Python SegmentStatisticsLogic.getStatistics方法代码示例

# 需要导入模块: from SegmentStatistics import SegmentStatisticsLogic [as 别名]
# 或者: from SegmentStatistics.SegmentStatisticsLogic import getStatistics [as 别名]
  def test_SegmentStatisticsBasic(self):
    """
    This tests some aspects of the label statistics
    """

    self.delayDisplay("Starting test_SegmentStatisticsBasic")

    import vtkSegmentationCorePython as vtkSegmentationCore
    import SampleData
    from SegmentStatistics import SegmentStatisticsLogic

    self.delayDisplay("Load master volume")

    sampleDataLogic = SampleData.SampleDataLogic()
    masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()

    self.delayDisplay("Create segmentation containing a few spheres")

    segmentationNode = slicer.vtkMRMLSegmentationNode()
    slicer.mrmlScene.AddNode(segmentationNode)
    segmentationNode.CreateDefaultDisplayNodes()
    segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

    # Geometry for each segment is defined by: radius, posX, posY, posZ
    segmentGeometries = [[10, -6,30,28], [20, 0,65,32], [15, 1, -14, 30], [12, 0, 28, -7], [5, 0,30,64],
                         [12, 31, 33, 27], [17, -42, 30, 27]]
    for segmentGeometry in segmentGeometries:
      sphereSource = vtk.vtkSphereSource()
      sphereSource.SetRadius(segmentGeometry[0])
      sphereSource.SetCenter(segmentGeometry[1], segmentGeometry[2], segmentGeometry[3])
      sphereSource.Update()
      uniqueSegmentID = segmentationNode.GetSegmentation().GenerateUniqueSegmentID("Test")
      segmentationNode.AddSegmentFromClosedSurfaceRepresentation(sphereSource.GetOutput(), uniqueSegmentID)

    self.delayDisplay("Compute statistics")

    segStatLogic = SegmentStatisticsLogic()
    segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
    segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
    segStatLogic.computeStatistics()

    self.delayDisplay("Check a few numerical results")
    self.assertEqual( segStatLogic.getStatistics()["Test_2","LabelmapSegmentStatisticsPlugin.voxel_count"], 9807)
    self.assertEqual( segStatLogic.getStatistics()["Test_4","ScalarVolumeSegmentStatisticsPlugin.voxel_count"], 380)

    self.delayDisplay("Export results to table")
    resultsTableNode = slicer.vtkMRMLTableNode()
    slicer.mrmlScene.AddNode(resultsTableNode)
    segStatLogic.exportToTable(resultsTableNode)
    segStatLogic.showTable(resultsTableNode)

    self.delayDisplay("Export results to string")
    logging.info(segStatLogic.exportToString())

    outputFilename = slicer.app.temporaryPath + '/SegmentStatisticsTestOutput.csv'
    self.delayDisplay("Export results to CSV file: "+outputFilename)
    segStatLogic.exportToCSVFile(outputFilename)

    self.delayDisplay('test_SegmentStatisticsBasic passed!')

# 需要导入模块: from SegmentStatistics import SegmentStatisticsLogic [as 别名]
# 或者: from SegmentStatistics.SegmentStatisticsLogic import getStatistics [as 别名]
  def test_SegmentStatisticsPlugins(self):
    """
    This tests some aspects of the segment statistics plugins
    """

    self.delayDisplay("Starting test_SegmentStatisticsPlugins")

    import vtkSegmentationCorePython as vtkSegmentationCore
    import SampleData
    from SegmentStatistics import SegmentStatisticsLogic

    self.delayDisplay("Load master volume")

    masterVolumeNode = SampleData.downloadSample('MRBrainTumor1')

    self.delayDisplay("Create segmentation containing a few spheres")

    segmentationNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
    segmentationNode.CreateDefaultDisplayNodes()
    segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

    # Geometry for each segment is defined by: radius, posX, posY, posZ
    segmentGeometries = [[10, -6,30,28], [20, 0,65,32], [15, 1, -14, 30], [12, 0, 28, -7], [5, 0,30,64],
                         [12, 31, 33, 27], [17, -42, 30, 27]]
    for segmentGeometry in segmentGeometries:
      sphereSource = vtk.vtkSphereSource()
      sphereSource.SetRadius(segmentGeometry[0])
      sphereSource.SetCenter(segmentGeometry[1], segmentGeometry[2], segmentGeometry[3])
      sphereSource.Update()
      segment = vtkSegmentationCore.vtkSegment()
      uniqueSegmentID = segmentationNode.GetSegmentation().GenerateUniqueSegmentID("Test")
      segmentationNode.AddSegmentFromClosedSurfaceRepresentation(sphereSource.GetOutput(), uniqueSegmentID)

