def createSampleLabelmapVolumeNode(self, volumeNode, name, label, colorNode=None):
self.assertTrue( volumeNode != None )
self.assertTrue( volumeNode.IsA('vtkMRMLScalarVolumeNode') )
self.assertTrue( label > 0 )
sampleLabelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
sampleLabelmapNode.SetName(name)
sampleLabelmapNode = slicer.mrmlScene.AddNode(sampleLabelmapNode)
sampleLabelmapNode.Copy(volumeNode)
imageData = vtk.vtkImageData()
imageData.DeepCopy(volumeNode.GetImageData())
sampleLabelmapNode.SetAndObserveImageData(imageData)
extent = imageData.GetExtent()
for x in xrange(extent[0], extent[1]+1):
for y in xrange(extent[2], extent[3]+1):
for z in xrange(extent[4], extent[5]+1):
if (x >= (extent[1]/4) and x <= (extent[1]/4) * 3) and (y >= (extent[3]/4) and y <= (extent[3]/4) * 3) and (z >= (extent[5]/4) and z <= (extent[5]/4) * 3):
imageData.SetScalarComponentFromDouble(x,y,z,0,label)
else:
imageData.SetScalarComponentFromDouble(x,y,z,0,0)
# Display labelmap
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
if colorNode == None:
colorNode = slicer.util.getNode('GenericAnatomyColors')
self.assertTrue( colorNode != None )
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelmapVolumeDisplayNode.VisibilityOn()
sampleLabelmapNodeName = slicer.mrmlScene.GenerateUniqueName(name)
sampleLabelmapNode.SetName(sampleLabelmapNodeName)
sampleLabelmapNode.SetAndObserveDisplayNodeID(labelmapVolumeDisplayNode.GetID())
return sampleLabelmapNode
def createSampleLabelmapVolumeNode(self, volumeNode, name, label, colorNode=None):
self.assertIsNotNone( volumeNode )
self.assertTrue( volumeNode.IsA('vtkMRMLScalarVolumeNode') )
self.assertTrue( label > 0 )
sampleLabelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
sampleLabelmapNode.SetName(name)
sampleLabelmapNode = slicer.mrmlScene.AddNode(sampleLabelmapNode)
sampleLabelmapNode.Copy(volumeNode)
imageData = sampleLabelmapNode.GetImageData()
extent = imageData.GetExtent()
for x in range(extent[0], extent[1]+1):
for y in range(extent[2], extent[3]+1):
for z in range(extent[4], extent[5]+1):
if ( (x >= (extent[1]/4) and x <= (extent[1]/4) * 3) and
(y >= (extent[3]/4) and y <= (extent[3]/4) * 3) and
(z >= (extent[5]/4) and z <= (extent[5]/4) * 3) ):
imageData.SetScalarComponentFromDouble(x,y,z,0,label)
else:
imageData.SetScalarComponentFromDouble(x,y,z,0,0)
# Display labelmap
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
if colorNode is None:
colorNode = slicer.util.getNode('GenericAnatomyColors')
self.assertIsNotNone( colorNode )
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelmapVolumeDisplayNode.VisibilityOn()
sampleLabelmapName = slicer.mrmlScene.GenerateUniqueName(name)
sampleLabelmapNode.SetName(sampleLabelmapName)
sampleLabelmapNode.SetAndObserveDisplayNodeID(labelmapVolumeDisplayNode.GetID())
return sampleLabelmapNode
def createStatsChart(self, labelNode, valueToPlot):
"""Make a MRML chart of the current stats
"""
self.setChartLayout()
chartViewNode = slicer.util.getNode('ChartView')
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
samples = len(self.regionTags)
tuples = samples
array.SetNumberOfTuples(tuples)
tuple = 0
for i in xrange(samples):
index = self.regionTags[i]
array.SetComponent(tuple, 0, i)
array.SetComponent(tuple, 1, self.labelStats[valueToPlot, index])
