def setup(self):
""" Setup all UI elements and prepare data """
# TODO: following line is only for the purpose of testing
self._loadedVolumeNodes = OrderedDict({volume.GetID: volume for volume
in slicer.util.getNodesByClass('vtkMRMLScalarVolumeNode')})
ScriptedLoadableModuleWidget.setup(self)
self._setupPatientWatchBox()
self._setupViewSettingGroupBox()
self._setupCollapsibleLayoutButton()
self._patientAssessmentWidget = AssessmentWidget(forms=self.getSetting("Patient_Assessment_Forms"),
title="Patient Level Assessment")
self._studyAssessmentWidget = AssessmentWidget(forms=self.getSetting("Study_Assessment_Forms"),
title="Study Level Assessment")
self._prostateMeasurementsWidget = ProstateWidget()
self._findingsWidget = FindingsWidget(maximumNumber=4)
self._exportToHTMLButton = UICreationHelpers.createButton("Export to HTML")
self.layout.addWidget(self._collapsibleLayoutButton)
self._setupCollapsibleMultiVolumeExplorerButton()
self.layout.addWidget(self._collapsibleMultiVolumeButton)
self.layout.addWidget(self._patientAssessmentWidget)
self.layout.addWidget(self._studyAssessmentWidget)
self.layout.addWidget(self._prostateMeasurementsWidget)
self.layout.addWidget(self._findingsWidget)
self.layout.addWidget(self._exportToHTMLButton)
self._stepButtonGroup = qt.QButtonGroup()
self._stepButtonGroup.addButton(self._patientAssessmentWidget, 1)
self._stepButtonGroup.addButton(self._studyAssessmentWidget, 2)
self._stepButtonGroup.addButton(self._prostateMeasurementsWidget, 3)
self._stepButtonGroup.addButton(self._findingsWidget, 4)
self.layout.addStretch(1)
self._setupConnections()
self.updateGUIFromData()
def __init__(self, parent=None):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.__init__(self, parent)
self.logic = None
self.subjects = None
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = EPISURGBrowserLogic()
self.makeGUI()
slicer.episurgBrowser = self
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent,
self.onSceneStartClose)
def __init__(self, parent=None): ScriptedLoadableModuleWidget.__init__(self, parent) VolumeSeriesTypeSceneObserver().refresh() # is a singleton and observes the mrmlScene self.modulePath = os.path.dirname(slicer.util.modulePath(self.moduleName)) SlicerPIRADSConfiguration(self.moduleName, os.path.join(self.modulePath, 'Resources', "default.cfg")) self._loadedVolumeNodes = OrderedDict() self.logic = SlicerPIRADSModuleLogic()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.testsCollapsibleButton = ctk.ctkCollapsibleButton()
self.testsCollapsibleButton.setLayout(qt.QFormLayout())
self.testsCollapsibleButton.text = "Slicer Layout Buttons Tests"
self.layout.addWidget(self.testsCollapsibleButton)
self.generateButtons()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.testsCollapsibleButton = ctk.ctkCollapsibleButton()
self.testsCollapsibleButton.setLayout(qt.QFormLayout())
self.testsCollapsibleButton.text = "Quantitative Reporting Tests"
self.layout.addWidget(self.testsCollapsibleButton)
self.generateButtons()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = ResectorLogic()
self.makeGUI()
self.onVolumeSelectorModified()
slicer.torchio = self
import SampleData
SampleData.downloadSample('MRHead')
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.testsCollapsibleButton = ctk.ctkCollapsibleButton()
self.testsCollapsibleButton.setLayout(qt.QFormLayout())
self.testsCollapsibleButton.text = "Quantitative Reporting Tests"
self.layout.addWidget(self.testsCollapsibleButton)
self.generateButtons()
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
global OPENCV2_AVAILABLE
try:
global cv2
import cv2
OPENCV2_AVAILABLE = True
except ImportError:
OPENCV2_AVAILABLE = False
if not OPENCV2_AVAILABLE:
logging.error("OpenCV2 python interface not available.")
