def __init__(self):
QToolBar.__init__(self)
VTKObservationMixin.__init__(self)
self.parameterNode = WarpDrive.WarpDriveLogic().getParameterNode()
self.addObserver(self.parameterNode, vtk.vtkCommand.ModifiedEvent,
self.updateToolbarFromParameterNode)
self.setWindowTitle(qt.QObject().tr("LeadDBS"))
self.name = 'LeadDBS'
#
# Modality
#
self.addWidget(qt.QLabel('Modality:'))
self.modalityComboBox = qt.QComboBox()
self.modalityComboBox.addItem('T1w')
self.modalityComboBox.view().pressed.connect(self.onModalityPressed)
self.addWidget(self.modalityComboBox)
#
# B <-> F slider
#
self.addSeparator()
self.addWidget(qt.QLabel('Template:'))
templateSlider = qt.QSlider(1)
templateSlider.singleStep = 10
templateSlider.minimum = 0
templateSlider.maximum = 100
templateSlider.value = 0
templateSlider.setFixedWidth(120)
templateSlider.connect(
'valueChanged(int)', lambda value: slicer.util.
setSliceViewerLayers(foregroundOpacity=value / 100.0))
self.addWidget(templateSlider)
#
# Space Separator
#
self.addSeparator()
empty = qt.QWidget()
empty.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Preferred)
self.addWidget(empty)
#
# Subject
#
self.subjectNameLabel = qt.QLabel('Subject: ')
self.addWidget(self.subjectNameLabel)
#
# Harden Changes
#
self.addSeparator()
self.hardenChangesCheckBox = qt.QCheckBox("Harden Changes")
self.hardenChangesCheckBox.checked = True
self.addWidget(self.hardenChangesCheckBox)
#
# Save
#
self.nextButton = qt.QPushButton("Exit")
self.nextButton.setFixedWidth(75)
self.nextButton.setStyleSheet("background-color: green")
self.addWidget(self.nextButton)
self.nextButton.connect("clicked(bool)", self.onNextButton)
#
# Update
#
self.updateModalities(self.parameterNode.GetParameter("subjectPath"))
self.initSubject()
self.updateToolbarFromParameterNode()
time.sleep(5)
exit()
else:
control = qt.QWidget()
layout = qt.QVBoxLayout()
control.setLayout(layout)
b0 = qt.QPushButton("0: VTK CPU ray cast")
layout.addWidget(b0)
b0.connect('clicked()', vr0)
b1 = qt.QPushButton("1: VTK GPU ray cast")
layout.addWidget(b1)
b1.connect('clicked()', vr1)
b2 = qt.QPushButton("2: VTK GPU texture mapping")
layout.addWidget(b2)
b2.connect('clicked()', vr2)
b3 = qt.QPushButton("3: NCI GPU ray cast")
layout.addWidget(b3)
b3.connect('clicked()', vr3)
b4 = qt.QPushButton("4: NCI GPU ray cast (multi-volume)")
layout.addWidget(b4)
b4.connect('clicked()', vr4)
s1 = qt.QSlider(qt.Qt.Horizontal, control)
layout.addWidget(s1)
s1.connect('valueChanged(int)', vrthres)
be = qt.QPushButton("Exit")
layout.addWidget(be)
be.connect('clicked()', exit)
p = mainWindow().geometry
control.setGeometry(p.x() - 30, p.y() - 30, 300, 700)
control.show()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.caseInfoCollapsibleButton = ctk.ctkCollapsibleButton()
self.caseInfoCollapsibleButton.text = "Case information"
self.caseInfoCollapsibleButton.collapsed = False
self.layout.addWidget(self.caseInfoCollapsibleButton)
self.caseAreaLayout = qt.QGridLayout(self.caseInfoCollapsibleButton)
# Select case
row = 0
self.loadCaseButton = ctk.ctkPushButton()
self.loadCaseButton.text = "Load case"
self.loadCaseButton.toolTip = "Load a case folder"
self.caseAreaLayout.addWidget(self.loadCaseButton, row, 0)
# Reset button
self.resetButton = ctk.ctkPushButton()
self.resetButton.text = "Close case"
self.resetButton.toolTip = "Close the current case"
self.caseAreaLayout.addWidget(self.resetButton, row, 1)
# Case info
row += 1
self.caseInfoFrame = qt.QFrame()
self.caseInfoFrame.setFrameStyle(0x0002 | 0x0010)
self.caseInfoFrame.lineWidth = 2
self.caseInfoFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.caseAreaLayout.addWidget(self.caseInfoFrame, row, 0, 1, 2)
self.caseInfoFrameLayout = qt.QGridLayout()
self.caseInfoFrame.setLayout(self.caseInfoFrameLayout)
self.caseIdLabel = qt.QLabel("Case id: ")
