def createUserInterface(self):
""" This step is mostly empty. A volume rendering threshold is added to be useful.
"""
self.__layout = self.__parent.createUserInterface()
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__threshRange.connect('valuesChanged(double,double)',
self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
ThreshGroupBox = qt.QGroupBox()
ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
ThreshGroupBoxLayout.addRow(self.__threshRange)
self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.__editorWidget = EditorWidget(parent=editorWidgetParent)
self.__editorWidget.setup()
self.__layout.addRow(editorWidgetParent)
self.hideUnwantedEditorUIElements()
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveCroppedSubtractionMap = qt.QCheckBox()
self.__RemoveCroppedSubtractionMap.checked = True
self.__RemoveCroppedSubtractionMap.setToolTip(
"Delete the cropped version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete cropped subtraction map: ",
self.__RemoveCroppedSubtractionMap)
self.__RemoveFullSubtracitonMap = qt.QCheckBox()
self.__RemoveFullSubtracitonMap.checked = True
self.__RemoveFullSubtracitonMap.setToolTip(
"Delete the full version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete full subtraction map: ",
self.__RemoveFullSubtracitonMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI resulting from your subtaction map.")
RestartGroupBoxLayout.addRow("Delete ROI: ", self.__RemoveROI)
# self.__RestartButton.setEnabled(0)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
def setupEditorWidget(self):
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent)
self.editorWidget.setup()
self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def __init__(self, parent=None, showVolumesFrame=False,
activeTools=("DefaultTool", "DrawEffect", "RectangleEffect", "EraseLabel",
"PreviousCheckPoint", "NextCheckPoint")):
"""Constructor. Just invokes the parent's constructor"""
self.activeTools = activeTools
# self.__masterVolume__ = scalarNode
# self.__labelmapVolume__ = labelmapNode
EditorWidget.__init__(self, parent, showVolumesFrame)
def __init__(self,
parent=None,
showVolumesFrame=True,
activeTools=("DefaultTool", "PaintEffect", "DrawEffect",
"LevelTracingEffect", "RectangleEffect",
"EraseLabel", "PreviousCheckPoint",
"NextCheckPoint")):
"""Constructor. Just invokes the parent's constructor"""
self.activeTools = activeTools
EditorWidget.__init__(self, parent, showVolumesFrame)
def __init__(self,
parent=None,
showVolumesFrame=False,
activeTools=("DefaultTool", "DrawEffect", "RectangleEffect",
"EraseLabel", "PreviousCheckPoint",
"NextCheckPoint")):
"""Constructor. Just invokes the parent's constructor"""
self.activeTools = activeTools
# self.__masterVolume__ = scalarNode
# self.__labelmapVolume__ = labelmapNode
EditorWidget.__init__(self, parent, showVolumesFrame)
def createUserInterface(self):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#endoSegmentButton = qt.QPushButton('Open Slicer Editor tool')
#self.__layout.addRow(endoSegmentButton)
#endoSegmentButton.connect('clicked()', self.startEditor)
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.updateParameters(self.parameterNode())
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background,
qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True)
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame,
showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
##TODO: How to set the required merge node?
wallCleanupSegLabel = qt.QLabel('Final Wall Segmentation Image:')
self.__wallCleanupSegSelector = slicer.qMRMLNodeComboBox()
self.__wallCleanupSegSelector.toolTip = "Choose the final wall segmentation label image."
self.__wallCleanupSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__wallCleanupSegSelector.setMRMLScene(slicer.mrmlScene)
self.__wallCleanupSegSelector.addEnabled = 0
self.__layout.addRow(wallCleanupSegLabel,
self.__wallCleanupSegSelector)
# Hide unnecessary button
findChildren(text='AutomaticLeft*')[0].hide()
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
def setupEditorWidget(self): editorWidgetParent = slicer.qMRMLWidget() editorWidgetParent.setLayout(qt.QVBoxLayout()) editorWidgetParent.setMRMLScene(slicer.mrmlScene) self.editorWidget = EditorWidget(parent=editorWidgetParent) self.editorWidget.setup() self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
endoSegLabel = qt.QLabel( 'Endo Segmentation Image:' )
self.__endoSegSelector = slicer.qMRMLNodeComboBox()
self.__endoSegSelector.toolTip = "Choose the endo segmentation label image."
self.__endoSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__endoSegSelector.setMRMLScene(slicer.mrmlScene)
self.__endoSegSelector.addEnabled = 0
self.__layout.addRow( endoSegLabel, self.__endoSegSelector )
def test_ThresholdThreading(self):
"""
Test for issue 2329, using the slicer EditorLib components
in outside of the editor.
"""
#
# first, get some sample data
#
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
head = sampleDataLogic.downloadMRHead()
#
# create a label map and set it for editing
#
volumesLogic = slicer.modules.volumes.logic()
# AF: intentionally use the naming convention that does not match the one
# used by Editor
headLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetActiveVolumeID( head.GetID() )
selectionNode.SetActiveLabelVolumeID( headLabel.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
#
# Instantiate a new widget, and add Editor widget to it
#
from Editor import EditorWidget
editorWidget = EditorWidget(showVolumesFrame=False)
def setupEditorWidget(self): self.editorWidgetParent = slicer.qMRMLWidget() self.editorWidgetParent.setLayout(qt.QVBoxLayout()) self.editorWidgetParent.setMRMLScene(slicer.mrmlScene) self.editUtil = EditorLib.EditUtil.EditUtil() self.editorWidget = EditorWidget(parent=self.editorWidgetParent, showVolumesFrame=False) self.editorWidget.setup() self.editorParameterNode = self.editUtil.getParameterNode()
def createUserInterface(self):
""" This UI takes advantage of a pre-built slicer thresholding widget.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Automatic segmentation with deep learning is not available in this demo, due to lack of computing resources. You may however create a segmentation using 3D Slicer's editor module in this step."""
)
step_label.setWordWrap(True)
self.__informationGroupBox = qt.QGroupBox()
self.__informationGroupBox.setTitle('Information')
self.__informationGroupBoxLayout = qt.QFormLayout(
self.__informationGroupBox)
self.__informationGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__informationGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.EditorWidget = EditorWidget(parent=editorWidgetParent)
self.EditorWidget.setup()
self.__layout.addRow(editorWidgetParent)
# self.__thresholdGroupBox = qt.QGroupBox()
# self.__thresholdGroupBox.setTitle('Threshold Range')
# self.__thresholdGroupBoxLayout = qt.QFormLayout(self.__thresholdGroupBox)
# threshLabel = qt.QLabel('Select Intensity Range:')
# threshLabel.alignment = 4
# self.__threshRange = slicer.qMRMLRangeWidget()
# self.__threshRange.decimals = 0
# self.__threshRange.singleStep = 1
# self.__thresholdGroupBoxLayout.addRow(threshLabel)
# self.__thresholdGroupBoxLayout.addRow(self.__threshRange)
# self.__layout.addRow(self.__thresholdGroupBox)
# self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface(self):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background,
qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True)
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame,
showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
endoSegLabel = qt.QLabel('Endo Segmentation Image:')
self.__endoSegSelector = slicer.qMRMLNodeComboBox()
self.__endoSegSelector.toolTip = "Choose the endo segmentation label image."
self.__endoSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__endoSegSelector.setMRMLScene(slicer.mrmlScene)
self.__endoSegSelector.addEnabled = 0
self.__layout.addRow(endoSegLabel, self.__endoSegSelector)
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#endoSegmentButton = qt.QPushButton('Open Slicer Editor tool')
#self.__layout.addRow(endoSegmentButton)
#endoSegmentButton.connect('clicked()', self.startEditor)
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.updateParameters(self.parameterNode())
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
##TODO: How to set the required merge node?
wallCleanupSegLabel = qt.QLabel( 'Final Wall Segmentation Image:' )
self.__wallCleanupSegSelector = slicer.qMRMLNodeComboBox()
self.__wallCleanupSegSelector.toolTip = "Choose the final wall segmentation label image."
self.__wallCleanupSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__wallCleanupSegSelector.setMRMLScene(slicer.mrmlScene)
self.__wallCleanupSegSelector.addEnabled = 0
self.__layout.addRow( wallCleanupSegLabel, self.__wallCleanupSegSelector )
# Hide unnecessary button
findChildren( text = 'AutomaticLeft*')[0].hide()
class LASegmentationWorkflowEndoSegmentationStep( LASegmentationWorkflowStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '3. Segmentation of endocardium' )
self.setDescription( 'Segment the endocardium using the Editor tools.' )
self.__parent = super( LASegmentationWorkflowEndoSegmentationStep, self )
def killButton(self):
# Hide unneccesary button
bl = slicer.util.findChildren(text='LAEndo*')
if len(bl):
bl[0].hide()
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
#def startEditor(self):
# from Editor import EditorWidget
# editorWidget = EditorWidget(showVolumesFrame=True)
def validate( self, desiredBranchId ):
self.__parent.validate( desiredBranchId )
if endoSegVolume != None :
self.__parent.validationSucceeded(desiredBranchId)
else:
self.__parent.validationFailed(desiredBranchId, 'Error','Endo segmentation step did not complete successfully.')
def onEntry(self, comingFrom, transitionType):
super(LASegmentationWorkflowEndoSegmentationStep, self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
self.editorWidget.exit()
super(LASegmentationWorkflowEndoSegmentationStep, self).onExit(goingTo, transitionType)
def setup(self):
EditorWidget.setup(self)
self.infoIconLabel.setVisible(False)
self.segmentEditorLabel.setVisible(False)
class CMRToolkitWizardWallCleanupStep(CMRToolkitWizardStep):
def __init__(self, stepid):
self.initialize(stepid)
self.setName('5. Edit Wall Segmentation')
self.setDescription(
'Set the wall segmentation image from the previous step as the merge volume in the Slicer Editor. Remove the pulmonary veins from the wall segmentation using the Slicer Editor erase tool and select the final label image to proceed.'
)
self.__parent = super(CMRToolkitWizardWallCleanupStep, self)
def killButton(self):
# Hide unneccesary button
bl = slicer.util.findChildren(text='AutomaticLeft*')
if len(bl):
bl[0].hide()
def createUserInterface(self):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#endoSegmentButton = qt.QPushButton('Open Slicer Editor tool')
#self.__layout.addRow(endoSegmentButton)
#endoSegmentButton.connect('clicked()', self.startEditor)
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.updateParameters(self.parameterNode())
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background,
qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True)
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame,
showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
##TODO: How to set the required merge node?
wallCleanupSegLabel = qt.QLabel('Final Wall Segmentation Image:')
self.__wallCleanupSegSelector = slicer.qMRMLNodeComboBox()
self.__wallCleanupSegSelector.toolTip = "Choose the final wall segmentation label image."
self.__wallCleanupSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__wallCleanupSegSelector.setMRMLScene(slicer.mrmlScene)
self.__wallCleanupSegSelector.addEnabled = 0
self.__layout.addRow(wallCleanupSegLabel,
self.__wallCleanupSegSelector)
# Hide unnecessary button
findChildren(text='AutomaticLeft*')[0].hide()
def validate(self, desiredBranchId):
self.__parent.validate(desiredBranchId)
wallCleanupSegVolume = self.__wallCleanupSegSelector.currentNode()
if wallCleanupSegVolume != None:
wallCleanupSegID = wallCleanupSegVolume.GetID()
pNode = self.parameterNode()
pNode.SetParameter('wallCleanupSegID', wallCleanupSegID)
Helper.SetLabelVolume(wallCleanupSegVolume.GetID())
self.__parent.validationSucceeded(desiredBranchId)
else:
self.__parent.validationFailed(
desiredBranchId, 'Error',
'Please select the wall segmentation image to proceed.')
def onEntry(self, comingFrom, transitionType):
super(CMRToolkitWizardWallCleanupStep,
self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
## TODO: Why does editor effect continue to the next workflow step?
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
#if goingTo.id() != 'PVAntrumCut':
# return
self.editorWidget.exit()
super(CMRToolkitWizardWallCleanupStep,
self).onExit(goingTo, transitionType)
def updateParameters(self, parameterNode):
global wallSegVolume
wallSegVolume = parameterNode.GetParameter('wallSegVolumeID')
class SegmentationStep(GBMWizardStep):
def __init__(self, stepid):
self.initialize(stepid)
self.setName('5. Threshold')
self.__vrDisplayNode = None
self.__threshold = [-1, -1]
# Initialize volume rendering.
self.__vrLogic = slicer.modules.volumerendering.logic()
self.__vrOpacityMap = None
self.__vrColorMap = None
self.__thresholdedLabelNode = None
self.__roiVolume = None
self.__visualizedVolume = None
self.__parent = super(SegmentationStep, self)
def createUserInterface(self):
""" This UI takes advantage of a pre-built slicer thresholding widget.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Automatic segmentation with deep learning is not available in this demo, due to lack of computing resources. You may however create a segmentation using 3D Slicer's editor module in this step."""
)
step_label.setWordWrap(True)
self.__informationGroupBox = qt.QGroupBox()
self.__informationGroupBox.setTitle('Information')
self.__informationGroupBoxLayout = qt.QFormLayout(
self.__informationGroupBox)
self.__informationGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__informationGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.EditorWidget = EditorWidget(parent=editorWidgetParent)
self.EditorWidget.setup()
self.__layout.addRow(editorWidgetParent)
# self.__thresholdGroupBox = qt.QGroupBox()
# self.__thresholdGroupBox.setTitle('Threshold Range')
# self.__thresholdGroupBoxLayout = qt.QFormLayout(self.__thresholdGroupBox)
# threshLabel = qt.QLabel('Select Intensity Range:')
# threshLabel.alignment = 4
# self.__threshRange = slicer.qMRMLRangeWidget()
# self.__threshRange.decimals = 0
# self.__threshRange.singleStep = 1
# self.__thresholdGroupBoxLayout.addRow(threshLabel)
# self.__thresholdGroupBoxLayout.addRow(self.__threshRange)
# self.__layout.addRow(self.__thresholdGroupBox)
# self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def onThresholdChanged(self):
""" Upon changing the slider (or intializing this step), this method
updates the volume rendering node and label volume accordingly.
"""
range0 = self.__threshRange.minimumValue
range1 = self.__threshRange.maximumValue
# Use vtk to threshold the label volume.
if self.__roiVolume != None:
thresh = vtk.vtkImageThreshold()
if vtk.VTK_MAJOR_VERSION <= 5:
thresh.SetInput(self.__roiVolume.GetImageData())
else:
thresh.SetInputData(self.__roiVolume.GetImageData())
thresh.ThresholdBetween(range0, range1)
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.ReplaceOutOn()
thresh.ReplaceInOn()
thresh.Update()
self.__thresholdedLabelNode.SetAndObserveImageData(
thresh.GetOutput())
def killButton(self):
# ctk creates a useless final page button. This method gets rid of it.
bl = slicer.util.findChildren(text='ReviewStep')
if len(bl):
bl[0].hide()
def validate(self, desiredBranchId):
# For now, no validation required.
self.__parent.validationSucceeded(desiredBranchId)
def onEntry(self, comingFrom, transitionType):
""" This method removes and adds nodes necessary to for a segementation
display, intializes color and opacity maps, and calls the main
thresholding function for the first time.
"""
super(SegmentationStep, self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
self.EditorWidget.setMergeNode(self.__thresholdedLabelNode)
self.EditorWidget.volumes.collapsed = True
self.EditorWidget.editLabelMapsFrame.collapsed = False
try:
self.EditorWidget.segmentEditorLabel.hide()
self.EditorWidget.infoIconLabel.hide()
except:
pass
# pNode = self.parameterNode()
# # What if someone goes to the Volume Rendering module, creates a new VRNode,
# # and then returns? Need some way to check if self.__vrNode is currently
# # being viewed.
# self.__vrDisplayNode = Helper.getNodeByID(pNode.GetParameter('vrDisplayNodeID'))
# self.updateWidgetFromParameters(pNode)
# # Retrieves necessary nodes.
# self.__roiVolume = Helper.getNodeByID(pNode.GetParameter('croppedVolumeID'))
# self.__thresholdedLabelNode = Helper.getNodeByID(pNode.GetParameter('thresholdedLabelID'))
# self.__nonThresholdedLabelNode = Helper.getNodeByID(pNode.GetParameter('nonThresholdedLabelID'))
# # self.InitVRDisplayNode()
# # Adds segementation label volume.
# Helper.SetLabelVolume(self.__thresholdedLabelNode.GetID())
# threshRange = [self.__threshRange.minimumValue, self.__threshRange.maximumValue]
# # Segments the entire vtk model. I assume there's a more concise way
# # to do it than thresholding over its entire intensity range, so TODO
# range0 = self.__threshRange.minimum
# range1 = self.__threshRange.maximum
# thresh = vtk.vtkImageThreshold()
# if vtk.VTK_MAJOR_VERSION <= 5:
# thresh.SetInput(self.__roiVolume.GetImageData())
# else:
# thresh.SetInputData(self.__roiVolume.GetImageData())
# thresh.ThresholdBetween(range0, range1)
# thresh.SetInValue(1)
# thresh.SetOutValue(0)
# thresh.ReplaceOutOn()
# thresh.ReplaceInOn()
# thresh.Update()
# self.__nonThresholdedLabelNode.SetAndObserveImageData(thresh.GetOutput())
# # Adjusts threshold information.
# self.onThresholdChanged()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def updateWidgetFromParameters(self, pNode):
""" Intializes the threshold and label volume established in the previous step.
"""
pass
# if pNode.GetParameter('followupVolumeID') == None or pNode.GetParameter('followupVolumeID') == '':
# Helper.SetBgFgVolumes(pNode.GetParameter('baselineVolumeID'), '')
# self.__visualizedVolume = Helper.getNodeByID(pNode.GetParameter('baselineVolumeID'))
# else:
# Helper.SetBgFgVolumes(pNode.GetParameter('subtractVolumeID'), pNode.GetParameter('followupVolumeID'))
# self.__visualizedVolume = Helper.getNodeByID(pNode.GetParameter('subtractVolumeID'))
# thresholdRange = [float(pNode.GetParameter('intensityThreshRangeMin')), float(pNode.GetParameter('intensityThreshRangeMax'))]
# if thresholdRange != '':
# self.__threshRange.maximum = thresholdRange[1]
# self.__threshRange.minimum = thresholdRange[0]
# self.__threshRange.maximumValue = thresholdRange[1]
# self.__threshRange.minimumValue = thresholdRange[0]
# else:
# Helper.Error('Unexpected parameter values! Error code CT-S03-TNA. Please report')
# labelID = pNode.GetParameter('thresholdedLabelID')
# self.__thresholdedLabelNode = Helper.getNodeByID(labelID)
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
# if self.__vrDisplayNode != None:
# # self.__vrDisplayNode.VisibilityOff()
# pNode.SetParameter('vrDisplayNodeID', self.__vrDisplayNode.GetID())
# roiRange = self.__threshRange
# pNode.SetParameter('intensityThreshRangeMin', str(roiRange.minimumValue))
# pNode.SetParameter('intensityThreshRangeMax', str(roiRange.maximumValue))
# pNode.SetParameter('vrThreshRangeMin', str(roiRange.minimumValue))
# pNode.SetParameter('vrThreshRangeMax', str(roiRange.maximumValue))
super(GBMWizardStep, self).onExit(goingTo, transitionType)
def InitVRDisplayNode(self):
""" This method calls a series of steps necessary to initailizing a volume
rendering node with an ROI.
