def __init__(self):
self.popupGeometry = qt.QRect()
settings = qt.QSettings()
if settings.contains('DICOM/headerPopup.geometry'):
self.popupGeometry = settings.value('DICOM/headerPopup.geometry')
self.popupPositioned = False
self.window = ctk.ctkDICOMObjectListWidget()
self.window.setWindowTitle('DICOM File Metadata')
self.layout = qt.QGridLayout()
self.window.setLayout(self.layout)
def setup(self):
# Instantiate and connect widgets ...
#PARCHEE"
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# INPUT MENU
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
#Descubriendo que seria esto#
self.__mvNode = None
#Entrada multivolume
label = qt.QLabel('Input multivolume')
self.mvSelector = slicer.qMRMLNodeComboBox()
self.mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.mvSelector.setMRMLScene(slicer.mrmlScene)
self.mvSelector.addEnabled = 0
self.mvSelector.noneEnabled = 1
inputFrameLayout.addRow(label, self.mvSelector)
#Entrada frame a mostrar
label = qt.QLabel('Frame a mostrar')
self.__veInitial = qt.QDoubleSpinBox()
self.__veInitial.value = 0
inputFrameLayout.addRow(label, self.__veInitial)
###PARTE HELLO WORLD## BUTTON DE ACTIVACION
# Collapsible button
sampleCollapsibleButton = ctk.ctkCollapsibleButton()
sampleCollapsibleButton.text = "A collapsible button"
self.layout.addWidget(sampleCollapsibleButton)
# Layout within the sample collapsible button
sampleFormLayout = qt.QFormLayout(sampleCollapsibleButton)
helloWorldButton = qt.QPushButton("Hello World")
helloWorldButton.toolTip = "Print 'Hello World' in standard output."
sampleFormLayout.addWidget(helloWorldButton)
helloWorldButton.connect('clicked(bool)',
self.onHelloWorldButtonClicked)
# Set local var as instance attribute
self.helloWorldButton = helloWorldButton
def __init__(self, parent):
layout = qt.QGridLayout(parent)
self.pathList = slicer.qSlicerDirectoryListView()
layout.addWidget(self.pathList, 0, 0, 3, 1)
self.addPathButton = qt.QToolButton()
self.addPathButton.icon = qt.QIcon.fromTheme("list-add")
self.addPathButton.text = "Add"
layout.addWidget(self.addPathButton, 0, 1)
self.removePathButton = qt.QToolButton()
self.removePathButton.icon = qt.QIcon.fromTheme("list-remove")
self.removePathButton.text = "Remove"
layout.addWidget(self.removePathButton, 1, 1)
def __init__(self,
parent,
logic,
configurationName='Default',
sliceletDockWidgetPosition=qt.Qt.LeftDockWidgetArea):
logging.debug('Guidelet.__init__')
self.sliceletDockWidgetPosition = sliceletDockWidgetPosition
self.parent = parent
self.logic = logic
self.configurationName = configurationName
self.parameterNodeObserver = None
self.parameterNode = self.logic.getParameterNode()
self.layoutManager = slicer.app.layoutManager()
self.layoutNameToIdMap = {}
self.layoutNameToSelectCallbackMap = {}
self.defaultLayoutName = self.VIEW_ULTRASOUND
self.logic.updateParameterNodeFromSettings(self.parameterNode,
self.configurationName)
self.setAndObserveParameterNode(self.parameterNode)
self.ultrasound = self.getUltrasoundClass()
self.fitUltrasoundImageToViewOnConnect = True
self.setupConnectorNode()
self.sliceletDockWidget = qt.QDockWidget(self.parent)
self.mainWindow = slicer.util.mainWindow()
self.sliceletDockWidget.setParent(self.mainWindow)
self.mainWindow.addDockWidget(self.sliceletDockWidgetPosition,
self.sliceletDockWidget)
self.sliceletPanel = qt.QFrame(self.sliceletDockWidget)
self.sliceletPanelLayout = qt.QVBoxLayout(self.sliceletPanel)
self.sliceletDockWidget.setWidget(self.sliceletPanel)
self.topPanelLayout = qt.QGridLayout(self.sliceletPanel)
self.sliceletPanelLayout.addLayout(self.topPanelLayout)
self.setupTopPanel()
self.setupFeaturePanelList()
self.setupAdvancedPanel()
self.setupAdditionalPanel()
self.addConnectorObservers()
self.setupConnections()
self.sliceletDockWidget.setStyleSheet(self.loadStyleSheet())
def __init__(self, MODULE = None):
""" Init function.
"""
super(XnatViewer, self).__init__(self)
self.MODULE = MODULE
#--------------------
# Make label to display when no search
# results are found.
#--------------------
self.noSearchResultsFound = qt.QLabel("<i>No results found.</i>", self)
self.noSearchResultsFound.setStyleSheet('color: gray; margin-left: 150px; text-align: center')
#--------------------
# Make a stackedLayout and stackedWidget
# of the XnatView and the 'noSearchResultsFound'
# label. We create a 'stackedWidget' because we need
# a widget to feed into the viewerLayout, which is a
# QGridLayout. We then set the index to the XnatView --
# the XnatView will call 'setNoResultsWidgetVisible'
# if there are no search results.
#--------------------
self.stackedLayout = qt.QStackedLayout(self)
self.stackedLayout.addWidget(self.noSearchResultsFound)
self.stackedLayout.addWidget(self.MODULE.XnatView)
self.stackedLayout.setCurrentIndex(1)
self.stackedLayout.setStackingMode(1)
self.stackedWidget = qt.QWidget(self)
self.stackedWidget.setLayout(self.stackedLayout)
#--------------------
# Make main layout.
#--------------------
self.viewerLayout = qt.QGridLayout()
self.viewerLayout.addWidget(self.MODULE.XnatSearchBar, 0, 0, 1, 1)
self.viewerLayout.addWidget(self.stackedWidget, 2, 0)
self.viewerLayout.addLayout(self.MODULE.XnatButtons.loadSaveButtonLayout, 2, 1)
self.setLayout(self.viewerLayout)
def makeLoginLayout(LoginMenu):
""" As stated.
"""
#--------------------
# Username/Password Row
#--------------------
credentialsRow = qt.QHBoxLayout()
credentialsRow.addWidget(LoginMenu.manageHostsButton)
credentialsRow.addWidget(LoginMenu.hostDropdown)
credentialsRow.addSpacing(20)
credentialsRow.addWidget(LoginMenu.usernameLine)
credentialsRow.addWidget(LoginMenu.passwordLine)
credentialsRow.addWidget(LoginMenu.loginButton)
#--------------------
# Everything related to logging in.
#--------------------
loginLayout = qt.QGridLayout()
loginLayout.addLayout(credentialsRow, 0, 2)
return loginLayout
def __init__(self, MODULE=None):
""" Init function.
"""
#--------------------
# Call parent init.
#--------------------
super(XnatNodeDetails, self).__init__()
self.MODULE = MODULE
#self.settingsButton = self.MODULE.utils.makeSettingsButton(self.MODULE.XnatDetailsSettings)
self.textEdit = qt.QTextEdit(self)
self.currFont = self.MODULE.GLOBALS.LABEL_FONT
self.textEdit.setFont(self.currFont)
self.textEdit.setReadOnly(True)
self._layout = qt.QGridLayout()
self._layout.setContentsMargins(0, 0, 0, 0)
#--------------------
# Call parent init.
#--------------------
self.numColumns = 2
self.textEdit.setStyleSheet(
'border: none; padding: 0px; margin-left: 0px; margin-right: 0px')
#--------------------
# NOTE: fixes a scaling error that occurs with the scroll
# bar. Have yet to pinpoint why this happens.
#--------------------
self.textEdit.verticalScrollBar().setStyleSheet('width: 15px;')
self._layout.addWidget(self.textEdit, 0, 0)
self.setLayout(self._layout)
def setupFieldsSection(self):
self.fieldsCollapsibleButton = ctk.ctkCollapsibleButton()
self.fieldsCollapsibleButton.objectName = "ReferencePoints"
self.fieldsCollapsibleButton.text = "Reference points"
self.fieldsCollapsibleButton.setToolTip(
"Mark reference points in 2D or 3D views.\nHold down Shift key while moving the mouse pointer to synchronize mouse pointer in all views."
)
self.layout.addWidget(self.fieldsCollapsibleButton)
self.fieldsCollapsibleButton.connect(
'toggled(bool)', lambda toggle: self.onWorkflowStepChanged(
self.fieldsCollapsibleButton, toggle))
fieldsFormLayout = qt.QFormLayout(self.fieldsCollapsibleButton)
self.inputFieldsCommentLabel = qt.QLabel()
self.wordWrap = True
self.inputFieldsCommentLabel.enabled = False # make it gray
self.inputFieldsCommentLabel.hide()
fieldsFormLayout.addRow(self.inputFieldsCommentLabel)
# Input field editor widgets be inserted into this frame
self.fieldsWidgetsFrame = qt.QFrame()
self.fieldsWidgetsFrame.setFrameShape(qt.QFrame.NoFrame)
self.fieldsWidgetsGridLayout = qt.QGridLayout(self.fieldsWidgetsFrame)
self.fieldsWidgetsGridLayout.setContentsMargins(0, 0, 0, 0)
fieldsFormLayout.addRow(self.fieldsWidgetsFrame)
def setup(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
plotFrameLayout.addWidget(self.plotSettingsFrame, 0, 1)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
label = qt.QLabel('Input secondary multivolume')
self.fgSelector = slicer.qMRMLNodeComboBox()
self.fgSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.fgSelector.setMRMLScene(slicer.mrmlScene)
self.fgSelector.addEnabled = 0
self.fgSelector.noneEnabled = 1
self.fgSelector.toolTip = "Secondary multivolume will be used for the secondary \
plot in interactive charting. As an example, this can be used to overlay the \
curve obtained by fitting a model to the data"
inputFrameLayout.addRow(label, self.fgSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
label = qt.QLabel('Current frame number')
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector, 1, 1, 1, 2)
ctrlFrameLayout.addWidget(self.extractButton, 2, 0, 1, 3)
# 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()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode', 'LabelMap',
'1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.chartButton = qt.QPushButton('Chart')
self.chartButton.checkable = False
self.chartButton.connect('clicked()', self.onChartRequested)
plotSettingsFrameLayout.addWidget(label, 0, 0)
plotSettingsFrameLayout.addWidget(self.__fSelector, 0, 1)
plotSettingsFrameLayout.addWidget(self.chartButton, 0, 2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotSettingsFrameLayout.addWidget(self.iCharting, 1, 0, 1, 3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
groupLabel = qt.QLabel('Interactive plotting mode:')
self.iChartingMode = qt.QButtonGroup()
self.iChartingIntensity = qt.QRadioButton('Signal intensity')
#self.iChartingIntensity.tooltip = 'Plot range adjusted dynamically to the range over the time course for the selected pixel'
self.iChartingIntensityFixedAxes = qt.QRadioButton(
'Fixed range intensity')
#self.iChartingIntensityFixedAxes.tooltip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.iChartingPercent = qt.QRadioButton('Percent change')
#self.iChartingPercent.tooltip = 'Percent change relative to the average of the first N frames (parameter set below)'
self.iChartingIntensity.setChecked(1)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(groupLabel)
self.groupLayout.addRow(self.iChartingIntensity)
self.groupLayout.addRow(self.iChartingIntensityFixedAxes)
self.groupLayout.addRow(self.iChartingPercent)
self.baselineFrames = qt.QSpinBox()
self.baselineFrames.minimum = 1
label = qt.QLabel('Number of frames for baseline calculation')
self.groupLayout.addRow(label, self.baselineFrames)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for X axis')
self.groupLayout.addRow(self.xLogScaleCheckBox, label)
self.xLogScaleCheckBox.connect('stateChanged(int)',
self.onXLogScaleRequested)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for Y axis')
self.groupLayout.addRow(self.yLogScaleCheckBox, label)
self.yLogScaleCheckBox.connect('stateChanged(int)',
self.onYLogScaleRequested)
plotSettingsFrameLayout.addWidget(self.groupWidget, 2, 0)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView, 3, 0, 1, 3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
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):
for cervicalVertebrae in range(
1, self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE + 1):
self.verterbraeNames.append("C" + str(cervicalVertebrae))
for thoracicVertebrae in range(
1, self.CONST_NUMBER_OF_THORACIC_VERTERBRAE + 1):
self.verterbraeNames.append("T" + str(thoracicVertebrae))
for lumbarVertebrae in range(
1, self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE + 1):
self.verterbraeNames.append("L" + str(lumbarVertebrae))
self.superiorAnglesList = [
None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
self.inferiorAnglesList = [
None
] * self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE * self.CONST_NUMBER_OF_THORACIC_VERTERBRAE * self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE
# Instantiate and connect widgets
#
# Brief Explanation Text
instructionsCollapsibleButton = ctk.ctkCollapsibleButton()
instructionsCollapsibleButton.text = "Instructions"
self.layout.addWidget(instructionsCollapsibleButton)
instructionsLayout = qt.QVBoxLayout(instructionsCollapsibleButton)
self.namingInstructions = ctk.ctkFittedTextBrowser()
self.namingInstructions.setReadOnly(True)
self.namingInstructions.setPlainText(
"C - Cervical, T - Thoracic, L - Lumbar\ns - Superior, i - Inferior\nName ruler annotations like so: T1-s, T1-i, T2-s, etc."
