def setUp(self): """ Do whatever is needed to reset the state - typically a scene clear will be enough. """ self.UID = '1.3.6.1.4.1.14519.5.2.1.2744.7002.886851941687931416391879144903' self.PatientName = 'QIN-HEADNECK-01-0139' self.tempDicomDatabase = os.path.join(slicer.app.temporaryPath,'PETTest') slicer.mrmlScene.Clear(0) self.originalDicomDatabase = DICOMUtils.openTemporaryDatabase(self.tempDicomDatabase)
def load_DICOM(self):
# create temporary database. Save original database path to restore
# it when finished
self.original_db_path = DICOMUtils.openTemporaryDatabase()
#assert temporary database is open
# import DICOM to database
DICOMUtils.importDicom(self.locations_dict['DICOM'],
slicer.dicomDatabase)
# get patient name
patient_name = slicer.dicomDatabase.nameForPatient(
slicer.dicomDatabase.patients()[0])
# open DICOM by name
DICOMUtils.loadPatientByName(patient_name)
slicer.util.selectModule('SegmentationExtractionModule')
def main(argv):
try:
logging.info("Start batch RTSTRUCT conversion")
# Parse command-line arguments
parser = argparse.ArgumentParser(
description="Batch Structure Set Conversion")
parser.add_argument(
"-i",
"--input-folder",
dest="input_folder",
metavar="PATH",
default="-",
required=True,
help=
"Folder of input DICOM study (or database path to use existing)")
parser.add_argument(
"-r",
"--ref-dicom-folder",
dest="ref_dicom_folder",
metavar="PATH",
default="",
required=False,
help=
"Folder containing reference anatomy DICOM image series, if stored outside the input study"
)
parser.add_argument(
"-u",
"--use-ref-image",
dest="use_ref_image",
default=False,
required=False,
action='store_true',
help=
"Use anatomy image as reference when converting structure set to labelmap"
)
parser.add_argument("-x",
"--exist-db",
dest="exist_db",
default=False,
required=False,
action='store_true',
help="Process an existing database")
parser.add_argument("-m",
"--export-images",
dest="export_images",
default=False,
required=False,
action='store_true',
help="Export image data with labelmaps")
parser.add_argument("-o",
"--output-folder",
dest="output_folder",
metavar="PATH",
default=".",
help="Folder for output labelmaps")
parser.add_argument("-s",
"--export-surfaces",
dest="export_surfaces",
default=False,
required=False,
action='store_true',
help="Export surface mesh representation")
parser.add_argument(
"-c",
"--show-python-console",
dest="show_python_console",
default=False,
required=False,
action='store_true',
help=
"If this flag is specified then messages are displayed in an interactive Python console and the application does not quit when the script is finished."
)
args = parser.parse_args(argv)
if args.show_python_console:
slicer.util.pythonShell().show()
slicer.exit_when_finished = False
# Check if SlicerRT is installed
try:
slicer.modules.dicomrtimportexport
except AttributeError:
logging.error("Please install SlicerRT extension")
return 1
# Check required arguments
if args.input_folder == "-":
logging.warning('Please specify input DICOM study folder!')
if args.output_folder == ".":
logging.info(
'Current directory is selected as output folder (default). To change it, please specify --output-folder'
)
# Convert to python path style
input_folder = args.input_folder.replace('\\', '/')
ref_dicom_folder = args.ref_dicom_folder.replace('\\', '/')
output_folder = args.output_folder.replace('\\', '/')
use_ref_image = args.use_ref_image
exist_db = args.exist_db
export_images = args.export_images
export_surfaces = args.export_surfaces
# Perform batch conversion
logic = BatchStructureSetConversionLogic()
def save_rtslices(output_dir, use_ref_image, ref_image_node_id=None):
# package the saving code into a subfunction
logging.info("Convert loaded structure set to labelmap volumes")
labelmaps = logic.ConvertStructureSetToLabelmap(
use_ref_image, ref_image_node_id)
logging.info("Save labelmaps to directory " + output_dir)
logic.SaveLabelmaps(labelmaps, output_dir)
if export_surfaces:
logic.SaveModels(output_dir)
if export_images:
logic.SaveImages(output_dir)
logging.info("DONE")
if exist_db:
logging.info('BatchStructureSet running in existing database mode')
DICOMUtils.openDatabase(input_folder)
all_patients = slicer.dicomDatabase.patients()
logging.info('Processing %d patients...' % len(all_patients))
for patient in all_patients:
try:
slicer.mrmlScene.Clear(0) # clear the scene
DICOMUtils.loadPatientByUID(patient)
output_dir = os.path.join(output_folder, patient)
if not os.access(output_dir, os.F_OK):
os.mkdir(output_dir)
save_rtslices(output_dir, use_ref_image)
except OSError as e:
# Failed to load data from this patient, continue with the next one
print(e)
else:
logging.info('BatchStructureSet running in file mode')
ref_volume_file_path = None
if os.path.isdir(ref_dicom_folder):
# If reference DICOM folder is given and valid, then import reference patient and save its ID
logging.info("Import reference anatomy DICOM data from " +
ref_dicom_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(ref_dicom_folder)
# Save first volume to be used as reference
logic.LoadFirstPatientIntoSlicer()
scalarVolumeNodes = list(
slicer.util.getNodes('vtkMRMLScalarVolume*').values())
if len(scalarVolumeNodes) > 0:
refVolNode = scalarVolumeNodes[0]
refVolStorageNode = refVolNode.CreateDefaultStorageNode()
ref_volume_file_path = os.path.join(
output_folder, 'refVolume.nrrd')
refVolStorageNode.SetFileName(ref_volume_file_path)
refVolStorageNode.WriteData(refVolNode)
logging.info("Import DICOM data from " + input_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(input_folder)
all_patients = slicer.dicomDatabase.patients()
logging.info('Processing %d patients...' % len(all_patients))
for patient in all_patients:
try:
slicer.mrmlScene.Clear(0) # clear the scene
DICOMUtils.loadPatientByUID(patient)
output_dir = os.path.join(output_folder, patient)
if not os.access(output_dir, os.F_OK):
os.mkdir(output_dir)
ref_volume_node_id = None
if ref_volume_file_path:
try:
refVolNode = slicer.util.loadVolume(
ref_volume_file_path)
ref_volume_node_id = refVolNode.GetID()
except:
pass
save_rtslices(output_dir, use_ref_image,
ref_volume_node_id)
except OSError as e:
# Failed to load data from this patient, continue with the next one
print(e)
except Exception as e:
import traceback
traceback.print_exc()
print(e)
return 1
return 0
def main(argv):
try:
# Parse command-line arguments
parser = argparse.ArgumentParser(description="Batch Structure Set Conversion")
parser.add_argument("-i", "--input-folder", dest="input_folder", metavar="PATH",
default="-", required=True, help="Folder of input DICOM study (or database path to use existing)")
parser.add_argument("-x", "--exist-db", dest="exist_db",
default=False, required=False, action='store_true',
help="Process an existing database")
parser.add_argument("-m", "--export-images", dest="export_images",
default=False, required=False, action='store_true',
help="Export image data with labelmaps")
parser.add_argument("-o", "--output-folder", dest="output_folder", metavar="PATH",
default=".", help="Folder for output labelmaps")
args = parser.parse_args(argv)
# Check required arguments
if args.input_folder == "-":
logging.warning('Please specify input DICOM study folder!')