"""
if self.__vrDisplayNode == None or self.__vrDisplayNode == '':
pNode = self.parameterNode()
self.__vrDisplayNode = self.__vrLogic.CreateVolumeRenderingDisplayNode(
)
slicer.mrmlScene.AddNode(self.__vrDisplayNode)
# Documentation on UnRegister is scant so far.
self.__vrDisplayNode.UnRegister(self.__vrLogic)
Helper.InitVRDisplayNode(self.__vrDisplayNode,
self.__roiVolume.GetID(), '')
self.__roiVolume.AddAndObserveDisplayNodeID(
self.__vrDisplayNode.GetID())
else:
self.__vrDisplayNode.SetAndObserveVolumeNodeID(
self.__roiVolume.GetID())
# This is a bit messy.
viewNode = slicer.util.getNode('vtkMRMLViewNode1')
self.__vrDisplayNode.AddViewNodeID(viewNode.GetID())
self.__vrLogic.CopyDisplayToVolumeRenderingDisplayNode(
self.__vrDisplayNode)
self.__vrOpacityMap = self.__vrDisplayNode.GetVolumePropertyNode(
).GetVolumeProperty().GetScalarOpacity()
self.__vrColorMap = self.__vrDisplayNode.GetVolumePropertyNode(
).GetVolumeProperty().GetRGBTransferFunction()
vrRange = self.__visualizedVolume.GetImageData().GetScalarRange()
# Renders in yellow, like the label map in the next steps.
self.__vrColorMap.RemoveAllPoints()
self.__vrColorMap.AddRGBPoint(vrRange[0], 0.8, 0.8, 0)
self.__vrColorMap.AddRGBPoint(vrRange[1], 0.8, 0.8, 0)
class CMRToolkitWizardWallCleanupStep( CMRToolkitWizardStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '5. Edit Wall Segmentation' )
self.setDescription( 'Set the wall segmentation image from the previous step as the merge volume in the Slicer Editor. Remove the pulmonary veins from the wall segmentation using the Slicer Editor erase tool and select the final label image to proceed.' )
self.__parent = super( CMRToolkitWizardWallCleanupStep, self )
def killButton(self):
# Hide unneccesary button
bl = slicer.util.findChildren(text='AutomaticLeft*')
if len(bl):
bl[0].hide()
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#endoSegmentButton = qt.QPushButton('Open Slicer Editor tool')
#self.__layout.addRow(endoSegmentButton)
#endoSegmentButton.connect('clicked()', self.startEditor)
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
self.updateParameters(self.parameterNode())
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
##TODO: How to set the required merge node?
wallCleanupSegLabel = qt.QLabel( 'Final Wall Segmentation Image:' )
self.__wallCleanupSegSelector = slicer.qMRMLNodeComboBox()
self.__wallCleanupSegSelector.toolTip = "Choose the final wall segmentation label image."
self.__wallCleanupSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__wallCleanupSegSelector.setMRMLScene(slicer.mrmlScene)
self.__wallCleanupSegSelector.addEnabled = 0
self.__layout.addRow( wallCleanupSegLabel, self.__wallCleanupSegSelector )
# Hide unnecessary button
findChildren( text = 'AutomaticLeft*')[0].hide()
def validate( self, desiredBranchId ):
self.__parent.validate( desiredBranchId )
wallCleanupSegVolume = self.__wallCleanupSegSelector.currentNode()
if wallCleanupSegVolume != None :
wallCleanupSegID = wallCleanupSegVolume.GetID()
pNode = self.parameterNode()
pNode.SetParameter('wallCleanupSegID', wallCleanupSegID)
Helper.SetLabelVolume(wallCleanupSegVolume.GetID())
self.__parent.validationSucceeded(desiredBranchId)
else:
self.__parent.validationFailed(desiredBranchId, 'Error','Please select the wall segmentation image to proceed.')
def onEntry(self, comingFrom, transitionType):
super(CMRToolkitWizardWallCleanupStep, self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
## TODO: Why does editor effect continue to the next workflow step?
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
#if goingTo.id() != 'PVAntrumCut':
# return
self.editorWidget.exit()
super(CMRToolkitWizardWallCleanupStep, self).onExit(goingTo, transitionType)
def updateParameters(self, parameterNode):
global wallSegVolume
wallSegVolume = parameterNode.GetParameter('wallSegVolumeID')
class CMRToolkitWizardEndoSegmentationStep( CMRToolkitWizardStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '2. Segmentation of endocardium' )
self.setDescription( 'Segment the endocardium using the Editor paint tool and select the final label image to proceed.' )
self.__parent = super( CMRToolkitWizardEndoSegmentationStep, self )
def killButton(self):
# Hide unneccesary button
bl = slicer.util.findChildren(text='AutomaticLeft*')
if len(bl):
bl[0].hide()
def createUserInterface( self ):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background, qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True);
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame, showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
endoSegLabel = qt.QLabel( 'Endo Segmentation Image:' )
self.__endoSegSelector = slicer.qMRMLNodeComboBox()
self.__endoSegSelector.toolTip = "Choose the endo segmentation label image."
self.__endoSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__endoSegSelector.setMRMLScene(slicer.mrmlScene)
self.__endoSegSelector.addEnabled = 0
self.__layout.addRow( endoSegLabel, self.__endoSegSelector )
#def startEditor(self):
# from Editor import EditorWidget
# editorWidget = EditorWidget(showVolumesFrame=True)
def validate( self, desiredBranchId ):
self.__parent.validate( desiredBranchId )
endoSegVolume = self.__endoSegSelector.currentNode()
if endoSegVolume != None :
endoSegID = endoSegVolume.GetID()
pNode = self.parameterNode()
pNode.SetParameter('endoSegVolumeID', endoSegID)
Helper.SetLabelVolume(endoSegVolume.GetID())
self.__parent.validationSucceeded(desiredBranchId)
else:
self.__parent.validationFailed(desiredBranchId, 'Error','Please select an endo segmentation image to proceed.')
def onEntry(self, comingFrom, transitionType):
super(CMRToolkitWizardEndoSegmentationStep, self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
#if goingTo.id() != 'AxialDilate':
# return
self.editorWidget.exit()
super(CMRToolkitWizardEndoSegmentationStep, self).onExit(goingTo, transitionType)
class SlicerPathologyWidget(ScriptedLoadableModuleWidget, ModuleWidgetMixin):
def __init__(self, parent = None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.modulePath = os.path.dirname(slicer.util.modulePath(self.moduleName))
self.currentStep = 1
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# this section is for custom color box
infoGroupBox = qt.QWidget()
hbox = qt.QHBoxLayout()
hbox.setMargin(0)
self.studySelectionGroupBoxLayout = qt.QGridLayout()
infoGroupBox.setLayout(hbox)
self.studySelectionGroupBoxLayout.addWidget(infoGroupBox, 0, 3, 1, 1)
infoIcon = qt.QPixmap(os.path.join(self.resourcesPath, 'Icons', 'icon-infoBox.png'))
self.customLUTInfoIcon = qt.QLabel()
self.customLUTInfoIcon.setPixmap(infoIcon)
self.customLUTInfoIcon.setSizePolicy(PythonQt.QtGui.QSizePolicy())
hbox.addWidget(self.customLUTInfoIcon)
self.customLUTLabel = qt.QLabel()
hbox.addWidget(self.customLUTLabel)
# end of custom color box section
self.setupIcons()
self.setupTabBarNavigation()
self.setupsetupUI()
self.setupimageSelectionUI()
self.setupsegmentationUI()
self.setupsubmissionUI()
self.setupEditorWidget()
editUtil = EditorLib.EditUtil.EditUtil()
self.parameterNode = editUtil.getParameterNode()
# 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)
#
# scale factor for screen shots
#
self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
self.screenshotScaleFactorSliderWidget.singleStep = 1.0
self.screenshotScaleFactorSliderWidget.minimum = 1.0
self.screenshotScaleFactorSliderWidget.maximum = 50.0
self.screenshotScaleFactorSliderWidget.value = 1.0
self.screenshotScaleFactorSliderWidget.setToolTip("Set scale factor for the screen shots.")
parametersFormLayout.addRow("Screenshot scale factor", self.screenshotScaleFactorSliderWidget)
#
# Apply Button
#
#self.applyButton = qt.QPushButton("Apply")
#self.applyButton.toolTip = "Run the algorithm."
#self.applyButton.enabled = False
#parametersFormLayout.addRow(self.applyButton)
# Add vertical spacer
self.layout.addStretch(1)
self.j = {}
def cleanup(self):
pass
def onSelect(self):
self.applyButton.enabled = self.inputSelector.currentNode() and self.outputSelector.currentNode()
def onApplyButton(self):
logic = SlicerPathologyLogic()
enableScreenshotsFlag = self.enableScreenshotsFlagCheckBox.checked
screenshotScaleFactor = int(self.screenshotScaleFactorSliderWidget.value)
print("Run the algorithm")
logic.run(self.inputSelector.currentNode(), self.outputSelector.currentNode(), enableScreenshotsFlag,screenshotScaleFactor)
def setupIcons(self):
self.setupIcon = self.createIcon('icon-setup.png')
self.imageSelectionIcon = self.createIcon('icon-imageselection.png')
self.segmentationIcon = self.createIcon('icon-segmentation.png')
self.submissionIcon = self.createIcon('icon-submission.png')
def setupTabBarNavigation(self):
self.tabWidget = qt.QTabWidget()
self.layout.addWidget(self.tabWidget)
setupGroupBox = qt.QGroupBox()
imageSelectionGroupBox = qt.QGroupBox()
segmentationGroupBox = qt.QGroupBox()
submissionGroupBox = qt.QGroupBox()
self.setupGroupBoxLayout = qt.QFormLayout()
self.imageSelectionGroupBoxLayout = qt.QFormLayout()
self.segmentationGroupBoxLayout = qt.QGridLayout()
self.submissionGroupBoxLayout = qt.QFormLayout()
setupGroupBox.setLayout(self.setupGroupBoxLayout)
imageSelectionGroupBox.setLayout(self.imageSelectionGroupBoxLayout)
segmentationGroupBox.setLayout(self.segmentationGroupBoxLayout)
submissionGroupBox.setLayout(self.submissionGroupBoxLayout)
self.tabWidget.setIconSize(qt.QSize(85, 30))
self.tabWidget.addTab(setupGroupBox, self.setupIcon, '')
self.tabWidget.addTab(imageSelectionGroupBox, self.imageSelectionIcon, '')
self.tabWidget.addTab(segmentationGroupBox, self.segmentationIcon, '')
self.tabWidget.addTab(submissionGroupBox, self.submissionIcon, '')
self.tabWidget.connect('currentChanged(int)',self.onTabWidgetClicked)
self.setTabsEnabled([1,2,3,4], True)
def onTabWidgetClicked(self, currentIndex):
if currentIndex == 0:
self.onStep1Selected()
if currentIndex == 1:
print ""
if currentIndex == 2:
print ""
if currentIndex == 3:
print ""
def setTabsEnabled(self, indexes, enabled):
for index in indexes:
self.tabWidget.childAt(1, 1).setTabEnabled(index, enabled)
def onStep1Selected(self):
#if self.checkStep3or4Leave() is True:
#return
if self.currentStep == 1:
return
self.currentStep = 1
self.setTabsEnabled([0],True)
self.setTabsEnabled([1,2,3], False)
def setupsetupUI(self):
self.setupUserName = qt.QLineEdit()
self.setupGroupBoxLayout.addRow("Username:"******"Password:"******"Data directory:") )
self.setupGroupBoxLayout.addWidget(self.dataDirButton)
self.setupExecutionID = qt.QLineEdit()
self.setupGroupBoxLayout.addRow("Execution ID:", self.setupExecutionID)
def setupimageSelectionUI(self):
self.loadDataButton = qt.QPushButton("Load Image from disk")
self.imageSelectionGroupBoxLayout.addWidget(self.loadDataButton)
self.loadDataButton.connect('clicked()', self.loadTCGAData)
self.WIP2 = qt.QPushButton("Select image from web")
self.WIP2.connect('clicked()', self.onWIP2ButtonClicked)
self.imageSelectionGroupBoxLayout.addWidget(self.WIP2)
self.WIP3 = qt.QPushButton("Load image from web")
self.WIP3.connect('clicked()', self.onWIP3ButtonClicked)
self.imageSelectionGroupBoxLayout.addWidget(self.WIP3)
self.RestoreButton = qt.QPushButton("Restore Session")
self.RestoreButton.connect('clicked()', self.RestoreSession)
self.imageSelectionGroupBoxLayout.addWidget(self.RestoreButton)
# def ebCenter(self):
# r = slicer.app.layoutManager().sliceWidget("Red").sliceController()
# r.fitSliceToBackground()
def onWIP2ButtonClicked(self):
self.openTargetImage0()
def onWIP3ButtonClicked(self):
self.openTargetImage()
r = slicer.app.layoutManager().sliceWidget("Red").sliceController()
r.fitSliceToBackground()
def setupsegmentationUI(self):
print ""
def setupsubmissionUI(self):
self.SaveButton = qt.QPushButton("Save")
self.submissionGroupBoxLayout.addWidget(self.SaveButton)
self.SaveButton.connect('clicked()', self.onSaveButtonClicked)
self.SaveButton.setEnabled(0)
#self.WebSaveButton = qt.QPushButton("Submit to web")
#self.submissionGroupBoxLayout.addWidget(self.WebSaveButton)
#self.WebSaveButton.connect('clicked()', self.onWebSaveButtonClicked)
def QImage2vtkImage(self, image):
i = vtk.vtkImageData().NewInstance()
i.SetDimensions(image.width(),image.height(),1)
i.AllocateScalars(vtk.VTK_UNSIGNED_CHAR,3)
for x in range(0,image.width()):
for y in range(0,image.height()):
c = qt.QColor(image.pixel(x,y))
i.SetScalarComponentFromDouble(x,y,0,0,c.red())
i.SetScalarComponentFromDouble(x,y,0,1,c.green())
i.SetScalarComponentFromDouble(x,y,0,2,c.blue())
return i
def onWIPButtonClicked(self):
import urllib2
reply = urllib2.urlopen('http://www.osa.sunysb.edu/erich.png')
byte_array = reply.read()
image = qt.QImage(qt.QImage.Format_RGB888)
image.loadFromData(byte_array)
imageData = self.QImage2vtkImage(image)
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("WEB")
volumeNode.SetAndObserveImageData(imageData)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(volumeNode)
slicer.mrmlScene.AddNode(displayNode)
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeGrey')
self.mutate()
def RestoreSession(self):
import zipfile
import os.path
f = qt.QFileDialog.getOpenFileName()
zf = zipfile.ZipFile(f)
for filename in zf.namelist():
try:
data = zf.read(filename)
except KeyError:
print 'ERROR: Did not find %s in zip file' % filename
else:
print filename
def onSaveButtonClicked(self):
import zipfile
import os.path
import uuid
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
self.j['layers'] = layers
self.j['username'] = self.setupUserName.text
self.j['sourcetile'] = self.tilename
self.j['generator'] = slicer.app.applicationVersion
self.j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
self.j['execution_id'] = self.setupExecutionID.text + "-"+ uuid.uuid4().get_urn()
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
zfname = os.path.join(self.dataDirButton.directory, self.tilename + "_" + datetime.datetime.now().strftime("%Y%m%d%H%M%S") + '.zip')
print "zipfile name"
print zfname
zf = zipfile.ZipFile(zfname, mode='w')
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fg = red_cn.GetForegroundVolumeID()
ff = slicer.util.getNode(fg)
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName("original.tif")
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(ff)
zf.write("original.tif")
os.remove("original.tif")
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
compFileName = os.path.join(self.dataDirButton.directory, labelName + '-comp.tif')
sNode.SetFileName(labelFileName)
success = sNode.WriteData(label)
if success:
print "adding "+labelFileName+" to zipfile"
zf.write(labelFileName,os.path.basename(labelFileName))
os.remove(labelFileName)
else:
print "failed writing "+labelFileName
comp = self.WriteLonI(label.GetImageData(),ff.GetImageData())
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("COMP")
volumeNode.SetAndObserveImageData(comp)
sNode.SetFileName(compFileName)
success = sNode.WriteData(volumeNode)
if success:
print "adding "+compFileName+" to zipfile"
zf.write(compFileName,os.path.basename(compFileName))
os.remove(compFileName)
else:
print "failed writing "+compFileName
jstr = json.dumps(self.j,sort_keys=True, indent=4, separators=(',', ': '))
mfname = os.path.join(self.dataDirButton.directory, 'manifest.json')
f = open(mfname,'w')
f.write(jstr)
f.close()
zf.write(mfname,os.path.basename(mfname))
zf.close()
os.remove(mfname)
#import sys
#reload(sys)
#sys.setdefaultencoding('utf8')
#opener = urllib2.build_opener(MultipartPostHandler)
#params = { "ss" : "0", # show source
# "doctype" : "Inline",
# "uploaded_file" : open(zfname, "rb") }
#print params
#print opener.open('http://quip1.bmi.stonybrook.edu:4000/upload', params).read()
def WriteLonI(self, src, dest):
dim = src.GetDimensions()
i = vtk.vtkImageData().NewInstance()
i.SetDimensions(dim[0],dim[1],1)
i.AllocateScalars(vtk.VTK_UNSIGNED_CHAR,3)
for x in range(0,dim[0]):
for y in range(0,dim[1]):
if (src.GetScalarComponentAsDouble(x,y,0,0)==0):
for c in range(0,3):
i.SetScalarComponentFromDouble(x,y,0,c,dest.GetScalarComponentAsDouble(x,y,0,c))
else:
if (
(src.GetScalarComponentAsDouble(x+1,y-1,0,0)==1) and
(src.GetScalarComponentAsDouble(x+1,y,0,0)==1) and
(src.GetScalarComponentAsDouble(x+1,y+1,0,0)==1) and
(src.GetScalarComponentAsDouble(x,y+1,0,0)==1) and
(src.GetScalarComponentAsDouble(x,y-1,0,0)==1) and
(src.GetScalarComponentAsDouble(x-1,y+1,0,0)==1) and
(src.GetScalarComponentAsDouble(x-1,y,0,0)==1) and
(src.GetScalarComponentAsDouble(x-1,y-1,0,0)==1)):
for c in range(0,3):
i.SetScalarComponentFromDouble(x,y,0,c,dest.GetScalarComponentAsDouble(x,y,0,c))
else:
i.SetScalarComponentFromDouble(x,y,0,0,0)
i.SetScalarComponentFromDouble(x,y,0,1,250)
i.SetScalarComponentFromDouble(x,y,0,2,0)
i.Modified()
return i
def onWebSaveButtonClicked(self):
print "Web Save to be implemented...."
