import os from subprocess import check_call from funlib.run import run, run_singularity import logging from micron import read_predict_config, read_worker_config, read_data_config import time import json predict_config = read_predict_config("predict_config.ini") worker_config = read_worker_config("worker_config.ini") data_config = read_data_config("data_config.ini") start = time.time() if worker_config["singularity_container"] != "None": run_singularity("python mknet.py", singularity_image=worker_config["singularity_container"], mount_dirs=worker_config["mount_dirs"], execute=True) else: check_call("python mknet.py", shell=True) check_call("python {} {} {} {}".format(predict_config["blockwise"], os.path.abspath("predict_config.ini"), os.path.abspath("worker_config.ini"), os.path.abspath("data_config.ini")), shell=True) end = time.time() with open("./time_prediction.json", "w") as f:
logger.info('Predict worker finished') def check_block(blocks_predicted, block): done = blocks_predicted.count({'block_id': block.block_id}) >= 1 return done if __name__ == "__main__": predict_config = sys.argv[1] worker_config = sys.argv[2] data_config = sys.argv[3] predict_config_dict = read_predict_config(predict_config) worker_config_dict = read_worker_config(worker_config) data_config_dict = read_data_config(data_config) full_config = predict_config_dict full_config.update(worker_config_dict) full_config.update(data_config_dict) start = time.time() predict_blockwise(**full_config) end = time.time() seconds = end - start logger.info('Total time to predict: %f seconds' % seconds)
import os from subprocess import check_call from funlib.run import run, run_singularity import logging from micron import read_worker_config, read_eval_config directory = os.path.dirname(os.path.abspath(__file__)) worker_config = read_worker_config(os.path.join(directory, "worker_config.ini")) eval_config = read_eval_config(os.path.join(directory, "eval_config.ini")) base_cmd = "python {} {} {} {} {} {} {}".format( eval_config["evaluation_pipeline"], os.path.abspath(os.path.join(directory, "predict_config.ini")), os.path.abspath(os.path.join(directory, "worker_config.ini")), os.path.abspath(os.path.join(directory, "data_config.ini")), os.path.abspath(os.path.join(directory, "graph_config.ini")), os.path.abspath(os.path.join(directory, "solve_config.ini")), os.path.abspath(os.path.join(directory, "eval_config.ini"))) if worker_config["singularity_container"] != "None" and worker_config[ "queue"] == "None": run_singularity(base_cmd, singularity_image=worker_config["singularity_container"], mount_dirs=worker_config["mount_dirs"], execute=True) elif worker_config["singularity_container"] != "None" and worker_config[ "queue"] != "None": run(base_cmd,