def onSaveButtonClicked(self):
bundle = EditUtil.EditUtil().getParameterNode().GetParameter('QuickTCGAEffect,erich')
tran = json.loads(bundle)
layers = []
for key in tran:
nn = tran[key]
nn["file"] = key + '.tif'
layers.append(tran[key])
j = {}
j['layers'] = layers
j['username'] = self.setupUserName.text
j['sourcetile'] = self.tilename
j['generator'] = "3DSlicer-4.5.0 with SlicerPathology v1.0a"
j['timestamp'] = datetime.datetime.now().strftime("%Y%m%d%H%M%S")
labelNodes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
savedMessage = 'Segmentations for the following series were saved:\n\n'
for label in labelNodes.values():
labelName = label.GetName()
labelFileName = os.path.join(self.dataDirButton.directory, labelName + '.tif')
print "labelFileName : "+labelFileName
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFileName)
sNode.SetWriteFileFormat('tif')
sNode.SetURI(None)
success = sNode.WriteData(label)
if success:
print "successful writing "+labelFileName
else:
print "failed writing "+labelFileName
jstr = json.dumps(j,sort_keys=True, indent=4, separators=(',', ': '))
f = open(os.path.join(self.dataDirButton.directory, self.tilename + '.json'),'w')
f.write(jstr)
f.close()
def readFrame(self, file):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
sNode.SetFileName(file)
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
success = sNode.ReadData(frame)
return (success, frame)
def readFrame(self, file):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
sNode.SetFileName(file)
sNode.SetSingleFile(1)
frame = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(frame)
return frame
def loadFilesWithArchetype(self, files, name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
vNode = slicer.vtkMRMLScalarVolumeNode()
sNode.SetFileName(files[0])
sNode.ResetFileNameList()
for f in files:
sNode.AddFileName(f)
sNode.SetSingleFile(0)
res = sNode.ReadData(vNode)
if res == 1:
vNode.SetScene(slicer.mrmlScene)
vNode.SetName(name)
slicer.mrmlScene.AddNode(vNode)
else:
vNode = None
return vNode
def loadFilesWithArchetype(self, files, name):
"""Load files in the traditional Slicer manner
using the volume logic helper class
and the vtkITK archetype helper code
"""
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
vNode = slicer.vtkMRMLScalarVolumeNode()
sNode.SetFileName(files[0])
sNode.ResetFileNameList()
for f in files:
sNode.AddFileName(f)
sNode.SetSingleFile(0)
res = sNode.ReadData(vNode)
if res == 1:
vNode.SetScene(slicer.mrmlScene)
vNode.SetName(name)
slicer.mrmlScene.AddNode(vNode)
else:
vNode = None
return vNode
def DoIt(inputDir, labelFile, outputDir, forceLabel, forceResample):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
if not hasattr(slicer.modules, 'reporting'):
print 'The Reporting module has not been loaded into Slicer, script cannot run!\n\tTry setting the --additional-module-path parameter.'
sys.exit(1)
reportingLogic = slicer.modules.reporting.logic()
print('Temporary directory location: '+dbDir1)
qt.QDir().mkpath(dbDir1)
dbDir0 = None
if slicer.dicomDatabase:
dbDir0 = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(dbDir1)
# import DICOM study
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir, None)
indexer.waitForImportFinished()
print('DICOM import finished!')
