def __init__(self,
database,
fileToBeAddedCallback=None,
fileAddedCallback=None):
super(DICOMListener, self).__init__()
self.dicomDatabase = database
self.indexer = ctk.ctkDICOMIndexer()
self.fileToBeAddedCallback = fileToBeAddedCallback
self.fileAddedCallback = fileAddedCallback
self.lastFileAdded = None
settings = qt.QSettings()
dir = settings.value('DatabaseDirectory')
if not dir:
raise (UserWarning(
'Database directory not set: cannot start DICOMListener'))
if not os.path.exists(dir):
os.mkdir(dir)
self.incomingDir = dir + "/incoming"
if not os.path.exists(self.incomingDir):
os.mkdir(self.incomingDir)
self.port = settings.value('StoragePort')
if not self.port:
settings.setValue('StoragePort', '11112')
self.port = settings.value('StoragePort')
def addFilesToDatabase(self):
indexer = ctk.ctkDICOMIndexer()
destinationDir = os.path.dirname(slicer.dicomDatabase.databaseFilename)
if self.sdbFile:
files = [self.sdbFile]
else:
files = glob.glob("%s/*" % self.dicomDirectory)
for file in files:
indexer.addFile(slicer.dicomDatabase, file, destinationDir)
slicer.util.showStatusMessage("Loaded: %s" % file, 1000)
def importDicomDir(self, outputDirPath):
"""
Utility function to import DICOM files from a directory
"""
self.addLog('Directory: '+outputDirPath)
self.addLog('DICOM importing started...')
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory( slicer.dicomDatabase, outputDirPath )
self.addLog('DICOM importing completed.')
def importDicomDir(self, outputDirPath):
"""
Utility function to import DICOM files from a directory
"""
self.addLog('Directory: '+outputDirPath)
self.addLog('DICOM importing started...')
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory( slicer.dicomDatabase, outputDirPath )
self.addLog('DICOM importing completed.')
def addFilesToDatabase(self):
indexer = ctk.ctkDICOMIndexer()
destinationDir = os.path.dirname(slicer.dicomDatabase.databaseFilename)
if self.sdbFile:
files = [self.sdbFile]
else:
files = glob.glob('%s/*' % self.dicomDirectory)
for file in files:
indexer.addFile(slicer.dicomDatabase, file, destinationDir)
slicer.util.showStatusMessage("Loaded: %s" % file, 1000)
def TestSection_2ImportStudy(self):
self.delayDisplay("Import study",self.delayMs)
indexer = ctk.ctkDICOMIndexer()
self.assertIsNotNone( indexer )
# Import study to database
indexer.addDirectory( slicer.dicomDatabase, self.dataDir )
indexer.waitForImportFinished()
self.assertEqual( len(slicer.dicomDatabase.patients()), 1 )
self.assertIsNotNone( slicer.dicomDatabase.patients()[0] )
def importStudy(self, inputDir, progressCallback=None):
self.progressCallback = progressCallback
self.canceled = False
print('Database location: '+self.dicomDatabaseDir)
print('FIXME: revert back to the original DB location when done!')
