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 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 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 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()
self.updateTreeView()
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 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 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 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 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 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 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 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 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 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 populateTreeView(self):
Helper.Debug('populateTreeView')
self.__markupTreeView.setHeader(self.__rNode)
return
Helper.Debug('populateTreeView')
if self.__rNode == None:
Helper.Debug('populateTreeView: no report node set!')
return
volumeID = self.__rNode.GetVolumeNodeID()
if volumeID == "":
Helper.Debug('populateTreeView: no active volume node id on report ' + self.__rNode.GetName())
return
volumeNode = Helper.getNodeByID(volumeID)
Helper.Debug('volumeID = ' + volumeID)
# find displayble nodes that are associated with this volume
numDisplayableNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLDisplayableNode")
nodeIDList = []
for n in range(numDisplayableNodes):
displayableNode = slicer.mrmlScene.GetNthNodeByClass(n, "vtkMRMLDisplayableNode")
inReport = self.__logic.IsInReport(displayableNode)
if inReport:
Helper.Debug('Found node associated with the volume node: ' + displayableNode.GetName())
nodeIDList.append(displayableNode.GetID())
print "Report: " + self.__rNode.GetName()
print "Volume: " + volumeNode.GetName()
row = 0
# volume name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(volumeNode.GetName())
self.__markupsModel.setItem(row,0,item)
self.items.append(item)
row += 1
# get the associated markups
for nodeID in nodeIDList:
node = Helper.getNodeByID(nodeID)
if node != None and node.IsA("vtkMRMLVolumeNode") and node.GetLabelMap() == 1:
Helper.Debug('Segmentation: ' + node.GetName())
item = qt.QStandardItem()
item.setEditable(False)
item.setText(node.GetName())
self.__markupsModel.setItem(row,0,item)
self.items.append(item)
row += 1
if node != None and node.IsA("vtkMRMLAnnotationNode"):
Helper.Debug('Annotation: ' + node.GetName())
# annotation name
item = qt.QStandardItem()
item.setEditable(False)
item.setText(node.GetName())
self.__markupsModel.setItem(row,0,item)
self.items.append(item)
# annotation visibility
item = qt.QStandardItem()
# todo: allow click to toggle visib
item.setEditable(False)
if node.GetDisplayVisibility() == 1:
item.setData(qt.QPixmap(":/Icons/Small/SlicerVisible.png"),qt.Qt.DecorationRole)
else:
item.setData(qt.QPixmap(":/Icons/Small/SlicerInvisible.png"),qt.Qt.DecorationRole)
self.__markupsModel.setItem(row,1,item)
self.items.append(item)
row += 1
def respondToAnnotationAdded(self, caller, event):
Helper.Debug("respondToAnnotationAdded: updating the tree view")
self.updateTreeView()
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 updateTreeView(self):
Helper.Debug('updateTreeView')
self.__markupTreeView.setHeader(self.__rNode)
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()
def test_RoundTrip(self):
"""
Test fiducial round trip to and from AIM XML file on disk
"""
print("ctest, please don't truncate my output: CTEST_FULL_OUTPUT")
# enter the module
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
# l = slicer.modulelogic.vtkSlicerReportingModuleLogic()
l = slicer.modules.reporting.logic()
l.GUIHiddenOff()
# testDataPath = os.path.normpath(os.path.join(os.path.realpath(__file__), "..", "..", "Prototype/TestData/DICOM.CT/")
print("Reporting round trip test, current working directory = " +
os.getcwd())
testDataPath = os.path.join(os.getcwd(),
"../../Testing/Temporary/DICOM.CT")
# testDataPath = "/projects/birn/nicole/Slicer4/Reporting/Prototype/TestData/DICOM.CT"
print("test data path = " + testDataPath)
# set up a new DICOM database
print("Creating a dicomDatabase!")
ddb = ctk.ctkDICOMDatabase()
if not ddb:
print("ERROR: failed to create a new dicom database!")