array.SetComponent(tuple, 2, 0)
tuple += 1
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray(valueToPlot, arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Parenchyma Statistics')
chartNode.SetProperty('default', 'xAxisLabel', 'Label')
chartNode.SetProperty('default', 'yAxisLabel', valueToPlot)
chartNode.SetProperty('default', 'type', 'Bar')
chartNode.SetProperty('default', 'xAxisType', 'categorical')
chartNode.SetProperty('default', 'showLegend', 'off')
# series level properties
if labelNode.GetDisplayNode() != None and labelNode.GetDisplayNode(
).GetColorNode() != None:
colorNode = labelNode.GetDisplayNode().GetColorNode()
newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
newDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
slicer.mrmlScene.AddNode(newDisplayNode)
newColorNode = newDisplayNode.GetColorNode()
colorNumber = 0
for tag in self.regionTags:
c = [0, 0, 0, 0]
value = self.valuesDictionary[tag]
if value[0] == value[1]:
colorNode.SetColorName(value[0], tag)
colorNode.GetColor(value[0], c)
newColorNode.SetColor(colorNumber, c[0], c[1], c[2])
newColorNode.SetColorName(colorNumber, tag)
colorNumber += 1
# chartNode.SetProperty(valueToPlot, 'lookupTable', labelNode.GetDisplayNode().GetColorNodeID())
chartNode.SetProperty(valueToPlot, 'lookupTable',
newColorNode.GetID())
def test_USGeometry_CreateScanlines(self):
""" Ideally you should have several levels of tests. At the lowest level
tests should exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting CreateScanlines test")
# Setup testing data
import urllib
xmlFileName = 'SpineUltrasound-Lumbar-C5_config.xml'
testDataPath = 'https://raw.githubusercontent.com/Mattel/USBoneSegmentation/master/USGeometry/Testing/Data/Curvilinear/'
downloads = (
(testDataPath+'SpineUltrasound-Lumbar-C5-Trimmed.mha', 'SpineUltrasound-Lumbar-C5-Trimmed.mha', slicer.util.loadLabelVolume),
(testDataPath+'SpineUltrasound-Lumbar-C5_config.xml', xmlFileName, None),
(testDataPath+'GroundTruth/SpineUltrasound-Lumbar-C5_Scanline_GroundTruth.mha', 'Curvilinear_Scanline_GroundTruth.mha', slicer.util.loadLabelVolume)
)
# Load testing data
for url,name,loader in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
logging.info('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
logging.info('Loading %s...' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading')
volumeNode = slicer.util.getNode(pattern="SpineUltrasound-Lumbar-C5-Trimmed")
groundTruthNode = slicer.util.getNode(pattern="Curvilinear_Scanline_GroundTruth")
logic = USGeometryLogic(slicer.app.temporaryPath+'/'+xmlFileName, volumeNode)
scanlineNode = slicer.vtkMRMLLabelMapVolumeNode()
scanlineNode.SetName("Scanline_Test")
slicer.mrmlScene.AddNode(scanlineNode)
scanlineDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
colorNode = slicer.util.getNode('GenericAnatomyColors')
scanlineDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
slicer.mrmlScene.AddNode(scanlineDisplayNode)
scanlineNode.AddAndObserveDisplayNodeID(scanlineDisplayNode.GetID())
self.delayDisplay("Running createScanlines...")
logic.createScanlines(scanlineNode)
volumeEqualityCheck = self.compareVolumes(groundTruthNode, scanlineNode)
if volumeEqualityCheck == True:
self.delayDisplay('Scanline test passed!')
else:
self.delayDisplay('Scanline test failed!')