self.openDatabase()
print('Input directory: ' + inputDir)
if not self.indexer:
self.indexer = ctk.ctkDICOMIndexer()
self.indexer.connect("progress(int)", self.updateProgress)
self.indexer.addDirectory(slicer.dicomDatabase, inputDir)
self.patients = slicer.dicomDatabase.patients()
print('Import completed, total '+str(len(slicer.dicomDatabase.patients()))+' patients imported')
def ImportStudy(self, dicomDataDir):
indexer = ctk.ctkDICOMIndexer()
# Import study to database
indexer.addDirectory( slicer.dicomDatabase, dicomDataDir )
indexer.waitForImportFinished()
# Check if import added any new patients to the database
if len(slicer.dicomDatabase.patients()) > self.databases[self.dbCounter]['NumberPatients']:
patientsAdded = slicer.dicomDatabase.patients()[self.databases[self.dbCounter]['NumberPatients']:]
self.databases[self.dbCounter]['NumberPatients'] = len(slicer.dicomDatabase.patients())
return patientsAdded
else:
return 0
def loadCheckedLoadables(self):
"""Invoke the load method on each plugin for the DICOMLoadable
instances that are selected"""
if self.advancedViewButton.checkState() == 0:
self.examineForLoading()
self.loadableTable.updateSelectedFromCheckstate()
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
loadingResult = ''
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
loadingResult = '%s\nCould not load: %s as a %s' % (loadingResult,loadable.name,plugin.loadType)
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
try:
for derivedItem in loadable.derivedItems:
indexer = ctk.ctkDICOMIndexer()
self.progress.labelText = '\nIndexing %s' % derivedItem
slicer.app.processEvents()
indexer.addFile(slicer.dicomDatabase, derivedItem)
except AttributeError:
# no derived items or some other attribute error
pass
self.progress.close()
self.progress = None
if loadingResult:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'DICOM loading', loadingResult)
if not self.browserPersistent:
self.close()
def loadCheckedLoadables(self):
"""Invoke the load method on each plugin for the loadable
(DICOMLoadable or qSlicerDICOMLoadable) instances that are selected"""
if self.advancedViewButton.checkState() == 0:
self.examineForLoading()
self.loadableTable.updateSelectedFromCheckstate()
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
loadingResult = ''
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
loadingResult = '%s\nCould not load: %s as a %s' % (loadingResult,loadable.name,plugin.loadType)
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
try:
for derivedItem in loadable.derivedItems:
indexer = ctk.ctkDICOMIndexer()
self.progress.labelText = '\nIndexing %s' % derivedItem
slicer.app.processEvents()
indexer.addFile(slicer.dicomDatabase, derivedItem)
except AttributeError:
# no derived items or some other attribute error
pass
self.progress.close()
self.progress = None
if loadingResult:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'DICOM loading', loadingResult)
if not self.browserPersistent:
self.close()
def ImportStudy(self, dicomDataDir):
indexer = ctk.ctkDICOMIndexer()
# Import study to database
indexer.addDirectory(slicer.dicomDatabase, dicomDataDir)
indexer.waitForImportFinished()
# Check if import added any new patients to the database
if len(slicer.dicomDatabase.patients()) > self.databases[
self.dbCounter]['NumberPatients']:
patientsAdded = slicer.dicomDatabase.patients(
)[self.databases[self.dbCounter]['NumberPatients']:]
self.databases[self.dbCounter]['NumberPatients'] = len(
slicer.dicomDatabase.patients())
return patientsAdded
else:
return 0
def __init__(self,database,fileToBeAddedCallback=None,fileAddedCallback=None):
super(DICOMListener,self).__init__()
self.dicomDatabase = database
self.indexer = ctk.ctkDICOMIndexer()
self.fileToBeAddedCallback = fileToBeAddedCallback
self.fileAddedCallback = fileAddedCallback
self.lastFileAdded = None
settings = qt.QSettings()
dir = settings.value('DatabaseDirectory')
if not dir:
raise( UserWarning('Database directory not set: cannot start DICOMListener') )
if not os.path.exists(dir):
os.mkdir(dir)
self.incomingDir = dir + "/incoming"
if not os.path.exists(self.incomingDir):
os.mkdir(self.incomingDir)
self.port = settings.value('StoragePort')
if not self.port:
settings.setValue('StoragePort', '11112')