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
sys.exit(1)
inputVolume = scalarVolumePlugin.load(loadables[0])
print 'Input volume loaded! ID = ', inputVolume.GetID()
# read the label volume
labelVolume = slicer.vtkMRMLLabelMapVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
if forceLabel>0:
# print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(labelImage)
else:
thresh.SetInputData(labelImage)
thresh.ThresholdBetween(1, labelImage.GetScalarRange()[1])
thresh.SetInValue(int(forceLabel))
thresh.SetOutValue(0)
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.Update()
labelImage = thresh.GetOutput()
labelVolume.SetAndObserveImageData(labelImage)
slicer.mrmlScene.AddNode(labelVolume)
print 'Label volume added, id = ', labelVolume.GetID()
# ensure that the label volume scalar type is unsigned short
if labelVolume.GetImageData() != None:
scalarType = labelVolume.GetImageData().GetScalarType()
if scalarType != vtk.VTK_UNSIGNED_SHORT:
print 'Label volume has pixel type of ',vtk.vtkImageScalarTypeNameMacro(scalarType),', casting to unsigned short'
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToUnsignedShort()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(labelVolume.GetImageData())
cast.Update()
labelVolume.SetAndObserveImageData(cast.GetOutput())
else:
cast.SetInputConnection(labelVolume.GetImageDataConnection())
cast.Update()
labelVolume.SetImageDataConnection(cast.GetOutputPort())
if labelVolume.GetImageData().GetScalarType() != vtk.VTK_UNSIGNED_SHORT:
print 'Failed to cast label volume to unsigned short, type is ', vtk.vtkImageScalarTypeNameMacro(labelVolume.GetImageData().GetScalarType())
sys.exit(1)
volumesLogic = slicer.modules.volumes.logic()
geometryCheckString = volumesLogic.CheckForLabelVolumeValidity(inputVolume, labelVolume)
if geometryCheckString != "":
# has the user specified that forced resampling is okay?
if forceResample == False:
print 'Label volume mismatch with input volume:\n',geometryCheckString,'\nForced resample not specified, aborting. Re-run with --force option to ignore geometric inconsistencies'
sys.exit(1)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
print 'Resampled label added, id = ', resampledLabel.GetID()
resampledLabel = volumesLogic.ResampleVolumeToReferenceVolume(labelVolume, inputVolume)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
# initialize the DICOM DB for Reporting logic, save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(labelVolume)
print('About to write DICOM SEG!')
dbFileName = slicer.dicomDatabase.databaseFilename
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
def load(self,loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = string.split(mvNode.GetAttribute('MultiVolume.FrameFileList'),',')
nFiles = len(files)
filesPerFrame = nFiles/nFrames
frames = []
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
# read each frame into scalar volume
for frameNumber in range(nFrames):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList();
frameFileList = files[frameNumber*filesPerFrame:(frameNumber+1)*filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
return
for f in svLoadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(frameFileList[0]) # only used when num files/frame = 1
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(frame)
if frame == None:
print('Failed to read a multivolume frame!')
return False
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
mvImage.SetExtent(frameExtent)
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.AllocateScalars()
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetScene(slicer.mrmlScene)
mvDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(mvDisplayNode)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
slicer.mrmlScene.AddNode(mvNode)
return True
def LoadAIMFile(newReportID, fileName):
dom = xml.dom.minidom.parse(fileName)
SlicerReportingModuleWidgetHelper.Debug('Parsed AIM report:')
SlicerReportingModuleWidgetHelper.Debug(dom.toxml())
volumeList = []
ddb = slicer.dicomDatabase
volId = 1
volume = None
# get the annotation element and retrieve its name
annotations = dom.getElementsByTagName('ImageAnnotation')
if len(annotations) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file does not contain any annotations!')
return
ann = annotations[0]
desc = ann.getAttribute('name')
# get the anatomic entity element and initialize the report node based on
# it
anatomics = dom.getElementsByTagName('AnatomicEntity')
if len(anatomics) != 1:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file does not contain any anatomic entities or contains more than one! This is not supported.')
return
anatomy = anatomics[0]
labelValue = anatomy.getAttribute('codeValue')
labelName = anatomy.getAttribute('codeMeaning')
codingSchemeDesignator = anatomy.getAttribute('codingSchemeDesignator')
if codingSchemeDesignator != '3DSlicer':
SlicerReportingModuleWidgetHelper.WarningPopup('Code scheme designator '+codingSchemeDesignator+' is not supported. Default will be used instead.')