)
instructionsLayout.addWidget(self.namingInstructions)
# Input Area
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Input"
self.layout.addWidget(parametersCollapsibleButton)
# Layout
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# Input Selector
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = (("vtkMRMLAnnotationHierarchyNode"), "")
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = True
self.inputSelector.removeEnabled = True
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 Rulers: ", self.inputSelector)
self.projectionPlaneBox = qt.QComboBox()
self.projectionPlaneBox.addItems(["Coronal", "Axial", "Sagittal"])
parametersFormLayout.addRow("Projection Plane: ",
self.projectionPlaneBox)
#
# Output Area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
self.layout.addWidget(outputCollapsibleButton)
# Layout
outputVerticalLayout = qt.QGridLayout(outputCollapsibleButton)
# Calculate Button
self.calculateButton = qt.QPushButton("Start Calculating")
outputVerticalLayout.addWidget(self.calculateButton, 0, 0, 1, 5)
# Save Button
self.saveButton = qt.QPushButton("Save as CSV")
outputVerticalLayout.addWidget(self.saveButton, 1, 0, 1, 5)
# Angle Table
horizontalHeaders = [
"Vertebrae", "Superior Angles (degrees)",
"Inferior Angles (degrees)"
]
self.angleTable = qt.QTableWidget(
self.CONST_NUMBER_OF_CERVICAL_VERTERBRAE +
self.CONST_NUMBER_OF_THORACIC_VERTERBRAE +
self.CONST_NUMBER_OF_LUMBAR_VERTERBRAE, 3)
self.angleTable.sortingEnabled = False
self.angleTable.setEditTriggers(0)
self.angleTable.setMinimumHeight(
self.angleTable.verticalHeader().length() + 25)
self.angleTable.horizontalHeader().setResizeMode(
qt.QHeaderView.Stretch)
self.angleTable.setSizePolicy(qt.QSizePolicy.MinimumExpanding,
qt.QSizePolicy.Preferred)
outputVerticalLayout.addWidget(self.angleTable, 2, 0, 1, 5)
self.angleTable.setHorizontalHeaderLabels(horizontalHeaders)
self.labelReferences = []
self.superiorAngleReferences = []
self.inferiorAngleReferences = []
for verterbraeIndex, verterbraeName in enumerate(self.verterbraeNames):
vertebraeLabel = qt.QTableWidgetItem(verterbraeName)
self.labelReferences.append(vertebraeLabel)
self.angleTable.setItem(verterbraeIndex, 0, vertebraeLabel)
superiorAngleItem = qt.QTableWidgetItem("")
self.superiorAngleReferences.append(superiorAngleItem)
self.angleTable.setItem(verterbraeIndex, 1, superiorAngleItem)
inferiorAngleItem = qt.QTableWidgetItem("")
self.inferiorAngleReferences.append(inferiorAngleItem)
self.angleTable.setItem(verterbraeIndex, 2, inferiorAngleItem)
# connections
self.calculateButton.connect('clicked(bool)', self.onCalculateButton)
self.saveButton.connect('clicked(bool)', self.onSaveButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.layout.addStretch(1)
def setup(self):
"""This is called one time when the module GUI is initialized
"""
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self.logic = CIP_PAARatioLogic()
#
# Create all the widgets. Example Area
mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
mainAreaCollapsibleButton.text = "Main parameters"
self.layout.addWidget(mainAreaCollapsibleButton)
self.mainAreaLayout = qt.QGridLayout(mainAreaCollapsibleButton)
self.label = qt.QLabel("Select the volume")
self.label.setStyleSheet("margin:10px 0 20px 7px")
self.mainAreaLayout.addWidget(self.label, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
# DEPRECATED. Now there is a new vtkMRMLLabelMapNode
#self.volumeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "0" ) # No labelmaps
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = True
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setStyleSheet(
"margin:0px 0 0px 0; padding:2px 0 2px 5px")
self.mainAreaLayout.addWidget(self.volumeSelector, 0, 1)
# self.label2 = qt.QLabel("Select the slice")
# self.label2.setStyleSheet("margin:0px 0 20px 7px; padding-top:20px")
# self.mainAreaLayout.addWidget(self.label2, 1, 0)
self.placeDefaultRulersButton = ctk.ctkPushButton()
self.placeDefaultRulersButton.text = "Place default rulers"
# self.placeDefaultRulersSliceButton.toolTip = "Navigate to the best estimated slice to place the rulers"
self.placeDefaultRulersButton.setIcon(
qt.QIcon("{0}/next.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeDefaultRulersButton.setIconSize(qt.QSize(20, 20))
self.placeDefaultRulersButton.setStyleSheet("font-weight: bold;")
# self.placeDefaultRulersButton.setFixedWidth(140)
self.mainAreaLayout.addWidget(self.placeDefaultRulersButton, 1, 1)
### Structure Selector
self.structuresGroupbox = qt.QGroupBox("Select the structure")
self.groupboxLayout = qt.QVBoxLayout()
self.structuresGroupbox.setLayout(self.groupboxLayout)
self.mainAreaLayout.addWidget(self.structuresGroupbox, 2, 0)
self.structuresButtonGroup = qt.QButtonGroup()
# btn = qt.QRadioButton("None")
# btn.visible = False
# self.structuresButtonGroup.addButton(btn)
# self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Both")
btn.checked = True
self.structuresButtonGroup.addButton(btn, 0)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Pulmonary Arterial")
self.structuresButtonGroup.addButton(btn, 1)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Aorta")
self.structuresButtonGroup.addButton(btn, 2)
self.groupboxLayout.addWidget(btn)
### Buttons toolbox
self.buttonsToolboxFrame = qt.QFrame()
self.buttonsToolboxLayout = qt.QGridLayout()
self.buttonsToolboxFrame.setLayout(self.buttonsToolboxLayout)
self.mainAreaLayout.addWidget(self.buttonsToolboxFrame, 2, 1)
self.placeRulersButton = ctk.ctkPushButton()
self.placeRulersButton.text = "Place ruler/s"
self.placeRulersButton.toolTip = "Place the ruler/s for the selected structure/s in the current slice"
self.placeRulersButton.setIcon(
qt.QIcon("{0}/ruler.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeRulersButton.setIconSize(qt.QSize(20, 20))
self.placeRulersButton.setFixedWidth(105)
self.placeRulersButton.setStyleSheet("font-weight:bold")
self.buttonsToolboxLayout.addWidget(self.placeRulersButton, 0, 0)
self.moveUpButton = ctk.ctkPushButton()
self.moveUpButton.text = "Move up"
self.moveUpButton.toolTip = "Move the selected ruler/s one slice up"
self.moveUpButton.setIcon(
qt.QIcon("{0}/move_up.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveUpButton.setIconSize(qt.QSize(20, 20))
self.moveUpButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveUpButton, 0, 1)
self.moveDownButton = ctk.ctkPushButton()
self.moveDownButton.text = "Move down"
self.moveDownButton.toolTip = "Move the selected ruler/s one slice down"
self.moveDownButton.setIcon(
qt.QIcon("{0}/move_down.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveDownButton.setIconSize(qt.QSize(20, 20))
self.moveDownButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveDownButton, 0, 2)
self.removeButton = ctk.ctkPushButton()
self.removeButton.text = "Remove ALL rulers"
self.removeButton.toolTip = "Remove all the rulers for this volume"
self.removeButton.setIcon(
qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeButton.setIconSize(qt.QSize(20, 20))
self.buttonsToolboxLayout.addWidget(self.removeButton, 1, 1, 1, 2, 2)
### Textboxes
self.textboxesFrame = qt.QFrame()
self.textboxesLayout = qt.QFormLayout()
self.textboxesFrame.setLayout(self.textboxesLayout)
self.textboxesFrame.setFixedWidth(190)
self.mainAreaLayout.addWidget(self.textboxesFrame, 3, 0)
self.paTextBox = qt.QLineEdit()
self.paTextBox.setReadOnly(True)
self.textboxesLayout.addRow("PA (mm): ", self.paTextBox)
self.aortaTextBox = qt.QLineEdit()
self.aortaTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Aorta (mm): ", self.aortaTextBox)
self.ratioTextBox = qt.QLineEdit()
self.ratioTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Ratio PA/A: ", self.ratioTextBox)
# Save case data
self.reportsCollapsibleButton = ctk.ctkCollapsibleButton()
self.reportsCollapsibleButton.text = "Reporting"
self.layout.addWidget(self.reportsCollapsibleButton)
self.reportsLayout = qt.QHBoxLayout(self.reportsCollapsibleButton)
self.storedColumnNames = [
"caseId", "paDiameter_mm", "aortaDiameter_mm", "pa1r", "pa1a",
"pa1s", "pa2r", "pa2a", "pa2s", "a1r", "a1a", "a1s", "a2r", "a2a",
"a2s"
]
self.reportsWidget = CaseReportsWidget(
"CIP_PAARatio",
columnNames=self.storedColumnNames,
parentWidget=self.reportsCollapsibleButton)
self.reportsWidget.setup()
self.switchToRedView()
#####
# Case navigator
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
self.layout.addStretch()
# Connections
self.observers = []
self.__addSceneObservables__()
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onVolumeSelectorChanged)
self.placeDefaultRulersButton.connect('clicked()',
self.oPlaceDefaultRulersClicked)
self.placeRulersButton.connect('clicked()', self.onPlaceRulersClicked)
self.moveUpButton.connect('clicked()', self.onMoveUpRulerClicked)
self.moveDownButton.connect('clicked()', self.onMoveDownRulerClicked)
self.removeButton.connect('clicked()', self.onRemoveRulerClicked)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
def setup(self):
"""This is called one time when the module GUI is initialized
"""
# Declare ALL the GUI components (depending on the context we will add different ones to the layout)
self.widgetMainFrame = qt.QFrame()
self.widgetMainLayout = qt.QGridLayout()
self.widgetMainFrame.setLayout(self.widgetMainLayout)
self.layout.addWidget(self.widgetMainFrame)
## Context
self.contextLabel = qt.QLabel("Context")
self.contextComboBox = qt.QComboBox()
for context in self.contexts.values():
self.contextComboBox.addItem(context)
## Operation
self.operationLabel = qt.QLabel("Optimization")
self.operationComboBox = qt.QComboBox()
for operation in self.operations.values():
if operation != self.OPERATION_NONE:
self.operationComboBox.addItem(operation)
## Plane
self.planeLabel = qt.QLabel("Plane")
# Buttons group
self.planesButtonGroup = qt.QButtonGroup()
# Axial
self.axialButton = qt.QPushButton()
self.axialButton.setCheckable(True)
self.axialButton.toolTip = "Axial plane"
self.axialButton.setFixedSize(40, 40)
self.axialButton.setIcon(SlicerUtil.getIcon("axial.png"))
self.planesButtonGroup.addButton(self.axialButton, self.PLANE_AXIAL)
# Sagittal
self.sagittalButton = qt.QPushButton()
self.sagittalButton.setCheckable(True)
self.sagittalButton.toolTip = "Sagittal plane"
self.sagittalButton.setFixedSize(40, 40)
self.sagittalButton.setIcon(SlicerUtil.getIcon("sagittal.png"))
self.widgetMainLayout.addWidget(self.sagittalButton, 2, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.planesButtonGroup.addButton(self.sagittalButton,
self.PLANE_SAGITTAL)
# Coronal
self.coronalButton = qt.QPushButton()
self.coronalButton.setCheckable(True)
self.coronalButton.toolTip = "coronal plane"
self.coronalButton.setFixedSize(40, 40)
self.coronalButton.setIcon(SlicerUtil.getIcon("coronal.png"))
self.planesButtonGroup.addButton(self.coronalButton,
self.PLANE_CORONAL)
# Null button (to uncheck all)
self.nullPlaneButton = qt.QPushButton()
self.nullPlaneButton.setCheckable(True)
self.planesButtonGroup.addButton(self.nullPlaneButton, -1)
# Buttons labels
self.axialButtonLabel = qt.QLabel("Axial")
self.axialButtonLabel.setStyleSheet("margin-bottom: 10px")
self.sagittalButtonLabel = qt.QLabel("Sagittal")
self.sagittalButtonLabel.setStyleSheet("margin-bottom: 10px")
self.coronalButtonLabel = qt.QLabel("Coronal")
self.coronalButtonLabel.setStyleSheet("margin-bottom: 10px")
## Layout
self.layoutLabel = qt.QLabel("Layout")
# Buttons group
self.layoutsButtonGroup = qt.QButtonGroup()
# Single slice Button
self.singleSlideViewButton = qt.QPushButton()
self.singleSlideViewButton.setCheckable(True)
self.singleSlideViewButton.toolTip = "Single slice view"
self.singleSlideViewButton.setFixedSize(40, 40)
self.singleSlideViewButton.setIcon(
qt.QIcon(":/Icons/LayoutOneUpRedSliceView.png"))
self.layoutsButtonGroup.addButton(self.singleSlideViewButton,
self.LAYOUT_RED_ONLY)
# Side by side Button
self.sideBySideViewButton = qt.QPushButton()
self.sideBySideViewButton.setCheckable(True)
self.sideBySideViewButton.toolTip = "Side by side view"
self.sideBySideViewButton.setFixedSize(40, 40)
self.sideBySideViewButton.setIcon(
qt.QIcon(":/Icons/LayoutSideBySideView.png"))
self.layoutsButtonGroup.addButton(self.sideBySideViewButton,
self.LAYOUT_SIDE_BY_SIDE)
# Three over three button
self.threeOverThreeViewButton = qt.QPushButton()
self.threeOverThreeViewButton.setCheckable(True)
self.threeOverThreeViewButton.toolTip = "Compare 2 images in their 3 planes"
self.threeOverThreeViewButton.setFixedSize(40, 40)
self.threeOverThreeViewButton.setIcon(
qt.QIcon(":/Icons/LayoutThreeOverThreeView.png"))
self.layoutsButtonGroup.addButton(self.threeOverThreeViewButton,
self.LAYOUT_THREE_OVER_THREE)
# Comparative MIP-MinIP button
self.maxMinCompareViewButton = qt.QPushButton()
self.maxMinCompareViewButton.setCheckable(True)
self.maxMinCompareViewButton.toolTip = "MIP and MinIP comparison"
self.maxMinCompareViewButton.setFixedSize(40, 40)
self.maxMinCompareViewButton.setIcon(
qt.QIcon(":/Icons/LayoutFourUpView.png"))
self.layoutsButtonGroup.addButton(self.maxMinCompareViewButton,
self.LAYOUT_COMPARE)
# Null button (to uncheck all)
self.nullLayoutButton = qt.QPushButton()
self.nullLayoutButton.setCheckable(True)
self.layoutsButtonGroup.addButton(self.nullLayoutButton, -2)
# Reset Button
self.resetViewButton = qt.QPushButton()
self.resetViewButton.toolTip = "Go back to the original layout"
self.resetViewButton.setFixedSize(40, 40)
# self.resetViewButton.setIconSize(qt.QSize(24, 24))
self.resetViewButton.setIcon(
qt.QIcon(os.path.join(SlicerUtil.CIP_ICON_DIR, "Reload.png")))
# Buttons labels
self.singleSlideButtonLabel = qt.QLabel("Single")
self.sideBySideButtonLabel = qt.QLabel("Side by side")
self.threeOverThreeButtonLabel = qt.QLabel("3x3")
self.maxMinCompareButtonLabel = qt.QLabel("MIP+MinIP")
self.resetLabel = qt.QLabel("Reset")
self.resetLabel.setStyleSheet("font-weight: bold")
# Number of slices (different for each operation). The size of the slider also changes
self.spacingSliderItems = OrderedDict()
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MIP])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 1000
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MIP] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MIP, 20)
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MinIP])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 200
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MinIP] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MinIP, 5)
spacingLabel = qt.QLabel("Slice size " +
self.operations[self.OPERATION_MEAN])
spacingSlider = qt.QSlider()
spacingSlider.orientation = 1
spacingSlider.setTickPosition(2)
spacingSlider.minimum = 0
spacingSlider.maximum = 200
spacingSlider.setPageStep(50)
spacingMmLabel = qt.QLabel()
self.spacingSliderItems[self.OPERATION_MEAN] = (spacingLabel,
spacingSlider,
spacingMmLabel)
self.setCurrentSpacingInMm(self.OPERATION_MEAN, 20)
# Crosshair
self.crosshairCheckbox = qt.QCheckBox()
self.crosshairCheckbox.setText("Crosshair cursor")
self.crosshairCheckbox.toolTip = "Activate/Desactivate the crosshair cursor for a better visualization"
self.crosshairCheckbox.setStyleSheet("margin-top:10px")
# Center button
self.centerButton = qt.QPushButton()
self.centerButton.setText("Center volumes")
self.centerButton.setFixedSize(100, 40)
self.centerButton.setStyleSheet("margin-top:10px")
if self.fullModeOn:
###### FULL MODE
# Context
self.widgetMainLayout.addWidget(self.contextLabel, 0, 0)
self.widgetMainLayout.addWidget(self.contextComboBox, 0, 1, 1, 3)
# Operation
self.widgetMainLayout.addWidget(self.operationLabel, 1, 0)
self.widgetMainLayout.addWidget(self.operationComboBox, 1, 1, 1, 3)
# Plane
self.widgetMainLayout.addWidget(self.planeLabel, 2, 0)
self.widgetMainLayout.addWidget(
self.axialButton, 2, 1, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButton, 2, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.axialButtonLabel, 3, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButtonLabel, 3, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButtonLabel, 3, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Layout
self.widgetMainLayout.addWidget(self.layoutLabel, 4, 0)
self.widgetMainLayout.addWidget(
self.singleSlideViewButton, 4, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sideBySideViewButton, 4, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeViewButton, 4, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.maxMinCompareViewButton, 4, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.resetViewButton, 4, 5,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.singleSlideButtonLabel, 5, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sideBySideButtonLabel, 5, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeButtonLabel, 5, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.maxMinCompareButtonLabel, 5, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.resetLabel, 5, 5, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Number of slices
row = 6
for structure in self.spacingSliderItems.values():
self.widgetMainLayout.addWidget(structure[0], row, 0, 1, 2)
self.widgetMainLayout.addWidget(structure[1], row, 2, 1, 3)
self.widgetMainLayout.addWidget(structure[2], row, 5)
row += 1
self.widgetMainLayout.addWidget(self.crosshairCheckbox, row, 0, 1,
2)
self.crosshairCheckbox.setChecked(True)
self.widgetMainLayout.addWidget(self.centerButton, row, 2, 1, 2)
else:
##### COLLAPSED MODE
# Plane
self.widgetMainLayout.addWidget(self.planeLabel, 0, 0)
self.widgetMainLayout.addWidget(
self.axialButton, 0, 1, SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButton, 0, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButton, 0, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeViewButton, 0, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.axialButtonLabel, 1, 1,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.sagittalButtonLabel, 1, 2,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.coronalButtonLabel, 1, 3,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
self.widgetMainLayout.addWidget(
self.threeOverThreeButtonLabel, 1, 4,
SlicerUtil.ALIGNMENT_HORIZONTAL_CENTER)
# Number of slices
row = 2
for structure in self.spacingSliderItems.values():
self.widgetMainLayout.addWidget(structure[0], row, 0)
self.widgetMainLayout.addWidget(structure[1], row, 1, 1, 3)
self.widgetMainLayout.addWidget(structure[2], row, 4)
row += 1
self.widgetMainLayout.addWidget(self.crosshairCheckbox, row, 0)
self.widgetMainLayout.addWidget(self.centerButton, row, 1, 1, 2)
self.layout.addStretch(1)
self.__refreshUI__()
# Connections
self.contextComboBox.connect("currentIndexChanged (int)",
self.__onContextIndexChanged__)
self.operationComboBox.connect("currentIndexChanged (int)",
self.__onOperationIndexChanged__)
self.planesButtonGroup.connect("buttonClicked(int)",
self.__onPlaneButtonClicked__)
self.singleSlideViewButton.connect("clicked()",
self.__onSingleSlideButtonClicked__)
self.sideBySideViewButton.connect("clicked()",
self.__onSideBySideButtonClicked__)
self.threeOverThreeViewButton.connect(
"clicked()", self.__onThreeOverThreeViewButtonClicked__)
self.maxMinCompareViewButton.connect(
"clicked()", self.__onMaxMinCompareViewButtonClicked__)
self.resetViewButton.connect("clicked()",
self.__onResetViewButtonClicked__)
for slicer in (item[1] for item in self.spacingSliderItems.values()):
slicer.connect('valueChanged(int)',
self.__onNumberOfSlicesChanged__)
self.crosshairCheckbox.connect("stateChanged(int)",
self.__onCrosshairCheckChanged__)
self.centerButton.connect("clicked()", self.__onCenterButtonClicked__)
def create(self, widgetType='window', showHeader=False, showPreview=False):
"""
main window is a frame with widgets from the app
widget repacked into it along with slicer-specific
extra widgets
"""
# find internals of widget for reference and repacking
self.toolBar = slicer.util.findChildren(self.dicomApp, 'ToolBar')[0]
self.databaseNameLabel = slicer.util.findChildren(
self.dicomApp, 'DatabaseNameLabel')[0]
self.databaseDirectoryButton = slicer.util.findChildren(
self.dicomApp, 'DirectoryButton')[0]
self.tree = slicer.util.findChildren(self.dicomApp, 'TreeView')[0]
self.userFrame = slicer.util.findChildren(self.dicomApp,
'UserFrame')[0]
self.thumbs = slicer.util.findChildren(self.dicomApp,
'ThumbnailsWidget')[0]
self.widthSlider = slicer.util.findChildren(self.dicomApp,
'ThumbnailWidthSlider')[0]
self.preview = slicer.util.findChildren(self.dicomApp,
'PreviewFrame')[0]
self.widgetType = widgetType
if widgetType == 'dialog':
self.window = qt.QDialog(self.dicomApp)
elif widgetType == 'window':
self.window = qt.QWidget()
elif widgetType == 'popup':
self.window = ctk.ctkPopupWidget(self.dicomApp)
self.window.orientation = 1
self.window.horizontalDirection = 0
self.window.alignment = 0x82
elif widgetType == 'dock':
self.dock = qt.QDockWidget(slicer.util.mainWindow())
self.dock.setFeatures(qt.QDockWidget.DockWidgetFloatable
| qt.QDockWidget.DockWidgetMovable
| qt.QDockWidget.DockWidgetClosable)
slicer.util.mainWindow().addDockWidget(0x15, self.dock)
self.window = qt.QFrame()
self.dock.setWidget(self.window)
else:
raise "Unknown widget type - should be dialog, window, dock or popup"
self.window.setWindowTitle('DICOM Details')
self.layout = qt.QGridLayout()
self.window.setLayout(self.layout)
# overall layout - tree on top, preview and selection below
toolRow = 0
treeRow = 1
selectionRow = 2
# tool row at top, with commands and database
self.toolLayout = qt.QHBoxLayout()
self.layout.addLayout(self.toolLayout, toolRow, 0, 1, 2)
self.toolLayout.addWidget(self.toolBar)
self.toolLayout.addWidget(self.databaseNameLabel)
self.toolLayout.addWidget(self.databaseDirectoryButton)
# tree goes next, spread across 1 row, 2 columns
self.layout.addWidget(self.tree, treeRow, 0, 1, 2)
#
# preview related column
#
self.previewLayout = qt.QVBoxLayout()
self.layout.addLayout(self.previewLayout, selectionRow, 0)
self.previewLayout.addWidget(self.thumbs)
self.previewLayout.addWidget(self.widthSlider)
if showPreview:
self.previewLayout.addWidget(self.preview)
else:
self.preview.hide()
#
# action related column (interacting with slicer)
#
self.actionLayout = qt.QVBoxLayout()
self.layout.addLayout(self.actionLayout, selectionRow, 1)
self.actionLayout.addWidget(self.userFrame)
tableWidth = 350 if showHeader else 700
self.loadableTable = DICOMLoadableTable(self.userFrame,
width=tableWidth)
self.actionLayout.addWidget(self.loadableTable.widget)
#
# button row for action column
#
self.actionButtonLayout = qt.QHBoxLayout()
self.actionLayout.addLayout(self.actionButtonLayout)
self.uncheckAllButton = qt.QPushButton('Uncheck All')
self.actionButtonLayout.addWidget(self.uncheckAllButton)
self.uncheckAllButton.connect('clicked()', self.uncheckAllLoadables)
self.loadButton = qt.QPushButton('Load Selection to Slicer')
self.loadButton.enabled = False
self.actionButtonLayout.addWidget(self.loadButton)
self.loadButton.connect('clicked()', self.loadCheckedLoadables)
self.closeButton = qt.QPushButton('Close')
self.actionButtonLayout.addWidget(self.closeButton)
self.closeButton.connect('clicked()', self.close)
if self.setBrowserPersistence:
self.browserPersistentButton = qt.QCheckBox(
'Make DICOM Browser Persistent')
self.browserPersistentButton.toolTip = 'When enabled, DICOM Broswer remains open and usable after leaving DICOM module'
self.actionLayout.addWidget(self.browserPersistentButton)
self.browserPersistentButton.connect('stateChanged(int)',
self.setBrowserPersistence)
#
# header related column (more details about the selected file)
#
if showHeader:
self.headerLayout = qt.QVBoxLayout()
self.layout.addLayout(self.headerLayout, selectionRow, 2)
self.header = DICOMHeaderWidget(self.window)
self.headerLayout.addWidget(self.header.widget)
def setup(self):
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
####################IMPORTAR VOLUMEN 4D#################################################3
### Se crea la sección para importar
importDataCollapsibleButton = ctk.ctkCollapsibleButton()
importDataCollapsibleButton.text = "Import DICOM"
self.layout.addWidget(importDataCollapsibleButton)
importDataFormLayout = qt.QFormLayout(importDataCollapsibleButton)
#### Crear desplegable para seleccionar dirección del volumen
self.__fDialog = ctk.ctkDirectoryButton()
self.__fDialog.caption = 'Input directory'
importDataFormLayout.addRow('Input directory:', self.__fDialog)
#### Crear desplegable para seleccionar dirección del volumen
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.inputSelector.addEnabled = True # Se habilita la posibildad al usuario de crear un nuevo nodo con este widget
self.inputSelector.removeEnabled = True # Se le quita al usuario la posibilidad de eliminar el nodo seleccionado en ese momento
self.inputSelector.setMRMLScene(slicer.mrmlScene)
importDataFormLayout.addRow("Input node:", self.inputSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputSelector, 'setMRMLScene(vtkMRMLScene*)')
self.__nameFrame = qt.QLineEdit()
self.__nameFrame.text = 'NA'
importDataFormLayout.addRow('Volume Name', self.__nameFrame)
# Botón de importar
self.buttonImport = qt.QPushButton("Import")
self.buttonImport.toolTip = "Run the algorithm."