self.caseIdLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.caseIdLabel, 0, 0)
self.showEnhancementCheckboxGroup = qt.QButtonGroup()
self.showJustOriginalButton = qt.QRadioButton("Original only")
self.showJustOriginalButton.setChecked(True)
self.showEnhancementCheckboxGroup.addButton(
self.showJustOriginalButton, 0)
self.caseInfoFrameLayout.addWidget(self.showJustOriginalButton, 1, 0)
self.showOriginalPlusEnhancedButton = qt.QRadioButton(
"Original and enhanced")
self.showEnhancementCheckboxGroup.addButton(
self.showOriginalPlusEnhancedButton, 1)
self.caseInfoFrameLayout.addWidget(self.showOriginalPlusEnhancedButton,
2, 0)
self.showJustEnhancedButton = qt.QRadioButton("Enhanced only")
self.showEnhancementCheckboxGroup.addButton(
self.showJustEnhancedButton, 2)
self.caseInfoFrameLayout.addWidget(self.showJustEnhancedButton, 3, 0)
# Center Volumes button
self.centerVolumesButton = ctk.ctkPushButton()
self.centerVolumesButton.text = "Center image/s"
self.centerVolumesButton.toolTip = "Center all the current visible images"
self.centerVolumesButton.setFixedWidth(200)
# self.centerVolumesButton.toolTip = "Load a case folder"
self.caseInfoFrameLayout.addWidget(self.centerVolumesButton, 4, 0)
# Enhancement fine tuning
self.vascularFactorLabel = qt.QLabel("Vascular factor")
self.vascularFactorLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.vascularFactorLabel, 0, 1)
self.vascularFactorSlider = qt.QSlider()
self.vascularFactorSlider.orientation = 2 # Vertical
self.vascularFactorSlider.value = 5
self.vascularFactorSlider.minimum = 0
self.vascularFactorSlider.maximum = 10
# self.vascularFactorSlider.setStyleSheet("margin-top:10px;padding-top:20px")
# self.vascularFactorSlider.setToolTip("Move the slider for a fine tuning segmentation")
self.caseInfoFrameLayout.addWidget(self.vascularFactorSlider, 1, 1, 4,
1, 0x0004)
self.enhancementFactorLabel = qt.QLabel("Enhancement factor")
self.enhancementFactorLabel.setStyleSheet("font-weight: bold")
self.caseInfoFrameLayout.addWidget(self.enhancementFactorLabel, 0, 2)
self.enhancementFactorSlider = qt.QSlider()
self.enhancementFactorSlider.orientation = 2 # Vertical
self.enhancementFactorSlider.minimum = 0
self.enhancementFactorSlider.maximum = 10
self.enhancementFactorSlider.value = 5
# self.vascularFactorSlider.setStyleSheet("margin-top:10px;padding-top:20px")
# self.vascularFactorSlider.setToolTip("Move the slider for a fine tuning segmentation")
self.caseInfoFrameLayout.addWidget(self.enhancementFactorSlider, 1, 2,
4, 1, 0x0004)
# Editor
row += 1
self.editorWidget = ui.CustomEditorWidget(self.parent)
self.editorWidget.setup()
self.editorCollapsibleButton = self.editorWidget.editLabelMapsFrame
self.editorCollapsibleButton.text = "Edit the current eye image"
self.editorCollapsibleButton.collapsed = False
self.editorWidget.toolsColor.terminologyCollapsibleButton.setVisible(
False)
self.layout.addWidget(self.editorCollapsibleButton)
### DIAGNOSIS
self.diagnosisCollapsibleButton = ctk.ctkCollapsibleButton()
self.diagnosisCollapsibleButton.text = "Diagnosis"
self.diagnosisCollapsibleButton.collapsed = False
self.layout.addWidget(self.diagnosisCollapsibleButton)
self.diagnosisAreaLayout = qt.QVBoxLayout(
self.diagnosisCollapsibleButton)
# Visual Acuity
label = qt.QLabel("Visual acuity (VA): ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
self.vaFrame = qt.QFrame()
self.vaFrame.setFrameStyle(0x0002 | 0x0010)
self.vaFrame.lineWidth = 2
self.vaFrame.setStyleSheet("background-color: #EEEEEE; margin: 10px")
self.vaFrame.setFixedWidth(240)
self.diagnosisAreaLayout.addWidget(self.vaFrame)
self.vaFrameLayout = qt.QGridLayout(self.vaFrame)
self.vaFrameLayout.addWidget(qt.QLabel("OS"), 0, 0)
self.osLineEdit = qt.QLineEdit()
self.osLineEdit.setFixedWidth(80)
self.osLineEdit.setStyleSheet("background-color: white")
self.vaFrameLayout.addWidget(self.osLineEdit, 0, 1)
