def __init__(self, parent, db):
self.view = qt.QTableView(parent)
self.model = qt.QSqlQueryModel()
self.statement = """ SELECT
Patients.PatientsName, Patients.PatientID, Patients.PatientsBirthDate,
Studies.StudyDate, Studies.StudyDescription, Studies.ModalitiesInStudy,
Studies.StudyInstanceUID
FROM
Patients,Studies
WHERE
Patients.UID=Studies.PatientsUID
ORDER BY
Patients.PatientsName
; """
self.query = qt.QSqlQuery(db)
self.query.prepare(self.statement)
self.query.exec_()
self.model.setQuery(self.query)
self.view.setModel(self.model)
self.view.sortingEnabled = False
self.view.setSelectionBehavior(self.view.SelectRows)
self.view.setSelectionMode(self.view.SingleSelection)
self.view.setColumnWidth(0, 250)
self.view.setColumnWidth(1, 100)
self.view.setColumnWidth(2, 150)
self.view.setColumnWidth(3, 100)
self.view.setColumnWidth(4, 180)
self.view.setColumnWidth(5, 180)
self.view.setColumnWidth(6, 180)
self.view.verticalHeader().visible = False
def __init__(self, parent, db):
self.view = qt.QTableView(parent)
self.model = qt.QSqlQueryModel()
self.statementFormat = """SELECT
Series.SeriesNumber, Series.SeriesDescription,
Series.SeriesDate, Series.SeriesTime, Series.SeriesInstanceUID
FROM
Series
WHERE
Series.StudyInstanceUID='{StudyInstanceUID}'
ORDER BY
Series.SeriesNumber
; """
self.query = qt.QSqlQuery(db)
self.query.prepare(
self.statementFormat.format(StudyInstanceUID='Nothing'))
self.query.exec_()
self.model.setQuery(self.query)
self.view.setModel(self.model)
self.view.sortingEnabled = False
self.view.setSelectionBehavior(self.view.SelectRows)
self.view.setSelectionMode(self.view.SingleSelection)
self.view.setColumnWidth(0, 250)
self.view.setColumnWidth(1, 100)
self.view.setColumnWidth(2, 150)
self.view.setColumnWidth(3, 100)
self.view.setColumnWidth(4, 180)
self.view.setColumnWidth(5, 180)
self.view.setColumnWidth(6, 180)
self.view.verticalHeader().visible = False
def __init__(self, parent):
super(CaseReportsWindow, self).__init__()
self.mainLayout = qt.QVBoxLayout(self)
self.setLayout(self.mainLayout)
self.resize(400, 300)
self.label = qt.QLabel("Data stored in the module: ")
self.label.setStyleSheet("margin: 10px 0 15px 0")
self.mainLayout.addWidget(self.label)
self.tableView = qt.QTableView()
self.tableView.setColumnWidth(0,125)
self.tableView.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.mainLayout.addWidget(self.tableView)
self.exportButton = ctk.ctkPushButton()
self.exportButton.text = "Export"
self.exportButton.setFixedWidth(150)
self.exportButton.setIcon(qt.QIcon("{0}/export-csv.png".format(SlicerUtil.CIP_ICON_DIR)))
self.exportButton.setIconSize(qt.QSize(24,24))
self.mainLayout.addWidget(self.exportButton)
self.removeButton = ctk.ctkPushButton()
self.removeButton.text = "Clean cache"
self.removeButton.setIcon(qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeButton.setIconSize(qt.QSize(24,24))
self.removeButton.setFixedWidth(150)
self.mainLayout.addWidget(self.removeButton)
self.exportButton.connect('clicked()', parent.onExport)
self.removeButton.connect('clicked()', parent.onRemoveStoredData)
def setup(self):
# Set the grayscaleNode and labelNode to the current active volume and label
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
self.grayscaleNode = slicer.util.getNode(
selectionNode.GetActiveVolumeID())
self.labelNode = slicer.util.getNode(
selectionNode.GetActiveLabelVolumeID())
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Statistics."
self.applyButton.setStyleSheet("background-color: rgb(230,241,255)")
self.applyButton.enabled = True
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.saveButton = qt.QPushButton("Save")
self.saveButton.toolTip = "Calculate Statistics."
self.saveButton.setStyleSheet("background-color: rgb(230,241,255)")
self.saveButton.enabled = False
self.parent.layout().addWidget(self.saveButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.saveButton.connect('clicked()', self.onSave)
def setup(self):
#
# 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.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", 0)
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 = ("vtkMRMLScalarVolumeNode", "")
self.labelSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
"1")
# 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 = False
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)
# Save button
self.saveButton = qt.QPushButton("Save")
self.saveButton.toolTip = "Calculate Statistics."
self.saveButton.enabled = False
self.parent.layout().addWidget(self.saveButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.saveButton.connect('clicked()', self.onSave)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
def setup(self):
#
# 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("Inspiratory CT: ",
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.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", 0)
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("Emphysema Subtypes: ")
self.labelSelectorFrame.layout().addWidget(self.labelSelectorLabel)
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.labelSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
"1")
# 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 = False
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.saveButton = qt.QPushButton("Save")
self.saveButton.toolTip = "Calculate Statistics."
self.saveButton.enabled = False
self.parent.layout().addWidget(self.saveButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.saveButton.connect('clicked()', self.onSave)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
def setup(self):
# Instantiate and connect widgets ...
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
#self.layout = layout
if self.isDeveloperMode:
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "SequenceLabelStatistics Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Parameter Area
#
parametersCollapsibleButton1 = ctk.ctkCollapsibleButton()
parametersCollapsibleButton1.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton1)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton1)
#
# the grayscale volume selector
#
self.grayscaleSelector = slicer.qMRMLNodeComboBox()
self.grayscaleSelector.nodeTypes = (("vtkMRMLSequenceNode"), "")
self.grayscaleSelector.selectNodeUponCreation = False
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = False
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene(slicer.mrmlScene)
self.grayscaleSelector.setToolTip(
"Select the grayscale volume (background grayscale scalar volume node) for statistics calculations."
)
# TODO: need to add a QLabel
# self.grayscaleSelector.SetLabelText( "Master Volume:" )
parametersFormLayout.addRow("Grayscale Volume Sequence: ",
self.grayscaleSelector)
#
# the label volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ("vtkMRMLSequenceNode",
"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 = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to edit")
parametersFormLayout.addRow("Labelmap/Sequence: ", self.labelSelector)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Statistics."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
parametersFormLayout.addRow(self.view)
# Chart button
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
parametersFormLayout.addRow(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.saveButton = qt.QPushButton("Save")
self.saveButton.toolTip = "Calculate Statistics."
