Python SegmentStatisticsLogic.computeStatistics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 computeStatistics [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 computeStatistics [as 别名]
  def test_ScriptedSegmentEditorEffectModuleTemplate1(self):
    """
    Basic automated test of the segmentation method:
    - Create segmentation by placing sphere-shaped seeds
    - Run segmentation
    - Verify results using segment statistics
    The test can be executed from SelfTests module (test name: SegmentEditorScriptedSegmentEditorEffectModuleTemplate)
    """

    self.delayDisplay("Starting test_ScriptedSegmentEditorEffectModuleTemplate1")

    import vtkSegmentationCorePython as vtkSegmentationCore
    import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
    import SampleData
    from SegmentStatistics import SegmentStatisticsLogic

    ##################################
    self.delayDisplay("Load master volume")

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

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

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

    # Segments are defined by a list of: name and a list of sphere [radius, posX, posY, posZ]
    segmentGeometries = [
      ['Tumor', [[10, -6,30,28]]],
      ['Background', [[10, 0,65,22], [15, 1, -14, 30], [12, 0, 28, -7], [5, 0,30,54], [12, 31, 33, 27], [17, -42, 30, 27], [6, -2,-17,71]]],
      ['Air', [[10, 76,73,0], [15, -70,74,0]]] ]
    for segmentGeometry in segmentGeometries:
      segmentName = segmentGeometry[0]
      appender = vtk.vtkAppendPolyData()
      for sphere in segmentGeometry[1]:
        sphereSource = vtk.vtkSphereSource()
        sphereSource.SetRadius(sphere[0])
        sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
        appender.AddInputConnection(sphereSource.GetOutputPort())
      segment = vtkSegmentationCore.vtkSegment()
      segment.SetName(segmentationNode.GetSegmentation().GenerateUniqueSegmentID(segmentName))
      appender.Update()
      segment.AddRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(), appender.GetOutput())
      segmentationNode.GetSegmentation().AddSegment(segment)

    ##################################
    self.delayDisplay("Create segment editor")

    segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
    segmentEditorWidget.show()
    segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
    segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
    slicer.mrmlScene.AddNode(segmentEditorNode)
    segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
    segmentEditorWidget.setSegmentationNode(segmentationNode)
    segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)

    ##################################
    self.delayDisplay("Run segmentation")
    segmentEditorWidget.setActiveEffectByName("ScriptedSegmentEditorEffectModuleTemplate")
    effect = segmentEditorWidget.activeEffect()
    effect.setParameter("ObjectScaleMm", 3.0)
    effect.self().onApply()

    ##################################
    self.delayDisplay("Make segmentation results nicely visible in 3D")
    segmentationDisplayNode = segmentationNode.GetDisplayNode()
    segmentationDisplayNode.SetSegmentVisibility("Air", False)
    segmentationDisplayNode.SetSegmentOpacity3D("Background",0.5)

    ##################################
    self.delayDisplay("Compute statistics")

    segStatLogic = SegmentStatisticsLogic()
    segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)

    # Export results to table (just to see all results)
    resultsTableNode = slicer.vtkMRMLTableNode()
    slicer.mrmlScene.AddNode(resultsTableNode)
    segStatLogic.exportToTable(resultsTableNode)
    segStatLogic.showTable(resultsTableNode)

    self.delayDisplay("Check a few numerical results")
    self.assertEqual( round(segStatLogic.statistics["Tumor","LM volume cc"]), 16)
    self.assertEqual( round(segStatLogic.statistics["Background","LM volume cc"]), 3010)

    self.delayDisplay('test_ScriptedSegmentEditorEffectModuleTemplate1 passed')

# 需要导入模块: from SegmentStatistics import SegmentStatisticsLogic [as 别名]
# 或者: from SegmentStatistics.SegmentStatisticsLogic import computeStatistics [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.........

