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b/train_within.py |
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#!/usr/bin/env python |
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# coding: utf-8 |
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'''Subject-specific classification with KU Data, |
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using Deep ConvNet model from [1]. |
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References |
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---------- |
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.. [1] Schirrmeister, R. T., Springenberg, J. T., Fiederer, L. D. J., |
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Glasstetter, M., Eggensperger, K., Tangermann, M., Hutter, F. & Ball, T. (2017). |
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Deep learning with convolutional neural networks for EEG decoding and |
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visualization. |
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Human Brain Mapping , Aug. 2017. Online: http://dx.doi.org/10.1002/hbm.23730 |
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''' |
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import argparse |
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import json |
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import logging |
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import sys |
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from os.path import join as pjoin |
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import h5py |
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import torch |
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import torch.nn.functional as F |
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from braindecode.models.deep4 import Deep4Net |
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from braindecode.torch_ext.optimizers import AdamW |
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from braindecode.torch_ext.util import set_random_seeds |
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logging.basicConfig(format='%(asctime)s %(levelname)s : %(message)s', |
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level=logging.INFO, stream=sys.stdout) |
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parser = argparse.ArgumentParser( |
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description='Subject-specific classification with KU Data') |
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parser.add_argument('datapath', type=str, help='Path to the h5 data file') |
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parser.add_argument('outpath', type=str, help='Path to the result folder') |
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parser.add_argument('-gpu', type=int, |
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help='The gpu device index to use', default=0) |
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parser.add_argument('-start', type=int, |
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help='Start of the subject index', default=1) |
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parser.add_argument( |
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'-end', type=int, help='End of the subject index (not inclusive)', default=55) |
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parser.add_argument('-subj', type=int, nargs='+', |
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help='Explicitly set the subject number. This will override the start and end argument') |
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args = parser.parse_args() |
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datapath = args.datapath |
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outpath = args.outpath |
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start = args.start |
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end = args.end |
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assert(start < end) |
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subjs = args.subj if args.subj else range(start, end) |
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dfile = h5py.File(datapath, 'r') |
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torch.cuda.set_device(args.gpu) |
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set_random_seeds(seed=20200205, cuda=True) |
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def get_data(subj): |
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dpath = '/s' + str(subj) |
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X = dfile[pjoin(dpath, 'X')] |
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Y = dfile[pjoin(dpath, 'Y')] |
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return X[:], Y[:] |
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for subj in subjs: |
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# Get data for within-subject classification |
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X, Y = get_data(subj) |
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X_train, Y_train = X[:200], Y[:200] |
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X_val, Y_val = X[200:300], Y[200:300] |
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X_test, Y_test = X[300:], Y[300:] |
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suffix = 's' + str(subj) |
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n_classes = 2 |
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in_chans = X.shape[1] |
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# final_conv_length = auto ensures we only get a single output in the time dimension |
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model = Deep4Net(in_chans=in_chans, n_classes=n_classes, |
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input_time_length=X.shape[2], |
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final_conv_length='auto').cuda() |
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# these are good values for the deep model |
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optimizer = AdamW(model.parameters(), lr=1 * 0.01, weight_decay=0.5*0.001) |
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model.compile(loss=F.nll_loss, optimizer=optimizer, iterator_seed=1, ) |
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model.fit(X_train, Y_train, epochs=200, batch_size=16, scheduler='cosine', |
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validation_data=(X_val, Y_val), remember_best_column='valid_loss') |
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test_loss = model.evaluate(X_test, Y_test) |
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model.epochs_df.to_csv(pjoin(outpath, 'epochs_' + suffix + '.csv')) |
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with open(pjoin(outpath, 'test_subj_' + str(subj) + '.json'), 'w') as f: |
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json.dump(test_loss, f) |
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dfile.close() |