self.saveButton.enabled = False
parametersFormLayout.addRow(self.saveButton)
# Add vertical spacer
self.layout.addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.saveButton.connect('clicked()', self.onSave)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
# Set initial state
self.grayscaleNode = self.grayscaleSelector.currentNode()
self.labelNode = self.labelSelector.currentNode()
self.applyButton.enabled = bool(self.grayscaleNode) and bool(
self.labelNode)
def setup(self):
# Instantiate and connect widgets ...
# #
# # Reload and Test area
# #
# reloadCollapsibleButton = ctk.ctkCollapsibleButton()
# reloadCollapsibleButton.text = "Reload && Test"
# self.layout.addWidget(reloadCollapsibleButton)
# reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# # reload button
# # (use this during development, but remove it when delivering
# # your module to users)
# self.reloadButton = qt.QPushButton("Reload")
# self.reloadButton.toolTip = "Reload this module."
# self.reloadButton.name = "PortPlacement Reload"
# reloadFormLayout.addWidget(self.reloadButton)
# self.reloadButton.connect('clicked()', self.onReload)
# # reload and test button
# # (use this during development, but remove it when delivering
# # your module to users)
# self.reloadAndTestButton = qt.QPushButton("Reload and Test")
# self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
# reloadFormLayout.addWidget(self.reloadAndTestButton)
# self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Ports Area
#
portsCollapsibleButton = ctk.ctkCollapsibleButton()
portsCollapsibleButton.text = "Surgical Ports"
self.layout.addWidget(portsCollapsibleButton)
portsFormLayout = qt.QFormLayout(portsCollapsibleButton)
#
# port fiducial list selector
#
self.portListSelector = slicer.qMRMLNodeComboBox()
self.portListSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.portListSelector.addEnabled = False
self.portListSelector.removeEnabled = False
self.portListSelector.noneEnabled = True
self.portListSelector.setMRMLScene(slicer.mrmlScene)
self.portListSelector.setToolTip("Add surgical ports from a markups node.")
portsFormLayout.addRow("Markups node of surgical ports", self.portListSelector)
#
# Add Port List button
#
self.addPortListButton = qt.QPushButton("Set Port Markups Node")
self.addPortListButton.enabled = False
portsFormLayout.addRow(self.addPortListButton)
#
# Port table
#
self.portsTable = qt.QTableView()
self.portsTableModel = qt.QStandardItemModel()
self.portsTable.setModel(self.portsTableModel)
portsFormLayout.addRow(self.portsTable)
#
# Remove Port button
#
self.removePortButton = qt.QPushButton("Remove Selected Port")
self.removePortButton.enabled = False
portsFormLayout.addRow(self.removePortButton)
#
# Target area
#
targetCollapsibleButton = ctk.ctkCollapsibleButton()
targetCollapsibleButton.text = "Surgical Target"
self.layout.addWidget(targetCollapsibleButton)
targetFormLayout = qt.QFormLayout(targetCollapsibleButton)
#
# target selector
#
self.targetSelector = slicer.qMRMLNodeComboBox()
self.targetSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.targetSelector.addEnabled = False
self.targetSelector.removeEnabled = False
self.targetSelector.noneEnabled = True
self.targetSelector.setMRMLScene(slicer.mrmlScene)
self.targetSelector.setToolTip("Pick the surgical target that the tools should face.")
targetFormLayout.addRow("Surgical Target Fiducial", self.targetSelector)
#
# Retarget button
#
self.retargetButton = qt.QPushButton("Aim Tools at Target")
self.retargetButton.toolTip = "Reset tool orientations to face target fiducial"
self.retargetButton.enabled = False
targetFormLayout.addRow(self.retargetButton)
#
# Port Tool Display Options
#
toolsCollapsibleButton = ctk.ctkCollapsibleButton()
toolsCollapsibleButton.text = "Port Tool Display Options"
self.layout.addWidget(toolsCollapsibleButton)
toolsFormLayout = qt.QFormLayout(toolsCollapsibleButton)
#
# Transform sliders
#
self.transformSliders = slicer.qMRMLTransformSliders()
self.transformSliders.TypeOfTransform = slicer.qMRMLTransformSliders.ROTATION
self.transformSliders.CoordinateReference = slicer.qMRMLTransformSliders.LOCAL
self.transformSliders.Title = 'Tool Orientation'
self.transformSliders.minMaxVisible = False
toolsFormLayout.addRow(self.transformSliders)
#
# radius spin box
#
self.radiusSpinBox = qt.QDoubleSpinBox()
self.radiusSpinBox.setMinimum(0.0)
self.radiusSpinBox.setMaximum(10.0)
self.radiusSpinBox.setValue(2.0)
toolsFormLayout.addRow("Tool radius", self.radiusSpinBox)
#
# length spin box
#
self.lengthSpinBox = qt.QDoubleSpinBox()
self.lengthSpinBox.setMinimum(0.0)
self.lengthSpinBox.setMaximum(250.0)
self.lengthSpinBox.setValue(150.0)
toolsFormLayout.addRow("Tool length", self.lengthSpinBox)
# connections
self.portListSelector.connect('currentNodeChanged(bool)', self.onPortListSelectorChanged)
self.targetSelector.connect('currentNodeChanged(bool)', self.onTargetSelectorChanged)
self.addPortListButton.connect('clicked(bool)', self.onAddPortListButton)
self.removePortButton.connect('clicked(bool)', self.onRemovePortButton)
self.retargetButton.connect('clicked(bool)', self.onRetargetButton)
self.radiusSpinBox.connect('valueChanged(double)', self.onToolShapeChanged)
self.lengthSpinBox.connect('valueChanged(double)', self.onToolShapeChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Add observer to scene for removal of fiducial nodes
self.sceneObserverTag = slicer.mrmlScene.AddObserver(slicer.mrmlScene.NodeRemovedEvent,
self.onNodeRemoved)
# instantiate port placement module logic
self.logic = PortPlacementLogic()
self.currentMarkupsNode = None
self.onMarkupAddedTag = None
def setup(self):
#
# Reload and Test area
#
#reloadCollapsibleButton = ctk.ctkCollapsibleButton()
#reloadCollapsibleButton.text = "Reload && Test"
#self.layout.addWidget(reloadCollapsibleButton)
#self.layout.setSpacing(6)
#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 = "InteractiveLobeSegmentation Reload"
#reloadFormLayout.addWidget(self.reloadButton)
#self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
#self.reloadAndTestButton = qt.QPushButton("Reload and Test")
#self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
#reloadFormLayout.addWidget(self.reloadAndTestButton)
#self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# the inps volume selector
#
self.inspSelectorFrame = qt.QFrame(self.parent)
self.inspSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.inspSelectorFrame)
self.inspSelectorLabel = qt.QLabel("Inspiratory CT: ",
self.inspSelectorFrame)
self.inspSelectorLabel.setToolTip(
"Select the Inspiratory CT for parenchymal analysis")
self.inspSelectorFrame.layout().addWidget(self.inspSelectorLabel)
self.inspSelector = slicer.qMRMLNodeComboBox(self.inspSelectorFrame)
self.inspSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inspSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.inspSelector.selectNodeUponCreation = False
self.inspSelector.addEnabled = False
self.inspSelector.removeEnabled = False
self.inspSelector.noneEnabled = True
self.inspSelector.showHidden = False
self.inspSelector.showChildNodeTypes = False
self.inspSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.inspSelector.SetLabelText( "Master Volume:" )
self.inspSelectorFrame.layout().addWidget(self.inspSelector)
#
# the exp volume selector
#
self.expSelectorFrame = qt.QFrame(self.parent)
self.expSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.expSelectorFrame)
self.expSelectorLabel = qt.QLabel("Expiratory CT: ",
self.expSelectorFrame)
self.expSelectorLabel.setToolTip(
"Select the Expiratory CT for parenchymal analysis")
self.expSelectorFrame.layout().addWidget(self.expSelectorLabel)
self.expSelector = slicer.qMRMLNodeComboBox(self.expSelectorFrame)
self.expSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.expSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.expSelector.selectNodeUponCreation = False
