def main(): # logger = logging.getLogger() logger.setLevel(logging.WARNING) ch = logging.StreamHandler() logger.addHandler(ch) #logger.debug('input params') # input parser parser = argparse.ArgumentParser( description='Module for segmentation of simple anatomical structures') parser.add_argument('-i', '--inputfile', default='organ.pkl', help='path to data dir') args = parser.parse_args() data = misc.obj_from_file(args.inputfile, filetype='pickle') data3d = data['data3d'] voxelsize_mm = data['voxelsize_mm'] ss = SimpleSegmentation() simple_seg = ss.simple_segmentation(data3d, voxelsize_mm) #visualization pyed = sed3.sed3(data['data3d'], seeds=simple_seg) pyed.show() # save savestring = raw_input('Save output data? (y/n): ') if savestring in ['Y', 'y']: misc.obj_to_file(data, "resection.pkl", filetype='pickle')
def main(): logger = logging.getLogger() logger.setLevel(logging.WARNING) ch = logging.StreamHandler() logger.addHandler(ch) #logger.debug('input params') # input parser parser = argparse.ArgumentParser( description='Module for segmentation of simple anatomical structures') parser.add_argument('-i', '--inputfile', default='organ.pkl', help='path to data dir') args = parser.parse_args() data = misc.obj_from_file(args.inputfile, filetype = 'pickle') data3d = data['data3d'] voxelsize_mm = data['voxelsize_mm'] ss = SimpleSegmentation() simple_seg = ss.simple_segmentation(data3d, voxelsize_mm) #visualization pyed = sed3.sed3(data['data3d'], seeds=simple_seg) pyed.show() # save savestring = raw_input('Save output data? (y/n): ') if savestring in ['Y', 'y']: misc.obj_to_file(data, "resection.pkl", filetype='pickle')
def test_obj_to_and_from_file_pickle(self): testdata = np.random.random([4, 4, 3]) test_object = {'a': 1, 'data': testdata} filename = 'test_obj_to_and_from_file.pkl' misc.obj_to_file(test_object, filename, 'pickle') saved_object = misc.obj_from_file(filename, 'pickle') self.assertTrue(saved_object['a'] == 1) self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1]) os.remove(filename)
def test_obj_to_and_from_file_with_directories(self): import shutil testdata = np.random.random([4, 4, 3]) test_object = {'a': 1, 'data': testdata} dirname = '__test_write_and_read' filename = '__test_write_and_read/test_obj_to_and_from_file.pkl' misc.obj_to_file(test_object, filename, 'pickle') saved_object = misc.obj_from_file(filename, 'pickle') self.assertTrue(saved_object['a'] == 1) self.assertTrue(saved_object['data'][1, 1, 1] == testdata[1, 1, 1]) shutil.rmtree(dirname)