def main(): # pragma: no cover
# import ipdb; ipdb.set_trace() # BREAKPOINT
try:
ch, fh = logger_init()
cfg = lisa_config_init()
args = parser_init(cfg)
# rint args["arg"]
oseg_argspec_keys = config.get_function_keys(
OrganSegmentation.__init__)
if args["debug"]:
ch.setLevel(logging.DEBUG)
args["debug_mode"] = True
if args["iparams"] is not None:
params = misc.obj_from_file(args["iparams"], filetype='pickle')
else:
params = config.subdict(args, oseg_argspec_keys)
logger.debug('params ' + str(params))
oseg = OrganSegmentation(**params)
if args["no_interactivity"]:
oseg.ninteractivity()
oseg.save_outputs()
else:
# mport_gui()
from lisaWindow import OrganSegmentationWindow
from PyQt4.QtGui import QApplication
app = QApplication(sys.argv)
oseg_w = OrganSegmentationWindow(oseg) # noqa
# import pdb; pdb.set_trace()
sys.exit(app.exec_())
except Exception as e:
# mport exceptionProcessing
exceptionProcessing.reportException(e)
print traceback.format_exc()
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
print 'version: ', qmisc.getVersionString()
###
# Configuration is has three sources:
# * Default function values
# * Config file 'organ_segmentation.config' in directory with application
# * Config file 'organ_segmentation.config' in output data directory
#
# It is read in this order so the last one has highest priority
###
## read confguraton from file, use default values from OrganSegmentation
cfgplus = {
'datapath': None,
'viewermax': 300,
'viewermin': -100,
'output_datapath': os.path.expanduser("~/lisa_data"),
'lisa_operator_identifier': "",
'experiment_caption': ''
}
cfg = config.get_default_function_config(OrganSegmentation.__init__)
cfg.update(cfgplus)
# now is in cfg default values
cfg = config.get_config("organ_segmentation.config", cfg)
# read user defined config in user data
cfg = config.get_config(
os.path.join(cfg['output_datapath'], "organ_segmentation.config"),
cfg
)
# input parser
parser = argparse.ArgumentParser(
description='Segment vessels from liver \n\
\npython organ_segmentation.py\n\
\npython organ_segmentation.py -mroi -vs 0.6')
parser.add_argument('-dd', '--datapath',
default=cfg["datapath"],
help='path to data dir')
parser.add_argument('-d', '--debug', action='store_true',
help='run in debug mode')
parser.add_argument(
'-vs', '--working_voxelsize_mm',
default=cfg["working_voxelsize_mm"],
type=eval, # type=str,
help='Insert working voxelsize. It can be number or \
array of three numbers. It is possible use original \n \
resolution or half of original resolution. \n \
-vs 3 \n \
-vs [3,3,5] \n \
-vs orig \n \
-vs orig*2 \n \
-vs orig*4 \n \
'
)
parser.add_argument('-mroi', '--manualroi', action='store_true',
help='manual crop before data processing',
default=cfg["manualroi"])
parser.add_argument('-op', '--output_datapath',
default=cfg["output_datapath"],
help='path for output data')
parser.add_argument('-ol', '--output_label', default=1,
help='label for segmented data')
parser.add_argument(
'--slab',
default=cfg["slab"],
type=eval,
help='labels for segmentation,\
example -slab "{\'liver\':1, \'lesions\':6}"')
parser.add_argument(
'-acr', '--autocrop',
help='automatic crop after data processing',
default=cfg["autocrop"])
parser.add_argument(
'-iparams', '--iparams',
default=None,
help='filename of ipars file with stored interactivity')
parser.add_argument(
'-sp', '--segparams', type=eval,
default=cfg["segparams"],
help='params for segmentation,\
example -sp "{\'pairwise_alpha_per_mm2\':90}"')
parser.add_argument(
'-tx', '--texture_analysis', action='store_true',
help='run with texture analysis')
parser.add_argument('-exd', '--exampledata', action='store_true',
help='run unittest')
parser.add_argument('-ed', '--edit_data', action='store_true',
help='Run data editor')
parser.add_argument(
'-vmax', '--viewermax', type=eval, # type=int,
help='Maximum of viewer window, set None for automatic maximum.',
default=cfg["viewermax"])
parser.add_argument(
'-vmin', '--viewermin', type=eval, # type=int,
help='Minimum of viewer window, set None for automatic minimum.',
default=cfg["viewermin"])
parser.add_argument(
'-so', '--show_output', action='store_true',
help='Show output data in viewer')
parser.add_argument('-a', '--arg', nargs='+', type=float)
parser.add_argument(
'-ec', '--experiment_caption', type=str, # type=int,
help='Short caption of experiment. No special characters.',
default=cfg["experiment_caption"])
parser.add_argument(
'-oi', '--lisa_operator_identifier', type=str, # type=int,
help='Identifier of Lisa operator.',
default=cfg["experiment_caption"])
parser.add_argument(
'-ss',
'--segmentation_smoothing',
action='store_true',
help='Smoothing of output segmentation',
default=cfg["segmentation_smoothing"]
)
args_obj = parser.parse_args()
args = vars(args_obj)
#print args["arg"]
oseg_argspec_keys = config.get_function_keys(OrganSegmentation.__init__)
# voxelsize_mm can be number or array
#if args.voxelsize_mm != 'orig':
#TODO easy way to set half of resolution
# if isinstance(args["working_voxelsize_mm"], numbers.Number)
# if args["working_voxelsize_mm"] == -1:
# args["working_voxelsize_mm"] = 'orig'
## todo and so on
# if not args["working_voxelsize_mm"].startswith('orig'):
# #import pdb; pdb.set_trace()
# args["working_voxelsize_mm"] = eval(args["working_voxelsize_mm"])
#
#args["segparams"] = eval(args["segparams"])
#args["slab"] = eval(args["slab"])
#args["viewermin"] = eval(args["viewermin"])
#args["viewermax"] = eval(args["viewermax"])
if args["debug"]:
logger.setLevel(logging.DEBUG)
if args["exampledata"]:
args["datapath"] = '../sample_data/\
matlab/examples/sample_data/DICOM/digest_article/'
if args["iparams"] is not None:
iparams = misc.obj_from_file(args["iparams"], filetype='pickle')
oseg = OrganSegmentation(**iparams)
else:
#else:
#dcm_read_from_dir('/home/mjirik/data/medical/data_orig/46328096/')
#data3d, metadata = dcmreaddata.dcm_read_from_dir()
data3d, metadata, qt_app = readData3d(args["datapath"])
args['datapath'] = metadata['datadir']
oseg_params = config.subdict(args, oseg_argspec_keys)
oseg_params["data3d"] = data3d
oseg_params["metadata"] = metadata
oseg_params['qt_app'] = qt_app
oseg = OrganSegmentation(**oseg_params)
oseg.interactivity(args["viewermin"], args["viewermax"])
#igc = pycut.ImageGraphCut(data3d, zoom = 0.5)
#igc.interactivity()
#igc.make_gc()
#igc.show_segmentation()
# volume
#volume_mm3 = np.sum(oseg.segmentation > 0) * np.prod(oseg.voxelsize_mm)
audiosupport.beep()
print(
"Volume " +
str(oseg.get_segmented_volume_size_mm3() / 1000000.0) + ' [l]')
#pyed = py3DSeedEditor.py3DSeedEditor(oseg.data3d, contour =
# oseg.segmentation)
#pyed.show()
print("Total time: " + str(oseg.processing_time))
if args["show_output"]:
oseg.show_output()
#print savestring
save_outputs(args, oseg, qt_app)
# import pdb; pdb.set_trace()
return