def test_USGeometry_SumManualSegmentations(self):
self.delayDisplay("Starting SumManualSegmentations test")
import urllib
xmlFileName = 'SpineUltrasound-Lumbar-C5_config.xml'
testDataPath = 'https://raw.githubusercontent.com/Mattel/USBoneSegmentation/master/USGeometry/Testing/Data/Curvilinear/'
downloads = (
(testDataPath+'SpineUltrasound-Lumbar-C5-Trimmed.mha', 'SpineUltrasound-Lumbar-C5-Trimmed.mha', slicer.util.loadLabelVolume),
(testDataPath+'SpineUltrasound-Lumbar-C5_config.xml', xmlFileName, None),
(testDataPath+'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg1.mha', 'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg1.mha', slicer.util.loadLabelVolume),
(testDataPath+'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg2.mha', 'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg2.mha', slicer.util.loadLabelVolume),
(testDataPath+'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg3.mha', 'TestManualSegmentations/SpineUltrasound-Lumbar-C5-TestSeg3.mha', slicer.util.loadLabelVolume),
(testDataPath+'GroundTruth/SummedManualSegmentations_GroundTruth.mha','SummedManualSegmentations_GroundTruth.mha', slicer.util.loadLabelVolume)
)
for url,name,loader in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
directoryName = os.path.dirname(filePath)
if not os.path.exists(directoryName):
os.makedirs(directoryName)
logging.info('Requesting download %s from %s...\n' % (name,url))
urllib.urlretrieve(url, filePath)
if loader:
logging.info('Loading %s...' % (name,))
loader(filePath)
self.delayDisplay('Finished with downloading and loading')
volumeNode = slicer.util.getNode(pattern="SpineUltrasound-Lumbar-C5-Trimmed")
groundTruthNode = slicer.util.getNode(pattern="SummedManualSegmentations_GroundTruth")
logic = USGeometryLogic(slicer.app.temporaryPath+'/'+xmlFileName, volumeNode)
summedManualSegNode = slicer.vtkMRMLLabelMapVolumeNode()
summedManualSegNode.SetName("SummedManualSegmentations_Test")
slicer.mrmlScene.AddNode(summedManualSegNode)
summedManualSegDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
colorNode = slicer.util.getNode('GenericAnatomyColors')
summedManualSegDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
slicer.mrmlScene.AddNode(summedManualSegDisplayNode)
summedManualSegNode.AddAndObserveDisplayNodeID(summedManualSegDisplayNode.GetID())
self.delayDisplay("Running sumManualSegmentations...")
logic.sumManualSegmentations(slicer.app.temporaryPath+'/TestManualSegmentations', summedManualSegNode)
volumeEqualityCheck = self.compareVolumes(groundTruthNode, summedManualSegNode)
if volumeEqualityCheck == True:
self.delayDisplay("Summed manual segmentations test passed!")
else:
self.delayDisplay("Summed manual segmentations test failed!")
def loadVoi(self,filePath,segmentationNode,motionState=0,voi=None):
if not segmentationNode:
print "No segmentation node"
return
if voi.slicerNodeID[motionState]:
return voi.slicerNodeID[motionState]
binaryLabelmapReprName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
segLogic = slicer.modules.segmentations.logic()
segLogic.SetMRMLScene(slicer.mrmlScene)
voi.slicerNodeID[motionState]=None
if not filePath or not os.path.isfile(filePath):
#Try to execute hed2nrrd.sh
filePrefix, fileExtension = os.path.splitext(filePath)
hed2nrrd = "/u/motion/share/bin/hed2nrrd.sh"
dirName = os.path.dirname(os.path.realpath(filePath) )
if os.path.isfile(hed2nrrd):
#If you have write access, nrrd file is created
if os.access(dirName, os.W_OK):
os.system(hed2nrrd + " " + dirName)
else:
print "No write access to " + dirName +"\n Either create .nrrd files or get write permission."
if not filePath or not os.path.isfile(filePath):
print "No file!" + filePath
return None
volumesLogic = slicer.vtkSlicerVolumesLogic()
volumesLogic.SetMRMLScene(slicer.mrmlScene)
slicerVolumeName = voi.name + "_" + str(motionState)
slicerVolume = volumesLogic.AddArchetypeVolume(filePath,slicerVolumeName,1)
#success, midV = slicer.util.loadVolume(os.path.basename(filePath),
#properties = {'name' : "Helo", 'labelmap' : True}, returnNode = True)
slicerVolume.SetOrigin(voi.getSlicerOrigin())
if not slicerVolume:
print "Can't load volume " + os.path.basename(filePath)
return None
colorNode = slicer.util.getNode("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
colorIndex = colorNode.GetColorIndexByName(voi.name.lower())
color = [0,0,0,1]
if colorIndex < 2:
colorIndex = colorNode.GetColorIndexByName("region 11")
if not colorNode.GetColor(colorIndex,color):
print "Can't set color for " + voi.name.lower()
color = [0,0,0,1]
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
displayNode.SetColor(color[0:3])
slicer.mrmlScene.AddNode(displayNode)
slicerVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
try:
array = slicer.util.array(slicerVolume.GetID())
except AttributeError:
import sys
sys.stderr.write('Cannot get array.')
array[:] = ( array[:] >> voi.motionStateBit[motionState] ) & 1
if colorIndex > -1:
array[:] *= colorIndex
slicerVolume.GetImageData().Modified()
if not slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode(slicerVolume,segmentationNode):
print "Can't load volume in segmentation"
return None
else:
print "Added " + slicerVolume.GetName() + " to " + segmentationNode.GetName()
return slicerVolume.GetID()
