def test_PETDicomExtensionSelfTest_Main(self):
""" test PET SUV Plugin and DICOM RWVM creation
"""
self.delayDisplay('Checking for PET DICOM plugins')
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomPluginCheckbox = dicomWidget.detailsPopup.pluginSelector.checkBoxByPlugin
self.assertIn('DICOMPETSUVPlugin', dicomPluginCheckbox)
self.assertIn('DICOMRWVMPlugin', dicomPluginCheckbox)
self.delayDisplay('Adding PET DICOM dataset to DICOM database (including download if necessary)')
self._downloadTestData()
self.delayDisplay('Loading data with DICOMPETSUVPlugin')
self._loadWithPlugin(self.UID, 'DICOMPETSUVPlugin')
imageNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLScalarVolumeNode')
self.assertIsNotNone(imageNode)
self.delayDisplay('Testing properties of loaded SUV normalized data')
self._testDataProperties(imageNode)
self.delayDisplay('Testing DICOM database for created RWVM file')
patientUID = DICOMUtils.getDatabasePatientUIDByPatientName(self.PatientName)
studies = slicer.dicomDatabase.studiesForPatient(patientUID)
series = slicer.dicomDatabase.seriesForStudy(studies[0])
RWVMSeries = None
for serie in series:
description = slicer.dicomDatabase.descriptionForSeries(serie)
if description=='PET SUV Factors':
RWVMSeries = serie
self.assertIsNotNone(RWVMSeries)
files = slicer.dicomDatabase.filesForSeries(RWVMSeries)
self.assertTrue(len(files)>0)
RWVMFile = files[0]
print(RWVMFile)
self.delayDisplay('Testing RealWorldValueSlope stored in RWVM file')
rwvm=dicom.read_file(RWVMFile)
self.assertIn('ReferencedImageRealWorldValueMappingSequence', rwvm)
rirwvms = rwvm.ReferencedImageRealWorldValueMappingSequence[0]
self.assertIn('RealWorldValueMappingSequence', rirwvms)
rwvms = rirwvms.RealWorldValueMappingSequence[0]
self.assertIn('RealWorldValueSlope', rwvms)
slope = rwvms.RealWorldValueSlope
self.assertTrue(abs(slope-0.000401664)<0.00001)
self.delayDisplay('Loading data with DICOMRWVMPlugin')
slicer.mrmlScene.Clear(0)
self._loadWithPlugin(RWVMSeries, 'DICOMRWVMPlugin')
imageNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLScalarVolumeNode')
self.assertIsNotNone(imageNode)
self.delayDisplay('Testing properties of loaded SUV normalized data')
self._testDataProperties(imageNode)
self.delayDisplay('Test passed!')
def test_PETPhantomAnalysis(self):
""" test standard processing
"""
try:
self.assertIsNotNone(slicer.modules.petphantomanalysis)
with DICOMUtils.TemporaryDICOMDatabase(
self.tempDicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)
self.delayDisplay(
'Loading PET DICOM dataset (including download if necessary)'
)
petNode = self.loadTestData()
self.delayDisplay('Running segmentation')
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('PETPhantomAnalysis')
qrWidget = slicer.modules.PETPhantomAnalysisWidget
qrWidget.inputSelector.setCurrentNode(petNode)
segmentationNode = qrWidget.segmentationSelector.addNode()
qrWidget.inputVolumeSelected()
qrWidget.segmentButton.click()
# assert measurements are correct
self.assertTrue(
abs(float(qrWidget.meanValueLineEdit.text) -
0.982502) < 0.01)
self.assertTrue(
abs(float(qrWidget.stdValueLineEdit.text) -
0.031612) < 0.01)
self.assertTrue(
abs(
float(qrWidget.maxRelDiffValueLineEdit.text) +
0.0203663) < 0.01)
## clean up data from DICOM database
patientUID = DICOMUtils.getDatabasePatientUIDByPatientName(
self.patienName)
db.removePatient(patientUID)
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),
self.delayMs * 2)
def test_PETLiverUptakeMeasurementQR2(self):
""" test segmentation options
"""
try:
self.assertIsNotNone( slicer.modules.petliveruptakemeasurement )
with DICOMUtils.TemporaryDICOMDatabase(self.tempDicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)
self.delayDisplay('Loading PET DICOM dataset (including download if necessary)')
petNode = self.loadTestData()
qrWidget = slicer.modules.PETLiverUptakeMeasurementQRWidget
qrWidget.inputSelector.setCurrentNode(petNode)
segmentationNode = qrWidget.segmentationSelector.addNode()
self.delayDisplay('Running segmentation with standard settings')
qrWidget.segmentButton.click()
self.assertTrue(abs(float(qrWidget.meanValueLineEdit.text)-2.36253)<0.01)
self.delayDisplay('Specifying annotation ROI')
roi=slicer.vtkMRMLAnnotationROINode()
roi.SetXYZ([-34,243,-1168])
roi.SetRadiusXYZ([85,102,82])
roi.SetName('ROI')
