def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace(self.moduleName+".py",""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath, "Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def mutate(self):
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
red_cn = red_logic.GetSliceCompositeNode()
fgrdVolID = red_cn.GetBackgroundVolumeID()
fgrdNode = slicer.util.getNode("WEB")
fgrdVolID = fgrdNode.GetID()
fMat=vtk.vtkMatrix4x4()
fgrdNode.GetIJKToRASDirectionMatrix(fMat)
bgrdName = fgrdNode.GetName() + '_gray'
magnitude = vtk.vtkImageMagnitude()
magnitude.SetInputData(fgrdNode.GetImageData())
magnitude.Update()
bgrdNode = slicer.vtkMRMLScalarVolumeNode()
bgrdNode.SetImageDataConnection(magnitude.GetOutputPort())
bgrdNode.SetName(bgrdName)
bgrdNode.SetIJKToRASDirectionMatrix(fMat)
slicer.mrmlScene.AddNode(bgrdNode)
bgrdVolID = bgrdNode.GetID()
red_cn.SetForegroundVolumeID(fgrdVolID)
red_cn.SetBackgroundVolumeID(bgrdVolID)
red_cn.SetForegroundOpacity(1)
resourcesPath = os.path.join(slicer.modules.slicerpathology.path.replace("SlicerPathology.py",""), 'Resources')
colorFile = os.path.join(resourcesPath, "Colors/SlicerPathology.csv")
try:
slicer.modules.EditorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
allColorTableNodes = slicer.util.getNodes('vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n-1)
colorNode.NamesInitialisedOn()
import csv
structureNames = []
with open(colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index,row in enumerate(reader):
success = colorNode.SetColor(index ,row['Label'],float(row['R'])/255,float(row['G'])/255,float(row['B'])/255,float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
structureNames.append(row['Label'])
volumesLogic = slicer.modules.volumes.logic()
labelName = bgrdName+'-label'
refLabel = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene,bgrdNode,labelName)
refLabel.GetDisplayNode().SetAndObserveColorNodeID(SlicerPathologyColorNode.GetID())
self.editorWidget.helper.setMasterVolume(bgrdNode)
def build_color_table(name, table_max):
table = slicer.vtkMRMLColorTableNode()
table.SetName(name)
table.SetHideFromEditors(0)
table.SetTypeToFile()
table.NamesInitialisedOff()
table.SetNumberOfColors(table_max)
table.GetLookupTable().SetTableRange(0, table_max)
table.NamesInitialisedOn()
slicer.mrmlScene.AddNode(table)
return table
def CreateDefaultGSIColorTable(self, overDoseOff):
colorTableNode = slicer.vtkMRMLColorTableNode()
if overDoseOff:
nodeName = "GSIStandard_NoOverDose"
else:
nodeName = "GSIStandard_OverDose"
colorTableNode.SetName(nodeName);
colorTableNode.SetTypeToUser();
colorTableNode.SetAttribute("Category", "User Generated");
colorTableNode.HideFromEditorsOn();
colorTableNode.SetNumberOfColors(256);
colorTableNode.GetLookupTable().SetTableRange(0,255)
darkBlue = 47.0
lightBlue = 95.0
darkGreen = 142.0
lightGreen = 189.0
yellow = 225.0
red = 248.0
if overDoseOff:
for i in range(0,256):
if i>=0 and i<darkBlue:
colorTableNode.AddColor(str(i), 0, 0 + i/darkBlue, 1, 0.2)
elif i>=darkBlue and i<lightBlue:
colorTableNode.AddColor(str(i), 0, 1-0.5*(i-darkBlue)/(lightBlue-darkBlue), 1 - (i-darkBlue)/(lightBlue-darkBlue), 0.2)
elif i>=lightBlue and i<darkGreen:
colorTableNode.AddColor(str(i), 0, 0.5 + 0.5*(i-lightBlue)/(darkGreen-lightBlue), 0, 0.2)
elif i>=darkGreen and i<lightGreen:
colorTableNode.AddColor(str(i), 0 + (i-darkGreen)/(lightGreen-darkGreen), 1, 0, 0.2)
elif i>=lightGreen and i<236:
colorTableNode.AddColor(str(i), 1, 1, 0, 0.2)
else:
colorTableNode.AddColor(str(i), 1, 0, 0, 0.2)
else:
for i in range(0,256):
if i>=0 and i<darkBlue:
colorTableNode.AddColor(str(i), 0, 0 + i/darkBlue, 1, 0.2)
elif i>=darkBlue and i<lightBlue:
colorTableNode.AddColor(str(i), 0, 1-0.5*(i-darkBlue)/(lightBlue-darkBlue), 1 - (i-darkBlue)/(lightBlue-darkBlue), 0.2)
elif i>=lightBlue and i<darkGreen:
colorTableNode.AddColor(str(i), 0, 0.5 + 0.5*(i-lightBlue)/(darkGreen-lightBlue), 0, 0.2)
elif i>=darkGreen and i<lightGreen:
colorTableNode.AddColor(str(i), 0 + (i-darkGreen)/(lightGreen-darkGreen), 1, 0, 0.2)
elif i>=lightGreen and i<yellow:
colorTableNode.AddColor(str(i), 1, 1, 0, 0.2)
elif i<=red:
colorTableNode.AddColor(str(i), 1, 0, 0, 0.2)
else:
colorTableNode.AddColor(str(i), 1, 0, 1, 0.2)
slicer.mrmlScene.AddNode( colorTableNode )
return colorTableNode
def onSelectROI(self):
merge=self.outputSelector.currentNode()
master=self.masterSelector.currentNode()
if master:
if merge:
if not merge.GetImageData():
self.newROI=True
imd=vtk.vtkImageData()
mim=master.GetImageData()
imd.SetDimensions(mim.GetDimensions())
imd.SetSpacing(mim.GetSpacing())
imd.SetOrigin(mim.GetOrigin())
#imd.SetScalarType(vtk.VTK_SHORT)
imd.AllocateScalars(vtk.VTK_SHORT,1)
masterIJKToRAS = vtk.vtkMatrix4x4()
master.GetIJKToRASMatrix(masterIJKToRAS)
merge.SetIJKToRASMatrix(masterIJKToRAS)
nd=slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(nd)
merge.AddAndObserveDisplayNodeID(nd.GetID())
merge.SetAndObserveImageData(imd)
#workaround to display ROI in Slicer??????
