def section_LoadDicomDataWitchBatchProcessing(self):
try:
# Open Data module so that a subject hierarchy scene model is active
# (which caused problems with batch processing)
slicer.util.selectModule('Data')
# Open test database and empty it
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue( db.isOpen )
self.assertEqual( slicer.dicomDatabase, db)
slicer.mrmlScene.StartState(slicer.vtkMRMLScene.BatchProcessState)
# Download, unzip, import, and load data. Verify loaded nodes.
loadedNodes = {'vtkMRMLScalarVolumeNode':1}
with DICOMUtils.LoadDICOMFilesToDatabase( \
self.dicomZipFileUrl, self.dicomZipFilePath, \
self.dicomDataDir, self.expectedNumOfFilesInDicomDataDir, \
{}, loadedNodes, checksum=self.dicomZipChecksum) as success:
self.assertTrue(success)
slicer.mrmlScene.EndState(slicer.vtkMRMLScene.BatchProcessState)
self.assertEqual( len( slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*') ), 1 )
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
self.assertIsNotNone( shNode )
loadedDicomVolumeItemID = shNode.GetItemByName(self.loadedDicomVolumeName)
loadedDicomStudyItemID = shNode.GetItemByName(self.loadedDicomStudyName)
self.assertEqual( shNode.GetItemParent(loadedDicomVolumeItemID), loadedDicomStudyItemID )
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)
def loadTestData(self):
#download data and add to dicom database
zipFileUrl = 'http://slicer.kitware.com/midas3/download/item/257234/QIN-HEADNECK-01-0139-PET.zip'
zipFilePath = self.tempDataDir + '/dicom.zip'
zipFileData = self.tempDataDir + '/dicom'
expectedNumOfFiles = 545
if not os.access(self.tempDataDir, os.F_OK):
os.mkdir(self.tempDataDir)
if not os.access(zipFileData, os.F_OK):
os.mkdir(zipFileData)
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['DICOMScalarVolumePlugin'].checked = True
# Download, unzip, import, and load data. Verify loaded nodes.
loadedNodes = {'vtkMRMLScalarVolumeNode': 1}
with DICOMUtils.LoadDICOMFilesToDatabase(zipFileUrl, zipFilePath,
zipFileData,
expectedNumOfFiles, {},
loadedNodes) as success:
self.assertTrue(success)
print('loading returned true')
self.assertEqual(
len(slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*')), 1)
imageNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLScalarVolumeNode')
for key, value in dicomPluginStates:
dicomPluginCheckbox[key].checked = value
# apply the SUVbw conversion factor and set units and quantity
suvNormalizationFactor = 0.00040166400000000007
quantity = slicer.vtkCodedEntry()
quantity.SetFromString(
'CodeValue:126400|CodingSchemeDesignator:DCM|CodeMeaning:Standardized Uptake Value'
)
units = slicer.vtkCodedEntry()
units.SetFromString(
'CodeValue:{SUVbw}g/ml|CodingSchemeDesignator:UCUM|CodeMeaning:Standardized Uptake Value body weight'
)
multiplier = vtk.vtkImageMathematics()
multiplier.SetOperationToMultiplyByK()
multiplier.SetConstantK(suvNormalizationFactor)
multiplier.SetInput1Data(imageNode.GetImageData())
multiplier.Update()
imageNode.GetImageData().DeepCopy(multiplier.GetOutput())
imageNode.GetVolumeDisplayNode().SetWindowLevel(6, 3)
imageNode.GetVolumeDisplayNode().SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeInvertedGrey')
imageNode.SetVoxelValueQuantity(quantity)
imageNode.SetVoxelValueUnits(units)
return imageNode
def TestSection_1_LoadDicomData(self):
try:
self.assertTrue( self.db.isOpen )
self.assertEqual( slicer.dicomDatabase, self.db)
# Download, unzip, import, and load data. Verify selected plugins and loaded nodes.
selectedPlugins = { 'Scalar Volume':1, 'RT':2 }
loadedNodes = { 'vtkMRMLScalarVolumeNode':2, \
'vtkMRMLSegmentationNode':1 }
with DICOMUtils.LoadDICOMFilesToDatabase( \
self.dicomZipFileUrl, self.dicomZipFilePath, \
self.dicomDataDir, self.expectedNumOfFilesInDicomDataDir, \
{}, loadedNodes) as success:
self.assertTrue(success)
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)
def section_LoadDicomData(self):
try:
# Open test database and empty it
with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
self.assertTrue( db.isOpen )
self.assertEqual( slicer.dicomDatabase, db)
# Download, unzip, import, and load data. Verify loaded nodes.
loadedNodes = {'vtkMRMLScalarVolumeNode':1}
with DICOMUtils.LoadDICOMFilesToDatabase( \
self.dicomZipFileUrl, self.dicomZipFilePath, \
self.dicomDataDir, self.expectedNumOfFilesInDicomDataDir, \
{}, loadedNodes, checksum=self.dicomZipChecksum) as success:
self.assertTrue(success)
self.assertEqual( len( slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*') ), 1 )
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)