# 需要导入模块: from SegmentStatistics import SegmentStatisticsLogic [as 别名]
# 或者: from SegmentStatistics.SegmentStatisticsLogic import computeStatistics [as 别名]

#.........这里部分代码省略.........
      self.parameterNodeSelector.setCurrentNode(parameterNode)
    if self.segmentationSelector.currentNode() is None:
      segmentationNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLSegmentationNode")
      self.segmentationSelector.setCurrentNode(segmentationNode)

  def cleanup(self):
    if self.parameterNode and self.parameterNodeObserver:
      self.parameterNode.RemoveObserver(self.parameterNodeObserver)

  def onNodeSelectionChanged(self):
    self.applyButton.enabled = (self.segmentationSelector.currentNode() is not None and
                                self.parameterNodeSelector.currentNode() is not None)
    if self.segmentationSelector.currentNode():
      self.outputTableSelector.baseName = self.segmentationSelector.currentNode().GetName() + ' statistics'

  def onApply(self):
    """Calculate the label statistics
    """
    if not self.outputTableSelector.currentNode():
      newTable = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
      self.outputTableSelector.setCurrentNode(newTable)
    # Lock GUI
    self.applyButton.text = "Working..."
    self.applyButton.setEnabled(False)
    slicer.app.processEvents()
    # set up parameters for computation
    self.logic.getParameterNode().SetParameter("Segmentation", self.segmentationSelector.currentNode().GetID())
    if self.scalarSelector.currentNode():
      self.logic.getParameterNode().SetParameter("ScalarVolume", self.scalarSelector.currentNode().GetID())
    else:
      self.logic.getParameterNode().UnsetParameter("ScalarVolume")
    self.logic.getParameterNode().SetParameter("MeasurementsTable", self.outputTableSelector.currentNode().GetID())
    # Compute statistics
    self.logic.computeStatistics()
    self.logic.exportToTable(self.outputTableSelector.currentNode())
    # Unlock GUI
    self.applyButton.setEnabled(True)
    self.applyButton.text = "Apply"

    self.logic.showTable(self.outputTableSelector.currentNode())

  def onEditParameters(self, pluginName=None):
    """Open dialog box to edit plugin's parameters"""
    if self.parameterNodeSelector.currentNode():
      SegmentStatisticsParameterEditorDialog.editParameters(self.parameterNodeSelector.currentNode(),pluginName)

  def addPluginOptionWidgets(self):
    self.pluginEnabledCheckboxes = {}
    self.parametersLayout.addRow(qt.QLabel("Enabled segment statistics plugins:"))
    for plugin in self.logic.plugins:
      checkbox = qt.QCheckBox(plugin.name+" Statistics")
      checkbox.checked = True
      checkbox.connect('stateChanged(int)', self.updateParameterNodeFromGui)
      optionButton = qt.QPushButton("Options")
      from functools import partial
      optionButton.connect('clicked()',partial(self.onEditParameters, plugin.name))
      editWidget = qt.QWidget()
      editWidget.setLayout(qt.QHBoxLayout())
      editWidget.layout().margin = 0
      editWidget.layout().addWidget(checkbox, 0)
      editWidget.layout().addStretch(1)
      editWidget.layout().addWidget(optionButton, 0)
      self.pluginEnabledCheckboxes[plugin.name] = checkbox
      self.parametersLayout.addRow(editWidget)
    # embed widgets for editing plugin' parameters
    #for plugin in self.logic.plugins:

# 需要导入模块: from SegmentStatistics import SegmentStatisticsLogic [as 别名]
# 或者: from SegmentStatistics.SegmentStatisticsLogic import computeStatistics [as 别名]
class SegmentStatisticsWidget(ScriptedLoadableModuleWidget):
  """Uses ScriptedLoadableModuleWidget base class, available at:
  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
  """

  def setup(self):
    ScriptedLoadableModuleWidget.setup(self)

    self.logic = SegmentStatisticsLogic()
    self.grayscaleNode = None
    self.labelNode = None
    self.fileName = None
    self.fileDialog = None