self.expSelector.addEnabled = False
self.expSelector.removeEnabled = False
self.expSelector.noneEnabled = True
self.expSelector.showHidden = False
self.expSelector.showChildNodeTypes = False
self.expSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.inspSelector.SetLabelText( "Master Volume:" )
self.expSelectorFrame.layout().addWidget(self.expSelector)
#
# the insp label volume selector
#
self.insplabelSelectorFrame = qt.QFrame()
self.insplabelSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.insplabelSelectorFrame)
self.insplabelSelectorLabel = qt.QLabel()
self.insplabelSelectorLabel.setText("Inspiratory Label Map: ")
self.insplabelSelectorFrame.layout().addWidget(
self.insplabelSelectorLabel)
self.insplabelSelector = slicer.qMRMLNodeComboBox()
#self.insplabelSelector.nodeTypes = ( "vtkMRMLScalarVolumeNode", "" )
#self.insplabelSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "1" )
self.insplabelSelector.nodeTypes = ("vtkMRMLLabelMapVolumeNode", "")
# todo addAttribute
self.insplabelSelector.selectNodeUponCreation = False
self.insplabelSelector.addEnabled = False
self.insplabelSelector.noneEnabled = True
self.insplabelSelector.removeEnabled = False
self.insplabelSelector.showHidden = False
self.insplabelSelector.showChildNodeTypes = False
self.insplabelSelector.setMRMLScene(slicer.mrmlScene)
self.insplabelSelector.setToolTip("Inspiratory label map")
self.insplabelSelectorFrame.layout().addWidget(self.insplabelSelector)
#
# the exp label volume selector
#
self.explabelSelectorFrame = qt.QFrame()
self.explabelSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.explabelSelectorFrame)
self.explabelSelectorLabel = qt.QLabel()
self.explabelSelectorLabel.setText("Expiratory Label Map: ")
self.explabelSelectorFrame.layout().addWidget(
self.explabelSelectorLabel)
self.explabelSelector = slicer.qMRMLNodeComboBox()
#self.explabelSelector.nodeTypes = ( "vtkMRMLScalarVolumeNode", "" )
#self.explabelSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "1" )
self.explabelSelector.nodeTypes = ("vtkMRMLLabelMapVolumeNode", "")
# todo addAttribute
self.explabelSelector.selectNodeUponCreation = False
self.explabelSelector.addEnabled = False
self.explabelSelector.noneEnabled = True
self.explabelSelector.removeEnabled = False
self.explabelSelector.showHidden = False
self.explabelSelector.showChildNodeTypes = False
self.explabelSelector.setMRMLScene(slicer.mrmlScene)
self.explabelSelector.setToolTip("Expiratory label map")
self.explabelSelectorFrame.layout().addWidget(self.explabelSelector)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Parenchyma Phenotypes."
self.applyButton.enabled = False
self.parent.layout().addWidget(self.applyButton)
# model and view for INSP 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)
# 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.saveButton = qt.QPushButton("Save")
self.saveButton.toolTip = "Save Statistics as a csv file."
self.saveButton.enabled = False
self.parent.layout().addWidget(self.saveButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.saveButton.connect('clicked()', self.onSave)
self.inspSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInspSelect)
self.insplabelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInspLabelSelect)
self.expSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onExpSelect)
self.explabelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onExpLabelSelect)
def setup(self):
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Radiomics Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
# self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
reloadCollapsibleButton.collapsed = True
#---------------------------------------------------------
#
# Compute Radiomics area
#
self.computeRadiomicsCollapsibleButton = ctk.ctkCollapsibleButton()
self.computeRadiomicsCollapsibleButton.text = "Slicer Radiomics Platform"
self.layout.addWidget(self.computeRadiomicsCollapsibleButton)
self.computeRadiomicsFormLayout = qt.QFormLayout(
self.computeRadiomicsCollapsibleButton)
#
# Universal Advanced Settings Collapsible Button
#
self.AdvancedSettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.AdvancedSettingsCollapsibleButton.text = "Advanced Settings"
self.AdvancedSettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.AdvancedSettingsCollapsibleButton.setLayout(qt.QHBoxLayout())
self.computeRadiomicsFormLayout.addWidget(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsCollapsibleButton.collapsed = True
self.AdvancedSettingsFrame = qt.QFrame(
self.AdvancedSettingsCollapsibleButton)
self.AdvancedSettingsFrameLayout = qt.QFormLayout()
self.AdvancedSettingsFrame.setLayout(self.AdvancedSettingsFrameLayout)
self.AdvancedSettingsCollapsibleButton.layout().addWidget(
self.AdvancedSettingsFrame)
# Label Values
self.inputLabelValues = qt.QLabel("Label Values:",
self.AdvancedSettingsFrame)
self.inputLabelValuesField = qt.QLineEdit("1",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputLabelValues,
self.inputLabelValuesField)
# Interpolation Settings
self.settingsRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.settingsRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.interpolationsGroup = qt.QButtonGroup(
self.settingsRadioButtonFrame)
self.ipRawButton = qt.QRadioButton("Raw")
self.ip1x1x1Button = qt.QRadioButton("(1,1,1)")
self.ip2x2x2Button = qt.QRadioButton("(2,2,2)")
self.ip3x3x3Button = qt.QRadioButton("(3,3,3)")
self.ipRawButton.checked = True
self.interpolationsGroup.addButton(self.ipRawButton)
self.interpolationsGroup.addButton(self.ip1x1x1Button)
self.interpolationsGroup.addButton(self.ip2x2x2Button)
self.interpolationsGroup.addButton(self.ip3x3x3Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ipRawButton)
self.settingsRadioButtonFrame.layout().addWidget(self.ip1x1x1Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip2x2x2Button)
self.settingsRadioButtonFrame.layout().addWidget(self.ip3x3x3Button)
self.interpHeader = qt.QLabel("Interpolation:")
self.AdvancedSettingsFrameLayout.addRow(self.interpHeader,
self.settingsRadioButtonFrame)
# Bin Width
self.inputBinWidth = qt.QLabel("Bin Width:",
self.AdvancedSettingsFrame)
self.inputBinWidthField = qt.QLineEdit("25",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.inputBinWidth,
self.inputBinWidthField)
# Modality Radio Buttons Frame
self.ModalityRadioButtonFrame = qt.QFrame(self.AdvancedSettingsFrame)
self.ModalityRadioButtonFrame.setLayout(qt.QHBoxLayout())
self.ModalityFileFormatGroup = qt.QButtonGroup(
self.ModalityRadioButtonFrame)
self.CTButton = qt.QRadioButton("CT")
self.CTButton.checked = True
self.MRIButton = qt.QRadioButton("MRI")
self.PETButton = qt.QRadioButton("PET")
self.ModalityFileFormatGroup.addButton(self.CTButton)
self.ModalityFileFormatGroup.addButton(self.MRIButton)
self.ModalityFileFormatGroup.addButton(self.PETButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.CTButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.MRIButton)
self.ModalityRadioButtonFrame.layout().addWidget(self.PETButton)
self.ModalityInputLabel = qt.QLabel("Image Modality:",
self.AdvancedSettingsFrame)
self.AdvancedSettingsFrameLayout.addRow(self.ModalityInputLabel,
self.ModalityRadioButtonFrame)
#
# End Universal Advanced Settings Collapsible Button
#
# Parent Tab Widget
self.computeRadiomicsTabWidget = qt.QTabWidget()
self.computeRadiomicsFormLayout.addWidget(
self.computeRadiomicsTabWidget)
# Radiomics Current Mode
self.tabComputeRadiomicsCurr = qt.QWidget()
self.singleCaseInputFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsCurr.setLayout(self.singleCaseInputFormLayout)
self.tabComputeRadiomicsCurrName = "Single Case Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsCurr,
self.tabComputeRadiomicsCurrName)
# Input 1: Input Image
self.input1Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input1Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input1Frame)
