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!')
def getStatForVol(self, volFile, folderSaveName, condition, seriesName=""):
# Load the volume, get a tuple of (success, vtkMRMLScalarVolumeNode)
vol = slicer.util.loadVolume(volFile, returnNode=True)
# If the volume was not successfully loaded, exit
if not vol[0]:
# Print error if volume does not exist or is inaccessible
raise IOError("Volume could not be loaded from: " + volFile)
# Get the volume node
volNode = vol[1]
# Instantiate a SegmentStatisticsLogic object to store the statistics
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
self.segNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
volNode.GetID())
# Compute the statistics using the specified volume as the master volume
segStatLogic.computeStatistics()
# If the --getsnr argument was specified
if self.getsnr:
statistics = segStatLogic.getStatistics()
# Get the noise segment's standard deviation
noiseStdev = statistics[(
self.noiseSegmentID,
"ScalarVolumeSegmentStatisticsPlugin.stdev")]
# Compute the SNRs of other segments
segStatLogic = self.computeSnrs(segStatLogic,
statistics['SegmentIDs'],
noiseStdev)
# If this object's statistics dictionary does not contain this series
if seriesName not in self.metaStats[condition]:
# Initialize it into an empty list
self.metaStats[condition][seriesName] = []
# Append current volume's statistics to the statistics dictionary
self.metaStats[condition][seriesName].append(
segStatLogic.getStatistics())
# Specify the folder name of output
documentsDir = os.path.normpath(
os.path.expanduser(
r"~\\Documents\\StatsCollector\\SegmentStatistics"))
# Specify the folder path of the output
fileParentDir = os.path.join(documentsDir, folderSaveName)
# Specify the full file path of the Excel file to output
filePath = os.path.join(fileParentDir, condition)
# Make the folder directories if they don't exist
if not os.path.exists(fileParentDir):
os.makedirs(fileParentDir)
# Export the stats to a file
self.exportStatsToXl(segStatLogic, filePath, volNode.GetName(),
seriesName)
def calculateStatistics(self):
from SegmentStatistics import SegmentStatisticsLogic
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter(
"Segmentation", self.segmentationEditorWidget.segmentationNodeID())
self.segmentationEditorWidget.segmentationNode(
).CreateDefaultDisplayNodes()
segStatLogic.computeStatistics()
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
def test_NvidiaAIAA1(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: SegmentEditorNvidiaAIAA)
"""
self.delayDisplay("Starting test_NvidiaAIAA1")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
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)
# 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("NvidiaAIAA")
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_NvidiaAIAA1 passed')
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')
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)
self.assertFalse('Volume [cm3] (3)' in columnHeaders)
self.delayDisplay("Test re-enabling of individual measurements")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.voxel_count.enabled", str(True))
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.volume_cm3.enabled", str(True))
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [
resultsTableNode.GetColumnName(i)
for i in range(resultsTableNode.GetNumberOfColumns())
]
self.assertTrue('Number of voxels [voxels] (1)' in columnHeaders)
self.assertTrue('Volume [mm3] (1)' in columnHeaders)
self.assertTrue('Volume [cm3] (1)' in columnHeaders)
# test enabling/disabling of individual plugins
self.delayDisplay("Test disabling of plugin")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.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] (3)' in columnHeaders)
self.assertFalse('Volume [mm3] (3)' in columnHeaders)
self.assertTrue('Volume [mm3] (2)' in columnHeaders)
self.delayDisplay("Test re-enabling of plugin")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.enabled", str(True))
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [
resultsTableNode.GetColumnName(i)
for i in range(resultsTableNode.GetNumberOfColumns())
]
self.assertTrue('Number of voxels [voxels] (2)' in columnHeaders)
self.assertTrue('Volume [mm3] (3)' in columnHeaders)
# test unregistering/registering of plugins
self.delayDisplay("Test of removing all registered plugins")
SegmentStatisticsLogic.registeredPlugins = [
] # remove all registered plugins
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [
resultsTableNode.GetColumnName(i)
for i in range(resultsTableNode.GetNumberOfColumns())
]
self.assertEqual(len(columnHeaders),
1) # only header element should be "Segment"
self.assertEqual(columnHeaders[0],
"Segment") # only header element should be "Segment"
self.delayDisplay("Test registering plugins")
SegmentStatisticsLogic.registerPlugin(
LabelmapSegmentStatisticsPlugin())
SegmentStatisticsLogic.registerPlugin(
ScalarVolumeSegmentStatisticsPlugin())
SegmentStatisticsLogic.registerPlugin(
ClosedSurfaceSegmentStatisticsPlugin())
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [
resultsTableNode.GetColumnName(i)
for i in range(resultsTableNode.GetNumberOfColumns())
]
self.assertTrue('Number of voxels [voxels] (1)' in columnHeaders)
self.assertTrue('Number of voxels [voxels] (2)' in columnHeaders)
self.assertTrue('Surface area [mm2]' in columnHeaders)
self.delayDisplay('test_SegmentStatisticsPlugins passed!')