self.vaFrameLayout.addWidget(qt.QLabel("OD"), 1, 0)
self.odLineEdit = qt.QLineEdit()
self.odLineEdit.setFixedWidth(80)
self.odLineEdit.setStyleSheet("background-color: white")
self.vaFrameLayout.addWidget(self.odLineEdit, 1, 1)
self.vaModalityButtonGroup = qt.QButtonGroup()
self.scvaRadioButton = qt.QRadioButton()
self.scvaRadioButton.setText("SCVA")
self.vaFrameLayout.addWidget(self.scvaRadioButton, 0, 2)
self.vaModalityButtonGroup.addButton(self.scvaRadioButton)
self.bcvaRadioButton = qt.QRadioButton()
self.bcvaRadioButton.setText("BCVA")
self.vaFrameLayout.addWidget(self.bcvaRadioButton, 1, 2)
self.vaModalityButtonGroup.addButton(self.bcvaRadioButton)
self.ucvaRadioButton = qt.QRadioButton()
self.ucvaRadioButton.setText("UCVA")
self.vaFrameLayout.addWidget(self.ucvaRadioButton, 2, 2)
self.vaModalityButtonGroup.addButton(self.ucvaRadioButton)
# Problems detected
label = qt.QLabel("Problems detected: ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
self.problemsFrame = qt.QFrame()
self.problemsFrame.setFrameStyle(0x0002 | 0x0010)
self.problemsFrame.lineWidth = 2
self.problemsFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.diagnosisAreaLayout.addWidget(self.problemsFrame)
self.problemsFrameLayout = qt.QGridLayout()
self.problemsFrame.setLayout(self.problemsFrameLayout)
self.problemsButtons = []
self.microaneurysmsCheckbox = qt.QCheckBox()
self.microaneurysmsCheckbox.setText("Microaneurysms")
self.problemsFrameLayout.addWidget(self.microaneurysmsCheckbox, 0, 0)
self.problemsButtons.append(self.microaneurysmsCheckbox)
self.exudatesCheckbox = qt.QCheckBox()
self.exudatesCheckbox.setText("Exudates")
self.problemsFrameLayout.addWidget(self.exudatesCheckbox, 0, 1)
self.problemsButtons.append(self.exudatesCheckbox)
self.haemorrhagesCheckbox = qt.QCheckBox()
self.haemorrhagesCheckbox.setText("Haemorrhages")
self.problemsFrameLayout.addWidget(self.haemorrhagesCheckbox, 0, 2)
self.problemsButtons.append(self.haemorrhagesCheckbox)
self.cottonWoolSpotsCheckbox = qt.QCheckBox()
self.cottonWoolSpotsCheckbox.setText("Cotton wool spots")
self.problemsFrameLayout.addWidget(self.cottonWoolSpotsCheckbox, 1, 0)
self.problemsButtons.append(self.cottonWoolSpotsCheckbox)
self.NeovascularisationCheckbox = qt.QCheckBox()
self.NeovascularisationCheckbox.setText("Neovascularisation")
self.problemsFrameLayout.addWidget(self.NeovascularisationCheckbox, 1,
1)
self.problemsButtons.append(self.NeovascularisationCheckbox)
label = qt.QLabel("Diabetic retinopathy diagnosis: ")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
# Diabetic Retinopathy diagnosis
self.diabeticRetinopathyDiagnosisFrame = qt.QFrame()
self.diabeticRetinopathyDiagnosisFrame.setFrameStyle(0x0002 | 0x0010)
self.diabeticRetinopathyDiagnosisFrame.lineWidth = 2
self.diabeticRetinopathyDiagnosisFrame.setStyleSheet(
"background-color: #EEEEEE; margin: 10px")
self.diagnosisAreaLayout.addWidget(
self.diabeticRetinopathyDiagnosisFrame)
self.diabeticRetinopathyDiagnosisFrameLayout = qt.QHBoxLayout()
self.diabeticRetinopathyDiagnosisFrame.setLayout(
self.diabeticRetinopathyDiagnosisFrameLayout)
self.diagnosisRadioButtonGroup = qt.QButtonGroup()
for i in range(5):
rb = qt.QRadioButton(str(i))
self.diagnosisRadioButtonGroup.addButton(rb, i)
self.diabeticRetinopathyDiagnosisFrameLayout.addWidget(rb)
self.diagnosisRadioButtonGroup.buttons()[0].setChecked(True)
# Additional comments
label = qt.QLabel("Additional comments:")
label.setStyleSheet("margin: 10px 0 0 10px; font-weight: bold")
self.diagnosisAreaLayout.addWidget(label)
row += 1
self.additionalCommentsText = qt.QTextEdit()
self.additionalCommentsText.setStyleSheet("margin: 10px")
self.diagnosisAreaLayout.addWidget(self.additionalCommentsText)
self.saveReportButton = ctk.ctkPushButton()
self.saveReportButton.text = "Save report"