labelValue = "1"
newReport = slicer.mrmlScene.GetNodeByID(newReportID)
newReport.SetFindingLabel(int(labelValue))
# pull all the volumes that are referenced into the scene
for node in dom.getElementsByTagName('ImageSeries'):
instanceUID = node.getAttribute('instanceUID')
filelist = ddb.filesForSeries(instanceUID)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
if len(scalarVolumeLoadables) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('Error loading AIM: Failed to load the volume node reference in the file')
volumeName = scalarVolumeLoadables[0].name
newReport.SetName('Report for Volume '+volumeName)
volume = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volume.SetName(volumeName)
if volume == None:
SlicerReportingModuleWidgetHelper.Error('Failed to read series!')
return
if len(volumeList) != 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('Error importing AIM report: Report references more than one volume, which is not allowed!')
return
volumeList.append(volume)
SlicerReportingModuleWidgetHelper.Debug('Volume read from AIM report:')
slicer.modules.reporting.logic().AddVolumeToReport(volume)
newReport.SetVolumeNodeID(volume.GetID())
if len(volumeList) > 1:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM does not allow to have more than one volume per file!')
return
if len(volumeList) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup('AIM file you requested to load does not reference any volumes, cannot process it!')
return
#if volume != None:
# self.__volumeSelector.setCurrentNode(volume)
instanceUIDs = volume.GetAttribute('DICOM.instanceUIDs')
instanceUIDList = instanceUIDs.split()
# AF: GeometricShape is inside geometricShapeCollection, but
# there's no need to parse at that level, I think
#
# geometricShapeCollection
# |
# +-spatialCoordinateCollection
# |
# +-SpatialCoordinate
#
for node in dom.getElementsByTagName('GeometricShape'):
ijCoordList = []
rasPointList = []
uidList = []
elementType = node.getAttribute('xsi:type')
for child in node.childNodes:
if child.nodeName == 'spatialCoordinateCollection':
for coord in child.childNodes:
if coord.nodeName == 'SpatialCoordinate':
ijCoordList.append(float(coord.getAttribute('x')))
ijCoordList.append(float(coord.getAttribute('y')))
uid = coord.getAttribute('imageReferenceUID')
uidList.append(uid)
SlicerReportingModuleWidgetHelper.Debug('Coordinate list: '+str(ijCoordList))
ijk2ras = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(ijk2ras)
# convert each point from IJ to RAS
for ij in range(len(uidList)):
pointUID = uidList[ij]
# locate the UID in the list assigned to the volume
totalSlices = len(instanceUIDList)
for k in range(len(instanceUIDList)):
if pointUID == instanceUIDList[k]:
break
# print "k = ",k,", totalSlices = ",totalSlices
pointIJK = [ijCoordList[ij*2], ijCoordList[ij*2+1], k, 1.]
pointRAS = ijk2ras.MultiplyPoint(pointIJK)
SlicerReportingModuleWidgetHelper.Debug('Input point: '+str(pointIJK))
SlicerReportingModuleWidgetHelper.Debug('Converted point: '+str(pointRAS))
rasPointList.append(pointRAS[0:3])
# instantiate the markup elements
if elementType == 'Point':
SlicerReportingModuleWidgetHelper.Debug("Importing a fiducial!")
if len(ijCoordList) != 2:
SlicerReportingModuleWidgetHelper.Error('Number of coordinates not good for a fiducial')
return
fiducial = slicer.mrmlScene.CreateNodeByClass('vtkMRMLAnnotationFiducialNode')
fiducial.SetReferenceCount(fiducial.GetReferenceCount()-1)
# associate it with the report
fiducial.SetAttribute('ReportingReportNodeID', newReport.GetID())
# associate it with the volume
fiducial.SetAttribute('AssociatedNodeID', volume.GetID())
# ??? Why the API is so inconsistent -- there's no SetPosition1() ???
fiducial.SetFiducialCoordinates(rasPointList[0])
fiducial.Initialize(slicer.mrmlScene)
# adding to hierarchy is handled by the Reporting logic
if elementType == 'MultiPoint':
SlicerReportingModuleWidgetHelper.Debug("Importing a ruler!")
