def initializeNewLabel(newLabel, sourceVolume):
displayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLLabelMapVolumeDisplayNode())
threshold = vtk.vtkImageThreshold()
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetInValue(0)
threshold.SetOutValue(0)
threshold.SetOutputScalarTypeToUnsignedShort()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
threshold.SetInput(sourceVolume.GetImageData())
else:
threshold.SetInputData(sourceVolume.GetImageData())
threshold.Update()
labelImage = vtk.vtkImageData()
labelImage.DeepCopy(threshold.GetOutput())
newLabel.SetAndObserveStorageNodeID(None)
newLabel.CopyOrientation(sourceVolume)
ras2ijk = vtk.vtkMatrix4x4()
sourceVolume.GetRASToIJKMatrix(ras2ijk)
newLabel.SetRASToIJKMatrix(ras2ijk)
newLabel.SetAttribute('ReportingReportNodeID', sourceVolume.GetAttribute('ReportingReportNodeID'))
newLabel.SetAttribute('AssociatedNodeID', sourceVolume.GetID())
newLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
newLabel.SetAndObserveImageData(labelImage)
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 test_LabelToDICOMSEGConverterRoundTrip(self):
print("CTEST_FULL_OUTPUT")
dir(slicer.modules)
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=10881', 'JANCT-CT.zip'),
)
self.delayDisplay("Downloading")
for url,name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
reportingTempDir = slicer.app.temporaryPath+'/LabelToDICOMSEGConverter'
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + '/dicomFiles'
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
self.importDICOM(slicer.dicomDatabase, dicomFilesDirectory)
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, 'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes('vtkMRMLScalarVolumeNode*')
self.assertTrue(len(volumes) == 1)
(name,volume) = volumes.items()[0]
self.delayDisplay('Loaded volume name %s' % volume.GetName())
self.delayDisplay('Configure Module')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('LabelToDICOMSEGConverter')
module = slicer.modules.labeltodicomsegconverter.widgetRepresentation().self()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volume, "Segmentation")
labelNode.SetAttribute('AssociatedNodeID', volume.GetID())
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10,400)
thresh.SetInValue(10)
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
module.segmentationSelector.setCurrentNode(labelNode)
module.volumeSelector.setCurrentNode(volume)
self.delayDisplay('Input label initialized')
module.outputDir = reportingTempDir+'/Output'
# Save the report
exportDir = reportingTempDir+'/Output'
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
module.onLabelExport()
self.delayDisplay('Report saved')
self.importDICOM(slicer.dicomDatabase, exportDir)
slicer.mrmlScene.Clear(0)
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, 'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Wait',10000)
dicomWidget.detailsPopup.loadCheckedLoadables()
volumes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
for n,v in volumes.items():
print('Label volume found: '+v.GetID())
self.assertTrue(len(volumes) == 1)
for name,volume in volumes.items():
image = volume.GetImageData()
previousImage = thresh.GetOutput()
diff = vtk.vtkImageDifference()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
diff.SetInput(thresh.GetOutput())
else:
diff.SetInputData(thresh.GetOutput())
diff.SetImage(image)
diff.Update()
if diff.GetThresholdedError() > 1:
self.delayDisplay('Reloaded image does not match')
self.assertTrue(False)
self.delayDisplay('Test passed')
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.assertTrue(False)
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 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 test_ReportingAIMRoundTrip(self):
print("CTEST_FULL_OUTPUT")
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download?items=10881', 'JANCT-CT.zip'),
)
self.delayDisplay("Downloading")
for url,name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
reportingTempDir = slicer.app.temporaryPath+'/Reporting'
print('Temporary directory location: '+reportingTempDir)
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + '/dicomFiles'
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
#dicomWidget.dicomApp.suspendModel()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, 'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes('vtkMRMLScalarVolumeNode*')
self.assertTrue(len(volumes) == 1)
(name,volume) = volumes.items()[0]
self.delayDisplay('Loaded volume name %s' % volume.GetName())
self.delayDisplay('Configure Module')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
reporting = slicer.modules.reporting.widgetRepresentation().self()
report = slicer.mrmlScene.CreateNodeByClass('vtkMRMLReportingReportNode')
report.SetReferenceCount(report.GetReferenceCount()-1)
slicer.mrmlScene.AddNode(report)
report.SetFindingLabel(7)
reporting.reportSelector.setCurrentNode(report)
self.delayDisplay('Setting volume to %s' % volume.GetName())
reporting.volumeSelector.setCurrentNode(volume)
slicer.app.processEvents()
# place some markups and add a segmentation label
# add fiducial
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(1)
fidNode.SetLocked(0)
# TODO: ask Nicole where this is assigned in the regular workflow
fidNode.SetAttribute('AssociatedNodeID',volume.GetID())
print("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0],startCoords[1],startCoords[2])
print("Starting fiducial coordinates: "+str(startCoords))
slicer.mrmlScene.AddNode(fidNode)
# add ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetName('Test Ruler')
m = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(m)
