import mxnet as mx
import logging
import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from arg_parsing import process_args
from logger import construct_run_id, configure_root_logger
from data_loaders.cifar10 import Cifar10
from models.resnet164_basic import resnet164Basic
from learners.gluon import GluonLearner
if __name__ == "__main__":
run_id = construct_run_id(__file__)
configure_root_logger(run_id)
logging.info(__file__)
args = process_args()
mx.random.seed(args.seed)
batch_size = 128
train_data, valid_data = Cifar10(
batch_size=batch_size,
data_shape=(3, 32, 32),
padding=4,
padding_value=0,
normalization_type="channel").return_dataloaders()
lr_schedule = {0: 0.01, 5: 0.1, 95: 0.01, 140: 0.001}
model = resnet164Basic(num_classes=10)
def run(args):
# Configures the root application logger.
# After these line, it's safe to log using src.poretitioner.logger.getLogger() throughout the application.
logger.configure_root_logger(verbosity=args.verbose, debug=args.debug)
log = logger.getLogger()
log.debug(f"Starting poretitioner with arguments: {vars(args)!s}")
# Get the command line args as a dictionary.
command_line_args = vars(args)
if "capture_directory" not in command_line_args and getattr(
args, ARG.GENERAL.CAPTURE_DIRECTORY, False):
command_line_args["capture_directory"] = command_line_args[
ARG.GENERAL.CAPTURE_DIRECTORY]
# Read configuration file, if it exists.
try:
configuration_path = Path(
command_line_args[ARG.GENERAL.CONFIG]).resolve()
except KeyError as e:
log.info(f"No config file found from arg: {ARG.GENERAL.CONFIG}.")
raise e
configuration = readconfig(configuration_path,
command_line_args=command_line_args,
log=log)
bulk_f5_filepath = Path(
command_line_args[ARG.GENERAL.BULK_FAST5]).resolve()
seg_config = configuration[CONFIG.SEGMENTATION]
filter_set: FilterSet = configuration[CONFIG.FILTER]
config = configuration[CONFIG.GENERAL]
save_location = Path(getattr(args,
ARG.GENERAL.CAPTURE_DIRECTORY)).resolve()
log.info(f"bulk_f5_filepath: {bulk_f5_filepath}")
log.info(f"Save location: {save_location}")
if args.command == COMMAND.SEGMENT:
segmentation_config_str = pprint.pformat(seg_config.__dict__)
general_config_str = pprint.pformat(config.__dict__)
capture_metadata = segment.segment(
bulk_f5_filepath,
config,
seg_config,
save_location=save_location,
sub_run_start_observations=0,
sub_run_end_observations=None,
)
segment_results = pprint.pformat(capture_metadata)
log.debug(f"All done segmenting: \n{segment_results}")
return
elif args.command == COMMAND.FILTER:
# TODO: Perform filter step.
return
elif args.command == COMMAND.CLASSIFY:
# TODO: Perform classification step.
return
elif args.command == COMMAND.QUANTIFY:
# TODO: Perform quantification step.
return
else:
# TODO: Perform all steps.
return