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_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
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=8610', 'dicom.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')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
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()
dicomWidget.dicomApp.resumeModel()
dicomWidget.detailsPopup.open()
# click on the first row of the tree
index = dicomWidget.tree.indexAt(qt.QPoint(0,0))
dicomWidget.onTreeClicked(index)
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
self.clickAndDrag(redWidget,start=(10,10),end=(10,40))
self.delayDisplay('Change Window')
self.clickAndDrag(redWidget,start=(10,10),end=(40,10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
self.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.delayDisplay('Pan')
self.clickAndDrag(redWidget,button='Middle',start=(10,10),end=(40,40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
self.clickAndDrag(redWidget,button='None',start=(100,100),end=(140,140),modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView,button='Right')
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def proceedWithReferencedLoadablesSelection(self):
# each check box corresponds to a referenced loadable
# that was selected by examine; if the user confirmed
# that reference should be loaded, add it to the self.loadablesByPlugin
# dictionary
if self.referencesDialog:
children = self.referencesDialog.children()
loadableCnt = 0
for plugin in self.referencedLoadables:
for loadable in self.referencedLoadables[plugin]:
if loadable.selected:
if children[loadableCnt+2].checked:
self.loadablesByPlugin[plugin].append(loadable)
self.referencesDialog.close()
self.referencesDialog = None
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
loadingResult = ''
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
loadingResult = '%s\nCould not load: %s as a %s' % (loadingResult,loadable.name,plugin.loadType)
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
try:
for derivedItem in loadable.derivedItems:
indexer = ctk.ctkDICOMIndexer()
self.progress.labelText = '\nIndexing %s' % derivedItem
slicer.app.processEvents()
indexer.addFile(slicer.dicomDatabase, derivedItem)
except AttributeError:
# no derived items or some other attribute error
pass
self.progress.close()
self.progress = None
if loadingResult:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'DICOM loading', loadingResult)
if not self.browserPersistent:
self.close()
return
def proceedWithReferencedLoadablesSelection(self):
# each check box corresponds to a referenced loadable
# that was selected by examine; if the user confirmed
# that reference should be loaded, add it to the self.loadablesByPlugin
# dictionary
if self.referencesDialog:
children = self.referencesDialog.children()
loadableCnt = 0
for plugin in self.referencedLoadables:
for loadable in self.referencedLoadables[plugin]:
if loadable.selected:
if children[loadableCnt+2].checked:
self.loadablesByPlugin[plugin].append(loadable)
self.referencesDialog.close()
self.referencesDialog = None
loadableCount = 0
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if loadable.selected:
loadableCount += 1
self.progress = qt.QProgressDialog(self.window)
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(loadableCount)
step = 0
loadingResult = ''
loadedNodeIDs = []
@vtk.calldata_type(vtk.VTK_OBJECT)
def onNodeAdded(caller, event, calldata):
node = calldata
if isinstance(node, slicer.vtkMRMLVolumeNode):
loadedNodeIDs.append(node.GetID())
self.addObserver(slicer.mrmlScene, slicer.vtkMRMLScene.NodeAddedEvent, onNodeAdded);
for plugin in self.loadablesByPlugin:
for loadable in self.loadablesByPlugin[plugin]:
if self.progress.wasCanceled:
break
slicer.app.processEvents()
self.progress.setValue(step)
slicer.app.processEvents()
if loadable.selected:
self.progress.labelText = '\nLoading %s' % loadable.name
slicer.app.processEvents()
if not plugin.load(loadable):
loadingResult = '%s\nCould not load: %s as a %s' % (loadingResult,loadable.name,plugin.loadType)
step += 1
self.progress.setValue(step)
slicer.app.processEvents()
try:
for derivedItem in loadable.derivedItems:
indexer = ctk.ctkDICOMIndexer()
self.progress.labelText = '\nIndexing %s' % derivedItem
slicer.app.processEvents()
indexer.addFile(slicer.dicomDatabase, derivedItem)
