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(), 4)
# 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(), 5)
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), 814)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 0)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 175)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 4)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(4,0,0,0), 7)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(self.sphereSegmentName)
self.assertEqual(self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(), 2)
self.assertEqual(colorTableNode.GetNumberOfColors(), 5)
sphereColorArray = [0]*4
colorTableNode.GetColor(4,sphereColorArray)
self.assertTrue(int(sphereColorArray[0]*100) == 50 and int(sphereColorArray[1]*100) == 50 and 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 add_layer(self):
# add layer to slicer
self.inputSegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
for layer in self.layer:
Segment = vtkSegmentationCore.vtkSegment()
Segment.SetName(layer[0])
Segment.SetColor(layer[1])
self.inputSegmentationNode.GetSegmentation().AddSegment(Segment)
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(), 4)
# 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(), 5)
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), 814)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 0)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 175)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 4)
self.assertEqual(
imageStatResult.GetScalarComponentAsDouble(4, 0, 0, 0), 7)
# Remove segment from segmentation
self.inputSegmentationNode.GetSegmentation().RemoveSegment(
self.sphereSegmentName)
self.assertEqual(
self.inputSegmentationNode.GetSegmentation().GetNumberOfSegments(),
2)
self.assertEqual(colorTableNode.GetNumberOfColors(), 5)
sphereColorArray = [0] * 4
colorTableNode.GetColor(4, sphereColorArray)
self.assertTrue(
int(sphereColorArray[0] * 100) == 50
and int(sphereColorArray[1] * 100) == 50
and 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 TestSection_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section: 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(self.bodySegmentName).GetColor()
logging.info(f"bodyColor: {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(self.tumorSegmentName).GetColor()
logging.info(f"tumorColor: {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(80)
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()
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info(f"Volume {i}: {imageStatResult.GetScalarComponentAsDouble(i,0,0,0)}")
self.assertEqual(imageStat.GetVoxelCount(), 1000)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 786)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 170)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 4)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3, 0, 0, 0), 40)
# 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()
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info(f"Volume {i}: {imageStatResult.GetScalarComponentAsDouble(i,0,0,0)}")
self.assertEqual(imageStat.GetVoxelCount(), 1000)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0, 0, 0, 0), 786)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1, 0, 0, 0), 170)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2, 0, 0, 0), 39)
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 TestSection_AddRemoveSegment(self):
# Add/remove segment from segmentation (check display properties, color table, etc.)
logging.info('Test section: 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(self.bodySegmentName).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(self.tumorSegmentName).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(80)
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()
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStat.GetVoxelCount(), 1000)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 786)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 170)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 4)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(3,0,0,0), 40)
# 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()
imageStatResult = imageStat.GetOutput()
for i in range(4):
logging.info("Volume {0}: {1}".format(i, imageStatResult.GetScalarComponentAsDouble(i,0,0,0)))
self.assertEqual(imageStat.GetVoxelCount(), 1000)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(0,0,0,0), 786)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(1,0,0,0), 170)