importDataFormLayout.addRow("", self.buttonImport)
self.buttonImport.connect('clicked(bool)', self.importFunction)
### Se crea la sección para exportar
exportDataCollapsibleButton = ctk.ctkCollapsibleButton()
exportDataCollapsibleButton.text = "Export DICOM"
self.layout.addWidget(exportDataCollapsibleButton)
exportDataFormLayout = qt.QFormLayout(exportDataCollapsibleButton)
###Selector de volumen donde se guardara el volumen de la direccion
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.outputSelector.addEnabled = False # Se habilita la posibildad al usuario de crear un nuevo nodo con este widget
self.outputSelector.removeEnabled = False # Se le quita al usuario la posibilidad de eliminar el nodo seleccionado en ese momento
self.outputSelector.setMRMLScene(slicer.mrmlScene)
exportDataFormLayout.addRow("Volumen to export:", self.outputSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputSelector, 'setMRMLScene(vtkMRMLScene*)')
#### Crear desplegable para seleccionar direccion del volumen
self.__fDialogOutput = ctk.ctkDirectoryButton()
self.__fDialogOutput.caption = 'DICOM directory'
exportDataFormLayout.addRow('DiCOM directory:', self.__fDialogOutput)
# Botón de exportar
self.buttonExport = qt.QPushButton("Export")
self.buttonExport.toolTip = "Run the algorithm."
exportDataFormLayout.addRow("", self.buttonExport)
self.buttonExport.connect('clicked(bool)', self.ExportFunction)
####################EXPORTAR MANUALMENTE#################################################3
### Se crea la sección para importar
exportManualDataCollapsibleButton = ctk.ctkCollapsibleButton()
exportManualDataCollapsibleButton.text = "Exportar manualmente"
self.layout.addWidget(exportManualDataCollapsibleButton)
exportManualDataFormLayout = qt.QFormLayout(
exportManualDataCollapsibleButton)
#### Crear desplegable para seleccionar dirección del volumen
self.__fDialogManual = ctk.ctkDirectoryButton()
self.__fDialogManual.caption = 'Input directory'
exportManualDataFormLayout.addRow('Input directory:',
self.__fDialogManual)
self.__dicomID = qt.QLineEdit()
self.__dicomID.text = 'NA'
exportManualDataFormLayout.addRow('Patient ID:', self.__dicomID)
self.__dicomName = qt.QLineEdit()
self.__dicomName.text = 'NA'
exportManualDataFormLayout.addRow('Patient ID:', self.__dicomName)
self.__dicomstudyID = qt.QLineEdit()
self.__dicomstudyID.text = 'NA'
exportManualDataFormLayout.addRow('Study ID:', self.__dicomstudyID)
self.__dicomstudyComments = qt.QLineEdit()
self.__dicomstudyComments.text = 'NA'
exportManualDataFormLayout.addRow('Study ID:',
self.__dicomstudyComments)
self.__dicomstudyDescription = qt.QLineEdit()
self.__dicomstudyDescription.text = 'NA'
exportManualDataFormLayout.addRow('study Description:',
self.__dicomstudyDescription)
self.__dicommodality = qt.QLineEdit()
self.__dicommodality.text = 'NA'
exportManualDataFormLayout.addRow('modality:', self.__dicommodality)
self.__dicommanufacturer = qt.QLineEdit()
self.__dicommanufacturer.text = 'NA'
exportManualDataFormLayout.addRow('manufacturer:',
self.__dicommanufacturer)
self.__dicomseriesNumber = qt.QLineEdit()
self.__dicomseriesNumber.text = 'NA'
exportManualDataFormLayout.addRow('series Number:',
self.__dicomseriesNumber)
self.__dicomseriesDescription = qt.QLineEdit()
self.__dicomseriesDescription.text = 'NA'
exportManualDataFormLayout.addRow('series Description:',
self.__dicomseriesDescription)
self.__dicomPrefix = qt.QLineEdit()
self.__dicomPrefix.text = 'IMG'
exportManualDataFormLayout.addRow('dicomPrefix:', self.__dicomPrefix)
self.__dicomNumberFormat = qt.QLineEdit()
self.__dicomNumberFormat.text = '%04d'
exportManualDataFormLayout.addRow('series Description:',
self.__dicomNumberFormat)
def construct(self):
""" Constructs the MetadataEditorSet widget.
"""
#--------------------
# Loop through all folders as per
# Xnat.path.DEFAULT_LEVELS. We create an AnimatedCollapsible
# for every folder, one MetadataEditor_Custom and one
# MetadataEditor_Default, along with the relevant buttons for
# very folder in XNAT_LEVELS.
#--------------------
for xnatLevel in Xnat.path.DEFAULT_LEVELS:
#
# Set DEFAULT label per xnat level.
#
self.labels[xnatLevel] = []
self.labels[xnatLevel].append(qt.QLabel('<b>DEFAULT<b>'))
self.labels[xnatLevel][0].setFont(
XnatSlicerGlobals.LABEL_FONT_BOLD)
#
# Set the collapsible's internal layout
# (a qt.QGridLayout) per folder.
#
self.collapsibleLayouts[xnatLevel] = qt.QGridLayout()
self.collapsibleLayouts[xnatLevel].\
addWidget(self.labels[xnatLevel][0], 0, 0)
#
# Set the MetadataEditor_Default,
# add to layout.
#
self.defaultMetadataEditors[xnatLevel] = \
MetadataEditor_Default(xnatLevel)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.defaultMetadataEditors[xnatLevel], 1, 0)
#
# Set the MetadataEditor_Custom,
# add to layout.
#
self.customMetadataEditors[xnatLevel] = \
MetadataEditor_Custom(xnatLevel)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.customMetadataEditors[xnatLevel], 1, 1, 1, 2)
#
# Set DEFAULT label per xnat level.
#
self.labels[xnatLevel].append(qt.QLabel('<b>CUSTOM<b>'))
self.labels[xnatLevel][1].setFont(
XnatSlicerGlobals.LABEL_FONT_BOLD)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.labels[xnatLevel][1], 0, 1)
#
# Add the 'editCustom' button.
#
# NOTE: The user can choose to hide/show these buttons,
# based on what's needed. For isntance, the Settings['METADATA']
# class hides these buttons as they are not necessary for
# its workflow.
#
self.editCustomButtons[xnatLevel] = \
XnatSlicerUtils.generateButton(iconOrLabel = \
"Edit custom tags for '%s'"%(xnatLevel),
toolTip = "Adds a custom metadata tag to display in the" +
" 'Info' column.",
font = XnatSlicerGlobals.LABEL_FONT,
size = qt.QSize(180, 20),
enabled = True)
self.collapsibleLayouts[xnatLevel].\
addWidget(self.editCustomButtons[xnatLevel], 0, 2)
self.editCustomButtonGroup.\
addButton(self.editCustomButtons[xnatLevel])
#
# Put all of the widgets into first, a contentsWidget.
# Then set the widget of the AnimatedCollapsible to the
# contentsWidget.
#
self.collapsibles[xnatLevel] = AnimatedCollapsible(self, \
xnatLevel.title())
self.collapsibles[xnatLevel].setMaxExpandedHeight(250)
self.collapsibles[xnatLevel].setMinExpandedHeight(250)
contentsWidget = qt.QWidget()
contentsWidget.setLayout(self.collapsibleLayouts[xnatLevel])
self.collapsibles[xnatLevel].setContents(contentsWidget)
self.collapsibles[xnatLevel].setFixedWidth(550)
#
# Add collapsible to self.mainLayout.
#
self.mainLayout.addWidget(self.collapsibles[xnatLevel])
self.mainLayout.addSpacing(10)
#--------------------
# Set callback to Update XNATSlicer's
# layout when animating.
#--------------------
for key, collapsible in self.collapsibles.items():
collapsible.onEvent('animate', self.updateLayout)
#--------------------
# Set mainLayout to the master layout.
#--------------------
self.mainLayout.addStretch()
self.setLayout(self.mainLayout)
#--------------------
# Set the current item tyype to label.
# The user can change it to 'checkbox'
# later.
#--------------------
self.setItemType('label')
def setup(self, wName, parent):
if self.ctrlWidget:
return
self.LinkViewers()
self.numFrames = len(self.nodeImgList[0][0])
if parent:
self.ctrlWidget = parent
else:
# Create seperate window
self.ctrlWidget = slicer.qMRMLWidget()
self.ctrlWidget.setMRMLScene(slicer.mrmlScene)
self.ctrlWidget.setLayout(qt.QFormLayout())
self.ctrlWidget.setWindowTitle(wName)
ctrlLayout = self.ctrlWidget.layout()
# Create Slider Panel
self.sliderPanel = qt.QWidget()
self.sliderPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.sliderPanel)
sliderLayout = self.sliderPanel.layout()
if self.numFrames > 1:
self.ctrlFrameLabel = qt.QLabel('Frame')
self.ctrlFrameSlider = ctk.ctkSliderWidget()
self.ctrlFrameSlider.connect('valueChanged(double)',
self.onSliderFrameChanged)
sliderLayout.addWidget(self.ctrlFrameLabel, 0, 0)
sliderLayout.addWidget(self.ctrlFrameSlider, 0, 1)
self.ctrlLevelLabel = qt.QLabel('Level')
self.ctrlLevelSlider = ctk.ctkSliderWidget()
self.ctrlLevelSlider.connect('valueChanged(double)',
self.onSliderLevelChanged)
sliderLayout.addWidget(self.ctrlLevelLabel, 1, 0)
sliderLayout.addWidget(self.ctrlLevelSlider, 1, 1)
self.ctrlWindowLabel = qt.QLabel('Window')
self.ctrlWindowSlider = ctk.ctkSliderWidget()
self.ctrlWindowSlider.connect('valueChanged(double)',
self.onSliderWindowChanged)
sliderLayout.addWidget(self.ctrlWindowLabel, 2, 0)
sliderLayout.addWidget(self.ctrlWindowSlider, 2, 1)
self.setSliderRangesAndValues()
if self.sliceNodeList:
self.orientPanel = qt.QWidget()
self.orientPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.orientPanel)
self.orientationButtons = {}
index = 0
for orientation in self.orientations:
self.orientationButtons[orientation] = qt.QRadioButton()
self.orientationButtons[orientation].text = orientation
# self.orientationBox.layout().addWidget(self.orientationButtons[orientation])
self.orientPanel.layout().addWidget(
self.orientationButtons[orientation], 0, index)
self.orientationButtons[orientation].connect(
"clicked()", lambda o=orientation: self.setOrientation(o))
index += 1
self.setOrientation(self.selectedOrientation)
if False:
#self.plotFrame = ctk.ctkCollapsibleButton()
#self.plotFrame.text = "Plotting"
#self.plotFrame.collapsed = 0
self.plotFrame = qt.QWidget()
plotFrameLayout = qt.QGridLayout(self.plotFrame)
ctrlLayout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
#plotFrameLayout.addWidget(self.plotSettingsFrame,0,1)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
# taken from https://github.com/fedorov/MultiVolumeExplorer
self.__chartView = ctk.ctkVTKChartView(self.ctrlWidget)
# self.plotFrame)
# self.ctrlWidget
plotFrameLayout.addWidget(self.__chartView, 0, 0)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.onInputChanged()
self.refreshObservers()
self.buttonPanel = qt.QWidget()
self.buttonPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.buttonPanel)
self.exitButton = qt.QPushButton("Exit")
self.exitButton.toolTip = "Close down slicer."