if args.output_folder == ".":
logging.info('Current directory is selected as output folder (default). To change it, please specify --output-folder')
# Convert to python path style
input_folder = args.input_folder.replace('\\', '/')
output_folder = args.output_folder.replace('\\', '/')
exist_db = args.exist_db
export_images = args.export_images
# Perform batch conversion
logic = BatchStructureSetConversionLogic()
def save_rtslices(output_dir):
# package the saving code into a subfunction
logging.info("Convert loaded structure set to labelmap volumes")
labelmaps = logic.ConvertStructureSetToLabelmap()
logging.info("Save labelmaps to directory " + output_dir)
logic.SaveLabelmaps(labelmaps, output_dir)
if export_images:
logic.SaveImages(output_dir)
logging.info("DONE")
if exist_db:
logging.info('BatchStructureSet running in existing database mode')
DICOMUtils.openDatabase(input_folder)
all_patients = slicer.dicomDatabase.patients()
logging.info('Must Process Patients %s' % len(all_patients))
for patient in all_patients:
slicer.mrmlScene.Clear(0) # clear the scene
DICOMUtils.loadPatientByUID(patient)
output_dir = os.path.join(output_folder,patient)
if not os.access(output_dir, os.F_OK):
os.mkdir(output_dir)
save_rtslices(output_dir)
else:
logging.info("Import DICOM data from " + input_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(input_folder)
logging.info("Load first patient into Slicer")
logic.LoadFirstPatientIntoSlicer()
save_rtslices(output_folder)
except Exception as e:
print(e)
sys.exit(0)
def test_Part1DICOM(self,enableScreenshotsFlag=0,screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
logic = RSNAVisTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='dataset1_Thorax_Abdomen.zip',
uris='http://slicer.kitware.com/midas3/download?items=124183')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget = slicer.modules.DICOMWidget
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()
logic.takeScreenshot('LoadingADICOMVolume-Loaded','Loaded DICOM Volume',-1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
logic.takeScreenshot('LoadingADICOMVolume-WL','Changed level and window',-1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True);
logic.takeScreenshot('LoadingADICOMVolume-LinkView','Linked and visible',-1)
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
logic.takeScreenshot('LoadingADICOMVolume-Zoom','Zoom',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('LoadingADICOMVolume-Rotate','Rotate',-1)
threeDView.resetFocalPoint()
logic.takeScreenshot('LoadingADICOMVolume-Center','Center the view',-1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView)
logic.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen','Conventional Widescreen Layout',-1)
slicer.util.mainWindow().moduleSelector().selectModule('VolumeRendering')
logic.takeScreenshot('VolumeRendering-Module','Volume Rendering',-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation()
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName('6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
logic.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)
logic.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)
logic.takeScreenshot('VolumeRendering-ViewRendering','View Volume Rendering',-1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False);
logic.takeScreenshot('VolumeRendering-SlicesOff','Turn off visibility of slices in 3D',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('VolumeRendering-RotateVolumeRendering','Rotate volume rendered image',-1)
volumeRenderingNode.SetVisibility(0)
logic.takeScreenshot('VolumeRendering-TurnOffVolumeRendering','Turn off volume rendered image',-1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName('AnnotationROI')
annotationROI.SetDisplayVisibility(1)
logic.takeScreenshot('VolumeRendering-DisplayROI','Enable cropping and display ROI',-1)
redWidget.sliceController().setSliceVisible(True)
logic.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)
logic.takeScreenshot('VolumeRendering-SizedROI','Position the ROI over a kidney',-1)
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ROIRendering','ROI volume rendered',-1)
annotationROI.SetXYZ(15,146,-186)
annotationROI.SetRadiusXYZ(138,57,61)
logic.takeScreenshot('VolumeRendering-BothKidneys','Rendered both kidneys',-1)
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
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")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
dicomWidget = slicer.modules.DICOMWidget
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')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
slicer.util.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)
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.takeScreenshot('LoadingADICOMVolume-Zoom','Zoom',-1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.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()
slicer.util.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 test_AlternateReaders(self):
""" Test the DICOM loading of sample testing data
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test", 100)
referenceData = json.JSONDecoder().decode('''[
{ "url": "http://slicer.kitware.com/midas3/download/item/292839/Mouse-MR-example-where-GDCM_fails.zip",
"fileName": "Mouse-MR-example-where-GDCM_fails.zip",
"name": "Mouse-MR-example-where-GDCM_fails",
"seriesUID": "1.3.6.1.4.1.9590.100.1.2.366426457713813178933224342280246227461",
"expectedFailures": ["GDCM", "Archetype"],
"voxelValueQuantity": "(110852, DCM, \\"MR signal intensity\\")",
"voxelValueUnits": "(1, UCUM, \\"no units\\")"
},
{ "url": "http://slicer.kitware.com/midas3/download/item/294857/deidentifiedMRHead-dcm-one-series.zip",
"fileName": "deidentifiedMRHead-dcm-one-series.zip",
"name": "deidentifiedMRHead-dcm-one-series",
"seriesUID": "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0",
"expectedFailures": [],
"voxelValueQuantity": "(110852, DCM, \\"MR signal intensity\\")",
"voxelValueUnits": "(1, UCUM, \\"no units\\")"
}
]''')
# another dataset that could be added in the future - currently fails for all readers
# due to invalid format - see https://issues.slicer.org/view.php?id=3569
#{ "url": "http://slicer.kitware.com/midas3/download/item/293587/RIDER_bug.zip",
#"fileName": "RIDER_bug.zip",
#"name": "RIDER_bug",
#"seriesUID": "1.3.6.1.4.1.9328.50.7.261772317324041365541450388603508531852",
#"expectedFailures": []
#}
loadingResult = {}
#
# first, get the data - a zip file of dicom data
#
self.delayDisplay("Downloading", 100)
for dataset in referenceData:
try:
filePath = slicer.app.temporaryPath + '/' + dataset['fileName']
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (dataset['fileName'], dataset['url']), 100)
urllib.urlretrieve(dataset['url'], filePath)
self.delayDisplay('Finished with download\n', 100)
self.delayDisplay("Unzipping", 100)
dicomFilesDirectory = slicer.app.temporaryPath + dataset['name']
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
#
# insert the data into th database
#
self.delayDisplay("Switching to temp database directory", 100)
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM', 100)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
#
# select the series
#
detailsPopup = slicer.modules.DICOMWidget.detailsPopup
detailsPopup.open()
# load the data by series UID
detailsPopup.offerLoadables(dataset['seriesUID'],'Series')
detailsPopup.examineForLoading()
loadable = detailsPopup.getAllSelectedLoadables().keys()[0]
#
# try loading using each of the selected readers, fail
# on enexpected load issue
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
readerApproaches = scalarVolumePlugin.readerApproaches()
basename = loadable.name
volumesByApproach = {}
for readerApproach in readerApproaches:
self.delayDisplay('Loading Selection with approach: %s' % readerApproach, 100)
loadable.name = basename + "-" + readerApproach
volumeNode = scalarVolumePlugin.load(loadable,readerApproach)
if not volumeNode and readerApproach not in dataset['expectedFailures']:
raise Exception("Expected to be able to read with %s, but couldn't" % readerApproach)