return
dbpath = slicer.app.slicerHome + '/Testing/Temporary/TestingDCMDB/ctkDICOM.sql'
print('database path set to ' + dbpath)
if not os.path.exists(os.path.dirname(dbpath)):
print('Creating dir ' + os.path.dirname(dbpath))
os.makedirs(os.path.dirname(dbpath))
ddb.openDatabase(dbpath, "ReportingTesting")
if not ddb.isOpen:
print("ERROR: failed to open a new dicom database at path " +
dbpath)
return
retval = ddb.initializeDatabase()
if not retval:
print("ERROR: failed to init database")
return
l.InitializeDICOMDatabase(dbpath)
testFileNames = []
for n in [487, 488, 489]:
filename = os.path.join(testDataPath,
"instance_" + str(n) + ".dcm")
print("Adding file " + filename)
testFileNames.append(filename)
# check to see if the test data is already in it
patients = ddb.patients()
if len(patients) == 0:
# add the files
for filename in testFileNames:
print("Inserting file " + filename)
retval = ddb.insert(filename)
patients = ddb.patients()
if len(patients) == 0:
print("ERROR: unable to add test files to database!")
print(str(testFileNames))
return
# get the UID for the series
study = ddb.studiesForPatient(patients[0])
series = ddb.seriesForStudy(study[0])
seriesUID = series[0]
# seriesUID = "1.2.392.200103.20080913.113635.2.2009.6.22.21.43.10.23432.1"
# seriesUID = "2.16.840.1.114362.1.759508.1251415878280.192"
# seriesUID = "1.3.12.2.1107.5.1.4.53031.30000011032906120157800000219"
print("For test, using the AIM sample volume with series UID of " +
seriesUID)
fileList = ddb.filesForSeries(seriesUID)
print("fileList = " + str(fileList))
if not fileList:
print("ERROR: sample series with id " + seriesUID +
" not found in database!")
return
# add a parameter node
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetModuleName('Reporting')
slicer.mrmlScene.AddNode(parameterNode)
# set it to be the active parameter node
l.SetActiveParameterNodeID(parameterNode.GetID())
#
# create a new report, make it the report in the parameter node, set up hierarchy
#
reportNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
reportNode.SetReferenceCount(reportNode.GetReferenceCount() - 1)
# set the color id
colorID = 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt'
reportNode.SetColorNodeID(colorID)
reportNode.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(reportNode)
parameterNode.SetParameter("reportID", reportNode.GetID())
print(
"Init hierarchy for report node, set parameter node to report id of "
+ reportNode.GetID())
l.InitializeHierarchyForReport(reportNode)
#
# get some sample data from the database
#
volId = 1
volumeNode = None
volName = 'AIM volume ' + str(volId)
print("Dicom data base = " + ddb)
slicer.dicomDatabase = ddb
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
volumeNode = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volumeNode.SetName(volName)
# print "volumeNode = ",volumeNode
print("Initialize Hierarchy For Volume with id " + volumeNode.GetID())
l.InitializeHierarchyForVolume(volumeNode)
print("---Now active mark up is " + l.GetActiveMarkupHierarchyID())
print("adding a fiducial")
#
# define a fiducial
#
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetVisible(1)
fidNode.SetLocked(0)
print("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0], startCoords[1],
startCoords[2])
print("Starting fiducial coordinates: " + str(startCoords))
# point it to the volume
fidNode.SetAttribute("AssociatedNodeID", volumeNode.GetID())
fidNode.SetScene(slicer.mrmlScene)
print("Adding text disp node")
fidNode.CreateAnnotationTextDisplayNode()
print("Adding point display node")
fidNode.CreateAnnotationPointDisplayNode()
print("add node:")
# slicer.mrmlScene.DebugOn()
# l.DebugOn()
slicer.mrmlScene.AddNode(fidNode)
print("getting slice uid")
uid = l.GetSliceUIDFromMarkUp(fidNode)
print("fidNode uid = " + uid)
#
# create a label volume
#
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateLabelVolume(slicer.mrmlScene,
volumeNode, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
l.AddNodeToReport(labelNode)
# initialize image content
labelImage = labelNode.GetImageData()
extent = labelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
if pixelCounter in initializedSegmentationVoxels:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 1)
else:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 0)
pixelCounter = pixelCounter + 1
# test save to mrml
# slicer.mrmlScene.SetURL('/spl/tmp/nicole/Testing/aim/RoundTripTest.mrml')
# slicer.mrmlScene.Commit()
#
# output AIM XML
#
dirName = slicer.app.slicerHome + '/Testing/Temporary/'
reportNode.SetStorageDirectoryName(dirName)
print("Saving report to " + dirName)
retval = l.SaveReportToAIM(reportNode)
if (retval != 0):
print("ERROR: unable to save report to aim file " + dirName +
", retval=" + retval)
else:
print("Saved report to " + dirName)
self.assertEqual(retval, 0)
print("\n\n\nReloading aim file...")