if len(ijCoordList) != 4:
SlicerReportingModuleWidgetHelper.Error('Number of coordinates not good for a ruler')
return
ruler = slicer.mrmlScene.CreateNodeByClass('vtkMRMLAnnotationRulerNode')
ruler.SetReferenceCount(ruler.GetReferenceCount()-1)
# associate it with the report
ruler.SetAttribute('ReportingReportNodeID', newReport.GetID())
# associate it with the volume
ruler.SetAttribute('AssociatedNodeID', volume.GetID())
SlicerReportingModuleWidgetHelper.Debug('Initializing with points '+str(rasPointList[0])+' and '+str(rasPointList[1]))
ruler.SetPosition1(rasPointList[0])
ruler.SetPosition2(rasPointList[1])
ruler.Initialize(slicer.mrmlScene)
# AF: Initialize() adds to the scene ...
for node in dom.getElementsByTagName('Segmentation'):
# read all labels that are available in the SEG object
# check if the referenced volume is already in the scene
# if not, load it
# initialize AssociatedNodeID for the label node to point to the
# reference
SlicerReportingModuleWidgetHelper.Debug('Importing a segmentation')
labelNodes = vtk.vtkCollection()
referenceNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeNode')
referenceNode.SetReferenceCount(referenceNode.GetReferenceCount()-1)
uid = node.getAttribute('sopInstanceUID')
res = False
colorNode = slicer.mrmlScene.GetNodeByID(newReport.GetColorNodeID())
res = slicer.modules.reporting.logic().DicomSegRead(labelNodes, uid, colorNode)
SlicerReportingModuleWidgetHelper.Debug('Read this many labels from the seg object:'+str(labelNodes.GetNumberOfItems()))
if labelNodes.GetNumberOfItems() == 0:
print("Error loading segmentation object, have 0 labels")
else:
# read the reference node
label0 = labelNodes.GetItemAsObject(0)
referenceUIDs = label0.GetAttribute('DICOM.referenceInstanceUIDs')
SlicerReportingModuleWidgetHelper.Debug('Seg object reference uids: '+referenceUIDs)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('ReportingReportNodeID', newReport.GetID())
labelNode.SetAttribute('AssociatedNodeID', volumeList[0].GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
# AF: this shuould not be necessary with the "proper" AIM input, since
# only one volume should be present in the report, and only one item in
# that volume should be annotated
if 0:
# if referenceUIDs != None:
reader = slicer.vtkMRMLVolumeArchetypeStorageNode()
reader.ResetFileNameList()
for uid in string.split(referenceUIDs, ' '):
fname = slicer.modules.reporting.logic().GetFileNameFromUID(uid)
reader.AddFileName(fname)
reader.SetFileName(string.split(referenceUIDs, ' ')[0])
reader.SetSingleFile(0)
referenceVolume = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeNode')
referenceVolumeUIDs = referenceVolume.GetAttribute('DICOM.instanceUIDs')
reader.ReadData(referenceVolume)
nodeToAdd = referenceVolume
allVolumeNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLScalarVolumeNode')
allVolumeNodes.SetReferenceCount(allVolumeNodes.GetReferenceCount()-1)
for i in range(allVolumeNodes.GetNumberOfItems()):
v = allVolumeNodes.GetItemAsObject(i)
uids = v.GetAttribute('DICOM.instanceUIDs')
if uids == referenceNodeUIDs:
print('Referenced node is already in the scene!')