if volumeNode and readerApproach in dataset['expectedFailures']:
raise Exception("Expected to NOT be able to read with %s, but could!" % readerApproach)
if volumeNode:
volumesByApproach[readerApproach] = volumeNode
self.delayDisplay('Test quantity and unit')
if 'voxelValueQuantity' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueQuantity().GetAsPrintableString(), dataset['voxelValueQuantity'])
if 'voxelValueUnits' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueUnits().GetAsPrintableString(), dataset['voxelValueUnits'])
#
# for each approach that loaded as expected, compare the volumes
# to ensure they match in terms of pixel data and metadata
#
failedComparisons = {}
approachesThatLoaded = volumesByApproach.keys()
print('approachesThatLoaded %s' % approachesThatLoaded)
for approachIndex in range(len(approachesThatLoaded)):
firstApproach = approachesThatLoaded[approachIndex]
firstVolume = volumesByApproach[firstApproach]
for secondApproachIndex in range(approachIndex+1,len(approachesThatLoaded)):
secondApproach = approachesThatLoaded[secondApproachIndex]
secondVolume = volumesByApproach[secondApproach]
print('comparing %s,%s' % (firstApproach, secondApproach))
comparison = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin'].compareVolumeNodes(firstVolume,secondVolume)
if comparison != "":
print('failed: %s', comparison)
failedComparisons[firstApproach,secondApproach] = comparison
if len(failedComparisons.keys()) > 0:
raise Exception("Loaded volumes don't match: %s" % failedComparisons)
self.delayDisplay('%s Test passed!' % dataset['name'], 200)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('%s Test caused exception!\n' % dataset['name'] + str(e), 2000)
testPass = 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 SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='Dcmtk-db.zip',
uris=TESTING_DATA_URL + 'MD5/7a43d121a51a631ab0df02071e5ba6ed',
checksums='MD5:7a43d121a51a631ab0df02071e5ba6ed')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
print("configFilePath: " + os.path.abspath(configFilePath))
print("processCurrentPath: " + os.path.abspath(processCurrentPath))
dcmqrscpExeOptions = ('/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
'/../DCMTK-build/bin/Release',
'/../DCMTK-build/bin/Debug',
'/../DCMTK-build/bin/RelWithDebInfo'
'/../DCMTK-build/bin/MinSizeRel')
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise UserWarning("Could not find dcmqrscp executable")
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
slicer.util.selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy(
'1.2.124.113932.1.170.223.162.178.20050502.160340.12640015')
popen.kill()
# Select first patient
browserWidget = slicer.modules.DICOMWidget.browserWidget
browserWidget.dicomBrowser.dicomTableManager().patientsTable(
).selectFirst()
browserWidget.examineForLoading()
self.delayDisplay('Loading Selection')
browserWidget.loadCheckedLoadables()
self.delayDisplay('Change Level')
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
self.delayDisplay('Change Window')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
slicer.util.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
self.delayDisplay('Pan')
slicer.util.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')
slicer.util.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()
slicer.util.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView, button='Right')
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
def main(argv):
# Parse command-line arguments
parser = argparse.ArgumentParser(description="Batch Structure Set Conversion")
parser.add_argument(
"-i",
"--input-folder",
dest="input_folder",
metavar="PATH",
default="-",
required=True,
help="Folder of input DICOM study (or database path to use existing)",
)
parser.add_argument(
"-o", "--output-folder", dest="output_folder", metavar="PATH", default=".", help="Folder for output labelmaps"
)
parser.add_argument(
"-r",
"--register",
dest="register",
metavar="PATH",
default="no_registration",
help='"T1" for registration to T1 image, "T2" for registration to T2 image. ' 'Defaults to "no_registration".',
)
parser.add_argument(
"--export_all_structures",
dest="export_all_structures",
action="store_true",
help="All available structures will be exported. By default, only the VS is exported.",
)
parser.set_defaults(export_all_structures=False)
args = parser.parse_args(argv)
# Check required arguments
if args.input_folder == "-":
logging.warning("Please specify input DICOM study folder!")
if args.output_folder == ".":
logging.info(
"Current directory is selected as output folder (default). To change it, please specify --output-folder"
)
if args.register not in ["no_registration", "T1", "T2"]:
logging.error('Invalid value for keyword "--register": choose "T1" or "T2" or "no_registration"')
# Convert to python path style
input_folder = args.input_folder.replace("\\", "/")
output_folder = args.output_folder.replace("\\", "/")
register = args.register
export_all_structures = args.export_all_structures
register_T1_image_and_contour_points_to_T2_image = False
register_T2_image_and_contour_points_to_T1_image = False
if register == "T1":
register_T2_image_and_contour_points_to_T1_image = True
elif register == "T2":
register_T1_image_and_contour_points_to_T2_image = True
if export_all_structures:
export_only_tumour_seg = False
else:
export_only_tumour_seg = True
if not os.access(output_folder, os.F_OK):
os.mkdir(output_folder)
DICOMUtils.openTemporaryDatabase()
patient_dirs = glob.glob(os.path.join(input_folder, "vs_gk_*"))
# create and compile a regex pattern
pattern = re.compile(r"_([0-9]+)_t[1-2]$")
case_numbers = []
# first_case = 1
# last_case = 2
# for case_number in range(first_case, last_case + 1):
# exclude cases
# if case_number in [39, 97, 130, 160, 168, 208, 219, 227]:
# continue
for i in range(len(patient_dirs)):
# get case number from folder name
print(pattern.findall(patient_dirs[i]))
case_number = pattern.findall(patient_dirs[i])[0]
# skip iteration if case has already been dealt with
if case_number in case_numbers:
continue
case_numbers.append(case_number)
print(f"case: {case_number}")
[ref1, ref2, RTSS1, RTSS2] = import_T1_and_T2_data(input_folder, case_number)
## REGISTRATION
if register_T1_image_and_contour_points_to_T2_image:
transform_path = os.path.join(input_folder, f"vs_gk_{case_number}" + "_t1", "inv_T1_LPS_to_T2_LPS.tfm")
transformNode = slicer.util.loadNodeFromFile(transform_path, filetype="TransformFile")
ref1 = register_and_resample(
input_node=ref1, reference_node=ref2, transform_node=transformNode, interpolationMode="Linear"
)
# also transform contour points
RTSS1.SetAndObserveTransformNodeID(transformNode.GetID())
elif register_T2_image_and_contour_points_to_T1_image:
transform_path = os.path.join(input_folder, f"vs_gk_{case_number}" + "_t2", "inv_T2_LPS_to_T1_LPS.tfm")
transformNode = slicer.util.loadNodeFromFile(transform_path, filetype="TransformFile")
ref2 = register_and_resample(
input_node=ref2, reference_node=ref1, transform_node=transformNode, interpolationMode="Linear"
)
# also transform contour points
RTSS2.SetAndObserveTransformNodeID(transformNode.GetID())
## Create segments from contour files
# Create segmentation node where we will store segments
segmentationNode_T1 = create_segmentation_node_with_reference_geometry(
"SegmentationFromContourPoints_refT1", ref_geometry_image_node=ref1
)
segmentationNode_T2 = create_segmentation_node_with_reference_geometry(
"SegmentationFromContourPoints_refT2", ref_geometry_image_node=ref2
)
# load structure contour list from json file
# these are registered to original T1 and T2 images (they are not affected by registrations of the ref_geometry
# node, which only defines extent and the IJK to RAS transformation)
structure_contour_list_T1 = load_LPS_contour_points(
os.path.join(input_folder, f"vs_gk_{case_number}" + "_t1", "contours.json")
)
structure_contour_list_T2 = load_LPS_contour_points(
os.path.join(input_folder, f"vs_gk_{case_number}" + "_t2", "contours.json")
)
# create segments for all structures
create_segments_from_structure_contour_list(segmentationNode_T1, structure_contour_list_T1)