self.saveReportButton.setFixedWidth(300)
self.diagnosisAreaLayout.addWidget(self.saveReportButton)
self.printReportButton = ctk.ctkPushButton()
self.printReportButton.text = "Save and generate PDF"
self.printReportButton.setFixedWidth(300)
self.diagnosisAreaLayout.addWidget(self.printReportButton)
self.expertModeCollapsibleButton = ctk.ctkCollapsibleButton()
self.expertModeCollapsibleButton.text = "Expert mode"
self.expertModeCollapsibleButton.collapsed = True
self.layout.addWidget(self.expertModeCollapsibleButton)
self.expertModeLayout = qt.QVBoxLayout(
self.expertModeCollapsibleButton)
self.expertModeCheckbox = qt.QCheckBox("Activate expert mode")
self.expertModeCheckbox.checked = False
self.expertModeLayout.addWidget(self.expertModeCheckbox)
self.layout.addStretch(1)
# Connections
self.loadCaseButton.connect('clicked()', self.__onLoadCaseClicked__)
# self.loadReportButton.connect('clicked()', self.__onLoadReportClicked__)
self.showEnhancementCheckboxGroup.connect(
"buttonClicked (int)", self.__onEnhancementButtonGroupClicked__)
self.centerVolumesButton.connect('clicked()',
SlicerUtil.centerAllVolumes)
self.vascularFactorSlider.connect('sliderReleased()',
self.__onEnhancementFineTuning__)
self.enhancementFactorSlider.connect('sliderReleased()',
self.__onEnhancementFineTuning__)
self.saveReportButton.connect('clicked()',
self.__onSaveReportClicked__)
self.printReportButton.connect('clicked()',
self.__onPrintReportClicked__)
self.resetButton.connect('clicked()', self.reset)
self.expertModeCheckbox.connect("stateChanged(int)",
self.__onExpertModeStateChanged__)
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.EndCloseEvent,
self.__onSceneClosed__)
# Set default layout Red
SlicerUtil.changeLayoutRedSingle()
self.refreshUI()
def create(self):
super(WatershedFromMarkerEffectOptions, self).create()
if not HAVE_SIMPLEITK:
self.warningLabel = qt.QLabel()
self.warningLabel.text = "WatershedFromMarker is not available because\nSimpleITK is not available in this build"
self.widgets.append(self.warningLabel)
self.frame.layout().addWidget(self.warningLabel)
return
labelVolume = EditUtil.getLabelVolume()
if labelVolume and labelVolume.GetImageData():
spacing = labelVolume.GetSpacing()
self.minimumSigma = 0.1 * min(spacing)
self.maximumSigma = 100 * self.minimumSigma
else:
self.minimumSigma = 0.1
self.maximumSigma = 10
self.sigmaFrame = qt.QFrame(self.frame)
self.sigmaFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.sigmaFrame)
self.widgets.append(self.sigmaFrame)
tip = "Increasing this value smooths the segmentation and reduces leaks. This is the sigma used for edge detection."
self.sigmaLabel = qt.QLabel("Object Scale: ", self.frame)
self.sigmaLabel.setToolTip(tip)
self.sigmaFrame.layout().addWidget(self.sigmaLabel)
self.widgets.append(self.sigmaLabel)
self.sigmaSlider = qt.QSlider(qt.Qt.Horizontal, self.frame)
self.sigmaFrame.layout().addWidget(self.sigmaSlider)
self.sigmaFrame.setToolTip(tip)
self.widgets.append(self.sigmaSlider)
self.sigmaSpinBox = qt.QDoubleSpinBox(self.frame)
self.sigmaSpinBox.setToolTip(tip)
self.sigmaSpinBox.suffix = "mm"
self.sigmaFrame.layout().addWidget(self.sigmaSpinBox)
self.widgets.append(self.sigmaSpinBox)
self.sigmaSpinBox.minimum = self.minimumSigma
self.sigmaSlider.minimum = self.minimumSigma
self.sigmaSpinBox.maximum = self.maximumSigma
self.sigmaSlider.maximum = self.maximumSigma
decimals = math.floor(math.log(self.minimumSigma, 10))
if decimals < 0:
self.sigmaSpinBox.decimals = -decimals + 2
self.apply = qt.QPushButton("Apply", self.frame)
self.apply.objectName = self.__class__.__name__ + 'Apply'
self.apply.setToolTip("Apply the extension operation")
self.frame.layout().addWidget(self.apply)
self.widgets.append(self.apply)
helpDoc = \
"""Use this effect to apply the watershed from markers segmentation from multiple initial labels.