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.parameterNode = None
self.parameterNodeObserver = None
# Instantiate and connect widgets ...
#
# Parameter set selector
self.parameterNodeSelector = slicer.qMRMLNodeComboBox()
self.parameterNodeSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.parameterNodeSelector.addAttribute("vtkMRMLScriptedModuleNode",
"ModuleName",
"SegmentStatistics")
self.parameterNodeSelector.selectNodeUponCreation = True
self.parameterNodeSelector.addEnabled = True
self.parameterNodeSelector.renameEnabled = True
self.parameterNodeSelector.removeEnabled = True
self.parameterNodeSelector.noneEnabled = False
self.parameterNodeSelector.showHidden = True
self.parameterNodeSelector.showChildNodeTypes = False
self.parameterNodeSelector.baseName = "SegmentStatistics"
self.parameterNodeSelector.setMRMLScene(slicer.mrmlScene)
self.parameterNodeSelector.setToolTip("Pick parameter set")
self.layout.addWidget(self.parameterNodeSelector)
# 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)
# Scalar volume selector
self.scalarSelector = slicer.qMRMLNodeComboBox()
self.scalarSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.scalarSelector.addEnabled = False
self.scalarSelector.removeEnabled = True
self.scalarSelector.renameEnabled = True
self.scalarSelector.noneEnabled = True
self.scalarSelector.showChildNodeTypes = False
self.scalarSelector.setMRMLScene(slicer.mrmlScene)
self.scalarSelector.setToolTip(
"Select the scalar volume for intensity statistics calculations")
inputsFormLayout.addRow("Scalar volume:", self.scalarSelector)
# Output table selector
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
self.outputTableSelector = slicer.qMRMLNodeComboBox()
self.outputTableSelector.noneDisplay = "Create new table"
self.outputTableSelector.setMRMLScene(slicer.mrmlScene)
self.outputTableSelector.nodeTypes = ["vtkMRMLTableNode"]
self.outputTableSelector.addEnabled = True
self.outputTableSelector.selectNodeUponCreation = True
self.outputTableSelector.renameEnabled = True
self.outputTableSelector.removeEnabled = True
self.outputTableSelector.noneEnabled = True
self.outputTableSelector.setToolTip(
"Select the table where statistics will be saved into")
self.outputTableSelector.setCurrentNode(None)
outputFormLayout.addRow("Output table:", self.outputTableSelector)
# Parameter set
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Advanced"
parametersCollapsibleButton.collapsed = True
self.layout.addWidget(parametersCollapsibleButton)
self.parametersLayout = qt.QFormLayout(parametersCollapsibleButton)
# Edit parameter set button to open SegmentStatisticsParameterEditorDialog
# Note: we add the plugins' option widgets to the module widget instead of using the editor dialog
#self.editParametersButton = qt.QPushButton("Edit Parameter Set")
#self.editParametersButton.toolTip = "Editor Statistics Plugin Parameter Set."