return
self.logic = PinholeCameraRayIntersectionLogic()
self.markupsLogic = slicer.modules.markups.logic()
self.canSelectFiducials = False
self.isManualCapturing = False
self.validPinholeCamera = False
self.centerFiducialSelectionNode = None
self.copyNode = None
self.widget = None
self.videoCameraIntrinWidget = None
self.videoCameraSelector = None
self.videoCameraNode = None
self.markupsNode = None
# Observer tags
self.videoCameraObserverTag = None
self.videoCameraTransformObserverTag = None
self.pointModifiedObserverTag = None
self.videoCameraTransformNode = None
self.videoCameraTransformStatusLabel = None
self.okPixmap = PinholeCameraRayIntersectionWidget.loadPixmap(
'icon_Ok', 20, 20)
self.notOkPixmap = PinholeCameraRayIntersectionWidget.loadPixmap(
'icon_NotOk', 20, 20)
# Inputs/Outputs
self.imageSelector = None
self.videoCameraTransformSelector = None
# Actions
self.captureButton = None
self.resetButton = None
self.actionContainer = None
# Results
self.resultsLabel = None
self.videoCameraToReference = None
self.identity3x3 = vtk.vtkMatrix3x3()
self.identity4x4 = vtk.vtkMatrix4x4()
def __init__(self, parent=None):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(
self) # needed for parameter node observation
self.logic = None
self.subjects = None
def __init__(self, parent):
ScriptedLoadableModuleWidget.__init__(self, parent)
slicer.mrmlScene.Clear()
self.logic = ResynthLogic()
self.logic.installLibraries()
self.modelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
self.modelNode.CreateDefaultDisplayNodes()
self.loadBrainMesh()
self.makeGUI()
slicer.resynth = self
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = TorchIOTransformsLogic()
if not self.logic.checkTorchIO():
return
self.transforms = []
self.currentTransform = None
self.makeGUI()
self.onVolumeSelectorModified()
slicer.torchio = self
self.backgroundNode = None
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
if not OPENCV2_AVAILABLE:
self.layout.addWidget(
qt.QLabel(
"OpenCV2 python is required and not available. Check installation/configuration of SlicerOpenCV."
))
else:
# Load the UI From file
scriptedModulesPath = eval('slicer.modules.%s.path' %
self.moduleName.lower())
scriptedModulesPath = os.path.dirname(scriptedModulesPath)
path = os.path.join(scriptedModulesPath, 'Resources', 'UI',
'q' + self.moduleName + 'Widget.ui')
self.widget = slicer.util.loadUI(path)
self.layout.addWidget(self.widget)
# Camera UI
layout = PinholeCameraRayIntersectionWidget.get(
self.widget, "gridLayout")
placeholder = PinholeCameraRayIntersectionWidget.get(
self.widget, "placeholder")
layout.removeWidget(placeholder)
self.videoCameraIntrinWidget = slicer.qMRMLPinholeCameraIntrinsicsWidget(
)
self.videoCameraIntrinWidget.setMRMLScene(slicer.mrmlScene)
layout.addWidget(self.videoCameraIntrinWidget, 0, 0)
# Workaround for videoCamera selector
self.videoCameraSelector = self.videoCameraIntrinWidget.children(
)[1].children()[1]
# Inputs/Outputs
self.imageSelector = PinholeCameraRayIntersectionWidget.get(
self.widget, "comboBox_ImageSelector")
self.videoCameraTransformSelector = PinholeCameraRayIntersectionWidget.get(
self.widget, "comboBox_PinholeCameraTransform")
self.actionContainer = PinholeCameraRayIntersectionWidget.get(
self.widget, "widget_ActionContainer")
self.captureButton = PinholeCameraRayIntersectionWidget.get(
self.widget, "pushButton_Capture")
self.resetButton = PinholeCameraRayIntersectionWidget.get(
self.widget, "pushButton_Reset")
self.actionContainer = PinholeCameraRayIntersectionWidget.get(
self.widget, "widget_ActionContainer")
self.resultsLabel = PinholeCameraRayIntersectionWidget.get(
self.widget, "label_Results")
self.videoCameraTransformStatusLabel = PinholeCameraRayIntersectionWidget.get(
self.widget, "label_PinholeCameraTransform_Status")
# Disable capture as image processing isn't active yet
self.actionContainer.setEnabled(False)
