Exemplo n.º 1
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    def loadPhilipsAffinity3DUS(self, loadable):
        """Load files in the traditional Slicer manner
    using the volume logic helper class
    and the vtkITK archetype helper code
    """
        name = slicer.util.toVTKString(loadable.name)
        filePath = loadable.files[0]
        fileList = vtk.vtkStringArray()
        fileList.InsertNextValue(slicer.util.toVTKString(filePath))
        volumesLogic = slicer.modules.volumes.logic()
        outputVolume = volumesLogic.AddArchetypeScalarVolume(
            filePath, name, 0, fileList)

        # Override spacing, as GDCM cannot retreive image spacing correctly for this type of image
        ds = dicom.read_file(filePath, stop_before_pixels=True)
        outputSpacingStr = ds[findPrivateTag(ds, 0x200d, 0x03,
                                             "Philips US Imaging DD 036")]
        outputVolume.SetSpacing(float(outputSpacingStr[0]),
                                float(outputSpacingStr[1]),
                                float(outputSpacingStr[2]))

        appLogic = slicer.app.applicationLogic()
        selectionNode = appLogic.GetSelectionNode()
        selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
        appLogic.PropagateVolumeSelection(0)
        appLogic.FitSliceToAll()

        return outputVolume
Exemplo n.º 2
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  def examineForImport(self,fileLists):
    """ Returns a list of qSlicerDICOMLoadable
    instances corresponding to ways of interpreting the 
    fileLists parameter.
    """    
    import vtkSlicerDicomRtImportExportModuleLogic

    # Create loadables for each file list
    loadables = []
    for fileList in fileLists: # Each file list corresponds to one series, so do loadables
      # Convert file list to VTK object to be able to pass it for examining
      # (VTK class cannot have Qt object as argument, otherwise it is not python wrapped)
      vtkFileList = vtk.vtkStringArray()
      for file in fileList:
        vtkFileList.InsertNextValue(file)

      # Examine files
      loadablesCollection = vtk.vtkCollection()
      slicer.modules.dicomrtimportexport.logic().ExamineForLoad(vtkFileList, loadablesCollection)

      for loadableIndex in xrange(0,loadablesCollection.GetNumberOfItems()):
        vtkLoadable = loadablesCollection.GetItemAsObject(loadableIndex)
        # Create Qt loadable if confidence is greater than 0
        if vtkLoadable.GetConfidence() > 0:
          # Convert to Qt loadable to pass it back
          qtLoadable = slicer.qSlicerDICOMLoadable()
          qtLoadable.copyFromVtkLoadable(vtkLoadable)
          qtLoadable.tooltip = 'Valid RT object in selection'
          qtLoadable.selected = True
          loadables.append(qtLoadable)

    return loadables
    def loadEigenArtemis3DUS(self, loadable):

        name = slicer.util.toVTKString(loadable.name)
        filePath = loadable.files[0]
        fileList = vtk.vtkStringArray()
        fileList.InsertNextValue(slicer.util.toVTKString(filePath))
        volumesLogic = slicer.modules.volumes.logic()
        outputVolume = volumesLogic.AddArchetypeScalarVolume(
            filePath, name, 0, fileList)

        outputVolume.SetSpacing(loadable.spacing, loadable.spacing,
                                loadable.spacing)
        outputVolume.SetOrigin(loadable.origin[0], loadable.origin[1],
                               loadable.origin[2])

        ijk2ras = vtk.vtkMatrix4x4()
        outputVolume.GetIJKToRASMatrix(ijk2ras)

        rot = vtk.vtkMatrix4x4()
        rot.DeepCopy((0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1))

        ijk2ras_updated = vtk.vtkMatrix4x4()
        ijk2ras.Multiply4x4(rot, ijk2ras, ijk2ras_updated)
        outputVolume.SetIJKToRASMatrix(ijk2ras_updated)

        appLogic = slicer.app.applicationLogic()
        selectionNode = appLogic.GetSelectionNode()
        selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
        appLogic.PropagateVolumeSelection(0)
        appLogic.FitSliceToAll()