#self.parametersLayout.addRow(self.editParametersButton)
#self.editParametersButton.connect('clicked()', self.onEditParameters)
# add caclulator's option widgets
self.addPluginOptionWidgets()
# 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.scalarSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onNodeSelectionChanged)
self.segmentationSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onNodeSelectionChanged)
self.outputTableSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onNodeSelectionChanged)
self.parameterNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onNodeSelectionChanged)
self.parameterNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onParameterSetSelected)
self.parameterNodeSelector.setCurrentNode(
self.logic.getParameterNode())
self.onNodeSelectionChanged()
self.onParameterSetSelected()
def enter(self):
"""Runs whenever the module is reopened
"""
if self.parameterNodeSelector.currentNode() is None:
parameterNode = self.logic.getParameterNode()
slicer.mrmlScene.AddNode(parameterNode)
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:
# pluginOptionsCollapsibleButton = ctk.ctkCollapsibleGroupBox()
# pluginOptionsCollapsibleButton.setTitle( plugin.name )
# pluginOptionsFormLayout = qt.QFormLayout(pluginOptionsCollapsibleButton)
# pluginOptionsFormLayout.addRow(plugin.optionsWidget)
# self.parametersLayout.addRow(pluginOptionsCollapsibleButton)
def onParameterSetSelected(self):
if self.parameterNode and self.parameterNodeObserver:
self.parameterNode.RemoveObserver(self.parameterNodeObserver)
self.parameterNode = self.parameterNodeSelector.currentNode()
if self.parameterNode:
self.logic.setParameterNode(self.parameterNode)
self.parameterNodeObserver = self.parameterNode.AddObserver(
vtk.vtkCommand.ModifiedEvent, self.updateGuiFromParameterNode)
self.updateGuiFromParameterNode()
def updateGuiFromParameterNode(self, caller=None, event=None):
if not self.parameterNode:
return
for plugin in self.logic.plugins:
pluginName = plugin.__class__.__name__
parameter = pluginName + '.enabled'
checkbox = self.pluginEnabledCheckboxes[plugin.name]
value = self.parameterNode.GetParameter(parameter) == 'True'
if checkbox.checked != value:
previousState = checkbox.blockSignals(True)
checkbox.checked = value
checkbox.blockSignals(previousState)
def updateParameterNodeFromGui(self):
if not self.parameterNode:
return
for plugin in self.logic.plugins:
pluginName = plugin.__class__.__name__
parameter = pluginName + '.enabled'
checkbox = self.pluginEnabledCheckboxes[plugin.name]
self.parameterNode.SetParameter(parameter, str(checkbox.checked))
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)
self.assertFalse('Volume [cm3] (3)' in columnHeaders)
self.delayDisplay("Test re-enabling of individual measurements")
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.voxel_count.enabled",str(True))
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.volume_cm3.enabled",str(True))
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [resultsTableNode.GetColumnName(i) for i in range(resultsTableNode.GetNumberOfColumns())]
self.assertTrue('Number of voxels [voxels] (1)' in columnHeaders)
self.assertTrue('Volume [mm3] (1)' in columnHeaders)
self.assertTrue('Volume [cm3] (1)' in columnHeaders)
# test enabling/disabling of individual plugins
self.delayDisplay("Test disabling of plugin")
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.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] (3)' in columnHeaders)
self.assertFalse('Volume [mm3] (3)' in columnHeaders)
self.assertTrue('Volume [mm3] (2)' in columnHeaders)
self.delayDisplay("Test re-enabling of plugin")
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.enabled",str(True))
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [resultsTableNode.GetColumnName(i) for i in range(resultsTableNode.GetNumberOfColumns())]
self.assertTrue('Number of voxels [voxels] (2)' in columnHeaders)
self.assertTrue('Volume [mm3] (3)' in columnHeaders)
# test unregistering/registering of plugins
self.delayDisplay("Test of removing all registered plugins")
SegmentStatisticsLogic.registeredPlugins = [] # remove all registered plugins
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [resultsTableNode.GetColumnName(i) for i in range(resultsTableNode.GetNumberOfColumns())]
self.assertEqual(len(columnHeaders),1) # only header element should be "Segment"
self.assertEqual(columnHeaders[0],"Segment") # only header element should be "Segment"
self.delayDisplay("Test registering plugins")
SegmentStatisticsLogic.registerPlugin(LabelmapSegmentStatisticsPlugin())
SegmentStatisticsLogic.registerPlugin(ScalarVolumeSegmentStatisticsPlugin())
SegmentStatisticsLogic.registerPlugin(ClosedSurfaceSegmentStatisticsPlugin())
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
columnHeaders = [resultsTableNode.GetColumnName(i) for i in range(resultsTableNode.GetNumberOfColumns())]
self.assertTrue('Number of voxels [voxels] (1)' in columnHeaders)
self.assertTrue('Number of voxels [voxels] (2)' in columnHeaders)
self.assertTrue('Surface area [mm2]' in columnHeaders)
self.delayDisplay('test_SegmentStatisticsPlugins passed!')