def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath, "Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def setupEditorWidget(self):
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent)
self.editorWidget.setup()
self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def mutate(self):
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fgrdVolID = red_cn.GetBackgroundVolumeID()
fgrdNode = slicer.util.getNode("WEB")
fgrdVolID = fgrdNode.GetID()
fMat=vtk.vtkMatrix4x4()
fgrdNode.GetIJKToRASDirectionMatrix(fMat)
bgrdName = fgrdNode.GetName() + '_gray'
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputData(fgrdNode.GetImageData())
magnitude.Update()
bgrdNode = slicer.vtkMRMLScalarVolumeNode()
bgrdNode.SetImageDataConnection(magnitude.GetOutputPort())
bgrdNode.SetName(bgrdName)
bgrdNode.SetIJKToRASDirectionMatrix(fMat)
slicer.mrmlScene.AddNode(bgrdNode)
bgrdVolID = bgrdNode.GetID()
red_cn.SetForegroundVolumeID(fgrdVolID)
red_cn.SetBackgroundVolumeID(bgrdVolID)
red_cn.SetForegroundOpacity(1)
resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace("SlicerPathology.py",""), 'Resources')
colorFile = os.path.join(resourcesPath, "Colors/SlicerPathology.csv")
try:
slicer.modules.EditorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
structureNames = []
with open(colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
structureNames.append(row['Label'])
volumesLogic = slicer.modules.volumes.logic()
labelName = bgrdName+'-label'
refLabel = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene,bgrdNode,labelName)
refLabel.GetDisplayNode().SetAndObserveColorNodeID(SlicerPathologyColorNode.GetID())
self.editorWidget.helper.setMasterVolume(bgrdNode)
def openTargetImage0(self):
self.v = qt.QWebView()
weburl='http://quip1.bmi.stonybrook.edu:4000/'
self.v.setUrl(qt.QUrl(weburl))
self.v.show()
def openTargetImage(self):
import string
p = self.v.page()
m = p.mainFrame()
imageBound=m.evaluateJavaScript('viewer.viewport.viewportToImageRectangle(viewer.viewport.getBounds().x, viewer.viewport.getBounds().y, viewer.viewport.getBounds().width, viewer.viewport.getBounds().height)')
x=imageBound[u'x']
y=imageBound[u'y']
width=imageBound[u'width']
height=imageBound[u'height']
self.j['x'] = x
self.j['y'] = y
self.j['width'] = width
self.j['height'] = height
imagedata = m.evaluateJavaScript('imagedata')
tmpfilename= imagedata[u'metaData'][1]
imageFileName=string.rstrip(tmpfilename,'.dzi')
self.tilename = imagedata[u'imageId']
print self.tilename
self.parameterNode.SetParameter("SlicerPathology,tilename", self.tilename)
current_weburl ='http://quip1.uhmc.sunysb.edu/fcgi-bin/iipsrv.fcgi?IIIF=' + imageFileName +'/' + str(x) + ','+ str(y) + ',' + str(width) + ',' + str(height) + '/full/0/default.jpg'
print current_weburl
self.v.setUrl(qt.QUrl(current_weburl))
self.v.show()
reply = urllib2.urlopen(current_weburl)
byte_array = reply.read()
image = qt.QImage(qt.QImage.Format_RGB888)
image.loadFromData(byte_array)
imageData = self.QImage2vtkImage(image)
volumeNode = slicer.vtkMRMLVectorVolumeNode()
volumeNode.SetName("WEB")
volumeNode.SetAndObserveImageData(imageData)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(volumeNode)
slicer.mrmlScene.AddNode(displayNode)
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
displayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeGrey')
self.mutate()
def Four2ThreeChannel(self, image):
dim = image.GetDimensions()
i = vtk.vtkImageData().NewInstance()
i.SetDimensions(dim[0],dim[1],1)
i.AllocateScalars(vtk.VTK_UNSIGNED_CHAR,3)
for x in range(0,dim[0]):
for y in range(0,dim[1]):
for c in range(0,3):
i.SetScalarComponentFromDouble(x,y,0,c,image.GetScalarComponentAsDouble(x,y,0,c))
i.Modified()
return i
def loadTCGAData(self):
slicer.util.openAddVolumeDialog()
import EditorLib
editUtil = EditorLib.EditUtil.EditUtil()
imsainode = editUtil.getBackgroundVolume()
imsai = imsainode.GetImageData()
print imsai.GetNumberOfScalarComponents()
if imsai.GetNumberOfScalarComponents() > 3:
lala = self.Four2ThreeChannel(imsai)
print lala.GetNumberOfScalarComponents()
imsainode.SetAndObserveImageData(lala)
imsainode.Modified()
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fgrdVolID = red_cn.GetBackgroundVolumeID()
fgrdNode = slicer.util.getNode(fgrdVolID)
fMat=vtk.vtkMatrix4x4()
fgrdNode.GetIJKToRASDirectionMatrix(fMat)
bgrdName = fgrdNode.GetName() + '_gray'
self.tilename = fgrdNode.GetName() + '_gray'
self.parameterNode.SetParameter("SlicerPathology,tilename", self.tilename)
# Create dummy grayscale image
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputData(fgrdNode.GetImageData())
magnitude.Update()
bgrdNode = slicer.vtkMRMLScalarVolumeNode()
bgrdNode.SetImageDataConnection(magnitude.GetOutputPort())
bgrdNode.SetName(bgrdName)
bgrdNode.SetIJKToRASDirectionMatrix(fMat)
slicer.mrmlScene.AddNode(bgrdNode)
bgrdVolID = bgrdNode.GetID()
red_cn.SetForegroundVolumeID(fgrdVolID)
red_cn.SetBackgroundVolumeID(bgrdVolID)
red_cn.SetForegroundOpacity(1)
self.checkAndSetLUT()
print bgrdName
cv = slicer.util.getNode(bgrdName)
self.volumesLogic = slicer.modules.volumes.logic()
labelName = bgrdName+'-label'
refLabel = self.volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene,cv,labelName)
refLabel.GetDisplayNode().SetAndObserveColorNodeID(self.SlicerPathologyColorNode.GetID())
self.editorWidget.helper.setMasterVolume(cv)
class SlicerPathologyWidget(ScriptedLoadableModuleWidget, ModuleWidgetMixin):
def __init__(self, parent = None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.modulePath = os.path.dirname(slicer.util.modulePath(self.moduleName))
self.currentStep = 1
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# this section is for custom color box
infoGroupBox = qt.QWidget()
hbox = qt.QHBoxLayout()
hbox.setMargin(0)
self.studySelectionGroupBoxLayout = qt.QGridLayout()
infoGroupBox.setLayout(hbox)
self.studySelectionGroupBoxLayout.addWidget(infoGroupBox, 0, 3, 1, 1)
infoIcon = qt.QPixmap(os.path.join(self.resourcesPath, 'Icons', 'icon-infoBox.png'))
self.customLUTInfoIcon = qt.QLabel()
self.customLUTInfoIcon.setPixmap(infoIcon)
self.customLUTInfoIcon.setSizePolicy(PythonQt.QtGui.QSizePolicy())
hbox.addWidget(self.customLUTInfoIcon)
self.customLUTLabel = qt.QLabel()
hbox.addWidget(self.customLUTLabel)
# end of custom color box section
self.setupIcons()
self.setupTabBarNavigation()
self.setupsetupUI()
self.setupimageSelectionUI()
self.setupsegmentationUI()
self.setupsubmissionUI()
self.setupEditorWidget()
editUtil = EditorLib.EditUtil.EditUtil()
self.parameterNode = editUtil.getParameterNode()
# 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)
#
# scale factor for screen shots
#
self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
self.screenshotScaleFactorSliderWidget.singleStep = 1.0
self.screenshotScaleFactorSliderWidget.minimum = 1.0
self.screenshotScaleFactorSliderWidget.maximum = 50.0
self.screenshotScaleFactorSliderWidget.value = 1.0
self.screenshotScaleFactorSliderWidget.setToolTip("Set scale factor for the screen shots.")
parametersFormLayout.addRow("Screenshot scale factor", self.screenshotScaleFactorSliderWidget)
#
# Apply Button
#
#self.applyButton = qt.QPushButton("Apply")
#self.applyButton.toolTip = "Run the algorithm."
#self.applyButton.enabled = False
#parametersFormLayout.addRow(self.applyButton)
# Add vertical spacer
self.layout.addStretch(1)
def cleanup(self):
pass
def onSelect(self):
self.applyButton.enabled = self.inputSelector.currentNode() and self.outputSelector.currentNode()
def onApplyButton(self):
logic = SlicerPathologyLogic()
enableScreenshotsFlag = self.enableScreenshotsFlagCheckBox.checked
screenshotScaleFactor = int(self.screenshotScaleFactorSliderWidget.value)
print("Run the algorithm")
logic.run(self.inputSelector.currentNode(), self.outputSelector.currentNode(), enableScreenshotsFlag,screenshotScaleFactor)
def setupIcons(self):
self.setupIcon = self.createIcon('icon-setup.png')
self.imageSelectionIcon = self.createIcon('icon-imageselection.png')
self.segmentationIcon = self.createIcon('icon-segmentation.png')
self.submissionIcon = self.createIcon('icon-submission.png')
def setupTabBarNavigation(self):
self.tabWidget = qt.QTabWidget()
self.layout.addWidget(self.tabWidget)
setupGroupBox = qt.QGroupBox()
imageSelectionGroupBox = qt.QGroupBox()
segmentationGroupBox = qt.QGroupBox()
submissionGroupBox = qt.QGroupBox()
self.setupGroupBoxLayout = qt.QFormLayout()
self.imageSelectionGroupBoxLayout = qt.QFormLayout()
self.segmentationGroupBoxLayout = qt.QGridLayout()
self.submissionGroupBoxLayout = qt.QFormLayout()
setupGroupBox.setLayout(self.setupGroupBoxLayout)
imageSelectionGroupBox.setLayout(self.imageSelectionGroupBoxLayout)
segmentationGroupBox.setLayout(self.segmentationGroupBoxLayout)
submissionGroupBox.setLayout(self.submissionGroupBoxLayout)
self.tabWidget.setIconSize(qt.QSize(85, 30))
self.tabWidget.addTab(setupGroupBox, self.setupIcon, '')
self.tabWidget.addTab(imageSelectionGroupBox, self.imageSelectionIcon, '')
self.tabWidget.addTab(segmentationGroupBox, self.segmentationIcon, '')
self.tabWidget.addTab(submissionGroupBox, self.submissionIcon, '')
self.tabWidget.connect('currentChanged(int)',self.onTabWidgetClicked)
self.setTabsEnabled([1,2,3,4], True)
def onTabWidgetClicked(self, currentIndex):
if currentIndex == 0:
self.onStep1Selected()
if currentIndex == 1:
print "to be implemented..."
if currentIndex == 2:
print "to be implemented..."
if currentIndex == 3:
print "to be implemented..."
def setTabsEnabled(self, indexes, enabled):
for index in indexes:
self.tabWidget.childAt(1, 1).setTabEnabled(index, enabled)
def onStep1Selected(self):
#if self.checkStep3or4Leave() is True:
#return
if self.currentStep == 1:
return
self.currentStep = 1
self.setTabsEnabled([0],True)
self.setTabsEnabled([1,2,3], False)
def setupsetupUI(self):
self.setupUserName = qt.QLineEdit()
self.setupGroupBoxLayout.addRow("Username:"******"Password:"******"Load Data")
self.imageSelectionGroupBoxLayout.addWidget(self.loadDataButton)
self.loadDataButton.connect('clicked()', self.loadTCGAData)
print "Adding WIP Button!"
self.WIP = qt.QPushButton("WIP")
self.WIP.connect('clicked()', self.onWIPButtonClicked)
self.imageSelectionGroupBoxLayout.addWidget(self.WIP)
def setupsegmentationUI(self):
print "adding this for now..."
def setupsubmissionUI(self):
self.dataDirButton = ctk.ctkDirectoryButton()
self.submissionGroupBoxLayout.addWidget(qt.QLabel("Data directory:") )
self.submissionGroupBoxLayout.addWidget(self.dataDirButton)
self.SaveButton = qt.QPushButton("Save")
self.submissionGroupBoxLayout.addWidget(self.SaveButton)
self.SaveButton.connect('clicked()', self.onSaveButtonClicked)
self.WebSaveButton = qt.QPushButton("Submit to web")
self.submissionGroupBoxLayout.addWidget(self.WebSaveButton)
self.WebSaveButton.connect('clicked()', self.onWebSaveButtonClicked)
def onWIPButtonClicked(self):
print "WIP ME!"
from EditorLib import EditUtil
self.editUtil = EditorLib.EditUtil.EditUtil()
self.labelNode = self.editUtil.getLabelVolume()
print self.labelNode.GetImageData()
self.labelNode.GetImageData().Modified()
self.labelNode.Modified()
self.currentMessage = "WIP Code is done being executed..."
slicer.util.showStatusMessage(self.currentMessage)
def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
print "labelFileName : "+labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing "+labelFileName
else:
print "failed writing "+labelFileName
jstr = json.dumps(j,sort_keys=True, indent=4, separators=(',', ': '))
f = open(os.path.join(self.dataDirButton.directory, self.tilename + '.json'),'w')
f.write(jstr)
f.close()
def onWebSaveButtonClicked(self):
print "Web Save to be implemented...."
def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath, "Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def setupEditorWidget(self):
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent)
self.editorWidget.setup()
self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def loadTCGAData(self):
slicer.util.openAddVolumeDialog()
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fgrdVolID = red_cn.GetBackgroundVolumeID()
fgrdNode = slicer.util.getNode(fgrdVolID)
fMat=vtk.vtkMatrix4x4()
fgrdNode.GetIJKToRASDirectionMatrix(fMat)
bgrdName = fgrdNode.GetName() + '_gray'
self.tilename = fgrdNode.GetName() + '_gray'
self.parameterNode.SetParameter("SlicerPathology,tilename", self.tilename)
# Get dummy grayscale image
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputData(fgrdNode.GetImageData())
magnitude.Update()
bgrdNode = slicer.vtkMRMLScalarVolumeNode()
bgrdNode.SetImageDataConnection(magnitude.GetOutputPort())
bgrdNode.SetName(bgrdName)
bgrdNode.SetIJKToRASDirectionMatrix(fMat)
slicer.mrmlScene.AddNode(bgrdNode)
bgrdVolID = bgrdNode.GetID()
# Reset slice configuration
red_cn.SetForegroundVolumeID(fgrdVolID)
red_cn.SetBackgroundVolumeID(bgrdVolID)
red_cn.SetForegroundOpacity(1)
self.checkAndSetLUT()
print bgrdName
cv = slicer.util.getNode(bgrdName)
self.volumesLogic = slicer.modules.volumes.logic()
labelName = bgrdName+'-label'
refLabel = self.volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene,cv,labelName)
refLabel.GetDisplayNode().SetAndObserveColorNodeID(self.SlicerPathologyColorNode.GetID())
self.editorWidget.helper.setMasterVolume(cv)
def createUserInterface(self):
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Review your segmentation. Use the 3D Visualization slider to see your segmentation in context with your image. Use the Editor panel to apply spot edits to your segmentation. If you would like to start over, see the Restart box below"""
)
step_label.setWordWrap(True)
self.__primaryGroupBox = qt.QGroupBox()
self.__primaryGroupBox.setTitle('Information')
self.__primaryGroupBoxLayout = qt.QFormLayout(self.__primaryGroupBox)
self.__primaryGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__primaryGroupBox)
# self.__threshRange = slicer.qMRMLRangeWidget()
# self.__threshRange.decimals = 0
# self.__threshRange.singleStep = 1
# self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
# qt.QTimer.singleShot(0, self.killButton)
# ThreshGroupBox = qt.QGroupBox()
# ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
# ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
# ThreshGroupBoxLayout.addRow(self.__threshRange)
# self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.EditorWidget = EditorWidget(parent=editorWidgetParent)
self.EditorWidget.setup()
self.__layout.addRow(editorWidgetParent)
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveRegisteredImage = qt.QCheckBox()
self.__RemoveRegisteredImage.checked = True
self.__RemoveRegisteredImage.setToolTip(
"Delete your registered images.")
RestartGroupBoxLayout.addRow("Delete Registered images: ",
self.__RemoveRegisteredImage)
self.__RemoveNormalizedImages = qt.QCheckBox()
self.__RemoveNormalizedImages.checked = True
self.__RemoveNormalizedImages.setToolTip(
"Delete your normalized images.")
RestartGroupBoxLayout.addRow("Delete Normalized images: ",
self.__RemoveNormalizedImages)
self.__RemoveSubtractionMap = qt.QCheckBox()
self.__RemoveSubtractionMap.checked = True
self.__RemoveSubtractionMap.setToolTip("Delete your subtraction map.")
RestartGroupBoxLayout.addRow("Delete Subtraction map: ",
self.__RemoveSubtractionMap)
self.__RemoveCroppedMap = qt.QCheckBox()
self.__RemoveCroppedMap.checked = True
self.__RemoveCroppedMap.setToolTip(
"Delete the cropped version of your input volume.")
RestartGroupBoxLayout.addRow("Delete Cropped Volume: ",
self.__RemoveCroppedMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI you made with your markup points.")
RestartGroupBoxLayout.addRow("Delete Full ROI: ", self.__RemoveROI)
self.__RemoveThresholdedROI = qt.QCheckBox()
self.__RemoveThresholdedROI.checked = False
self.__RemoveThresholdedROI.setToolTip(
"Delete the intensity-thresholded version of your ROI.")
RestartGroupBoxLayout.addRow("Delete Thresholded ROI: ",
self.__RemoveThresholdedROI)
self.__RemoveMarkups = qt.QCheckBox()
self.__RemoveMarkups.checked = True
self.__RemoveMarkups.setToolTip(
"Delete the markup points you used to create your 3D ROI.")
RestartGroupBoxLayout.addRow("Delete Markup Points: ",
self.__RemoveMarkups)
self.__RemoveModels = qt.QCheckBox()
self.__RemoveModels.checked = True
self.__RemoveModels.setToolTip(
"Delete the 3D model you created from your markup points.")
RestartGroupBoxLayout.addRow("Delete 3D Model: ", self.__RemoveModels)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
class SlicerPathologyWidget(ScriptedLoadableModuleWidget, ModuleWidgetMixin):
def __init__(self, parent=None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.resourcesPath = os.path.join(
slicer.modules.slicerpathology.path.replace(
self.moduleName + ".py", ""), 'Resources')
self.modulePath = os.path.dirname(
slicer.util.modulePath(self.moduleName))
self.currentStep = 1
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# this section is for custom color box
infoGroupBox = qt.QWidget()
hbox = qt.QHBoxLayout()
hbox.setMargin(0)
self.studySelectionGroupBoxLayout = qt.QGridLayout()
infoGroupBox.setLayout(hbox)
self.studySelectionGroupBoxLayout.addWidget(infoGroupBox, 0, 3, 1, 1)
infoIcon = qt.QPixmap(
os.path.join(self.resourcesPath, 'Icons', 'icon-infoBox.png'))
self.customLUTInfoIcon = qt.QLabel()
self.customLUTInfoIcon.setPixmap(infoIcon)
self.customLUTInfoIcon.setSizePolicy(PythonQt.QtGui.QSizePolicy())
hbox.addWidget(self.customLUTInfoIcon)
self.customLUTLabel = qt.QLabel()
hbox.addWidget(self.customLUTLabel)
# end of custom color box section
self.setupIcons()
self.setupTabBarNavigation()
self.setupsetupUI()
self.setupimageSelectionUI()
self.setupsegmentationUI()
self.setupsubmissionUI()
self.setupEditorWidget()
editUtil = EditorLib.EditUtil.EditUtil()
self.parameterNode = editUtil.getParameterNode()
# 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)
#
# scale factor for screen shots
#
self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
self.screenshotScaleFactorSliderWidget.singleStep = 1.0
self.screenshotScaleFactorSliderWidget.minimum = 1.0
self.screenshotScaleFactorSliderWidget.maximum = 50.0
self.screenshotScaleFactorSliderWidget.value = 1.0
self.screenshotScaleFactorSliderWidget.setToolTip(
"Set scale factor for the screen shots.")
parametersFormLayout.addRow("Screenshot scale factor",
self.screenshotScaleFactorSliderWidget)
#
# Apply Button
#
#self.applyButton = qt.QPushButton("Apply")
#self.applyButton.toolTip = "Run the algorithm."