# UI file method does not do mrml scene connections, do them manually
self.videoCameraIntrinWidget.setMRMLScene(slicer.mrmlScene)
self.imageSelector.setMRMLScene(slicer.mrmlScene)
self.videoCameraTransformSelector.setMRMLScene(slicer.mrmlScene)
# Connections
self.videoCameraSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onPinholeCameraSelected)
self.imageSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onImageSelected)
self.videoCameraTransformSelector.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.onPinholeCameraTransformSelected)
self.captureButton.connect('clicked(bool)', self.onCapture)
self.resetButton.connect('clicked(bool)', self.onReset)
# Choose red slice only
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
# Refresh Apply button state
self.onSelect()
def __init__(self, parent=None): ScriptedLoadableModuleWidget.__init__(self, parent)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.tutorials = {
"ShapeAnalysisModule":
"https://bit.ly/2Fyn97v", # SPHARM-PDM Generator
"GroupWiseRegistrationModule": "https://bit.ly/2WsFiun",
"RegressionComputation": "https://bit.ly/2uVYche",
"ShapeVariationAnalyzer":
"https://bit.ly/2HYbHVA", # Population Analysis
"SRep": "https://bit.ly/3sTEG3H",
"SRepCreator": "https://bit.ly/3sTEG3H",
"SRepRefinement": "https://bit.ly/3sTEG3H",
}
# The anchor associated with each link corresponds to the name of the module to select.
# For example, after the user click on the link associated with `href="#DataImporter"`,
# the "DataImporter" module is selected.
text = """
<br>
<u>Workflow quick-reference:</u><br>
<br>
The drop-down Modules are ordered to follow the basic workflow for choosing and using data. As a quick reference, the basic steps involve:<br>
<br>
1. Use the <a href="#DataImporter"><b>Data importer</b></a> module to load your segmentations from FreeSurf, FSL, Autoseg, or a bunch of vtp's<br><br>
2. Use <a href="#ShapePopulationViewer"><b>Shape Population Viewer</b></a> to do a quality check on the imported data<br><br>
3. Use <a href="#ShapeAnalysisModule"><b>SPHARM-PDM Generator</b></a> to do spherical harmonics based analysis<br><br>
4. Use the <a href="#GroupWiseRegistrationModule"><b>Study-specific Shape Analysis</b></a> module.<br><br>
5. Use the <a href="#SkeletalRepresentationVisualizer"><b>S-Rep Shape Analysis</b></a> module to do shape analysis via skeletal representations.<br><br>
6. Use the <a href="#ShapeVariationAnalyzer"><b>Shape Evaluator</b></a> module to compute a mean shape and see how the population varies.<br><br>
7. Use <a href="#RegressionComputation"><b>Shape Regressions</b></a> module to do regression based analysis.<br><br>
8. Use the <a href="#MFSDA"><b>Shape Statistics</b></a> module.<br><br>
"""
# TEXTEDIT
self.HomeTextSection = qt.QTextBrowser()
self.HomeTextSection.setHtml(text)
self.HomeTextSection.setMinimumHeight(400)
self.HomeTextSection.connect('anchorClicked(QUrl)',
self.onAnchorClicked)
self.layout.addWidget(self.HomeTextSection)
# SPACER
self.layout.addStretch()
# SAMPLE DATA REGISTRATION
for json_file in [
'DataImporterInputData.json', 'MFSDAInputData.json',
'ShapeRegressionInputData.json', 'SPHARM-PDMTestData.json',
'SPHARM-PDMFiducials.json', 'SRepCreatorData.json',
'SVAInputData.json'
]:
with open(
self.resourcePath('SampleDataDescription/%s' % json_file),
'r') as json_data:
source_data = json.load(json_data)
if 'iconPath' in source_data:
iconPath = self.resourcePath(source_data['iconPath'])
else:
iconPath = None
SampleDataLogic.registerCustomSampleDataSource(
category=source_data['category'],
sampleName=source_data['sampleName'],
uris=source_data['uris'],
checksums=source_data.get('checksums', None),
fileNames=source_data['fileNames'],
nodeNames=None,
thumbnailFileName=iconPath,
loadFileType=None,
customDownloader=self.downloadSampleDataInFolder,
)