self.exitButton.name = "sviewer exit"
self.buttonPanel.layout().addWidget(self.exitButton, 0, 0)
self.exitButton.connect('clicked()', exit)
# do not do ctrlWin.show() here - for some reason window does not pop up then
return self.ctrlWidget
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
#
# 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 = "SequenceRegistration 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)
#
# Input Area
#
parametersCollapsibleButton1 = ctk.ctkCollapsibleButton()
parametersCollapsibleButton1.text = "Inputs"
self.layout.addWidget(parametersCollapsibleButton1)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton1)
#
# Input fixed image
#
self.fixedImageSelector = slicer.qMRMLNodeComboBox()
self.fixedImageSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.fixedImageSelector.selectNodeUponCreation = True
self.fixedImageSelector.addEnabled = False
self.fixedImageSelector.removeEnabled = False
self.fixedImageSelector.noneEnabled = False
self.fixedImageSelector.showHidden = False
self.fixedImageSelector.showChildNodeTypes = False
self.fixedImageSelector.setMRMLScene( slicer.mrmlScene )
self.fixedImageSelector.setToolTip( "Please select the fixed image node for tracking." )
parametersFormLayout.addRow("Reference sequence/image node: ", self.fixedImageSelector)
#
# Input moving sequence image
#
self.movingImageSequenceSelector = slicer.qMRMLNodeComboBox()
self.movingImageSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.movingImageSequenceSelector.selectNodeUponCreation = True
self.movingImageSequenceSelector.addEnabled = False
self.movingImageSequenceSelector.removeEnabled = False
self.movingImageSequenceSelector.noneEnabled = False
self.movingImageSequenceSelector.showHidden = False
self.movingImageSequenceSelector.showChildNodeTypes = False
self.movingImageSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.movingImageSequenceSelector.setToolTip( "Please select the moving sequence image node for tracking." )
parametersFormLayout.addRow("Moving sequence/image node: ", self.movingImageSequenceSelector)
#
# Input rigid transform
#
self.linearTransformSelector = slicer.qMRMLNodeComboBox()
self.linearTransformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.linearTransformSelector.selectNodeUponCreation = True
self.linearTransformSelector.addEnabled = True
self.linearTransformSelector.removeEnabled = True
self.linearTransformSelector.noneEnabled = True
self.linearTransformSelector.showHidden = False
self.linearTransformSelector.showChildNodeTypes = False
self.linearTransformSelector.setMRMLScene( slicer.mrmlScene )
self.linearTransformSelector.setToolTip( "Please select a transform." )
parametersFormLayout.addRow("Initial transform node: ", self.linearTransformSelector)
#
# ROI
#
self.InputROISelector = slicer.qMRMLNodeComboBox()
self.InputROISelector.nodeTypes = ( ("vtkMRMLAnnotationROINode"), "" )
self.InputROISelector.selectNodeUponCreation = True
self.InputROISelector.addEnabled = True
self.InputROISelector.removeEnabled = True
self.InputROISelector.noneEnabled = True
self.InputROISelector.showHidden = False
self.InputROISelector.showChildNodeTypes = False
self.InputROISelector.setMRMLScene( slicer.mrmlScene )
parametersFormLayout.addRow("ROI: ", self.InputROISelector)
self.ROIVisibilityButton = qt.QPushButton("Off")
self.ROIVisibilityButton.checkable = True
self.ROIVisibilityButton.checked = False
self.ROIVisibilityButton.enabled = False
parametersFormLayout.addRow("ROI Visibility: ", self.ROIVisibilityButton)
self.InitializeTransformModeOptions = ("Off","useGeometryAlign","useMomentsAlign")
#
#Initialization
#
self.groupBox = qt.QGroupBox("Initialize Transform Mode")
self.groupBoxLayout = qt.QHBoxLayout(self.groupBox)
parametersFormLayout.addRow(self.groupBox)
#
# layout selection
#
for initializeTransformModeOption in self.InitializeTransformModeOptions:
initializeTransformModeButton = qt.QRadioButton(initializeTransformModeOption)
initializeTransformModeButton.connect('clicked()', lambda itmo=initializeTransformModeOption: self.selectInitializeTransformMode(itmo))
self.groupBoxLayout.addWidget(initializeTransformModeButton)
#self.groupBoxLayout.addRow("Layout", layoutHolder)
#
# Register Button
#
self.registerButton = qt.QPushButton("Register")
self.registerButton.toolTip = "Run the algorithm."
self.registerButton.enabled = False
parametersFormLayout.addRow(self.registerButton)
# Connections
self.fixedImageSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.movingImageSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.InputROISelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.ROIVisibilityButton.connect('clicked(bool)', self.onROIVisible)
self.registerButton.connect('clicked(bool)', self.onApply)
#
# Output Area
#
outputsCollapsibleButton1 = ctk.ctkCollapsibleButton()
outputsCollapsibleButton1.text = "Outputs (at least one output must be specified)"
self.layout.addWidget(outputsCollapsibleButton1)
# Layout within the dummy collapsible button
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton1)
#
# Output rigid transform
#
self.outputTransformSequenceSelector = slicer.qMRMLNodeComboBox()
self.outputTransformSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.outputTransformSequenceSelector.selectNodeUponCreation = True
self.outputTransformSequenceSelector.addEnabled = True
self.outputTransformSequenceSelector.removeEnabled = True
self.outputTransformSequenceSelector.noneEnabled = True
self.outputTransformSequenceSelector.showHidden = False
self.outputTransformSequenceSelector.showChildNodeTypes = False
self.outputTransformSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.outputTransformSequenceSelector.setToolTip( "Please select a sequence transform node." )
outputsFormLayout.addRow("Output sequence transform node: ", self.outputTransformSequenceSelector)
#
# Output images
#
self.outputImageSequenceSelector = slicer.qMRMLNodeComboBox()
self.outputImageSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.outputImageSequenceSelector.selectNodeUponCreation = True
self.outputImageSequenceSelector.addEnabled = True
self.outputImageSequenceSelector.removeEnabled = True
self.outputImageSequenceSelector.noneEnabled = True
self.outputImageSequenceSelector.showHidden = False
self.outputImageSequenceSelector.showChildNodeTypes = False
self.outputImageSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.outputImageSequenceSelector.setToolTip( "Please select a sequence image node." )
outputsFormLayout.addRow("Output sequence image node: ", self.outputImageSequenceSelector)
# Comment out the following code as this functionality is not moved to Sequence Browser module
# plottingCollapsibleButton = ctk.ctkCollapsibleButton()
# plottingCollapsibleButton.text = "Plotting"
# plottingCollapsibleButton.collapsed = 0
# self.layout.addWidget(plottingCollapsibleButton)
# plottingFrameLayout = qt.QGridLayout(plottingCollapsibleButton)
# self.ChartingDisplayOptions = ("LR","AP","SI")
# self.chartingDisplayOption = 'LR'
# #
# #Initialization
# #
# self.chartGroupBox = qt.QGroupBox("Display options:")
# self.chartGroupBoxLayout = qt.QHBoxLayout(self.chartGroupBox)
# plottingFrameLayout.addWidget(self.chartGroupBox,0,0,1,3)
# #
# # layout selection
# #
# for chartingDisplayOption in self.ChartingDisplayOptions:
# chartingDisplayOptionButton = qt.QRadioButton(chartingDisplayOption)
# chartingDisplayOptionButton.connect('clicked()', lambda cdo=chartingDisplayOption: self.selectChartingDisplayOption(cdo))
# self.chartGroupBoxLayout.addWidget(chartingDisplayOptionButton)
# #self.groupBoxLayout.addRow("Layout", layoutHolder)
# # add chart container widget
# self.__chartView = ctk.ctkVTKChartView(w)
# plottingFrameLayout.addWidget(self.__chartView,1,0,1,3)
# self.__chart = self.__chartView.chart()
# self.__chartTable = vtk.vtkTable()
# self.__xArray = vtk.vtkFloatArray()
# self.__yArray = vtk.vtkFloatArray()
# self.__zArray = vtk.vtkFloatArray()
# self.__mArray = vtk.vtkFloatArray()
# # will crash if there is no name
# self.__xArray.SetName('')
# self.__yArray.SetName('signal intensity')
# self.__zArray.SetName('')
# self.__mArray.SetName('signal intensity')
# self.__chartTable.AddColumn(self.__xArray)
# self.__chartTable.AddColumn(self.__yArray)
# self.__chartTable.AddColumn(self.__zArray)
# self.__chartTable.AddColumn(self.__mArray)
self.outputTransformSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputSelect)
self.outputImageSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputSelect)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
"""Init the widget """
# ScriptedLoadableModuleWidget.setup(self)
settings = qt.QSettings()
if (SlicerUtil.IsDevelopment):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onBtnReloadClicked)
self.logic = PicasaSnapLogic()
self.__addObservers__()
######## Credentials
self.credentialsCollapsibleButton = ctk.ctkCollapsibleButton()
self.credentialsCollapsibleButton.text = "Credentials"
self.layout.addWidget(self.credentialsCollapsibleButton)
self.credentialsLayout = qt.QFormLayout(
self.credentialsCollapsibleButton)
self.isUserLogged = False
self.loginLineEdit = qt.QLineEdit()
self.credentialsLayout.addRow("Login: "******"Password: "******"Remember my credentials")
self.rememberCredentialsCheckBox.toolTip = "Check for an automatic login when the application starts"
self.loginButton = qt.QPushButton("Login")
self.loginButton.toolTip = "Login in Picassa service (Google credentials)"
self.logoutButton = qt.QPushButton("Logout")
self.logoutButton.toolTip = "Logout to connect with another user's credentials"
# Add all the items, they will be shown/hidden in refreshCredentialsUI function
self.credentialsLayout.addRow(self.rememberCredentialsCheckBox,
self.loginButton)
self.credentialsLayout.addRow(None, self.logoutButton)
######## Snapshots (main frame)
self.mainCollapsibleButton = ctk.ctkCollapsibleButton()
self.mainCollapsibleButton.text = "Snapshots"
self.layout.addWidget(self.mainCollapsibleButton)
self.mainLayout = qt.QVBoxLayout(self.mainCollapsibleButton)
############### Current snapshots
self.currentSnapshotsFrame = qt.QFrame()
self.currentSnapshotsLayout = qt.QVBoxLayout()
self.currentSnapshotsFrame.setLayout(self.currentSnapshotsLayout)
self.currentSnapshotsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.mainLayout.addWidget(self.currentSnapshotsFrame)
self.snapshotsLabel = qt.QLabel("Snapshots to upload:")
self.snapshotsLabel.setStyleSheet(
"font-weight:bold; font-size:14px; margin-bottom:10px")
self.currentSnapshotsLayout.addWidget(self.snapshotsLabel)
# Subframe that contains the checkbox list
self.currentSnapshotsInnerFrame = qt.QFrame()
self.currentSnapshotsInnerLayout = qt.QVBoxLayout()
self.currentSnapshotsInnerFrame.setLayout(
self.currentSnapshotsInnerLayout)
self.currentSnapshotsLayout.addWidget(self.currentSnapshotsInnerFrame)
self.noItemsLabel = qt.QLabel(
"(There are not any snapshots at the moment)")
# Add the label by default. It will be hidden if there is any snapshot
self.currentSnapshotsInnerLayout.addWidget(self.noItemsLabel)
self.loadExistingSnapshotsFirstLoad()
############### Albums
# Try to login before getting the albums
self.login()
msgBox = None
if self.isUserLogged:
# Show message box while loading the data
msgBox = qt.QMessageBox(qt.QMessageBox.Information, 'Login',
'Connecting with Picasa. Please wait...',
qt.QMessageBox.Cancel)
msgBox.show()
try:
self.albumNameFrame = qt.QFrame()
self.albumNameLayout = qt.QHBoxLayout()
self.albumNameFrame.setLayout(self.albumNameLayout)
self.albumNameFrame.setFrameShape(qt.QFrame.StyledPanel)
self.albumNameLabel = qt.QLabel("Album name:")
self.albumNameLabel.setStyleSheet("font-weight:bold;")
self.albumNamesComboBox = qt.QComboBox()
self.loadAlbums()
self.albumNameLayout.addWidget(self.albumNameLabel)
self.albumNameLayout.addWidget(self.albumNamesComboBox)
self.mainLayout.addWidget(self.albumNameFrame)
############### Tags
self.tagsFrame = qt.QFrame()
self.tagsLayout = qt.QGridLayout()
self.tagsFrame.setLayout(self.tagsLayout)
self.tagsFrame.setFrameShape(qt.QFrame.StyledPanel)
self.tagsLabel = qt.QLabel(
"Tags (select all that apply, you can filter o create new tags):"
)
self.tagsLabel.setStyleSheet(
"font-weight: bold; margin-bottom: 10px; margin-top: 5px")
self.tagsLayout.addWidget(self.tagsLabel, 0, 0, 1, 3)
# Add input to filter tags and button to add a new one
self.tagsFilterLineEdit = qt.QLineEdit()
self.tagsFilterLineEdit.toolTip = "Type here to filter your tags. If you press the return key all the visible tags will be checked"
#self.tagsFilterLineEdit.setStyleSheet(style)
self.tagsLayout.addWidget(self.tagsFilterLineEdit, 1, 0, 1, 2)
self.newTagButton = qt.QPushButton("New tag")
#self.newTagButton.setStyleSheet("background-color: #5D74C6; color:white")
self.newTagButton.setIconSize(qt.QSize(20, 20))
self.newTagButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Plus - 48.png"))
self.newTagButton.setFixedWidth(75)
self.newTagButton.toolTip = "Add a new tag (the tag will not be created until you upload any picture with it)"
self.tagsLayout.addWidget(self.newTagButton, 1, 2)
self.loadTags()
############### Upload snapshots controls
self.uploadSnapsButtonFrame = qt.QFrame()
self.uploadSnapsLayout = qt.QHBoxLayout()
self.uploadSnapsButtonFrame.setLayout(self.uploadSnapsLayout)
#self(qt.QFrame.HLine)
self.mainLayout.addWidget(self.uploadSnapsButtonFrame)
self.uploadSnapshotsButton = qt.QPushButton()
self.uploadSnapshotsButton.text = "Upload to Picasa!"
self.uploadSnapshotsButton.toolTip = "Upload selected screenshots to Picassa"
self.uploadSnapshotsButton.setStyleSheet(
"background-color: #5D74C6; color: white; font-weight: bold; font-size:14px"
)
self.uploadSnapshotsButton.setIcon(
qt.QIcon(self.CIP_ICON_DIR + "/Upload - 64.png"))
self.uploadSnapshotsButton.setIconSize(qt.QSize(24, 24))
self.uploadSnapshotsButton.setFixedSize(170, 35)
self.uploadSnapsLayout.addWidget(self.uploadSnapshotsButton)
############### Progress bar
self.progressBar = qt.QProgressDialog()
self.progressBar.setMinimum(0)
self.progressBar.setMinimumDuration(0)
self.progressBar.setWindowModality(True)
# Check for updates in CIP
#autoUpdate = SlicerUtil.settingGetOrSetDefault("PicasaSnap", "AutoUpdate", 1)
#uw = AutoUpdateWidget(parent=self.parent, autoUpdate=autoUpdate)
#uw.addAutoUpdateCheckObserver(self.onAutoUpdateStateChanged)
# self.uploadProgressFrame = qt.QFrame()
# self.uploadProgressLayout = qt.QVBoxLayout()
# self.uploadProgressFrame.setLayout(self.uploadProgressLayout)
#
# # Gif image
# self.imUploading = qt.QMovie("%s/loading.gif" % self.CIP_ICON_DIR, qt.QByteArray())
# # Label to contain the gif
# self.lblImLoading = qt.QLabel()
# # Fix the dimensions of the image (by fixing the dimensions of the label that contains it)
# self.lblImLoading.setFixedWidth(40)
# # Other image parameters
# self.imUploading.setCacheMode(qt.QMovie.CacheAll)
# self.imUploading.setSpeed(100)
# # Assign the label to the image (don't start it yet, it will be started when we are uploading)
# self.lblImLoading.setMovie(self.imUploading)
# #self.imUploading.start()
# self.uploadProgressLayout.addWidget(self.lblImLoading)
#
# # Label that will show the progress
# self.lblUploading = qt.QLabel("Uploading %i/%i images...")
# self.uploadProgressLayout.addWidget(self.lblUploading)
#
# Cancel uploading button
# self.btnCancelUpload = qt.QPushButton("Cancel")
# self.btnCancelUpload.toolTip = "Cancel the process"
# self.btnCancelUpload.setFixedWidth(100)
# self.uploadProgressLayout.addWidget(self.btnCancelUpload)
# self.mainLayout.addWidget(self.uploadProgressFrame)
#
# # Hide the progress frame
# self.uploadProgressFrame.hide()
######## Connections
self.uploadSnapshotsButton.connect(
'clicked (bool)', self.onUploadSnapshotsButtonClicked)
self.loginButton.connect('clicked (bool)',
self.onLoginButtonClicked)
self.logoutButton.connect('clicked (bool)',
self.onLogoutButtonClicked)
self.loginLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.passwordLineEdit.returnPressed.connect(
self.onLoginPasswordReturnKeyPressed)
self.albumNamesComboBox.connect("currentIndexChanged (int)",
self.onAlbumsCurrentIndexChanged)
self.newTagButton.connect('clicked (bool)',
self.onNewTagButtonClicked)
self.tagsFilterLineEdit.connect('textEdited (QString)',
self.onFilterTagsEdited)
self.tagsFilterLineEdit.returnPressed.connect(
self.onFilterTagsReturnKeyPressed)
# Add vertical spacer
self.layout.addStretch(1)
finally:
# Hide MesageBox if it was visible
if msgBox:
msgBox.close()
def setup(self):
#Collapsible button
autoMRIBrainCollapsibleButton = ctk.ctkCollapsibleButton()
autoMRIBrainCollapsibleButton.text = "Collapsible button for Brain MRI auto-segmentation"
self.layout.addWidget(autoMRIBrainCollapsibleButton)
#Layout within the collapsible button
autoMRIBrainFormLayout = qt.QFormLayout(autoMRIBrainCollapsibleButton)
#Load Brain MRI image button
# loadMRIBrainButton = qt.QPushButton("Load Brain MRI image and add ROI annotation")
# loadMRIBrainButton.toolTip = "Click to load Brain MRI image and annotate tumor center location"
# autoMRIBrainFormLayout.addWidget(loadMRIBrainButton)
# loadMRIBrainButton.connect('clicked(bool)', self.onloadMRIBrainButtonClicked)
#Load Brain MRI T1 image button
loadMRIT1Button = qt.QPushButton("Load Brain MRI T1 image")
loadMRIT1Button.toolTip = "Click to load Brain MRI T1 image and annotate tumor center location"
# autoMRIBrainFormLayout.addWidget(loadMRIT1Button)
loadMRIT1Button.connect('clicked(bool)', self.onloadMRIT1ButtonClicked)
#Load Brain MRI T2 FLAIR
loadMRIFLAIRButton = qt.QPushButton("Load Brain MRI T2 FLAIR image")
loadMRIFLAIRButton.toolTip = "Click to load Brain MRI image and annotate tumor center location"
# autoMRIBrainFormLayout.addWidget(loadMRIFLAIRButton)
loadMRIFLAIRButton.connect('clicked(bool)',
self.onloadMRIFLAIRButtonClicked)
loadMRIBrainButtons = qt.QGridLayout()
loadMRIBrainButtons.addWidget(loadMRIT1Button, 0, 0)
loadMRIBrainButtons.addWidget(loadMRIFLAIRButton, 0, 1)
autoMRIBrainFormLayout.addRow(loadMRIBrainButtons)
#load ATLAS
loadATLASButton = qt.QPushButton("Load ALTAS Images")
loadATLASlabelButton = qt.QPushButton("Load ALTAS Labels")
loadATLASButton.connect('clicked(bool)', self.onloadATLASButtonClicked)
loadATLASlabelButton.connect('clicked(bool)',
self.onloadATLASlabelButtonClicked)
autoMRIBrainFormLayout.addWidget(loadATLASButton)
autoMRIBrainFormLayout.addWidget(loadATLASlabelButton)
# Segment T1
SegT1Button = qt.QPushButton("Segment T1")
SegT1Button.toolTip = "Click this button to segment tumor if loaded image is T1."