self.input1Selector = qt.QLabel("Input Image: ", self.input1Frame)
self.input1Frame.layout().addWidget(self.input1Selector)
self.input1Selector = slicer.qMRMLNodeComboBox(self.input1Frame)
self.input1Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input1Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.input1Selector.addEnabled = False
self.input1Selector.removeEnabled = False
self.input1Selector.setMRMLScene(slicer.mrmlScene)
self.input1Frame.layout().addWidget(self.input1Selector)
# Input 2: Input Segmentation
self.input2Frame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.input2Frame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.input2Frame)
self.input2Selector = qt.QLabel("Input Label: ", self.input2Frame)
self.input2Frame.layout().addWidget(self.input2Selector)
self.input2Selector = slicer.qMRMLNodeComboBox(self.input2Frame)
self.input2Selector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.input2Selector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
1)
self.input2Selector.addEnabled = False
self.input2Selector.removeEnabled = False
self.input2Selector.setMRMLScene(slicer.mrmlScene)
self.input2Frame.layout().addWidget(self.input2Selector)
# Settings Collapsible Button
self.SettingsCollapsibleButtonCurr = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButtonCurr.text = "Settings"
self.SettingsCollapsibleButtonCurrLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButtonCurr.setLayout(
self.SettingsCollapsibleButtonCurrLayout)
self.singleCaseInputFormLayout.addWidget(
self.SettingsCollapsibleButtonCurr)
self.SettingsCollapsibleButtonCurr.collapsed = False
self.SettingsFrameCurr = qt.QFrame(self.SettingsCollapsibleButtonCurr)
self.SettingsFrameCurr.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonCurrLayout.addWidget(
self.SettingsFrameCurr)
# Settings
self.para2curr = qt.QCheckBox("Use MatlabBridge",
self.tabComputeRadiomicsCurr)
self.para2curr.toolTip = "When checked: Matlab features extracted"
self.para2curr.checked = False
self.SettingsFrameCurr.layout().addRow(self.para2curr)
# Apply Radiomics button
self.RadiomicCurrButtonsFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicCurrButtonsFrame.setLayout(qt.QHBoxLayout())
self.singleCaseInputFormLayout.addWidget(self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton = qt.QPushButton(
"Compute Radiomics Features (Single Case)",
self.RadiomicCurrButtonsFrame)
self.radiomicsCurrButton.enabled = True
self.radiomicsCurrButton.toolTip = "Run the feature extraction for a single case."
self.RadiomicCurrButtonsFrame.layout().addWidget(
self.radiomicsCurrButton)
# Chart
self.RadiomicsTableFrame = qt.QFrame(self.tabComputeRadiomicsCurr)
self.RadiomicsTableFrameLayout = qt.QHBoxLayout()
self.RadiomicsTableFrame.setLayout(self.RadiomicsTableFrameLayout)
self.singleCaseInputFormLayout.addWidget(self.RadiomicsTableFrame)
self.RadiomicsTableView = qt.QTableView(self.RadiomicsTableFrame)
self.RadiomicsTableView.sortingEnabled = True
self.RadiomicsTableView.minimumHeight = 175
self.RadiomicsTableView.verticalHeader().visible = False
self.RadiomicsTableView.setColumnWidth(0, 30)
self.RadiomicsTableFrameLayout.addWidget(self.RadiomicsTableView)
self.RadiomicsTableModel = qt.QStandardItemModel()
# Save Table Button
self.saveButton = qt.QPushButton("Save Table to CSV File",
self.RadiomicCurrButtonsFrame)
self.saveButton.toolTip = "Save Radiomics Feature from table to CSV file"
self.saveButton.enabled = False
self.singleCaseInputFormLayout.layout().addWidget(self.saveButton)
"""
#
# The interface we use for batch mode (not part of this module)
#
#---------------------------------------------------------
# Radiomics Batch
self.tabComputeRadiomicsBatch = qt.QWidget()
self.RadiomicsFormLayout = qt.QFormLayout()
self.tabComputeRadiomicsBatch.setLayout(self.RadiomicsFormLayout)
self.tabComputeRadiomicsBatchName = "Batch Mode"
self.computeRadiomicsTabWidget.addTab(self.tabComputeRadiomicsBatch, self.tabComputeRadiomicsBatchName)
# Input 3: Database selection
self.input3Frame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.input3Frame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.input3Frame)
self.DatabaseButton = qt.QPushButton("Set Root Patient Directory")
self.DatabaseButton.toolTip = "Set the main Patient Data location"
self.DatabaseButton.enabled = True
self.input3Frame.layout().addWidget(self.DatabaseButton)
self.PatientSelector = qt.QComboBox()
self.PatientSelector.enabled = False
self.input3Frame.layout().addWidget(self.PatientSelector)
# Settings Collapsible Button
self.SettingsCollapsibleButton = ctk.ctkCollapsibleButton()
self.SettingsCollapsibleButton.text = "Settings"
self.SettingsCollapsibleButtonLayout = qt.QHBoxLayout()
self.SettingsCollapsibleButton.setLayout(self.SettingsCollapsibleButtonLayout)
self.RadiomicsFormLayout.addWidget(self.SettingsCollapsibleButton)
self.SettingsCollapsibleButton.collapsed = False
self.SettingsFrame = qt.QFrame(self.SettingsCollapsibleButton)
self.SettingsFrame.setLayout(qt.QFormLayout())
self.SettingsCollapsibleButtonLayout.addWidget(self.SettingsFrame)
# Settings
self.para2 = qt.QCheckBox("Use MatlabBridge", self.SettingsFrame)
self.para2.toolTip = "When checked: Matlab features extracted"
self.para2.checked = True
self.SettingsFrame.layout().addRow(self.para2)
self.para3 = qt.QCheckBox("Clear Database", self.SettingsFrame)
self.para3.toolTip = "When checked: old database is cleared"
self.para3.checked = True
self.SettingsFrame.layout().addRow(self.para3)
# Keywords Collapsible Button
self.KeywordsCollapsibleButton = ctk.ctkCollapsibleButton()
self.KeywordsCollapsibleButton.text = "Keyword Matching"
self.KeywordsCollapsibleButtonLayout = qt.QHBoxLayout()
self.KeywordsCollapsibleButton.setLayout(self.KeywordsCollapsibleButtonLayout)
self.SettingsFrame.layout().addRow(self.KeywordsCollapsibleButton)
self.KeywordsCollapsibleButton.collapsed = True
self.keywordsFrame = qt.QFrame(self.KeywordsCollapsibleButton)
self.keywordsFrame.setLayout(qt.QFormLayout())
self.KeywordsCollapsibleButtonLayout.addWidget(self.keywordsFrame)
self.keywordsHeader = qt.QLabel("Keyword Matching:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.keywordsHeader)
# File Type Radio Buttons Frame
self.radioButtonFrame = qt.QFrame(self.keywordsFrame)
self.radioButtonFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.radioButtonFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.radioButtonFrame.layout().addRow(self.nrrdButton, self.niftiButton)
self.inputMaskHeader = qt.QLabel("Input Image File Type:", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputMaskHeader, self.radioButtonFrame)
# Keywords Frame
self.inputImageKeywords = qt.QLabel("Input Image Keywords:", self.keywordsFrame)
self.inputImageKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageKeywords, self.inputImageKeywordsField )
self.inputImageExclusionKeywords = qt.QLabel("Input Image Exclusion Keywords:", self.keywordsFrame)
self.inputImageExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageExclusionKeywords, self.inputImageExclusionKeywordsField )
self.inputLabelKeywords = qt.QLabel("Input Label Keywords:", self.keywordsFrame)
self.inputLabelKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelKeywords, self.inputLabelKeywordsField )
self.inputLabelExclusionKeywords = qt.QLabel("Input Label Exclusion Keywords:", self.keywordsFrame)
self.inputLabelExclusionKeywordsField = qt.QLineEdit("",self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelExclusionKeywords, self.inputLabelExclusionKeywordsField )
# Radiomic Mode Buttons
self.RadiomicButtonsFrame = qt.QFrame(self.tabComputeRadiomicsBatch)
self.RadiomicButtonsFrame.setLayout(qt.QHBoxLayout())
self.RadiomicsFormLayout.addWidget(self.RadiomicButtonsFrame)
self.radiomicsBatchButton = qt.QPushButton("Compute Radiomics Features (Batch Mode)")
self.radiomicsBatchButton.toolTip = "Run the feature extraction for database batch."
