def load_DICOM(self):
# create temporary database. Save original database path to restore
# it when finished
self.original_db_path = DICOMUtils.openTemporaryDatabase()
#assert temporary database is open
# import DICOM to database
DICOMUtils.importDicom(self.locations_dict['DICOM'],
slicer.dicomDatabase)
# get patient name
patient_name = slicer.dicomDatabase.nameForPatient(
slicer.dicomDatabase.patients()[0])
# open DICOM by name
DICOMUtils.loadPatientByName(patient_name)
slicer.util.selectModule('SegmentationExtractionModule')
def _test_PETLiverUptakeMeasurementQR2_WithQRExtension(self):
""" verify SR measurements assuming QuantiativeReporting Extension is installed and enabled
"""
from DICOMLib import DICOMUtils
self.delayDisplay('Loading DICOM SEG and SR')
# note: introduces dependency on QuantiativeReporting and DICOMPETExtension
# with QuantiativeReporting installed, this should load the DICOM SR and SEG together with the PET scan
# disable all dicom plugins except those necessary
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomPluginCheckbox = dicomWidget.detailsPopup.pluginSelector.checkBoxByPlugin
dicomPluginStates = {(key,value.checked) for key,value in dicomPluginCheckbox.iteritems()}
for cb in dicomPluginCheckbox.itervalues():
cb.checked=False
dicomPluginCheckbox['DICOMRWVMPlugin'].checked = True
dicomPluginCheckbox['DICOMPETSUVPlugin'].checked = True
dicomPluginCheckbox['DICOMSegmentationPlugin'].checked = True
dicomPluginCheckbox['DICOMTID1500Plugin'].checked = True
DICOMUtils.loadPatientByName(self.patienName)
for key,value in dicomPluginStates:
dicomPluginCheckbox[key].checked=value
# with QuantiativeReporting installed, this should load the DICOM SR and SEG together with the PET scan
DICOMUtils.loadPatientByName(self.patienName)
tableNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLTableNode")
self.assertIsNotNone(tableNode, "Loading SR into mrmlScene failed. No vtkMRMLTableNodes were found within the scene.")
self.assertEqual(tableNode.GetNumberOfRows(),1)
self.assertTrue(tableNode.GetNumberOfColumns()>3)
self.assertEqual(tableNode.GetColumnName(0),'Segment')
self.assertEqual(tableNode.GetColumnName(1),'Mean [{SUVbw}g/ml]')
self.assertEqual(tableNode.GetColumnName(2),'Standard Deviation [{SUVbw}g/ml]')
self.assertEqual(tableNode.GetColumnName(3),'Median [{SUVbw}g/ml]')
self.assertEqual(tableNode.GetCellText(0,0),'Liver reference region')
self.assertTrue(abs(float(tableNode.GetCellText(0,1))-2.36253)<0.01)
self.assertTrue(abs(float(tableNode.GetCellText(0,2))-0.402997)<0.01)
self.assertTrue(abs(float(tableNode.GetCellText(0,3))-2.335)<0.01)
self.delayDisplay('Test passed!')
for key,value in dicomPluginStates:
dicomPluginCheckbox[key].checked=value
