def TestSection_01_GenerateInputData(self):
self.inputSegmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(self.inputSegmentationNode)
# Create new segments
import random
for segmentName in ['first', 'second', 'third']:
sphereSegment = vtkSegmentationCore.vtkSegment()
sphereSegment.SetName(segmentName)
sphereSegment.SetColor(random.uniform(0.0,1.0), random.uniform(0.0,1.0), random.uniform(0.0,1.0))
sphere = vtk.vtkSphereSource()
sphere.SetCenter(random.uniform(0,100),random.uniform(0,100),random.uniform(0,100))
sphere.SetRadius(random.uniform(20,30))
sphere.Update()
spherePolyData = sphere.GetOutput()
sphereSegment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(),
spherePolyData)
self.inputSegmentationNode.GetSegmentation().AddSegment(sphereSegment)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
def TestSection_01_GenerateInputData(self):
logging.info('Test section 1: GenerateInputData')
self.inputSegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
# Create new segments
import random
for segmentName in ['first', 'second', 'third']:
sphereSegment = vtkSegmentationCore.vtkSegment()
sphereSegment.SetName(segmentName)
sphereSegment.SetColor(random.uniform(0.0, 1.0),
random.uniform(0.0, 1.0),
random.uniform(0.0, 1.0))
sphere = vtk.vtkSphereSource()
sphere.SetCenter(random.uniform(0, 100), random.uniform(0, 100),
random.uniform(0, 100))
sphere.SetRadius(random.uniform(20, 30))
sphere.Update()
spherePolyData = sphere.GetOutput()
sphereSegment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
spherePolyData)
self.inputSegmentationNode.GetSegmentation().AddSegment(
sphereSegment)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
3)
self.inputSegmentationNode.CreateDefaultDisplayNodes()
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
def test_SegmentStatisticsBasic(self):
"""
This tests some aspects of the label statistics
"""
self.delayDisplay("Starting test_SegmentStatisticsBasic")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
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()
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentationNode.GetSegmentation().GenerateUniqueSegmentID("Test"))
segment.AddRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(), sphereSource.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)
self.delayDisplay("Check a few numerical results")
self.assertEqual( segStatLogic.statistics["Test_2","LM voxel count"], 9807)
self.assertEqual( segStatLogic.statistics["Test_4","GS 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 _createAndObserveSegment(self):
import vtkSegmentationCorePython as vtkSegmentationCore
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(self._masterVolume.GetName())
# TODO need to think about the reference more in detail. After loading the volume nodes don't occupy the same address
self.mrmlNode.SetReferenceImageGeometryParameterFromVolumeNode(
self._masterVolume)
self.mrmlNode.GetSegmentation().AddSegment(segment)
self.mrmlNode.AddObserver(
vtkSegmentationCore.vtkSegmentation.SegmentModified,
self._onSegmentModified)
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = displayNode.GetSegmentColor('Body_Contour')
self.assertTrue(int(bodyColor[0]*100) == 33 and int(bodyColor[1]*100) == 66 and bodyColor[2] == 0.0)
tumorColor = displayNode.GetSegmentColor('Tumor_Contour')
self.assertTrue(tumorColor[0] == 1.0 and tumorColor[1] == 0.0 and tumorColor[2] == 0.0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0,50,0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetDefaultColor(0.0,0.0,1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName, spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(self.sphereSegment)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.0 and sphereColor[1] == 0.0 and sphereColor[2] == 1.0)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0,4,0,0,0,0)
imageStat.SetComponentOrigin(0,0,0)
imageStat.SetComponentSpacing(1,1,1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 5)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 6)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 2)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.5 and sphereColor[1] == 0.5 and sphereColor[2] == 0.5)
def test_Autoscroll(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: SegmentEditorAutoscroll)
"""
self.delayDisplay("Starting test_Autoscroll")
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 with an empty segment")
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
segment = vtkSegmentationCore.vtkSegment()
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 autoscroll for 10 seconds")
segmentEditorWidget.setActiveEffectByName("Autoscroll")
effect = segmentEditorWidget.activeEffect()
qt.QTimer.singleShot(10000, effect.self().onApply)
effect.self().onApply()
self.delayDisplay('test_Autoscroll passed')
def test_create_report(self):
self.delayDisplay('Starting %s' % inspect.stack()[0][3])
qrWidget = slicer.modules.QuantitativeReportingWidget
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)
self.loadTestVolume()
success, err = qrWidget.saveReport()
self.assertFalse(success)
self.delayDisplay('Add segments')
qrWidget = slicer.modules.QuantitativeReportingWidget
segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()
segmentGeometries = {
'Tumor': [[2, 30, 30, -127.7], [2, 40, 40, -127.7], [2, 50, 50, -127.7], [2, 40, 80, -127.7]],
'Air': [[2, 60, 100, -127.7], [2, 80, 30, -127.7]]
}
for segmentName, segmentGeometry in segmentGeometries.iteritems():
appender = vtk.vtkAppendPolyData()
for sphere in segmentGeometry:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentation.GenerateUniqueSegmentID(segmentName))
appender.Update()
representationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName()
segment.AddRepresentation(representationName, appender.GetOutput())
segmentation.AddSegment(segment)
self.delayDisplay('Save report')
success, err = qrWidget.saveReport()
self.assertTrue(success)
self.delayDisplay('Test passed!')