self.radiomicsBatchButton.enabled = True
self.RadiomicButtonsFrame.layout().addWidget(self.radiomicsBatchButton)
self.RadiomicButtonsFrame.enabled = True
"""
#---------------------------------------------------------
# Connections
#self.DatabaseButton.connect('clicked(bool)', self.onDatabaseButton)
self.radiomicsCurrButton.connect('clicked(bool)', self.onRadiomicsCurr)
#self.radiomicsBatchButton.connect('clicked(bool)', self.onRadiomicsBatch)
self.saveButton.connect('clicked()', self.onSave)
self.layout.addStretch(1) # Add vertical spacer
def setup(self):
#Instantiate and Connect Widgets
#################################################
#HeterogeneityCAD Inputs Collapsible Button
self.inputHeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton(
)
self.inputHeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Input"
self.layout.addWidget(self.inputHeterogeneityCADCollapsibleButton)
self.inputHeterogeneityCADLayout = qt.QFormLayout(
self.inputHeterogeneityCADCollapsibleButton)
##Input Volume as a PET/CT/MRI image or parameter map converted to a volume
self.inputVolHetFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.inputVolHetFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputVolHetFrame)
# label for selecting individual node
self.inputVolHet = qt.QLabel("Input Node: ", self.inputVolHetFrame)
self.inputVolHetFrame.layout().addWidget(self.inputVolHet)
# select individual nodes
self.inputSelectorVolHet = slicer.qMRMLNodeComboBox(
self.inputVolHetFrame)
self.inputSelectorVolHet.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorVolHet.selectNodeUponCreation = False
self.inputSelectorVolHet.addEnabled = False
self.inputSelectorVolHet.removeEnabled = False
self.inputSelectorVolHet.setMRMLScene(slicer.mrmlScene)
self.inputVolHetFrame.layout().addWidget(self.inputSelectorVolHet)
# add Data Node button
self.addDataNodeButton = qt.QPushButton("Add Node",
self.inputVolHetFrame)
self.addDataNodeButton.objectName = 'AddDataNodeButton'
self.addDataNodeButton.setToolTip("Add a Node to Queue")
self.addDataNodeButton.connect('clicked()',
self.onAddDataNodeButtonClicked)
self.inputVolHetFrame.layout().addWidget(self.addDataNodeButton)
## data nodes Frame
self.dataNodesFrame = ctk.ctkCollapsibleGroupBox(
self.inputHeterogeneityCADCollapsibleButton)
self.dataNodesFrame.title = "Nodes List"
self.dataNodesFrame.collapsed = False
self.dataNodesFrame.setLayout(qt.QVBoxLayout())
# all buttons frame
self.allButtonsFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.allButtonsFrame.objectName = 'AllButtonsFrameButton'
self.allButtonsFrame.setLayout(qt.QVBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.dataNodesFrame,
self.allButtonsFrame)
# Data Nodes view
# Use list view here with scroll area widget.
self.dataScrollArea = qt.QScrollArea()
self.dataNodesListWidget = qt.QListWidget()
self.dataNodesListWidget.name = 'dataNodesListWidget'
self.dataScrollArea.setWidget(self.dataNodesListWidget)
self.dataNodesListWidget.resize(350, 100)
self.dataNodesFrame.layout().addWidget(self.dataScrollArea)
#self.listWidget.setProperty('SH_ItemView_ActivateItemOnSingleClick', 1)
#self.listWidget.connect('activated(QModelIndex)', self.onActivated)
# add all Data Nodes from scene button
self.addAllDataNodesButton = qt.QPushButton("Add All Nodes From Scene",
self.allButtonsFrame)
self.addAllDataNodesButton.objectName = 'AddAllDataNodesButton'
self.addAllDataNodesButton.setToolTip(
"Add all Nodes from the Scene to Queue")
self.addAllDataNodesButton.connect('clicked()',
self.onAddAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.addAllDataNodesButton)
# remove single Data Node
self.removeDataNodeButton = qt.QPushButton("Remove Node",
self.allButtonsFrame)
self.removeDataNodeButton.objectName = 'RemoveDataNodeButton'
self.removeDataNodeButton.setToolTip(
"Removes Selected Node from the Queue.")
self.removeDataNodeButton.connect('clicked()',
self.onRemoveDataNodeButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeDataNodeButton)
# remove all Data Nodes button
self.removeAllDataNodesButton = qt.QPushButton("Remove All Nodes",
self.allButtonsFrame)
self.removeAllDataNodesButton.objectName = 'RemoveAllDataNodesButton'
self.removeAllDataNodesButton.setToolTip(
"Removes All Nodes from the Queue.")