create_segments_from_structure_contour_list(segmentationNode_T2, structure_contour_list_T2)
## export all files
if register_T1_image_and_contour_points_to_T2_image:
lm_node_in_T2_list = save_labelmaps_from_planar_contour(
segmentationNode_T2, ref2, export_only_tumour_seg, case_number, output_folder
) # save contour points registered to T2 image
if register_T2_image_and_contour_points_to_T1_image:
lm_node_in_T1_list = save_labelmaps_from_planar_contour(
segmentationNode_T1, ref1, export_only_tumour_seg, case_number, output_folder
)
if not register_T1_image_and_contour_points_to_T2_image and not register_T2_image_and_contour_points_to_T1_image:
lm_node_in_T2_list = save_labelmaps_from_planar_contour(
segmentationNode_T2, ref2, export_only_tumour_seg, case_number, output_folder
) # save contour points registered to T2 image
lm_node_in_T1_list = save_labelmaps_from_planar_contour(
segmentationNode_T1, ref1, export_only_tumour_seg, case_number, output_folder
)
# save images as nifti files
if register_T1_image_and_contour_points_to_T2_image:
slicer.util.saveNode(
ref1, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t1_refT2.nii.gz")
) # pass vol node and destination filename
slicer.util.saveNode(
ref2, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t2_refT2.nii.gz")
) # pass vol node and destination filename
if register_T2_image_and_contour_points_to_T1_image:
slicer.util.saveNode(
ref1, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t1_refT1.nii.gz")
) # pass vol node and destination filename
slicer.util.saveNode(
ref2, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t2_refT1.nii.gz")
) # pass vol node and destination filename
if not register_T1_image_and_contour_points_to_T2_image and not register_T2_image_and_contour_points_to_T1_image:
slicer.util.saveNode(
ref1, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t1_refT1.nii.gz")
) # pass vol node and destination filename
slicer.util.saveNode(
ref2, os.path.join(output_folder, f"vs_gk_{case_number}", f"vs_gk_t2_refT2.nii.gz")
) # pass vol node and destination filename
sys.exit(0)
parser.add_argument("--input", help="Input DICOM directory")
parser.add_argument("--output", help="Output directory")
parser.add_argument("--filename", help="File name")
args = parser.parse_args()
if args.dcmtk and args.gdcm:
raise ValueError("Cannot specify both gdcm and dcmtk")
if args.dcmtk:
setDICOMReaderApproach('DCMTK')
if args.gdcm:
setDICOMReaderApproach('GDCM')
indexer = ctk.ctkDICOMIndexer()
dbDir = "/tmp/SlicerDB"
print("Temporary directory: " + dbDir)
DICOMUtils.openTemporaryDatabase(dbDir)
db = slicer.dicomDatabase
print("indexing {}".format(args.input))
indexer.addDirectory(db, args.input)
indexer.waitForImportFinished()
slicer.util.selectModule('DICOM')
fileLists = []
for patient in db.patients():
print("Patient:" + patient)
for study in db.studiesForPatient(patient):
print("Study:" + study)
for series in db.seriesForStudy(study):
print("Series:" + series)
fileLists.append(db.filesForSeries(series))
def main(argv):
try:
# Parse command-line arguments
parser = argparse.ArgumentParser(
description="Batch Structure Set Conversion")
parser.add_argument(
"-i",
"--input-folder",
dest="input_folder",
metavar="PATH",
default="-",
required=True,
help=
"Folder of input DICOM study (or database path to use existing)")
parser.add_argument(
"-r",
"--ref-dicom-folder",
dest="ref_dicom_folder",
metavar="PATH",
default="",
required=False,
help=
"Folder containing reference anatomy DICOM image series, if stored outside the input study"
)
parser.add_argument(
"-u",
"--use-ref-image",
dest="use_ref_image",
default=False,
required=False,
action='store_true',
help=
"Use anatomy image as reference when converting structure set to labelmap"
)
parser.add_argument("-x",
"--exist-db",
dest="exist_db",
default=False,
required=False,
action='store_true',
help="Process an existing database")
parser.add_argument("-m",
"--export-images",
dest="export_images",
default=False,
required=False,
action='store_true',
help="Export image data with labelmaps")
parser.add_argument("-o",
"--output-folder",
dest="output_folder",
metavar="PATH",
default=".",
help="Folder for output labelmaps")
args = parser.parse_args(argv)
# Check required arguments
if args.input_folder == "-":
logging.warning('Please specify input DICOM study folder!')
if args.output_folder == ".":
logging.info(
'Current directory is selected as output folder (default). To change it, please specify --output-folder'
)
# Convert to python path style
input_folder = args.input_folder.replace('\\', '/')
ref_dicom_folder = args.ref_dicom_folder.replace('\\', '/')
output_folder = args.output_folder.replace('\\', '/')
use_ref_image = args.use_ref_image
exist_db = args.exist_db
export_images = args.export_images
# Perform batch conversion
logic = BatchStructureSetConversionLogic()
def save_rtslices(output_dir, use_ref_image, ref_image_node_id=None):
# package the saving code into a subfunction
logging.info("Convert loaded structure set to labelmap volumes")
labelmaps = logic.ConvertStructureSetToLabelmap(
use_ref_image, ref_image_node_id)
logging.info("Save labelmaps to directory " + output_dir)
logic.SaveLabelmaps(labelmaps, output_dir)
if export_images:
logic.SaveImages(output_dir)
logging.info("DONE")
if exist_db:
logging.info('BatchStructureSet running in existing database mode')
DICOMUtils.openDatabase(input_folder)
all_patients = slicer.dicomDatabase.patients()
logging.info('Must Process Patients %s' % len(all_patients))
for patient in all_patients:
slicer.mrmlScene.Clear(0) # clear the scene
DICOMUtils.loadPatientByUID(patient)
output_dir = os.path.join(output_folder, patient)
if not os.access(output_dir, os.F_OK):
os.mkdir(output_dir)
save_rtslices(output_dir, use_ref_image)
else:
ref_image_node_id = None
if os.path.isdir(ref_dicom_folder):
# If reference DICOM folder is given and valid, then load that volume
logging.info("Import reference anatomy DICOM data from " +
ref_dicom_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(ref_dicom_folder)
logic.LoadFirstPatientIntoSlicer()
# Remember first volume
scalarVolumeNodes = list(
slicer.util.getNodes('vtkMRMLScalarVolume*').values())
if len(scalarVolumeNodes) > 0:
ref_image_node_id = scalarVolumeNodes[0].GetID()
logging.info("Import DICOM data from " + input_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(input_folder)
logging.info("Load first patient into Slicer")
logic.LoadFirstPatientIntoSlicer()
save_rtslices(output_folder, use_ref_image, ref_image_node_id)
except Exception as e:
print(e)
sys.exit(0)
def test_Part1DICOM(self):
""" Test the DICOM loading of sample testing data
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test", 100)
referenceData = json.JSONDecoder().decode('''[
{ "url": "http://slicer.kitware.com/midas3/download/item/292839/Mouse-MR-example-where-GDCM_fails.zip",
"fileName": "Mouse-MR-example-where-GDCM_fails.zip",
"name": "Mouse-MR-example-where-GDCM_fails",
"seriesUID": "1.3.6.1.4.1.9590.100.1.2.366426457713813178933224342280246227461",
"expectedFailures": ["GDCM", "Archetype"]
},
{ "url": "http://slicer.kitware.com/midas3/download/item/294857/deidentifiedMRHead-dcm-one-series.zip",
"fileName": "deidentifiedMRHead-dcm-one-series.zip",
"name": "deidentifiedMRHead-dcm-one-series",
"seriesUID": "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0",
"expectedFailures": []
}
]''')
# another dataset that could be added in the future - currently fails for all readers
# due to invalid format - see https://issues.slicer.org/view.php?id=3569
#{ "url": "http://slicer.kitware.com/midas3/download/item/293587/RIDER_bug.zip",
#"fileName": "RIDER_bug.zip",
#"name": "RIDER_bug",
#"seriesUID": "1.3.6.1.4.1.9328.50.7.261772317324041365541450388603508531852",
#"expectedFailures": []
#}
loadingResult = {}
#
# first, get the data - a zip file of dicom data
#
self.delayDisplay("Downloading", 100)
for dataset in referenceData:
try:
filePath = slicer.app.temporaryPath + '/' + dataset['fileName']
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (dataset['fileName'], dataset['url']), 100)