# HIDE SAMPLE DATA 'BUILTIN' CATEGORY
slicer.modules.sampledata.widgetRepresentation().self(
).setCategoryVisible('BuiltIn', False)
self.sampleDataModuleTab = None
self.sampleDataTabTextEdit = None
self.moduleNameToSampleDataCategory = {
"DataImporter": "Data Importer",
"MFSDA": "Covariate Significance Testing",
"ShapeAnalysisModule": "SPHARM-PDM",
"RegressionComputation": "Shape Regression",
"ShapeVariationAnalyzer": "Population Analysis",
"SRepCreator": "Skeletal Representation Creator"
}
self.sampleDataModuleTab = self.addSampleDataTab()
self.updateSampleDataTab("Home")
moduleMenu = slicer.util.mainWindow().moduleSelector().modulesMenu()
moduleMenu.connect("currentModuleChanged(QString)",
self.updateSampleDataTab)
def __init__(self, parent=None): ScriptedLoadableModuleWidget.__init__(self, parent)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = EPISURGSegmentLogic()
self.makeGUI()
slicer.episurgSegment = self
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
#
# input mesh selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLModelNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick input model to use as mesh.")
parametersFormLayout.addRow("Input Model: ", self.inputSelector)
#
# Create Problem Button
#
self.createProblemButton = qt.QPushButton("Create Problem")
self.createProblemButton.toolTip = "Create a new FEniCS problem from the selected model."
self.createProblemButton.enabled = True
parametersFormLayout.addRow(self.createProblemButton)
#
# displacement value
#
self.displacementSliderWidget = ctk.ctkSliderWidget()
self.displacementSliderWidget.singleStep = 0.1
self.displacementSliderWidget.minimum = -1.0
self.displacementSliderWidget.maximum = 4.0
self.displacementSliderWidget.value = 0.0
self.displacementSliderWidget.setToolTip("Set displacement.")
parametersFormLayout.addRow("Displacement",
self.displacementSliderWidget)
#
# rotation angle value
#
self.rotationAngleSliderWidget = ctk.ctkSliderWidget()
self.rotationAngleSliderWidget.singleStep = 1
self.rotationAngleSliderWidget.minimum = -90
self.rotationAngleSliderWidget.maximum = 90
self.rotationAngleSliderWidget.value = 0.0
self.rotationAngleSliderWidget.setToolTip("Set rotation angle.")
parametersFormLayout.addRow("Rotation (degrees)",
self.rotationAngleSliderWidget)
#
# body force value
#
self.bodyForceSliderWidget = ctk.ctkSliderWidget()
self.bodyForceSliderWidget.singleStep = 0.1
self.bodyForceSliderWidget.minimum = -10
self.bodyForceSliderWidget.maximum = 10
self.bodyForceSliderWidget.value = 0.0
self.bodyForceSliderWidget.setToolTip("Set body force value.")
parametersFormLayout.addRow("Body Force", self.bodyForceSliderWidget)
#
# traction force value
#
self.tractionForceSliderWidget = ctk.ctkSliderWidget()
self.tractionForceSliderWidget.singleStep = 0.1
self.tractionForceSliderWidget.minimum = -2
self.tractionForceSliderWidget.maximum = 2
self.tractionForceSliderWidget.value = 0.0
self.tractionForceSliderWidget.setToolTip("Set traction force value.")
parametersFormLayout.addRow("Traction Force",
self.tractionForceSliderWidget)
#
# Defaults Button
#
self.defaultsButton = qt.QPushButton("Default parameters")
self.defaultsButton.toolTip = "Set default parameters."
self.defaultsButton.enabled = True
parametersFormLayout.addRow(self.defaultsButton)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# Squash and Stretch Buttons
#
self.squashButton = qt.QPushButton("Squash")
self.squashButton.toolTip = "Squash"
self.squashButton.enabled = False
self.stretchButton = qt.QPushButton("Stretch")
self.stretchButton.toolTip = "Stretch"
self.stretchButton.enabled = False
rowLayout = qt.QHBoxLayout()
rowLayout.addWidget(self.squashButton)
rowLayout.addWidget(self.stretchButton)
parametersFormLayout.addRow(rowLayout)
#
# Rotate Buttons
#
self.rotateLeftButton = qt.QPushButton("Rotate Left")
self.rotateLeftButton.toolTip = "Rotate left."