#self.applyButton.enabled = False
#parametersFormLayout.addRow(self.applyButton)
# Add vertical spacer
self.layout.addStretch(1)
def cleanup(self):
pass
def onSelect(self):
self.applyButton.enabled = self.inputSelector.currentNode(
) and self.outputSelector.currentNode()
def onApplyButton(self):
logic = SlicerPathologyLogic()
enableScreenshotsFlag = self.enableScreenshotsFlagCheckBox.checked
screenshotScaleFactor = int(
self.screenshotScaleFactorSliderWidget.value)
print("Run the algorithm")
logic.run(self.inputSelector.currentNode(),
self.outputSelector.currentNode(), enableScreenshotsFlag,
screenshotScaleFactor)
def setupIcons(self):
self.setupIcon = self.createIcon('icon-setup.png')
self.imageSelectionIcon = self.createIcon('icon-imageselection.png')
self.segmentationIcon = self.createIcon('icon-segmentation.png')
self.submissionIcon = self.createIcon('icon-submission.png')
def setupTabBarNavigation(self):
self.tabWidget = qt.QTabWidget()
self.layout.addWidget(self.tabWidget)
setupGroupBox = qt.QGroupBox()
imageSelectionGroupBox = qt.QGroupBox()
segmentationGroupBox = qt.QGroupBox()
submissionGroupBox = qt.QGroupBox()
self.setupGroupBoxLayout = qt.QFormLayout()
self.imageSelectionGroupBoxLayout = qt.QFormLayout()
self.segmentationGroupBoxLayout = qt.QGridLayout()
self.submissionGroupBoxLayout = qt.QFormLayout()
setupGroupBox.setLayout(self.setupGroupBoxLayout)
imageSelectionGroupBox.setLayout(self.imageSelectionGroupBoxLayout)
segmentationGroupBox.setLayout(self.segmentationGroupBoxLayout)
submissionGroupBox.setLayout(self.submissionGroupBoxLayout)
self.tabWidget.setIconSize(qt.QSize(85, 30))
self.tabWidget.addTab(setupGroupBox, self.setupIcon, '')
self.tabWidget.addTab(imageSelectionGroupBox, self.imageSelectionIcon,
'')
self.tabWidget.addTab(segmentationGroupBox, self.segmentationIcon, '')
self.tabWidget.addTab(submissionGroupBox, self.submissionIcon, '')
self.tabWidget.connect('currentChanged(int)', self.onTabWidgetClicked)
self.setTabsEnabled([1, 2, 3, 4], True)
def onTabWidgetClicked(self, currentIndex):
if currentIndex == 0:
self.onStep1Selected()
if currentIndex == 1:
print "to be implemented..."
if currentIndex == 2:
print "to be implemented..."
if currentIndex == 3:
print "to be implemented..."
def setTabsEnabled(self, indexes, enabled):
for index in indexes:
self.tabWidget.childAt(1, 1).setTabEnabled(index, enabled)
def onStep1Selected(self):
#if self.checkStep3or4Leave() is True:
#return
if self.currentStep == 1:
return
self.currentStep = 1
self.setTabsEnabled([0], True)
self.setTabsEnabled([1, 2, 3], False)
def setupsetupUI(self):
self.setupUserName = qt.QLineEdit()
self.setupGroupBoxLayout.addRow("Username:"******"Password:"******"Load Data")
self.imageSelectionGroupBoxLayout.addWidget(self.loadDataButton)
self.loadDataButton.connect('clicked()', self.loadTCGAData)
print "Adding WIP Button!"
self.WIP = qt.QPushButton("WIP")
self.WIP.connect('clicked()', self.onWIPButtonClicked)
self.imageSelectionGroupBoxLayout.addWidget(self.WIP)
def setupsegmentationUI(self):
print "adding this for now..."
def setupsubmissionUI(self):
self.dataDirButton = ctk.ctkDirectoryButton()
self.submissionGroupBoxLayout.addWidget(qt.QLabel("Data directory:"))
self.submissionGroupBoxLayout.addWidget(self.dataDirButton)
self.SaveButton = qt.QPushButton("Save")
self.submissionGroupBoxLayout.addWidget(self.SaveButton)
self.SaveButton.connect('clicked()', self.onSaveButtonClicked)
self.WebSaveButton = qt.QPushButton("Submit to web")
self.submissionGroupBoxLayout.addWidget(self.WebSaveButton)
self.WebSaveButton.connect('clicked()', self.onWebSaveButtonClicked)
def onWIPButtonClicked(self):
print "WIP ME!"
from EditorLib import EditUtil
self.editUtil = EditorLib.EditUtil.EditUtil()
self.labelNode = self.editUtil.getLabelVolume()
print self.labelNode.GetImageData()
self.labelNode.GetImageData().Modified()
self.labelNode.Modified()
self.currentMessage = "WIP Code is done being executed..."
slicer.util.showStatusMessage(self.currentMessage)
def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter(
'QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory,
labelName + '.tif')
print "labelFileName : " + labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing " + labelFileName
else:
print "failed writing " + labelFileName
jstr = json.dumps(j, sort_keys=True, indent=4, separators=(',', ': '))
f = open(
os.path.join(self.dataDirButton.directory,
self.tilename + '.json'), 'w')
f.write(jstr)
f.close()
def onWebSaveButtonClicked(self):
print "Web Save to be implemented...."
def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(
slicer.modules.slicerpathology.path.replace(
self.moduleName + ".py", ""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath,
"Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes(
'vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n - 1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index, row in enumerate(reader):
success = colorNode.SetColor(index, row['Label'],
float(row['R']) / 255,
float(row['G']) / 255,
float(row['B']) / 255,
float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def setupEditorWidget(self):
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent)
self.editorWidget.setup()
self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def loadTCGAData(self):
slicer.util.openAddVolumeDialog()
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fgrdVolID = red_cn.GetBackgroundVolumeID()
fgrdNode = slicer.util.getNode(fgrdVolID)
fMat = vtk.vtkMatrix4x4()
fgrdNode.GetIJKToRASDirectionMatrix(fMat)
bgrdName = fgrdNode.GetName() + '_gray'
self.tilename = fgrdNode.GetName() + '_gray'
self.parameterNode.SetParameter("SlicerPathology,tilename",
self.tilename)
# Get dummy grayscale image
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputData(fgrdNode.GetImageData())
magnitude.Update()
bgrdNode = slicer.vtkMRMLScalarVolumeNode()
bgrdNode.SetImageDataConnection(magnitude.GetOutputPort())
bgrdNode.SetName(bgrdName)
bgrdNode.SetIJKToRASDirectionMatrix(fMat)
slicer.mrmlScene.AddNode(bgrdNode)
bgrdVolID = bgrdNode.GetID()
# Reset slice configuration
red_cn.SetForegroundVolumeID(fgrdVolID)
red_cn.SetBackgroundVolumeID(bgrdVolID)
red_cn.SetForegroundOpacity(1)
self.checkAndSetLUT()
print bgrdName
cv = slicer.util.getNode(bgrdName)
self.volumesLogic = slicer.modules.volumes.logic()
labelName = bgrdName + '-label'
refLabel = self.volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, cv, labelName)
refLabel.GetDisplayNode().SetAndObserveColorNodeID(
self.SlicerPathologyColorNode.GetID())
self.editorWidget.helper.setMasterVolume(cv)
class ReviewStep(BeersSingleStep):
def __init__(self, stepid):
""" This method creates a drop-down menu that includes the whole step.
The description also acts as a tooltip for the button. There may be
some way to override this. The initialize method is inherited
from ctk.
"""
self.initialize(stepid)
self.setName('6. Review')
self.setDescription(
'The segment from the subtraction map is now overlaid on your post-contrast image. Use the threshold bar below to edit the volume rendering node. Use the official Volume Rendering module for more specific visualization.'
)
self.__pNode = None
self.__vrDisplayNode = None
self.__threshold = [-1, -1]
# initialize VR stuff
self.__vrLogic = slicer.modules.volumerendering.logic()
self.__vrOpacityMap = None
self.__roiSegmentationNode = None
self.__roiVolume = None
self.__parent = super(ReviewStep, self)
self.__RestartActivated = False
def createUserInterface(self):
""" This step is mostly empty. A volume rendering threshold is added to be useful.
"""
self.__layout = self.__parent.createUserInterface()
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__threshRange.connect('valuesChanged(double,double)',
self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
ThreshGroupBox = qt.QGroupBox()
ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
ThreshGroupBoxLayout.addRow(self.__threshRange)
self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.__editorWidget = EditorWidget(parent=editorWidgetParent)
self.__editorWidget.setup()
self.__layout.addRow(editorWidgetParent)
self.hideUnwantedEditorUIElements()
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveCroppedSubtractionMap = qt.QCheckBox()
self.__RemoveCroppedSubtractionMap.checked = True
self.__RemoveCroppedSubtractionMap.setToolTip(
"Delete the cropped version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete cropped subtraction map: ",
self.__RemoveCroppedSubtractionMap)
self.__RemoveFullSubtracitonMap = qt.QCheckBox()
self.__RemoveFullSubtracitonMap.checked = True
self.__RemoveFullSubtracitonMap.setToolTip(
"Delete the full version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete full subtraction map: ",
self.__RemoveFullSubtracitonMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI resulting from your subtaction map.")
RestartGroupBoxLayout.addRow("Delete ROI: ", self.__RemoveROI)
# self.__RestartButton.setEnabled(0)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
def hideUnwantedEditorUIElements(self):
print self.__editorWidget.editBoxFrame
self.__editorWidget.volumes.hide()
print dir(self.__editorWidget)
print slicer.util.findChildren()
# for widgetName in slicer.util.findChildren(self.__editorWidget.editBoxFrame):
for widgetName in slicer.util.findChildren(self.__editorWidget.helper):
# widget = slicer.util.findChildren(self.__editorWidget.editBoxFrame)
print widgetName.objectName
# print widgetName.parent.name
# widgetName.hide()
for widget in [
'DrawEffectToolButton', 'RectangleEffectToolButton',
'IdentifyIslandsEffectToolButton',
'RemoveIslandsEffectToolButton', 'SaveIslandEffectToolButton',
'RowFrame2'
]:
slicer.util.findChildren(self.__editorWidget.editBoxFrame,
widget)[0].hide()
print slicer.util.findChildren('', 'EditColorFrame')
def Restart(self):
print self.__pNode
slicer.mrmlScene.RemoveNode(testVolume)
self.__pNode.SetParameter('baselineVolumeID', None)
self.__pNode.SetParameter('croppedSubtractVolumeID', None)
self.__pNode.SetParameter('croppedSubtractVolumeSegmentationID', None)
self.__pNode.SetParameter('followupVolumeID', None)
self.__pNode.SetParameter('roiNodeID', None)
self.__pNode.SetParameter('roiTransformID', None)
self.__pNode.SetParameter('subtractVolumeID', None)
self.__pNode.SetParameter('vrDisplayNodeID', None)
self.__pNode.SetParameter('thresholdRange', None)
if self.__RestartActivated:
self.workflow().goForward()
def onThresholdChanged(self):
if self.__vrOpacityMap == None:
return
range0 = self.__threshRange.minimumValue
range1 = self.__threshRange.maximumValue
self.__vrOpacityMap.RemoveAllPoints()
self.__vrOpacityMap.AddPoint(range0 - 75, 0)
self.__vrOpacityMap.AddPoint(range0, 1)
self.__vrOpacityMap.AddPoint(range1, 1)
self.__vrOpacityMap.AddPoint(range1 + 75, 0)
def killButton(self):
# ctk creates a useless final page button. This method gets rid of it.
bl = slicer.util.findChildren(text='ReviewStep')
ex = slicer.util.findChildren('', 'EditColorFrame')
if len(bl):
bl[0].hide()
if len(ex):
ex[0].hide()
print 'success'
else:
print 'fail'
self.__editLabelMapsFrame = slicer.util.findChildren(
'', 'EditLabelMapsFrame')[0]
self.__toolsColor = EditorLib.EditColor(self.__editLabelMapsFrame)
def validate(self, desiredBranchId):
# For now, no validation required.
self.__parent.validationSucceeded(desiredBranchId)
def onEntry(self, comingFrom, transitionType):
super(ReviewStep, self).onEntry(comingFrom, transitionType)
# self.__RestartButton.setEnabled(1)
self.__RestartActivated = True
pNode = self.parameterNode()
self.__pNode = pNode
self.__clippingModelNode = Helper.getNodeByID(
pNode.GetParameter('clippingModelNodeID'))
print self.__clippingModelNode
print pNode.GetParameter('clippingModelNodeID')
self.__baselineVolumeID = pNode.GetParameter('baselineVolumeID')
self.__followupVolumeID = pNode.GetParameter('followupVolumeID')
self.__subtractVolumeID = pNode.GetParameter('subtractVolumeID')
self.__roiNodeID = pNode.GetParameter('roiNodeID')
self.__followupVolumeNode = Helper.getNodeByID(self.__followupVolumeID)
self.__subtractVolumeNode = Helper.getNodeByID(self.__subtractVolumeID)
self.__vrDisplayNodeID = pNode.GetParameter('vrDisplayNodeID')
self.__roiSegmentationNode = Helper.getNodeByID(
pNode.GetParameter('croppedSubtractVolumeSegmentationID'))
self.__roiVolumeNode = Helper.getNodeByID(
pNode.GetParameter('croppedSubtractVolumeID'))
self.__editorWidget.setMergeNode(self.__roiSegmentationNode)
self.__clippingModelNode.GetDisplayNode().VisibilityOn()
followupRange = self.__followupVolumeNode.GetImageData(
).GetScalarRange()
ROIRange = self.__roiSegmentationNode.GetImageData().GetScalarRange()
if self.__vrDisplayNode == None:
if self.__vrDisplayNodeID != '':
self.__vrDisplayNode = slicer.mrmlScene.GetNodeByID(
self.__vrDisplayNodeID)
self.__vrDisplayNode.SetCroppingEnabled(1)
self.__followupVolumeNode.AddAndObserveDisplayNodeID(
self.__vrDisplayNode.GetID())
Helper.InitVRDisplayNode(self.__vrDisplayNode, self.__followupVolumeID,
self.__roiNodeID)
self.__threshRange.minimum = followupRange[0]
self.__threshRange.maximum = followupRange[1]
self.__threshRange.setValues(followupRange[1] / 3,
2 * followupRange[1] / 3)
self.__vrOpacityMap = self.__vrDisplayNode.GetVolumePropertyNode(
).GetVolumeProperty().GetScalarOpacity()
vrColorMap = self.__vrDisplayNode.GetVolumePropertyNode(
).GetVolumeProperty().GetRGBTransferFunction()
vrColorMap.RemoveAllPoints()
vrColorMap.AddRGBPoint(followupRange[0], 0.8, 0.8, 0)
vrColorMap.AddRGBPoint(followupRange[1], 0.8, 0.8, 0)
self.__vrDisplayNode.VisibilityOn()
# threshRange = [self.__threshRange.minimumValue, self.__threshRange.maximumValue]
# self.__vrOpacityMap.RemoveAllPoints()
# self.__vrOpacityMap.AddPoint(threshRange[1]/2-75,0)
# self.__vrOpacityMap.AddPoint(threshRange[1]/2,1)
# self.__vrOpacityMap.AddPoint(threshRange[1]/2+200,1)
# self.__vrOpacityMap.AddPoint(threshRange[1]/2+250,0)
Helper.SetBgFgVolumes(self.__baselineVolumeID, self.__followupVolumeID)
Helper.SetLabelVolume(self.__roiSegmentationNode.GetID())
self.onThresholdChanged()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
# extra error checking, in case the user manages to click ReportROI button
super(BeersSingleStep, self).onExit(goingTo, transitionType)
class qSlicerReportingModuleWidget:
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
self.parent.show()
else:
self.parent = parent
self.layout = parent.layout()
# Reference to the logic that Slicer instantiated
self.__logic = slicer.modules.reporting.logic()
if not self.__logic:
# create a new instance
self.__logic = slicer.modulelogic.vtkSlicerReportingModuleLogic()
# Get the location and initialize the DICOM DB
settings = qt.QSettings()
self.__dbFileName = settings.value("DatabaseDirectory", "")
if self.__dbFileName == "":
Helper.Warning("DICOM Database is not accessible.")
else:
self.__dbFileName = self.__dbFileName + "/ctkDICOM.sql"
if self.__logic.InitializeDICOMDatabase(self.__dbFileName):
Helper.Info('DICOM database initialized correctly!')
else:
Helper.Error('Failed to initialize DICOM database at ' +
self.__dbFileName)
if not self.__logic.GetMRMLScene():
# set the logic's mrml scene
self.__logic.SetMRMLScene(slicer.mrmlScene)
# for export
self.exportFileName = None
self.exportFileDialog = None
# initialize parameter node
self.__parameterNode = None
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLScriptedModuleNode')
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(
n, 'vtkMRMLScriptedModuleNode')
compNode.SetReferenceCount(compNode.GetReferenceCount() - 1)
nodeid = None
if compNode.GetModuleName() == 'Reporting':
self.__parameterNode = compNode
'Found existing Reporting parameter node'
break
if self.__parameterNode == None:
self.__parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.__parameterNode.SetModuleName('Reporting')
self.__parameterNode.SetSingletonTag('Reporting')
slicer.mrmlScene.AddNode(self.__parameterNode)
# keep active report and volume
self.__rNode = None
self.__vNode = None
if self.__parameterNode != None:
paramID = self.__parameterNode.GetID()
self.__logic.SetActiveParameterNodeID(paramID)
else:
Helper.Error('Unable to set logic active parameter node')
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
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 onEditorParameterNodeChanged(self, caller, event):
print('Editor parameter node changed')
label = self.__editorParameterNode.GetParameter('label')
if self.__rNode:
print("Updating report label")
self.__rNode.SetFindingLabel(int(label))
def enter(self):
# switch to Two-over-Two layout
lm = slicer.app.layoutManager()
lm.setLayout(26) # two over two
# update the logic to know that the module has been entered
self.__logic.GUIHiddenOff()
self.updateWidgetFromParameters()
# respond to error events
Helper.Info(
'Enter: Setting up connection to respond to logic error events')
hasObserver = self.__logic.HasObserver(vtk.vtkCommand.ErrorEvent)
if hasObserver == 0:
tag = self.__logic.AddObserver(vtk.vtkCommand.ErrorEvent,
self.respondToErrorMessage)
# print '\tobserver tag = ',tag
else:
Helper.Debug('Logic already has an observer on the ErrorEvent')
vnode = self.__volumeSelector.currentNode()
if vnode != None:
# print "Enter: setting active hierarchy from node ",vnode.GetID()
# update the logic active markup
self.__logic.SetActiveMarkupHierarchyIDFromNode(vnode)
self.updateTreeView()
self.__editorWidget.enter()
def exit(self):
self.updateParametersFromWidget()
Helper.Debug(
"Reporting Exit. Letting logic know that module has been exited")
# let the module logic know that the GUI is hidden, so that fiducials can go elsewehre
self.__logic.GUIHiddenOn()
# disconnect observation
self.__logic.RemoveObservers(vtk.vtkCommand.ErrorEvent)
self.__editorWidget.exit()
# respond to error events from the logic
def respondToErrorMessage(self, caller, event):
errorMessage = self.__logic.GetErrorMessage()
# inform user only if the message is not empty since vtkErrorMacro invokes this event as well
if errorMessage != None:
Helper.Debug('respondToErrorMessage, event = ' + str(event) +
', message =\n\t' + str(errorMessage))
errorDialog = qt.QErrorMessage(self.parent)
errorDialog.showMessage(errorMessage)
def onMRMLSceneChanged(self, mrmlScene):
if mrmlScene != self.__logic.GetMRMLScene():
self.__logic.SetMRMLScene(mrmlScene)
self.__logic.RegisterNodes()
self.__reportSelector.setMRMLScene(slicer.mrmlScene)
def updateTreeView(self):
# make the tree view update
if self.__useNewTreeView == 1:
self.__markupTreeView.updateTreeView()
else:
self.__markupTreeView.sceneModelType = "Displayable"
nodeTypes = [
'vtkMRMLDisplayableHierarchyNode',
'vtkMRMLAnnotationHierarchyNode', 'vtkMRMLAnnotationNode',
'vtkMRMLVolumeNode', 'vtkMRMLReportingReportNode'
]
self.__markupTreeView.nodeTypes = nodeTypes
self.__markupTreeView.listenNodeModifiedEvent = 1
self.__markupTreeView.sceneModelType = "Displayable"
# show these nodes even if they're hidden by being children of hidden hierarchy nodes
showHiddenNodeTypes = [
'vtkMRMLAnnotationNode', 'vtkMRMLVolumeNode',
'vtkMRMLDisplayableHierarchyNode'
]
self.__markupTreeView.model(
).showHiddenForTypes = showHiddenNodeTypes
# set the root to be the current report hierarchy root
if self.__rNode == None:
Helper.Error("updateTreeView: report node is not initialized!")
self.__markupTreeView.setRootNode(None)
return
else:
# the tree root node has to be a hierarchy node, so get the associated hierarchy node for the active report node
rootNode = slicer.vtkMRMLHierarchyNode(
).GetAssociatedHierarchyNode(self.__rNode.GetScene(),
self.__rNode.GetID())
if rootNode:
self.__markupTreeView.setRootNode(rootNode)
Helper.Debug("Setting tree view root to be " +
rootNode.GetID())
self.__markupTreeView.expandAll()
else:
Helper.Debug("Setting tree view root to be None")
self.__markupTreeView.setRootNode(None)
def onAnnotatedVolumeNodeChanged(self):
Helper.Debug("onAnnotatedVolumeNodeChanged()")
# get the current volume node
selectedVolume = self.__volumeSelector.currentNode()
# do the error checks
if selectedVolume == None or self.__rNode == None:
self.__volumeSelector.setCurrentNode(None)
return
uids = selectedVolume.GetAttribute('DICOM.instanceUIDs')
if uids == None:
Helper.ErrorPopup(
"Volume \"" + selectedVolume.GetName() +
"\" was not loaded from DICOM. Only volumes loaded from DICOM data can be annotated in the Reporting module."