SegT1Button.connect('clicked(bool)', self.onloadSegT1ButtonClicked)
# autoMRIBrainFormLayout.addWidget(loadSegT1Button)
#Segment FLAIR
SegFLAIRButton = qt.QPushButton("Segment FLAIR")
SegFLAIRButton.toolTip = "Click this button to segment tumor if loaded image is FLAIR"
SegFLAIRButton.connect('clicked(bool)',
self.onloadSegFLAIRButtonClicked)
#Buttons to form
segMRIBrainButtons = qt.QGridLayout()
segMRIBrainButtons.addWidget(SegT1Button, 0, 0)
segMRIBrainButtons.addWidget(SegFLAIRButton, 0, 1)
autoMRIBrainFormLayout.addRow(segMRIBrainButtons)
##### Ajust value for volume to keep ##########
##########################################
# sigmalabel = qt.QLabel()
# sigmalabel.setText("Ajust ROI size value for better segmentation (1-10)")
# autoMRIBrainFormLayout.addWidget(sigmalabel)
# sigmaSlider = qt.QSlider(qt.Qt.Horizontal)
# sigmaSlider.toolTip = "Slide to change threshold value"
# sigmaSlider.setMinimum(1)
# sigmaSlider.setMaximum(10)
# sigmaSlider.setValue(1)
# sigmaSlider.setTickPosition(qt.QSlider.TicksBelow)
# sigmaSlider.setTickInterval(1)
# self.sigmaSlider = sigmaSlider
# #label for ticks
# sigmavalues = qt.QGridLayout()
# r1 = qt.QLabel("1")
# # r2 = qt.QLabel("3")
# # r3 = qt.QLabel("5")
# # r4 = qt.QLabel("7")
# # r5 = qt.QLabel("9")
# sigmavalues.addWidget(sigmaSlider, 0,0,1,5)
# sigmavalues.addWidget(r1,1,0,1,1)
# # sigmavalues.addWidget(r2,1,1,1,1)
# # sigmavalues.addWidget(r3,1,2,1,1)
# # sigmavalues.addWidget(r4,1,3,1,1)
# # sigmavalues.addWidget(r5,1,4,1,1)
# #Apply the changes
# sigmaApplyButton = qt.QPushButton("Apply")
# sigmaApplyButton.toolTip = "Click to apply new sigma value"
# sigmavalues.addWidget(sigmaApplyButton, 0,5,2,1)
# sigmaApplyButton.connect('clicked(bool)', self.changesApplyButtonClicked)
# autoMRIBrainFormLayout.addRow(sigmavalues)
# # Add vertical spacer
# self.layout.addStretch(1)
#ATLAS directories
# self.atlas_T1_dir = '/Users/lingdao.sha/Documents/Images/Radiology/Brain_MRI_auto/Brain/mni_icbm152_nlin_sym_09a/mni_icbm152_t1_tal_nlin_sym_09a.nii'
# self.atlas_label_T1_dir = '/Users/lingdao.sha/Documents/Images/Radiology/Brain_MRI_auto/Brain/mni_icbm152_nlin_sym_09a/mni_icbm152_t1_tal_nlin_sym_09a_mask.nii'
### Parameters for tweaking ###
# Elongation threshold (0 = perfect sphere)
self.elong_thresh = -1 # default = 0.25; switch to -1 to remove threshold altogether (may be needed in cases where algorithm gives nans or segmented tumor region is not correct)
# Segmentation to select when refining segmentation
self.seg_number = 1 # 1 (default) corresponds to largest volume, 2 corresponds to second largest volume, etc. This may need to be changed if eyes are getting segmented instead of tumor
# change which thresholded segment to keep during t1p segmentation
self.lowIntEnhance = 0 # 0 (default) takes highest intensity region; 1 takes second highest intensity region
### End tweak parameters ###
# register and resample FLAIR to T1p and perform skull stripping
self.registerSkullStripImages = 1 # 1 yes; 0 load registered/resampled and sull stripped images from file
# Output file names
self.name_T1p_label = 'T1p_label.nrrd'
self.name_T1p_image = 'T1p_image.nrrd'
# Output file names
self.name_FLAIR_label = 'FLAIR_label.nrrd'
self.name_FLAIR_image = 'FLAIR_image.nrrd'
# volume thresholds for FLAIR segmented tumors (derived through empiracal results)
self.volume_FLAIR_lower_threshold = 3000 # Regions with volumes less than this was never the tumor
self.volume_FLAIR_upper_threshold = 185000 # Regions with volumes greater than this always included many (non-tumor) regions of the brain
def setup(self):
# make an instance of the logic
self.logic = TwoTensorModelVizLogic()
#
# Model Selection Area
#
modelCollapsibleButton = ctk.ctkCollapsibleButton()
modelCollapsibleButton.text = "Basic"
self.layout.addWidget(modelCollapsibleButton)
modelFormLayout = qt.QFormLayout(modelCollapsibleButton)
# ============Fiber model selector===================
self.modelSelector = slicer.qMRMLNodeComboBox()
self.modelSelector.nodeTypes = ( ("vtkMRMLFiberBundleNode"), "" )
self.modelSelector.selectNodeUponCreation = True
self.modelSelector.addEnabled = False
self.modelSelector.removeEnabled = False
self.modelSelector.noneEnabled = False
self.modelSelector.showHidden = False
self.modelSelector.showChildNodeTypes = False
self.modelSelector.setMRMLScene( slicer.mrmlScene )
self.modelSelector.setToolTip( "Pick a bundle of fibers." )
modelFormLayout.addRow("Fiber bundles: ", self.modelSelector)
self.modelSelector.connect('currentNodeChanged(vtkMRMLNode*)', \
self.onModelSelect)
# ============Glyph Space scroller=================
self.sliderGlyphSpace = ctk.ctkSliderWidget()
self.sliderGlyphSpace.decimals = 0
self.sliderGlyphSpace.minimum=1
self.sliderGlyphSpace.maximum=100
self.sliderGlyphSpace.value=10
self.sliderGlyphSpace.enabled = False
modelFormLayout.addRow("Glyph Space:", self.sliderGlyphSpace)
self.sliderGlyphSpace.connect('valueChanged(double)', \
self.onGlyphSpaceChanged)
# ============Glyph Scale scroller=================
self.sliderGlyphScale = ctk.ctkSliderWidget()
self.sliderGlyphScale.decimals = 0
self.sliderGlyphScale.minimum=1
self.sliderGlyphScale.maximum=10000
self.sliderGlyphScale.value=2000
self.sliderGlyphScale.enabled = False
modelFormLayout.addRow("Glyph Scale:", self.sliderGlyphScale)
self.sliderGlyphScale.connect('valueChanged(double)', \
self.onGlyphScaleChanged)
modelGridLayout=qt.QGridLayout()
modelFormLayout.addRow("View Items:",modelGridLayout)
# ============Check Box for showing lines==============
self.checkboxLines=qt.QCheckBox("Lines")
self.checkboxLines.toolTip="When checked, fiber lines are shown."
self.checkboxLines.checked=True
self.checkboxLines.enabled=False
#modelFormLayout.addRow(self.checkboxLines)
modelGridLayout.addWidget(self.checkboxLines,0,0)
# ============Check Box for showing tensor 1==============
self.checkboxTensor1=qt.QCheckBox("Tensor 1")
self.checkboxTensor1.toolTip="When checked, cylinder glyphs are shown for tensor 1."
self.checkboxTensor1.checked=True
self.checkboxTensor1.enabled=False
modelGridLayout.addWidget(self.checkboxTensor1,0,1)
# ============Check Box for showing tensor 2==============
self.checkboxTensor2=qt.QCheckBox("Tensor 2")
self.checkboxTensor2.toolTip="When checked, cylinder glyphs are shown for tensor 2."
self.checkboxTensor2.checked=True
self.checkboxTensor2.enabled=False
modelGridLayout.addWidget(self.checkboxTensor2,0,2)
# ============Check Box for showing tube==============
self.checkboxTubes=qt.QCheckBox("Tubes")
self.checkboxTubes.toolTip="When checked, tubes will be shown."
self.checkboxTubes.checked=True
self.checkboxTubes.enabled=False
modelGridLayout.addWidget(self.checkboxTubes,0,3)
#
# Fiber Filter Area
#
filterCollapsibleButton = ctk.ctkCollapsibleButton()
filterCollapsibleButton.text = "Fiber Filter"
self.layout.addWidget(filterCollapsibleButton)
filterFormLayout = qt.QFormLayout(filterCollapsibleButton)
# ============Line Space scroller=================
self.sliderLineSpace = ctk.ctkSliderWidget()
self.sliderLineSpace.decimals = 0
self.sliderLineSpace.minimum=1
self.sliderLineSpace.maximum=100
self.sliderLineSpace.value=10
self.sliderLineSpace.enabled = False
filterFormLayout.addRow("One of n Fibers:", self.sliderLineSpace)
self.sliderLineSpace.connect('valueChanged(double)', \
self.onLineSpaceChanged)
# ============Line Num scroller=================
self.sliderLineNum = ctk.ctkSliderWidget()
self.sliderLineNum.decimals = 0
self.sliderLineNum.minimum=1
self.sliderLineNum.maximum=100
self.sliderLineNum.value=1
self.sliderLineNum.enabled = False
filterFormLayout.addRow("Specific Fiber No:", self.sliderLineNum)
self.sliderLineNum.connect('valueChanged(double)', \
self.onLineNumChanged)
# ============Check Box for showing one fiber==============
self.checkboxOnlyOneLine=qt.QCheckBox("Only show the specific fiber")
self.checkboxOnlyOneLine.toolTip="When checked, only the specified fiber is shown."
self.checkboxOnlyOneLine.checked=False
self.checkboxOnlyOneLine.enabled=False
filterFormLayout.addWidget(self.checkboxOnlyOneLine)
#
# Cylinder Color Mapping Area
#
cylinderColorCollapsibleButton = ctk.ctkCollapsibleButton()
cylinderColorCollapsibleButton.text = "Cylinder Boby Color"
self.layout.addWidget(cylinderColorCollapsibleButton)
cylinderVBoxLayOut = qt.QVBoxLayout(cylinderColorCollapsibleButton)
# Add a TabWidget
cylinderTabWidget=qt.QTabWidget()
cylinderVBoxLayOut.addWidget(cylinderTabWidget)
# Create four pages and the GridLayOut
redPage=qt.QWidget()
redGrid=qt.QGridLayout(redPage)
cylinderTabWidget.addTab(redPage,'Red')
greenPage=qt.QWidget()
greenGrid=qt.QGridLayout(greenPage)
cylinderTabWidget.addTab(greenPage,'Green')
bluePage=qt.QWidget()
blueGrid=qt.QGridLayout(bluePage)
cylinderTabWidget.addTab(bluePage,'Blue')
alphaPage=qt.QWidget()
alphaGrid=qt.QGridLayout(alphaPage)
cylinderTabWidget.addTab(alphaPage,'Alpha')
#========= Set the Red page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
redGrid.addWidget(groupBox,0,1)
self.bodRadioR1=qt.QRadioButton("Fixed to:")
self.bodRadioR2=qt.QRadioButton("Mapped to:")
self.bodRadioR1.checked=True
self.bodSliderR = ctk.ctkSliderWidget()
self.bodSliderR.decimals = 0
self.bodSliderR.minimum=0
self.bodSliderR.maximum=255
self.bodSliderR.value=1
self.bodSliderR.enabled = True
self.bodComboR = qt.QComboBox()
self.bodComboR.duplicatesEnabled= False
grid.addWidget(self.bodRadioR1,0,0)
grid.addWidget(self.bodRadioR2,1,0)
grid.addWidget(self.bodSliderR,0,1)
grid.addWidget(self.bodComboR,1,1)
#========= Set the Green page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
greenGrid.addWidget(groupBox,0,1)
self.bodRadioG1=qt.QRadioButton("Fixed to:")
self.bodRadioG2=qt.QRadioButton("Mapped to:")
self.bodRadioG1.checked=True
self.bodSliderG = ctk.ctkSliderWidget()
self.bodSliderG.decimals = 0
self.bodSliderG.minimum=0
self.bodSliderG.maximum=255
self.bodSliderG.value=1
self.bodSliderG.enabled = True
self.bodComboG = qt.QComboBox()
self.bodComboG.duplicatesEnabled= False
grid.addWidget(self.bodRadioG1,0,0)
grid.addWidget(self.bodRadioG2,1,0)
grid.addWidget(self.bodSliderG,0,1)
grid.addWidget(self.bodComboG,1,1)
#========= Set the Blue page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
blueGrid.addWidget(groupBox,0,1)
self.bodRadioB1=qt.QRadioButton("Fixed to:")
self.bodRadioB2=qt.QRadioButton("Mapped to:")
self.bodRadioB1.checked=True
self.bodSliderB = ctk.ctkSliderWidget()
self.bodSliderB.decimals = 0
self.bodSliderB.minimum=0
self.bodSliderB.maximum=255
self.bodSliderB.value=1
self.bodSliderB.enabled = True
self.bodComboB = qt.QComboBox()
self.bodComboB.duplicatesEnabled= False
grid.addWidget(self.bodRadioB1,0,0)
grid.addWidget(self.bodRadioB2,1,0)
grid.addWidget(self.bodSliderB,0,1)
grid.addWidget(self.bodComboB,1,1)
#========= Set the Alpha page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
alphaGrid.addWidget(groupBox,0,1)
self.bodRadioA1=qt.QRadioButton("Fixed to:")
self.bodRadioA2=qt.QRadioButton("Mapped to:")
self.bodRadioA1.checked=True
self.bodSliderA = ctk.ctkSliderWidget()
self.bodSliderA.decimals = 0
self.bodSliderA.minimum=0
self.bodSliderA.maximum=255
self.bodSliderA.value=1
self.bodSliderA.enabled = True
self.bodComboA = qt.QComboBox()
self.bodComboA.duplicatesEnabled= False
grid.addWidget(self.bodRadioA1,0,0)
grid.addWidget(self.bodRadioA2,1,0)
grid.addWidget(self.bodSliderA,0,1)
grid.addWidget(self.bodComboA,1,1)
#
# Tube Mapping Area
#
tubeColorCollapsibleButton = ctk.ctkCollapsibleButton()
tubeColorCollapsibleButton.text = "Tube Mapping"
self.layout.addWidget(tubeColorCollapsibleButton)
tubeVboxLayOut = qt.QVBoxLayout(tubeColorCollapsibleButton)
# Add a TabWidget
tubeTabWidget=qt.QTabWidget()
tubeVboxLayOut.addWidget(tubeTabWidget)
# Create three pages and the GridLayOut
tubeColorPage=qt.QWidget()
tubeColorGrid=qt.QGridLayout(tubeColorPage)
tubeTabWidget.addTab(tubeColorPage,'Color')
tubeSizePage=qt.QWidget()
tubeSizeGrid=qt.QGridLayout(tubeSizePage)
tubeTabWidget.addTab(tubeSizePage,'Size')
#========= Set the color page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
tubeColorGrid.addWidget(groupBox,0,0)
self.tubeRadioFixedTo=qt.QRadioButton("Fixed to")
self.tubeRadioByOrientation=qt.QRadioButton("Color by orientation")
self.tubeRadioSameAsCylinderBody=qt.QRadioButton("Same as Cylinder Body")
self.tubeRadioByOrientation.checked=True
grid.addWidget(self.tubeRadioFixedTo,0,0)
grid.addWidget(self.tubeRadioByOrientation,1,0)
grid.addWidget(self.tubeRadioSameAsCylinderBody,2,0)
self.tubeColorButton=qt.QPushButton('Specifying Color')
self.tubeColorButton.setAutoFillBackground(True)
grid.addWidget(self.tubeColorButton,0,1)
self.tubeColorButton.connect('clicked()', \
self.onTubeFixedColor)
#========= Set the size page ==============
self.tubeSizeRadio1=qt.QRadioButton("Fixed to:")
self.tubeSizeRadio2=qt.QRadioButton("Mapped to:")
self.tubeSizeRadio1.checked=True
self.tubeSizeSlider = ctk.ctkSliderWidget()
self.tubeSizeSlider.decimals = 2
self.tubeSizeSlider.minimum=0.0
self.tubeSizeSlider.maximum=5.0
self.tubeSizeSlider.value=0.1
self.tubeSizeSlider.enabled = True
self.tubeComboBox = qt.QComboBox()
self.tubeComboBox.duplicatesEnabled= False
tubeSizeGrid.addWidget(self.tubeSizeRadio1,0,0)
tubeSizeGrid.addWidget(self.tubeSizeRadio2,1,0)
tubeSizeGrid.addWidget(self.tubeSizeSlider,0,1)
tubeSizeGrid.addWidget(self.tubeComboBox,1,1)
# ============Scale scroller=================
label=qt.QLabel('Tube Scale:')
self.sliderTubeScale = ctk.ctkSliderWidget()
self.sliderTubeScale.decimals = 0
self.sliderTubeScale.minimum=1
self.sliderTubeScale.maximum=100
self.sliderTubeScale.value=5
self.sliderTubeScale.enabled = False
tubeSizeGrid.addWidget(label,2,0)
tubeSizeGrid.addWidget(self.sliderTubeScale,2,1)
self.sliderTubeScale.connect('valueChanged(double)', \
self.onTubeScaleChanged)
#
# ============Apply button=================
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Apply the visualization."
self.applyButton.enabled = False
self.applyButton.setPalette(qt.QPalette(qt.QColor(128,255,128)))
self.parent.layout().addWidget(self.applyButton)
self.applyButton.connect('clicked()', \
self.onApply)
#
# ============Clear button=================
#
self.clearButton = qt.QPushButton("Clear")
self.clearButton.toolTip = "Clear objects rendered in 3D view windows."
self.clearButton.enabled = False
self.clearButton.setPalette(qt.QPalette(qt.QColor(255,128,128)))
self.parent.layout().addWidget(self.clearButton)
self.clearButton.connect('clicked()', \
self.onClear)
# ===========Finally, Add vertical spacer================
self.layout.addStretch(2)
def __init__(self, parent, MODULE=None):
""" Init function.