nodeToAdd = None
referenceNode = v
break
if nodeToAdd != None:
slicer.mrmlScene.AddNode(nodeToAdd)
slicer.modules.reporting.logic().AddVolumeToReport(referenceNode)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount()-1)
displayNode.SetAndObserveColorNodeID(newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('ReportingReportNodeID', newReport.GetID())
labelNode.SetAttribute('AssociatedNodeID', referenceNode.GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNodes.GetItemAsObject(i))
def DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
print 'Will examine: ',dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb)-rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir+'/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir+'/'+f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.')+1:len(rgbList[0])]
print 'Extension for RGBs: ',rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ',len(dcmFileList), ' and rgb files: ',len(rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/')+1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx),5)
rgbCnt = rgbCnt+1
src = rgbDir+'/'+rgb
dest = tmpDir+'/'+name+'.'+rgbExt
rgbRenamedList.append(dest)
shutil.copy(src,dest)
break
rgbIdx = rgbIdx+1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file '+dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx+1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0,1,2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID',inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory','')
if dbFileName =='':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName +'/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def writeVolume(self,volume,name): path = slicer.app.temporaryPath + '/%s.nrrd' % name s = slicer.vtkMRMLVolumeArchetypeStorageNode() s.SetFileName(path) s.WriteData(volume) return path
def DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm) - dcm.rfind('.dcm') == 4:
dcmList.append(inputDir + '/' + dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
print 'Will examine: ', dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb) - rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir + '/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir + '/' + f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.') + 1:len(rgbList[0])]
print 'Extension for RGBs: ', rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ', len(dcmFileList), ' and rgb files: ', len(
rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/') + 1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx), 5)
rgbCnt = rgbCnt + 1
src = rgbDir + '/' + rgb
dest = tmpDir + '/' + name + '.' + rgbExt
rgbRenamedList.append(dest)
shutil.copy(src, dest)
break
rgbIdx = rgbIdx + 1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file ' +
dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx + 1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0, 1, 2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(
reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID', inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory', '')
if dbFileName == '':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName + '/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def load(self,loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return None
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = string.split(mvNode.GetAttribute('MultiVolume.FrameFileList'),',')
nFiles = len(files)
filesPerFrame = nFiles/nFrames
frames = []
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
instanceUIDs = ""
for file in files:
uid = slicer.dicomDatabase.fileValue(file,self.tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid+" "
instanceUIDs = instanceUIDs[:-1]
mvNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
# read each frame into scalar volume
for frameNumber in range(nFrames):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList();
frameFileList = files[frameNumber*filesPerFrame:(frameNumber+1)*filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
return None
for f in svLoadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(frameFileList[0]) # only used when num files/frame = 1
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(frame)
if frame.GetImageData() == None:
print('Failed to read a multivolume frame!')
return None
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
mvImage.SetExtent(frameExtent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(frame.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(frame.GetImageData().GetScalarType(), nFrames)
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetScene(slicer.mrmlScene)
mvDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(mvDisplayNode)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(mvNode)
#
# automatically select the volume to display
#
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(mvNode.GetID())
appLogic.PropagateVolumeSelection()
# file list is no longer needed - remove the attribute
mvNode.RemoveAttribute('MultiVolume.FrameFileList')
return mvNode
def DoIt(inputDir, labelFile, outputDir, forceLabel):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
reportingLogic = slicer.modules.reporting.logic()
print('Temporary directory location: '+dbDir1)
qt.QDir().mkpath(dbDir1)
dbDir0 = None
if slicer.dicomDatabase:
dbDir0 = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
try:
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(dbDir1)
# import DICOM study
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir, None)
indexer.waitForImportFinished()
print('DICOM import finished!')
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
slicer.mrmlScene.AddNode(inputVolume)
print('Input volume loaded!')
# read the label volume
labelVolume = slicer.vtkMRMLScalarVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
labelVolume.LabelMapOn()
if forceLabel>0:
print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
thresh.SetInput(labelImage)
thresh.ThresholdBetween(1, labelImage.GetScalarRange()[1])
thresh.SetInValue(int(forceLabel))
thresh.SetOutValue(0)
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.Update()
labelImage = thresh.GetOutput()
labelVolume.SetAndObserveImageData(labelImage)
slicer.mrmlScene.AddNode(labelVolume)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
eye = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(eye)
parameters = {}
parameters['inputVolume'] = labelVolume.GetID()
parameters['referenceVolume'] = inputVolume.GetID()
parameters['outputVolume'] = resampledLabel.GetID()
parameters['warpTransform'] = eye.GetID()
parameters['interpolationMode'] = 'NearestNeighbor'
parameters['pixelType'] = 'ushort'
cliNode = None
cliNode = slicer.cli.run(slicer.modules.brainsresample, None, parameters, 1)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.LabelMapOn()
labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
# initialize the DICOM DB for Reporting logic, save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(labelVolume)
print('About to write DICOM SEG!')
dbFileName = slicer.dicomDatabase.databaseFilename
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
except:
print('Error occurred!')