)
self.__volumeSelector.setCurrentNode(None)
return
nSlices = selectedVolume.GetImageData().GetExtent()[-1] + 1
if nSlices != len(string.split(uids)):
Helper.ErrorPopup(
"Volume \"" + selectedVolume.GetName() +
"\" was loaded from multi-frame DICOM. Multi-frame DICOM is currently not supported by the Reporting module"
)
self.__volumeSelector.setCurrentNode(None)
return
# volume node is valid!
self.__vNode = selectedVolume
# update the report node
if self.__rNode != None:
self.__rNode.SetVolumeNodeID(self.__vNode.GetID())
self.__rNode.SetName('Report for Volume ' + self.__vNode.GetName())
Helper.SetBgFgVolumes(self.__vNode.GetID(), '')
Helper.RotateToVolumePlanes()
# go over all label nodes in the scene
# if there is a label that has the selected volume as associated node,
# initialize label selector to show that label
volumeNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLScalarVolumeNode')
volumeNodes.SetReferenceCount(volumeNodes.GetReferenceCount() - 1)
associatedLabelFound = False
for i in range(volumeNodes.GetNumberOfItems()):
vol = volumeNodes.GetItemAsObject(i)
associatedNodeID = vol.GetAttribute('AssociatedNodeID')
label = vol.GetAttribute('LabelMap')
if associatedNodeID == self.__vNode.GetID() and label == '1':
Helper.SetLabelVolume(vol.GetID())
associatedLabelFound = True
# if there is no associated label node, set the selector to none
if associatedLabelFound == False:
Helper.SetLabelVolume("")
orientation = Helper.GetScanOrderSliceName(self.__vNode)
message = "Slice viewers to be used for markup: "
for sliceViewer in orientation:
message = message + sliceViewer
if orientation.index(sliceViewer) < (len(orientation) - 1):
message = message + ", "
Helper.Debug(message)
self.__markupSliceText.text = message
# take the first one
self.__parameterNode.SetParameter('acquisitionSliceViewer',
orientation[0])
# print "Calling logic to set up hierarchy"
self.__logic.InitializeHierarchyForVolume(self.__vNode)
self.updateTreeView()
def onSegmentationNodeChanged(self):
Helper.Debug('onSegmentationNodeChanged()')
if self.__vNode == None:
Helper.Error(
'Should not be possible to select segmentation unless annotated volume is initialized!'
)
return
# get the current segmentation (label) node
sNode = self.__segmentationSelector.currentNode()
if sNode == None:
self.updateWidgets()
return
# if it's a new label, it should have/will be added to the report
# automatically
image = sNode.GetImageData()
if image == None:
Helper.initializeNewLabel(sNode, self.__vNode)
else:
# if it's an existing label, we need to check that the geometry matches
# the annotated label geometry, and if so, add it to the hierarchy
if Helper.GeometriesMatch(sNode, self.__vNode) == False:
Helper.ErrorPopup(
'The geometry of the segmentation label you attempted to select does not match the geometry of the volume being annotated! Please select a different label or create a new one.'
)
self.__segmentationSelector.setCurrentNode(None)
self.updateWidgets()
return
# assign the color LUT we use
dNode = sNode.GetDisplayNode()
dNode.SetAndObserveColorNodeID(self.__defaultColorNode.GetID())
sNode.SetAttribute('AssociatedNodeID', self.__vNode.GetID())
self.__logic.AddNodeToReport(sNode)
# assign the volume and the selected color to the editor parameter node
Helper.SetLabelVolume(sNode.GetID())
# TODO: disable adding new label node to the hierarchy if it was added
# outside the reporting module
self.__segmentationSelector.setCurrentNode(sNode)
self.__editorWidget.setMasterNode(self.__vNode)
self.__editorWidget.setMergeNode(sNode)
self.__editorParameterNode.Modified()
self.updateWidgets()
def onReportNodeChanged(self):
Helper.Debug("onReportNodeChanged()")
# cancel the active effect in Editor
if self.__editorWidget:
self.__editorWidget.toolsBox.defaultEffect()
# TODO
# -- initialize annotations and markup frames based on the report node
# content
self.__rNode = self.__reportSelector.currentNode()
self.__segmentationSelector.setCurrentNode(None)
# disable editor frame
self.onSegmentationNodeChanged()
if self.__rNode != None:
Helper.Debug("Selected report has changed to " +
self.__rNode.GetID())
if self.__rNode.GetDICOMDatabaseFileName() == "":
self.__rNode.SetDICOMDatabaseFileName(self.__dbFileName)
self.__parameterNode.SetParameter('reportID', self.__rNode.GetID())
# setup the default color node, if not initialized
if self.__rNode.GetColorNodeID() == "":
self.__rNode.SetColorNodeID(self.__defaultColorNode.GetID())
Helper.Debug('Set color node id to ' +
self.__defaultColorNode.GetID())
else:
Helper.Debug('Color node has already been set to ' +
self.__rNode.GetColorNodeID())
self.__logic.InitializeHierarchyForReport(self.__rNode)
self.updateTreeView()
vID = self.__rNode.GetVolumeNodeID()
if vID:
Helper.Debug('Have a volume node id in the report ' + vID +
', setting current volume node selector')
self.__vNode = slicer.mrmlScene.GetNodeByID(vID)
self.__volumeSelector.setCurrentNode(self.__vNode)
else:
Helper.Debug(
'Do not have a volume id in the report, setting current volume node selector to none'
)
# set the volume to be none
self.__vNode = None
self.__volumeSelector.setCurrentNode(None)
# hide the markups that go with other report nodes
self.__logic.HideAnnotationsForOtherReports(self.__rNode)
# update the GUI annotation name/label/color
self.updateWidgets()
# initialize the label used by the EditorWidget
if self.__editorParameterNode:
self.__editorParameterNode.SetParameter(
'label', str(self.__rNode.GetFindingLabel()))
'''
Load report and initialize GUI based on .xml report file content
'''
def onReportImport(self):
print('onReportImport here!!!')
# TODO
# -- popup file open dialog to choose the .xml AIM file
# -- warn the user if the selected report node is not empty
# -- populate the selected report node, initializing annotation template,
# content, markup hierarchy and content
if not self.__importAIMFile:
Helper.Debug('onReportImport: import file name not specified')
return
Helper.Debug('onReportImport')
# For now, always create a new report node
newReport = slicer.modulemrml.vtkMRMLReportingReportNode()
# always use the default color map
newReport.SetColorNodeID(self.__defaultColorNode.GetID())
slicer.mrmlScene.AddNode(newReport)
self.__reportSelector.setCurrentNode(newReport)
self.onReportNodeChanged()
# initialize the report hierarchy
# -- assume that report node has been created and is in the selector
Helper.LoadAIMFile(newReport.GetID(), self.__importAIMFile)
# update the GUI
Helper.Debug('onReportImport --> calling onReportNodeChanged()')
self.onReportNodeChanged()
def onSelectAIMFile(self):
# -- popup file dialog prompting output file
if not self.__importAIMFile:
fileName = qt.QFileDialog.getOpenFileName(self.parent,
"Choose AIM report", "/",
"XML Files (*.xml)")
else:
lastDir = self.__importAIMFile[0:string.
rfind(self.__importAIMFile, '/')]
fileName = qt.QFileDialog.getOpenFileName(self.parent,
"Choose AIM report",
lastDir,
"XML Files (*.xml)")
if fileName == '':
return
self.__importAIMFile = fileName
try:
label = string.split(fileName, '/')[-1]
except:
label = fileName
self.__aimFilePicker.text = label
'''
Save report to an xml file
'''
def onReportExport(self):
if self.__rNode == None:
return
Helper.Debug('onReportExport')
exportDirectory = self.__exportFolderPicker.directory
self.__rNode.SetStorageDirectoryName(exportDirectory)
Helper.Debug('Will export to ' + exportDirectory)
# use the currently selected report
self.__rNode = self.__reportSelector.currentNode()
if self.__rNode == None:
return
# -- traverse markup hierarchy and translate
retval = self.__logic.SaveReportToAIM(self.__rNode)
if retval == EXIT_FAILURE:
Helper.Error("Failed to save report to '" + exportDirectory + "'")
else:
Helper.Debug("Saved report to '" + exportDirectory + "'")
# This code is commented out because repeated insertion into the database
# leads to database lockout (illustrated in Testing/RepeatInsertTest.py).
# For now, the solution will be to import the created DICOM objects
# manually.
# attempt to insert each of the saved items into the database
#filesToInsert = glob.glob(exportDirectory+'/*')
#for f in filesToInsert:
# Helper.Debug('Inserting '+f+' into DICOM database...')
# slicer.dicomDatabase.insert(f)
# Helper.Debug('Done')
def updateWidgetFromParameters(self):
pn = self.__parameterNode
if pn == None:
return
reportID = pn.GetParameter('reportID')
if reportID != None:
self.__rNode = Helper.getNodeByID(reportID)
# AF: looks like this does not trigger event, why?
self.__reportSelector.setCurrentNode(self.__rNode)
def updateParametersFromWidget(self):
pn = self.__parameterNode
if pn == None:
return
report = self.__reportSelector.currentNode()
if report != None:
pn.SetParameter('reportID', report.GetID())
def updateWidgets(self):
Helper.Debug("updateWidgets()")
report = self.__rNode
volume = None
label = self.__segmentationSelector.currentNode()
if report != None:
self.__reportSelector.setCurrentNode(self.__rNode)
volume = slicer.mrmlScene.GetNodeByID(report.GetVolumeNodeID())
# TODO: get the label node from volume hieararchy
if volume != None:
self.__volumeSelector.setCurrentNode(volume)
self.__markupFrame.enabled = 1
self.__annotationsFrame.enabled = 1
self.__volumeSelector.enabled = 0
else:
self.__volumeSelector.enabled = 1
self.__markupFrame.enabled = 0
self.__annotationsFrame.enabled = 0
else:
self.__volumeSelector.enabled = 0
self.__markupFrame.enabled = 0
self.__annotationsFrame.enabled = 0
if not label:
self.__editorWidget.editLabelMapsFrame.collapsed = True
self.__editorWidget.editLabelMapsFrame.setEnabled(False)
else:
self.__editorWidget.editLabelMapsFrame.collapsed = False
self.__editorWidget.editLabelMapsFrame.setEnabled(True)
class qSlicerReportingModuleWidget:
def __init__( self, parent=None ):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
self.parent.show()
else:
self.parent = parent
self.layout = parent.layout()
# Reference to the logic that Slicer instantiated
self.__logic = slicer.modules.reporting.logic()
if not self.__logic:
# create a new instance
self.__logic = slicer.modulelogic.vtkSlicerReportingModuleLogic()
# Get the location and initialize the DICOM DB
settings = qt.QSettings()
self.__dbFileName = settings.value("DatabaseDirectory","")
if self.__dbFileName == "":
Helper.Warning("DICOM Database is not accessible.")
else:
self.__dbFileName = self.__dbFileName+"/ctkDICOM.sql"
if self.__logic.InitializeDICOMDatabase(self.__dbFileName):
Helper.Info('DICOM database initialized correctly!')
else:
Helper.Error('Failed to initialize DICOM database at '+self.__dbFileName)
if not self.__logic.GetMRMLScene():
# set the logic's mrml scene
self.__logic.SetMRMLScene(slicer.mrmlScene)
# for export
self.exportFileName = None
self.exportFileDialog = None
# initialize parameter node
self.__parameterNode = None
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLScriptedModuleNode')
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLScriptedModuleNode')
compNode.SetReferenceCount(compNode.GetReferenceCount() - 1)
nodeid = None
if compNode.GetModuleName() == 'Reporting':
self.__parameterNode = compNode
'Found existing Reporting parameter node'
break
if self.__parameterNode == None:
self.__parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.__parameterNode.SetModuleName('Reporting')
self.__parameterNode.SetSingletonTag('Reporting')
slicer.mrmlScene.AddNode(self.__parameterNode)
# keep active report and volume
self.__rNode = None
self.__vNode = None
if self.__parameterNode != None:
paramID = self.__parameterNode.GetID()
self.__logic.SetActiveParameterNodeID(paramID)
else:
Helper.Error('Unable to set logic active parameter node')
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
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 onEditorParameterNodeChanged(self,caller,event):
print('Editor parameter node changed')
label = self.__editorParameterNode.GetParameter('label')
if self.__rNode:
print("Updating report label")
self.__rNode.SetFindingLabel(int(label))
def enter(self):
# switch to Two-over-Two layout
lm = slicer.app.layoutManager()
lm.setLayout(26) # two over two
# update the logic to know that the module has been entered
self.__logic.GUIHiddenOff()
self.updateWidgetFromParameters()
# respond to error events
Helper.Info('Enter: Setting up connection to respond to logic error events')
hasObserver = self.__logic.HasObserver(vtk.vtkCommand.ErrorEvent)
if hasObserver == 0:
tag = self.__logic.AddObserver(vtk.vtkCommand.ErrorEvent, self.respondToErrorMessage)
# print '\tobserver tag = ',tag
else:
Helper.Debug('Logic already has an observer on the ErrorEvent')
vnode = self.__volumeSelector.currentNode()
if vnode != None:
# print "Enter: setting active hierarchy from node ",vnode.GetID()
# update the logic active markup
self.__logic.SetActiveMarkupHierarchyIDFromNode(vnode)
self.updateTreeView()
self.__editorWidget.enter()
def exit(self):
self.updateParametersFromWidget()
Helper.Debug("Reporting Exit. Letting logic know that module has been exited")
# let the module logic know that the GUI is hidden, so that fiducials can go elsewehre
self.__logic.GUIHiddenOn()
# disconnect observation
self.__logic.RemoveObservers(vtk.vtkCommand.ErrorEvent)
self.__editorWidget.exit()
# respond to error events from the logic
def respondToErrorMessage(self, caller, event):
errorMessage = self.__logic.GetErrorMessage()
# inform user only if the message is not empty since vtkErrorMacro invokes this event as well
if errorMessage != None:
Helper.Debug('respondToErrorMessage, event = '+str(event)+', message =\n\t'+str(errorMessage))
errorDialog = qt.QErrorMessage(self.parent)
errorDialog.showMessage(errorMessage)
def onMRMLSceneChanged(self, mrmlScene):
if mrmlScene != self.__logic.GetMRMLScene():
self.__logic.SetMRMLScene(mrmlScene)
self.__logic.RegisterNodes()
self.__reportSelector.setMRMLScene(slicer.mrmlScene)
def updateTreeView(self):
# make the tree view update
if self.__useNewTreeView == 1:
self.__markupTreeView.updateTreeView()
else:
self.__markupTreeView.sceneModelType = "Displayable"
nodeTypes = ['vtkMRMLDisplayableHierarchyNode', 'vtkMRMLAnnotationHierarchyNode', 'vtkMRMLAnnotationNode', 'vtkMRMLVolumeNode', 'vtkMRMLReportingReportNode']
self.__markupTreeView.nodeTypes = nodeTypes
self.__markupTreeView.listenNodeModifiedEvent = 1
self.__markupTreeView.sceneModelType = "Displayable"
# show these nodes even if they're hidden by being children of hidden hierarchy nodes
showHiddenNodeTypes = ['vtkMRMLAnnotationNode', 'vtkMRMLVolumeNode', 'vtkMRMLDisplayableHierarchyNode']
self.__markupTreeView.model().showHiddenForTypes = showHiddenNodeTypes
# set the root to be the current report hierarchy root
if self.__rNode == None:
Helper.Error("updateTreeView: report node is not initialized!")
self.__markupTreeView.setRootNode(None)
return
else:
# the tree root node has to be a hierarchy node, so get the associated hierarchy node for the active report node
rootNode = slicer.vtkMRMLHierarchyNode().GetAssociatedHierarchyNode(self.__rNode.GetScene(), self.__rNode.GetID())
if rootNode:
self.__markupTreeView.setRootNode(rootNode)
Helper.Debug("Setting tree view root to be " + rootNode.GetID())
self.__markupTreeView.expandAll()
else:
Helper.Debug("Setting tree view root to be None")
self.__markupTreeView.setRootNode(None)
def onAnnotatedVolumeNodeChanged(self):
Helper.Debug("onAnnotatedVolumeNodeChanged()")
# get the current volume node
selectedVolume = self.__volumeSelector.currentNode()
# do the error checks
if selectedVolume == None or self.__rNode == None:
self.__volumeSelector.setCurrentNode(None)
return
uids = selectedVolume.GetAttribute('DICOM.instanceUIDs')
if uids == None:
Helper.ErrorPopup("Volume \""+selectedVolume.GetName()+"\" was not loaded from DICOM. Only volumes loaded from DICOM data can be annotated in the Reporting module.")
self.__volumeSelector.setCurrentNode(None)
return
nSlices = selectedVolume.GetImageData().GetExtent()[-1]+1
if nSlices != len(string.split(uids)):
Helper.ErrorPopup("Volume \""+selectedVolume.GetName()+"\" was loaded from multi-frame DICOM. Multi-frame DICOM is currently not supported by the Reporting module")
self.__volumeSelector.setCurrentNode(None)
return
# volume node is valid!
self.__vNode = selectedVolume
# update the report node
if self.__rNode != None:
self.__rNode.SetVolumeNodeID(self.__vNode.GetID())
self.__rNode.SetName('Report for Volume '+self.__vNode.GetName())
Helper.SetBgFgVolumes(self.__vNode.GetID(), '')
Helper.RotateToVolumePlanes()
# go over all label nodes in the scene
# if there is a label that has the selected volume as associated node,
# initialize label selector to show that label
volumeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
volumeNodes.SetReferenceCount(volumeNodes.GetReferenceCount()-1)
associatedLabelFound = False
for i in range(volumeNodes.GetNumberOfItems()):
vol = volumeNodes.GetItemAsObject(i)
associatedNodeID = vol.GetAttribute('AssociatedNodeID')
label = vol.GetAttribute('LabelMap')
if associatedNodeID == self.__vNode.GetID() and label == '1':
Helper.SetLabelVolume(vol.GetID())
associatedLabelFound = True
# if there is no associated label node, set the selector to none
if associatedLabelFound == False:
Helper.SetLabelVolume("")
orientation = Helper.GetScanOrderSliceName(self.__vNode)
message = "Slice viewers to be used for markup: "
for sliceViewer in orientation:
message = message + sliceViewer
if orientation.index(sliceViewer) < (len(orientation) - 1 ):
message = message + ", "
Helper.Debug(message)
self.__markupSliceText.text = message
# take the first one
self.__parameterNode.SetParameter('acquisitionSliceViewer',orientation[0])
# print "Calling logic to set up hierarchy"
self.__logic.InitializeHierarchyForVolume(self.__vNode)
self.updateTreeView()
def onSegmentationNodeChanged(self):
Helper.Debug('onSegmentationNodeChanged()')
if self.__vNode == None:
Helper.Error('Should not be possible to select segmentation unless annotated volume is initialized!')
return
# get the current segmentation (label) node
sNode = self.__segmentationSelector.currentNode()
if sNode == None:
self.updateWidgets()
return
# if it's a new label, it should have/will be added to the report
# automatically
image = sNode.GetImageData()
if image == None:
Helper.initializeNewLabel(sNode, self.__vNode)
else:
# if it's an existing label, we need to check that the geometry matches
# the annotated label geometry, and if so, add it to the hierarchy
if Helper.GeometriesMatch(sNode, self.__vNode) == False:
Helper.ErrorPopup('The geometry of the segmentation label you attempted to select does not match the geometry of the volume being annotated! Please select a different label or create a new one.')
self.__segmentationSelector.setCurrentNode(None)
self.updateWidgets()
return
# assign the color LUT we use
dNode = sNode.GetDisplayNode()
dNode.SetAndObserveColorNodeID(self.__defaultColorNode.GetID())
sNode.SetAttribute('AssociatedNodeID',self.__vNode.GetID())
self.__logic.AddNodeToReport(sNode)
# assign the volume and the selected color to the editor parameter node
Helper.SetLabelVolume(sNode.GetID())
# TODO: disable adding new label node to the hierarchy if it was added
# outside the reporting module
self.__segmentationSelector.setCurrentNode(sNode)
self.__editorWidget.setMasterNode(self.__vNode)
self.__editorWidget.setMergeNode(sNode)
self.__editorParameterNode.Modified()
self.updateWidgets()
def onReportNodeChanged(self):
Helper.Debug("onReportNodeChanged()")
# cancel the active effect in Editor
if self.__editorWidget:
self.__editorWidget.toolsBox.defaultEffect()
# TODO
# -- initialize annotations and markup frames based on the report node
# content
self.__rNode = self.__reportSelector.currentNode()
self.__segmentationSelector.setCurrentNode(None)
# disable editor frame
self.onSegmentationNodeChanged()
if self.__rNode != None:
Helper.Debug("Selected report has changed to " + self.__rNode.GetID())
if self.__rNode.GetDICOMDatabaseFileName() == "":
self.__rNode.SetDICOMDatabaseFileName(self.__dbFileName)
self.__parameterNode.SetParameter('reportID', self.__rNode.GetID())
# setup the default color node, if not initialized
if self.__rNode.GetColorNodeID() == "":
self.__rNode.SetColorNodeID(self.__defaultColorNode.GetID())
Helper.Debug('Set color node id to '+self.__defaultColorNode.GetID())
else:
Helper.Debug('Color node has already been set to '+self.__rNode.GetColorNodeID())
self.__logic.InitializeHierarchyForReport(self.__rNode)
self.updateTreeView()
vID = self.__rNode.GetVolumeNodeID()
if vID:
Helper.Debug('Have a volume node id in the report ' + vID + ', setting current volume node selector')
self.__vNode = slicer.mrmlScene.GetNodeByID(vID)
self.__volumeSelector.setCurrentNode(self.__vNode)
else:
Helper.Debug('Do not have a volume id in the report, setting current volume node selector to none')
# set the volume to be none
self.__vNode = None
self.__volumeSelector.setCurrentNode(None)
# hide the markups that go with other report nodes
self.__logic.HideAnnotationsForOtherReports(self.__rNode)
# update the GUI annotation name/label/color
self.updateWidgets()
# initialize the label used by the EditorWidget
if self.__editorParameterNode:
self.__editorParameterNode.SetParameter('label',str(self.__rNode.GetFindingLabel()))
'''
Load report and initialize GUI based on .xml report file content
'''
def onReportImport(self):
print('onReportImport here!!!')