"""
self.MODULE = MODULE
#--------------------
# Call parent init.
#--------------------
super(XnatFolderMaker, self).__init__()
#--------------------
# Adjust window features.
#--------------------
self.setWindowTitle("Add Folder to Xnat")
self.setWindowModality(2)
#--------------------
# Hide the widget initially.
#--------------------
self.hide()
#--------------------
# Set fixed width.
#--------------------
self.setFixedWidth(500)
self.setFixedHeight(250)
#--------------------
# Make the xsiList for experiment
# creation.
#--------------------
self.xsiList = qt.QComboBox()
self.xsiList.addItems([
key
for key, value in self.MODULE.GLOBALS.XNAT_XSI_TYPES.iteritems()
])
#--------------------
# Displayable wigets.
#--------------------
self.levelLabels = {}
self.nameLabels = {}
self.lineEdits = {}
self.errorLines = {}
self.levelLayouts = {}
self.labelLineStacks = {}
self.levelRows = {}
#--------------------
# Make the buttons:
# create, cancel,
# etc.
#--------------------
self.addButton = qt.QPushButton()
self.addButton.setText("Add")
self.addButton.setEnabled(False)
self.cancelButton = qt.QPushButton()
self.cancelButton.setText("Cancel")
buttonRow = qt.QDialogButtonBox()
buttonRow.addButton(self.cancelButton, 2)
buttonRow.addButton(self.addButton, 0)
#-------------------
# Create the keys in the displayable widgets.
#--------------------
self.addFolderXnatLevels = ['projects', 'subjects', 'experiments']
for level in self.addFolderXnatLevels:
#
# Labels (name and level)
#
self.levelLabels[level] = qt.QLabel(self)
self.levelLabels[level].setFixedHeight(25)
self.nameLabels[level] = qt.QLabel(self)
self.nameLabels[level].setFixedHeight(25)
#
# Line edits
#
self.lineEdits[level] = qt.QLineEdit(self)
self.lineEdits[level].installEventFilter(self)
self.lineEdits[level].setFixedHeight(25)
#
# Error lines
#
self.errorLines[level] = qt.QLabel(self)
self.errorLines[level].setTextFormat(1)
self.errorLines[level].setFixedHeight(25)
#
# Make the label-line stacks, adjusting
# for 'experiments' as necessary.
#
self.labelLineStacks[level] = qt.QStackedLayout()
if level == 'experiments':
experimentRow = qt.QHBoxLayout()
experimentRow.addWidget(self.xsiList)
experimentRow.addWidget(self.lineEdits[level])
experimentWidget = qt.QWidget()
experimentWidget.setLayout(experimentRow)
self.labelLineStacks[level].addWidget(experimentWidget)
else:
self.labelLineStacks[level].addWidget(self.nameLabels[level])
self.labelLineStacks[level].addWidget(self.lineEdits[level])
#
# make row widgets
#
self.levelRows[level] = qt.QWidget(self)
levelRowLayout = qt.QGridLayout()
levelRowLayout.addWidget(self.levelLabels[level], 0, 0)
levelRowLayout.addLayout(self.labelLineStacks[level], 0, 1)
levelRowLayout.addWidget(self.errorLines[level], 1, 1)
self.levelRows[level].setLayout(levelRowLayout)
#--------------------
# Connect button click events.
#--------------------
buttonRow.connect('clicked(QAbstractButton*)', self.onAddButtonClicked)
#--------------------
# Make the mainLayout and add all widgets.
#--------------------
self.mainLayout = qt.QVBoxLayout()
for level in self.addFolderXnatLevels:
self.mainLayout.addWidget(self.levelRows[level])
self.mainLayout.addStretch()
self.mainLayout.addWidget(buttonRow)
self.setLayout(self.mainLayout)
def setup(self):
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
####################IMPORTAR VOLUMEN 4D#################################################3
### Se crea la sección para cargar el volumen 4D en una pestaña desplegable
importDataCollapsibleButton = ctk.ctkCollapsibleButton()
importDataCollapsibleButton.text = "Import Data"
self.layout.addWidget(importDataCollapsibleButton)
importDataFormLayout = qt.QFormLayout(importDataCollapsibleButton)
#### Crear desplegable para seleccionar dirección del volumen
self.__fDialog = ctk.ctkDirectoryButton()
self.__fDialog.caption = 'Input directory'
importDataFormLayout.addRow('Input directory:', self.__fDialog)
###Selector de volumen donde se guardara el volumen de la direccion
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.outputSelector.addEnabled = True # Se habilita la posibildad al usuario de crear un nuevo nodo con este widget
self.outputSelector.removeEnabled = False # Se le quita al usuario la posibilidad de eliminar el nodo seleccionado en ese momento
self.outputSelector.setMRMLScene(slicer.mrmlScene)
importDataFormLayout.addRow("Output node:", self.outputSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputSelector, 'setMRMLScene(vtkMRMLScene*)')
### Parametros avanzados
self.__dicomTag = qt.QLineEdit()
self.__dicomTag.text = 'NA'
importDataFormLayout.addRow('Frame identifying DICOM tag:',
self.__dicomTag)
self.__veLabel = qt.QLineEdit()
self.__veLabel.text = 'na'
importDataFormLayout.addRow('Frame identifying units:', self.__veLabel)
self.__veInitial = qt.QDoubleSpinBox()
self.__veInitial.value = 0
importDataFormLayout.addRow('Initial value:', self.__veInitial)
self.__veStep = qt.QDoubleSpinBox()
self.__veStep.value = 1
importDataFormLayout.addRow('Step:', self.__veStep)
self.__te = qt.QDoubleSpinBox()
self.__te.value = 1
importDataFormLayout.addRow('EchoTime:', self.__te)
self.__tr = qt.QDoubleSpinBox()
self.__tr.value = 1
importDataFormLayout.addRow('RepetitionTime:', self.__tr)
self.__fa = qt.QDoubleSpinBox()
self.__fa.value = 1
importDataFormLayout.addRow('FlipAngle:', self.__fa)
# Botón de importar
self.buttonImport = qt.QPushButton("Import")
self.buttonImport.toolTip = "Run the algorithm."
##self.buttonImport.enabled = True
importDataFormLayout.addRow(" ",
self.buttonImport)
self.buttonImport.connect('clicked(bool)', self.importFunction)
##self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
###########################REGISTRO##########################################
## # Se crea una sección de parámetros en una pestaña desplegable
registerCollapsibleButton = ctk.ctkCollapsibleButton()
registerCollapsibleButton.text = "Register"
self.layout.addWidget(registerCollapsibleButton)
registerFormLayout = qt.QFormLayout(registerCollapsibleButton)
#Se crea una ventana desplegable en la cual se ingresa el volumen 4D de
#entrada que se quiere registrar, este volumen debe ser de tipo
#"vtkMRMLMultiVolumeNode", además si se tienen varios multivolumenes cargados
#se puede elegir entre ellos el que se desea registrar
self.inputRegSelector = slicer.qMRMLNodeComboBox()
self.inputRegSelector.nodeTypes = ["vtkMRMLMultiVolumeNode"]
self.inputRegSelector.selectNodeUponCreation = True
self.inputRegSelector.addEnabled = True
self.inputRegSelector.removeEnabled = False
self.inputRegSelector.noneEnabled = True
self.inputRegSelector.showHidden = False
self.inputRegSelector.showChildNodeTypes = False
self.inputRegSelector.setMRMLScene(slicer.mrmlScene)
self.inputRegSelector.setToolTip("Pick the input to the algorithm.")
registerFormLayout.addRow("Volumen 4D: ", self.inputRegSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputRegSelector,
'setMRMLScene(vtkMRMLScene*)')
###Selector de volumen donde se guardara el volumen de la direccion
self.outputRegSelector = slicer.qMRMLNodeComboBox()
self.outputRegSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.outputRegSelector.addEnabled = True # Se habilita la posibildad al usuario de crear un nuevo nodo con este widget
self.outputRegSelector.removeEnabled = False # Se le quita al usuario la posibilidad de eliminar el nodo seleccionado en ese momento
self.outputRegSelector.setMRMLScene(slicer.mrmlScene)
registerFormLayout.addRow("Output node:", self.outputRegSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputRegSelector,
'setMRMLScene(vtkMRMLScene*)')
# Botón de Registro
#Este botón solo se activa si el multivolumen ha sido seleccionado en la
#ventana desplegable de Volumen 4D. Al presionarlo, el algoritmo
#realiza el registro de los diferentes volumenes en el volumen 4D
self.applyButton = qt.QPushButton("Registrar")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
registerFormLayout.addRow(self.applyButton)
# Conexiones necesarias para el algoritmo
#entrega al algoritmo el volumen 4D de entrada y conecta la función del botón
#con la ejecución del registro
self.applyButton.connect('clicked(bool)', self.registrarButton)
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
autoCTCollapsibleButton = ctk.ctkCollapsibleButton()
autoCTCollapsibleButton.text = "Collapsible button for CT auto-segmentation"
self.layout.addWidget(autoCTCollapsibleButton)
# Layout within the sample collapsible button
autoCTFormLayout = qt.QFormLayout(autoCTCollapsibleButton)
#Load CT image button
loadCTButton = qt.QPushButton("Load CT image and add ROI annotation")
loadCTButton.toolTip = "Click to load CT image and then annotate tumor location"
autoCTFormLayout.addWidget(loadCTButton)
loadCTButton.connect('clicked(bool)', self.onloadCTButtonClicked)
#Number of nodule to operate
# loadCTnodulelabel = qt.QInputDialog()
# loadCTnodulelabel.toolTip = "The tumor number to segment"
# loadCTnodulelabel.getInt(self, "Get integer","Percentage:")
# autoCTFormLayout.addWidget(loadCTnodulelabel)
# loadCTnodulelabel.connect('clicked(bool)', self.onloadCTnodulelabelButtonClicked)
#
####Ajust sigma value for CT##########
#########################################
# nodulelabel1 = qt.QLabel()
# nodulelabel1.setText("Enter the nodule number to process")
# autoCTFormLayout.addWidget(nodulelabel1)
# noduleSlider1 = qt.QInputDialog()
# noduleSlider1.toolTip = "Slide to change nodule number"
# autoCTFormLayout.addWidget(noduleSlider1)
## noduleSlider1.setMinimum(0.0)
## noduleSlider1.setMaximum(20)
## noduleSlider1.setValue(1.0)
## noduleSlider.setTickPosition(qt.QSlider.TicksBelow)
## noduleSlider.setTickInterval(1)
# self.noduleSlider1 = noduleSlider1
nodulelabel = qt.QLabel()
nodulelabel.setText("Enter the nodule number to segment (1-10)")
autoCTFormLayout.addWidget(nodulelabel)
noduleSlider = qt.QSlider(qt.Qt.Horizontal)
noduleSlider.toolTip = "Slide to change nodule number"
noduleSlider.setMinimum(0.0)
noduleSlider.setMaximum(20)
noduleSlider.setValue(1.0)
noduleSlider.setTickPosition(qt.QSlider.TicksBelow)
noduleSlider.setTickInterval(1)
self.noduleSlider = noduleSlider
#label for ticks
nodulevalues = qt.QGridLayout()
r1 = qt.QLabel("0")
r2 = qt.QLabel("2")
r3 = qt.QLabel("4")
r4 = qt.QLabel("6")
r5 = qt.QLabel("8")
nodulevalues.addWidget(noduleSlider, 0, 0, 1, 5)
nodulevalues.addWidget(r1, 1, 0, 1, 1)
nodulevalues.addWidget(r2, 1, 1, 1, 1)
nodulevalues.addWidget(r3, 1, 2, 1, 1)
nodulevalues.addWidget(r4, 1, 3, 1, 1)
nodulevalues.addWidget(r5, 1, 4, 1, 1)
#Apply the changes
# noduleApplyButton = qt.QPushButton("Apply")
# noduleApplyButton.toolTip = "Click to apply new sigma value"
# nodulevalues.addWidget(noduleApplyButton, 0,5,2,1)
# noduleApplyButton.connect('clicked(bool)', self.changesApplyButtonClicked)
autoCTFormLayout.addRow(nodulevalues)
# Add vertical spacer
self.layout.addStretch(1)
#########Button for CT segmentation and 3D generation##########
###########################################################
CTSeg3D_tumorButton = qt.QPushButton("CTSeg3D_tumor")
CTSeg3D_tumorButton.toolTip = "Click to generate auto segmentation and 3D view of tumor"
autoCTFormLayout.addWidget(CTSeg3D_tumorButton)
CTSeg3D_tumorButton.connect('clicked(bool)',
self.onCTSeg3D_tumorButtonClicked)
####Ajust multipler value for CT (fine tuning)##########
#########################################
# CTfinetuneButton = qt.QPushButton("Fine_tuning")
# CTfinetuneButton.toolTip = "Fine tuning segmentation for better ROI"
# autoCTFormLayout.addWidget(CTfinetuneButton)
# CTfinetuneButton.connect('clicked(bool)', self.onCTfinetuneButtonClicked)
############## Button segment out lung ############
CTSeg3D_lungButton = qt.QPushButton("CTSeg3D_lung")
CTSeg3D_lungButton.toolTip = "Click to generate auto segmentation and 3D view of lung"
autoCTFormLayout.addWidget(CTSeg3D_lungButton)
CTSeg3D_lungButton.connect('clicked(bool)',
self.onCTSeg3D_lungButtonClicked)
self.image_loaded = False
def setup(self):
#
# Input frame
#
self.__inputFrame = ctk.ctkCollapsibleButton()
self.__inputFrame.text = "Input"
self.__inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.__inputFrame)
self.layout.addWidget(self.__inputFrame)
# Active report node
label = qt.QLabel('Report: ')
self.__reportSelector = slicer.qMRMLNodeComboBox()
self.__reportSelector.nodeTypes = ['vtkMRMLReportingReportNode']
self.__reportSelector.setMRMLScene(slicer.mrmlScene)
self.__reportSelector.addEnabled = 1
self.__reportSelector.removeEnabled = 0
inputFrameLayout.addRow(label, self.__reportSelector)
self.__reportSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onMRMLSceneChanged)
self.__reportSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onReportNodeChanged)
# Volume being annotated (only one is allowed for the report)
label = qt.QLabel(
'NOTE: Only volumes loaded from DICOM can be annotated!')
inputFrameLayout.addRow(label)
label = qt.QLabel('Annotated volume: ')
self.__volumeSelector = slicer.qMRMLNodeComboBox()
self.__volumeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
# only allow volumes with the attribute DICOM.instanceUIDs
self.__volumeSelector.addAttribute('vtkMRMLScalarVolumeNode',
'DICOM.instanceUIDs')
self.__volumeSelector.setMRMLScene(slicer.mrmlScene)
self.__volumeSelector.addEnabled = False
inputFrameLayout.addRow(label, self.__volumeSelector)
self.__volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onAnnotatedVolumeNodeChanged)
self.__volumeSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onMRMLSceneChanged)
#
# Annotation frame -- vocabulary-based description of what is
# being annotated/marked up in this report
#
self.__annotationsFrame = ctk.ctkCollapsibleButton()
self.__annotationsFrame.text = "Annotation"
self.__annotationsFrame.collapsed = 0
annotationsFrameLayout = qt.QFormLayout(self.__annotationsFrame)
self.layout.addWidget(self.__annotationsFrame)
self.__defaultColorNode = self.__logic.GetDefaultColorNode()
self.__toolsColor = EditColor(self.__annotationsFrame,
colorNode=self.__defaultColorNode)
#
# Markup frame -- summary of all the markup elements contained in the
# report
#
self.__markupFrame = ctk.ctkCollapsibleButton()
self.__markupFrame.text = "Markup"
self.__markupFrame.collapsed = 0
markupFrameLayout = qt.QFormLayout(self.__markupFrame)
self.layout.addWidget(self.__markupFrame)
# Add a flag to switch between different tree view models
self.__useNewTreeView = 1
# Add the tree widget
if self.__useNewTreeView == 1:
self.__markupTreeView = slicer.modulewidget.qMRMLReportingTreeView(
)
self.__markupTreeView.sceneModelType = "DisplayableHierarchy"
else:
self.__markupTreeView = slicer.qMRMLTreeView()
self.__markupTreeView.sceneModelType = "Displayable"
self.__markupTreeView.setMRMLScene(self.__logic.GetMRMLScene())
self.__markupSliceText = qt.QLabel()
markupFrameLayout.addRow(self.__markupSliceText)
markupFrameLayout.addRow(self.__markupTreeView)
# Editor frame
self.__editorFrame = ctk.ctkCollapsibleButton()
self.__editorFrame.text = 'Segmentation'
self.__editorFrame.collapsed = 0
editorFrameLayout = qt.QFormLayout(self.__editorFrame)
label = qt.QLabel('Segmentation volume: ')
self.__segmentationSelector = slicer.qMRMLNodeComboBox()
self.__segmentationSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__segmentationSelector.setMRMLScene(slicer.mrmlScene)
self.__segmentationSelector.addEnabled = 1
self.__segmentationSelector.noneEnabled = 1
self.__segmentationSelector.removeEnabled = 0
self.__segmentationSelector.showHidden = 0
self.__segmentationSelector.showChildNodeTypes = 0
self.__segmentationSelector.selectNodeUponCreation = 1
self.__segmentationSelector.addAttribute('vtkMRMLScalarVolumeNode',
'LabelMap', 1)
editorFrameLayout.addRow(label, self.__segmentationSelector)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.__editorWidget = EditorWidget(parent=editorWidgetParent,
showVolumesFrame=False)
self.__editorWidget.setup()
self.__editorWidget.toolsColor.frame.setVisible(False)
editorFrameLayout.addRow(editorWidgetParent)
markupFrameLayout.addRow(self.__editorFrame)
self.__segmentationSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSegmentationNodeChanged)
self.__segmentationSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onMRMLSceneChanged)
# IO frame
self.__ioFrame = ctk.ctkCollapsibleButton()
self.__ioFrame.text = 'Import/Export'
self.__ioFrame.collapsed = 1
ioFrameLayout = qt.QGridLayout(self.__ioFrame)
self.layout.addWidget(self.__ioFrame)
# Buttons to save/load report using AIM XML serialization
label = qt.QLabel('Export folder')
self.__exportFolderPicker = ctk.ctkDirectoryButton()
exportButton = qt.QPushButton('Export')
exportButton.connect('clicked()', self.onReportExport)
ioFrameLayout.addWidget(label, 0, 0)
ioFrameLayout.addWidget(self.__exportFolderPicker, 0, 1)
ioFrameLayout.addWidget(exportButton, 0, 2)
label = qt.QLabel('AIM file to import')
self.__aimFilePicker = qt.QPushButton('N/A')
self.__aimFilePicker.connect('clicked()', self.onSelectAIMFile)
button = qt.QPushButton('Import')
button.connect('clicked()', self.onReportImport)
ioFrameLayout.addWidget(label, 1, 0)
ioFrameLayout.addWidget(self.__aimFilePicker, 1, 1)
ioFrameLayout.addWidget(button, 1, 2)
self.__importAIMFile = None
self.__reportSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.updateWidgets)
self.__volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.updateWidgets)
self.updateWidgets()
self.layout.addStretch(1)
self.__editorParameterNode = self.editUtil.getParameterNode()
self.__editorParameterNode.AddObserver(
vtk.vtkCommand.ModifiedEvent, self.onEditorParameterNodeChanged)
def createUserInterface(self):
self.__layout = self.__parent.createUserInterface()
'''
# Input fiducials node selector
#self.inputFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.inputFiducialsNodeSelector.toolTip = "Select a fiducial to define an insertion point for a screw."
