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 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 + "'")
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 __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 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
volumesLogic = slicer.modules.volumes.logic()
geometryCheckString = volumesLogic.CheckForLabelVolumeValidity(self.__vNode, sNode)
if geometryCheckString != "":
newNodeAnswer = Helper.QuestionPopup('The geometry of the segmentation label you selected does not match the geometry of the volume being annotated!\nDo you want to create a new label to match the geometry, resampling data to fit?\n' + geometryCheckString)
if newNodeAnswer == True:
# create a new resampled label node from the input image
resampledSegmentationNode = volumesLogic.ResampleVolumeToReferenceVolume(sNode, self.__vNode)
# reselect it
self.segmentationSelector.setCurrentNode(resampledSegmentationNode)
# reset vars
sNode = self.segmentationSelector.currentNode()
Helper.InfoPopup('Created a new segmentation label named ' + sNode.GetName() + ' resampled from the input label map')
image = sNode.GetImageData()
else:
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()
self.updateTreeView()