except AttributeError:
# no derived items or some other attribute error
pass
self.removeObserver(slicer.mrmlScene, slicer.vtkMRMLScene.NodeAddedEvent, onNodeAdded);
loadedFileParameters = {}
loadedFileParameters['nodeIDs'] = loadedNodeIDs
slicer.app.ioManager().emitNewFileLoaded(loadedFileParameters)
self.progress.close()
self.progress = None
if loadingResult:
qt.QMessageBox.warning(slicer.util.mainWindow(), 'DICOM loading', loadingResult)
if not self.browserPersistent:
self.close()
return
def test_Part1DICOM(self,
enableScreenshotsFlag=0,
screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
self.enableScreenshots = enableScreenshotsFlag
self.screenshotScaleFactor = screenshotScaleFactor
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=124183',
'dataset1_Thorax_Abdomen.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')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatabase'
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(
slicer.dicomDatabase.databaseFilename)[0]
else:
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')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory,
None)
indexer.waitForImportFinished()
dicomWidget.detailsPopup.open()
# load the data by series UID
dicomWidget.detailsPopup.offerLoadables(
'1.3.12.2.1107.5.1.4.50025.30000005060811542834300000776',
'Series')
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.takeScreenshot('LoadingADICOMVolume-Loaded',
'Loaded DICOM Volume', -1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
self.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.takeScreenshot('LoadingADICOMVolume-WL',
'Changed level and window', -1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot('LoadingADICOMVolume-LinkView',
'Linked and visible', -1)
self.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
self.takeScreenshot('LoadingADICOMVolume-Zoom', 'Zoom', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.takeScreenshot('LoadingADICOMVolume-Rotate', 'Rotate', -1)
threeDView.resetFocalPoint()
self.takeScreenshot('LoadingADICOMVolume-Center',
'Center the view', -1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.
SlicerLayoutConventionalWidescreenView)
self.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen',
'Conventional Widescreen Layout', -1)
slicer.util.mainWindow().moduleSelector().selectModule(
'VolumeRendering')
self.takeScreenshot('VolumeRendering-Module', 'Volume Rendering',
-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation(
)
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName(
'6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
self.takeScreenshot('VolumeRendering-SelectVolume',
'Select the volume 6: CT_Thorax_Abdomen', -1)
presetsScene = slicer.modules.volumerendering.logic(
).GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.applyPreset(ctCardiac3)
self.takeScreenshot('VolumeRendering-SelectPreset',
'Select the Preset CT-Cardiac-3')
self.delayDisplay('Skipping: Select VTK CPU Ray Casting')
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName(
'VolumeRendering')
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot('VolumeRendering-ViewRendering',
'View Volume Rendering', -1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False)
self.takeScreenshot('VolumeRendering-SlicesOff',
'Turn off visibility of slices in 3D', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.takeScreenshot('VolumeRendering-RotateVolumeRendering',
'Rotate volume rendered image', -1)
volumeRenderingNode.SetVisibility(0)
self.takeScreenshot('VolumeRendering-TurnOffVolumeRendering',
'Turn off volume rendered image', -1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName(
'AnnotationROI')
annotationROI.SetDisplayVisibility(1)
self.takeScreenshot('VolumeRendering-DisplayROI',
'Enable cropping and display ROI', -1)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot('VolumeRendering-SlicesOn',
'Turn on visibility of slices in 3D', -1)
annotationROI.SetXYZ(-79.61, 154.16, -232.591)
annotationROI.SetRadiusXYZ(43.4, 65.19, 70.5)
self.takeScreenshot('VolumeRendering-SizedROI',
'Position the ROI over a kidney', -1)
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot('VolumeRendering-ROIRendering',
'ROI volume rendered', -1)
annotationROI.SetXYZ(15, 146, -186)