self.removeAllDataNodesButton.connect(
'clicked()', self.onRemoveAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeAllDataNodesButton)
# Use Label Map as ROI(segmentation output or user-selected ROI)
self.inputLabelROIFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.inputLabelROIFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputLabelROIFrame)
# Enable Input Label Map as ROI
self.inputLabelROI = qt.QLabel("Label Map ROI: ",
self.inputLabelROIFrame)
self.inputLabelROIFrame.layout().addWidget(self.inputLabelROI)
# Select Input Label Map as ROI
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(
self.inputLabelROIFrame)
self.inputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.inputLabelROIFrame.layout().addWidget(self.inputSelectorLabel)
#End HeterogeneityCAD Inputs Collapsible Button
#################################################
#HeterogeneityCAD Features Collapsible Button
self.HeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton()
self.HeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Features Selection"
self.layout.addWidget(self.HeterogeneityCADCollapsibleButton)
self.featuresHeterogeneityCADLayout = qt.QFormLayout(
self.HeterogeneityCADCollapsibleButton)
# auto-generate QTabWidget Tabs and QCheckBoxes (subclassed in FeatureWidgetHelperLib)
self.tabsFeatureClasses = FeatureWidgetHelperLib.CheckableTabWidget()
self.featuresHeterogeneityCADLayout.addRow(self.tabsFeatureClasses)
gridWidth, gridHeight = 3, 9
for featureClass in self.featureClassKeys:
# by default, features from the following features classes are checked:
if featureClass in [
"Node Information", "First-Order Statistics",
"Morphology and Shape", "Texture: GLCM", "Texture: GLRL"
]:
check = True
else:
check = False
tabFeatureClass = qt.QWidget()
tabFeatureClass.setLayout(qt.QGridLayout())
#featureList = (feature for feature in self.featureClassKeys[featureClass])
gridLayoutCoordinates = ((row, col) for col in range(gridWidth)
for row in range(gridHeight))
for featureName in self.featureClassKeys[featureClass]:
row, col = next(gridLayoutCoordinates, None)
if featureName is None or row is None or col is None:
break
featureCheckboxWidget = FeatureWidgetHelperLib.FeatureWidget()
featureCheckboxWidget.Setup(featureName=featureName,
checkStatus=check)
tabFeatureClass.layout().addWidget(featureCheckboxWidget, row,
col)
self.featureWidgets[featureClass].append(featureCheckboxWidget)
self.tabsFeatureClasses.addTab(tabFeatureClass,
featureClass,
self.featureWidgets[featureClass],
checkStatus=check)
self.tabsFeatureClasses.setCurrentIndex(1)
# note: try using itertools list merging with lists of GLRL diagonal
self.heterogeneityFeatureWidgets = list(
itertools.chain.from_iterable(self.featureWidgets.values()))
self.classes = list(self.featureWidgets.keys())
# or reduce(lambda x,y: x+y, self.featureWidgets.values())
########## Parameter options
# add parameters for top-level feature classes
self.tabsFeatureClasses.addParameter("Geometrical Measures",
"Extrusion Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLCM",
"GLCM Matrix Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLRL",
"GLRL Matrix Parameter 1")
# compile dict of feature classes with parameter names and values
self.featureClassParametersDict = collections.OrderedDict()
for featureClassWidget in self.tabsFeatureClasses.getFeatureClassWidgets(
):
featureClassName = featureClassWidget.getName()
self.featureClassParametersDict[
featureClassName] = collections.OrderedDict()
self.updateFeatureClassParameterDict(0, featureClassWidget)
for parameterName in featureClassWidget.widgetMenu.parameters:
featureClassWidget.getParameterEditWindow(
parameterName).connect(
'intValueChanged(int)',
lambda intValue, featureClassWidget=featureClassWidget:
self.updateFeatureClassParameterDict(
intValue, featureClassWidget))
# add parameters for individual features
for featureWidget in self.heterogeneityFeatureWidgets:
if featureWidget.getName() == "Voxel Count":
featureWidget.addParameter("Example Parameter 1")
featureWidget.addParameter("Example Parameter 2")
if featureWidget.getName() == "Gray Levels":
featureWidget.addParameter("Example Parameter 1-GL")
featureWidget.addParameter("Example Parameter 2-GL")
# compile dict of features with parameter names and values
self.featureParametersDict = collections.OrderedDict()
for featureWidget in self.heterogeneityFeatureWidgets:
featureName = featureWidget.getName()
self.featureParametersDict[featureName] = collections.OrderedDict()
self.updateFeatureParameterDict(0, featureWidget)
for parameterName in featureWidget.widgetMenu.parameters:
featureWidget.getParameterEditWindow(parameterName).connect(
'intValueChanged(int)',
lambda intValue, featureWidget=featureWidget: self.
updateFeatureParameterDict(intValue, featureWidget)
) #connect intvaluechanged signals to updateParamaterDict function
##########
# Feature Buttons Frame and Layout
self.featureButtonFrame = qt.QFrame(
self.HeterogeneityCADCollapsibleButton)
self.featureButtonFrame.setLayout(qt.QHBoxLayout())
self.featuresHeterogeneityCADLayout.addRow(self.featureButtonFrame)
# HeterogeneityCAD Apply Button
self.HeterogeneityCADButton = qt.QPushButton("Apply HeterogeneityCAD",
self.featureButtonFrame)
self.HeterogeneityCADButton.toolTip = "Analyze input volume using selected Heterogeneity Features."
self.featureButtonFrame.layout().addWidget(self.HeterogeneityCADButton)
self.HeterogeneityCADButton.connect(
'clicked()', self.onHeterogeneityCADButtonClicked)
# Save Button
self.saveButton = qt.QPushButton("Save to File",
self.featureButtonFrame)
self.saveButton.toolTip = "Save analyses to CSV file"
self.saveButton.enabled = False
self.featureButtonFrame.layout().addWidget(self.saveButton)
self.saveButton.connect('clicked()', self.onSave)
#End HeterogeneityCAD Features Collapsible Button
#################################################
#Feature Summary Chart
#Complete chart options, export list of user-selected options identified via connections to labelstatistics module
self.chartOptions = ("Count", "Volume mm^3", "Volume cc", "Min", "Max",
"Mean", "StdDev")
self.StatisticsChartCollapsibleButton = ctk.ctkCollapsibleButton()
self.StatisticsChartCollapsibleButton.text = "HeterogeneityCAD Features Summary"
self.layout.addWidget(self.StatisticsChartCollapsibleButton)
self.StatisticsChartLayout = qt.QFormLayout(
self.StatisticsChartCollapsibleButton)
self.StatisticsChartCollapsibleButton.collapsed = False
#Table View to display Label statistics
self.view = qt.QTableView(self.StatisticsChartCollapsibleButton)
self.view.sortingEnabled = True
self.StatisticsChartLayout.addWidget(self.view)
self.view.minimumHeight = 175
def setup(self):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "HeterogeneityCAD Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Tumor Segmentation Collapsible Button
self.TumorSegmentationCollapsibleButton = ctk.ctkCollapsibleButton()
self.TumorSegmentationCollapsibleButton.text = "SegmentCAD Segmentation"
self.layout.addWidget(self.TumorSegmentationCollapsibleButton)
self.TumorSegmentationLayout = qt.QFormLayout(
self.TumorSegmentationCollapsibleButton)
# Select Volumes Collapsible Button
self.selectionsCollapsibleButton = ctk.ctkCollapsibleButton()
self.selectionsCollapsibleButton.text = "Select DCE-MRI Volumes for Segmentation"
self.TumorSegmentationLayout.addWidget(
self.selectionsCollapsibleButton)
# Layout within the collapsible button
self.volumesLayout = qt.QFormLayout(self.selectionsCollapsibleButton)
# Use Multivolume Node as input
self.enableMultiVolume = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableMultiVolume.setText('Input Multi-Volume Node')
self.enableMultiVolume.checked = True
self.enableMultiVolume.setToolTip(
'Use Multi-Volume Node, with volumes imported in the correct order'
)
self.inputSelectorMultiVolume = slicer.qMRMLNodeComboBox(
self.selectionsCollapsibleButton)
self.inputSelectorMultiVolume.nodeTypes = (("vtkMRMLMultiVolumeNode"),
"")
self.inputSelectorMultiVolume.selectNodeUponCreation = False
self.inputSelectorMultiVolume.renameEnabled = True
self.inputSelectorMultiVolume.removeEnabled = False
self.inputSelectorMultiVolume.noneEnabled = True
self.inputSelectorMultiVolume.addEnabled = False
self.inputSelectorMultiVolume.setMRMLScene(slicer.mrmlScene)
self.inputSelectorMultiVolume.setToolTip(
'Use Multi-Volume Node, with volumes imported in the correct order'
)
self.volumesLayout.addRow(self.enableMultiVolume,
self.inputSelectorMultiVolume)
self.nodeInputFrame = ctk.ctkCollapsibleGroupBox(
self.selectionsCollapsibleButton)
self.nodeInputFrame.title = "Input Scalar Volume Nodes"
self.nodeInputFrame.collapsed = True
self.nodeInputFrame.enabled = False
self.nodeInputFrame.setLayout(qt.QFormLayout())
self.volumesLayout.addRow(self.nodeInputFrame)
# Select Pre Node
self.inputPre = qt.QLabel("Pre-contrast Volume", self.nodeInputFrame)
self.inputPre.setToolTip(
'Select the initial pre-contrast volume node.')
self.inputSelectorPre = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorPre.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorPre.selectNodeUponCreation = False
self.inputSelectorPre.addEnabled = False
self.inputSelectorPre.removeEnabled = False
self.inputSelectorPre.noneEnabled = True
self.inputSelectorPre.noneDisplay = 'Please Select Volume'
self.inputSelectorPre.setMRMLScene(slicer.mrmlScene)
self.inputSelectorPre.setToolTip(
'Select the initial pre-contrast volume node.')