# TODO
# -- popup file open dialog to choose the .xml AIM file
# -- warn the user if the selected report node is not empty
# -- populate the selected report node, initializing annotation template,
# content, markup hierarchy and content
if not self.__importAIMFile:
Helper.Debug('onReportImport: import file name not specified')
return
Helper.Debug('onReportImport')
# For now, always create a new report node
newReport = slicer.modulemrml.vtkMRMLReportingReportNode()
# always use the default color map
newReport.SetColorNodeID(self.__defaultColorNode.GetID())
slicer.mrmlScene.AddNode(newReport)
self.__reportSelector.setCurrentNode(newReport)
self.onReportNodeChanged()
# initialize the report hierarchy
# -- assume that report node has been created and is in the selector
Helper.LoadAIMFile(newReport.GetID(),self.__importAIMFile)
# update the GUI
Helper.Debug('onReportImport --> calling onReportNodeChanged()')
self.onReportNodeChanged()
def onSelectAIMFile(self):
# -- popup file dialog prompting output file
if not self.__importAIMFile:
fileName = qt.QFileDialog.getOpenFileName(self.parent, "Choose AIM report","/","XML Files (*.xml)")
else:
lastDir = self.__importAIMFile[0:string.rfind(self.__importAIMFile,'/')]
fileName = qt.QFileDialog.getOpenFileName(self.parent, "Choose AIM report",lastDir,"XML Files (*.xml)")
if fileName == '':
return
self.__importAIMFile = fileName
try:
label = string.split(fileName,'/')[-1]
except:
label = fileName
self.__aimFilePicker.text = label
'''
Save report to an xml file
'''
def onReportExport(self):
if self.__rNode == None:
return
Helper.Debug('onReportExport')
exportDirectory = self.__exportFolderPicker.directory
self.__rNode.SetStorageDirectoryName(exportDirectory)
Helper.Debug('Will export to '+exportDirectory)
# use the currently selected report
self.__rNode = self.__reportSelector.currentNode()
if self.__rNode == None:
return
# -- traverse markup hierarchy and translate
retval = self.__logic.SaveReportToAIM(self.__rNode)
if retval == EXIT_FAILURE:
Helper.Error("Failed to save report to '"+exportDirectory+"'")
else:
Helper.Debug("Saved report to '"+exportDirectory+"'")
# This code is commented out because repeated insertion into the database
# leads to database lockout (illustrated in Testing/RepeatInsertTest.py).
# For now, the solution will be to import the created DICOM objects
# manually.
# attempt to insert each of the saved items into the database
#filesToInsert = glob.glob(exportDirectory+'/*')
#for f in filesToInsert:
# Helper.Debug('Inserting '+f+' into DICOM database...')
# slicer.dicomDatabase.insert(f)
# Helper.Debug('Done')
def updateWidgetFromParameters(self):
pn = self.__parameterNode
if pn == None:
return
reportID = pn.GetParameter('reportID')
if reportID != None:
self.__rNode = Helper.getNodeByID(reportID)
# AF: looks like this does not trigger event, why?
self.__reportSelector.setCurrentNode(self.__rNode)
def updateParametersFromWidget(self):
pn = self.__parameterNode
if pn == None:
return
report = self.__reportSelector.currentNode()
if report != None:
pn.SetParameter('reportID', report.GetID())
def updateWidgets(self):
Helper.Debug("updateWidgets()")
report = self.__rNode
volume = None
label = self.__segmentationSelector.currentNode()
if report != None:
self.__reportSelector.setCurrentNode(self.__rNode)
volume = slicer.mrmlScene.GetNodeByID(report.GetVolumeNodeID())
# TODO: get the label node from volume hieararchy
if volume != None:
self.__volumeSelector.setCurrentNode(volume)
self.__markupFrame.enabled = 1
self.__annotationsFrame.enabled = 1
self.__volumeSelector.enabled = 0
else:
self.__volumeSelector.enabled = 1
self.__markupFrame.enabled = 0
self.__annotationsFrame.enabled = 0
else:
self.__volumeSelector.enabled = 0
self.__markupFrame.enabled = 0
self.__annotationsFrame.enabled = 0
if not label:
self.__editorWidget.editLabelMapsFrame.collapsed = True
self.__editorWidget.editLabelMapsFrame.setEnabled(False)
else:
self.__editorWidget.editLabelMapsFrame.collapsed = False
self.__editorWidget.editLabelMapsFrame.setEnabled(True)
class VisAIReWidget:
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
def setup(self):
self.viewMode = 'compare'
self.compare0 = None
self.compare1 = None
self.sidebyside0 = None
self.sidebyside1 = None
# Instantiate and connect widgets ...
# 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 = "VisAIRe Reload"
self.layout.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."
#self.layout.addWidget(self.reloadAndTestButton)
#self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# entry for the rater name
label = qt.QLabel('Rater name:')
self.raterName = qt.QLineEdit()
self.layout.addWidget(label)
self.layout.addWidget(self.raterName)
# Configuration file picker
label = qt.QLabel('Configuration file:')
self.configFilePicker = qt.QPushButton('N/A')
self.configFilePicker.connect('clicked()',self.onConfigFileSelected)
self.layout.addWidget(label)
self.layout.addWidget(self.configFilePicker)
self.makeSnapshots = qt.QPushButton('Make snapshots')
self.layout.addWidget(self.makeSnapshots)
self.makeSnapshots.connect('clicked()', self.onMakeSnapshots)
# Opacity control
label = qt.QLabel('Foreground/Background opacity:')
self.opacitySlider = ctk.ctkSliderWidget()
self.opacitySlider.connect('valueChanged(double)',self.onOpacityChangeRequested)
self.opacitySlider.minimum = 0.
self.opacitySlider.maximum = 1.
self.opacitySlider.decimals = 1
self.opacitySlider.singleStep = 0.1
self.layout.addWidget(label)
self.layout.addWidget(self.opacitySlider)
# Button to switch between showing background/foreground volumes
self.bgfgButton = qt.QPushButton("Switch Background/Foreground")
self.layout.addWidget(self.bgfgButton)
self.bgfgButton.connect('clicked()', self.onbgfgButtonPressed)
# Select between compare view and editing layouts
groupLabel = qt.QLabel('Review mode:')
self.viewGroup = qt.QButtonGroup()
self.compareSelector = qt.QRadioButton('Compare view')
self.sideBySideSelector = qt.QRadioButton('Side by side')
self.compareSelector.setChecked(1)
self.viewGroup.addButton(self.compareSelector,1)
self.viewGroup.addButton(self.sideBySideSelector,2)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(self.compareSelector, self.sideBySideSelector)
self.layout.addWidget(self.groupWidget)
# step4Layout.addRow(groupLabel, self.viewGroup)
self.viewGroup.connect('buttonClicked(int)', self.onViewUpdateRequested)
# setup Editor widget
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent,showVolumesFrame=False)
self.editorWidget.setup()
self.editorParameterNode = self.editUtil.getParameterNode()
self.layout.addWidget(editorWidgetParent)
# Slice control
#label = qt.QLabel('Slice selector:')
#self.sliceSlider = ctk.ctkSliderWidget()
#self.sliceSlider.connect('valueChanged(double)',self.onSliceChangeRequested)
#self.sliceSlider.minimum = 0.
#self.sliceSlider.maximum = 1.
#self.sliceSlider.decimals = 1
#self.sliceSlider.singleStep = 0.1
#self.layout.addWidget(label)
#self.layout.addWidget(self.opacitySlider)
# Collapsible button to keep the content of the form
self.evaluationFrame = ctk.ctkCollapsibleButton()
self.evaluationFrame.text = "Assessment Form"
self.evaluationFrame.collapsed = 0
self.evaluationFrameLayout = qt.QFormLayout(self.evaluationFrame)
self.layout.addWidget(self.evaluationFrame)
self.formEntries = []
self.questions = {'Improved compared to non-registered?':'binary','Diagnostic quality?':'binary','Error quantification (if available)':'numeric'}
self.formEntryMapper = qt.QSignalMapper()
self.formEntryMapper.connect('mapped(const QString&)', self.entrySelected)
self.maxFormEntries = 30
for i in range(self.maxFormEntries):
# populate the assessment form
# create a new sub-frame with the questions
cb = ctk.ctkCollapsibleButton()
cb.visible = False
cb.collapsed = True
self.formEntries.append(cb)
self.formEntryMapper.setMapping(cb, str(i))
cb.connect('contentsCollapsed(bool)', self.formEntryMapper, 'map()')
layout = qt.QFormLayout(cb)
self.evaluationFrameLayout.addRow(cb)
for (q,c) in self.questions.items():
if c == 'binary':
self.addBinaryEntry(q, layout)
elif c == 'numeric':
self.addNumericEntry(q, layout)
# Save button
self.doneButton = qt.QPushButton("Save")
self.doneButton.toolTip = "Click this when done."
self.layout.addWidget(self.doneButton)
self.doneButton.connect('clicked(bool)', self.onDoneButtonClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Initialize internal persistent variables
self.configFile = None
self.movingVolume = None
self.perVolumeForms = []
self.fixedVolumes = []
self.registeredVolumes = []
self.transforms = []
self.caseName = None
# add custom layout for comparing two pairs of volumes
compareViewTwoRows ="<layout type=\"vertical\">"
for i in range(2):
compareViewTwoRows = compareViewTwoRows+" <item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"Compare"+str(i)+"\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">"+str(i)+"</property>\
<property name=\"viewcolor\" action=\"default\">#E17012</property>\
<property name=\"lightboxrows\" action=\"default\">1</property>\
<property name=\"lightboxcolumns\" action=\"default\">6</property>\
<property name=\"lightboxrows\" action=\"relayout\">1</property>\
<property name=\"lightboxcolumns\" action=\"relayout\">6</property>\
</view>\
</item>"
compareViewTwoRows = compareViewTwoRows+"</layout>"
sideBySide = "<layout type=\"horizontal\">\
<item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"SideBySide0\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">Moving</property>\
<property name=\"viewcolor\" action=\"default\">#F34A33</property>\
</view>\
</item>\
<item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"SideBySide1\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">Reference</property>\
<property name=\"viewcolor\" action=\"default\">#EDD54C</property>\
</view>\
</item>\
</layout>"
print(sideBySide)
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
self.layoutNode = layoutNodes.GetItemAsObject(0)
self.CompareLayout = 123
self.ContouringLayout = 124
self.layoutNode.AddLayoutDescription(self.CompareLayout,compareViewTwoRows)
self.layoutNode.AddLayoutDescription(self.ContouringLayout,sideBySide)
self.layoutNode.SetViewArrangement(self.ContouringLayout)
self.layoutNode.SetViewArrangement(self.CompareLayout)
sliceCompositeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
sliceCompositeNodes.SetReferenceCount(sliceCompositeNodes.GetReferenceCount()-1)
sliceNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
sliceNodes.SetReferenceCount(sliceNodes.GetReferenceCount()-1)
for i in range(sliceCompositeNodes.GetNumberOfItems()):
scn = sliceCompositeNodes.GetItemAsObject(i)
sn = sliceNodes.GetItemAsObject(i)
sn.SetUseLabelOutline(1)
if sn.GetName() == 'Compare0':
self.compare0 = scn
if sn.GetName() == 'Compare1':
self.compare1 = scn
if sn.GetName() == 'SideBySide0':
self.sidebyside0 = scn
if sn.GetName() == 'SideBySide1':
self.sidebyside1 = scn
def compositeNodeForWidget(self,name):
sliceCompositeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
sliceCompositeNodes.SetReferenceCount(sliceCompositeNodes.GetReferenceCount()-1)
sliceNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
sliceNodes.SetReferenceCount(sliceNodes.GetReferenceCount()-1)
for i in range(sliceCompositeNodes.GetNumberOfItems()):
scn = sliceCompositeNodes.GetItemAsObject(i)
sn = sliceNodes.GetItemAsObject(i)
sn.SetUseLabelOutline(1)
if sn.GetName() == name:
return scn
return None
def onViewUpdateRequested(self,id):
if id == 1:
self.viewMode = 'compare'
if id == 2:
self.viewMode = 'sidebyside'
self.entrySelected('0')
def onOpacityChangeRequested(self,value):
if self.viewMode == 'compare':
viewer0 = self.compare0
viewer1 = self.compare1
else:
viewer0 = self.sidebyside0
viewer1 = self.sidebyside1
if viewer0:
viewer0.SetForegroundOpacity(value)
if viewer1:
viewer1.SetForegroundOpacity(value)
def onbgfgButtonPressed(self):
if self.viewMode == 'compare':
viewer0 = self.compare0
viewer1 = self.compare1
else:
viewer0 = self.sidebyside0
viewer1 = self.sidebyside1
if viewer0.GetForegroundOpacity() == 1:
viewer0.SetForegroundOpacity(0)
viewer1.SetForegroundOpacity(0)
else:
viewer0.SetForegroundOpacity(1)
viewer1.SetForegroundOpacity(1)
def onMakeSnapshots(self):
for key in range(len(self.transforms)):
print('Key :'+str(key))
if not self.transforms[key]:
continue
self.makeSnapshotsForKey(key)
def makeSnapshotsForKey(self,name,snapshots=True):
movingID = self.movingVolume.GetID()
registeredID = self.registeredVolumes[int(name)].GetID()
fixedID = self.fixedVolumes[int(name)].GetID()
snapshotsDir = '/Users/fedorov/Temp/RegistrationSnapshots'
# assume this is full path, and the file name has the format
# <CaseID>_<junk>
caseId = os.path.split(self.configFileName)[-1].split('_')[0]
redSliceCompositeNode = self.compositeNodeForWidget('Red')
redSliceCompositeNode.SetForegroundOpacity(0)
self.setupLightbox(fixedID,movingID)
if snapshots:
snapshotName = os.path.join(snapshotsDir,caseId+'_'+str(name)+'_fixed.png')
self.makeSnapshot('Red',snapshotName)
self.setupLightbox(registeredID,movingID)
if snapshots:
snapshotName = os.path.join(snapshotsDir,caseId+'_'+str(name)+'_registered.png')
self.makeSnapshot('Red',snapshotName)
# make snapshots of the moving image for the first one
# (same for all keys)
if str(name) == '0':
redSliceCompositeNode.SetForegroundOpacity(1)
if snapshots:
snapshotName = os.path.join(snapshotsDir,caseId+'_moving.png')
self.makeSnapshot('Red',snapshotName)
def makeSnapshot(self, widgetName, snapshotName):
w = slicer.app.layoutManager().sliceWidget(widgetName)
if w:
qt.QPixmap().grabWidget(w).toImage().save(snapshotName)
def setupSliceWidget(self,swName):
w = slicer.app.layoutManager().sliceWidget(swName)
w.fitSliceToBackground()
sn = self.compositeNodeForWidget(swName)
sn.SetForegroundOpacity(0)
n = w.sliceLogic().GetSliceNode()
fov = n.GetFieldOfView()
n.SetFieldOfView(fov[0]/2.,fov[1]/2.,fov[2]/2.)