        return outputVolume
 def loadFilesWithArchetype(self,files,name):
   """Load files in the traditional Slicer manner
   using the volume logic helper class
   and the vtkITK archetype helper code
   """
   fileList = vtk.vtkStringArray()
   for f in files:
     fileList.InsertNextValue(f)
   volumesLogic = slicer.modules.volumes.logic()
   return (volumesLogic.AddArchetypeVolume( files[0], name, 0, fileList ))
Exemplo n.º 5
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 def loadFilesWithArchetype(self, files, name):
     """Load files in the traditional Slicer manner
 using the volume logic helper class
 and the vtkITK archetype helper code
 """
     fileList = vtk.vtkStringArray()
     for f in files:
         fileList.InsertNextValue(f)
     volumesLogic = slicer.modules.volumes.logic()
     return (volumesLogic.AddArchetypeVolume(files[0], name, 0, fileList))
Exemplo n.º 6
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 def loadFilesWithArchetype(self):
   """Load files in the traditional Slicer manner
   using the volume logic helper class
   and the vtkITK archetype helper code
   """
   fileList = vtk.vtkStringArray()
   for f in self.files:
     fileList.InsertNextValue(f)
   vl = slicer.modules.volumes.logic()
   self.volumeNode = vl.AddArchetypeVolume( self.files[0], self.name, 0, fileList )
Exemplo n.º 7
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 def loadFilesWithArchetype(self):
   """Load files in the traditional Slicer manner
   using the volume logic helper class
   and the vtkITK archetype helper code
   """
   fileList = vtk.vtkStringArray()
   for f in self.files:
     fileList.InsertNextValue(f)
   vl = slicer.modules.volumes.logic()
   self.volumeNode = vl.AddArchetypeVolume( self.files[0], self.name, 0, fileList )
Exemplo n.º 8
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 def loadFiles(self, files, name):
   fileList = vtk.vtkStringArray()
   for f in files:
     fileList.InsertNextValue(f)
   vl = slicer.modules.volumes.logic()
   # TODO: pass in fileList once it is known to be in the right order
   volumeNode = vl.AddArchetypeVolume( files[0], name, 0 )
   # automatically select the volume to display
   appLogic = slicer.app.applicationLogic()
   selNode = appLogic.GetSelectionNode()
   selNode.SetReferenceActiveVolumeID(volumeNode.GetID())
   appLogic.PropagateVolumeSelection()
 def InitializeMetricsTable( metricsTable ):
   if ( metricsTable == None ):
     return
 
   metricsTable.GetTable().Initialize()
   
   # TODO: Make the more robust (e.g. qSlicerMetricsTableWidget::METRIC_TABLE_COLUMNS) 
   metricsTableColumnNames = [ "MetricName", "MetricRoles", "MetricUnit", "MetricValue" ]
   for columnName in metricsTableColumnNames:
     column = vtk.vtkStringArray()
     column.SetName( columnName )
     metricsTable.GetTable().AddColumn( column )
Exemplo n.º 10
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 def loadFilesWithArchetype(self,files,name):
   """Load files in the traditional Slicer manner
   using the volume logic helper class
   and the vtkITK archetype helper code
   """
   #name = slicer.util.unicodeify(name)
   name = name.encode('latin1', 'ignore')
   fileList = vtk.vtkStringArray()
   for f in files:
     fileList.InsertNextValue(f)
   volumesLogic = slicer.modules.volumes.logic()
   return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))
Exemplo n.º 11
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 def loadFilesWithArchetype(self,files,name):
   """Load files in the traditional Slicer manner
   using the volume logic helper class
   and the vtkITK archetype helper code
   """
   #name = slicer.util.unicodeify(name)
   name = name.encode('latin1', 'ignore')
   fileList = vtk.vtkStringArray()
   for f in files:
     fileList.InsertNextValue(f)
   volumesLogic = slicer.modules.volumes.logic()
   return(volumesLogic.AddArchetypeScalarVolume(files[0],name,0,fileList))
Exemplo n.º 12
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    def requestDeviceIDsCompleted(self, object=None, event=None, caller=None):
        wasBlocked = self.deviceIDComboBox.blockSignals(True)
        self.deviceIDComboBox.clear()
        deviceIDs = vtk.vtkStringArray()
        self.plusRemoteNode.GetDeviceIDs(deviceIDs)
        currentDeviceID = self.plusRemoteNode.GetCurrentDeviceID()

        for valueIndex in range(deviceIDs.GetNumberOfValues()):
            deviceID = deviceIDs.GetValue(valueIndex)
            self.deviceIDComboBox.addItem(deviceID)

        currentIndex = self.deviceIDComboBox.findText(currentDeviceID)
        self.deviceIDComboBox.setCurrentIndex(currentIndex)
        self.deviceIDComboBox.blockSignals(wasBlocked)
        self.onDeviceIdChanged()
Exemplo n.º 13
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  def ConvertStructureSetToLabelmap(self):
    import vtkSlicerDicomRtImportExportModuleLogic
    import vtkSegmentationCore
    import vtkSlicerSegmentationsModuleMRML
    import vtkSlicerSegmentationsModuleLogic

    labelmapsToSave = []
    