slicer.mrmlScene.AddNode(roi)
qrWidget.regionSelector.setCurrentNode(roi)
qrWidget.segmentButton.click()
self.assertTrue(abs(float(qrWidget.meanValueLineEdit.text)-2.91891)<0.01)
self.delayDisplay('Changing erosion range')
originalErosion = qrWidget.erosionSlider.value
qrWidget.erosionSlider.value = 0
qrWidget.segmentButton.click()
self.assertTrue(abs(float(qrWidget.meanValueLineEdit.text)-2.71982)<0.01)
self.delayDisplay('Changing thresholds')
originalMinimValue = qrWidget.thresholdRangeSlider.minimumValue
originalMaximumValue = qrWidget.thresholdRangeSlider.maximumValue
qrWidget.thresholdRangeSlider.minimumValue = 2
qrWidget.thresholdRangeSlider.maximumValue = 20
qrWidget.segmentButton.click()
self.assertTrue(abs(float(qrWidget.meanValueLineEdit.text)-3.72669)<0.01)
self.delayDisplay('Completing and writing DICOM report')
qrWidget.readerValueLineEdit.text = 'semiautotest'
self.assertTrue(qrWidget.saveReport(completed=True))
self.delayDisplay('Testing that report was saved as semiautomatic result')
import dicom
patientUID = DICOMUtils.getDatabasePatientUIDByPatientName('QIN-HEADNECK-01-0139')
studies = slicer.dicomDatabase.studiesForPatient(patientUID)
series = slicer.dicomDatabase.seriesForStudy(studies[0])
SEGSeries = None
for serie in series:
description = slicer.dicomDatabase.descriptionForSeries(serie)
if description=='Semiautomatic Liver Reference Region Segmentation':
SEGSeries = serie
self.assertIsNotNone(SEGSeries)
# reset values
qrWidget.regionSelector.removeCurrentNode()
qrWidget.erosionSlider.value = originalErosion
qrWidget.thresholdRangeSlider.minimumValue = originalMinimValue
qrWidget.thresholdRangeSlider.maximumValue = originalMaximumValue
# clean up data from DICOM database
db.removePatient(patientUID)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)
def test_PETLiverUptakeMeasurementQR1(self):
""" test standard segmentation and report generation
"""
try:
self.assertIsNotNone( slicer.modules.petliveruptakemeasurement )
with DICOMUtils.TemporaryDICOMDatabase(self.tempDicomDatabaseDir) as db:
self.assertTrue(db.isOpen)
self.assertEqual(slicer.dicomDatabase, db)
self.delayDisplay('Loading PET DICOM dataset (including download if necessary)')
petNode = self.loadTestData()
self.delayDisplay('Running segmentation')
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('PETLiverUptakeMeasurementQR')
qrWidget = slicer.modules.PETLiverUptakeMeasurementQRWidget
qrWidget.inputSelector.setCurrentNode(petNode)
segmentationNode = qrWidget.segmentationSelector.addNode()
qrWidget.segmentButton.click()
self.assertTrue(abs(float(qrWidget.meanValueLineEdit.text)-2.36253)<0.01)
self.assertTrue(abs(float(qrWidget.stdValueLineEdit.text)-0.402997)<0.01)
self.assertTrue(abs(float(qrWidget.medianValueLineEdit.text)-2.335)<0.01)
self.delayDisplay('Completing and writing DICOM report')
qrWidget.readerValueLineEdit.text = 'autotest'
self.assertTrue(qrWidget.saveReport(completed=True))
self.delayDisplay('Checking for DICOM SEG and SR')
import dicom
patientUID = DICOMUtils.getDatabasePatientUIDByPatientName(self.patienName)
studies = slicer.dicomDatabase.studiesForPatient(patientUID)
series = slicer.dicomDatabase.seriesForStudy(studies[0])
SRSeries = None
SEGSeries = None
for serie in series:
description = slicer.dicomDatabase.descriptionForSeries(serie)
if description=='Automatic Liver Reference Region Segmentation':
SEGSeries = serie
if description=='Liver Reference Region Measurement Report':
SRSeries = serie
self.assertIsNotNone(SRSeries)
self.assertIsNotNone(SEGSeries)
SRFile = slicer.dicomDatabase.filesForSeries(SRSeries)[0]
self.delayDisplay('Loading DICOM SR and verifying stored measurements')
sr = dicom.read_file(SRFile)
dicomMean = self._getMeasuredValue(sr,'Mean')
self.assertIsNotNone(dicomMean)
self.assertEqual(dicomMean.MeasuredValueSequence[0].NumericValue, 2.36253)
dicomStandardDeviation = self._getMeasuredValue(sr,'Standard Deviation')
self.assertIsNotNone(dicomStandardDeviation)
self.assertEqual(dicomStandardDeviation.MeasuredValueSequence[0].NumericValue, 0.402997)
dicomMedian = self._getMeasuredValue(sr,'Median')
self.assertIsNotNone(dicomMedian)
self.assertEqual(dicomMedian.MeasuredValueSequence[0].NumericValue, 2.335)
# clean up data from DICOM database
db.removePatient(patientUID)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)
