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')