annotationROI.SetRadiusXYZ(138, 57, 61)
self.takeScreenshot('VolumeRendering-BothKidneys',
'Rendered both kidneys', -1)
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
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_Part1DICOM(self, enableScreenshotsFlag=0, screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
self.enableScreenshots = enableScreenshotsFlag
self.screenshotScaleFactor = screenshotScaleFactor
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=124183", "dataset1_Thorax_Abdomen.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")
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + "/dicomFiles"
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + "/tempDICOMDatabase"
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
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")
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget.detailsPopup.open()
# load the data by series UID
dicomWidget.detailsPopup.offerLoadables("1.3.12.2.1107.5.1.4.50025.30000005060811542834300000776", "Series")
dicomWidget.detailsPopup.examineForLoading()
self.delayDisplay("Loading Selection")
dicomWidget.detailsPopup.loadCheckedLoadables()
self.takeScreenshot("LoadingADICOMVolume-Loaded", "Loaded DICOM Volume", -1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget("Red")
self.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.takeScreenshot("LoadingADICOMVolume-WL", "Changed level and window", -1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot("LoadingADICOMVolume-LinkView", "Linked and visible", -1)
self.clickAndDrag(redWidget, button="Right", start=(10, 10), end=(10, 40))
self.takeScreenshot("LoadingADICOMVolume-Zoom", "Zoom", -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.takeScreenshot("LoadingADICOMVolume-Rotate", "Rotate", -1)
threeDView.resetFocalPoint()
self.takeScreenshot("LoadingADICOMVolume-Center", "Center the view", -1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView)
self.takeScreenshot("LoadingADICOMVolume-ConventionalWidescreen", "Conventional Widescreen Layout", -1)
slicer.util.mainWindow().moduleSelector().selectModule("VolumeRendering")
self.takeScreenshot("VolumeRendering-Module", "Volume Rendering", -1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation()
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName("6: CT_Thorax_Abdomen")
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
self.takeScreenshot("VolumeRendering-SelectVolume", "Select the volume 6: CT_Thorax_Abdomen", -1)
presetsScene = slicer.modules.volumerendering.logic().GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName("CT-Cardiac3")
volumeRenderingWidgetRep.applyPreset(ctCardiac3)
self.takeScreenshot("VolumeRendering-SelectPreset", "Select the Preset CT-Cardiac-3")
self.delayDisplay("Skipping: Select VTK CPU Ray Casting")
volumeRenderingNode = slicer.mrmlScene.GetFirstNodeByName("VolumeRendering")
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot("VolumeRendering-ViewRendering", "View Volume Rendering", -1)
self.delayDisplay("Skipping Move the Shift slider")
redWidget.sliceController().setSliceVisible(False)
self.takeScreenshot("VolumeRendering-SlicesOff", "Turn off visibility of slices in 3D", -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.takeScreenshot("VolumeRendering-RotateVolumeRendering", "Rotate volume rendered image", -1)
volumeRenderingNode.SetVisibility(0)
self.takeScreenshot("VolumeRendering-TurnOffVolumeRendering", "Turn off volume rendered image", -1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName("AnnotationROI")
annotationROI.SetDisplayVisibility(1)
self.takeScreenshot("VolumeRendering-DisplayROI", "Enable cropping and display ROI", -1)
redWidget.sliceController().setSliceVisible(True)
self.takeScreenshot("VolumeRendering-SlicesOn", "Turn on visibility of slices in 3D", -1)
annotationROI.SetXYZ(-79.61, 154.16, -232.591)
annotationROI.SetRadiusXYZ(43.4, 65.19, 70.5)
self.takeScreenshot("VolumeRendering-SizedROI", "Position the ROI over a kidney", -1)
volumeRenderingNode.SetVisibility(1)
self.takeScreenshot("VolumeRendering-ROIRendering", "ROI volume rendered", -1)
annotationROI.SetXYZ(15, 146, -186)
annotationROI.SetRadiusXYZ(138, 57, 61)
self.takeScreenshot("VolumeRendering-BothKidneys", "Rendered both kidneys", -1)
self.delayDisplay("Test passed!")