def test_create_report(self):
self.delayDisplay('Starting %s' % inspect.stack()[0][3])
qrWidget = slicer.modules.QuantitativeReportingWidget
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)
self.loadTestVolume()
success, err = qrWidget.saveReport()
self.assertFalse(success)
self.delayDisplay('Add segments')
qrWidget = slicer.modules.QuantitativeReportingWidget
segmentation = qrWidget.segmentEditorWidget.segmentationNode.GetSegmentation()
segmentGeometries = {
'Tumor': [[2, 30, 30, -127.7], [2, 40, 40, -127.7], [2, 50, 50, -127.7], [2, 40, 80, -127.7]],
'Air': [[2, 60, 100, -127.7], [2, 80, 30, -127.7]]
}
for segmentName, segmentGeometry in six.iteritems(segmentGeometries):
appender = vtk.vtkAppendPolyData()
for sphere in segmentGeometry:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentation.GenerateUniqueSegmentID(segmentName))
appender.Update()
representationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName()
segment.AddRepresentation(representationName, appender.GetOutput())
segmentation.AddSegment(segment)
self.delayDisplay('Save report')
success, err = qrWidget.saveReport()
self.assertTrue(success)
self.delayDisplay('Test passed!')
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
previewNode = self.getPreviewNode()
previewOpacity = self.getPreviewOpacity()
previewShow3D = self.getPreviewShow3D()
# If the selectedSegmentIds have been specified, then they shouldn't be overwritten here
currentSelectedSegmentIds = self.selectedSegmentIds
if self.effectiveExtentChanged():
self.reset()
# Restore the selectedSegmentIds
self.selectedSegmentIds = currentSelectedSegmentIds
if self.selectedSegmentIds is None:
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(
self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues(
) < self.minimumNumberOfSegments:
logging.error(
"Auto-complete operation skipped: at least {0} visible segments are required"
.format(self.minimumNumberOfSegments))
self.selectedSegmentIds = None
return
# Compute merged labelmap extent (effective extent slightly expanded)
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = slicer.vtkOrientedImageData(
)
commonGeometryString = segmentationNode.GetSegmentation(
).DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info(
"Auto-complete operation skipped: all visible segments are empty"
)
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(
commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageData = self.scriptedEffect.masterVolumeImageData()
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent(
)
# Margin size is relative to combined seed region size, but minimum of 3 voxels
print("self.extentGrowthRatio = {0}".format(
self.extentGrowthRatio))
margin = [
int(
max(
3,
self.extentGrowthRatio * (labelsEffectiveExtent[1] -
labelsEffectiveExtent[0]))),
int(
max(
3,
self.extentGrowthRatio * (labelsEffectiveExtent[3] -
labelsEffectiveExtent[2]))),
int(
max(
3,
self.extentGrowthRatio *
(labelsEffectiveExtent[5] - labelsEffectiveExtent[4])))
]
labelsExpandedExtent = [
max(masterImageExtent[0],
labelsEffectiveExtent[0] - margin[0]),
min(masterImageExtent[1],
labelsEffectiveExtent[1] + margin[0]),
max(masterImageExtent[2],
labelsEffectiveExtent[2] - margin[1]),
min(masterImageExtent[3],
labelsEffectiveExtent[3] + margin[1]),
max(masterImageExtent[4],
labelsEffectiveExtent[4] - margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5] + margin[2])
]
print("masterImageExtent = " + repr(masterImageExtent))
print("labelsEffectiveExtent = " + repr(labelsEffectiveExtent))
print("labelsExpandedExtent = " + repr(labelsExpandedExtent))
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
# Create and setup preview node
previewNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(
segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(
ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter(
"SegmentationResultPreviewOwnerEffect",
self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
# Disable smoothing for closed surface generation to make it fast
previewNode.GetSegmentation().SetConversionParameter(
slicer.vtkBinaryLabelmapToClosedSurfaceConversionRule.
GetSmoothingFactorParameterName(), "-0.5")
inputContainsClosedSurfaceRepresentation = segmentationNode.GetSegmentation(
).ContainsRepresentation(
slicer.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName())
self.setPreviewShow3D(inputContainsClosedSurfaceRepresentation)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = slicer.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(
self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(
masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(
self.mergedLabelmapGeometryImage)
self.clippedMaskImageData = None
if self.clippedMaskImageDataRequired:
self.clippedMaskImageData = slicer.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode(
).GetMasterVolumeIntensityMask()
success = segmentationNode.GenerateEditMask(
self.clippedMaskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
self.clippedMasterImageData, # reference geometry
"", # edited segment ID
self.scriptedEffect.parameterSetNode().GetMaskSegmentID()
if
self.scriptedEffect.parameterSetNode().GetMaskSegmentID()
else "",
self.clippedMasterImageData
if intensityBasedMasking else None,
self.scriptedEffect.parameterSetNode(
).GetMasterVolumeIntensityMaskRange()
if intensityBasedMasking else None)
if not success:
logging.error("Failed to create edit mask")
self.clippedMaskImageData = None
previewNode.SetName(segmentationNode.GetName() + " preview")
mergedImage = slicer.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS,
self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = slicer.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in range(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = slicer.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(
segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
self.scriptedEffect.modifySegmentByLabelmap(
previewNode, segmentID, newSegmentLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
# Automatically hide result segments that are background (all eight corners are non-zero)
previewNode.GetDisplayNode().SetSegmentVisibility3D(
segmentID, not self.isBackgroundLabelmap(newSegmentLabelmap))
# If the preview was reset, we need to restore the visibility options
self.setPreviewOpacity(previewOpacity)
self.setPreviewShow3D(previewShow3D)
self.updateGUIFromMRML()
def TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0], [0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(1,1,1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test 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!')