self.assertEqual(imageStatResult.GetScalarComponentAsDouble(2,0,0,0), 39)
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)
layers = []
for label in labels:
print(label)
layers.append([
label,
[
random.uniform(0.0, 1.0),
random.uniform(0.0, 1.0),
random.uniform(0.0, 1.0)
]
])
print layers[1]
# In[11]:
inputSegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
# In[12]:
Segment = vtkSegmentationCore.vtkSegment()
for layer in layers:
print layer[0]
print layer[1]
Segment = vtkSegmentationCore.vtkSegment()
Segment.SetName(layer[0])
Segment.SetColor(layer[1])
inputSegmentationNode.GetSegmentation().AddSegment(Segment)
# In[ ]:
def load(self,loadable):
""" Load the DICOM SEG object
"""
print('DICOM SEG load()')
labelNodes = vtk.vtkCollection()
uid = None
try:
uid = loadable.uid
print ('in load(): uid = ', uid)
except AttributeError:
return False
res = False
# make the output directory
outputDir = os.path.join(slicer.app.temporaryPath,"QIICR","SEG",loadable.uid)
try:
os.makedirs(outputDir)
except:
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:
print 'Failed to get the filename from the DICOM database for ', uid
return False
parameters = {
"inputSEGFileName": segFileName,
"outputDirName": outputDir,
}
seg2nrrd = None
try:
seg2nrrd = slicer.modules.seg2nrrd
except AttributeError:
print 'Unable to find CLI module SEG2NRRD, unable to load DICOM Segmentation object'
return False
cliNode = None
cliNode = slicer.cli.run(seg2nrrd, cliNode, parameters, wait_for_completion=True)
if cliNode.GetStatusString() != 'Completed':
print 'SEG2NRRD did not complete successfully, unable to load DICOM Segmentation'
return False
# create a new color node to be set up with the colors in these segments
colorLogic = slicer.modules.colors.logic()
segmentationColorNode = slicer.vtkMRMLColorTableNode()
segmentationColorNode.SetName(loadable.name)
segmentationColorNode.SetTypeToUser();
segmentationColorNode.SetHideFromEditors(0)
segmentationColorNode.SetAttribute("Category", "File")
segmentationColorNode.NamesInitialisedOff()
slicer.mrmlScene.AddNode(segmentationColorNode)
# also create a new terminology and associate it with this color node
colorLogic.CreateNewTerminology(segmentationColorNode.GetName())
import glob
numberOfSegments = len(glob.glob(os.path.join(outputDir,'*.nrrd')))
# resize the color table to include the segments plus 0 for the background
print ('number of segments = ',numberOfSegments)
segmentationColorNode.SetNumberOfColors(numberOfSegments + 1)
segmentationColorNode.SetColor(0, 'background', 0.0, 0.0, 0.0, 0.0)
seriesName = self.referencedSeriesName(loadable)
segmentNodes = []
for segmentId in range(numberOfSegments):
# 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
rgb = (0., 0., 0.)
colorIndex = segmentId + 1
categoryCode = 'T-D0050'
categoryCodingScheme = 'SRT'
categoryCodeMeaning = 'Tissue'
typeCode = 'T-D0050'
typeCodeMeaning = 'Tissue'
typeCodingScheme = 'SRT'
typeModCode = ''
typeModCodingScheme = ''
typeModCodeMeaning = ''
regionCode = 'T-D0010'
regionCodingScheme = 'SRT'
regionCodeMeaning = 'Entire Body'
regionModCode = ''
regionModCodingScheme = ''
regionModCodeMeaning = ''
infoFileName = os.path.join(outputDir,str(segmentId+1)+".info")
print ('Parsing info file', infoFileName)
with open(infoFileName, 'r') as infoFile:
for line in infoFile:
line = line.rstrip()
if len(line) == 0:
# empty line
continue
terms = line.split(';')
for term in terms:
# label number is the first thing, no key
if len(term.split(':')) == 1:
colorIndex = int(term)
else:
key = term.split(':')[0]
if key == "RGB":
rgb255 = term.split(':')[1].split(',')
rgb = map(lambda c: float(c) / 255., rgb255)
elif key == "AnatomicRegion":
# Get the Region information
region = term.split(':')[1]
# use partition to deal with any commas in the meaning
regionCode, sep, regionCodingSchemeAndCodeMeaning = region.partition(',')
regionCodingScheme, sep, regionCodeMeaning = regionCodingSchemeAndCodeMeaning.partition(',')
elif key == "AnatomicRegionModifier":
regionMod = term.split(':')[1]
regionModCode, sep, regionModCodingSchemeAndCodeMeaning = regionMod.partition(',')
regionModCodingScheme, sep, regionModCodeMeaning = regionModCodingSchemeAndCodeMeaning.partition(',')
elif key == "SegmentedPropertyCategory":
# Get the Category information
category = term.split(':')[1]
categoryCode, sep, categoryCodingSchemeAndCodeMeaning = category.partition(',')