The input to this filter is current labelmap image which is expected to contain multiple labels as initial marks. The marks or labels are grown to fill the image and with edges defining the bondaries between. To segment a single object, mark the object, and then it is suggested to surround the object with a negative label on each axis.
The "Object Scale" parameter is use to adjust the smoothness of the output image and prevent leakage. It is used internally for the sigma of the gradient magnitude.
"""
HelpButton(self.frame, helpDoc)
self.sigmaSlider.connect('valueChanged(int)',
self.sigmaSpinBox.setValue)
self.sigmaSpinBox.connect('valueChanged(double)',
self.sigmaSlider.setValue)
# if either widget is changed both should change and this should be triggered
self.connections.append((self.sigmaSpinBox, 'valueChanged(double)',
self.onSigmaValueChanged))
self.connections.append((self.apply, 'clicked()', self.onApply))
# Add vertical spacer
self.frame.layout().addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
sampleCollapsibleButton = ctk.ctkCollapsibleButton()
sampleCollapsibleButton.text = "Main Panel"
self.layout.addWidget(sampleCollapsibleButton)
# Set layout
self.formFrame = qt.QFrame(sampleCollapsibleButton)
self.formFrame.setLayout(qt.QHBoxLayout())
self.formFrame1 = qt.QFrame(sampleCollapsibleButton)
self.formFrame1.setLayout(qt.QHBoxLayout())
self.formFrame2 = qt.QFrame(sampleCollapsibleButton)
self.formFrame2.setLayout(qt.QHBoxLayout())
self.formFrame3 = qt.QFrame(sampleCollapsibleButton)
self.formFrame3.setLayout(qt.QHBoxLayout())
# bind new frame to the layout menu
self.layout.addWidget(self.formFrame)
self.layout.addWidget(self.formFrame1)
self.layout.addWidget(self.formFrame2)
self.layout.addWidget(self.formFrame3)
#create volume selector
self.inputSelector = qt.QLabel("Input Volume", self.formFrame)
self.formFrame.layout().addWidget(self.inputSelector)
self.inputSelector = slicer.qMRMLNodeComboBox(self.formFrame)
self.inputSelector.nodeTypes = ("vtkMRMLScalarVolumeNode","")
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
#bind the current volume selector to the current scene of slicer
self.inputSelector.setMRMLScene(slicer.mrmlScene)
#bind the input selector to the frame
self.formFrame.layout().addWidget(self.inputSelector)
#Set up buttons
Button_volume = qt.QPushButton("Show Volume")
Button_volume.toolTip = "Show Volume of selected file."
self.formFrame.layout().addWidget(Button_volume)
Button_volume.connect('clicked(bool)', self.onButton_volumeClicked)
Button_clip=qt.QPushButton("Crop Volume")
Button_clip.toolTip="Crop Volume of selected file."
self.formFrame.layout().addWidget(Button_clip)
Button_clip.connect('clicked(bool)',self.onButton_cropClicked)
Button_remove=qt.QPushButton("Remove Volume")
Button_remove.toolTip="remove current scene's volume."
self.formFrame.layout().addWidget(Button_remove)
Button_remove.connect('clicked(bool)',self.onButton_removeClicked)
#Set up sliders
self.xLabel = qt.QLabel("LR", self.formFrame1)
self.xLabel.setMinimumWidth(80)
self.xsld = qt.QSlider(qt.Qt.Horizontal,self.formFrame1)
self.xsld.setRange(0, 100)
self.xsld.setValue(100)
self.xsld.setFixedWidth(400)
self.xsld.setFocusPolicy(qt.Qt.NoFocus)
self.xsld.setPageStep(5)
self.xsld.valueChanged.connect(self.xchangeValue)
self.xnumber = qt.QLabel('100',self.formFrame1)
self.xnumber.setMinimumWidth(50)
self.formFrame1.layout().addWidget(self.xLabel)
self.formFrame1.layout().addWidget(self.xsld)
self.formFrame1.layout().addWidget(self.xnumber)
self.yLabel = qt.QLabel("AP", self.formFrame2)
self.yLabel.setMinimumWidth(80)
self.ysld = qt.QSlider(qt.Qt.Horizontal,self.formFrame2)
self.ysld.setRange(0, 100)
self.ysld.setValue(100)
self.ysld.setFixedWidth(400)
self.ysld.setFocusPolicy(qt.Qt.NoFocus)
self.ysld.setPageStep(5)
self.ysld.valueChanged.connect(self.ychangeValue)
self.ynumber = qt.QLabel('100',self.formFrame2)
self.ynumber.setMinimumWidth(50)
self.formFrame2.layout().addWidget(self.yLabel)