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')
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
previewNode = self.getPreviewNode()
if not previewNode or not self.mergedLabelmapGeometryImage \
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(
self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues(
) < self.minimumNumberOfSegments:
logging.error(
"Auto-complete operation skipped: at least {0} visible segments are required"
.format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData(
)
commonGeometryString = segmentationNode.GetSegmentation(
).DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info(
"Auto-complete operation skipped: all visible segments are empty"
)
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(
commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent(
)
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0],
labelsEffectiveExtent[0] - margin[0]),
min(masterImageExtent[1],
labelsEffectiveExtent[1] + margin[0]),
max(masterImageExtent[2],
labelsEffectiveExtent[2] - margin[1]),
min(masterImageExtent[3],
labelsEffectiveExtent[3] + margin[1]),
max(masterImageExtent[4],
labelsEffectiveExtent[4] - margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5] + margin[2])
]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(
segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(
ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter(
"SegmentationResultPreviewOwnerEffect",
self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData(
)
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(
self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(
masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(
self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName() + " preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS,
self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue)
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(
segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
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!')
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 TestSection_2_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
# Use MRHead and Tinypatient for testing
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
mrVolumeNode = sampleDataLogic.downloadMRHead()
[tinyVolumeNode, tinySegmentationNode] = sampleDataLogic.downloadSample('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.GetSegmentation().SetMasterRepresentationName(binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.GetReferenceImageGeometryParameterName(), geometryStr)
slicer.mrmlScene.AddNode(segmentationNode)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0,0.0,1.0)
segment.AddRepresentation(binaryLabelmapReprName, segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData() # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with no transforms - OK')
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0,3,24.5)
translationTransformMatrix.SetElement(1,3,24.5)
translationTransformMatrix.SetElement(2,3,11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (224.3439, 223.7890, -135.25),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Transformed volume source - OK')
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(23,23,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with isotropic spacing - OK')
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(24.5, 24.5, 11.5), (261.0939, 260.5390, -129.5),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Volume source with oversampling - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(self.compareOutputGeometry(geometryImageData,
(49,49,23), (248.8439, 248.2890, -123.75),
[[0.0, 0.0, 1.0], [0.0, 0.0, 1.0], [0.0, 0.0, 1.0]]))
slicer.util.delayDisplay('Segmentation source with binary labelmap master - OK')
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter('Smoothing factor', '0.0')
self.assertTrue(tinySegmentationNode.GetSegmentation().CreateRepresentation(closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(closedSurfaceReprName)
tinySegmentationNode.Modified() # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
# Manually resample and check if the output is non-empty
# Note: This is done for all poly data based geometry calculations below
#TODO: Come up with proper geometry baselines for these too
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Segmentation source with closed surface master - OK')
# Model source with no transform
outputModelHierarchy = slicer.vtkMRMLModelHierarchyNode()
slicer.mrmlScene.AddNode(outputModelHierarchy)
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModelHierarchy(
tinySegmentationNode, outputModelHierarchy )
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Model source with no transform - OK')
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('Transformed model source - OK')
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0]*3
center = [0]*3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = map(lambda x: x/2.0, xyz)
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData, False, True)
self.assertTrue(self.imageDataContainsData(geometryImageData))
slicer.util.delayDisplay('ROI source - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
colorTableNode = displayNode.GetColorNode()
self.assertIsNotNone(colorTableNode)
self.assertEqual(colorTableNode.GetNumberOfColors(), 3)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = displayNode.GetSegmentColor('Body_Contour')
self.assertTrue(
int(bodyColor[0] * 100) == 33 and int(bodyColor[1] * 100) == 66
and bodyColor[2] == 0.0)
tumorColor = displayNode.GetSegmentColor('Tumor_Contour')
self.assertTrue(tumorColor[0] == 1.0 and tumorColor[1] == 0.0
and tumorColor[2] == 0.0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0, 50, 0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetDefaultColor(0.0, 0.0, 1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName,
spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(
self.sphereSegment)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
3)
self.assertEqual(colorTableNode.GetNumberOfColors(), 4)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.0 and sphereColor[1] == 0.0
and sphereColor[2] == 1.0)
# Check merged labelmap
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(self.inputSegmentationNode.GetImageData())
imageStat.SetComponentExtent(0, 4, 0, 0, 0, 0)
imageStat.SetComponentOrigin(0, 0, 0)
imageStat.SetComponentSpacing(1, 1, 1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 795)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 194)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 5)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 6)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(
self.sphereSegmentName)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
2)
self.assertEqual(colorTableNode.GetNumberOfColors(), 4)
sphereColorArray = [0] * 4
colorTableNode.GetColor(3, sphereColorArray)
self.assertEqual(int(sphereColorArray[0] * 100), 50)
self.assertEqual(int(sphereColorArray[1] * 100), 50)
self.assertEqual(int(sphereColorArray[2] * 100), 50)
sphereColor = displayNode.GetSegmentColor(self.sphereSegmentName)
self.assertTrue(sphereColor[0] == 0.5 and sphereColor[1] == 0.5
and sphereColor[2] == 0.5)
def test_SegmentEditorHollow1(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: SegmentEditorHollow)
"""
self.delayDisplay("Starting test_SegmentEditorHollow1")
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("Hollow")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("ShellThicknessMm", 3.0)
effect.setParameter("ShellMode", "MEDIAL_SURFACE")
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('test_SegmentEditorHollow1 passed')
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = self.inputSegmentationNode.GetSegmentation().GetSegment('Body_Contour').GetColor()
logging.info("bodyColor: {0}".format(bodyColor))
self.assertEqual(int(bodyColor[0]*100), 33)
self.assertEqual(int(bodyColor[1]*100), 66)
self.assertEqual(int(bodyColor[2]*100), 0)
tumorColor = self.inputSegmentationNode.GetSegmentation().GetSegment('Tumor_Contour').GetColor()
logging.info("tumorColor: {0}".format(tumorColor))
self.assertEqual(int(tumorColor[0]*100), 100)
self.assertEqual(int(tumorColor[1]*100), 0)
