def __init__( self ):
super(VesselExtractionStep, self).__init__()
self.initialize( 'VesselExtractionStep' )
self.setName( 'Extract the vessels skeletons' )
self.setDescription('Extract the shape of the vessels of the input image')
self.createExtractVesselOutputConnected = False
self.createExtractVesselSeed = False
self.logic = SegmentTubesLogic()
class VesselExtractionStep( WorkflowStep ) :
# \todo Revise tooltips in GUI
def __init__( self ):
super(VesselExtractionStep, self).__init__()
self.initialize( 'VesselExtractionStep' )
self.setName( 'Extract the vessels skeletons' )
self.setDescription('Extract the shape of the vessels of the input image')
self.createExtractVesselOutputConnected = False
self.createExtractVesselSeed = False
self.logic = SegmentTubesLogic()
def setupUi( self ):
self.loadUi('VesselExtractionStep.ui')
saveIcon = self.style().standardIcon(qt.QStyle.SP_DialogSaveButton)
self.get('VesselExtractionSavePushButton').setVisible(False)
self.get('VesselExtractionSavePushButton').icon = saveIcon
self.get('VesselExtractionSavePushButton').connect('clicked()', self.saveVesselExtractionImage)
self.get('VesselExtractionOutputNodeComboBox').connect(
'nodeAddedByUser(vtkMRMLNode*)', self.logic.addDisplayNodes)
self.get('VesselExtractionApplyPushButton').connect('clicked(bool)', self.runVesselExtraction)
self.get('VesselExtractionGoToModulePushButton').connect('clicked()', self.openVesselExtractionModule)
def validate( self, desiredBranchId = None ):
validExtraction = True
cliNode = self.getCLINode(slicer.modules.segmenttubes)
validExtraction = (cliNode.GetStatusString() == 'Completed')
self.get('VesselExtractionSavePushButton').setVisible(validExtraction)
self.get('VesselExtractionSavePushButton').enabled = validExtraction
self.validateStep(validExtraction, desiredBranchId)
def onEntry(self, comingFrom, transitionType):
self.Workflow.updateLayout(self.Workflow.maximumNumberOfInput + 1)
self.get('VesselExtractionInputNodeComboBox').setCurrentNode(
self.step('VesselEnhancementStep').getVesselNode())
# Create output if necessary
if not self.createExtractVesselOutputConnected:
self.get('VesselExtractionInputNodeComboBox').connect('currentNodeChanged(vtkMRMLNode*)', self.createVesselExtractionOutput)
self.createExtractVesselOutputConnected = True
self.createVesselExtractionOutput()
if not self.createExtractVesselSeed:
self.get('VesselExtractionSeedPointNodeComboBox').connect('currentNodeChanged(vtkMRMLNode*)', self.createVesselExtractSeed)
self.createExtractVesselSeed = True
self.createVesselExtractSeed()
self.updateViews()
slicer.modules.markups.logic().StartPlaceMode(False)
super(VesselExtractionStep, self).onEntry(comingFrom, transitionType)
def saveVesselExtractionImage( self ):
self.saveFile('Tube objects', 'SpatialObject', '.tre', self.get('VesselExtractionOutputNodeComboBox'))
def createVesselExtractionOutput( self ):
self.createOutputIfNeeded( self.get('VesselExtractionInputNodeComboBox').currentNode(),
'tubes',
self.get('VesselExtractionOutputNodeComboBox') )
self.updateViews()
def createVesselExtractSeed( self ):
nodeName = 'VesselExtractionSeed'
node = self.getFirstNodeByNameAndClass(nodeName, 'vtkMRMLMarkupsFiducialNode')
if node == None:
nodeID = slicer.modules.markups.logic().AddNewFiducialNode(nodeName)
node = slicer.mrmlScene.GetNodeByID(nodeID)
node.SetMarkupLabelFormat('')
selectionNodeID = slicer.modules.markups.logic().GetSelectionNodeID()
selectionNode = slicer.mrmlScene.GetNodeByID(selectionNodeID)
selectionNode.SetReferenceActivePlaceNodeID(nodeID)
self.get('VesselExtractionSeedPointNodeComboBox').setCurrentNode(node)
def vesselExtractionParameters( self ):
parameters = self.getJsonParameters(slicer.modules.segmenttubes)
parameters['inputVolume'] = self.get('VesselExtractionInputNodeComboBox').currentNode()
parameters['OutputNode'] = self.get('VesselExtractionOutputNodeComboBox').currentNode()
parameters['outputTubeFile'] = self.logic.getFilenameFromNode(parameters['OutputNode'])
parameters['seedP'] = self.get('VesselExtractionSeedPointNodeComboBox').currentNode()
return parameters
def updateFromCLIParameters( self ):
cliNode = self.getCLINode(slicer.modules.segmenttubes)
self.get('VesselExtractionInputNodeComboBox').setCurrentNodeID(cliNode.GetParameterAsString('inputVolume'))
self.get('VesselExtractionOutputNodeComboBox').setCurrentNodeID(cliNode.GetParameterAsString('outputTubeFile'))
self.get('VesselExtractionSeedPointNodeComboBox').setCurrentNodeID(cliNode.GetParameterAsString('seedPhysicalPoint'))
def runVesselExtraction( self, run ):
parameters = {}
if run:
parameters = self.vesselExtractionParameters()
self.get('VesselExtractionApplyPushButton').setChecked(True)
else:
self.get('VesselExtractionApplyPushButton').enabled = False
self.logic.run(run, parameters, self.onVesselExtractionCLIModified)
def onVesselExtractionCLIModified( self, cliNode, *unused ):
if cliNode.GetStatusString() == 'Completed':
self.validate()
if not cliNode.IsBusy():
self.logic.removeObservers(self.onVesselExtractionCLIModified)
self.get('VesselExtractionApplyPushButton').setChecked(False)
self.get('VesselExtractionApplyPushButton').enabled = True
print 'Segment Tubes %s' % cliNode.GetStatusString()
self.Workflow.getProgressBar().setCommandLineModuleNode(cliNode)
def openVesselExtractionModule( self ):
self.openModule('SegmentTubes')
cliNode = self.getCLINode(slicer.modules.segmenttubes)
parameters = self.vesselExtractionParameters()
slicer.cli.setNodeParameters(cliNode, parameters)
def updateConfiguration( self, config ):
self.get('VesselExtractionInputLabel').setText('Enhanced ' + config['Workflow']['Organ'] + ' image')
self.get('VesselExtractiontSeedPointLabel').setText(config['Workflow']['Organ'] + ' vessel seed')
def getHelp( self ):
return '''Extract the vessels from the vessely image based on the seed
position and the seed image.
'''
def updateViews( self ):
viewDictionnary = {}
subDictionnary = {}
backgroundNode = self.get('VesselExtractionInputNodeComboBox').currentNode()
subDictionnary['Background'] = backgroundNode.GetID() if backgroundNode is not None else ''
subDictionnary['Foreground'] = ''
subDictionnary['Label'] = ''
viewDictionnary['Input1'] = subDictionnary
self.setViews(viewDictionnary)