def entrySelected(self, name):
# prepare fixed volume label, if it is not available
if self.movingVolumeSeg and not self.fixedVolumesSegmentations[int(name)] and self.transforms[int(name)]:
tfm = self.transforms[int(name)]
print('Resampled segmentation is missing, but will resample with '+tfm.GetID())
resample = slicer.modules.brainsresample
volumesLogic = slicer.modules.volumes.logic()
labelName = self.fixedVolumes[int(name)].GetName()+'-label'
self.fixedVolumesSegmentations[int(name)] = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, self.fixedVolumes[int(name)], labelName)
parameters = {}
parameters['inputVolume'] = self.movingVolumeSeg.GetID()
parameters['referenceVolume'] = self.fixedVolumes[int(name)].GetID()
parameters['warpTransform'] = self.transforms[int(name)].GetID()
parameters['outputVolume'] = self.fixedVolumesSegmentations[int(name)]
parameters['pixelType'] = 'short'
parameters['interpolationMode'] = 'NearestNeighbor'
slicer.cli.run(resample, None, parameters, wait_for_completion = True)
# initialize the file name for the segmentation
storageNode = self.fixedVolumesSegmentations[int(name)].GetStorageNode()
fixedVolumeIdStr = str(self.fixedVolumeIds[int(name)])
segFileName = os.path.join(os.path.split(self.config.get('MovingData','Segmentation'))[0],fixedVolumeIdStr+'-label.nrrd')
storageNode.SetFileName(segFileName)
storageNode.SetWriteFileFormat('.nrrd')
# update the config file to keep reference to the newly created
# segmentation label
self.config.set('FixedData','Segmentation'+fixedVolumeIdStr,segFileName)
# setup the Editor
self.editorWidget.setMasterNode(self.fixedVolumes[int(name)])
self.editorWidget.setMergeNode(self.fixedVolumesSegmentations[int(name)])
self.editorParameterNode.Modified()
if self.viewMode == 'compare':
self.layoutNode.SetViewArrangement(self.CompareLayout)
viewer0 = self.compare0
viewer1 = self.compare1
else:
self.layoutNode.SetViewArrangement(self.ContouringLayout)
viewer0 = self.sidebyside0
viewer1 = self.sidebyside1
entry = self.formEntries[int(name)]
if entry.collapsed == True:
return
print 'Entry selected: ',name
for i in range(len(self.fixedVolumes)):
#self.formEntries[i].blockSignals(True)
if i == int(name):
self.formEntries[i].collapsed = False
continue
else:
self.formEntries[i].collapsed = True
#self.formEntries[i].blockSignals(False)
viewer0.SetLinkedControl(False)
viewer1.SetLinkedControl(False)
v0fgID = self.movingVolume.GetID()
v1fgID = self.registeredVolumes[int(name)].GetID()
bgID = self.fixedVolumes[int(name)].GetID()
print('Will be setting ids: '+v0fgID+','+v1fgID+','+bgID)
viewer0.SetForegroundVolumeID(v0fgID)
if self.movingVolumeSeg:
viewer0.SetLabelVolumeID(self.movingVolumeSeg.GetID())
viewer1.SetForegroundVolumeID(v1fgID)
# if segmentation is available for the registered node, display it
if self.fixedVolumesSegmentations[int(name)]:
viewer1.SetLabelVolumeID(self.fixedVolumesSegmentations[int(name)].GetID())
# otherwise, if the transform is available, resample the moving volume
# segmentation, populate the entry in the list of segmentations and
# initialize the view
viewer0.SetLinkedControl(True)
viewer1.SetLinkedControl(True)
viewer0.SetBackgroundVolumeID(bgID)
viewer1.SetBackgroundVolumeID(bgID)
def setupLightbox(self,fixedID,movingID):
lm = slicer.app.layoutManager()
lm.setLayout(6) # Red
w = lm.sliceWidget('Red')
cn = self.compositeNodeForWidget('Red')
cn.SetForegroundVolumeID(movingID)
cn.SetBackgroundVolumeID(fixedID)
slicer.app.processEvents()
sc = w.sliceController()
sc.setLightbox(3,6)
w.fitSliceToBackground()
slider = sc.children()[1].children()[-1]
n = w.sliceLogic().GetSliceNode()
fov = n.GetFieldOfView()
# zoom into the prostate region
n.SetFieldOfView(fov[0]/2.5,fov[1]/2.5,fov[2])
sc.setSliceOffsetValue(slider.minimum)
def initializeViews(self, name):
if self.viewMode == 'compare':
self.layoutNode.SetViewArrangement(self.CompareLayout)
viewer0 = self.compare0
viewer1 = self.compare1
else:
self.layoutNode.SetViewArrangement(self.ContouringLayout)
viewer0 = self.sidebyside0
viewer1 = self.sidebyside1
viewer0.SetLinkedControl(False)
viewer1.SetLinkedControl(False)
v0fgID = self.movingVolume.GetID()
v1fgID = self.registeredVolumes[int(name)].GetID()
bgID = self.fixedVolumes[int(name)].GetID()
print('Will be setting ids: '+v0fgID+','+v1fgID+','+bgID)
viewer0.SetForegroundVolumeID(v0fgID)
if self.movingVolumeSeg:
viewer0.SetLabelVolumeID(self.movingVolumeSeg.GetID())
viewer1.SetForegroundVolumeID(v1fgID)
# if segmentation is available for the registered node, display it
if self.fixedVolumesSegmentations[int(name)]:
viewer1.SetLabelVolumeID(self.fixedVolumesSegmentations[int(name)].GetID())
# otherwise, if the transform is available, resample the moving volume
# segmentation, populate the entry in the list of segmentations and
# initialize the view
viewer0.SetLinkedControl(True)
viewer1.SetLinkedControl(True)
viewer0.SetBackgroundVolumeID(bgID)
viewer1.SetBackgroundVolumeID(bgID)
def onConfigFileSelected(self):
if not self.configFile:
fileName = qt.QFileDialog.getOpenFileName(self.parent, "Choose assessment for configuration file","/","Conf Files (*.ini)")
else:
lastDir = self.configFile[0:string.rfind(self.configFile,'/')]
fileName = qt.QFileDialog.getOpenFileName(self.parent, "Choose assessment for configuration file",lastDir,"Conf Files (*.ini)")
if fileName == '':
return
self.configFile = fileName
try:
label = string.split(fileName,'/')[-1]
except:
label = fileName
self.configFilePicker.text = label
self.initFromFile(fileName)
def initFromFile(self, fileName):
# parse config file and load all of the volumes referenced
slicer.mrmlScene.Clear(0)
self.clearForm()
self.fixedVolumes = []
self.fixedVolumeIds = []
self.registeredVolumes = []
self.movingVolume = None
self.movingVolumeSeg = None
self.config = config.SafeConfigParser()
cf = self.config
cf.optionxform = str
cf.read(fileName)
self.configFileName = fileName
assert cf.has_section('Info')
assert cf.has_section('MovingData')
assert cf.has_section('FixedData')
assert cf.has_section('RegisteredData')
# there should only be one moving image
self.movingVolume = slicer.util.loadVolume(cf.get('MovingData','Image'),returnNode=True)[1]
dn = self.movingVolume.GetDisplayNode()
mwl = [dn.GetWindow(), dn.GetLevel()]
# (optional) segmentation of the moving image
print('Set moving volume seg')
try:
self.movingVolumeSeg = slicer.util.loadLabelVolume(cf.get('MovingData','Segmentation'),{},returnNode=True)[1]
self.movingVolumeSeg.SetAttribute('LabelMap','1')
self.movingVolumeSeg.GetDisplayNode().SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
print('Setup color node: '+self.movingVolumeSeg.GetDisplayNode().GetColorNodeID())
except:
print(' ... to None')
self.movingVolumeSeg = None
# fixedVolumes: Slicer volume nodes corresponding to fixed images from the
# config file
# fixedVolumeIds: Each volume appears as "Image<id>" in the config file;
# this list stores the ids assigned to the volumes
# registeredVolumes: results of registration
# transforms: transformations mapping moving volume to the corresponding
# fixed volume
# fixedVolumesSegmentations: masks of a structure contoured in each of the
# fixed volumes
# movingFiducials: fiducial points corresponding to image landmarks
# fixedFiducials: fiducial points corresponding to the same landmarks in
# the fixed images
# and an arbitrary number of fixed images
fixedImageFiles = cf.options('FixedData')
print(str(fixedImageFiles))
for fi in fixedImageFiles:
if re.match('Image\d+',fi):
self.fixedVolumes.append(slicer.util.loadVolume(cf.get('FixedData',fi),returnNode=True)[1])
fixedDisplNode = self.fixedVolumes[-1].GetDisplayNode()
fixedDisplNode.SetAutoWindowLevel(0)
fixedDisplNode.SetWindow(mwl[0])
fixedDisplNode.SetLevel(mwl[1])
self.fixedVolumeIds.append(fi.split('Image')[1])
print('Fixed volumes: '+str(self.fixedVolumes))
# (optional) segmentations of the structure in the fixed images
self.registeredVolumes = [None] * len(self.fixedVolumes)
self.fixedVolumesSegmentations = [None] * len(self.fixedVolumes)
self.transforms = [None] * len(self.fixedVolumes)
for fvId in range(len(self.fixedVolumes)):
imageId = 'Image'+self.fixedVolumeIds[fvId]
segId = 'Segmentation'+self.fixedVolumeIds[fvId]
tfmId = 'Transform'+self.fixedVolumeIds[fvId]
try:
self.registeredVolumes[fvId] = slicer.util.loadVolume(cf.get('RegisteredData',imageId),{},returnNode=True)[1]
registeredDisplNode = self.registeredVolumes[fvId].GetDisplayNode()
registeredDisplNode.SetAutoWindowLevel(0)
registeredDisplNode.SetWindow(mwl[0])
registeredDisplNode.SetLevel(mwl[1])
except:
print('Failed to read RegisteredData/'+imageId)
pass
try:
self.fixedVolumesSegmentations[fvId] = slicer.util.loadLabelVolume(cf.get('FixedData',segId),{},returnNode=True)[1]
except:
print('Failed to read FixedData/'+segId)
pass
#try:
self.transforms[fvId] = slicer.util.loadTransform(cf.get('RegisteredData',tfmId),returnNode=True)[1]
#except:
# print('Failed to read RegisteredData/'+tfmId)
# pass
print('Number of fixed images: '+str(self.registeredVolumes))
print('Number of transformations: '+str(self.transforms))
print('Number of fixed image segmentations: '+str(self.fixedVolumesSegmentations))
assert len(self.fixedVolumes) == len(self.registeredVolumes)
self.caseName = cf.get('Info','CaseName')
self.evaluationFrame.text = "Assessment Form for "+self.caseName
# populate the assessment form
for fv in range(len(self.fixedVolumes)):
self.formEntries[fv].visible = True
self.formEntries[fv].text = self.fixedVolumes[fv].GetName()
# self.entrySelected('0')
def clearForm(self):
for i in range(self.maxFormEntries):
self.formEntries[i].visible = False
def onDoneButtonClicked(self):
# save the config file
self.config.write(open(self.configFileName,'w'))
return
path = self.configFile[0:string.rfind(self.configFile,'/')]
reportName = path+'/'+self.caseName+'-'+self.raterName.text+'-report.log'
report = open(reportName,'w')
report.write(self.configFile+'\n')
for i in range(len(self.fixedVolumes)):
report.write(self.fixedVolumes[i].GetName()+';')
item = 2
print 'num children: ',len(self.formEntries[i].children())
for (q,c) in self.questions.items():
report.write(q+';')
widget = self.formEntries[i].children()[item]
print widget
if c == 'binary':
checked = str(int(widget.checked))
report.write(str(checked)+';')
elif c == 'numeric':
error = str(widget.text)
report.write(error+';')
item = item+2
report.write('\n')
report.close()
def addBinaryEntry(self,question,layout):
self.questions[question] = 'binary'
label = qt.QLabel(question)
item = qt.QCheckBox()
layout.addRow(label,item)
#self.formEntries.append(item)
def addNumericEntry(self,question,layout):
self.questions[question] = 'numeric'
label = qt.QLabel(question)
item = qt.QLineEdit()
layout.addRow(label,item)
#self.formEntries.append(item)
def onReload(self,moduleName="VisAIRe"):
"""Generic reload method for any scripted module.
ModuleWizard will subsitute correct default moduleName.
"""
import imp, sys, os, slicer
widgetName = moduleName + "Widget"
# reload the source code
# - set source file path
# - load the module to the global space
filePath = eval('slicer.modules.%s.path' % moduleName.lower())
p = os.path.dirname(filePath)
if not sys.path.__contains__(p):
sys.path.insert(0,p)
fp = open(filePath, "r")
globals()[moduleName] = imp.load_module(
moduleName, fp, filePath, ('.py', 'r', imp.PY_SOURCE))
fp.close()
# rebuild the widget
# - find and hide the existing widget
# - create a new widget in the existing parent
parent = slicer.util.findChildren(name='%s Reload' % moduleName)[0].parent()
for child in parent.children():
try:
child.hide()
except AttributeError:
pass
# Remove spacer items
item = parent.layout().itemAt(0)
while item:
parent.layout().removeItem(item)
item = parent.layout().itemAt(0)
# delete the old widget instance
'''
widgetName = moduleName+'Widget'
if hasattr(globals()['slicer'].modules, widgetName):
getattr(globals()['slicer'].modules, widgetName).cleanup()
'''
# create new widget inside existing parent
globals()[widgetName.lower()] = eval(
'globals()["%s"].%s(parent)' % (moduleName, widgetName))
globals()[widgetName.lower()].setup()
def onReloadAndTest(self,moduleName="VisAIRe"):
self.onReload()
evalString = 'globals()["%s"].%sTest()' % (moduleName, moduleName)
tester = eval(evalString)
tester.runTest()
class SliceTrackerZFrameRegistrationWidget(ScriptedLoadableModuleWidget, ModuleWidgetMixin):
ZFRAME_MODEL_PATH = 'Resources/zframe/zframe-model.vtk'
ZFRAME_MODEL_NAME = 'ZFrameModel'
def __init__(self, parent=None):
ScriptedLoadableModuleWidget.__init__(self, parent)
self.logic = SliceTrackerZFrameRegistrationLogic()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.setupSliceWidget()
self.tag = None
self.zFrameModelNode = None
self.registrationGroupBox = qt.QGroupBox()
self.registrationGroupBoxLayout = qt.QFormLayout()
self.registrationGroupBox.setLayout(self.registrationGroupBoxLayout)
self.zFrameTemplateVolumeSelector = self.createComboBox(nodeTypes=["vtkMRMLScalarVolumeNode", ""], showChildNodeTypes=False,
selectNodeUponCreation=True, toolTip="Pick algorithm input.")
self.applyRegistrationButton = self.createButton("Run Registration")
self.registrationGroupBoxLayout.addRow("ZFrame template: ", self.zFrameTemplateVolumeSelector)
self.registrationGroupBoxLayout.addRow(self.applyRegistrationButton)
self.layout.addWidget(self.registrationGroupBox)
self.layout.addStretch()
self.setupConnections()
self.setupEditorWidget()
self.loadZFrameModel()
def loadZFrameModel(self):
collection = slicer.mrmlScene.GetNodesByName(self.ZFRAME_MODEL_NAME)
for index in range(collection.GetNumberOfItems()):
slicer.mrmlScene.RemoveNode(collection.GetItemAsObject(index))
self.modulePath = os.path.dirname(slicer.util.modulePath(self.moduleName))
zFrameModelPath = os.path.join(self.modulePath, self.ZFRAME_MODEL_PATH)
if not self.zFrameModelNode:
_, self.zFrameModelNode = slicer.util.loadModel(zFrameModelPath, returnNode=True)
self.zFrameModelNode.SetName(self.ZFRAME_MODEL_NAME)
slicer.mrmlScene.AddNode(self.zFrameModelNode)
modelDisplayNode = self.zFrameModelNode.GetDisplayNode()
modelDisplayNode.SetColor(1, 1, 0)
def setupSliceWidget(self, name):
self.redWidget = self.layoutManager.sliceWidget("Red")
self.redCompositeNode = self.redWidget.mrmlSliceCompositeNode()
self.redSliceView = self.redWidget.sliceView()
self.redSliceLogic = self.redWidget.sliceLogic()
self.redSliceNode = self.redSliceLogic.GetSliceNode()
def setupEditorWidget(self):
self.editorWidgetParent = slicer.qMRMLWidget()
self.editorWidgetParent.setLayout(qt.QVBoxLayout())
self.editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editUtil = EditorLib.EditUtil.EditUtil()
self.editorWidget = EditorWidget(parent=self.editorWidgetParent, showVolumesFrame=False)
self.editorWidget.setup()
self.editorParameterNode = self.editUtil.getParameterNode()
def setupConnections(self):
self.applyRegistrationButton.clicked.connect(self.runRegistration)
self.zFrameTemplateVolumeSelector.connect('currentNodeChanged(bool)', self.loadVolumeAndEnableEditor)
def processEvent(self, caller=None, event=None):
if event == "LeftButtonReleaseEvent":
interactor = self.redSliceView.interactorStyle().GetInteractor()
xy = interactor.GetEventPosition()
interactor.RemoveObserver(self.tag)
self.tag = None
self.onCenterPointSet(xy)
def loadVolumeAndEnableEditor(self):
zFrameTemplateVolume = self.zFrameTemplateVolumeSelector.currentNode()
self.redCompositeNode.SetBackgroundVolumeID(zFrameTemplateVolume.GetID())
interactor = self.redSliceView.interactorStyle().GetInteractor()
if self.tag:
interactor.RemoveObserver(self.tag)
self.tag = interactor.AddObserver(vtk.vtkCommand.LeftButtonReleaseEvent, self.processEvent, 1.0)
def onCenterPointSet(self, xy):
import vtk.util.numpy_support as vnp
zFrameTemplateVolume = self.zFrameTemplateVolumeSelector.currentNode()
volumesLogic = slicer.modules.volumes.logic()
zFrameTemplateMask = volumesLogic.CreateLabelVolume(slicer.mrmlScene, zFrameTemplateVolume, 'zFrameTemplateMask')
imageDataWorkingCopy = vtk.vtkImageData()
imageDataWorkingCopy.DeepCopy(zFrameTemplateMask.GetImageData())
newLabelNodeImage=vtk.vtkImageData()
newLabelNodeImage.AllocateScalars(vtk.VTK_SHORT, 1)
newLabelNodeImage.SetExtent(zFrameTemplateMask.GetImageData().GetExtent())
numpyArray = vnp.vtk_to_numpy(imageDataWorkingCopy.GetPointData().GetScalars()).reshape(imageDataWorkingCopy.GetDimensions()).transpose(2,1,0)
numpyArray[6:10,70:185,65:190].fill(1)
spacing = imageDataWorkingCopy.GetSpacing()
vtk_data = vnp.numpy_to_vtk(num_array=numpyArray.ravel(), deep=True, array_type=vtk.VTK_SHORT)
newLabelNodeImage.GetPointData().SetScalars(vtk_data)
dims = numpyArray.shape
newLabelNodeImage.SetDimensions(dims[2], dims[1], dims[0])
newLabelNodeImage.SetOrigin(0,0,0)
newLabelNodeImage.SetSpacing(spacing[0], spacing[1], spacing[2])
zFrameTemplateMask.SetAndObserveImageData(newLabelNodeImage)
# update the default label map to the generic anatomy colors
labelDisplayNode = zFrameTemplateMask.GetDisplayNode()
labelColorTable = slicer.util.getNode('GenericAnatomyColors')
labelDisplayNode.SetAndObserveColorNodeID(labelColorTable.GetID())
self.redCompositeNode.SetBackgroundVolumeID(zFrameTemplateVolume.GetID())
self.redCompositeNode.SetLabelVolumeID(zFrameTemplateMask.GetID())
self.redCompositeNode.SetLabelOpacity(0.6)
self.maskedVolume = self.createMaskedVolume(zFrameTemplateVolume, zFrameTemplateMask)
def createMaskedVolume(self, inputVolume, labelVolume):
maskedVolume = slicer.vtkMRMLScalarVolumeNode()
maskedVolume.SetName("maskedTemplateVolume")
slicer.mrmlScene.AddNode(maskedVolume)
params = {'InputVolume': inputVolume, 'MaskVolume': labelVolume, 'OutputVolume': maskedVolume}
slicer.cli.run(slicer.modules.maskscalarvolume, None, params, wait_for_completion=True)
return maskedVolume
def isRegistrationPossible(self):
return False
def runRegistration(self):
registration = OpenSourceZFrameRegistration(self.maskedVolume)
registration.runRegistration()
self.zFrameModelNode.SetAndObserveTransformNodeID(registration.outputTransform.GetID())
def setup(self):
self.viewMode = 'compare'
self.compare0 = None
self.compare1 = None
self.sidebyside0 = None
self.sidebyside1 = None
# Instantiate and connect widgets ...
# 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 = "VisAIRe Reload"
self.layout.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."
#self.layout.addWidget(self.reloadAndTestButton)
#self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# entry for the rater name
label = qt.QLabel('Rater name:')
self.raterName = qt.QLineEdit()
self.layout.addWidget(label)
self.layout.addWidget(self.raterName)
# Configuration file picker
label = qt.QLabel('Configuration file:')
self.configFilePicker = qt.QPushButton('N/A')
self.configFilePicker.connect('clicked()',self.onConfigFileSelected)
self.layout.addWidget(label)
self.layout.addWidget(self.configFilePicker)
self.makeSnapshots = qt.QPushButton('Make snapshots')
self.layout.addWidget(self.makeSnapshots)
self.makeSnapshots.connect('clicked()', self.onMakeSnapshots)
# Opacity control
label = qt.QLabel('Foreground/Background opacity:')
self.opacitySlider = ctk.ctkSliderWidget()
self.opacitySlider.connect('valueChanged(double)',self.onOpacityChangeRequested)
self.opacitySlider.minimum = 0.
self.opacitySlider.maximum = 1.
self.opacitySlider.decimals = 1
self.opacitySlider.singleStep = 0.1
self.layout.addWidget(label)
self.layout.addWidget(self.opacitySlider)
# Button to switch between showing background/foreground volumes
self.bgfgButton = qt.QPushButton("Switch Background/Foreground")
self.layout.addWidget(self.bgfgButton)
self.bgfgButton.connect('clicked()', self.onbgfgButtonPressed)
# Select between compare view and editing layouts
groupLabel = qt.QLabel('Review mode:')
self.viewGroup = qt.QButtonGroup()
self.compareSelector = qt.QRadioButton('Compare view')
self.sideBySideSelector = qt.QRadioButton('Side by side')
self.compareSelector.setChecked(1)
self.viewGroup.addButton(self.compareSelector,1)
self.viewGroup.addButton(self.sideBySideSelector,2)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(self.compareSelector, self.sideBySideSelector)
self.layout.addWidget(self.groupWidget)
# step4Layout.addRow(groupLabel, self.viewGroup)
self.viewGroup.connect('buttonClicked(int)', self.onViewUpdateRequested)
# setup Editor widget
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.editorWidget = EditorWidget(parent=editorWidgetParent,showVolumesFrame=False)
self.editorWidget.setup()
self.editorParameterNode = self.editUtil.getParameterNode()
self.layout.addWidget(editorWidgetParent)
# Slice control
#label = qt.QLabel('Slice selector:')
#self.sliceSlider = ctk.ctkSliderWidget()
#self.sliceSlider.connect('valueChanged(double)',self.onSliceChangeRequested)
#self.sliceSlider.minimum = 0.