self.inputFiducialsNodeSelector.nodeTypes = (("vtkMRMLMarkupsFiducialNode"), "")
self.inputFiducialsNodeSelector.addEnabled = False
self.inputFiducialsNodeSelector.removeEnabled = False
self.inputFiducialsNodeSelector.setMRMLScene( slicer.mrmlScene )
self.inputFiducialsNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.fidChanged)
self.__layout.addRow("Select Insertion Point:", self.inputFiducialsNodeSelector)
self.fid = self.inputFiducialsNodeSelector.currentNode()
self.sliceChange()
'''
'''
# Input model selector
self.inputScrewSelector = ctk.ctkComboBox()
self.inputScrewSelector.toolTip = "Select a screw to insert."
screwList = ['Select a screw','475x30', '475x35', '475x45', '550x30', '550x40', '550x45', '625x35', '625x40', '625x45', '625x50', '700x35', '700x40', '700x45', '700x50']
self.inputScrewSelector.addItems(screwList)
self.connect(self.inputScrewSelector, PythonQt.QtCore.SIGNAL('activated(QString)'), self.combo_chosen)
self.__layout.addRow("Choose Screw:", self.inputScrewSelector)
vText = qt.QLabel("1st Instrumented Level:")
iText = qt.QLabel("# to Instrument:")
aText = qt.QLabel("Approach Direction:")
self.vSelector = qt.QComboBox()
self.vSelector.setMaximumWidth(120)
self.levels = ("C1","C2","C3","C4","C5","C6","C7","T1","T2","T3","T4","T5","T6","T7","T8","T9","T10","T11","T12","L1", "L2", "L3", "L4", "L5","S1")
self.vSelector.addItems(self.levels)
self.iSelector = qt.QComboBox()
self.iSelector.setMaximumWidth(120)
self.iSelector.addItems(['1','2','3','4','5','6','7','8','9','10','11','12'])
self.aSelector = qt.QComboBox()
self.aSelector.setMaximumWidth(120)
self.aSelector.addItems(['Posterior','Anterior','Left','Right'])
blank = qt.QLabel(" ")
blank.setMaximumWidth(30)
#self.__layout.addWidget(vText)
#self.__layout.addWidget(self.vSelector)
#self.__layout.addWidget(iText)
#self.__layout.addWidget(self.iSelector)
self.vertebraeGridBox = qt.QGridLayout()
self.vertebraeGridBox.addWidget(vText,0,0)
self.vertebraeGridBox.addWidget(self.vSelector,1,0)
self.vertebraeGridBox.addWidget(blank,0,1)
self.vertebraeGridBox.addWidget(iText,0,2)
self.vertebraeGridBox.addWidget(blank,1,1)
self.vertebraeGridBox.addWidget(self.iSelector,1,2)
self.vertebraeGridBox.addWidget(blank,0,3)
self.vertebraeGridBox.addWidget(aText,0,4)
self.vertebraeGridBox.addWidget(blank,1,3)
self.vertebraeGridBox.addWidget(self.aSelector,1,4)
self.__layout.addRow(self.vertebraeGridBox)
'''
self.fiducial = ctk.ctkComboBox()
self.fiducial.toolTip = "Select an insertion site."
self.fiducial.addItems(self.fiduciallist)
self.connect(self.fiducial,
PythonQt.QtCore.SIGNAL('activated(QString)'),
self.fiducial_chosen)
#self.screwGridLayout.addWidget(self.fiducial,0,0)
self.__layout.addRow("Insertion Site:", self.fiducial)
self.__fiducial = ''
measuredText1 = qt.QLabel(" Measured:")
measuredText2 = qt.QLabel(" Measured:")
lengthText = qt.QLabel("Screw Length: ")
widthText = qt.QLabel("Screw Width: ")
self.length = ctk.ctkComboBox()
self.length.toolTip = "Select a screw to insert."
screwList = ['Select a length (mm)', '475', '550', '625', '700']
self.length.addItems(screwList)
self.connect(self.length, PythonQt.QtCore.SIGNAL('activated(QString)'),
self.length_chosen)
self.lengthMeasure = qt.QLineEdit()
#self.__layout.addRow("Screw Length:", self.length)
#self.__layout.addRow("Measured Pedicle Length:", self.lengthMeasure)
self.__length = ''
self.QHBox1 = qt.QHBoxLayout()
self.QHBox1.addWidget(lengthText)
self.QHBox1.addWidget(self.length)
self.QHBox1.addWidget(measuredText1)
self.QHBox1.addWidget(self.lengthMeasure)
self.__layout.addRow(self.QHBox1)
self.diameter = ctk.ctkComboBox()
self.diameter.toolTip = "Select a screw to insert."
screwList = ['Select a diameter (mm)', '30', '35', '45', '50']
self.diameter.addItems(screwList)
self.widthMeasure = qt.QLineEdit()
self.connect(self.diameter,
PythonQt.QtCore.SIGNAL('activated(QString)'),
self.diameter_chosen)
#self.__layout.addRow("Screw Diameter:", self.diameter)
#self.__layout.addRow("Measured Pedicle Width:", self.widthMeasure)
self.__diameter = ''
self.QHBox2 = qt.QHBoxLayout()
self.QHBox2.addWidget(widthText)
self.QHBox2.addWidget(self.diameter)
self.QHBox2.addWidget(measuredText2)
self.QHBox2.addWidget(self.widthMeasure)
self.__layout.addRow(self.QHBox2)
# Load Screw Button
self.__loadScrewButton = qt.QPushButton("Load Screw")
self.__loadScrewButton.enabled = False
#self.__layout.addWidget(self.__loadScrewButton)
self.__loadScrewButton.connect('clicked(bool)', self.loadScrew)
# Delete Screw Button
self.__delScrewButton = qt.QPushButton("Delete Screw")
self.__delScrewButton.enabled = True
#self.__layout.addWidget(self.__delScrewButton)
self.__delScrewButton.connect('clicked(bool)', self.delScrew)
self.QHBox3 = qt.QHBoxLayout()
self.QHBox3.addWidget(self.__loadScrewButton)
self.QHBox3.addWidget(self.__delScrewButton)
self.__layout.addRow(self.QHBox3)
# Input model node selector
self.modelNodeSelector = slicer.qMRMLNodeComboBox()
self.modelNodeSelector.toolTip = "."
self.modelNodeSelector.nodeTypes = (("vtkMRMLModelNode"), "")
self.modelNodeSelector.addEnabled = False
self.modelNodeSelector.removeEnabled = False
self.modelNodeSelector.setMRMLScene(slicer.mrmlScene)
#self.__layout.addRow("Current Screws:", self.modelNodeSelector)
self.transformGrid = qt.QGridLayout()
vText = qt.QLabel("Vertical Adjustment:")
iText = qt.QLabel("Horizontal Adjustment:")
self.transformGrid.addWidget(vText, 0, 0)
self.transformGrid.addWidget(iText, 0, 2)
self.b = ctk.ctkDoubleSpinBox()
self.b.minimum = -45
self.b.maximum = 45
self.transformGrid.addWidget(self.b, 1, 0)
# Transform Sliders
self.transformSlider1 = ctk.ctkDoubleSlider()
self.transformSlider1.minimum = -45
self.transformSlider1.maximum = 45
self.transformSlider1.connect('valueChanged(double)',
self.transformSlider1ValueChanged)
self.transformSlider1.connect('valueChanged(double)', self.b.setValue)
self.transformSlider1.setMinimumHeight(120)
#self.__layout.addRow("Rotate IS", self.transformSlider1)
self.transformGrid.addWidget(self.transformSlider1, 1, 1)
self.b.connect('valueChanged(double)', self.transformSlider1.setValue)
# Transform Sliders
self.transformSlider2 = ctk.ctkSliderWidget()
self.transformSlider2.minimum = -45
self.transformSlider2.maximum = 45
self.transformSlider2.connect('valueChanged(double)',
self.transformSlider2ValueChanged)
self.transformSlider2.setMaximumWidth(200)
#self.__layout.addRow("Rotate LR", self.transformSlider2)
self.transformGrid.addWidget(self.transformSlider2, 1, 2)
self.__layout.addRow(self.transformGrid)
'''
# Transfors Sliders
self.transformSlider3 = ctk.ctkSliderWidget()
self.transformSlider3.minimum = 0
self.transformSlider3.maximum = 100
self.transformSlider3.connect('valueChanged(double)', self.transformSlider3ValueChanged)
self.__layout.addRow("Drive Screw", self.transformSlider3)
'''
# Insert Screw Button
self.insertScrewButton = qt.QPushButton("Insert Screw")
self.insertScrewButton.enabled = True
#self.__layout.addWidget(self.__loadScrewButton)
self.insertScrewButton.connect('clicked(bool)', self.insertScrew)
# Backout Screw Button
self.backoutScrewButton = qt.QPushButton("Backout Screw")
self.backoutScrewButton.enabled = False
#self.__layout.addWidget(self.__delScrewButton)
self.backoutScrewButton.connect('clicked(bool)', self.backoutScrew)
# Reset Screw Button
self.resetScrewButton = qt.QPushButton("Reset Screw")
self.resetScrewButton.enabled = True
#self.__layout.addWidget(self.__delScrewButton)
self.resetScrewButton.connect('clicked(bool)', self.resetScrew)
self.QHBox4 = qt.QHBoxLayout()
self.QHBox4.addWidget(self.insertScrewButton)
self.QHBox4.addWidget(self.backoutScrewButton)
self.QHBox4.addWidget(self.resetScrewButton)
self.__layout.addRow(self.QHBox4)
# Hide ROI Details
#measurementsTable = ctk.ctkCollapsibleButton()
#measurementsTable.text = "Measurements Table"
#self.__layout.addWidget(measurementsTable)
#measurementsTable.collapsed = True
'''
self.view = qt.QTableView()
self.model = qt.QStandardItemModel()
self.view.setModel(self.model)
item = qt.QStandardItem()
item.setText("item")
self.model.setItem(0,0,item)
self.__layout.addWidget(self.view)
'''
#self.__layout.addRow(self.screwGridLayout)
# self.updateWidgetFromParameters(self.parameterNode())
qt.QTimer.singleShot(0, self.killButton)
self.currentFidIndex = self.fiducial.currentIndex
self.currentFidLabel = self.fiducial.currentText
self.fidNode.GetNthFiducialPosition(self.currentFidIndex, self.coords)
logging.debug("Coords: {0}".format(self.coords))
self.updateMeasurements()
self.cameraFocus(self.coords)
def open(self):
# main dialog
self.dialog = qt.QDialog(slicer.util.mainWindow())
self.dialog.setWindowTitle('Export to DICOM Study')
self.dialog.setWindowModality(1)
layout = qt.QVBoxLayout()
self.dialog.setLayout(layout)
self.studyLabel = qt.QLabel('Attach Data to Study: %s' % self.studyUID)
layout.addWidget(self.studyLabel)
# scene or volume option
self.selectFrame = qt.QFrame(self.dialog)
layout.addWidget(self.selectFrame)
self.selectLayout = qt.QGridLayout()
self.selectFrame.setLayout(self.selectLayout)
self.exportScene = qt.QRadioButton("Export Entire Scene",
self.selectFrame)
self.exportScene.setToolTip(
"Create a Slicer Data Bundle in a DICOM Private Creator\n(Only compatible with Slicer)"
)
self.exportVolume = qt.QRadioButton("Export Selected Volume",
self.selectFrame)
self.exportVolume.setToolTip(
"Create a compatible DICOM series of slice images")
self.exportVolume.checked = True
self.selectLayout.addWidget(self.exportScene, 0, 0)
self.selectLayout.addWidget(self.exportVolume, 1, 0)
self.exportScene.connect('toggled(bool)', self.onExportRadio)
self.exportVolume.connect('toggled(bool)', self.onExportRadio)
# select volume
self.volumeSelector = slicer.qMRMLNodeComboBox(self.dialog)
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.volumeSelector.selectNodeUponCreation = False
self.volumeSelector.addEnabled = False
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setToolTip("Pick the label map to edit")
self.selectLayout.addWidget(self.volumeSelector, 1, 1)
# DICOM Parameters
self.dicomFrame = qt.QFrame(self.dialog)
self.dicomFormLayout = qt.QFormLayout()
self.dicomFrame.setLayout(self.dicomFormLayout)
self.dicomEntries = {}
exporter = DICOMLib.DICOMExporter(self.studyUID)
self.dicomParameters = exporter.parametersFromStudy()
self.dicomParameters['Series Description'] = '3D Slicer Export'
for label in self.dicomParameters.keys():
self.dicomEntries[label] = qt.QLineEdit()
self.dicomEntries[label].text = self.dicomParameters[label]
self.dicomFormLayout.addRow(label + ": ", self.dicomEntries[label])
layout.addWidget(self.dicomFrame)
# button box
bbox = qt.QDialogButtonBox(self.dialog)
bbox.addButton(bbox.Ok)
bbox.addButton(bbox.Cancel)
bbox.connect('accepted()', self.onOk)
bbox.connect('rejected()', self.onCancel)
layout.addWidget(bbox)
self.dialog.open()
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 = "PlusRemote 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)
# Module requires openigtlinkremote
try:
slicer.modules.openigtlinkremote
except:
self.errorLabel = qt.QLabel(
"Could not find OpenIGTLink Remote module")
self.layout.addWidget(self.errorLabel)
return
# IGTLink Connector
connectorCollapsibleButton = ctk.ctkCollapsibleButton()
connectorCollapsibleButton.text = "OpenIGTLink Connector"
self.layout.addWidget(connectorCollapsibleButton)
connectorLayout = qt.QFormLayout(connectorCollapsibleButton)
self.linkInputSelector = slicer.qMRMLNodeComboBox()
self.linkInputSelector.nodeTypes = (("vtkMRMLIGTLConnectorNode"), "")
self.linkInputSelector.selectNodeUponCreation = True
self.linkInputSelector.addEnabled = False
self.linkInputSelector.removeEnabled = True
self.linkInputSelector.noneEnabled = False
self.linkInputSelector.showHidden = False
self.linkInputSelector.showChildNodeTypes = False
self.linkInputSelector.setMRMLScene(slicer.mrmlScene)
self.linkInputSelector.setToolTip("Pick connector node")
connectorLayout.addRow("OpenIGTLinkConnector: ",
self.linkInputSelector)
# Recording
recordingCollapsibleButton = ctk.ctkCollapsibleButton()
recordingCollapsibleButton.text = "Recording"
self.layout.addWidget(recordingCollapsibleButton)
recordingLayout = qt.QFormLayout(recordingCollapsibleButton)
self.captureIDBox = qt.QLineEdit()
recordingLayout.addRow("Capture Device ID: ", self.captureIDBox)
self.fileNameBox = qt.QLineEdit()
recordingLayout.addRow("Filename: ", self.fileNameBox)
# Move to the same row, use grid layout
recordingControlsLayout = qt.QGridLayout()
self.startRecordingButton = qt.QPushButton("Start Recording")
recordingControlsLayout.addWidget(self.startRecordingButton, 0, 0)
self.stopRecordingButton = qt.QPushButton("Stop Recording")
recordingControlsLayout.addWidget(self.stopRecordingButton, 0, 1)
recordingLayout.addRow(recordingControlsLayout)
# Reconstruction
reconstructionCollapsibleButton = ctk.ctkCollapsibleButton()
reconstructionCollapsibleButton.text = "Reconstruction"
self.layout.addWidget(reconstructionCollapsibleButton)
reconstructionLayout = qt.QFormLayout(reconstructionCollapsibleButton)
liveReconstructionLayout = qt.QGridLayout()
self.startReconstuctionButton = qt.QPushButton(
"Start Live Reconstruction")
liveReconstructionLayout.addWidget(self.startReconstuctionButton, 0, 0)
self.stopReconstructionButton = qt.QPushButton(
"Stop Live Reconstruction")
liveReconstructionLayout.addWidget(self.stopReconstructionButton, 0, 1)
reconstructionLayout.addRow(liveReconstructionLayout)
self.reconstructVolumeButton = qt.QPushButton(
"Reconstruct Recorded Volume")
reconstructionLayout.addRow(self.reconstructVolumeButton)
# Transform Update
transformUpdateCollapsibleButton = ctk.ctkCollapsibleButton()
transformUpdateCollapsibleButton.text = "Transform Update"
self.layout.addWidget(transformUpdateCollapsibleButton)
transformUpdateLayout = qt.QFormLayout(
transformUpdateCollapsibleButton)
self.transformUpdateInputSelector = slicer.qMRMLNodeComboBox()
self.transformUpdateInputSelector.nodeTypes = ((
"vtkMRMLLinearTransformNode"), "")
self.transformUpdateInputSelector.selectNodeUponCreation = True
self.transformUpdateInputSelector.addEnabled = False
self.transformUpdateInputSelector.removeEnabled = True
self.transformUpdateInputSelector.renameEnabled = True
self.transformUpdateInputSelector.noneEnabled = False
