def test_run_pipeline_3d():
ExperimentPipeline(log_base_path='../../hn_perf/3d_xs').from_full_config(
'tests/json/sample_dataset_xs_3d_full.json').run_experiment(
train_history_log=True,
model_checkpoint_period=1,
prediction_checkpoint_period=1,
epochs=1).apply_post_processors(
map_meta_data='patient_idx').load_best_model().run_test(
).apply_post_processors(map_meta_data='patient_idx',
run_test=True,
recipe='3d')
def test_run_pipeline():
ExperimentPipeline(log_base_path='../../hn_perf/2d_xs').from_full_config(
'tests/json/sample_dataset_xs_config_diff_size.json').run_experiment(
train_history_log=True,
model_checkpoint_period=1,
prediction_checkpoint_period=1,
epochs=2
).apply_post_processors(map_meta_data='patient_idx').plot_prediction(
masked_images=[i for i in range(3)], best_num=1,
worst_num=1).load_best_model(
monitor='val_dice', use_raw_log=True).run_test(
masked_images=[i for i in range(3)]).apply_post_processors(
map_meta_data='patient_idx',
run_test=True,
recipe='2d').plot_3d_test_images(best_num=1,
worst_num=1)
except RuntimeError as e:
# Virtual devices must be set before GPUs have been initialized
print(e)
if 'patch' in args.log_folder:
analysis_folder = args.analysis_folder
else:
analysis_folder = ''
if '2d' in args.log_folder:
meta = args.meta
else:
meta = args.meta.split(',')[0]
# # copy to another location
log_folder = args.log_folder + '_' + args.dataset_file[:-5].split('/')[-1]
if not os.path.exists(log_folder):
shutil.copytree(args.log_folder, log_folder)
if not os.path.exists(log_folder + '_temp'):
shutil.copytree(log_folder, log_folder + '_temp')
ex = ExperimentPipeline(log_base_path=log_folder,
temp_base_path=log_folder + '_temp')
ex.from_file(args.config_file).run_external(
args.dataset_file, map_meta_data=meta).apply_post_processors(
recipe='auto',
analysis_base_path=analysis_folder,
map_meta_data=meta,
run_test=True)
# .plot_3d_test_images(best_num=2, worst_num=2)