urllib.urlretrieve(dataset['url'], filePath)
self.delayDisplay('Finished with download\n', 100)
self.delayDisplay("Unzipping", 100)
dicomFilesDirectory = slicer.app.temporaryPath + dataset['name']
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
#
# insert the data into th database
#
self.delayDisplay("Switching to temp database directory", 100)
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM', 100)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
#
# selct the series
#
detailsPopup = slicer.modules.DICOMWidget.detailsPopup
detailsPopup.open()
# load the data by series UID
detailsPopup.offerLoadables(dataset['seriesUID'],'Series')
detailsPopup.examineForLoading()
loadable = detailsPopup.getAllSelectedLoadables().keys()[0]
#
# try loading using each of the selected readers, fail
# on enexpected load issue
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
readerApproaches = scalarVolumePlugin.readerApproaches()
basename = loadable.name
volumesByApproach = {}
for readerApproach in readerApproaches:
self.delayDisplay('Loading Selection with approach: %s' % readerApproach, 100)
loadable.name = basename + "-" + readerApproach
volumeNode = scalarVolumePlugin.load(loadable,readerApproach)
if not volumeNode and readerApproach not in dataset['expectedFailures']:
raise Exception("Expected to be able to read with %s, but couldn't" % readerApproach)
if volumeNode and readerApproach in dataset['expectedFailures']:
raise Exception("Expected to NOT be able to read with %s, but could!" % readerApproach)
if volumeNode:
volumesByApproach[readerApproach] = volumeNode
#
# for each approach that loaded as expected, compare the volumes
# to ensure they match in terms of pixel data and metadata
#
failedComparisons = {}
approachesThatLoaded = volumesByApproach.keys()
print('approachesThatLoaded %s' % approachesThatLoaded)
for approachIndex in range(len(approachesThatLoaded)):
firstApproach = approachesThatLoaded[approachIndex]
firstVolume = volumesByApproach[firstApproach]
for secondApproachIndex in range(approachIndex+1,len(approachesThatLoaded)):
secondApproach = approachesThatLoaded[secondApproachIndex]
secondVolume = volumesByApproach[secondApproach]
print('comparing %s,%s' % (firstApproach, secondApproach))
comparison = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin'].compareVolumeNodes(firstVolume,secondVolume)
if comparison != "":
print('failed: %s', comparison)
failedComparisons[firstApproach,secondApproach] = comparison
if len(failedComparisons.keys()) > 0:
raise Exception("Loaded volumes don't match: %s" % failedComparisons)
self.delayDisplay('%s Test passed!' % dataset['name'], 200)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('%s Test caused exception!\n' % dataset['name'] + str(e), 2000)
testPass = False
def main(argv):
try:
# Parse command-line arguments
parser = argparse.ArgumentParser(description="Batch Structure Set Conversion")
parser.add_argument("-i", "--input-folder", dest="input_folder", metavar="PATH",
default="-", required=True, help="Folder of input DICOM study (or database path to use existing)")
parser.add_argument("-x", "--exist-db", dest="exist_db",
default=False, required=False, action='store_true',
help="Process an existing database")
parser.add_argument("-m", "--export-images", dest="export_images",
default=False, required=False, action='store_true',
help="Export image data with labelmaps")
parser.add_argument("-o", "--output-folder", dest="output_folder", metavar="PATH",
default=".", help="Folder for output labelmaps")
args = parser.parse_args(argv)
# Check required arguments
if args.input_folder == "-":
logging.warning('Please specify input DICOM study folder!')
if args.output_folder == ".":
logging.info('Current directory is selected as output folder (default). To change it, please specify --output-folder')
# Convert to python path style
input_folder = args.input_folder.replace('\\', '/')
output_folder = args.output_folder.replace('\\', '/')
exist_db = args.exist_db
export_images = args.export_images
# Perform batch conversion
logic = BatchStructureSetConversionLogic()
def save_rtslices(output_dir):
# package the saving code into a subfunction
logging.info("Convert loaded structure set to labelmap volumes")
labelmaps = logic.ConvertStructureSetToLabelmap()
logging.info("Save labelmaps to directory " + output_dir)
logic.SaveLabelmaps(labelmaps, output_dir)
if export_images:
logic.SaveImages(output_dir)
logging.info("DONE")
if exist_db:
logging.info('BatchStructureSet running in existing database mode')
DICOMUtils.openDatabase(input_folder)
all_patients = slicer.dicomDatabase.patients()
logging.info('Must Process Patients %s' % len(all_patients))
for patient in all_patients:
slicer.mrmlScene.Clear(0) # clear the scene
DICOMUtils.loadPatientByUID(patient)
output_dir = os.path.join(output_folder,patient)
if not os.access(output_dir, os.F_OK):
os.mkdir(output_dir)
save_rtslices(output_dir)
else:
logging.info("Import DICOM data from " + input_folder)
DICOMUtils.openTemporaryDatabase()
DICOMUtils.importDicom(input_folder)
logging.info("Load first patient into Slicer")
logic.LoadFirstPatientIntoSlicer()
save_rtslices(output_folder)
except Exception, e:
print(e)
def test_MissingSlices(self):
""" Test behavior of the readers when slices are missing
To edit and run this test from the python console, paste this below:
reloadScriptedModule('DICOMReaders'); import DICOMReaders; tester = DICOMReaders.DICOMReadersTest(); tester.setUp(); tester.test_MissingSlices()
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
settings = qt.QSettings()
settings.setValue("DICOM/ScalarVolume/AcquisitionGeometryRegularization", "transform")
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='deidentifiedMRHead-dcm-one-series.zip',
uris='http://slicer.kitware.com/midas3/download?items=294857',
checksums='SHA256:899f3f8617ca53bad7dca0b2908478319e708b48ff41dfa64b6bac1d76529928')[0]
self.delayDisplay('Finished with download\n')
seriesUID = "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0"
seriesRASBounds = [-87.29489517211913, 81.70450973510744,
-121.57139587402344, 134.42860412597656,
-138.71430206298828, 117.28569793701172]
seriesDirectory = "Series 004 [MR - SAG RF FAST VOL FLIP 20]"
lastSliceCorners = [[[81.05451202, 133.92860413, 116.78569794], [81.05451202, -122.07139587, 116.78569794]],
[[81.05451202, 133.92860413, -139.21429443], [81.05451202, -122.07139587, -139.21429443]]]
filesToRemove = [
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.361.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.362.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.363.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.364.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.365.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.366.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.367.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.368.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.369.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.370.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.371.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.372.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.373.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.374.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.375.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.376.0.dcm",
]
try:
print('Removing %d files from the middle of the series' % len(filesToRemove))
for file in filesToRemove:
filePath = os.path.join(dicomFilesDirectory, seriesDirectory, file)
os.remove(filePath)
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
slicer.util.selectModule("DICOM")
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory, dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
#
# select the series
#
browserWidget.onSeriesSelected([seriesUID])
# load the data by series UID
browserWidget.examineForLoading()
loadable = list(browserWidget.getAllSelectedLoadables().keys())[0]
if len(loadable.warning) == 0:
raise Exception("Expected warning about geometry issues due to missing slices!")