self.assertEqual(int(tumorColor[2]*100), 0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0,50,0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetColor(0.0,0.0,1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName, spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(self.sphereSegment)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 3)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0,4,0,0,0,0)
imageStat.SetComponentOrigin(0,0,0)
imageStat.SetComponentSpacing(1,1,1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 4)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 7)
# Check if segment reorder is taken into account in merged labelmap generation
# Change segment order
sphereSegmentId = self.inputSegmentationNode.GetSegmentation().GetSegmentIdBySegment(self.sphereSegment)
self.inputSegmentationNode.GetSegmentation().SetSegmentIndex(sphereSegmentId, 1)
# Re-generate merged labelmap
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(mergedLabelmap, 0)
imageStat.SetInputData(mergedLabelmap)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 795)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 194)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 6)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 5)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 2)
def test_SegmentStatisticsBasic(self):
"""
This tests some aspects of the label statistics
"""
self.delayDisplay("Starting test_SegmentStatisticsBasic")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
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()
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
"Test"))
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
sphereSource.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)
self.delayDisplay("Check a few numerical results")
self.assertEqual(segStatLogic.statistics["Test_2", "LM voxel count"],
9807)
self.assertEqual(segStatLogic.statistics["Test_4", "GS 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 test_Engrave1(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: SegmentEditorEngrave)
"""
self.delayDisplay("Starting test_Engrave1")
##################################
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("ENgrave")
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.AddControlPoint(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_Engrave1 passed')
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
previewNode = self.getPreviewNode()
if (not previewNode or not self.mergedLabelmapGeometryImage
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData)):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues() < self.minimumNumberOfSegments:
logging.error("Auto-complete operation skipped: at least {0} visible segments are required".format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
# Margin size is relative to combined seed region size, but minimum of 3 voxels
print("self.extentGrowthRatio = {0}".format(self.extentGrowthRatio))
margin = [
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[1]-labelsEffectiveExtent[0]))),
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[3]-labelsEffectiveExtent[2]))),
int(max(3, self.extentGrowthRatio * (labelsEffectiveExtent[5]-labelsEffectiveExtent[4]))) ]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
print("masterImageExtent = "+repr(masterImageExtent))
print("labelsEffectiveExtent = "+repr(labelsEffectiveExtent))
print("labelsExpandedExtent = "+repr(labelsExpandedExtent))
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
# Create and setup preview node
previewNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter("SegmentationResultPreviewOwnerEffect", self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
# Disable smoothing for closed surface generation to make it fast
previewNode.GetSegmentation().SetConversionParameter(
slicer.vtkBinaryLabelmapToClosedSurfaceConversionRule.GetSmoothingFactorParameterName(),
"-0.5");
inputContainsClosedSurfaceRepresentation = segmentationNode.GetSegmentation().ContainsRepresentation(
slicer.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName())
self.setPreviewShow3D(inputContainsClosedSurfaceRepresentation)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
self.clippedMaskImageData = None
if self.clippedMaskImageDataRequired:
self.clippedMaskImageData = vtkSegmentationCore.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMask()
success = segmentationNode.GenerateEditMask(self.clippedMaskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
self.clippedMasterImageData, # reference geometry
"", # edited segment ID
self.scriptedEffect.parameterSetNode().GetMaskSegmentID() if self.scriptedEffect.parameterSetNode().GetMaskSegmentID() else "",
self.clippedMasterImageData if intensityBasedMasking else None,
self.scriptedEffect.parameterSetNode().GetMasterVolumeIntensityMaskRange() if intensityBasedMasking else None)
if not success:
logging.error("Failed to create edit mask")
self.clippedMaskImageData = None
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
# Automatically hide result segments that are background (all eight corners are non-zero)
previewNode.GetDisplayNode().SetSegmentVisibility3D(segmentID, not self.isBackgroundLabelmap(newSegmentLabelmap))
self.updateGUIFromMRML()
def preview(self):
# Get source volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
previewNode = self.getPreviewNode()
previewOpacity = self.getPreviewOpacity()
previewShow3D = self.getPreviewShow3D()
# If the selectedSegmentIds have been specified, then they shouldn't be overwritten here
currentSelectedSegmentIds = self.selectedSegmentIds
if self.effectiveExtentChanged():
self.reset()
# Restore the selectedSegmentIds
self.selectedSegmentIds = currentSelectedSegmentIds
if self.selectedSegmentIds is None:
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(
self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues(
) < self.minimumNumberOfSegments:
logging.error(
f"Auto-complete operation skipped: at least {self.minimumNumberOfSegments} visible segments are required"
)
self.selectedSegmentIds = None
return
# Compute merged labelmap extent (effective extent slightly expanded)
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = slicer.vtkOrientedImageData(
)
commonGeometryString = segmentationNode.GetSegmentation(
).DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info(
"Auto-complete operation skipped: all visible segments are empty"
)
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(
commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageData = self.scriptedEffect.sourceVolumeImageData()
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent(
)
# Margin size is relative to combined seed region size, but minimum of 3 voxels
print(f"self.extentGrowthRatio = {self.extentGrowthRatio}")
margin = [
int(
max(
3,
self.extentGrowthRatio * (labelsEffectiveExtent[1] -
labelsEffectiveExtent[0]))),
int(
max(
3,
self.extentGrowthRatio * (labelsEffectiveExtent[3] -
labelsEffectiveExtent[2]))),
int(
max(
3,
self.extentGrowthRatio *
(labelsEffectiveExtent[5] - labelsEffectiveExtent[4])))
]
labelsExpandedExtent = [
max(masterImageExtent[0],
labelsEffectiveExtent[0] - margin[0]),
min(masterImageExtent[1],
labelsEffectiveExtent[1] + margin[0]),
max(masterImageExtent[2],
labelsEffectiveExtent[2] - margin[1]),
min(masterImageExtent[3],
labelsEffectiveExtent[3] + margin[1]),
max(masterImageExtent[4],
labelsEffectiveExtent[4] - margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5] + margin[2])
]
print("masterImageExtent = " + repr(masterImageExtent))
print("labelsEffectiveExtent = " + repr(labelsEffectiveExtent))
print("labelsExpandedExtent = " + repr(labelsExpandedExtent))
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
# Create and setup preview node
previewNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(
segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(
ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter(
"SegmentationResultPreviewOwnerEffect",
self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
# Disable smoothing for closed surface generation to make it fast
previewNode.GetSegmentation().SetConversionParameter(
slicer.vtkBinaryLabelmapToClosedSurfaceConversionRule.