self.transformUpdateInputSelector.showHidden = False
self.transformUpdateInputSelector.showChildNodeTypes = False
self.transformUpdateInputSelector.setMRMLScene(slicer.mrmlScene)
self.transformUpdateInputSelector.setToolTip("Pick transform node")
transformUpdateLayout.addRow("Transform node: ",
self.transformUpdateInputSelector)
self.updateTransformButton = qt.QPushButton("Update")
transformUpdateLayout.addRow(self.updateTransformButton)
self.configFileNameBox = qt.QLineEdit()
transformUpdateLayout.addRow("Filename: ", self.configFileNameBox)
self.saveTransformButton = qt.QPushButton("Save Config")
transformUpdateLayout.addRow(self.saveTransformButton)
replyUpdateCollapsibleButton = ctk.ctkCollapsibleButton()
replyUpdateCollapsibleButton.text = "Reply"
self.layout.addWidget(replyUpdateCollapsibleButton)
replyLayout = qt.QFormLayout(replyUpdateCollapsibleButton)
self.replyBox = qt.QPlainTextEdit()
self.replyBox.setReadOnly(True)
replyLayout.addRow(self.replyBox)
# connections
self.startRecordingButton.connect('clicked(bool)',
self.onStartRecording)
self.stopRecordingButton.connect('clicked(bool)', self.onStopRecording)
self.startReconstuctionButton.connect('clicked(bool)',
self.onStartReconstruction)
self.stopReconstructionButton.connect('clicked(bool)',
self.onStopReconstruction)
self.reconstructVolumeButton.connect('clicked(bool)',
self.onReconstVolume)
self.updateTransformButton.connect('clicked(bool)',
self.onUpdateTransform)
self.saveTransformButton.connect('clicked(bool)', self.onSaveTransform)
self.layout.addStretch(1)
def createUserInterface(self):
self.__layout = self.__parent.createUserInterface()
vText = qt.QLabel("1st Instrumented Level:")
iText = qt.QLabel("# to Instrument:")
aText = qt.QLabel("Approach Direction:")
self.vSelector = qt.QComboBox()
self.vSelector.setMaximumWidth(120)
self.levels = ("C1", "C2", "C3", "C4", "C5", "C6", "C7", "T1", "T2",
"T3", "T4", "T5", "T6", "T7", "T8", "T9", "T10", "T11",
"T12", "L1", "L2", "L3", "L4", "L5", "S1")
self.vSelector.addItems(self.levels)
self.iSelector = qt.QComboBox()
self.iSelector.setMaximumWidth(120)
self.iSelector.addItems(
['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12'])
self.aSelector = qt.QComboBox()
self.aSelector.setMaximumWidth(120)
self.aSelector.addItems(['Posterior', 'Anterior', 'Left', 'Right'])
blank = qt.QLabel(" ")
blank.setMaximumWidth(30)
#self.__layout.addWidget(vText)
#self.__layout.addWidget(self.vSelector)
#self.__layout.addWidget(iText)
#self.__layout.addWidget(self.iSelector)
self.vertebraeGridBox = qt.QGridLayout()
self.vertebraeGridBox.addWidget(vText, 0, 0)
self.vertebraeGridBox.addWidget(self.vSelector, 1, 0)
self.vertebraeGridBox.addWidget(blank, 0, 1)
self.vertebraeGridBox.addWidget(iText, 0, 2)
self.vertebraeGridBox.addWidget(blank, 1, 1)
self.vertebraeGridBox.addWidget(self.iSelector, 1, 2)
self.vertebraeGridBox.addWidget(blank, 0, 3)
self.vertebraeGridBox.addWidget(aText, 0, 4)
self.vertebraeGridBox.addWidget(blank, 1, 3)
self.vertebraeGridBox.addWidget(self.aSelector, 1, 4)
self.__layout.addRow(self.vertebraeGridBox)
#self.__layout.addRow("Starting Instrumented Vertebra:",self.vSelector)
#self.__layout.addRow("Number of Vertebrae to Instrument:",self.iSelector)
# Hide ROI Details
roiCollapsibleButton = ctk.ctkCollapsibleButton()
#roiCollapsibleButton.setMaximumWidth(320)
roiCollapsibleButton.text = "ROI Details"
self.__layout.addWidget(roiCollapsibleButton)
roiCollapsibleButton.collapsed = True
# Layout
roiLayout = qt.QFormLayout(roiCollapsibleButton)
#label for ROI selector
roiLabel = qt.QLabel('Select ROI:')
font = roiLabel.font
font.setBold(True)
roiLabel.setFont(font)
#creates combobox and populates it with all vtkMRMLAnnotationROINodes in the scene
self.__roiSelector = slicer.qMRMLNodeComboBox()
self.__roiSelector.nodeTypes = ['vtkMRMLAnnotationROINode']
self.__roiSelector.toolTip = "ROI defining the structure of interest"
self.__roiSelector.setMRMLScene(slicer.mrmlScene)
self.__roiSelector.addEnabled = 1
#add label + combobox
roiLayout.addRow(roiLabel, self.__roiSelector)
self.__roiSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onROIChanged)
# the ROI parameters
# GroupBox to hold ROI Widget
voiGroupBox = qt.QGroupBox()
voiGroupBox.setTitle('Define VOI')
roiLayout.addRow(voiGroupBox)
# create form layout for GroupBox
voiGroupBoxLayout = qt.QFormLayout(voiGroupBox)
# create ROI Widget and add it to the form layout of the GroupBox
self.__roiWidget = PythonQt.qSlicerAnnotationsModuleWidgets.qMRMLAnnotationROIWidget(
)
voiGroupBoxLayout.addRow(self.__roiWidget)
# # Hide VR Details
# vrCollapsibleButton = ctk.ctkCollapsibleButton()
# #roiCollapsibleButton.setMaximumWidth(320)
# vrCollapsibleButton.text = "Rendering Details"
# self.__layout.addWidget(vrCollapsibleButton)
# vrCollapsibleButton.collapsed = True
# # Layout
# vrLayout = qt.QFormLayout(vrCollapsibleButton)
# # the ROI parameters
# # GroupBox to hold ROI Widget
# vrGroupBox = qt.QGroupBox()
# vrGroupBox.setTitle( 'Define Rendering' )
# vrLayout.addRow( vrGroupBox )
# # create form layout for GroupBox
# vrGroupBoxLayout = qt.QFormLayout( vrGroupBox )
# # create ROI Widget and add it to the form layout of the GroupBox
# self.__vrWidget = PythonQt.qSlicerVolumeRenderingModuleWidgets.qSlicerPresetComboBox()
# #self.__vrWidget = PythonQt.qSlicerVolumeRenderingModuleWidgets.qMRMLVolumePropertyNodeWidget()
# vrGroupBoxLayout.addRow( self.__vrWidget )
# # initialize VR
# self.__vrLogic = slicer.modules.volumerendering.logic()
# self.updateWidgetFromParameters(self.parameterNode())
qt.QTimer.singleShot(0, self.killButton)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.dbpath = None
self.dbcsvpath = None
self.flirttemplate = '/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz'
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
self.clearButton = qt.QPushButton("Clear Scene")
self.clearButton.toolTip = "Clear all the volumes and models in 3D views"
self.clearButton.name = "AdniDemonsDatabase Clear"
reloadFormLayout.addWidget(self.clearButton)
self.clearButton.connect('clicked()', self.onClear)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload AdniDemonsDatabase"
self.reloadButton.name = "AdniDemonsDatabase Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Get the test methods create a button for each of them
testklsdir = dir(AdniDemonsDatabaseTest)
# reload and test button
# (use this during development, but remove it when delivering your module to users)
# reload and run specific tests
# scenarios = ('All', 'Model', 'Volume', 'SceneView_Simple', 'SceneView_Complex')
scenarios = [n for n in testklsdir if n.startswith('test_')]
for scenario in scenarios:
button = qt.QPushButton("Reload and Test %s" % scenario)
button.toolTip = "Reload this module and then run the self test on %s." % scenario
reloadFormLayout.addWidget(button)
button.connect('clicked()', lambda s = scenario: self.onReloadAndTest(scenario = s))
#
# Test All Button
#
self.testallButton = qt.QPushButton("Test All")
self.testallButton.toolTip = "Run all the logic tests"
self.testallButton.name = "Reload & Test All"
reloadFormLayout.addWidget(self.testallButton)
self.testallButton.connect('clicked()', self.onTestAll)
#
# Settings Area
#
settingCollapsibleButton = ctk.ctkCollapsibleButton()
settingCollapsibleButton.text = "ADNI Demons Database Generation"
self.layout.addWidget(settingCollapsibleButton)
settingFormLayout = qt.QGridLayout(settingCollapsibleButton)
#
# DB Directory Selection Button
#
self.dbButton = qt.QPushButton("Set ADNI Database Directory")
self.dbButton.toolTip = "Set ANDI Database Directory"
self.dbButton.enabled = True
settingFormLayout.addWidget(self.dbButton, 0, 0)
self.dblabel = qt.QLabel(self.dbpath if self.dbpath != None else 'Empty')
settingFormLayout.addWidget(self.dblabel, 0, 1)
#
# DB csv file Selection Button
#
csvbtntxt = "Set *.csv File For DB Record"
self.dbcsvpath = '' if self.dbButton.text.find(':') == -1 else join(self.dbpath, 'db.csv')
self.csvButton = qt.QPushButton(csvbtntxt if len(self.dbcsvpath) == 0 else csvbtntxt + ' : ' + self.dbcsvpath)
self.csvButton.toolTip = "Set ANDI Database csv file path, which can be downloaded in the data collection"
self.csvButton.enabled = True
settingFormLayout.addWidget(self.csvButton, 1, 0)
self.csvlabel = qt.QLabel(self.dbcsvpath if self.dbcsvpath != None and self.dbpath != None else 'Empty')
settingFormLayout.addWidget(self.csvlabel, 1, 1)
#
# Flirt Template Selection Button
#
self.betflirt_templatebutton = qt.QPushButton("Select Flirt Template")
self.betflirt_templatebutton.toolTip = "Select Flirt Template"
self.betflirt_templatebutton.enabled = True
settingFormLayout.addWidget(self.betflirt_templatebutton, 2, 0)
self.flirtlabel = qt.QLabel(self.flirttemplate if self.flirttemplate != None else 'Empty')
settingFormLayout.addWidget(self.flirtlabel, 2, 1)
# They should be connected afterwards their initiation
self.dbButton.connect('clicked(bool)', lambda: self.onFileButton('db'))
self.csvButton.connect('clicked(bool)', lambda: self.onFileButton('csv'))
self.betflirt_templatebutton.connect('clicked(bool)', lambda: self.onFileButton('flirt'))
#
# Bet & Flirt Threshold
#
self.betflirtspin = qt.QDoubleSpinBox()
self.betflirtspin.setRange(0.0, 1.0)
self.betflirtspin.setSingleStep(0.05)
self.betflirtspin.setValue(0.2)
settingFormLayout.addWidget(qt.QLabel("Bet Threashold"), 3 ,0)
settingFormLayout.addWidget(self.betflirtspin, 3, 1)
#
# Checkbox for Bet & Flirt
#
self.betflirtcheck = qt.QCheckBox("Run Bet + Flirt")
self.betflirtcheck.setToolTip("Only the image IDs listed in the csv file will be processed. flirted images will be saved in path/to/db/flirted")
self.betflirtcheck.checked = 0
settingFormLayout.addWidget(self.betflirtcheck, 4, 0)
#
# Checkbox for Running Demons Registration
#
self.demonscheck = qt.QCheckBox("Run Demons")
self.demonscheck.setToolTip("Only the image IDs listed in the csv file will be processed. Image sources will only be retrieved from path/to/db/flirted")
self.demonscheck.checked = 0
self.demonscheck.enabled = True
settingFormLayout.addWidget(self.demonscheck, 4, 1)
#
# Interval Selection : 6m | 12m
#
self.intervalCombo = qt.QComboBox()
self.intervalCombo.addItem("6 Month")
self.intervalCombo.addItem("12 Month")
settingFormLayout.addWidget(qt.QLabel("Extract Interval"), 5 ,0)
settingFormLayout.addWidget(self.intervalCombo, 5, 1)
#
# Sequence Label Selection: All, Stable: NL, Stable: MCI, Stable: AD, NL2MCI, MCI2AD
#
self.seqCombo = qt.QComboBox()
self.seqCombo.enabled = False
self.seqCombo.addItems(["All", "Stable: NL", "Stable: MCI", "Stable: AD", "NL2MCI", "MCI2AD"])
settingFormLayout.addWidget(qt.QLabel("Sequence Type"), 6 ,0)
settingFormLayout.addWidget(self.seqCombo, 6, 1)
actionCollapsibleButton = ctk.ctkCollapsibleButton()
actionCollapsibleButton.text = "Database Generation Actions"
self.layout.addWidget(actionCollapsibleButton)
actionFormLayout = qt.QFormLayout(actionCollapsibleButton)
#
# Generate Database csv
#
self.dbgenButton = qt.QPushButton("Generate Database Sequence csv")
self.dbgenButton.toolTip = "Generate A csv with required fields by merging the image collection csv and the dxsum. To make this button functional, pls make sure R language is installed in your system and \'RScript\' is in the $PATH. \'dbgen.csv\' will be generated in the database directory"
self.dbgenButton.enabled = False
actionFormLayout.addRow(self.dbgenButton)
self.dbgenButton.connect('clicked(bool)', self.onDbgenButton)
#
# Validate Database see if all the images exist
#
self.validateDbButton = qt.QPushButton("Validate Database")
self.validateDbButton.toolTip = "Check if all the image ids in the dbgen.csv exist in the data folder"
self.validateDbButton.enabled = False
actionFormLayout.addRow(self.validateDbButton)
self.validateDbButton.connect('clicked(bool)', self.onValidateDbButton)
#
# Validate Bet and Flirt see if all the images were flirted and betted successfully
#
self.validateBetAndFlirtButton = qt.QPushButton("Validate Bet&Flirt")
self.validateBetAndFlirtButton.toolTip = "Check if all the image were successfully betted and flirted"
self.validateBetAndFlirtButton.enabled = True
actionFormLayout.addRow(self.validateBetAndFlirtButton)
self.validateBetAndFlirtButton.connect('clicked(bool)', self.onValidateBetAndFlirtButton)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
actionFormLayout.addRow(self.applyButton)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
#
# Flirt Clear Button
#
self.clearFlirtButton = qt.QPushButton("Clear Flirt")
self.clearFlirtButton.toolTip = "Clear the files created by flirt."
self.clearFlirtButton.enabled = False
actionFormLayout.addRow(self.clearFlirtButton)
self.clearFlirtButton.connect('clicked(bool)', self.onFlirtClear)
#
# Evaluate DB Area
#
evaluateCollapsibleButton = ctk.ctkCollapsibleButton()
evaluateCollapsibleButton.text = "Evaluate DB"
self.layout.addWidget(evaluateCollapsibleButton)
evaluateFormLayout = qt.QGridLayout(evaluateCollapsibleButton)
#
# MAP setting
#
self.kmapspin = qt.QDoubleSpinBox()
self.kmapspin.setRange(0.0, 10.0)
self.kmapspin.setSingleStep(1.0)
self.kmapspin.setValue(5)
evaluateFormLayout.addWidget(qt.QLabel("K value for MAP"), 1 ,0)
evaluateFormLayout.addWidget(self.kmapspin, 1, 1)
#
# DB Evaluate Button
#
self.evaluateDbButton = qt.QPushButton('Evaluate DB')
self.evaluateDbButton.toolTip = "Set ANDI Database Directory. Assume in this folder, you have already generated a database with ADNI Demons DB Creator"
self.evaluateDbButton.enabled = True
evaluateFormLayout.addWidget(self.evaluateDbButton, 2, 0)
self.evaluateDbButton.connect('clicked(bool)', self.onEvaluateDbButton)
#
# Regenerate DB matrix check
#
self.regenMatCheck = qt.QCheckBox('Regenerate Dissimilarity Matrix')
self.regenMatCheck.checked = False
self.regenMatCheck.enabled = True
evaluateFormLayout.addWidget(self.regenMatCheck, 2, 1)
#
# Testing Ariea
#
statusCollapsibleButton = ctk.ctkCollapsibleButton()
statusCollapsibleButton.text = "Console"
self.layout.addWidget(statusCollapsibleButton)
self.statusLayout = qt.QFormLayout(statusCollapsibleButton)
#
# Show a Return Message
#
self.returnMsg = qt.QLabel("Ready")
self.statusLayout.addRow(self.returnMsg)
# Add vertical spacer
self.layout.addStretch(1)