#
# load and correct for acquisition then check the geometry
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
volumeNode = scalarVolumePlugin.load(loadable)
if not numpy.allclose(scalarVolumePlugin.acquisitionModeling.fixedCorners[-1], lastSliceCorners):
raise Exception("Acquisition transform didn't fix slice corners!")
self.delayDisplay('test_MissingSlices passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Missing Slices Test caused exception!\n' + str(e))
testPass = False
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
slicer.util.selectModule('DICOMReaders')
return testPass
def test_MissingSlices(self):
""" Test behavior of the readers when slices are missing
To edit and run this test from the python console, paste this below:
reloadScriptedModule('DICOMReaders'); import DICOMReaders; tester = DICOMReaders.DICOMReadersTest(); tester.setUp(); tester.test_MissingSlices()
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='deidentifiedMRHead-dcm-one-series.zip',
uris='http://slicer.kitware.com/midas3/download?items=294857')[0]
self.delayDisplay('Finished with download\n')
seriesUID = "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0"
seriesRASBounds = [
-87.29489517211913, 81.70450973510744, -121.57139587402344,
134.42860412597656, -138.71430206298828, 117.28569793701172
]
seriesDirectory = "Series 004 [MR - SAG RF FAST VOL FLIP 20]"
lastSliceCorners = [[[81.05451202, 133.92860413, 116.78569794],
[81.05451202, -122.07139587, 116.78569794]],
[[81.05451202, 133.92860413, -139.21429443],
[81.05451202, -122.07139587, -139.21429443]]]
filesToRemove = [
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.361.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.362.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.363.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.364.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.365.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.366.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.367.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.368.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.369.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.370.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.371.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.372.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.373.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.374.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.375.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.376.0.dcm",
]
try:
print('Removing %d files from the middle of the series' %
len(filesToRemove))
for file in filesToRemove:
filePath = os.path.join(dicomFilesDirectory, seriesDirectory,
file)
os.remove(filePath)
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory,
None)
indexer.waitForImportFinished()
#
# select the series
#
detailsPopup = slicer.modules.DICOMWidget.detailsPopup
detailsPopup.open()
# load the data by series UID
detailsPopup.offerLoadables(seriesUID, 'Series')
detailsPopup.examineForLoading()
loadable = detailsPopup.getAllSelectedLoadables().keys()[0]
if len(loadable.warning) == 0:
raise Exception(
"Expected warning about geometry issues due to missing slices!"
)
#
# load and correct for acquisition then check the geometry
#
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
volumeNode = scalarVolumePlugin.load(loadable)
if not numpy.allclose(
scalarVolumePlugin.acquisitionModeling.fixedCorners[-1],
lastSliceCorners):
raise Exception(
"Acquisition transform didn't fix slice corners!")
self.delayDisplay('test_MissingSlices passed!')
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Missing Slices Test caused exception!\n' +
str(e))
testPass = False
def test_AlternateReaders(self):
""" Test the DICOM loading of sample testing data
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
referenceData = [
{ "url": "http://slicer.kitware.com/midas3/download?items=292839",
"checksum": "SHA256:3450ef9372a3460a2f181c8d3bb35a74b4f0acb10c6e18cfcf7804e1d99bf843",
"fileName": "Mouse-MR-example-where-GDCM_fails.zip",
"name": "Mouse-MR-example-where-GDCM_fails",
"seriesUID": "1.3.6.1.4.1.9590.100.1.2.366426457713813178933224342280246227461",
# GDCM rejects loading.
# DCMTK reads it but then ITK rejects loading the image with 0 spacing.
"expectedFailures": ["GDCM", "Archetype", "DCMTK", "GDCM with DCMTK fallback"],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
},
{ "url": "http://slicer.kitware.com/midas3/download?items=294857",
"checksum": "SHA256:899f3f8617ca53bad7dca0b2908478319e708b48ff41dfa64b6bac1d76529928",
"fileName": "deidentifiedMRHead-dcm-one-series.zip",
"name": "deidentifiedMRHead-dcm-one-series",
"seriesUID": "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0",
"expectedFailures": [],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
}
]
# another dataset that could be added in the future - currently fails for all readers
# due to invalid format - see https://issues.slicer.org/view.php?id=3569
#{ "url": "http://slicer.kitware.com/midas3/download/item/293587/RIDER_bug.zip",
#"fileName": "RIDER_bug.zip",
#"name": "RIDER_bug",
#"seriesUID": "1.3.6.1.4.1.9328.50.7.261772317324041365541450388603508531852",
#"expectedFailures": []
#}
loadingResult = {}
#
# first, get the data - a zip file of dicom data
#
self.delayDisplay("Downloading")
for dataset in referenceData:
try:
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames=dataset['fileName'], uris=dataset['url'], checksums=dataset['checksum'])[0]
self.delayDisplay('Finished with download')
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
slicer.util.selectModule("DICOM")
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory, dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
#
# select the series
#
browserWidget.onSeriesSelected([dataset['seriesUID']])
# load the data by series UID
browserWidget.examineForLoading()
loadable = list(browserWidget.getAllSelectedLoadables().keys())[0]
#
# try loading using each of the selected readers, fail
# on enexpected load issue
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
readerApproaches = scalarVolumePlugin.readerApproaches()
basename = loadable.name
volumesByApproach = {}
for readerApproach in readerApproaches:
self.delayDisplay('Loading Selection with approach: %s' % readerApproach)
loadable.name = basename + "-" + readerApproach
volumeNode = scalarVolumePlugin.load(loadable,readerApproach)
if not volumeNode and readerApproach not in dataset['expectedFailures']:
raise Exception("Expected to be able to read with %s, but couldn't" % readerApproach)
if volumeNode and readerApproach in dataset['expectedFailures']:
raise Exception("Expected to NOT be able to read with %s, but could!" % readerApproach)
if volumeNode:
volumesByApproach[readerApproach] = volumeNode
self.delayDisplay('Test quantity and unit')
if 'voxelValueQuantity' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueQuantity().GetAsPrintableString(), dataset['voxelValueQuantity'])
if 'voxelValueUnits' in dataset.keys():
self.assertEqual(volumeNode.GetVoxelValueUnits().GetAsPrintableString(), dataset['voxelValueUnits'])
#
# for each approach that loaded as expected, compare the volumes
# to ensure they match in terms of pixel data and metadata
#
failedComparisons = {}
approachesThatLoaded = list(volumesByApproach.keys())
print('approachesThatLoaded %s' % approachesThatLoaded)
for approachIndex in range(len(approachesThatLoaded)):
firstApproach = approachesThatLoaded[approachIndex]
firstVolume = volumesByApproach[firstApproach]
for secondApproachIndex in range(approachIndex+1,len(approachesThatLoaded)):
secondApproach = approachesThatLoaded[secondApproachIndex]
secondVolume = volumesByApproach[secondApproach]
print('comparing %s,%s' % (firstApproach, secondApproach))
comparison = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin'].compareVolumeNodes(firstVolume,secondVolume)
if comparison != "":
print(('failed: %s', comparison))
failedComparisons[firstApproach,secondApproach] = comparison
if len(failedComparisons.keys()) > 0:
raise Exception("Loaded volumes don't match: %s" % failedComparisons)
self.delayDisplay('%s Test passed!' % dataset['name'])
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('%s Test caused exception!\n' % dataset['name'] + str(e))
testPass = False
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
slicer.util.selectModule('DICOMReaders')
logging.info(loadingResult)
return testPass
def test_AlternateReaders(self):
""" Test the DICOM loading of sample testing data
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test")
referenceData = [{
"url": "http://slicer.kitware.com/midas3/download?items=292839",
"fileName": "Mouse-MR-example-where-GDCM_fails.zip",
"name": "Mouse-MR-example-where-GDCM_fails",
"seriesUID":
"1.3.6.1.4.1.9590.100.1.2.366426457713813178933224342280246227461",
"expectedFailures": ["GDCM", "Archetype"],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
}, {
"url": "http://slicer.kitware.com/midas3/download?items=294857",
"fileName": "deidentifiedMRHead-dcm-one-series.zip",
"name": "deidentifiedMRHead-dcm-one-series",
"seriesUID":
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0",
"expectedFailures": [],
"voxelValueQuantity": "(110852, DCM, \"MR signal intensity\")",
"voxelValueUnits": "(1, UCUM, \"no units\")"
}]
# another dataset that could be added in the future - currently fails for all readers
# due to invalid format - see https://issues.slicer.org/view.php?id=3569
#{ "url": "http://slicer.kitware.com/midas3/download/item/293587/RIDER_bug.zip",
#"fileName": "RIDER_bug.zip",
#"name": "RIDER_bug",
#"seriesUID": "1.3.6.1.4.1.9328.50.7.261772317324041365541450388603508531852",
#"expectedFailures": []
#}
loadingResult = {}
#
# first, get the data - a zip file of dicom data
#
self.delayDisplay("Downloading")
for dataset in referenceData:
try:
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames=dataset['fileName'], uris=dataset['url'])[0]
self.delayDisplay('Finished with download')
#
# insert the data into th database
#
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatabase')
self.delayDisplay('Importing DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory,
None)
indexer.waitForImportFinished()
#
# select the series
#
detailsPopup = slicer.modules.DICOMWidget.detailsPopup
detailsPopup.open()
# load the data by series UID
detailsPopup.offerLoadables(dataset['seriesUID'], 'Series')
detailsPopup.examineForLoading()
loadable = detailsPopup.getAllSelectedLoadables().keys()[0]
#
# try loading using each of the selected readers, fail
# on enexpected load issue
#
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
readerApproaches = scalarVolumePlugin.readerApproaches()
basename = loadable.name
volumesByApproach = {}
for readerApproach in readerApproaches:
self.delayDisplay('Loading Selection with approach: %s' %
readerApproach)
loadable.name = basename + "-" + readerApproach
volumeNode = scalarVolumePlugin.load(
loadable, readerApproach)
if not volumeNode and readerApproach not in dataset[
'expectedFailures']:
raise Exception(
"Expected to be able to read with %s, but couldn't"
% readerApproach)
if volumeNode and readerApproach in dataset[
'expectedFailures']:
raise Exception(
"Expected to NOT be able to read with %s, but could!"