#self.volumesLayout.addRow(self.inputPre, self.inputSelectorPre)
self.nodeInputFrame.layout().addRow(self.inputPre,
self.inputSelectorPre)
# Select First Node
self.inputFirst = qt.QLabel("First Post-contrast Volume",
self.nodeInputFrame)
self.inputFirst.setToolTip(
'Select the first post-contrast volume node to calculate intitial enhancement and curve type.'
)
self.inputSelectorFirst = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorFirst.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorFirst.selectNodeUponCreation = False
self.inputSelectorFirst.addEnabled = False
self.inputSelectorFirst.removeEnabled = False
self.inputSelectorFirst.noneEnabled = True
self.inputSelectorFirst.noneDisplay = 'Please Select Volume'
self.inputSelectorFirst.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFirst.setToolTip(
'Select the first post-contrast volume node to calculate intitial enhancement and curve type.'
)
#self.volumesLayout.addRow(self.inputFirst, self.inputSelectorFirst)
self.nodeInputFrame.layout().addRow(self.inputFirst,
self.inputSelectorFirst)
# Select Second Node
self.inputSecond = qt.QLabel("Second Post-contrast Volume",
self.nodeInputFrame)
self.inputSecond.setToolTip(
'Select a second post-contrast volume node (not required).')
self.inputSelectorSecond = slicer.qMRMLNodeComboBox(
self.nodeInputFrame)
self.inputSelectorSecond.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorSecond.selectNodeUponCreation = False
self.inputSelectorSecond.addEnabled = False
self.inputSelectorSecond.removeEnabled = False
self.inputSelectorSecond.noneEnabled = True
self.inputSelectorSecond.noneDisplay = 'Please Select Volume'
self.inputSelectorSecond.setMRMLScene(slicer.mrmlScene)
self.inputSelectorSecond.setToolTip(
'Select a second post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputSecond, self.inputSelectorSecond)
self.nodeInputFrame.layout().addRow(self.inputSecond,
self.inputSelectorSecond)
# Select Third Node
self.inputThird = qt.QLabel("Third Post-contrast Volume",
self.nodeInputFrame)
self.inputThird.setToolTip(
'Select a third post-contrast volume node (not required).')
self.inputSelectorThird = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorThird.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorThird.selectNodeUponCreation = False
self.inputSelectorThird.addEnabled = False
self.inputSelectorThird.removeEnabled = False
self.inputSelectorThird.noneEnabled = True
self.inputSelectorThird.noneDisplay = 'Please Select Volume'
self.inputSelectorThird.setMRMLScene(slicer.mrmlScene)
self.inputSelectorThird.setToolTip(
'Select a third post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputThird, self.inputSelectorThird)
self.nodeInputFrame.layout().addRow(self.inputThird,
self.inputSelectorThird)
# Select Fourth Node
self.inputFourth = qt.QLabel("Fourth Post-contrast Volume",
self.nodeInputFrame)
self.inputFourth.setToolTip(
'Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.'
)
self.inputSelectorFourth = slicer.qMRMLNodeComboBox(
self.nodeInputFrame)
self.inputSelectorFourth.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorFourth.selectNodeUponCreation = False
self.inputSelectorFourth.addEnabled = False
self.inputSelectorFourth.removeEnabled = False
self.inputSelectorFourth.noneEnabled = True
self.inputSelectorFourth.noneDisplay = 'Please Select Volume'
self.inputSelectorFourth.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFourth.setToolTip(
'Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.'
)
#self.volumesLayout.addRow(self.inputFourth, self.inputSelectorFourth)
self.nodeInputFrame.layout().addRow(self.inputFourth,
self.inputSelectorFourth)
# Enable and Select Input Label Map as ROI
self.enableLabel = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableLabel.setText('Use Label Map as ROI')
self.enableLabel.checked = True
self.enableLabel.setToolTip(
'Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.'
)
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(
self.selectionsCollapsibleButton)
self.inputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.inputSelectorLabel.setToolTip(
'Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.'
)
self.volumesLayout.addRow(self.enableLabel, self.inputSelectorLabel)
# Select output SegmentCAD Label collapsible button
self.outlabelCollapsibleButton = ctk.ctkCollapsibleButton()
self.outlabelCollapsibleButton.text = "Select or Create Output SegmentCAD Label Map"
self.TumorSegmentationLayout.addWidget(self.outlabelCollapsibleButton)
# Layout within the collapsible button
self.outlabelLayout = qt.QFormLayout(self.outlabelCollapsibleButton)
# Select or create output SegmentCAD Label Map
self.outputLabel = qt.QLabel("Output SegmentCAD Label Map",
self.outlabelCollapsibleButton)
self.outputLabel.setToolTip(
'Select or create a label map volume node as the SegmentCAD segmentation output.'
)
self.outputSelectorLabel = slicer.qMRMLNodeComboBox(
self.outlabelCollapsibleButton)
self.outputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"),
"")
self.outputSelectorLabel.baseName = "SegmentCAD Label Map"
self.outputSelectorLabel.selectNodeUponCreation = True
self.outputSelectorLabel.renameEnabled = True
self.outputSelectorLabel.removeEnabled = True
self.outputSelectorLabel.noneEnabled = False
self.outputSelectorLabel.addEnabled = True
self.outputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.outputSelectorLabel.setToolTip(
'Select or create a label map volume node as the SegmentCAD segmentation output.'
)
self.outlabelLayout.addRow(self.outputLabel, self.outputSelectorLabel)
# SegmentCAD Label Map Legend
self.outputLegend = qt.QLabel(
"| Type I Persistent: Blue | Type II Plateau: Yellow | Type III Washout: Red |",
self.outlabelCollapsibleButton)
self.outputLegend.setToolTip(
'SegmentCAD Label Map Legend | Blue: Type I Persistent curve | Yellow: Type II Plateau curve | Red: Type III Washout curve |'
)
self.outlabelLayout.addRow(self.outputLegend)
# Enable Volume Rendering of the SegmentCAD label map
self.enableVolumeRendering = qt.QCheckBox(
self.selectionsCollapsibleButton)
self.enableVolumeRendering.setText('Display Volume Rendering')
self.enableVolumeRendering.checked = True
self.enableVolumeRendering.setToolTip(
'Display volume rendering of the SegmentCAD Label Map in the 3D View'
)
self.outlabelLayout.addRow(self.enableVolumeRendering)
# Enable Label Statistics Table and Data
self.enableStats = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableStats.setText('Calculate SegmentCAD Label statistics')
self.enableStats.checked = False
self.enableStats.setToolTip(
'Use logic from Label Statistics Module to calculate statistics for first post-contrast voxels within the SegmentCAD Label Map.'