GetSmoothingFactorParameterName(), "-0.5")
inputContainsClosedSurfaceRepresentation = segmentationNode.GetSegmentation(
).ContainsRepresentation(
slicer.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName())
self.setPreviewShow3D(inputContainsClosedSurfaceRepresentation)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = slicer.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(
self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(
masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(
self.mergedLabelmapGeometryImage)
self.clippedMaskImageData = None
if self.clippedMaskImageDataRequired:
self.clippedMaskImageData = slicer.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode(
).GetSourceVolumeIntensityMask()
maskSegmentID = self.scriptedEffect.parameterSetNode(
).GetMaskSegmentID() if self.scriptedEffect.parameterSetNode(
).GetMaskSegmentID() else ""
intensityRange = self.scriptedEffect.parameterSetNode(
).GetSourceVolumeIntensityMaskRange(
) if intensityBasedMasking else None
success = segmentationNode.GenerateEditMask(
self.clippedMaskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
self.clippedMasterImageData, # reference geometry
"", # edited segment ID
maskSegmentID,
self.clippedMasterImageData
if intensityBasedMasking else None,
intensityRange)
if not success:
logging.error("Failed to create edit mask")
self.clippedMaskImageData = None
previewNode.SetName(segmentationNode.GetName() + " preview")
previewNode.RemoveClosedSurfaceRepresentation(
) # Force the closed surface representation to update
# TODO: This will no longer be required when we can use the segment editor to set multiple segments
# as the closed surfaces will be converted as necessary by the segmentation logic.
mergedImage = slicer.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage, vtkSegmentationCore.vtkSegmentation.
EXTENT_UNION_OF_EFFECTIVE_SEGMENTS,
self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = slicer.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
if previewNode.GetSegmentation().GetNumberOfSegments(
) != self.selectedSegmentIds.GetNumberOfValues():
# first update (or number of segments changed), need a full reinitialization
previewNode.GetSegmentation().RemoveAllSegments()
for index in range(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
previewSegment = previewNode.GetSegmentation().GetSegment(
segmentID)
if not previewSegment:
inputSegment = segmentationNode.GetSegmentation().GetSegment(
segmentID)
previewSegment = vtkSegmentationCore.vtkSegment()
previewSegment.SetName(inputSegment.GetName())
previewSegment.SetColor(inputSegment.GetColor())
previewNode.GetSegmentation().AddSegment(
previewSegment, segmentID)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
previewSegment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName(),
outputLabelmap)
previewSegment.SetLabelValue(labelValue)
# Automatically hide result segments that are background (all eight corners are non-zero)
previewNode.GetDisplayNode().SetSegmentVisibility3D(
segmentID,
not self.isBackgroundLabelmap(outputLabelmap, labelValue))
# If the preview was reset, we need to restore the visibility options
self.setPreviewOpacity(previewOpacity)
self.setPreviewShow3D(previewShow3D)
self.updateGUIFromMRML()
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
previewNode = self.getPreviewNode()
if not previewNode or not self.mergedLabelmapGeometryImage \
or (self.clippedMasterImageDataRequired and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
if self.selectedSegmentIds.GetNumberOfValues() < self.minimumNumberOfSegments:
logging.error("Auto-complete operation skipped: at least {0} visible segments are required".format(self.minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.scriptedEffect.setCommonParameter("SegmentationResultPreviewOwnerEffect", self.scriptedEffect.name)
self.setPreviewOpacity(0.6)
if self.clippedMasterImageDataRequired:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.computePreviewLabelmap(mergedImage, outputLabelmap)
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
def TestSection_1_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section 1: Add/remove segment')
# Get baseline values
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
# If segments are not found then the returned color is the pre-defined invalid color
bodyColor = self.inputSegmentationNode.GetSegmentation().GetSegment(
'Body_Contour').GetColor()
logging.info("bodyColor: {0}".format(bodyColor))
self.assertEqual(int(bodyColor[0] * 100), 33)
self.assertEqual(int(bodyColor[1] * 100), 66)
self.assertEqual(int(bodyColor[2] * 100), 0)
tumorColor = self.inputSegmentationNode.GetSegmentation().GetSegment(
'Tumor_Contour').GetColor()
logging.info("tumorColor: {0}".format(tumorColor))
self.assertEqual(int(tumorColor[0] * 100), 100)
self.assertEqual(int(tumorColor[1] * 100), 0)
self.assertEqual(int(tumorColor[2] * 100), 0)
# Create new segment
sphere = vtk.vtkSphereSource()
sphere.SetCenter(0, 50, 0)
sphere.SetRadius(50)
sphere.Update()
spherePolyData = vtk.vtkPolyData()
spherePolyData.DeepCopy(sphere.GetOutput())
self.sphereSegment = vtkSegmentationCore.vtkSegment()
self.sphereSegment.SetName(self.sphereSegmentName)
self.sphereSegment.SetColor(0.0, 0.0, 1.0)
self.sphereSegment.AddRepresentation(self.closedSurfaceReprName,
spherePolyData)
# Add segment to segmentation
self.inputSegmentationNode.GetSegmentation().AddSegment(
self.sphereSegment)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