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.parameterNode = None
self.parameterNodeObserver = None
# Instantiate and connect widgets ...
#
# Parameter set selector
self.parameterNodeSelector = slicer.qMRMLNodeComboBox()
self.parameterNodeSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.parameterNodeSelector.addAttribute( "vtkMRMLScriptedModuleNode", "ModuleName", "SegmentStatistics" )
self.parameterNodeSelector.selectNodeUponCreation = True
self.parameterNodeSelector.addEnabled = True
self.parameterNodeSelector.renameEnabled = True
self.parameterNodeSelector.removeEnabled = True
self.parameterNodeSelector.noneEnabled = False
self.parameterNodeSelector.showHidden = True
self.parameterNodeSelector.showChildNodeTypes = False
self.parameterNodeSelector.baseName = "SegmentStatistics"
self.parameterNodeSelector.setMRMLScene( slicer.mrmlScene )
self.parameterNodeSelector.setToolTip( "Pick parameter set" )
self.layout.addWidget(self.parameterNodeSelector)
# 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)
# Scalar volume selector
self.scalarSelector = slicer.qMRMLNodeComboBox()
self.scalarSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.scalarSelector.addEnabled = False
self.scalarSelector.removeEnabled = True
self.scalarSelector.renameEnabled = True
self.scalarSelector.noneEnabled = True
self.scalarSelector.showChildNodeTypes = False
self.scalarSelector.setMRMLScene( slicer.mrmlScene )
self.scalarSelector.setToolTip( "Select the scalar volume for intensity statistics calculations")
inputsFormLayout.addRow("Scalar volume:", self.scalarSelector)
# Output table selector
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
self.outputTableSelector = slicer.qMRMLNodeComboBox()
self.outputTableSelector.noneDisplay = "Create new table"
self.outputTableSelector.setMRMLScene(slicer.mrmlScene)
self.outputTableSelector.nodeTypes = ["vtkMRMLTableNode"]
self.outputTableSelector.addEnabled = True
self.outputTableSelector.selectNodeUponCreation = True
self.outputTableSelector.renameEnabled = True
self.outputTableSelector.removeEnabled = True
self.outputTableSelector.noneEnabled = True
self.outputTableSelector.setToolTip("Select the table where statistics will be saved into")
self.outputTableSelector.setCurrentNode(None)
outputFormLayout.addRow("Output table:", self.outputTableSelector)
# Parameter set
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Advanced"
parametersCollapsibleButton.collapsed = True
self.layout.addWidget(parametersCollapsibleButton)
self.parametersLayout = qt.QFormLayout(parametersCollapsibleButton)
# Edit parameter set button to open SegmentStatisticsParameterEditorDialog
# Note: we add the plugins' option widgets to the module widget instead of using the editor dialog
#self.editParametersButton = qt.QPushButton("Edit Parameter Set")
#self.editParametersButton.toolTip = "Editor Statistics Plugin Parameter Set."
#self.parametersLayout.addRow(self.editParametersButton)
#self.editParametersButton.connect('clicked()', self.onEditParameters)
# add caclulator's option widgets
self.addPluginOptionWidgets()
# 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.scalarSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
self.segmentationSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
self.outputTableSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
self.parameterNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onNodeSelectionChanged)
self.parameterNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onParameterSetSelected)
self.parameterNodeSelector.setCurrentNode(self.logic.getParameterNode())
self.onNodeSelectionChanged()
self.onParameterSetSelected()
def enter(self):
"""Runs whenever the module is reopened
"""
if self.parameterNodeSelector.currentNode() is None:
parameterNode = self.logic.getParameterNode()
slicer.mrmlScene.AddNode(parameterNode)
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:
# pluginOptionsCollapsibleButton = ctk.ctkCollapsibleGroupBox()
# pluginOptionsCollapsibleButton.setTitle( plugin.name )
# pluginOptionsFormLayout = qt.QFormLayout(pluginOptionsCollapsibleButton)
# pluginOptionsFormLayout.addRow(plugin.optionsWidget)
# self.parametersLayout.addRow(pluginOptionsCollapsibleButton)
def onParameterSetSelected(self):
if self.parameterNode and self.parameterNodeObserver:
self.parameterNode.RemoveObserver(self.parameterNodeObserver)
self.parameterNode = self.parameterNodeSelector.currentNode()
if self.parameterNode:
self.logic.setParameterNode(self.parameterNode)
self.parameterNodeObserver = self.parameterNode.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.updateGuiFromParameterNode)
self.updateGuiFromParameterNode()
def updateGuiFromParameterNode(self, caller=None, event=None):
if not self.parameterNode:
return
for plugin in self.logic.plugins:
pluginName = plugin.__class__.__name__
parameter = pluginName+'.enabled'