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
def writeVolume(self, volume, name):
path = slicer.app.temporaryPath + '/%s.nrrd' % name
s = slicer.vtkMRMLVolumeArchetypeStorageNode()
s.SetFileName(path)
s.WriteData(volume)
return path
def LoadAIMFile(newReportID, fileName):
dom = xml.dom.minidom.parse(fileName)
SlicerReportingModuleWidgetHelper.Debug('Parsed AIM report:')
SlicerReportingModuleWidgetHelper.Debug(dom.toxml())
volumeList = []
ddb = slicer.dicomDatabase
volId = 1
volume = None
# get the annotation element and retrieve its name
annotations = dom.getElementsByTagName('ImageAnnotation')
if len(annotations) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file does not contain any annotations!')
return
ann = annotations[0]
desc = ann.getAttribute('name')
# get the anatomic entity element and initialize the report node based on
# it
anatomics = dom.getElementsByTagName('AnatomicEntity')
if len(anatomics) != 1:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file does not contain any anatomic entities or contains more than one! This is not supported.'
)
return
anatomy = anatomics[0]
labelValue = anatomy.getAttribute('codeValue')
labelName = anatomy.getAttribute('codeMeaning')
codeSchemeDesignator = anatomy.getAttribute('codeSchemeDesignator')
if codeSchemeDesignator != '3DSlicer':
SlicerReportingModuleWidgetHelper.WarningPopup(
'Code scheme designator ' + codeSchemeDesignator +
' is not supported. Default will be used instead.')
labelValue = "1"
newReport = slicer.mrmlScene.GetNodeByID(newReportID)
newReport.SetFindingLabel(int(labelValue))
# pull all the volumes that are referenced into the scene
for node in dom.getElementsByTagName('ImageSeries'):
instanceUID = node.getAttribute('instanceUID')
filelist = ddb.filesForSeries(instanceUID)
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
if len(scalarVolumeLoadables) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'Error loading AIM: Failed to load the volume node reference in the file'
)
volumeName = scalarVolumeLoadables[0].name
newReport.SetName('Report for Volume ' + volumeName)
volume = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volume.SetName(volumeName)
if volume == None:
SlicerReportingModuleWidgetHelper.Error(
'Failed to read series!')
return
if len(volumeList) != 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'Error importing AIM report: Report references more than one volume, which is not allowed!'
)
return
volumeList.append(volume)
SlicerReportingModuleWidgetHelper.Debug(
'Volume read from AIM report:')
slicer.modules.reporting.logic().InitializeHierarchyForVolume(
volume)
newReport.SetVolumeNodeID(volume.GetID())
if len(volumeList) > 1:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM does not allow to have more than one volume per file!')
return
if len(volumeList) == 0:
SlicerReportingModuleWidgetHelper.ErrorPopup(
'AIM file you requested to load does not reference any volumes, cannot process it!'
)
return
#if volume != None:
# self.__volumeSelector.setCurrentNode(volume)
instanceUIDs = volume.GetAttribute('DICOM.instanceUIDs')
instanceUIDList = instanceUIDs.split()
# AF: GeometricShape is inside geometricShapeCollection, but
# there's no need to parse at that level, I think
#
# geometricShapeCollection
# |
# +-spatialCoordinateCollection
# |
# +-SpatialCoordinate
#
for node in dom.getElementsByTagName('GeometricShape'):
ijCoordList = []
rasPointList = []
uidList = []
elementType = node.getAttribute('xsi:type')
for child in node.childNodes:
if child.nodeName == 'spatialCoordinateCollection':
for coord in child.childNodes:
if coord.nodeName == 'SpatialCoordinate':
ijCoordList.append(float(coord.getAttribute('x')))
ijCoordList.append(float(coord.getAttribute('y')))
uid = coord.getAttribute('imageReferenceUID')
uidList.append(uid)
SlicerReportingModuleWidgetHelper.Debug('Coordinate list: ' +
str(ijCoordList))
ijk2ras = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(ijk2ras)
# convert each point from IJ to RAS
for ij in range(len(uidList)):
pointUID = uidList[ij]
# locate the UID in the list assigned to the volume
totalSlices = len(instanceUIDList)
for k in range(len(instanceUIDList)):
if pointUID == instanceUIDList[k]:
break
# print "k = ",k,", totalSlices = ",totalSlices
pointIJK = [
ijCoordList[ij * 2], ijCoordList[ij * 2 + 1], k, 1.