#self.sliceSlider.maximum = 1.
#self.sliceSlider.decimals = 1
#self.sliceSlider.singleStep = 0.1
#self.layout.addWidget(label)
#self.layout.addWidget(self.opacitySlider)
# Collapsible button to keep the content of the form
self.evaluationFrame = ctk.ctkCollapsibleButton()
self.evaluationFrame.text = "Assessment Form"
self.evaluationFrame.collapsed = 0
self.evaluationFrameLayout = qt.QFormLayout(self.evaluationFrame)
self.layout.addWidget(self.evaluationFrame)
self.formEntries = []
self.questions = {'Improved compared to non-registered?':'binary','Diagnostic quality?':'binary','Error quantification (if available)':'numeric'}
self.formEntryMapper = qt.QSignalMapper()
self.formEntryMapper.connect('mapped(const QString&)', self.entrySelected)
self.maxFormEntries = 30
for i in range(self.maxFormEntries):
# populate the assessment form
# create a new sub-frame with the questions
cb = ctk.ctkCollapsibleButton()
cb.visible = False
cb.collapsed = True
self.formEntries.append(cb)
self.formEntryMapper.setMapping(cb, str(i))
cb.connect('contentsCollapsed(bool)', self.formEntryMapper, 'map()')
layout = qt.QFormLayout(cb)
self.evaluationFrameLayout.addRow(cb)
for (q,c) in self.questions.items():
if c == 'binary':
self.addBinaryEntry(q, layout)
elif c == 'numeric':
self.addNumericEntry(q, layout)
# Save button
self.doneButton = qt.QPushButton("Save")
self.doneButton.toolTip = "Click this when done."
self.layout.addWidget(self.doneButton)
self.doneButton.connect('clicked(bool)', self.onDoneButtonClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Initialize internal persistent variables
self.configFile = None
self.movingVolume = None
self.perVolumeForms = []
self.fixedVolumes = []
self.registeredVolumes = []
self.transforms = []
self.caseName = None
# add custom layout for comparing two pairs of volumes
compareViewTwoRows ="<layout type=\"vertical\">"
for i in range(2):
compareViewTwoRows = compareViewTwoRows+" <item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"Compare"+str(i)+"\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">"+str(i)+"</property>\
<property name=\"viewcolor\" action=\"default\">#E17012</property>\
<property name=\"lightboxrows\" action=\"default\">1</property>\
<property name=\"lightboxcolumns\" action=\"default\">6</property>\
<property name=\"lightboxrows\" action=\"relayout\">1</property>\
<property name=\"lightboxcolumns\" action=\"relayout\">6</property>\
</view>\
</item>"
compareViewTwoRows = compareViewTwoRows+"</layout>"
sideBySide = "<layout type=\"horizontal\">\
<item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"SideBySide0\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">Moving</property>\
<property name=\"viewcolor\" action=\"default\">#F34A33</property>\
</view>\
</item>\
<item>\
<view class=\"vtkMRMLSliceNode\" singletontag=\"SideBySide1\">\
<property name=\"orientation\" action=\"default\">Axial</property>\
<property name=\"viewlabel\" action=\"default\">Reference</property>\
<property name=\"viewcolor\" action=\"default\">#EDD54C</property>\
</view>\
</item>\
</layout>"
print(sideBySide)
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.SetReferenceCount(layoutNodes.GetReferenceCount()-1)
self.layoutNode = layoutNodes.GetItemAsObject(0)
self.CompareLayout = 123
self.ContouringLayout = 124
self.layoutNode.AddLayoutDescription(self.CompareLayout,compareViewTwoRows)
self.layoutNode.AddLayoutDescription(self.ContouringLayout,sideBySide)
self.layoutNode.SetViewArrangement(self.ContouringLayout)
self.layoutNode.SetViewArrangement(self.CompareLayout)
sliceCompositeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceCompositeNode')
sliceCompositeNodes.SetReferenceCount(sliceCompositeNodes.GetReferenceCount()-1)
sliceNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLSliceNode')
sliceNodes.SetReferenceCount(sliceNodes.GetReferenceCount()-1)
for i in range(sliceCompositeNodes.GetNumberOfItems()):
scn = sliceCompositeNodes.GetItemAsObject(i)
sn = sliceNodes.GetItemAsObject(i)
sn.SetUseLabelOutline(1)
if sn.GetName() == 'Compare0':
self.compare0 = scn
if sn.GetName() == 'Compare1':
self.compare1 = scn
if sn.GetName() == 'SideBySide0':
self.sidebyside0 = scn
if sn.GetName() == 'SideBySide1':
self.sidebyside1 = scn
class CMRToolkitWizardEndoSegmentationStep(CMRToolkitWizardStep):
def __init__(self, stepid):
self.initialize(stepid)
self.setName('2. Segmentation of endocardium')
self.setDescription(
'Segment the endocardium using the Editor paint tool and select the final label image to proceed.'
)
self.__parent = super(CMRToolkitWizardEndoSegmentationStep, self)
def killButton(self):
# Hide unneccesary button
bl = slicer.util.findChildren(text='AutomaticLeft*')
if len(bl):
bl[0].hide()
def createUserInterface(self):
from Editor import EditorWidget
self.__layout = self.__parent.createUserInterface()
#TODO: Create label map and set it for editing by user?
#volumesLogic = slicer.modules.volumes.logic()
#headLabel = volumesLogic.CreateLabelVolume( slicer.mrmlScene, head, head.GetName() + '-segmentation' )
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID( head.GetID() )
#selectionNode.SetReferenceActiveLabelVolumeID( headLabel.GetID() )
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
editorFrame = qt.QFrame()
editorFrame.setLayout(qt.QVBoxLayout())
palette = editorFrame.palette
bgColor = 230
palette.setColor(qt.QPalette.Background,
qt.QColor(bgColor, bgColor, bgColor))
editorFrame.setPalette(palette)
editorFrame.setAutoFillBackground(True)
self.__layout.addRow(editorFrame)
self.editorFrame = editorFrame
global editorWidget
self.editorWidget = EditorWidget(parent=self.editorFrame,
showVolumesFrame=True)
self.editorWidget.setup()
self.editorWidget.enter()
endoSegLabel = qt.QLabel('Endo Segmentation Image:')
self.__endoSegSelector = slicer.qMRMLNodeComboBox()
self.__endoSegSelector.toolTip = "Choose the endo segmentation label image."
self.__endoSegSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__endoSegSelector.setMRMLScene(slicer.mrmlScene)
self.__endoSegSelector.addEnabled = 0
self.__layout.addRow(endoSegLabel, self.__endoSegSelector)
#def startEditor(self):
# from Editor import EditorWidget
# editorWidget = EditorWidget(showVolumesFrame=True)
def validate(self, desiredBranchId):
self.__parent.validate(desiredBranchId)
endoSegVolume = self.__endoSegSelector.currentNode()
if endoSegVolume != None:
endoSegID = endoSegVolume.GetID()
pNode = self.parameterNode()
pNode.SetParameter('endoSegVolumeID', endoSegID)
Helper.SetLabelVolume(endoSegVolume.GetID())
self.__parent.validationSucceeded(desiredBranchId)
else:
self.__parent.validationFailed(
desiredBranchId, 'Error',
'Please select an endo segmentation image to proceed.')
def onEntry(self, comingFrom, transitionType):
super(CMRToolkitWizardEndoSegmentationStep,
self).onEntry(comingFrom, transitionType)
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
pNode = self.parameterNode()
#if goingTo.id() != 'AxialDilate':
# return
self.editorWidget.exit()
super(CMRToolkitWizardEndoSegmentationStep,
self).onExit(goingTo, transitionType)
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)
class ReviewStep(GBMWizardStep):
def __init__(self, stepid):
self.initialize(stepid)
self.setName('6. Review')
self.__vrDisplayNode = None
self.__threshold = [-1, -1]
# initialize VR stuff
self.__vrLogic = slicer.modules.volumerendering.logic()
self.__vrOpacityMap = None
self.__vrColorMap = None
self.__thresholdedLabelNode = None
self.__roiVolume = None
self.__parent = super(ReviewStep, self)
self.__RestartActivated = False
def createUserInterface(self):
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Review your segmentation. Use the 3D Visualization slider to see your segmentation in context with your image. Use the Editor panel to apply spot edits to your segmentation. If you would like to start over, see the Restart box below"""
)
step_label.setWordWrap(True)
self.__primaryGroupBox = qt.QGroupBox()
self.__primaryGroupBox.setTitle('Information')
self.__primaryGroupBoxLayout = qt.QFormLayout(self.__primaryGroupBox)
self.__primaryGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__primaryGroupBox)
# self.__threshRange = slicer.qMRMLRangeWidget()
# self.__threshRange.decimals = 0
# self.__threshRange.singleStep = 1
# self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
# qt.QTimer.singleShot(0, self.killButton)
# ThreshGroupBox = qt.QGroupBox()
# ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
# ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
# ThreshGroupBoxLayout.addRow(self.__threshRange)
# self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.EditorWidget = EditorWidget(parent=editorWidgetParent)
self.EditorWidget.setup()
self.__layout.addRow(editorWidgetParent)
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveRegisteredImage = qt.QCheckBox()
self.__RemoveRegisteredImage.checked = True
self.__RemoveRegisteredImage.setToolTip(
"Delete your registered images.")
RestartGroupBoxLayout.addRow("Delete Registered images: ",
self.__RemoveRegisteredImage)
self.__RemoveNormalizedImages = qt.QCheckBox()
self.__RemoveNormalizedImages.checked = True
self.__RemoveNormalizedImages.setToolTip(
"Delete your normalized images.")
RestartGroupBoxLayout.addRow("Delete Normalized images: ",
self.__RemoveNormalizedImages)
self.__RemoveSubtractionMap = qt.QCheckBox()
self.__RemoveSubtractionMap.checked = True
self.__RemoveSubtractionMap.setToolTip("Delete your subtraction map.")
RestartGroupBoxLayout.addRow("Delete Subtraction map: ",
self.__RemoveSubtractionMap)
self.__RemoveCroppedMap = qt.QCheckBox()
self.__RemoveCroppedMap.checked = True
self.__RemoveCroppedMap.setToolTip(
"Delete the cropped version of your input volume.")
RestartGroupBoxLayout.addRow("Delete Cropped Volume: ",
self.__RemoveCroppedMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI you made with your markup points.")
RestartGroupBoxLayout.addRow("Delete Full ROI: ", self.__RemoveROI)
self.__RemoveThresholdedROI = qt.QCheckBox()
self.__RemoveThresholdedROI.checked = False
self.__RemoveThresholdedROI.setToolTip(
"Delete the intensity-thresholded version of your ROI.")
RestartGroupBoxLayout.addRow("Delete Thresholded ROI: ",
self.__RemoveThresholdedROI)
self.__RemoveMarkups = qt.QCheckBox()
self.__RemoveMarkups.checked = True
self.__RemoveMarkups.setToolTip(
"Delete the markup points you used to create your 3D ROI.")
RestartGroupBoxLayout.addRow("Delete Markup Points: ",
self.__RemoveMarkups)
self.__RemoveModels = qt.QCheckBox()
self.__RemoveModels.checked = True
self.__RemoveModels.setToolTip(
"Delete the 3D model you created from your markup points.")
RestartGroupBoxLayout.addRow("Delete 3D Model: ", self.__RemoveModels)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
def hideUnwantedEditorUIElements(self):
""" We import the Editor module wholesale, which is useful, but it means
we have to manually hide parts we don't want after the fact..
If we could somehow import the segmentations module instead, that
might be better. On the other hand, first-time users often don't know
how to use the segmentations module.
"""
self.EditorWidget.setMergeNode(self.__thresholdedLabelNode)
self.EditorWidget.volumes.collapsed = True
self.EditorWidget.editLabelMapsFrame.collapsed = False
try:
self.EditorWidget.segmentEditorLabel.hide()
self.EditorWidget.infoIconLabel.hide()
except:
pass
def Restart(self):
# Unclick any selected editor tools..
self.__DefaultToolButton.click()
pNode = self.parameterNode()
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('clippingModelNodeID')))
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('clippingMarkupNodeID')))
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('vrDisplayNodeID')))
if self.__RemoveRegisteredImage.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('registrationVolumeID')))
if self.__RemoveNormalizedImages.checked:
for node in [
pNode.GetParameter('baselineNormalizeVolumeID'),
pNode.GetParameter('followupNormalizeVolumeID')
]:
if node != pNode.GetParameter(
'baselineVolumeID') and node != pNode.GetParameter(
'followupVolumeID'):
slicer.mrmlScene.RemoveNode(Helper.getNodeByID(node))
if self.__RemoveSubtractionMap.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('subtractVolumeID')))
if self.__RemoveCroppedMap.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('croppedVolumeID')))
if self.__RemoveROI.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(
pNode.GetParameter('nonThresholdedLabelID')))
if self.__RemoveThresholdedROI.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('thresholdedLabelID')))
if self.__RemoveMarkups.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('clippingMarkupNodeID')))
if self.__RemoveModels.checked:
slicer.mrmlScene.RemoveNode(
Helper.getNodeByID(pNode.GetParameter('clippingModelNodeID')))
pNode.SetParameter('baselineVolumeID', '')
pNode.SetParameter('followupVolumeID', '')
pNode.SetParameter('originalBaselineVolumeID', '')
pNode.SetParameter('originalFollowupVolumeID', '')
pNode.SetParameter('registrationVolumeID', '')
pNode.SetParameter('baselineNormalizeVolumeID', '')
pNode.SetParameter('followupNormalizeVolumeID', '')
pNode.SetParameter('subtractVolumeID', '')
pNode.SetParameter('clippingMarkupNodeID', '')
pNode.SetParameter('clippingModelNodeID', '')
pNode.SetParameter('outputList', '')
pNode.SetParameter('markupList', '')
pNode.SetParameter('modelList', '')
pNode.SetParameter('thresholdedLabelID', '')
pNode.SetParameter('croppedVolumeID', '')
pNode.SetParameter('nonThresholdedLabelID', '')
pNode.SetParameter('roiNodeID', '')
pNode.SetParameter('roiTransformID', '')
pNode.SetParameter('vrDisplayNodeID', '')
pNode.SetParameter('intensityThreshRangeMin', '')
pNode.SetParameter('intensityThreshRangeMax', '')
pNode.SetParameter('vrThreshRange', '')
Helper.SetLabelVolume('')
self.EditorWidget.exit()
if self.__RestartActivated:
self.workflow().goForward()
def onThresholdChanged(self):
if self.__vrOpacityMap == None:
return
range0 = self.__threshRange.minimumValue
range1 = self.__threshRange.maximumValue
self.__vrOpacityMap.RemoveAllPoints()
self.__vrOpacityMap.AddPoint(range0 - 75, 0)
self.__vrOpacityMap.AddPoint(range0, .02)
self.__vrOpacityMap.AddPoint(range1, .04)
self.__vrOpacityMap.AddPoint(range1 + 75, .1)
def killButton(self):
stepButtons = slicer.util.findChildren(className='ctkPushButton')
backButton = ''
nextButton = ''
for stepButton in stepButtons:
if stepButton.text == 'Next':
nextButton = stepButton
if stepButton.text == 'Back':
backButton = stepButton
nextButton.hide()
# ctk creates a useless final page button. This method gets rid of it.
bl = slicer.util.findChildren(text='ReviewStep')
ex = slicer.util.findChildren('', 'EditColorFrame')
if len(bl):
bl[0].hide()
if len(ex):
ex[0].hide()
self.__editLabelMapsFrame = slicer.util.findChildren(
'', 'EditLabelMapsFrame')[0]
self.__toolsColor = EditorLib.EditColor(self.__editLabelMapsFrame)
def validate(self, desiredBranchId):
# For now, no validation required.
self.__parent.validationSucceeded(desiredBranchId)
def onEntry(self, comingFrom, transitionType):
super(ReviewStep, self).onEntry(comingFrom, transitionType)
self.__RestartActivated = True
self.__DefaultToolButton = slicer.util.findChildren(
name='DefaultToolToolButton')[0]
pNode = self.parameterNode()
self.updateWidgetFromParameters(pNode)
Helper.SetBgFgVolumes(self.__visualizedID, '')
Helper.SetLabelVolume(self.__thresholdedLabelNode.GetID())
self.onThresholdChanged()
pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def updateWidgetFromParameters(self, pNode):
self.__clippingModelNode = Helper.getNodeByID(
pNode.GetParameter('clippingModelNodeID'))
self.__baselineVolumeID = pNode.GetParameter('baselineVolumeID')
self.__followupVolumeID = pNode.GetParameter('followupVolumeID')
self.__subtractVolumeID = pNode.GetParameter('subtractVolumeID')
self.__croppedVolumeID = pNode.GetParameter('cropedVolumeID')
self.__baselineVolumeNode = Helper.getNodeByID(self.__baselineVolumeID)
self.__followupVolumeNode = Helper.getNodeByID(self.__followupVolumeID)
self.__subtractVolumeNode = Helper.getNodeByID(self.__subtractVolumeID)
self.__vrDisplayNodeID = pNode.GetParameter('vrDisplayNodeID')
self.__thresholdedLabelNode = Helper.getNodeByID(
pNode.GetParameter('thresholdedLabelID'))
self.__clippingModelNode.GetDisplayNode().VisibilityOn()
if self.__followupVolumeID == None or self.__followupVolumeID == '':
self.__visualizedNode = self.__baselineVolumeNode
self.__visualizedID = self.__baselineVolumeID
else:
self.__visualizedID = self.__followupVolumeID
self.__visualizedNode = self.__followupVolumeNode
# vrRange = self.__visualizedNode.GetImageData().GetScalarRange()
# if self.__vrDisplayNode == None:
# if self.__vrDisplayNodeID != '':
# self.__vrDisplayNode = slicer.mrmlScene.GetNodeByID(self.__vrDisplayNodeID)
# Replace this, most likely.
# self.__visualizedNode.AddAndObserveDisplayNodeID(self.__vrDisplayNode.GetID())
# Helper.InitVRDisplayNode(self.__vrDisplayNode, self.__visualizedID, self.__croppedVolumeID)
# self.__threshRange.minimum = vrRange[0]
# self.__threshRange.maximum = vrRange[1]
# if pNode.GetParameter('vrThreshRangeMin') == '' or pNode.GetParameter('vrThreshRangeMin') == None:
# self.__threshRange.setValues(vrRange[1]/3, 2*vrRange[1]/3)
# else:
# self.__threshRange.setValues(float(pNode.GetParameter('vrThreshRangeMin')), float(pNode.GetParameter('vrThreshRangeMax')))
# self.__vrOpacityMap = self.__vrDisplayNode.GetVolumePropertyNode().GetVolumeProperty().GetScalarOpacity()
# self.__vrColorMap = self.__vrDisplayNode.GetVolumePropertyNode().GetVolumeProperty().GetRGBTransferFunction()
# self.__vrColorMap.RemoveAllPoints()
# self.__vrColorMap.AddRGBPoint(vrRange[0], 0.8, 0.8, 0)
# self.__vrColorMap.AddRGBPoint(vrRange[1], 0.8, 0.8, 0)
self.hideUnwantedEditorUIElements()
def onExit(self, goingTo, transitionType):
self.__DefaultToolButton.click()
super(GBMWizardStep, self).onExit(goingTo, transitionType)
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 __init__(self, parent=None, showVolumesFrame=True, activeTools=("DefaultTool", "PaintEffect", "DrawEffect", "LevelTracingEffect", "RectangleEffect", "EraseLabel", "PreviousCheckPoint", "NextCheckPoint")):
"""Constructor. Just invokes the parent's constructor"""
self.activeTools = activeTools
EditorWidget.__init__(self, parent, showVolumesFrame)