categoryCodingScheme, sep, categoryCodeMeaning = categoryCodingSchemeAndCodeMeaning.partition(',')
elif key == "SegmentedPropertyType":
# Get the Type information
types = term.split(':')[1]
typeCode, sep, typeCodingSchemeAndCodeMeaning = types.partition(',')
typeCodingScheme, sep, typeCodeMeaning = typeCodingSchemeAndCodeMeaning.partition(',')
elif key == "SegmentedPropertyTypeModifier":
typeMod = term.split(':')[1]
typeModCode, sep, typeModCodingSchemeAndCodeMeaning = typeMod.partition(',')
typeModCodingScheme, sep, typeModCodeMeaning = typeModCodingSchemeAndCodeMeaning.partition(',')
# set the color name from the terminology
colorName = typeCodeMeaning
segmentationColorNode.SetColor(colorIndex, colorName, *rgb)
colorLogic.AddTermToTerminology(segmentationColorNode.GetName(), colorIndex,
categoryCode, categoryCodingScheme, categoryCodeMeaning,
typeCode, typeCodingScheme, typeCodeMeaning,
typeModCode, typeModCodingScheme, typeModCodeMeaning,
regionCode, regionCodingScheme, regionCodeMeaning,
regionModCode, regionModCodingScheme, regionModCodeMeaning)
# end of processing a line of terminology
infoFile.close()
#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(outputDir,str(segmentId+1)+".nrrd")
segmentName = seriesName + "-" + colorName + "-label"
(success,labelNode) = slicer.util.loadLabelVolume(labelFileName,
properties = {'name' : segmentName},
returnNode=True)
segmentNodes.append(labelNode)
# point the label node to the color node we're creating
labelDisplayNode = labelNode.GetDisplayNode()
if labelDisplayNode == None:
print ('Warning: no label map display node for segment ',segmentId,', creating!')
labelNode.CreateDefaultDisplayNodes()
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID(segmentationColorNode.GetID())
# TODO: initialize referenced UID (and segment number?) attribute(s)
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, labelNode)
# create a combined (merge) label volume node (only if a segment was created)
if labelNode:
volumeLogic = slicer.modules.volumes.logic()
mergeNode = volumeLogic.CloneVolume(labelNode, seriesName + "-label")
combiner = slicer.vtkImageLabelCombine()
for segmentNode in segmentNodes:
combiner.SetInputConnection(0, mergeNode.GetImageDataConnection() )
combiner.SetInputConnection(1, segmentNode.GetImageDataConnection() )
combiner.Update()
mergeNode.GetImageData().DeepCopy( combiner.GetOutput() )
for segmentNode in segmentNodes:
segmentNode.Modified() # sets the MTime so the editor won't think they are older than mergeNode
# display the mergeNode
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveLabelVolumeID( mergeNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection(0)
# finalize the color node
segmentationColorNode.NamesInitialisedOn()
# TODO: the outputDir should be cleaned up
if hasattr(slicer.modules, 'segmentations'):
import vtkSlicerSegmentationsModuleLogic
import vtkSlicerSegmentationsModuleMRML
import vtkSegmentationCore
segmentationNode = vtkSlicerSegmentationsModuleMRML.vtkMRMLSegmentationNode()
segmentationNode.SetName(seriesName)
segmentationNode.AddNodeReferenceID('colorNodeID', segmentationColorNode.GetID())
slicer.mrmlScene.AddNode(segmentationNode)
segmentationDisplayNode = vtkSlicerSegmentationsModuleMRML.vtkMRMLSegmentationDisplayNode()
segmentationNode.SetAndObserveDisplayNodeID(segmentationDisplayNode.GetID())
slicer.mrmlScene.AddNode(segmentationDisplayNode)
segmentation = vtkSegmentationCore.vtkSegmentation()
segmentation.SetMasterRepresentationName(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
segmentationNode.SetAndObserveSegmentation(segmentation)
self.addSeriesInSubjectHierarchy(loadable, segmentationNode)
colorID = 1
for segmentNode in segmentNodes:
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentNode.GetName())
segmentColor = [0,0,0,0]
segmentationColorNode.GetColor(colorID, segmentColor)
segment.SetDefaultColor(segmentColor[0:3])
colorID += 1
#TODO: when the logic class is created, this will need to be changed
logic = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic()
orientedImage = logic.CreateOrientedImageDataFromVolumeNode(segmentNode)
segment.AddRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName(), orientedImage)
segmentation.AddSegment(segment)
segmentDisplayNode = segmentNode.GetDisplayNode()
slicer.mrmlScene.RemoveNode(segmentDisplayNode)
slicer.mrmlScene.RemoveNode(segmentNode)
segmentation.CreateRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(), True)
slicer.mrmlScene.RemoveNode(mergeNode)
return True