parameters={}
parameters["InputVolume"]=merge.GetID()
parameters["OutputVolume"]=merge.GetID()
parameters["Type"]="Short"
castIM=slicer.modules.castscalarvolume
slicer.cli.run(castIM,None,parameters)
coln=slicer.vtkMRMLColorTableNode()
coln.SetTypeToUser()
coln.SetNumberOfColors(2)
coln.SetColor(0,'bg',0,0,0)
coln.SetColor(1,'fg',1,0,0)
coln.SetOpacity(0,0)
coln.SetOpacity(1,1)
slicer.mrmlScene.AddNode(coln)
merge.GetDisplayNode().SetAndObserveColorNodeID(coln.GetID())
else:
self.newROI=False
warnings = self.checkForVolumeWarnings(master,merge)
if warnings != "":
self.errorDialog( "Warning: %s" % warnings )
self.outputSelector.setCurrentNode(None)
def createFociVisualizationColorMap(self,minimumValue,maximumValue):
if (minimumValue<0):
numberOfCoolColors = -(minimumValue)
else:
numberOfCoolColors = 0
if (maximumValue>0):
numberOfHotColors = maximumValue+1 # includes zero
else:
numberOfHotColors = 0
if self.displayDebugInformation:
print "number of cool colors = " + str(numberOfCoolColors)
print "number of hot colors (including zero) = " + str(numberOfHotColors)
colorNode = slicer.util.getNode(self.FOCI_ACONTRARIO_DETECTION_COLORMAP_NAME)
if colorNode is None:
colorNode = slicer.vtkMRMLColorTableNode()
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetName(self.FOCI_ACONTRARIO_DETECTION_COLORMAP_NAME)
colorNode.SetTypeToUser()
colorNode.SetNumberOfColors(numberOfCoolColors + numberOfHotColors);
colorNode.SetNamesFromColors()
''' cool color map in Matlab
r = (0:m-1)'/max(m-1,1);
c = [r 1-r ones(m,1)];
'''
for colorIndex in xrange(0,numberOfCoolColors):
r = np.double(numberOfCoolColors -1 - colorIndex) / (numberOfCoolColors)
colorNode.SetColor(colorIndex, r, 1-r, 1, 1.0);
''' hot color table in Matlab
r = [(1:n)'/n; ones(m-n,1)];
g = [zeros(n,1); (1:n)'/n; ones(m-2*n,1)];
b = [zeros(2*n,1); (1:m-2*n)'/(m-2*n)];
'''
n=3*numberOfHotColors/8 # fix
''' hot color table in Python '''
r=np.concatenate((np.double(range(1,n+1))/n , np.ones(numberOfHotColors-n)))
g=np.concatenate((np.zeros(n),np.double(range(1,n+1))/n,np.ones(numberOfHotColors-2*n)))
b=np.concatenate((np.zeros(2*n),np.double(range(1,numberOfHotColors-2*n+1))/(numberOfHotColors-2*n)))
for colorIndex in xrange(0,numberOfHotColors):
colorNode.SetColor(numberOfCoolColors + colorIndex, r[colorIndex], g[colorIndex], b[colorIndex], 1.0);
#print "hot color index = " + str(numberOfCoolColors + colorIndex)
colorNode.SetOpacity(numberOfCoolColors,0);
def setupLobesColorTable():
if len(slicer.util.getNodes('lapdMouseLobes')) > 0: return
colors = slicer.vtkMRMLColorTableNode()
colors.SetTypeToUser()
colors.SetAttribute("Category", "lapdMouse")
colors.SetName('lapdMouseLobes')
colors.SetHideFromEditors(True)
colors.SetNumberOfColors(6)
colors.NamesInitialisedOn()
colors.GetLookupTable().SetRange(0, 5)
colors.SetColor(0, 'background', 0, 0, 0, 0)
colors.SetColor(1, 'left lobe', 1, 0, 0, 1)
colors.SetColor(2, 'right cranial lobe', 0, 1, 0, 1)
colors.SetColor(3, 'right middle lobe', 0, 0, 1, 1)
colors.SetColor(4, 'right caudal lobe', 1, 1, 0, 1)
colors.SetColor(5, 'right accessory lobe', 0, 1, 1, 1)
slicer.mrmlScene.AddNode(colors)
def checkAndSetLUT(self):
# Default to module color table
self.resourcesPath = os.path.join(
slicer.modules.slicerpathology.path.replace(
self.moduleName + ".py", ""), 'Resources')
