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,
