Transformation Matrix:"))
self.parametersFormLayout.addRow(self.transformTable)
self.copyButton = qt.QPushButton()
self.copyButton.setDefault(False)
self.copyButton.text = "Copy Transform"
self.parametersFormLayout.addWidget(self.copyButton)
self.errorString = qt.QLabel()
self.errorString.text = "RMSE: " + str(self.error)
self.parametersFormLayout.addRow(self.errorString)
self.connectButton.connect('clicked(bool)',
self.onConnectButtonClicked)
self.TransformSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onTransformChanged)
self.collectButton.connect('clicked(bool)',
self.onCollectButtonClicked)
self.shortcut.connect('activated()', self.onCollectButtonClicked)
self.deleteButton.connect('clicked(bool)', self.onDeleteButtonClicked)
self.calculateButton.connect('clicked(bool)',
self.onCalculateButtonClicked)
self.copyButton.connect('clicked(bool)', self.onCopyButtonClicked)
self.layout.addStretch(1)
slicer.app.layoutManager().setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Metadata Area
metadataCollapsibleButton = ctk.ctkCollapsibleButton()
metadataCollapsibleButton.text = "Metadata"
self.layout.addWidget(metadataCollapsibleButton)
# Layout within the dummy collapsible button
metadataFormLayout = qt.QFormLayout(metadataCollapsibleButton)
# userID input
self.userIDField = qt.QLineEdit()
metadataFormLayout.addRow("UserID: ", self.userIDField)
# studyID input
self.studyIDField = qt.QLineEdit()
metadataFormLayout.addRow("StudyID: ", self.studyIDField)
# trialID input
self.trialIDField = qt.QLineEdit()
metadataFormLayout.addRow("TrialID: ", self.trialIDField)
# skill level selector
self.skillOptions = ("Novice", "Trainee", "Expert")
self.skillSelector = qt.QComboBox()
self.skillSelector.addItems(self.skillOptions)
metadataFormLayout.addRow("Select skill level: ", self.skillSelector)
# session completed selector
self.sessionCompletionOptions = ("Complete", "Incomplete")
self.sessionCompletionSelector = qt.QComboBox()
self.sessionCompletionSelector.addItems(self.sessionCompletionOptions)
metadataFormLayout.addRow("Session status: ", self.sessionCompletionSelector)
# Save Button
self.saveButton = qt.QPushButton("Save session")
self.saveButton.toolTip = "Uploading data to database."
self.saveButton.enabled = True
metadataFormLayout.addRow(self.saveButton)
# Load Scene Area
loadSceneCollapsibleButton = ctk.ctkCollapsibleButton()
loadSceneCollapsibleButton.text = "Search For Session"
self.layout.addWidget(loadSceneCollapsibleButton)
# Layout within the dummy collapsible button
loadSceneFormLayout = qt.QFormLayout(loadSceneCollapsibleButton)
# search fields text
self.searchText = qt.QLabel()
self.searchText.text = "Search by fields:"
loadSceneFormLayout.addRow(self.searchText)
# Search user ID field
self.searchUserID = qt.QLineEdit()
loadSceneFormLayout.addRow("UserID: ", self.searchUserID)
# Search study ID field
self.searchStudyID = qt.QLineEdit()
loadSceneFormLayout.addRow("StudyID: ", self.searchStudyID)
# Search trial ID field
self.searchTrialID = qt.QLineEdit()
loadSceneFormLayout.addRow("TrialID: ", self.searchTrialID)
# Search skill level field
self.skillOptions = ("All", "Novice", "Trainee", "Expert")
self.searchSkill = qt.QComboBox()
self.searchSkill.addItems(self.skillOptions)
loadSceneFormLayout.addRow("Select skill level: ", self.searchSkill)
# Search Button
self.searchButton = qt.QPushButton("Search for session")
