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(
"-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 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 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)