checkbox = self.pluginEnabledCheckboxes[plugin.name]
value = self.parameterNode.GetParameter(parameter)=='True'
if checkbox.checked!=value:
previousState = checkbox.blockSignals(True)
checkbox.checked = value
checkbox.blockSignals(previousState)
def updateParameterNodeFromGui(self):
if not self.parameterNode:
return
for plugin in self.logic.plugins:
pluginName = plugin.__class__.__name__
parameter = pluginName+'.enabled'
checkbox = self.pluginEnabledCheckboxes[plugin.name]
self.parameterNode.SetParameter(parameter, str(checkbox.checked))
def test_WrapSolidify1(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: SegmentEditorWrapSolidify)
"""
self.delayDisplay("Starting test_WrapSolidify1")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
import SampleData
from SegmentStatistics import SegmentStatisticsLogic
##################################
self.delayDisplay("Load master volume")
masterVolumeNode = SampleData.downloadSample('MRBrainTumor1')
##################################
self.delayDisplay("Create segmentation containing a two spheres")
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
features = ["none", "carveCavities", "createShell", "both"]
spheres = [[20, 5, 5, 5], [20, -5, -5, -5]]
appender = vtk.vtkAppendPolyData()
for sphere in spheres:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
for m in features:
segmentName = str(m)
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 WrapSolidify Effect")
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
for t in ["SEGMENTATION", "MODEL"]:
effect.setParameter("outputType", t)
self.delayDisplay(
"Creating Output Type %s, activated feature none" % (t))
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'none'))
effect.setParameter("carveCavities", False)
effect.setParameter("createShell", False)
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature carveCavities" %
(t))
effect.setParameter("carveCavities", True)
effect.setParameter("createShell", False)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'carveCavities'))
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature createShell" % (t))
effect.setParameter("carveCavities", False)
effect.setParameter("createShell", True)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'createShell'))
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature both" % (t))
effect.setParameter("carveCavities", True)
effect.setParameter("createShell", True)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'both'))
effect.self().onApply()
##################################
self.delayDisplay("Creating Segments from Models")
for m in features:
model = slicer.util.getNode(m)
segmentName = "MODEL_%s" % m
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
segmentName))
segment.SetColor(model.GetDisplayNode().GetColor())
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
model.GetPolyData())
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.computeStatistics()
statistics = segStatLogic.getStatistics()
##################################
self.delayDisplay("Check a few numerical results")
# logging.info(round(statistics["none",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_none",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["carveCavities",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_carveCavities",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["createShell",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_createShell",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["both",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_both",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
self.assertEqual(
round(
statistics["none",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46605)
self.assertEqual(
round(
statistics["MODEL_none",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46320)
self.assertEqual(
round(
statistics["carveCavities",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46605)
self.assertEqual(
round(
statistics["MODEL_carveCavities",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46321)
self.assertEqual(
round(
statistics["createShell",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9257)
self.assertEqual(
round(
statistics["MODEL_createShell",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9230)
self.assertEqual(
round(
statistics["both",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9254)
self.assertEqual(
round(
statistics["MODEL_both",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9245)
self.delayDisplay('test_WrapSolidify1 passed')
def test_SurfaceCut1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing fiducials around tumor
- Apply
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorSurfaceCut)
"""
self.delayDisplay("Starting test_SurfaceCut1")
##################################
self.delayDisplay("Load master volume")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