self.searchButton.enabled = True
loadSceneFormLayout.addRow(self.searchButton)
# Query Results Area
self.queryResultsCollapsibleButton = ctk.ctkCollapsibleButton()
self.queryResultsCollapsibleButton.text = "Query Results"
self.queryResultsCollapsibleButton.setVisible(False)
self.layout.addWidget(self.queryResultsCollapsibleButton)
self.queryResultsLayout = qt.QFormLayout(self.queryResultsCollapsibleButton)
self.table = qt.QTableWidget(1, 5)
self.queryResultsLayout.addRow(self.table)
#load session button
self.loadButton = qt.QPushButton("Load Session")
self.queryResultsLayout.addWidget(self.loadButton)
# Connections
self.saveButton.connect('clicked(bool)', self.onSaveButton)
self.searchButton.connect('clicked(bool)', self.onSearchButton)
self.loadButton.connect('clicked(bool)', self.onLoadButton)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Data Area
#
dataGroupBox = ctk.ctkCollapsibleGroupBox()
dataGroupBox.setTitle('Data')
self.layout.addWidget(dataGroupBox)
dataGridLayout = qt.QGridLayout(dataGroupBox)
self.dirButton = ctk.ctkDirectoryButton()
dirButtonLabel = qt.QLabel('DICOM Directory: ')
dataGridLayout.addWidget(dirButtonLabel, 1, 1, 1, 1)
dataGridLayout.addWidget(self.dirButton, 1, 2, 1, 3)
self.dirButton.setMaximumWidth(500)
orLabel = qt.QLabel(' - or - ')
dataGridLayout.addWidget(orLabel, 2, 1, 1, 1)
collectionsComboBoxLabel = qt.QLabel('TCIA Collection: ')
dataGridLayout.addWidget(collectionsComboBoxLabel, 3, 1, 1, 1)
try:
m = slicer.modules.tciabrowser
self.tcia = slicer.modules.tciabrowser.widgetRepresentation().self(
)
self.connectTCIAButton = qt.QPushButton('Connect')
self.connectTCIAButton.toolTip = "Connect to TCIA Server."
dataGridLayout.addWidget(self.connectTCIAButton, 3, 2, 1, 1)
self.collectionsComboBox = qt.QComboBox()
dataGridLayout.addWidget(self.collectionsComboBox, 3, 3, 1, 2)
# connections
self.connectTCIAButton.connect('clicked(bool)',
self.getTCIACollectionValues)
# TODO disable scrolling event for collectionsComboBox
self.collectionsComboBox.connect('currentIndexChanged(QString)',
self.onTCIACollectionChanged)
except AttributeError:
# TODO add button to open Extensions Manager
noConnectionLabel = qt.QLabel('TCIA Browser not installed.')
dataGridLayout.addWidget(noConnectionLabel, 3, 2, 1, 1)
#
# Patient Table Area
#
self.patientGroupBox = ctk.ctkCollapsibleGroupBox()
self.patientGroupBox.setTitle('Patient Selection')
self.layout.addWidget(self.patientGroupBox)
self.patientGroupBoxLayout = qt.QGridLayout(self.patientGroupBox)
self.patientsTable = qt.QTableWidget()
self.patientsTableHeaderLabels = [
'ID', 'Name', 'BirthDate', 'Sex', 'Modalities'
]
self.patientsTable.setColumnCount(5)
self.patientsTable.sortingEnabled = True
self.patientsTable.setHorizontalHeaderLabels(
self.patientsTableHeaderLabels)
self.patientsTableHeader = self.patientsTable.horizontalHeader()
self.patientsTableHeader.setStretchLastSection(True)
self.patientGroupBoxLayout.addWidget(self.patientsTable, 1, 1, 1, 5)
abstractItemView = qt.QAbstractItemView()
self.patientsTable.setSelectionBehavior(abstractItemView.SelectRows)
self.examinePatientButton = qt.QPushButton('Examine')
self.examinePatientButton.setEnabled(False)
self.patientGroupBoxLayout.addWidget(self.examinePatientButton, 2, 4,
1, 2)
#
# Other Connections
#
self.dirButton.connect('directoryChanged(const QString &)',
self.onDICOMDirectoryChanged)