3)
# Check merged labelmap
mergedLabelmap = vtkSegmentationCore.vtkOrientedImageData()
self.inputSegmentationNode.GetSegmentation().CreateRepresentation(
self.binaryLabelmapReprName)
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(
mergedLabelmap, 0)
imageStat = vtk.vtkImageAccumulate()
imageStat.SetInputData(mergedLabelmap)
imageStat.SetComponentExtent(0, 4, 0, 0, 0, 0)
imageStat.SetComponentOrigin(0, 0, 0)
imageStat.SetComponentSpacing(1, 1, 1)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(
i, imageStatResult.GetScalarComponentAsDouble(i, 0, 0, 0)))
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 795)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 194)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 4)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 7)
# Check if segment reorder is taken into account in merged labelmap generation
# Change segment order
sphereSegmentId = self.inputSegmentationNode.GetSegmentation(
).GetSegmentIdBySegment(self.sphereSegment)
self.inputSegmentationNode.GetSegmentation().SetSegmentIndex(
sphereSegmentId, 1)
# Re-generate merged labelmap
self.inputSegmentationNode.GenerateMergedLabelmapForAllSegments(
mergedLabelmap, 0)
imageStat.SetInputData(mergedLabelmap)
imageStat.Update()
self.assertEqual(imageStat.GetVoxelCount(), 1000)
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(
i, imageStatResult.GetScalarComponentAsDouble(i, 0, 0, 0)))
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 795)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 194)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 6)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 5)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(
self.sphereSegmentName)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
2)
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 _addInitialSegment(self):
import vtkSegmentationCorePython as vtkSegmentationCore
segment = vtkSegmentationCore.vtkSegment()
segment.SetName("Prostate Segmentation")
self._segmentationNode.GetSegmentation().AddSegment(segment)
def TestSection_03_qMRMLSegmentationGeometryWidget(self):
logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
import vtkSegmentationCore
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName(
)
closedSurfaceReprName = vtkSegmentationCore.vtkSegmentationConverter.GetClosedSurfaceRepresentationName(
)
# Use MRHead and Tinypatient for testing
import SampleData
mrVolumeNode = SampleData.downloadSample("MRHead")
[tinyVolumeNode,
tinySegmentationNode] = SampleData.downloadSamples('TinyPatient')
# Convert MRHead to oriented image data
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
mrOrientedImageData = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(
mrVolumeNode)
mrOrientedImageData.UnRegister(None)
# Create segmentation node with binary labelmap master and one segment with MRHead geometry
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.GetSegmentation().SetMasterRepresentationName(
binaryLabelmapReprName)
geometryStr = vtkSegmentationCore.vtkSegmentationConverter.SerializeImageGeometry(
mrOrientedImageData)
segmentationNode.GetSegmentation().SetConversionParameter(
vtkSegmentationCore.vtkSegmentationConverter.
GetReferenceImageGeometryParameterName(), geometryStr)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(mrOrientedImageData)
threshold.ThresholdByUpper(16.0)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
threshold.Update()
segmentOrientedImageData = vtkSegmentationCore.vtkOrientedImageData()
segmentOrientedImageData.DeepCopy(threshold.GetOutput())
mrImageToWorldMatrix = vtk.vtkMatrix4x4()
mrOrientedImageData.GetImageToWorldMatrix(mrImageToWorldMatrix)
segmentOrientedImageData.SetImageToWorldMatrix(mrImageToWorldMatrix)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName('Brain')
segment.SetColor(0.0, 0.0, 1.0)
segment.AddRepresentation(binaryLabelmapReprName,
segmentOrientedImageData)
segmentationNode.GetSegmentation().AddSegment(segment)
# Create geometry widget
geometryWidget = slicer.qMRMLSegmentationGeometryWidget()
geometryWidget.setSegmentationNode(segmentationNode)
geometryWidget.editEnabled = True
geometryImageData = vtkSegmentationCore.vtkOrientedImageData(
) # To contain the output later
# Volume source with no transforms
geometryWidget.setSourceNode(tinyVolumeNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Transformed volume source
translationTransformMatrix = vtk.vtkMatrix4x4()
translationTransformMatrix.SetElement(0, 3, 24.5)
translationTransformMatrix.SetElement(1, 3, 24.5)
translationTransformMatrix.SetElement(2, 3, 11.5)
translationTransformNode = slicer.vtkMRMLLinearTransformNode()
translationTransformNode.SetName('TestTranslation')
slicer.mrmlScene.AddNode(translationTransformNode)
translationTransformNode.SetMatrixTransformToParent(
translationTransformMatrix)
tinyVolumeNode.SetAndObserveTransformNodeID(
translationTransformNode.GetID())
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (224.3439, 223.7890, -135.25),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 94)
# Volume source with isotropic spacing
tinyVolumeNode.SetAndObserveTransformNodeID(None)
geometryWidget.setIsotropicSpacing(True)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (23, 23, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 414)
# Volume source with oversampling
geometryWidget.setIsotropicSpacing(False)