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay("Test caused exception!\n" + str(e))
def onHButtonClicked(self):
i = ctk.ctkDICOMIndexer()
i.addDirectory(slicer.dicomDatabase,
'/Users/Research/Documents/DICOM Files/TAC MONSERRAT')
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('DICOM')
def importDICOM(self, dicomDatabase, dicomFilesDirectory):
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
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_Part1DICOM(self):
""" Test the DICOM part of the test using the head atlas
"""
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=8610', 'dicom.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')
self.delayDisplay("Unzipping")
dicomFilesDirectory = slicer.app.temporaryPath + '/dicomFiles'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
try:
self.delayDisplay("Switching to temp database directory")
tempDatabaseDirectory = slicer.app.temporaryPath + '/tempDICOMDatbase'
qt.QDir().mkpath(tempDatabaseDirectory)
if slicer.dicomDatabase:
originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
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()
dicomWidget.dicomApp.resumeModel()
dicomWidget.detailsPopup.open()
# click on the first row of the tree
index = dicomWidget.tree.indexAt(qt.QPoint(0,0))
dicomWidget.onTreeClicked(index)
self.delayDisplay('Loading Selection')
dicomWidget.detailsPopup.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
self.clickAndDrag(redWidget,start=(10,10),end=(10,40))
self.delayDisplay('Change Window')
self.clickAndDrag(redWidget,start=(10,10),end=(40,10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
self.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.delayDisplay('Pan')
self.clickAndDrag(redWidget,button='Middle',start=(10,10),end=(40,40))
self.delayDisplay('Center')
redWidget.sliceController().fitSliceToBackground()
self.delayDisplay('Lightbox')
redWidget.sliceController().setLightboxTo6x6()
self.delayDisplay('Conventional Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
self.delayDisplay('No Lightbox')
redWidget.sliceController().setLightboxTo1x1()
self.delayDisplay('Four Up Layout')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
self.delayDisplay('Shift Mouse')
self.clickAndDrag(redWidget,button='None',start=(100,100),end=(140,140),modifiers=['Shift'])
self.delayDisplay('Conventional, Link, Slice Model')
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
self.delayDisplay('Rotate')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
self.clickAndDrag(threeDView,button='Right')
self.delayDisplay('Test passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
def ImportStudy(self,dicomDataDir):
indexer = ctk.ctkDICOMIndexer()
# Import study to database
indexer.addDirectory( slicer.dicomDatabase, dicomDataDir )
indexer.waitForImportFinished()
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 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 section_LoadDicomData(self):
try:
# Download and unzip test CT DICOM data
import urllib
downloads = (
('http://slicer.kitware.com/midas3/download/item/137843/TestDicomCT.zip', self.dicomZipFilePath),
)
downloaded = 0
for url,filePath in downloads:
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
if downloaded == 0:
self.delayDisplay('Downloading input data to folder\n' + self.dicomZipFilePath + '.\n\n It may take a few minutes...',self.delayMs)
print('Requesting download from %s...' % (url))
urllib.urlretrieve(url, filePath)
downloaded += 1
else:
self.delayDisplay('Input data has been found in folder ' + self.dicomZipFilePath, self.delayMs)
if downloaded > 0:
self.delayDisplay('Downloading input data finished',self.delayMs)
numOfFilesInDicomDataDir = len([name for name in os.listdir(self.dicomDataDir) if os.path.isfile(self.dicomDataDir + '/' + name)])
if (numOfFilesInDicomDataDir != self.expectedNumOfFilesInDicomDataDir):
slicer.app.applicationLogic().Unzip(self.dicomZipFilePath, self.dicomDataDir)
self.delayDisplay("Unzipping done",self.delayMs)
numOfFilesInDicomDataDirTest = len([name for name in os.listdir(self.dicomDataDir) if os.path.isfile(self.dicomDataDir + '/' + name)])
self.assertTrue( numOfFilesInDicomDataDirTest == self.expectedNumOfFilesInDicomDataDir )