    # test calculating only measurements for selected segments
    self.delayDisplay("Test calculating only measurements for individual segments")
    segStatLogic = SegmentStatisticsLogic()
    segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
    segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
    segStatLogic.updateStatisticsForSegment('Test_2')
    resultsTableNode = slicer.vtkMRMLTableNode()
    slicer.mrmlScene.AddNode(resultsTableNode)
    segStatLogic.exportToTable(resultsTableNode)
    segStatLogic.showTable(resultsTableNode)
    self.assertEqual( segStatLogic.getStatistics()["Test_2","LabelmapSegmentStatisticsPlugin.voxel_count"], 9807)
    with self.assertRaises(KeyError): segStatLogic.getStatistics()["Test_4","ScalarVolumeSegmentStatisticsPlugin.voxel count"]
    # assert there are no result for this segment
    segStatLogic.updateStatisticsForSegment('Test_4')
    segStatLogic.exportToTable(resultsTableNode)
    segStatLogic.showTable(resultsTableNode)
    self.assertEqual( segStatLogic.getStatistics()["Test_2","LabelmapSegmentStatisticsPlugin.voxel_count"], 9807)
    self.assertEqual( segStatLogic.getStatistics()["Test_4","LabelmapSegmentStatisticsPlugin.voxel_count"], 380)
    with self.assertRaises(KeyError): segStatLogic.getStatistics()["Test_5","ScalarVolumeSegmentStatisticsPlugin.voxel count"]
    # assert there are no result for this segment

    # calculate measurements for all segments
    segStatLogic.computeStatistics()
    self.assertEqual( segStatLogic.getStatistics()["Test","LabelmapSegmentStatisticsPlugin.voxel_count"], 2948)
    self.assertEqual( segStatLogic.getStatistics()["Test_1","LabelmapSegmentStatisticsPlugin.voxel_count"], 23281)

    # test updating measurements for segments one by one
    self.delayDisplay("Update some segments in the segmentation")
    segmentGeometriesNew = [[5, -6,30,28], [21, 0,65,32]]
    # We add/remove representations, so we temporarily block segment modifications
    # to make sure display managers don't try to access data while it is in an
    # inconsistent state.
    wasModified = segmentationNode.StartModify()
    for i in range(len(segmentGeometriesNew)):
      segmentGeometry  = segmentGeometriesNew[i]
      sphereSource = vtk.vtkSphereSource()
      sphereSource.SetRadius(segmentGeometry[0])
      sphereSource.SetCenter(segmentGeometry[1], segmentGeometry[2], segmentGeometry[3])
      sphereSource.Update()
      segment = segmentationNode.GetSegmentation().GetNthSegment(i)
      segment.RemoveAllRepresentations()
      closedSurfaceName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName()
      segment.AddRepresentation(closedSurfaceName,
                                sphereSource.GetOutput())
    segmentationNode.EndModify(wasModified)
    self.assertEqual( segStatLogic.getStatistics()["Test","LabelmapSegmentStatisticsPlugin.voxel_count"], 2948)
    self.assertEqual( segStatLogic.getStatistics()["Test_1","LabelmapSegmentStatisticsPlugin.voxel_count"], 23281)
    segStatLogic.updateStatisticsForSegment('Test_1')
    self.assertEqual( segStatLogic.getStatistics()["Test","LabelmapSegmentStatisticsPlugin.voxel_count"], 2948)
    self.assertTrue( segStatLogic.getStatistics()["Test_1","LabelmapSegmentStatisticsPlugin.voxel_count"]!=23281)
    segStatLogic.updateStatisticsForSegment('Test')
    self.assertTrue( segStatLogic.getStatistics()["Test","LabelmapSegmentStatisticsPlugin.voxel_count"]!=2948)
    self.assertTrue( segStatLogic.getStatistics()["Test_1","LabelmapSegmentStatisticsPlugin.voxel_count"]!=23281)

    # test enabling/disabling of individual measurements
    self.delayDisplay("Test disabling of individual measurements")
    segStatLogic = SegmentStatisticsLogic()
    segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
    segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
    segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.voxel_count.enabled",str(False))
    segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.volume_cm3.enabled",str(False))
    segStatLogic.computeStatistics()
    segStatLogic.exportToTable(resultsTableNode)
    segStatLogic.showTable(resultsTableNode)
    columnHeaders = [resultsTableNode.GetColumnName(i) for i in range(resultsTableNode.GetNumberOfColumns())]
    self.assertFalse('Number of voxels [voxels] (1)' in columnHeaders)
    self.assertTrue('Volume [mm3] (1)' in columnHeaders)
#.........这里部分代码省略.........