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 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 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 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)
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 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')