def saveReport(self, currentValuesDict):
""" Save a JSON text file with the current values of the GUI stored in a dictionary.
It also saves the current enhanced and labelmap volumes
:param currentValuesDict: dictionary of values
:return: file where the report was stored
"""
p = os.path.join(self.getCurrentDataFolder(), "report.json")
with open(p, "w+b") as f:
json.dump(currentValuesDict, f)
# Save the labelmap
if self.currentLabelmapVolume.GetStorageNode() is None:
SlicerUtil.saveNewNode(
self.currentLabelmapVolume,
os.path.join(self.getCurrentDataFolder(),
self.currentLabelmapVolume.GetName() + ".nrrd"))
else:
self.currentLabelmapVolume.GetStorageNode().WriteData(
self.currentLabelmapVolume)
# Save the enhanced volume
if self.getEnhancedVolume().GetStorageNode() is None:
SlicerUtil.saveNewNode(
self.currentEnhancedVolume,
os.path.join(self.getCurrentDataFolder(),
self.currentEnhancedVolume.GetName() + ".nrrd"))
else:
self.currentEnhancedVolume.GetStorageNode().WriteData(
self.currentEnhancedVolume)
self.isCurrentReportSaved = True
return p
def refreshUI(self):
SlicerUtil.showToolbars(self.isExpertMode)
lm = slicer.app.layoutManager()
for key in ("Red", "Yellow"):
sliceWidget = lm.sliceWidget(key)
controller = sliceWidget.sliceController()
controller.showLabelOutline(True)
controller.visible = self.isExpertMode
# Hide DataProbe module
dataProbeCollapsibleButton = [
b for b in slicer.util.mainWindow().findChildren(
"ctkCollapsibleButton") if b.text == "Data Probe"
][0]
dataProbeCollapsibleButton.setVisible(self.isExpertMode)
# Link windows
compNodes = slicer.util.getNodes("vtkMRMLSliceCompositeNode*")
for compNode in compNodes.itervalues():
compNode.SetLinkedControl(True)
self.resetButton.visible = self.caseInfoFrame.visible = \
self.editorCollapsibleButton.visible = self.diagnosisCollapsibleButton.visible = \
self.isCaseLoaded or self.isExpertMode
if self.isCaseLoaded:
self.caseIdLabel.text = "Case Id: " + self.logic.current2DVectorVolume.GetName(
)
for button in self.showEnhancementCheckboxGroup.buttons():
button.setEnabled(self.logic.current2DVectorVolume is not None)
if self.showEnhancementCheckboxGroup.checkedId() == 0:
# Just original. Red Slice only
SlicerUtil.changeLayout(6)
# Hide enhancement fine tuning controls
self.vascularFactorLabel.visible = self.vascularFactorSlider.visible = \
self.enhancementFactorLabel.visible = self.enhancementFactorSlider.visible = \
False
elif self.showEnhancementCheckboxGroup.checkedId() == 1:
# Original + Enhanced
SlicerUtil.changeLayout(29)
# Show enhancement fine tuning controls
self.vascularFactorLabel.visible = self.vascularFactorSlider.visible = \
self.enhancementFactorLabel.visible = self.enhancementFactorSlider.visible = \
True
elif self.showEnhancementCheckboxGroup.checkedId() == 2:
# Just enhanced. Yellow Slice
SlicerUtil.changeLayout(7)
# Show enhancement fine tuning controls
self.vascularFactorLabel.visible = self.vascularFactorSlider.visible = \
self.enhancementFactorLabel.visible = self.enhancementFactorSlider.visible = \
True
def __printSnapshots__(self):
""" Generate snapshots of all the volumes to be displayed in the report
"""
# Save a png file from different images.
# We manipulate the widget to have the aspect that we want for the screenshot
lm = slicer.app.layoutManager()
# Take original image with Labelmap
# Change to Red
SlicerUtil.changeLayoutRedSingle()
sliceWidget = lm.sliceWidget("Red")
controller = sliceWidget.sliceController()
controller.fitSliceToBackground()
# Hide the slider bar (just show the picture)
controller.hide()
sliceView = sliceWidget.sliceView()
sliceView.cornerAnnotation().ClearAllTexts()
sliceView.scheduleRender()
# Take the snapshot
SlicerUtil.takeSnapshot(os.path.join(self.getCurrentDataFolder(),
self.__getReportImagePath__(1)),
type=slicer.qMRMLScreenShotDialog.Red,
hideAnnotations=True)
# Restore the regular controller
controller.show()
# Enhanced (with and without labelmap)
SlicerUtil.changeLayoutYellowSingle()
# If the user didn't open the enhanced volume yet, force it
enhancedVol = self.getEnhancedVolume()
yellowCompositeNode = slicer.mrmlScene.GetNodeByID(
'vtkMRMLSliceCompositeNodeYellow')
if yellowCompositeNode.GetBackgroundVolumeID() != enhancedVol.GetID():
yellowCompositeNode.SetBackgroundVolumeID(enhancedVol.GetID())
yellowSliceNode = slicer.mrmlScene.GetNodeByID(
'vtkMRMLSliceNodeYellow')
yellowSliceNode.SetOrientationToAxial()
# Assign the labelmap
yellowCompositeNode.SetLabelVolumeID(
self.currentLabelmapVolume.GetID())
controller = lm.sliceWidget("Yellow").sliceController()
controller.fitSliceToBackground()
# Hide the slider bar (just show the picture)
controller.hide()
# Take the snapshot
SlicerUtil.takeSnapshot(os.path.join(self.getCurrentDataFolder(),
self.__getReportImagePath__(3)),
type=slicer.qMRMLScreenShotDialog.Yellow,
hideAnnotations=True)
# Remove the labelmap
controller.setLabelMapHidden(True)
# Take the snapshot
SlicerUtil.takeSnapshot(os.path.join(self.getCurrentDataFolder(),
self.__getReportImagePath__(2)),
type=slicer.qMRMLScreenShotDialog.Yellow,
hideAnnotations=True)
# Restore the regular controller
controller.show()
controller.setLabelMapHidden(False)
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 enter(self):
"""This is invoked every time that we select this module as the active module in Slicer (not only the first time)"""
self.__setLabelmapOutlines__()
SlicerUtil.showToolbars(SlicerUtil.IsDevelopment)