ijk0 = [0,0,1,1]
ijk1 = [50,50,1,1]
ras0 = m.MultiplyPoint(ijk0)
ras1 = m.MultiplyPoint(ijk1)
rulerNode.SetPosition1(19.386751174926758, 68.528785705566406, -127.69000244140625)
rulerNode.SetPosition2(132.72709655761719, -34.349384307861328, -127.69000244140625)
rulerNode.SetAttribute('AssociatedNodeID',volume.GetID())
slicer.mrmlScene.AddNode(rulerNode)
slicer.app.processEvents()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volume, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10,400)
thresh.SetInValue(report.GetFindingLabel())
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
reporting.segmentationSelector.setCurrentNode(labelNode)
# Save the report
exportDir = reportingTempDir+'/Output'
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
report.SetStorageDirectoryName(exportDir)
reportingLogic = slicer.modules.reporting.logic()
print("Before saving report")
reportingLogic.SaveReportToAIM(report)
self.delayDisplay('Report saved')
slicer.mrmlScene.Clear(0)
# parse on patient level, find segmentation object, load and make sure
# it matches the input
# close the scene and load the report, check consistency
# try to load back the saved AIM
import glob
print glob.glob(exportDir+'/*')
xmlFiles = glob.glob(exportDir+'/*xml')
print xmlFiles
self.assertTrue(len(xmlFiles) == 1)
reporting.importAIMFile = xmlFiles[0]
reporting.onReportImport()
self.delayDisplay('Report loaded from AIM! Test passed.')
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.assertTrue(False)
def test_ReportingAIMRoundTrip(self):
print ("CTEST_FULL_OUTPUT")
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (("http://slicer.kitware.com/midas3/download?items=10881", "JANCT-CT.zip"),)
self.delayDisplay("Downloading")
for url, name in downloads:
filePath = slicer.app.temporaryPath + "/" + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay("Requesting download %s from %s...\n" % (name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay("Finished with download\n")
reportingTempDir = slicer.app.temporaryPath + "/Reporting"
print ("Temporary directory location: " + reportingTempDir)
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + "/dicomFiles"
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + "/tempDICOMDatbase"
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue("DatabaseDirectory", tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay("Importing DICOM")
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule("DICOM")
# dicomWidget.dicomApp.suspendModel()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [slicer.dicomDatabase.seriesForStudy(study) for study in studies]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs, "SeriesUIDList")
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay("Loading Selection")
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes("vtkMRMLScalarVolumeNode*")
self.assertTrue(len(volumes) == 1)
(name, volume) = volumes.items()[0]
self.delayDisplay("Loaded volume name %s" % volume.GetName())
self.delayDisplay("Configure Module")
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule("Reporting")
reporting = slicer.modules.reporting.widgetRepresentation().self()
report = slicer.mrmlScene.CreateNodeByClass("vtkMRMLReportingReportNode")
report.SetReferenceCount(report.GetReferenceCount() - 1)
slicer.mrmlScene.AddNode(report)
report.SetFindingLabel(7)
reporting.reportSelector.setCurrentNode(report)
self.delayDisplay("Setting volume to %s" % volume.GetName())
reporting.volumeSelector.setCurrentNode(volume)
slicer.app.processEvents()
# place some markups and add a segmentation label
# add fiducial
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(1)
fidNode.SetLocked(0)
# TODO: ask Nicole where this is assigned in the regular workflow
fidNode.SetAttribute("AssociatedNodeID", volume.GetID())
print ("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0], startCoords[1], startCoords[2])
print ("Starting fiducial coordinates: " + str(startCoords))
slicer.mrmlScene.AddNode(fidNode)
# add ruler
rulerNode = slicer.vtkMRMLAnnotationRulerNode()
rulerNode.SetName("Test Ruler")
m = vtk.vtkMatrix4x4()
volume.GetIJKToRASMatrix(m)
ijk0 = [0, 0, 1, 1]
ijk1 = [50, 50, 1, 1]
ras0 = m.MultiplyPoint(ijk0)
ras1 = m.MultiplyPoint(ijk1)
rulerNode.SetPosition1(19.386751174926758, 68.528785705566406, -127.69000244140625)
rulerNode.SetPosition2(132.72709655761719, -34.349384307861328, -127.69000244140625)
rulerNode.SetAttribute("AssociatedNodeID", volume.GetID())
slicer.mrmlScene.AddNode(rulerNode)
slicer.app.processEvents()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volume, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10, 400)
thresh.SetInValue(report.GetFindingLabel())
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
reporting.segmentationSelector.setCurrentNode(labelNode)
# Save the report
exportDir = reportingTempDir + "/Output"
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
report.SetStorageDirectoryName(exportDir)
reportingLogic = slicer.modules.reporting.logic()
print ("Before saving report")
reportingLogic.SaveReportToAIM(report)
self.delayDisplay("Report saved")
slicer.mrmlScene.Clear(0)
# parse on patient level, find segmentation object, load and make sure
# it matches the input
# close the scene and load the report, check consistency
# try to load back the saved AIM
import glob
print glob.glob(exportDir + "/*")
xmlFiles = glob.glob(exportDir + "/*xml")
print xmlFiles
self.assertTrue(len(xmlFiles) == 1)
reporting.importAIMFile = xmlFiles[0]
reporting.onReportImport()
self.delayDisplay("Report loaded from AIM! Test passed.")