    # Get all segmentation nodes from the scene
    segmentationNodes = slicer.util.getNodes('vtkMRMLSegmentationNode*')

    for segmentationNode in segmentationNodes.values():
      logging.info('  Converting structure set ' + segmentationNode.GetName())
      # Set referenced volume as rasterization reference
      referenceVolume = vtkSlicerDicomRtImportExportModuleLogic.vtkSlicerDicomRtImportExportModuleLogic.GetReferencedVolumeByDicomForSegmentation(segmentationNode)
      if referenceVolume == None:
        logging.error('No reference volume found for segmentation ' + segmentationNode.GetName())
        continue
        
      # Perform conversion
      binaryLabelmapRepresentationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
      segmentation = segmentationNode.GetSegmentation()
      segmentation.CreateRepresentation(binaryLabelmapRepresentationName)
      
      # Create labelmap volume nodes from binary labelmaps
      segmentIDs = vtk.vtkStringArray()
      segmentation.GetSegmentIDs(segmentIDs)
      for segmentIndex in xrange(0,segmentIDs.GetNumberOfValues()):
        segmentID = segmentIDs.GetValue(segmentIndex)
        segment = segmentation.GetSegment(segmentID)
        binaryLabelmap = segment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
        if not binaryLabelmap:
          logging.error('Failed to retrieve binary labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
          continue
        labelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
        slicer.mrmlScene.AddNode(labelmapNode)
        labelmapName = segmentationNode.GetName() + "_" + segmentID
        labelmapNode.SetName(labelmapName)
        if not vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateLabelmapVolumeFromOrientedImageData(binaryLabelmap,labelmapNode):
          logging.error('Failed to create labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
          continue

        # Append volume to list
        labelmapsToSave.append(labelmapNode)
      
    return labelmapsToSave
Exemplo n.º 14
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 def loadFiles(self,files=None,name=None):
   if not files:
     files = self.files
   if not name:
     name = self.name
   fileList = vtk.vtkStringArray()
   for f in files:
     fileList.InsertNextValue(f)
   vl = slicer.modules.volumes.logic()
   # TODO: pass in fileList once it is known to be in the right order
   self.volumeNode = vl.AddArchetypeVolume( files[0], name, 0 )
   # automatically select the volume to display
   appLogic = slicer.app.applicationLogic()
   selNode = appLogic.GetSelectionNode()
   if self.volumeNode:
     selNode.SetReferenceActiveVolumeID(self.volumeNode.GetID())
     appLogic.PropagateVolumeSelection()
Exemplo n.º 15
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def copyNodeContentToNewScriptedModuleNode(oldDataNode, shNode):
    newDataNode = slicer.vtkMRMLScriptedModuleNode()
    newDataNode.HideFromEditorsOff()
    # Copy node attributes
    attributeNames = vtk.vtkStringArray()
    oldDataNode.GetAttributeNames(attributeNames)
    for index in range(attributeNames.GetNumberOfValues()):
        attributeName = attributeNames.GetValue(index)
        newDataNode.SetAttribute(attributeName,
                                 oldDataNode.GetAttribute(attributeName))
    slicer.mrmlScene.AddNode(newDataNode)
    newDataNode.SetName(oldDataNode.GetName())
    # Copy node references
    newDataNode.CopyReferences(oldDataNode)
    # Move children
    childItemIDs = vtk.vtkIdList()
    #shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
    shNode.GetItemChildren(shNode.GetItemByDataNode(oldDataNode), childItemIDs)
    for index in range(childItemIDs.GetNumberOfIds()):
        childItemID = childItemIDs.GetId(index)
        shNode.ReparentItemByDataNode(childItemID, newDataNode)
    return newDataNode