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 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)
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 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 enter(self):
# switch to Two-over-Two layout
lm = slicer.app.layoutManager()
if lm != None:
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutTwoOverTwoView)
# 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 events')
hasObserver = self.__logic.HasObserver(self.__logic.ErrorEvent)
if hasObserver == 0:
tag = self.__logic.AddObserver(self.__logic.ErrorEvent, self.respondToErrorMessage)
# print '\tobserver tag = ',tag
else:
Helper.Debug('Logic already has an observer on the ErrorEvent')
# respond to logic annotation added events
hasObserver = self.__logic.HasObserver(self.__logic.AnnotationAdded)
if hasObserver == 0:
tag = self.__logic.AddObserver(self.__logic.AnnotationAdded, self.respondToAnnotationAdded)
vnode = self.volumeSelector.currentNode()
if vnode != None:
# print "Enter: updating the tree view"
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()
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()))
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 setHeader(self,reportNode):
"""Load the table widget with annotations for the report
"""
Helper.Debug('setHeader() called')
self.widget.clearContents()
self.widget.setColumnCount(2)
self.widget.setHorizontalHeaderLabels(['Markup','Visibility'])
self.widget.horizontalHeader().setResizeMode(0, qt.QHeaderView.Stretch)
self.widget.horizontalHeader().setResizeMode(1, qt.QHeaderView.Fixed)
self.widget.setEditTriggers(qt.QAbstractItemView.NoEditTriggers)
if not reportNode:
return
# get the volume node associated with this report
volumeID = reportNode.GetVolumeNodeID()
Helper.Debug('volumeID = '+volumeID)
if volumeID == "":
return
volumeNode = slicer.mrmlScene.GetNodeByID(volumeID)
if not volumeNode:
return
# get the annotations associated with this report
# find displayble nodes that are associated with this volume
numDisplayableNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLDisplayableNode")
nodeIDList = [volumeID]
for n in range(numDisplayableNodes):
displayableNode = slicer.mrmlScene.GetNthNodeByClass(n, "vtkMRMLDisplayableNode")
# how best to get at module widget logic?
Helper.Debug('Will check if in report here for '+displayableNode.GetID())
inReport = slicer.modules.reporting.logic().IsInReport(displayableNode)
Helper.Debug('Checked for report')
if inReport:
Helper.Debug('Found node associated with the report node: ' + displayableNode.GetName())
nodeIDList.append(displayableNode.GetID())
else:
Helper.Debug('Failed to found associated node')
self.widget.setRowCount(len(nodeIDList))
row = 0
for nodeID in nodeIDList:
node = Helper.getNodeByID(nodeID)
item = qt.QTableWidgetItem(node.GetName())
self.widget.setItem(row,0,item)
self.items.append(item)
if node.IsA("vtkMRMLAnnotationNode"):
item = qt.QTableWidgetItem()
# save the id for toggling visibility on the node
# TODO: make this more elegant instead of overloading the what's this role with the id
item.setData(qt.Qt.WhatsThisRole, node.GetID())
if node.GetDisplayVisibility() == 1:
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerVisible.png"))
else:
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerInvisible.png"))
self.widget.setItem(row,1,item)
self.items.append(item)
row += 1
def onItemClicked(self, item):
# column 0 is the name, do jump to annotation
if item.column() == 0:
# get the id from the item in column 1
idItem = self.widget.item(item.row(), 1)
if idItem == None:
# volumes don't have anything in this column
return
nodeID = idItem.data(qt.Qt.WhatsThisRole)
if nodeID == None:
return
controlPointsNode = slicer.mrmlScene.GetNodeByID(nodeID)
if controlPointsNode == None:
return
# is it an annotation?
if controlPointsNode.IsA('vtkMRMLAnnotationControlPointsNode') == 0:
return
# get the coordinates of this annotation
rasCoordinates = [0,0,0]
if controlPointsNode.IsA('vtkMRMLAnnotationFiducialNode'):
controlPointsNode.GetFiducialCoordinates(rasCoordinates)
if controlPointsNode.IsA('vtkMRMLAnnotationRulerNode'):
controlPointsNode.GetPosition1(rasCoordinates)
sliceNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLSliceNode')
if sliceNode != None:
Helper.Debug("Jumping to first point in annotation")
# jump the other slices and then this slice
sliceNode.JumpAllSlices(rasCoordinates[0],rasCoordinates[1],rasCoordinates[2])
sliceNode.JumpSlice(rasCoordinates[0],rasCoordinates[1],rasCoordinates[2])
# column 1 is the visibility column
if item.column() == 1:
# is it a displayable?
nodeID = item.data(qt.Qt.WhatsThisRole)
if id == None:
return
node = slicer.mrmlScene.GetNodeByID(nodeID)
if node == None:
return
# update the visibility and the eye icon
if node.GetDisplayVisibility() == 0:
node.SetDisplayVisibility(1)
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerVisible.png"))
else:
node.SetDisplayVisibility(0)
item.setData(qt.Qt.DecorationRole,qt.QPixmap(":/Icons/Small/SlicerInvisible.png"))
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
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()
def updateTreeView(self):
Helper.Debug('updateTreeView')
self.__markupTreeView.setHeader(self.__rNode)
def respondToAnnotationAdded(self, caller, event):
Helper.Debug("respondToAnnotationAdded: updating the tree view")
self.updateTreeView()