geometryWidget.setOversamplingFactor(2.0)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (24.5, 24.5, 11.5),
(261.0939, 260.5390, -129.5),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 751)
slicer.util.delayDisplay('Volume source cases - OK')
# Segmentation source with binary labelmap master
geometryWidget.setOversamplingFactor(1.0)
geometryWidget.setSourceNode(tinySegmentationNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (49, 49, 23), (248.8439, 248.2890, -123.75),
[[-1.0, 0.0, 0.0], [0.0, -1.0, 0.0], [0.0, 0.0, 1.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData), 92)
# Segmentation source with closed surface master
tinySegmentationNode.GetSegmentation().SetConversionParameter(
'Smoothing factor', '0.0')
self.assertTrue(
tinySegmentationNode.GetSegmentation().CreateRepresentation(
closedSurfaceReprName))
tinySegmentationNode.GetSegmentation().SetMasterRepresentationName(
closedSurfaceReprName)
tinySegmentationNode.Modified(
) # Trigger re-calculation of geometry (only generic Modified event is observed)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Segmentation source cases - OK')
# Model source with no transform
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
outputFolderId = shNode.CreateFolderItem(shNode.GetSceneItemID(),
'ModelsFolder')
success = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.ExportVisibleSegmentsToModels(
tinySegmentationNode, outputFolderId)
self.assertTrue(success)
modelNode = slicer.util.getNode('Body_Contour')
geometryWidget.setSourceNode(modelNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
# Transformed model source
rotationTransform = vtk.vtkTransform()
rotationTransform.RotateX(45)
rotationTransformMatrix = vtk.vtkMatrix4x4()
rotationTransform.GetMatrix(rotationTransformMatrix)
rotationTransformNode = slicer.vtkMRMLLinearTransformNode()
rotationTransformNode.SetName('TestRotation')
slicer.mrmlScene.AddNode(rotationTransformNode)
rotationTransformNode.SetMatrixTransformToParent(
rotationTransformMatrix)
modelNode.SetAndObserveTransformNodeID(rotationTransformNode.GetID())
modelNode.Modified()
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-167.156, -58.6623, -249.228),
[[0.0, 0.0, 1.0], [-0.7071, -0.7071, 0.0],
[0.7071, -0.7071, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5221241)
# ROI source
roiNode = slicer.vtkMRMLAnnotationROINode()
roiNode.SetName('SourceROI')
slicer.mrmlScene.AddNode(roiNode)
roiNode.UnRegister(None)
xyz = [0] * 3
center = [0] * 3
slicer.vtkMRMLSliceLogic.GetVolumeRASBox(tinyVolumeNode, xyz, center)
radius = [x / 2.0 for x in xyz]
roiNode.SetXYZ(center)
roiNode.SetRadiusXYZ(radius)
geometryWidget.setSourceNode(roiNode)
geometryWidget.geometryImageData(geometryImageData)
self.assertTrue(
self.compareOutputGeometry(
geometryImageData, (1, 1, 1), (-216.156, -217.711, -135.75),
[[0.0, 0.0, 1.0], [-1.0, 0.0, 0.0], [0.0, -1.0, 0.0]]))
vtkSegmentationCore.vtkOrientedImageDataResample.ResampleOrientedImageToReferenceOrientedImage(
segmentOrientedImageData, geometryImageData, geometryImageData,
False, True)
self.assertEqual(self.getForegroundVoxelCount(geometryImageData),
5223846)
slicer.util.delayDisplay('Model and ROI source cases - OK')
slicer.util.delayDisplay('Segmentation geometry widget test passed')
def load(self, loadable):
""" Load the DICOM SEG object
"""
logging.debug('DICOM SEG load()')
try:
uid = loadable.uid
logging.debug('in load(): uid = ', uid)
except AttributeError:
return False
self.tempDir = os.path.join(slicer.app.temporaryPath, "QIICR", "SEG",
self.currentDateTime, loadable.uid)
try:
os.makedirs(self.tempDir)
except OSError:
pass
# produces output label map files, one per segment, and information files with
# the terminology information for each segment
segFileName = slicer.dicomDatabase.fileForInstance(uid)
if segFileName is None:
logging.error(
'Failed to get the filename from the DICOM database for ' +
uid)
self.cleanup()
return False
parameters = {
"inputSEGFileName": segFileName,
"outputDirName": self.tempDir,
}
try:
segimage2itkimage = slicer.modules.segimage2itkimage
except AttributeError:
logging.error(
'Unable to find CLI module segimage2itkimage, unable to load DICOM Segmentation object'
)
self.cleanup()
return False
cliNode = None
cliNode = slicer.cli.run(segimage2itkimage,
cliNode,
parameters,
wait_for_completion=True)
if cliNode.GetStatusString() != 'Completed':
logging.error(
'SEG2NRRD did not complete successfully, unable to load DICOM Segmentation'
)
self.cleanup()
return False
numberOfSegments = len(glob.glob(os.path.join(self.tempDir, '*.nrrd')))
# resize the color table to include the segments plus 0 for the background
seriesName = self.referencedSeriesName(loadable)
segmentLabelNodes = []
metaFileName = os.path.join(self.tempDir, "meta.json")
# Load terminology in the metafile into context
terminologiesLogic = slicer.modules.terminologies.logic()
terminologiesLogic.LoadTerminologyFromSegmentDescriptorFile(
loadable.name, metaFileName)
terminologiesLogic.LoadAnatomicContextFromSegmentDescriptorFile(
loadable.name, metaFileName)
with open(metaFileName) as metaFile:
data = json.load(metaFile)
logging.debug('number of segmentation files = ' +
str(numberOfSegments))
if numberOfSegments != len(data["segmentAttributes"]):
logging.error(
'Loading failed: Inconsistent number of segments in the descriptor file and on disk'
)
return
for segmentAttributes in data["segmentAttributes"]:
# TODO: only handles the first item of lists
for segment in segmentAttributes:
# load each of the segments' segmentations
# Initialize color and terminology from .info file
# See SEG2NRRD.cxx and EncodeSEG.cxx for how it's written.
# Format of the .info file (no leading spaces, labelNum, RGBColor, SegmentedPropertyCategory and
# SegmentedPropertyCategory are required):
# labelNum;RGB:R,G,B;SegmentedPropertyCategory:code,scheme,meaning;SegmentedPropertyType:code,scheme,meaning;SegmentedPropertyTypeModifier:code,scheme,meaning;AnatomicRegion:code,scheme,meaning;AnatomicRegionModifier:code,scheme,meaning
# R, G, B are 0-255 in file, but mapped to 0-1 for use in color node
# set defaults in case of missing fields, modifiers are optional
try:
rgb255 = segment["recommendedDisplayRGBValue"]
rgb = map(lambda c: float(c) / 255., rgb255)
except KeyError:
rgb = (0., 0., 0.)
segmentId = segment["LabelID"]
defaults = ['T-D0050', 'Tissue', 'SRT']
categoryCode, categoryCodingScheme, categoryCodeMeaning = \
self.getValuesFromCodeSequence(segment, "SegmentedPropertyCategoryCodeSequence", defaults)
typeCode, typeCodingScheme, typeCodeMeaning = \
self.getValuesFromCodeSequence(segment, "SegmentedPropertyTypeCodeSequence", defaults)
typeModCode, typeModCodingScheme, typeModCodeMeaning = \
self.getValuesFromCodeSequence(segment, "SegmentedPropertyTypeModifierCodeSequence")
anatomicRegionDefaults = ['T-D0010', 'SRT', 'Entire Body']
regionCode, regionCodingScheme, regionCodeMeaning = \
self.getValuesFromCodeSequence(segment, "AnatomicRegionCodeSequence", anatomicRegionDefaults)
regionModCode, regionModCodingScheme, regionModCodeMeaning = \
self.getValuesFromCodeSequence(segment, "AnatomicRegionModifierCodeSequence")
dummyTerminologyWidget = slicer.qSlicerTerminologyNavigatorWidget(
) # Still cannot call static methods from python
segmentTerminologyTag = dummyTerminologyWidget.serializeTerminologyEntry(
loadable.name, categoryCode, categoryCodingScheme,
categoryCodeMeaning, typeCode, typeCodingScheme,
typeCodeMeaning, typeModCode, typeModCodingScheme,
typeModCodeMeaning, loadable.name, regionCode,
regionCodingScheme, regionCodeMeaning, regionModCode,
regionModCodingScheme, regionModCodeMeaning)
# end of processing a line of terminology
# TODO: Create logic class that both CLI and this plugin uses so that we don't need to have temporary NRRD files and labelmap nodes
# if not hasattr(slicer.modules, 'segmentations'):
# load the segmentation volume file and name it for the reference series and segment color
labelFileName = os.path.join(self.tempDir,
str(segmentId) + ".nrrd")
segmentName = seriesName + "-" + typeCodeMeaning + "-label"
(success, labelNode) = slicer.util.loadLabelVolume(
labelFileName,
properties={'name': segmentName},
returnNode=True)
if not success:
raise ValueError(
"{} could not be loaded into Slicer!".format(
labelFileName))
segmentLabelNodes.append(labelNode)
# Set terminology properties as attributes to the label node (which is a temporary node)
#TODO: This is a quick solution, maybe there is a better one
labelNode.SetAttribute("Terminology",
segmentTerminologyTag)
labelNode.SetAttribute("ColorR", str(rgb[0]))
labelNode.SetAttribute("ColorG", str(rgb[1]))
labelNode.SetAttribute("ColorB", str(rgb[2]))
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, labelNode)
metaFile.close()
self.cleanup()
import vtkSegmentationCorePython as vtkSegmentationCore
segmentationNode = slicer.vtkMRMLSegmentationNode()
segmentationNode.SetName(seriesName)
slicer.mrmlScene.AddNode(segmentationNode)
segmentationDisplayNode = slicer.vtkMRMLSegmentationDisplayNode()
slicer.mrmlScene.AddNode(segmentationDisplayNode)
segmentationNode.SetAndObserveDisplayNodeID(
segmentationDisplayNode.GetID())
segmentation = vtkSegmentationCore.vtkSegmentation()
segmentation.SetMasterRepresentationName(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName())
segmentationNode.SetAndObserveSegmentation(segmentation)
self.addSeriesInSubjectHierarchy(loadable, segmentationNode)
for segmentLabelNode in segmentLabelNodes:
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentLabelNode.GetName())
segmentColor = [
float(segmentLabelNode.GetAttribute("ColorR")),
float(segmentLabelNode.GetAttribute("ColorG")),
float(segmentLabelNode.GetAttribute("ColorB"))
]
segment.SetColor(segmentColor)
segment.SetTag(
vtkSegmentationCore.vtkSegment.GetTerminologyEntryTagName(),
segmentLabelNode.GetAttribute("Terminology"))
#TODO: when the logic class is created, this will need to be changed
orientedImage = slicer.vtkSlicerSegmentationsModuleLogic.CreateOrientedImageDataFromVolumeNode(
segmentLabelNode)
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName(),
orientedImage)
segmentation.AddSegment(segment)
segmentDisplayNode = segmentLabelNode.GetDisplayNode()
if segmentDisplayNode is not None:
slicer.mrmlScene.RemoveNode(segmentDisplayNode)
slicer.mrmlScene.RemoveNode(segmentLabelNode)
segmentation.CreateRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(), True)
return True