self.formFrame2.layout().addWidget(self.ysld)
self.formFrame2.layout().addWidget(self.ynumber)
self.zLabel = qt.QLabel("SI", self.formFrame3)
self.zLabel.setMinimumWidth(80)
self.zsld = qt.QSlider(qt.Qt.Horizontal,self.formFrame3)
self.zsld.setRange(0, 100)
self.zsld.setValue(100)
self.zsld.setFixedWidth(400)
self.zsld.setFocusPolicy(qt.Qt.NoFocus)
self.zsld.setPageStep(5)
self.zsld.valueChanged.connect(self.zchangeValue)
self.znumber = qt.QLabel('100',self.formFrame3)
self.znumber.setMinimumWidth(50)
self.formFrame3.layout().addWidget(self.zLabel)
self.formFrame3.layout().addWidget(self.zsld)
self.formFrame3.layout().addWidget(self.znumber)
#set up initial roi region
self.x = self.xsld.value
self.y = self.ysld.value
self.z = self.zsld.value
self.Button_volume = Button_volume
self.r = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLAnnotationROINode")
self.r.SetRadiusXYZ(100, 100, 100)
time.sleep(5)
sizeROIX(50)
slicer.app.processEvents()
time.sleep(5)
sizeROIY(50)
slicer.app.processEvents()
time.sleep(5)
sizeROIZ(50)
slicer.app.processEvents()
time.sleep(5)
exit()
else:
control = qt.QWidget()
layout = qt.QVBoxLayout()
control.setLayout(layout)
sX = qt.QSlider(qt.Qt.Horizontal,control)
layout.addWidget(sX)
sX.connect('valueChanged(int)', moveROIX)
sY = qt.QSlider(qt.Qt.Horizontal,control)
layout.addWidget(sY)
sY.connect('valueChanged(int)', moveROIY)
sZ = qt.QSlider(qt.Qt.Horizontal,control)
layout.addWidget(sZ)
sZ.connect('valueChanged(int)', moveROIZ)
sX1 = qt.QSlider(qt.Qt.Horizontal,control)
layout.addWidget(sX1)
sX1.connect('valueChanged(int)', sizeROIX)
sY1 = qt.QSlider(qt.Qt.Horizontal,control)
layout.addWidget(sY1)
sY1.connect('valueChanged(int)', sizeROIY)
sZ1 = qt.QSlider(qt.Qt.Horizontal,control)
def __init__(self):
QToolBar.__init__(self)
VTKObservationMixin.__init__(self)
self.parameterNode = SmudgeModule.SmudgeModuleLogic().getParameterNode()
self.addObserver(self.parameterNode, vtk.vtkCommand.ModifiedEvent, self.updateToolbarFromMRML)
self.setWindowTitle(qt.QObject().tr("LeadDBS"))
self.name = 'LeadDBS'
#
# Modality
#
self.addWidget(qt.QLabel('Modality:'))
self.modalityComboBox = qt.QComboBox()
self.modalityComboBox.addItem('t1')
self.modalityComboBox.view().pressed.connect(self.onModalityPressed)
self.addWidget(self.modalityComboBox)
#
# B <-> F slider
#
self.addSeparator()
self.addWidget(qt.QLabel('Template:'))
templateSlider = qt.QSlider(1)
templateSlider.singleStep = 10
templateSlider.minimum = 0
templateSlider.maximum = 100
templateSlider.value = 0
templateSlider.setFixedWidth(120)
templateSlider.connect('valueChanged(int)', lambda value: slicer.util.setSliceViewerLayers(foregroundOpacity = value / 100.0))
self.addWidget(templateSlider)
#
# Resolution
#
self.addSeparator()
self.addWidget(qt.QLabel('Warp Resolution: '))
self.resolutionComboBox = qt.QComboBox()
avalibaleResolutions = [0.5, 1, 2, 5, 10]
self.resolutionComboBox.addItems([str(r)+'mm' for r in avalibaleResolutions])
self.resolutionComboBox.setCurrentIndex(avalibaleResolutions.index(float(self.parameterNode.GetParameter("resolution"))))
self.resolutionComboBox.connect('currentIndexChanged(int)', self.onResolutionChanged)
self.addWidget(self.resolutionComboBox)
#
# Space Separator
#
empty = qt.QWidget()
empty.setSizePolicy(qt.QSizePolicy.Expanding,qt.QSizePolicy.Preferred)
self.addWidget(empty)
#
# Subject
#
self.subjectNameLabel = qt.QLabel('Subject: ')
self.addWidget(self.subjectNameLabel)
#
# Save
#
self.saveButton = qt.QPushButton("Finish and Exit")
self.saveButton.setFixedWidth(200)
self.saveButton.setStyleSheet("background-color: green")
self.addWidget(self.saveButton)
ImportAtlas.ImportAtlasLogic().run(os.path.join(self.parameterNode.GetParameter("MNIAtlasPath"), 'DISTAL Minimal (Ewert 2017)'))
self.saveButton.connect("clicked(bool)", self.onSaveButton)
#
# Update
#
self.updateModalities(self.parameterNode.GetParameter("subjectPath"))
reducedToolbarLogic().loadSubjectTransforms()
self.onModalityPressed([],self.modalityComboBox.currentText)
