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)