diff --git a/diann_lib_processing.py b/diann_lib_processing.py index 25d3811fd4c156aeea1d242cf21fc59152a368f4..53594b148989f8dca59429573d5040bf3edee6a1 100644 --- a/diann_lib_processing.py +++ b/diann_lib_processing.py @@ -5,7 +5,7 @@ import pyarrow.parquet as pq import pyarrow as pa import torch import matplotlib.pyplot as plt -from loess.loess_1d import loess_1d +# from loess.loess_1d import loess_1d from model.model import ModelTransformer from config import load_args @@ -95,9 +95,9 @@ def predict(data_pred, model, output_path): if __name__ =='__main__': - df = load_lib('spectral_lib/1-240711_ident_resistance_idbioriv_fluoroquinolones_conta_human_sang.parquet') - df = extract_sequence(df) - df.to_csv('spectral_lib/1-240711_ident_resistance_idbioriv_fluoroquinolones_conta_human_sang.csv') + # df = load_lib('spectral_lib/1-240711_ident_resistance_idbioriv_fluoroquinolones_conta_human_sang.parquet') + # df = extract_sequence(df) + # df.to_csv('spectral_lib/1-240711_ident_resistance_idbioriv_fluoroquinolones_conta_human_sang.csv') # plt.hist(df['RT']) # plt.savefig('test.png') # @@ -174,19 +174,19 @@ if __name__ =='__main__': # - # args = load_args() - # - # model = ModelTransformer(encoder_ff=args.encoder_ff, decoder_rt_ff=args.decoder_rt_ff, - # n_head=args.n_head, encoder_num_layer=args.encoder_num_layer, - # decoder_rt_num_layer=args.decoder_rt_num_layer, drop_rate=args.drop_rate, - # embedding_dim=args.embedding_dim, acti=args.activation, norm=args.norm_first, seq_length=30) - # - # if torch.cuda.is_available(): - # model = model.cuda() - # - # model.load_state_dict(torch.load(args.model_weigh, weights_only=True)) - # - # data_test = load_data(data_source=args.dataset_test, batch_size=args.batch_size, length=30, mode=args.split_test, - # seq_col=args.seq_test) - # - # predict(data_test, model, args.output) + args = load_args() + + model = ModelTransformer(encoder_ff=args.encoder_ff, decoder_rt_ff=args.decoder_rt_ff, + n_head=args.n_head, encoder_num_layer=args.encoder_num_layer, + decoder_rt_num_layer=args.decoder_rt_num_layer, drop_rate=args.drop_rate, + embedding_dim=args.embedding_dim, acti=args.activation, norm=args.norm_first, seq_length=30) + + if torch.cuda.is_available(): + model = model.cuda() + + model.load_state_dict(torch.load(args.model_weigh, weights_only=True)) + + data_test = load_data(data_source=args.dataset_test, batch_size=args.batch_size, length=30, mode=args.split_test, + seq_col=args.seq_test) + + predict(data_test, model, args.output)