self.colorFile = os.path.join(self.resourcesPath,
"Colors/SlicerPathology.csv")
self.customLUTLabel.setText('Using Default LUT')
try:
self.editorWidget.helper.structureListWidget.merge = None
except AttributeError:
pass
# setup the color table, make sure SlicerPathology LUT is a singleton
allColorTableNodes = slicer.util.getNodes(
'vtkMRMLColorTableNode*').values()
for ctn in allColorTableNodes:
#print "color: "+ctn.GetName()
if ctn.GetName() == 'SlicerPathologyColor':
slicer.mrmlScene.RemoveNode(ctn)
break
self.SlicerPathologyColorNode = slicer.vtkMRMLColorTableNode()
colorNode = self.SlicerPathologyColorNode
colorNode.SetName('SlicerPathologyColor')
slicer.mrmlScene.AddNode(colorNode)
colorNode.SetTypeToUser()
with open(self.colorFile) as f:
n = sum(1 for line in f)
colorNode.SetNumberOfColors(n - 1)
colorNode.NamesInitialisedOn()
import csv
self.structureNames = []
with open(self.colorFile, 'rb') as csvfile:
reader = csv.DictReader(csvfile, delimiter=',')
for index, row in enumerate(reader):
success = colorNode.SetColor(index, row['Label'],
float(row['R']) / 255,
float(row['G']) / 255,
float(row['B']) / 255,
float(row['A']))
if not success:
print "color %s could not be set" % row['Label']
self.structureNames.append(row['Label'])
def setupOutletsColorTable():
if len(slicer.util.getNodes('lapdMouseOutlets')) > 0: return
numSegments = 5000
colors = slicer.vtkMRMLColorTableNode()
colors.SetTypeToUser()
colors.SetAttribute("Category", "lapdMouse")
colors.SetName('lapdMouseOutlets')
colors.SetHideFromEditors(True)
colors.SetNumberOfColors(numSegments)
colors.NamesInitialisedOn()
colors.GetLookupTable().SetRange(0, numSegments)
colors.SetColor(0, 'wall', 1, 0.67, 0, 1)
import random
random.seed(
3
) # seed 3: nothing too dark and first few generations reasonably well contrasted
for i in range(1, numSegments):
colors.SetColor(i, str(i), random.uniform(0.0, 1.0),
random.uniform(0.0, 1.0), random.uniform(0.0, 1.0),
1)
slicer.mrmlScene.AddNode(colors)
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
def load(self, loadable):
""" Call Reporting logic to load the DICOM SEG object
"""
print('DICOM SEG load()')
labelNodes = vtk.vtkCollection()
uid = None
try:
reportingLogic = slicer.modules.reporting.logic()
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
res = reportingLogic.DicomSegRead(labelNodes, uid)
# 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()
# 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
return True
import math
import slicer
# Test that a custom color table is consistent across scene view saves
# and restores
colorNode = slicer.vtkMRMLColorTableNode()
colorNode.SetName('CustomTest')
colorNode.SetHideFromEditors(0)
colorNode.SetTypeToFile()
colorNode.NamesInitialisedOff()
colorNode.SetNumberOfColors(3)
if colorNode.GetLookupTable() is not None:
colorNode.GetLookupTable().SetTableRange(0, 2)
colorNode.SetColor(0, 'zero', 0.0, 0.0, 0.0, 0.0)
colorNode.SetColor(1, 'one', 1.0, 1.0, 1.0, 1.0)
colorNode.SetColor(2, 'two', 0.5, 0.5, 0.5)
colorNode.SetColorName(0, 'zero')
colorNode.SetColorName(1, 'one')
colorNode.SetColorName(2, 'two')
colorNode.NamesInitialisedOn()
slicer.mrmlScene.AddNode(colorNode)
filePath = slicer.app.temporaryPath + "/customColorTableSceneViewRestore.ctbl"
colorStorageNode = slicer.vtkMRMLColorTableStorageNode()
colorStorageNode.SetFileName(filePath)