##################################
self.delayDisplay("Create tumor segmentation")
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
segmentName = "Tumor"
import vtkSegmentationCorePython as vtkSegmentationCore
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentationNode.GetSegmentation().GenerateUniqueSegmentID(segmentName))
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("Surface cut")
effect = segmentEditorWidget.activeEffect()
effect.self().fiducialPlacementToggle.placeButton().click()
points =[[2.589283578714074, 44.60536690073953, 27.299999999999997], [8.515228351086698, 35.22262101114956, 27.299999999999997],
[13.700430026912741, 25.099132025013006, 27.299999999999997], [5.799170330415919, 19.17318725264039, 27.299999999999997],
[2.589283578714074, 9.296612632019361, 27.299999999999997], [-10.250263428093263, 12.25958501820567, 27.299999999999997],
[-16.17620820046588, 18.185529790578286, 27.299999999999997], [-20.373752414229813, 27.568275680168263, 27.299999999999997],
[-15.929293834950343, 38.679422128366916, 27.299999999999997], [-11.484835255670887, 44.11153816970849, 27.299999999999997],
[6.539913426962492, 33.49422045254088, 31.499999999999993], [1.354711751136449, 42.383137611099805, 31.499999999999993],
[-8.768777235000101, 44.35845253522401, 31.499999999999993], [-14.200893276341674, 36.70410720424271, 31.499999999999993],
[-18.398437490105607, 27.07444694913721, 31.499999999999993], [-12.719407083248512, 16.704043597485132, 31.499999999999993],
[-7.534205407422476, 11.765756287174618, 31.499999999999993], [0.12013992355882408, 12.25958501820567, 31.499999999999993],
[5.799170330415919, 16.21021486645408, 31.499999999999993], [8.268313985571176, 21.642330907795646, 31.499999999999993],
[13.947344392428263, 26.827532583621682, 31.499999999999993], [-3.0897468281430065, 32.50656299047878, 45.49999999999998],
[2.589283578714074, 27.32136131465274, 45.49999999999998], [-5.3119761177827485, 21.642330907795646, 45.49999999999998],
[-8.02803413845352, 27.32136131465274, 45.49999999999998], [-14.694722007372718, 30.778162431870093, 38.499999999999986],
[-8.02803413845352, 12.01267065269014, 38.499999999999986], [-3.583575559174065, 39.66707959042902, 11.900000000000007],
[3.576941040776184, 31.765819893932196, 11.900000000000007], [0.12013992355882408, 20.901587811249065, 11.900000000000007],
[-9.26260596603116, 28.555933142230366, 11.900000000000007], [6.046084695931441, 38.432507762851394, 17.500000000000007],
[-17.163865662527982, 33.7411348180564, 17.500000000000007], [-14.200893276341674, 21.889245273311168, 17.500000000000007]]
for p in points:
effect.self().segmentMarkupNode.AddFiducialFromArray(p)
effect.self().onApply()
##################################
self.delayDisplay("Make segmentation results nicely visible in 3D")
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility(segmentName, True)
slicer.util.findChild(segmentEditorWidget, "Show3DButton").checked = True
segmentationDisplayNode.SetSegmentOpacity3D("Background",0.5)
##################################
self.delayDisplay("Compute statistics")
from SegmentStatistics import SegmentStatisticsLogic
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter("visibleSegmentsOnly", "False")
segStatLogic.computeStatistics()
# 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")
stats = segStatLogic.getStatistics()
self.assertEqual( round(stats['Tumor', 'LabelmapSegmentStatisticsPlugin.volume_mm3']), 19498.0)
self.delayDisplay('test_SurfaceCut1 passed')
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())
def test_SplitVolume1(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: SegmentEditorSplitVolume)
"""
self.delayDisplay("Starting test_SplitVolume1")
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.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
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("SplitVolume")
effect = segmentEditorWidget.activeEffect()
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("Check extent of cropped volumes")
expectedBounds = [[
100.31225000000003, 119.99975000000003, 101.24974999999999,
119.99974999999999, -78.4, -58.8
],
[
19.68725000000002, 119.99975000000003,
16.874749999999977, 119.99974999999999, -78.4,
16.80000000000001
],
[
-49.687749999999994, 119.99975000000003,
90.93724999999999, 119.99974999999999, -78.4,
-47.6
]]
for segmentIndex in range(
segmentationNode.GetSegmentation().GetNumberOfSegments()):
segmentID = segmentationNode.GetSegmentation().GetNthSegmentID(
segmentIndex)
outputVolumeName = masterVolumeNode.GetName() + '_' + segmentID
outputVolume = slicer.util.getNode(outputVolumeName)
bounds = [0, 0, 0, 0, 0, 0]
outputVolume.GetBounds(bounds)
self.assertEqual(bounds, expectedBounds)
##################################
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_SplitVolume1 passed')
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())