]
pointRAS = ijk2ras.MultiplyPoint(pointIJK)
SlicerReportingModuleWidgetHelper.Debug('Input point: ' +
str(pointIJK))
SlicerReportingModuleWidgetHelper.Debug('Converted point: ' +
str(pointRAS))
rasPointList.append(pointRAS[0:3])
# instantiate the markup elements
if elementType == 'Point':
SlicerReportingModuleWidgetHelper.Debug(
"Importing a fiducial!")
if len(ijCoordList) != 2:
SlicerReportingModuleWidgetHelper.Error(
'Number of coordinates not good for a fiducial')
return
fiducial = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLAnnotationFiducialNode')
fiducial.SetReferenceCount(fiducial.GetReferenceCount() - 1)
# associate it with the volume
fiducial.SetAttribute("AssociatedNodeID", volume.GetID())
# ??? Why the API is so inconsistent -- there's no SetPosition1() ???
fiducial.SetFiducialCoordinates(rasPointList[0])
fiducial.Initialize(slicer.mrmlScene)
# adding to hierarchy is handled by the Reporting logic
if elementType == 'MultiPoint':
SlicerReportingModuleWidgetHelper.Debug("Importing a ruler!")
if len(ijCoordList) != 4:
SlicerReportingModuleWidgetHelper.Error(
'Number of coordinates not good for a ruler')
return
ruler = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLAnnotationRulerNode')
ruler.SetReferenceCount(ruler.GetReferenceCount() - 1)
# associate it with the volume
ruler.SetAttribute("AssociatedNodeID", volume.GetID())
SlicerReportingModuleWidgetHelper.Debug(
'Initializing with points ' + str(rasPointList[0]) +
' and ' + str(rasPointList[1]))
ruler.SetPosition1(rasPointList[0])
ruler.SetPosition2(rasPointList[1])
ruler.Initialize(slicer.mrmlScene)
# AF: Initialize() adds to the scene ...
for node in dom.getElementsByTagName('Segmentation'):
# read all labels that are available in the SEG object
# check if the referenced volume is already in the scene
# if not, load it
# initialize AssociatedNodeID for the label node to point to the
# reference
SlicerReportingModuleWidgetHelper.Debug('Importing a segmentation')
labelNodes = vtk.vtkCollection()
referenceNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeNode')
referenceNode.SetReferenceCount(referenceNode.GetReferenceCount() -
1)
uid = node.getAttribute('sopInstanceUID')
res = False
colorNode = slicer.mrmlScene.GetNodeByID(
newReport.GetColorNodeID())
res = slicer.modules.reporting.logic().DicomSegRead(
labelNodes, uid, colorNode)
SlicerReportingModuleWidgetHelper.Debug(
'Read this many labels from the seg object:' +
str(labelNodes.GetNumberOfItems()))
# read the reference node
label0 = labelNodes.GetItemAsObject(0)
referenceUIDs = label0.GetAttribute('DICOM.referenceInstanceUIDs')
SlicerReportingModuleWidgetHelper.Debug(
'Seg object reference uids: ' + referenceUIDs)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLLabelMapVolumeDisplayNode')
displayNode.SetReferenceCount(displayNode.GetReferenceCount() -
1)
displayNode.SetAndObserveColorNodeID(
newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('AssociatedNodeID',
volumeList[0].GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNode)
# AF: this shuould not be necessary with the "proper" AIM input, since
# only one volume should be present in the report, and only one item in
# that volume should be annotated
if 0:
# if referenceUIDs != None:
reader = slicer.vtkMRMLVolumeArchetypeStorageNode()
reader.ResetFileNameList()
for uid in string.split(referenceUIDs, ' '):
fname = slicer.modules.reporting.logic(
).GetFileNameFromUID(uid)
reader.AddFileName(fname)
reader.SetFileName(string.split(referenceUIDs, ' ')[0])
reader.SetSingleFile(0)
referenceVolume = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeNode')
referenceVolumeUIDs = referenceVolume.GetAttribute(
'DICOM.instanceUIDs')
reader.ReadData(referenceVolume)
nodeToAdd = referenceVolume
allVolumeNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLScalarVolumeNode')
allVolumeNodes.SetReferenceCount(
allVolumeNodes.GetReferenceCount() - 1)
for i in range(allVolumeNodes.GetNumberOfItems()):
v = allVolumeNodes.GetItemAsObject(i)
uids = v.GetAttribute('DICOM.instanceUIDs')
if uids == referenceNodeUIDs:
print('Referenced node is already in the scene!')