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay("Test caused exception!\n" + str(e))
self.assertTrue(False)
def test_LabelToDICOMSEGConverterRoundTrip(self):
print("CTEST_FULL_OUTPUT")
dir(slicer.modules)
""" Load the data using DICOM module
"""
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import urllib
downloads = (('http://slicer.kitware.com/midas3/download?items=10881',
'JANCT-CT.zip'), )
self.delayDisplay("Downloading")
for url, name in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' %
(name, url))
urllib.urlretrieve(url, filePath)
self.delayDisplay('Finished with download\n')
reportingTempDir = slicer.app.temporaryPath + '/LabelToDICOMSEGConverter'
qt.QDir().mkpath(reportingTempDir)
dicomFilesDirectory = reportingTempDir + '/dicomFiles'
self.cleanupDir(dicomFilesDirectory)
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = reportingTempDir + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
self.cleanupDir(tempDatabaseDirectory)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(
slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', tempDatabaseDirectory)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(tempDatabaseDirectory)
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
self.importDICOM(slicer.dicomDatabase, dicomFilesDirectory)
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [
slicer.dicomDatabase.seriesForStudy(study) for study in studies
]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs,
'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
# initialize the module with the report and volume
volumes = slicer.util.getNodes('vtkMRMLScalarVolumeNode*')
self.assertTrue(len(volumes) == 1)
(name, volume) = volumes.items()[0]
self.delayDisplay('Loaded volume name %s' % volume.GetName())
self.delayDisplay('Configure Module')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule(
'LabelToDICOMSEGConverter')
module = slicer.modules.labeltodicomsegconverter.widgetRepresentation(
).self()
# add label node
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(
slicer.mrmlScene, volume, "Segmentation")
labelNode.SetAttribute('AssociatedNodeID', volume.GetID())
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
image = volume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(image)
else:
thresh.SetInputData(image)
thresh.ThresholdBetween(10, 400)
thresh.SetInValue(10)
thresh.SetOutValue(0)
thresh.Update()
labelNode.SetAndObserveImageData(thresh.GetOutput())
module.segmentationSelector.setCurrentNode(labelNode)
module.volumeSelector.setCurrentNode(volume)
self.delayDisplay('Input label initialized')
module.outputDir = reportingTempDir + '/Output'
# Save the report
exportDir = reportingTempDir + '/Output'
qt.QDir().mkpath(exportDir)
self.cleanupDir(exportDir)
module.onLabelExport()
self.delayDisplay('Report saved')
self.importDICOM(slicer.dicomDatabase, exportDir)
slicer.mrmlScene.Clear(0)
patient = slicer.dicomDatabase.patients()[0]
studies = slicer.dicomDatabase.studiesForPatient(patient)
series = [
slicer.dicomDatabase.seriesForStudy(study) for study in studies
]
seriesUIDs = [uid for uidList in series for uid in uidList]
dicomWidget.detailsPopup.offerLoadables(seriesUIDs,
'SeriesUIDList')
dicomWidget.detailsPopup.examineForLoading()
loadablesByPlugin = dicomWidget.detailsPopup.loadablesByPlugin
self.delayDisplay('Wait', 10000)
dicomWidget.detailsPopup.loadCheckedLoadables()
volumes = slicer.util.getNodes('vtkMRMLLabelMapVolumeNode*')
for n, v in volumes.items():
print('Label volume found: ' + v.GetID())
self.assertTrue(len(volumes) == 1)
for name, volume in volumes.items():
image = volume.GetImageData()
previousImage = thresh.GetOutput()
diff = vtk.vtkImageDifference()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
diff.SetInput(thresh.GetOutput())
else:
diff.SetInputData(thresh.GetOutput())
diff.SetImage(image)
diff.Update()
if diff.GetThresholdedError() > 1:
self.delayDisplay('Reloaded image does not match')
self.assertTrue(False)
self.delayDisplay('Test passed')
self.delayDisplay("Restoring original database directory")
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(
self.originalDatabaseDirectory)
except Exception, e:
if self.originalDatabaseDirectory:
dicomWidget.onDatabaseDirectoryChanged(
self.originalDatabaseDirectory)
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.assertTrue(False)
