def mergeStructures(self,label="all"):
"""merge the named or all structure labels into the master label"""
merge = self.merge
if not merge:
return
rows = self.structures.rowCount()
# check that structures are all the same size as the merge volume
dims = merge.GetImageData().GetDimensions()
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
if not structureVolume:
mergeName = merge.GetName()
slicer.util.errorDisplay( "Merge Aborted: No image data for volume node %s."%(structureName) )
return
if structureVolume.GetImageData().GetDimensions() != dims:
mergeName = merge.GetName()
slicer.util.errorDisplay( "Merge Aborted: Volume %s does not have the same dimensions as the target merge volume. Use the Resample Scalar/Vector/DWI module to resample. Use %s as the Reference Volume and select Nearest Neighbor (nn) Interpolation Type."%(structureName,mergeName) )
return
# check that user really wants to merge
rows = self.structures.rowCount()
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName)
if structureVolume.GetImageData().GetMTime() < merge.GetImageData().GetMTime():
mergeName = merge.GetName()
slicer.util.errorDisplay( "Note: Merge volume has been modified more recently than structure volumes.\nCreating backup copy as %s-backup"%mergeName )
self.volumesLogic.CloneVolume( slicer.mrmlScene, merge, mergeName+"-backup" )
#
# find the Image Label Combine
# - call Enter to be sure GUI has been built
#
combiner = slicer.vtkImageLabelCombine()
#
# iterate through structures merging into merge volume
#
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
if row == 0:
# first row, just copy into merge volume
merge.GetImageData().DeepCopy( structureVolume.GetImageData() )
continue
combiner.SetInputConnection(0, merge.GetImageDataConnection() )
combiner.SetInputConnection(1, structureVolume.GetImageDataConnection() )
self.statusText( "Merging %s" % structureName )
combiner.Update()
merge.GetImageData().DeepCopy( combiner.GetOutput() )
# mark all volumes as modified so we will be able to tell if the
# merged volume gets edited after these
for row in xrange(rows):
structureName = self.structures.item(row,2).text()
structureVolume = self.structureVolume( structureName )
structureVolume.GetImageData().Modified()
EditUtil.setActiveVolumes(self.master, merge)
self.statusText( "Finished merging." )
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 mergeStructures(self, label="all"):
"""merge the named or all structure labels into the master label"""
merge = self.merge
if not merge:
return
rows = self.structures.rowCount()
# check that structures are all the same size as the merge volume
dims = merge.GetImageData().GetDimensions()
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if not structureVolume:
mergeName = merge.GetName()
slicer.util.errorDisplay(
"Merge Aborted: No image data for volume node %s." %
(structureName))
return
if structureVolume.GetImageData().GetDimensions() != dims:
mergeName = merge.GetName()
slicer.util.errorDisplay(
"Merge Aborted: Volume %s does not have the same dimensions as the target merge volume. Use the Resample Scalar/Vector/DWI module to resample. Use %s as the Reference Volume and select Nearest Neighbor (nn) Interpolation Type."
% (structureName, mergeName))
return
# check that user really wants to merge
rows = self.structures.rowCount()
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if structureVolume.GetImageData().GetMTime() < merge.GetImageData(
).GetMTime():
mergeName = merge.GetName()
slicer.util.errorDisplay(
"Note: Merge volume has been modified more recently than structure volumes.\nCreating backup copy as %s-backup"
% mergeName)
self.volumesLogic.CloneVolume(slicer.mrmlScene, merge,
mergeName + "-backup")
#
# find the Image Label Combine
# - call Enter to be sure GUI has been built
#
combiner = slicer.vtkImageLabelCombine()
#
# iterate through structures merging into merge volume
#
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
if row == 0:
# first row, just copy into merge volume
merge.GetImageData().DeepCopy(structureVolume.GetImageData())
continue
if vtk.VTK_MAJOR_VERSION <= 5:
combiner.SetInput1(merge.GetImageData())
combiner.SetInput2(structureVolume.GetImageData())
else:
combiner.SetInputConnection(0, merge.GetImageDataConnection())
combiner.SetInputConnection(
1, structureVolume.GetImageDataConnection())
self.statusText("Merging %s" % structureName)
combiner.Update()
merge.GetImageData().DeepCopy(combiner.GetOutput())
# mark all volumes as modified so we will be able to tell if the
# merged volume gets edited after these
for row in xrange(rows):
structureName = self.structures.item(row, 2).text()
structureVolume = self.structureVolume(structureName)
structureVolume.GetImageData().Modified()
EditUtil.setActiveVolumes(self.master, merge)
self.statusText("Finished merging.")
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