self.updateToolbarFromMRML()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = CNN_Image_ClassifierLogic()
self.moduleDir = os.path.dirname(
slicer.modules.collect_training_images.path)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.modelSelector = qt.QComboBox()
self.modelSelector.addItems(["Select model"])
modelDirectoryContents = os.listdir(
os.path.join(self.moduleDir, os.pardir, "Models/retrainContainer"))
modelNames = [
dir for dir in modelDirectoryContents
if dir.find(".") == -1 and dir != "Dockerfile"
]
self.modelSelector.addItems(["Create new model"])
self.modelSelector.addItems(modelNames)
parametersFormLayout.addRow(self.modelSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Start")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# Object table
#
self.objectTable = qt.QTableWidget()
self.objectTable.setColumnCount(3)
self.objectTable.setHorizontalHeaderLabels(
["Name", "Found", "Confidence"])
parametersFormLayout.addRow(self.objectTable)
#
# Adjust Confidence Thresholds
#
confidenceThresholdsCollapsibleButton = ctk.ctkCollapsibleButton()
confidenceThresholdsCollapsibleButton.text = "Confidence Thresholds"
self.layout.addWidget(confidenceThresholdsCollapsibleButton)
confidenceFormLayout = qt.QFormLayout(
confidenceThresholdsCollapsibleButton)
self.confidenceSlider = qt.QSlider(0x1) #horizontal slider
self.confidenceSlider.setRange(0, 100)
self.confidenceSlider.setTickInterval(5)
self.confidenceSlider.setTickPosition(2) #Ticks appear below slider
self.confidenceSlider.setSliderPosition(80)
self.confidenceSlider.setToolTip(
"Set the minimum degree of confidence that must be met for an object to be considered found"
)
confidenceFormLayout.addRow("Confidence: ", self.confidenceSlider)
self.confidenceLabel = qt.QLabel("80%")
confidenceFormLayout.addRow(self.confidenceLabel)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.modelSelector.connect('currentIndexChanged(int)',
self.onModelSelected)
self.confidenceSlider.connect('sliderMoved(int)',
self.onConfidenceChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
self.webcamReference = slicer.util.getNode('Webcam_Reference')
if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
def setup(self):
self.developerMode = True
ScriptedLoadableModuleWidget.setup(self)
# inspect current Scene and search for files called ?h_pial and ?h_white
# if found fill the lists with relative nodes
lhPialNode = slicer.mrmlScene.GetNodesByName(
'lh_pial').GetItemAsObject(0)
rhPialNode = slicer.mrmlScene.GetNodesByName(
'rh_pial').GetItemAsObject(0)
lhWhiteNode = slicer.mrmlScene.GetNodesByName(
'lh_white').GetItemAsObject(0)
rhWhiteNode = slicer.mrmlScene.GetNodesByName(
'rh_white').GetItemAsObject(0)
reconFileNode = slicer.mrmlScene.GetNodesByName(
'recon').GetItemAsObject(0)
self.gmpiCB = ctk.ctkCollapsibleButton()
self.gmpiCB.text = "GMPI Computation"
self.layout.addWidget(self.gmpiCB)
self.gmpiFL = qt.QFormLayout(self.gmpiCB)
#### Left Pial selection box
self.leftPialCBox = slicer.qMRMLNodeComboBox()
self.leftPialCBox.nodeTypes = (("vtkMRMLModelNode"), "")
self.leftPialCBox.selectNodeUponCreation = True
self.leftPialCBox.addEnabled = False
self.leftPialCBox.removeEnabled = False
self.leftPialCBox.noneEnabled = True
self.leftPialCBox.showHidden = False
self.leftPialCBox.showChildNodeTypes = False
self.leftPialCBox.setMRMLScene(slicer.mrmlScene)
self.leftPialCBox.setToolTip("Pick the left pial.")
self.gmpiFL.addRow("Left Pial: ", self.leftPialCBox)
#### Left White selection box
self.leftWhiteCBox = slicer.qMRMLNodeComboBox()
self.leftWhiteCBox.nodeTypes = (("vtkMRMLModelNode"), "")
self.leftWhiteCBox.selectNodeUponCreation = True
self.leftWhiteCBox.addEnabled = False
self.leftWhiteCBox.removeEnabled = False
self.leftWhiteCBox.noneEnabled = True
self.leftWhiteCBox.showHidden = False
self.leftWhiteCBox.showChildNodeTypes = False
self.leftWhiteCBox.setMRMLScene(slicer.mrmlScene)
self.leftWhiteCBox.setToolTip("Pick the left pial.")
