def test_get_subdirs(self):
dirpath = os.path.join(path_to_script, "..")
dirlist = experiments.get_subdirs(dirpath)
#import pdb; pdb.set_trace()
self.assertTrue('tests' in dirlist)
self.assertTrue('extern' in dirlist)
self.assertTrue('src' in dirlist)
self.assertFalse('README.md' in dirlist)
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
# input parser
params = {'datadir':None, 'working_voxelsize_mm':3}
dirpath = os.path.join(path_to_script, "../../../data/medical/data_orig/volumetrie")
experiment_results = {'params':params,'dirpath':dirpath, 'volume_l':{}}
output_dirpath = os.path.join(path_to_script, '../../../data/medical')
dirlist = experiments.get_subdirs(dirpath)
for key in dirlist:
print key
# import pdb; pdb.set_trace()
try:
dirname = dirlist[key]['abspath']
params['datadir'] = dirname
oseg = organ_segmentation.OrganSegmentation(**params)
oseg.interactivity()
print (
"Volume " +
str(oseg.get_segmented_volume_size_mm3() / 1000000.0)
+ ' [l]')
volume_l = (oseg.get_segmented_volume_size_mm3() / 1000000.0)
experiment_results['volume_l'][key] = volume_l
head, teil = os.path.split(dirname)
filename_organ = os.path.join(output_dirpath, teil)
data = oseg.export()
misc.obj_to_file(data, filename_organ + "-organ.pkl", filetype='pickle')
#misc.obj_to_file(data, "organ.pkl", filetype='pickle')
misc.obj_to_file(oseg.get_iparams(), filename_organ + '-iparams.pkl', filetype='pickle')
misc.obj_to_file(experiment_results, filename_organ + "-info.yaml", filetype='yaml')
except:
print 'Selhani, pokracujeme dal'
print traceback.format_exc()
import pdb; pdb.set_trace()
misc.obj_to_file(experiment_results, "results.yaml", filetype='yaml')
def main():
#logger = logging.getLogger(__name__)
logger = logging.getLogger()
logger.setLevel(logging.WARNING)
ch = logging.StreamHandler()
logger.addHandler(ch)
#logger.debug('input params')
# input parser
params = {'datadir': None, 'working_voxelsize_mm': 3}
dirpath = os.path.join(path_to_script,
"../../../data/medical/data_orig/volumetrie")
experiment_results = {'params': params, 'dirpath': dirpath, 'volume_l': {}}
output_dirpath = os.path.join(path_to_script, '../../../data/medical')
dirlist = experiments.get_subdirs(dirpath)
for key in dirlist:
print key
# import pdb; pdb.set_trace()
try:
dirname = dirlist[key]['abspath']
params['datadir'] = dirname
oseg = organ_segmentation.OrganSegmentation(**params)
oseg.interactivity()
print("Volume " +
str(oseg.get_segmented_volume_size_mm3() / 1000000.0) +
' [l]')
volume_l = (oseg.get_segmented_volume_size_mm3() / 1000000.0)
experiment_results['volume_l'][key] = volume_l
head, teil = os.path.split(dirname)
filename_organ = os.path.join(output_dirpath, teil)
data = oseg.export()
misc.obj_to_file(data,
filename_organ + "-organ.pkl",
filetype='pickle')
#misc.obj_to_file(data, "organ.pkl", filetype='pickle')
misc.obj_to_file(oseg.get_iparams(),
filename_organ + '-iparams.pkl',
filetype='pickle')
misc.obj_to_file(experiment_results,
filename_organ + "-info.yaml",
filetype='yaml')
except:
print 'Selhani, pokracujeme dal'
print traceback.format_exc()
import pdb
pdb.set_trace()
misc.obj_to_file(experiment_results, "results.yaml", filetype='yaml')