nodeToAdd = None
referenceNode = v
break
if nodeToAdd != None:
slicer.mrmlScene.AddNode(nodeToAdd)
slicer.modules.reporting.logic().InitializeHierarchyForVolume(
referenceNode)
for i in range(labelNodes.GetNumberOfItems()):
displayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLScalarVolumeDisplayNode')
displayNode.SetReferenceCount(
displayNode.GetReferenceCount() - 1)
displayNode.SetAndObserveColorNodeID(
newReport.GetColorNodeID())
slicer.mrmlScene.AddNode(displayNode)
labelNode = labelNodes.GetItemAsObject(i)
labelNode.SetAttribute('AssociatedNodeID',
referenceNode.GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
slicer.mrmlScene.AddNode(labelNodes.GetItemAsObject(i))
def load(self, loadable):
"""Load the selection as a MultiVolume, if multivolume attribute is
present
"""
mvNode = ''
try:
mvNode = loadable.multivolume
except AttributeError:
return None
nFrames = int(mvNode.GetAttribute('MultiVolume.NumberOfFrames'))
files = string.split(mvNode.GetAttribute('MultiVolume.FrameFileList'),
',')
nFiles = len(files)
filesPerFrame = nFiles / nFrames
frames = []
mvImage = vtk.vtkImageData()
mvImageArray = None
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
instanceUIDs = ""
for file in files:
uid = slicer.dicomDatabase.fileValue(file,
self.tags['instanceUID'])
if uid == "":
uid = "Unknown"
instanceUIDs += uid + " "
instanceUIDs = instanceUIDs[:-1]
mvNode.SetAttribute("DICOM.instanceUIDs", instanceUIDs)
# read each frame into scalar volume
for frameNumber in range(nFrames):
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
frameFileList = files[frameNumber *
filesPerFrame:(frameNumber + 1) *
filesPerFrame]
# sv plugin will sort the filenames by geometric order
svLoadables = scalarVolumePlugin.examine([frameFileList])
if len(svLoadables) == 0:
return None
for f in svLoadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(
frameFileList[0]) # only used when num files/frame = 1
sNode.SetSingleFile(0)
frame = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(frame)
if frame.GetImageData() == None:
print('Failed to read a multivolume frame!')
return None
if frameNumber == 0:
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1] * frameExtent[3] * frameExtent[5]
mvImage.SetExtent(frameExtent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(frame.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(
frame.GetImageData().GetScalarType(), nFrames)
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars())
mvNode.SetScene(slicer.mrmlScene)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameNumber] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetScene(slicer.mrmlScene)
mvDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(mvDisplayNode)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(mvNode)
#
# automatically select the volume to display
#
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(mvNode.GetID())
appLogic.PropagateVolumeSelection()
# file list is no longer needed - remove the attribute
mvNode.RemoveAttribute('MultiVolume.FrameFileList')
return mvNode