# Open test database and empty it
qt.QDir().mkpath(self.dicomDatabaseDir)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', self.dicomDatabaseDir)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(self.dicomDatabaseDir)
self.assertTrue( slicer.dicomDatabase.isOpen )
# Import test data in database
indexer = ctk.ctkDICOMIndexer()
self.assertTrue( indexer )
indexer.addDirectory( slicer.dicomDatabase, self.dicomDataDir )
self.assertTrue( len(slicer.dicomDatabase.patients()) == 1 )
self.assertTrue( slicer.dicomDatabase.patients()[0] )
# Load test data
numOfScalarVolumeNodesBeforeLoad = len( slicer.util.getNodes('vtkMRMLScalarVolumeNode*') )
numOfSubjectHierarchyNodesBeforeLoad = len( slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*') )
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.loadCheckedLoadables()
self.assertTrue( len( slicer.util.getNodes('vtkMRMLScalarVolumeNode*') ) == numOfScalarVolumeNodesBeforeLoad + 1 )
self.assertTrue( len( slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*') ) == numOfSubjectHierarchyNodesBeforeLoad + 3 )
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)
def importDICOM(self, dicomDatabase, dicomFilesDirectory): dicomWidget = slicer.modules.dicom.widgetRepresentation().self() indexer = ctk.ctkDICOMIndexer() indexer.addDirectory(dicomDatabase, dicomFilesDirectory, None) indexer.waitForImportFinished()
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 section_LoadDicomData(self):
try:
# Download and unzip test CT DICOM data
import urllib
downloads = ((
'http://slicer.kitware.com/midas3/download/item/137843/TestDicomCT.zip',
self.dicomZipFilePath), )
downloaded = 0
for url, filePath in downloads:
if not os.path.exists(filePath) or os.stat(
filePath).st_size == 0:
if downloaded == 0:
self.delayDisplay(
'Downloading input data to folder\n' +
self.dicomZipFilePath +
'.\n\n It may take a few minutes...',
self.delayMs)
print('Requesting download from %s...' % (url))
urllib.urlretrieve(url, filePath)
downloaded += 1
else:
self.delayDisplay(
'Input data has been found in folder ' +
self.dicomZipFilePath, self.delayMs)
if downloaded > 0:
self.delayDisplay('Downloading input data finished',
self.delayMs)
numOfFilesInDicomDataDir = len([
name for name in os.listdir(self.dicomDataDir)
if os.path.isfile(self.dicomDataDir + '/' + name)
])
if (numOfFilesInDicomDataDir !=
self.expectedNumOfFilesInDicomDataDir):
slicer.app.applicationLogic().Unzip(self.dicomZipFilePath,
self.dicomDataDir)
self.delayDisplay("Unzipping done", self.delayMs)
numOfFilesInDicomDataDirTest = len([
name for name in os.listdir(self.dicomDataDir)
if os.path.isfile(self.dicomDataDir + '/' + name)
])
self.assertTrue(numOfFilesInDicomDataDirTest ==
self.expectedNumOfFilesInDicomDataDir)
# Open test database and empty it
qt.QDir().mkpath(self.dicomDatabaseDir)
if slicer.dicomDatabase:
self.originalDatabaseDirectory = os.path.split(
slicer.dicomDatabase.databaseFilename)[0]
else:
self.originalDatabaseDirectory = None
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', self.dicomDatabaseDir)
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(self.dicomDatabaseDir)
self.assertTrue(slicer.dicomDatabase.isOpen)
# Import test data in database
indexer = ctk.ctkDICOMIndexer()
self.assertTrue(indexer)
indexer.addDirectory(slicer.dicomDatabase, self.dicomDataDir)
self.assertTrue(len(slicer.dicomDatabase.patients()) == 1)
self.assertTrue(slicer.dicomDatabase.patients()[0])
# Load test data
numOfScalarVolumeNodesBeforeLoad = len(
slicer.util.getNodes('vtkMRMLScalarVolumeNode*'))
numOfSubjectHierarchyNodesBeforeLoad = len(
slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*'))
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.loadCheckedLoadables()
self.assertTrue(
len(slicer.util.getNodes('vtkMRMLScalarVolumeNode*')) ==
numOfScalarVolumeNodesBeforeLoad + 1)
self.assertTrue(
len(slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*')) ==
numOfSubjectHierarchyNodesBeforeLoad + 3)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e),
self.delayMs * 2)
def onHButtonClicked(self):
i = ctk.ctkDICOMIndexer()
i.addDirectory(slicer.dicomDatabase, '/Users/Research/Documents/DICOM Files/TAC MONSERRAT')
m = slicer.util.mainWindow()
m.moduleSelector().selectModule('DICOM')