self.rotateLeftButton.enabled = False
self.rotateRightButton = qt.QPushButton("Rotate Right")
self.rotateRightButton.toolTip = "Rotate right."
self.rotateRightButton.enabled = False
rowLayout = qt.QHBoxLayout()
rowLayout.addWidget(self.rotateLeftButton)
rowLayout.addWidget(self.rotateRightButton)
parametersFormLayout.addRow(rowLayout)
#
# Reset Button
#
self.resetButton = qt.QPushButton("Reset")
self.resetButton.toolTip = "Reset the model."
self.resetButton.enabled = False
parametersFormLayout.addRow(self.resetButton)
# connections
self.createProblemButton.connect('clicked(bool)',
self.onCreateProblemButton)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.defaultsButton.connect('clicked(bool)', self.onDefaultsButton)
self.inputSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelect)
self.squashButton.connect('clicked(bool)', self.onSquashButton)
self.stretchButton.connect('clicked(bool)', self.onStretchButton)
self.rotateLeftButton.connect('clicked(bool)', self.onRotateLeftButton)
self.rotateRightButton.connect('clicked(bool)',
self.onRotateRightButton)
self.resetButton.connect('clicked(bool)', self.onResetButton)
# Add vertical spacer
self.layout.addStretch(1)
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
# Input file
# Text + Button invoking QFileDialog
self.inputFileLayout = qt.QHBoxLayout()
self.inputFileLabelHeader = qt.QLabel()
self.inputFileLabelHeader.text = "Input File: "
self.inputFileLabelFile = qt.QLabel()
self.inputFileLabelFile.text = "Input header.xml or .m3d"
self.inputFileButton = qt.QPushButton()
self.inputFileButton.text = "Browse"
self.inputFileLayout.addWidget(self.inputFileLabelHeader)
self.inputFileLayout.addWidget(self.inputFileLabelFile)
self.inputFileLayout.addWidget(self.inputFileButton)
self.layout.addLayout(self.inputFileLayout)
#
# Parameters Area
#
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.collapsed = True
self.parametersCollapsibleButton.text = "Parameters for legacy m3d format"
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(self.parametersCollapsibleButton)
# set distance of fold curve from interior points
self.distSlider = slicer.qMRMLSliderWidget()
self.distSlider.setProperty('maximum', 0.6)
self.distSlider.setProperty('minimum', 0.0)
self.distSlider.setProperty('singleStep', 0.01)
self.distSlider.setToolTip(
"Parameter used in transformation from legacy s-rep to new s-rep")
parametersFormLayout.addRow("Set distance to expand fold curve",
self.distSlider)
self.outputFolderLayout = qt.QHBoxLayout()
self.outputFolderLabelHeader = qt.QLabel()
self.outputFolderLabelHeader.text = "Output folder: "
self.outputFolderLabelFile = qt.QLabel()
self.outputFolderLabelFile.text = "Folder to save the new xml format"
self.outputFolderButton = qt.QPushButton()
self.outputFolderButton.text = "Browse"
self.outputFolderLayout.addWidget(self.outputFolderLabelHeader)
self.outputFolderLayout.addWidget(self.outputFolderLabelFile)
self.outputFolderLayout.addWidget(self.outputFolderButton)
parametersFormLayout.addRow(self.outputFolderLayout)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Visualize s-rep file")
self.applyButton.toolTip = "Parse and visualize s-rep."
self.layout.addWidget(self.applyButton)
# Unused
# self.boundarySurfaceRendering = qt.QCheckBox()
# self.boundarySurfaceRendering.checked = 0
# self.boundarySurfaceRendering.setToolTip("If checked, set the visibility of the boundary mesh")
# self.layout.addWidget(self.boundarySurfaceRendering)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputFileButton.connect('clicked(bool)',
self.onInputFileButtonClicked)
self.outputFolderButton.connect('clicked(bool)',
self.onOutputFolderButtonClicked)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)