    # Instantiate and connect widgets ...
    #

    # Inputs
    inputsCollapsibleButton = ctk.ctkCollapsibleButton()
    inputsCollapsibleButton.text = "Inputs"
    self.layout.addWidget(inputsCollapsibleButton)
    inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)

    # Segmentation selector
    self.segmentationSelector = slicer.qMRMLNodeComboBox()
    self.segmentationSelector.nodeTypes = ["vtkMRMLSegmentationNode"]
    self.segmentationSelector.addEnabled = False
    self.segmentationSelector.removeEnabled = True
    self.segmentationSelector.renameEnabled = True
    self.segmentationSelector.setMRMLScene( slicer.mrmlScene )
    self.segmentationSelector.setToolTip( "Pick the segmentation to compute statistics for" )
    inputsFormLayout.addRow("Segmentation:", self.segmentationSelector)

    # Grayscale volume selector
    self.grayscaleSelector = slicer.qMRMLNodeComboBox()
    self.grayscaleSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
    self.grayscaleSelector.addEnabled = False
    self.grayscaleSelector.removeEnabled = True
    self.grayscaleSelector.renameEnabled = True
    self.grayscaleSelector.noneEnabled = True
    self.grayscaleSelector.showChildNodeTypes = False
    self.grayscaleSelector.setMRMLScene( slicer.mrmlScene )
    self.grayscaleSelector.setToolTip( "Select the grayscale volume for intensity statistics calculations")
    inputsFormLayout.addRow("Grayscale volume:", self.grayscaleSelector)

    # Output table selector
    outputCollapsibleButton = ctk.ctkCollapsibleButton()
    outputCollapsibleButton.text = "Output"
    self.layout.addWidget(outputCollapsibleButton)
    outputFormLayout = qt.QFormLayout(outputCollapsibleButton)

    self.outputTableSelector = slicer.qMRMLNodeComboBox()
    self.outputTableSelector.nodeTypes = ["vtkMRMLTableNode"]
    self.outputTableSelector.addEnabled = True
    self.outputTableSelector.selectNodeUponCreation = True
    self.outputTableSelector.renameEnabled = True
    self.outputTableSelector.removeEnabled = True
    self.outputTableSelector.noneEnabled = False
    self.outputTableSelector.setMRMLScene( slicer.mrmlScene )
    self.outputTableSelector.setToolTip( "Select the table where statistics will be saved into")
    outputFormLayout.addRow("Output table:", self.outputTableSelector)

    # Apply Button
    self.applyButton = qt.QPushButton("Apply")
    self.applyButton.toolTip = "Calculate Statistics."
    self.applyButton.enabled = False
    self.parent.layout().addWidget(self.applyButton)

    # Add vertical spacer
    self.parent.layout().addStretch(1)

    # connections
    self.applyButton.connect('clicked()', self.onApply)
    self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
    self.segmentationSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
    self.outputTableSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)

    self.onNodeSelectionChanged()

  def onNodeSelectionChanged(self):
    self.applyButton.enabled = (self.segmentationSelector.currentNode() is not None) and (self.outputTableSelector.currentNode() is not None)
    if self.segmentationSelector.currentNode():
      self.outputTableSelector.baseName = self.segmentationSelector.currentNode().GetName() + ' statistics'

  def onApply(self):
    """Calculate the label statistics
    """
    # Lock GUI
    self.applyButton.text = "Working..."
    self.applyButton.setEnabled(False)
    slicer.app.processEvents()
    # Compute statistics
    self.logic.computeStatistics(self.segmentationSelector.currentNode(), self.grayscaleSelector.currentNode())
    self.logic.exportToTable(self.outputTableSelector.currentNode())
    # Unlock GUI
    self.applyButton.setEnabled(True)
    self.applyButton.text = "Apply"

    self.logic.showTable(self.outputTableSelector.currentNode())