)
self.outlabelLayout.addRow(self.enableStats)
# Set Advanced Parameters Collapsible Button
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Set Advanced Segmentation Parameters"
self.TumorSegmentationLayout.addWidget(
self.parametersCollapsibleButton)
self.parametersCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.parametersLayout = qt.QFormLayout(
self.parametersCollapsibleButton)
# Set Minimum Threshold of Percentage Increase to First Post-Contrast Image
self.inputMinimumThreshold = qt.QLabel(
"Minimum Threshold of Increase", self.parametersCollapsibleButton)
self.inputMinimumThreshold.setToolTip(
'Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)'
)
self.inputSelectorMinimumThreshold = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorMinimumThreshold.setSuffix("%")
self.inputSelectorMinimumThreshold.singleStep = (1)
self.inputSelectorMinimumThreshold.minimum = (10)
self.inputSelectorMinimumThreshold.maximum = (150)
self.inputSelectorMinimumThreshold.value = (75)
self.inputSelectorMinimumThreshold.setToolTip(
'Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)'
)
self.parametersLayout.addRow(self.inputMinimumThreshold,
self.inputSelectorMinimumThreshold)
# Curve 1 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve1 = qt.QLabel("Type 1 (Persistent) Curve Minimum Slope",
self.parametersCollapsibleButton)
self.inputCurve1.setToolTip(
'Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)'
)
self.inputSelectorCurve1 = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorCurve1.singleStep = (0.02)
self.inputSelectorCurve1.minimum = (0.02)
self.inputSelectorCurve1.maximum = (0.3)
self.inputSelectorCurve1.value = (0.20)
self.inputSelectorCurve1.setToolTip(
'Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)'
)
self.parametersLayout.addRow(self.inputCurve1,
self.inputSelectorCurve1)
# Curve 3 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve3 = qt.QLabel("Type 3 (Washout) Curve Maximum Slope",
self.parametersCollapsibleButton)
self.inputCurve3.setToolTip(
'Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)'
)
self.inputSelectorCurve3 = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorCurve3.singleStep = (0.02)
self.inputSelectorCurve3.setPrefix("-")
self.inputSelectorCurve3.minimum = (0.02)
self.inputSelectorCurve3.maximum = (0.30)
self.inputSelectorCurve3.value = (0.20)
self.inputSelectorCurve3.setToolTip(
'Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)'
)
self.parametersLayout.addRow(self.inputCurve3,
self.inputSelectorCurve3)
# Apply Tumor Adaptive Segmentation button
self.SegmentCADButton = qt.QPushButton("Apply SegmentCAD")
self.SegmentCADButton.toolTip = "Apply SegmentCAD segmentation to selected volumes."
self.TumorSegmentationLayout.addWidget(self.SegmentCADButton)
# LabelStatistics Table Collapsible Button
self.labelstatisticsCollapsibleButton = ctk.ctkCollapsibleButton()
self.labelstatisticsCollapsibleButton.text = "SegmentCAD Label Statistics"
self.layout.addWidget(self.labelstatisticsCollapsibleButton)
self.labelstatisticsCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.labelstatisticsLayout = qt.QFormLayout(
self.labelstatisticsCollapsibleButton)
# Table View to display Label statistics
self.labelStatisticsTableView = qt.QTableView()
self.labelStatisticsTableView.sortingEnabled = True
self.labelstatisticsLayout.addWidget(self.labelStatisticsTableView)
self.labelStatisticsTableView.minimumHeight = 200
# Charting Statistics Button
self.chartOptions = ("Volume", "Curve Type", "Voxel Count",
"Volume mm^3", "Volume cc", "Minimum Intensity",
"Maximum Intensity", "Mean Intensity",
"Standard Deviation")
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
self.labelstatisticsLayout.addWidget(self.chartFrame)
self.chartButton = qt.QPushButton(
"Chart Statistics", self.labelstatisticsCollapsibleButton)
self.chartButton.toolTip = "Make a chart from the current statistics."
self.chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox(self.labelstatisticsCollapsibleButton)
self.chartOption.addItems(self.chartOptions)
self.chartFrame.layout().addWidget(self.chartOption)
self.chartIgnoreZero = qt.QCheckBox(
self.labelstatisticsCollapsibleButton)
self.chartIgnoreZero.setText('Ignore Zero Label')
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.chartButton.enabled = False
# Interactive Charting Settings Collapsible Button
self.iChartingCollapsibleButton = ctk.ctkCollapsibleButton()
self.iChartingCollapsibleButton.text = "Interactive Charting Settings"
self.iChartingCollapsibleButton.collapsed = True
self.layout.addWidget(self.iChartingCollapsibleButton)
# Layout within the collapsible button
self.iChartingLayout = qt.QFormLayout(self.iChartingCollapsibleButton)
# iCharting toggle button
self.iCharting = qt.QPushButton("Enable Interactive Charting")
self.iCharting.checkable = True
self.iCharting.setChecked(False)
self.iCharting.enabled = False
self.iCharting.toolTip = "Toggle the real-time charting of the %increase from baseline of the selected voxel from each input volume."
self.iChartingLayout.addRow(self.iCharting)
# Initialize slice observers (from DataProbe.py)
# Keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# Keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# Connections
self.SegmentCADButton.connect('clicked()',
self.onSegmentCADButtonClicked)
self.enableLabel.connect('stateChanged(int)', self.onEnableLabel)
self.enableMultiVolume.connect('stateChanged(int)',
self.onEnableMultiVolume)
self.chartButton.connect('clicked()', self.onChart)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
def setup(self):
# Instantiate and connect widgets ...
# reload button
# (use this during development, but remove it when delivering
# your module to users)
# Collapsible button
dummyCollapsibleButton = ctk.ctkCollapsibleButton()
dummyCollapsibleButton.text = "Parameters"
self.layout.addWidget(dummyCollapsibleButton)
# Layout within the dummy collapsible button
dummyFormLayout = qt.QFormLayout(dummyCollapsibleButton)
#LABEL VOLUME SELECTOR
self.labelSelectorFrame = qt.QFrame()
self.labelSelectorFrame.setLayout(qt.QHBoxLayout())
dummyFormLayout.addWidget(self.labelSelectorFrame)
self.labelSelectorLabel = qt.QLabel()
self.labelSelectorLabel.setText("Label Map: ")
dummyFormLayout.addWidget(self.labelSelectorLabel)
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.labelSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
"1")
# 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 = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to edit")
dummyFormLayout.addWidget(self.labelSelector)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
# the grayscale volume selector
#
self.grayscaleSelectorFrame = qt.QFrame(self.parent)
self.grayscaleSelectorFrame.setLayout(qt.QHBoxLayout())
dummyFormLayout.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"
)
dummyFormLayout.addWidget(self.grayscaleSelectorLabel)
self.grayscaleSelector = slicer.qMRMLNodeComboBox(
self.grayscaleSelectorFrame)
self.grayscaleSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.grayscaleSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", 0)
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:" )
dummyFormLayout.addWidget(self.grayscaleSelector)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "diagnosis Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Calculate button
self.calcButton = qt.QPushButton("Calculates")
self.calcButton.toolTip = "Calculates the level of stenosis on the most patological slice"
dummyFormLayout.addWidget(self.calcButton)
self.calcButton.enabled = False
self.calcButton.connect('clicked(bool)', self.onCalcButtonClicked)
# Botton temporal para llenar tabla ***************************************
self.fillTable = qt.QPushButton("Fill")
self.fillTable.toolTip = "Testing"
dummyFormLayout.addWidget(self.fillTable)
self.fillTable.enabled = True
self.fillTable.connect('clicked(bool)', self.onFillButtonClicked)
# Add Vertical Spacer
self.layout.addStretch(1)
# Parametros tabla
self.vista = qt.QTableView()
self.vista.sortingEnabled = False
self.vista.visible = False
self.vista.verticalHeader().visible = False
self.vista.horizontalHeader().visible = False
self.vista.setAlternatingRowColors(True)
dummyFormLayout.addWidget(self.vista)
# Add vertical spacer
self.layout.addStretch(1)