% readerApproach)
if volumeNode:
volumesByApproach[readerApproach] = volumeNode
self.delayDisplay('Test quantity and unit')
if 'voxelValueQuantity' in dataset.keys():
self.assertEqual(
volumeNode.GetVoxelValueQuantity(
).GetAsPrintableString(),
dataset['voxelValueQuantity'])
if 'voxelValueUnits' in dataset.keys():
self.assertEqual(
volumeNode.GetVoxelValueUnits(
).GetAsPrintableString(),
dataset['voxelValueUnits'])
#
# for each approach that loaded as expected, compare the volumes
# to ensure they match in terms of pixel data and metadata
#
failedComparisons = {}
approachesThatLoaded = volumesByApproach.keys()
print('approachesThatLoaded %s' % approachesThatLoaded)
for approachIndex in range(len(approachesThatLoaded)):
firstApproach = approachesThatLoaded[approachIndex]
firstVolume = volumesByApproach[firstApproach]
for secondApproachIndex in range(
approachIndex + 1, len(approachesThatLoaded)):
secondApproach = approachesThatLoaded[
secondApproachIndex]
secondVolume = volumesByApproach[secondApproach]
print('comparing %s,%s' %
(firstApproach, secondApproach))
comparison = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin'].compareVolumeNodes(
firstVolume, secondVolume)
if comparison != "":
print('failed: %s', comparison)
failedComparisons[firstApproach,
secondApproach] = comparison
if len(failedComparisons.keys()) > 0:
raise Exception("Loaded volumes don't match: %s" %
failedComparisons)
self.delayDisplay('%s Test passed!' % dataset['name'])
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('%s Test caused exception!\n' %
dataset['name'] + str(e))
testPass = 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 SampleData
SampleData.downloadFromURL(
fileNames='Dcmtk-db.zip',
uris='http://slicer.kitware.com/midas3/download?items=18822')[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise( UserWarning("Could not find dcmqrscp executable") )
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args, stdout=subprocess.PIPE, cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy('1.2.124.113932.1.170.223.162.178.20050502.160340.12640015');
popen.kill()
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')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(10,40))
self.delayDisplay('Change Window')
slicer.util.clickAndDrag(redWidget,start=(10,10),end=(40,10))
self.delayDisplay('Change Layout')
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.delayDisplay('Zoom')
slicer.util.clickAndDrag(redWidget,button='Right',start=(10,10),end=(10,40))
self.delayDisplay('Pan')
slicer.util.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')
slicer.util.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()
slicer.util.clickAndDrag(threeDView)
self.delayDisplay('Zoom')
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.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 test_Part1DICOM(self,
enableScreenshotsFlag=0,
screenshotScaleFactor=1):
""" Test the DICOM part of the test using the head atlas
"""
logic = RSNAVisTutorialLogic()
logic.enableScreenshots = enableScreenshotsFlag
logic.screenshotScaleFactor = screenshotScaleFactor
import os
self.delayDisplay("Starting the DICOM test")
#
# first, get the data - a zip file of dicom data
#
import SampleData
dicomFilesDirectory = SampleData.downloadFromURL(
fileNames='dataset1_Thorax_Abdomen.zip',
uris=TESTING_DATA_URL +
'SHA256/17a4199aad03a373dab27dc17e5bfcf84fc194d0a30975b4073e5b595d43a56a',
checksums=
'SHA256:17a4199aad03a373dab27dc17e5bfcf84fc194d0a30975b4073e5b595d43a56a'
)[0]
try:
self.delayDisplay("Switching to temp database directory")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatabase')
slicer.util.selectModule('DICOM')
browserWidget = slicer.modules.DICOMWidget.browserWidget
dicomBrowser = browserWidget.dicomBrowser
dicomBrowser.importDirectory(dicomFilesDirectory,
dicomBrowser.ImportDirectoryAddLink)
dicomBrowser.waitForImportFinished()
# load the data by series UID
dicomBrowser.dicomTableManager().patientsTable().selectFirst()
browserWidget.examineForLoading()
self.delayDisplay('Loading Selection')
browserWidget.loadCheckedLoadables()
logic.takeScreenshot('LoadingADICOMVolume-Loaded',
'Loaded DICOM Volume', -1)
layoutManager = slicer.app.layoutManager()
redWidget = layoutManager.sliceWidget('Red')
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(10, 40))
slicer.util.clickAndDrag(redWidget, start=(10, 10), end=(40, 10))
logic.takeScreenshot('LoadingADICOMVolume-WL',
'Changed level and window', -1)
redWidget.sliceController().setSliceLink(True)
redWidget.sliceController().setSliceVisible(True)
logic.takeScreenshot('LoadingADICOMVolume-LinkView',
'Linked and visible', -1)
slicer.util.clickAndDrag(redWidget,
button='Right',
start=(10, 10),
end=(10, 40))
logic.takeScreenshot('LoadingADICOMVolume-Zoom', 'Zoom', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('LoadingADICOMVolume-Rotate', 'Rotate', -1)
threeDView.resetFocalPoint()
logic.takeScreenshot('LoadingADICOMVolume-Center',
'Center the view', -1)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.