#
# now clear the scene so can read in
#
# TBD: this causes a crash
# slicer.mrmlScene.Clear(0)
#
# load in the aim file
#
newReport = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
newReport.SetReferenceCount(newReport.GetReferenceCount() - 1)
# set the default color map
newReport.SetColorNodeID(colorID)
newReport.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(newReport)
parameterNode.SetParameter("reportID", newReport.GetID())
Helper.LoadAIMFile(newReport.GetID(), aimFileName)
# check the fiducial
endCoords = [0, 0, 0]
col = slicer.mrmlScene.GetNodesByClass("vtkMRMLAnnotationFiducialNode")
col.SetReferenceCount(col.GetReferenceCount() - 1)
# if the scene is not cleared, we should have 2 fiducials
nFiducials = col.GetNumberOfItems()
if nFiducials != 2:
print("Failed to read fiducial form the saved report!")
self.assertTrue(False)
f = col.GetItemAsObject(1)
f.GetFiducialCoordinates(endCoords)
print("Start Coords = " + str(startCoords[0]) + "," +
str(startCoords[1]) + "," + str(startCoords[2]))
print("End Coords = " + str(endCoords))
xdiff = endCoords[0] - startCoords[0]
ydiff = endCoords[1] - startCoords[1]
zdiff = endCoords[2] - startCoords[2]
diffTotal = xdiff + ydiff + zdiff
print(
"Difference between coordinates after loaded the aim file and value from before stored the aim file: "
+ str(xdiff) + "," + str(ydiff) + "," + str(zdiff) +
". Total difference = " + str(diffTotal))
if diffTotal > 0.1:
print("Fiducial coordinates error exceeds the allowed bounds")
self.assertTrue(False)
# check the label node
sceneVolumes = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLScalarVolumeNode")
sceneVolumes.SetReferenceCount(sceneVolumes.GetReferenceCount() - 1)
sceneLabels = []
for i in range(sceneVolumes.GetNumberOfItems()):
vol = sceneVolumes.GetItemAsObject(i)
if vol.GetLabelMap():
sceneLabels.append(vol)
if len(sceneLabels) != 2:
print(
"Scene does not have two label nodes after reloading from AIM!"
)
self.assertTrue(False)
newLabelNode = sceneLabels[1]
newLabelImage = newLabelNode.GetImageData()
extent = newLabelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
pixel = newLabelImage.GetScalarComponentAsFloat(i, j, k, 0)
if ((pixelCounter in initializedSegmentationVoxels)
and pixel != 1) or (not (
pixelCounter in initializedSegmentationVoxels)
and pixel != 0):
print("Segmentation content not recovered correctly!")
print("Pixel counter " + str(pixelCounter) +
" is set to " + str(pixel))
self.assertTrue(False)
pixelCounter = pixelCounter + 1
self.assertTrue(True)