#### Right Pial selection box
self.rightPialCBox = slicer.qMRMLNodeComboBox()
self.rightPialCBox.nodeTypes = (("vtkMRMLModelNode"), "")
self.rightPialCBox.selectNodeUponCreation = True
self.rightPialCBox.addEnabled = False
self.rightPialCBox.removeEnabled = False
self.rightPialCBox.noneEnabled = True
self.rightPialCBox.showHidden = False
self.rightPialCBox.showChildNodeTypes = False
self.rightPialCBox.setMRMLScene(slicer.mrmlScene)
self.rightPialCBox.setToolTip("Pick the right pial.")
self.gmpiFL.addRow("Right Pial: ", self.rightPialCBox)
#### Right White selection box
self.rightWhiteCBox = slicer.qMRMLNodeComboBox()
self.rightWhiteCBox.nodeTypes = (("vtkMRMLModelNode"), "")
self.rightWhiteCBox.selectNodeUponCreation = True
self.rightWhiteCBox.addEnabled = False
self.rightWhiteCBox.removeEnabled = False
self.rightWhiteCBox.noneEnabled = True
self.rightWhiteCBox.showHidden = False
self.rightWhiteCBox.showChildNodeTypes = False
self.rightWhiteCBox.setMRMLScene(slicer.mrmlScene)
self.rightWhiteCBox.setToolTip("Pick the right pial.")
self.gmpiFL.addRow("Right White: ", self.rightWhiteCBox)
self.gmpiFL.addRow("Left White: ", self.leftWhiteCBox)
#### Fiducials list Combo Box
self.fiducialsCBox = slicer.qMRMLNodeComboBox()
self.fiducialsCBox.nodeTypes = (("vtkMRMLMarkupsFiducialNode"), "")
self.fiducialsCBox.selectNodeUponCreation = False
self.fiducialsCBox.addEnabled = False
self.fiducialsCBox.removeEnabled = False
self.fiducialsCBox.noneEnabled = True
self.fiducialsCBox.setMRMLScene(slicer.mrmlScene)
self.fiducialsCBox.setToolTip("Select a fiducial list")
self.gmpiFL.addRow("Fiducial : ", self.fiducialsCBox)
# if nodes already exist load them in ComboBoxes
if lhWhiteNode:
self.leftWhiteCBox.setCurrentNode(lhWhiteNode)
if rhWhiteNode:
self.rightWhiteCBox.setCurrentNode(rhWhiteNode)
if rhPialNode:
self.rightPialCBox.setCurrentNode(rhPialNode)
if lhPialNode:
self.leftPialCBox.setCurrentNode(lhPialNode)
if reconFileNode:
self.fiducialsCBox.setCurrentNode(reconFileNode)
#### GMPI Threshold Slider
self.gmpiSlider = qt.QSlider(qt.Qt.Horizontal)
self.gmpiSlider.setMinimum(-9)
self.gmpiSlider.setMaximum(9)
self.gmpiSlider.setValue(-3)
#### GMPI Spin Box
self.gmpiSpinBox = qt.QDoubleSpinBox()
self.gmpiSpinBox.setRange(-1, 1)
self.gmpiSpinBox.setSingleStep(0.1)
self.gmpiSpinBox.setValue(float(self.gmpiSlider.value) / 10)
#### GMPI Slider e SpinBox Layout
# self.gmpiverticalLayout = qt.QHBoxLayout()
#
# self.gmpiverticalLayout.addWidget(self.gmpiSlider)
# self.gmpiverticalLayout.addWidget(self.gmpiSpinBox)
# self.gmpiFL.addRow("GMPI Threshold : ", self.gmpiverticalLayout)
# GMPI Computation Detection button
self.gmpiPB = qt.QPushButton("Apply")
self.gmpiPB.toolTip = "Run the algorithm."
self.gmpiPB.enabled = True
# Create montage files
self.montagePB = qt.QPushButton("Create Montage")
self.montagePB.toolTip = "Create Montage"
self.montagePB.enabled = True
#### Aggiungo il bottone al layout
self.gmpiFL.addRow(self.gmpiPB)
# self.gmpiFL.addRow(self.montagePB)
# connections
self.gmpiPB.connect('clicked(bool)', self.onGMPIComputation)