SlicerLayoutConventionalWidescreenView)
logic.takeScreenshot('LoadingADICOMVolume-ConventionalWidescreen',
'Conventional Widescreen Layout', -1)
slicer.util.mainWindow().moduleSelector().selectModule(
'VolumeRendering')
logic.takeScreenshot('VolumeRendering-Module', 'Volume Rendering',
-1)
volumeRenderingWidgetRep = slicer.modules.volumerendering.widgetRepresentation(
)
abdomenVolume = slicer.mrmlScene.GetFirstNodeByName(
'6: CT_Thorax_Abdomen')
volumeRenderingWidgetRep.setMRMLVolumeNode(abdomenVolume)
logic.takeScreenshot('VolumeRendering-SelectVolume',
'Select the volume 6: CT_Thorax_Abdomen', -1)
presetsScene = slicer.modules.volumerendering.logic(
).GetPresetsScene()
ctCardiac3 = presetsScene.GetFirstNodeByName('CT-Cardiac3')
volumeRenderingWidgetRep.mrmlVolumePropertyNode().Copy(ctCardiac3)
logic.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)
logic.takeScreenshot('VolumeRendering-ViewRendering',
'View Volume Rendering', -1)
self.delayDisplay('Skipping Move the Shift slider')
redWidget.sliceController().setSliceVisible(False)
logic.takeScreenshot('VolumeRendering-SlicesOff',
'Turn off visibility of slices in 3D', -1)
threeDView = layoutManager.threeDWidget(0).threeDView()
slicer.util.clickAndDrag(threeDView)
logic.takeScreenshot('VolumeRendering-RotateVolumeRendering',
'Rotate volume rendered image', -1)
volumeRenderingNode.SetVisibility(0)
logic.takeScreenshot('VolumeRendering-TurnOffVolumeRendering',
'Turn off volume rendered image', -1)
volumeRenderingNode.SetCroppingEnabled(1)
annotationROI = slicer.mrmlScene.GetFirstNodeByName(
'AnnotationROI')
annotationROI.SetDisplayVisibility(1)
logic.takeScreenshot('VolumeRendering-DisplayROI',
'Enable cropping and display ROI', -1)
redWidget.sliceController().setSliceVisible(True)
logic.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)
logic.takeScreenshot('VolumeRendering-SizedROI',
'Position the ROI over a kidney', -1)
volumeRenderingNode.SetVisibility(1)
logic.takeScreenshot('VolumeRendering-ROIRendering',
'ROI volume rendered', -1)
annotationROI.SetXYZ(15, 146, -186)
annotationROI.SetRadiusXYZ(138, 57, 61)
logic.takeScreenshot('VolumeRendering-BothKidneys',
'Rendered both kidneys', -1)
self.delayDisplay('Test passed!')
except Exception as e:
import traceback
traceback.print_exc()
self.delayDisplay('Test caused exception!\n' + str(e))
self.delayDisplay("Restoring original database directory")
DICOMUtils.closeTemporaryDatabase(originalDatabaseDirectory)
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=18822',
'Dcmtk-db.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")
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase(
'tempDICOMDatbase')
self.delayDisplay('Start Local DICOM Q/R SCP')
import subprocess
import os
configFilePath = dicomFilesDirectory + '/Dcmtk-db/dcmqrscp.cfg'
processCurrentPath = dicomFilesDirectory + '/Dcmtk-db/'
dcmqrscpExeOptions = (
'/bin',
'/../CTK-build/CMakeExternals/Install/bin',
'/../DCMTK-install/bin',
'/../DCMTK-build/bin',
)
dcmqrscpExePath = None
dcmqrscpExeName = '/dcmqrscp'
if slicer.app.os == 'win':
dcmqrscpExeName = dcmqrscpExeName + '.exe'
for path in dcmqrscpExeOptions:
testPath = slicer.app.slicerHome + path + dcmqrscpExeName
if os.path.exists(testPath):
dcmqrscpExePath = testPath
break
if not dcmqrscpExePath:
raise (UserWarning("Could not find dcmqrscp executable"))
args = (dcmqrscpExePath, '-c', configFilePath)
popen = subprocess.Popen(args,
stdout=subprocess.PIPE,
cwd=processCurrentPath)
self.delayDisplay('Retrieve DICOM')
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
dicomRetrieve = ctk.ctkDICOMRetrieve()
dicomRetrieve.setKeepAssociationOpen(True)
dicomRetrieve.setDatabase(slicer.dicomDatabase)
dicomRetrieve.setCallingAETitle('SlicerAE')
dicomRetrieve.setCalledAETitle('DCMTK')
dicomRetrieve.setPort(12345)
dicomRetrieve.setHost('localhost')
dicomRetrieve.getStudy(
'1.2.124.113932.1.170.223.162.178.20050502.160340.12640015')
popen.kill()
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 test_MissingSlices(self):
""" Test behavior of the readers when slices are missing
To edit and run this test from the python console, paste this below:
reloadScriptedModule('DICOMReaders'); import DICOMReaders; tester = DICOMReaders.DICOMReadersTest(); tester.setUp(); tester.test_MissingSlices()
"""
testPass = True
import os, json
self.delayDisplay("Starting the DICOM test", 100)
datasetURL = "http://slicer.kitware.com/midas3/download/item/294857/deidentifiedMRHead-dcm-one-series.zip"
fileName = "deidentifiedMRHead-dcm-one-series.zip"
filePath = os.path.join(slicer.app.temporaryPath,fileName)
seriesUID = "1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.270.0"
seriesRASBounds = [-87.29489517211913, 81.70450973510744,
-121.57139587402344, 134.42860412597656,
-138.71430206298828, 117.28569793701172]
seriesDirectory = "Series 004 [MR - SAG RF FAST VOL FLIP 20]"
lastSliceCorners = [[[81.05451202, 133.92860413, 116.78569794], [81.05451202, -122.07139587, 116.78569794]],
[[81.05451202, 133.92860413, -139.21429443], [81.05451202, -122.07139587, -139.21429443]]]
filesToRemove = [
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.361.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.362.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.363.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.364.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.365.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.366.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.367.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.368.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.369.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.370.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.371.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.372.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.373.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.374.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.375.0.dcm",
"1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.376.0.dcm",
]
try:
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
self.delayDisplay('Requesting download %s from %s...\n' % (fileName, datasetURL), 100)
urllib.urlretrieve(datasetURL, filePath)
self.delayDisplay('Finished with download\n', 100)
self.delayDisplay("Unzipping", 100)
dicomFilesDirectory = slicer.app.temporaryPath + 'MRhead'
qt.QDir().mkpath(dicomFilesDirectory)
slicer.app.applicationLogic().Unzip(filePath, dicomFilesDirectory)
print('Removing %d files from the middle of the series' % len(filesToRemove))
for file in filesToRemove:
filePath = os.path.join(dicomFilesDirectory, seriesDirectory, file)
os.remove(filePath)
#
# insert the data into the database
#
self.delayDisplay("Switching to temp database directory", 100)
originalDatabaseDirectory = DICOMUtils.openTemporaryDatabase('tempDICOMDatabase')
self.delayDisplay('Importing DICOM', 100)
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('DICOM')
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, dicomFilesDirectory, None)
indexer.waitForImportFinished()
#
# select the series
#
detailsPopup = slicer.modules.DICOMWidget.detailsPopup
detailsPopup.open()
# load the data by series UID
detailsPopup.offerLoadables(seriesUID,'Series')
detailsPopup.examineForLoading()
loadable = detailsPopup.getAllSelectedLoadables().keys()[0]
if len(loadable.warning) == 0:
raise Exception("Expected warning about geometry issues due to missing slices!")
#
# load and correct for acquisition then check the geometry
#
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
volumeNode = scalarVolumePlugin.load(loadable)
if not numpy.allclose(scalarVolumePlugin.acquisitionModeling.fixedCorners[-1], lastSliceCorners):
raise Exception("Acquisition transform didn't fix slice corners!")
self.delayDisplay('test_MissingSlices passed!', 200)
except Exception, e:
import traceback
traceback.print_exc()
self.delayDisplay('Missing Slices Test caused exception!\n' + str(e), 2000)
testPass = False
