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b/train_adapt.py |
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#!/usr/bin/env python |
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# coding: utf-8 |
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'''Subject-adaptative 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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from torch import nn |
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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-adaptative 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('modelpath', type=str, |
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help='Path to the base model folder') |
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parser.add_argument('outpath', type=str, help='Path to the result folder') |
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parser.add_argument('-scheme', type=int, help='Adaptation scheme', default=4) |
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parser.add_argument( |
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'-trfrate', type=int, help='The percentage of data for adaptation', default=100) |
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parser.add_argument('-lr', type=float, help='Learning rate', default=0.0005) |
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parser.add_argument('-gpu', type=int, help='The gpu device to use', default=0) |
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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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modelpath = args.modelpath |
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scheme = args.scheme |
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rate = args.trfrate |
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lr = args.lr |
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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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BATCH_SIZE = 16 |
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TRAIN_EPOCH = 200 |
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# Randomly shuffled subject. |
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subjs = [35, 47, 46, 37, 13, 27, 12, 32, 53, 54, 4, 40, 19, 41, 18, 42, 34, 7, |
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49, 9, 5, 48, 29, 15, 21, 17, 31, 45, 1, 38, 51, 8, 11, 16, 28, 44, 24, |
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52, 3, 26, 39, 50, 6, 23, 2, 14, 25, 20, 10, 33, 22, 43, 36, 30] |
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# Get data from single subject. |
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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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X, Y = get_data(subjs[0]) |
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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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# Deprecated. |
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def reset_conv_pool_block(network, block_nr): |
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suffix = "_{:d}".format(block_nr) |
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conv = getattr(network, 'conv' + suffix) |
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kernel_size = conv.kernel_size |
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n_filters_before = conv.in_channels |
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n_filters = conv.out_channels |
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setattr(network, 'conv' + suffix, |
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nn.Conv2d( |
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n_filters_before, |
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n_filters, |
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kernel_size, |
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stride=(1, 1), |
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bias=False, |
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)) |
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setattr(network, 'bnorm' + suffix, |
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nn.BatchNorm2d( |
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n_filters, |
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momentum=0.1, |
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affine=True, |
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eps=1e-5, |
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)) |
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# Initialize the layers. |
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conv = getattr(network, 'conv' + suffix) |
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bnorm = getattr(network, 'bnorm' + suffix) |
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nn.init.xavier_uniform_(conv.weight, gain=1) |
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nn.init.constant_(bnorm.weight, 1) |
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nn.init.constant_(bnorm.bias, 0) |
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def reset_model(checkpoint): |
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# Load the state dict of the model. |
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model.network.load_state_dict(checkpoint['model_state_dict']) |
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# # Resets the last conv block |
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# reset_conv_pool_block(model.network, block_nr=4) |
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# reset_conv_pool_block(model.network, block_nr=3) |
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# reset_conv_pool_block(model.network, block_nr=2) |
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# # Resets the fully-connected layer. |
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# # Parameters of newly constructed modules have requires_grad=True by default. |
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# n_final_conv_length = model.network.conv_classifier.kernel_size[0] |
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# n_prev_filter = model.network.conv_classifier.in_channels |
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# n_classes = model.network.conv_classifier.out_channels |
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# model.network.conv_classifier = nn.Conv2d( |
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# n_prev_filter, n_classes, (n_final_conv_length, 1), bias=True) |
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# nn.init.xavier_uniform_(model.network.conv_classifier.weight, gain=1) |
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# nn.init.constant_(model.network.conv_classifier.bias, 0) |
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if scheme != 5: |
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# Freeze all layers. |
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for param in model.network.parameters(): |
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param.requires_grad = False |
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if scheme in {1, 2, 3, 4}: |
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# Unfreeze the FC layer. |
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for param in model.network.conv_classifier.parameters(): |
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param.requires_grad = True |
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if scheme in {2, 3, 4}: |
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# Unfreeze the conv4 layer. |
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for param in model.network.conv_4.parameters(): |
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param.requires_grad = True |
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for param in model.network.bnorm_4.parameters(): |
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param.requires_grad = True |
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if scheme in {3, 4}: |
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# Unfreeze the conv3 layer. |
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for param in model.network.conv_3.parameters(): |
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param.requires_grad = True |
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for param in model.network.bnorm_3.parameters(): |
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param.requires_grad = True |
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if scheme == 4: |
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# Unfreeze the conv2 layer. |
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for param in model.network.conv_2.parameters(): |
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param.requires_grad = True |
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for param in model.network.bnorm_2.parameters(): |
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param.requires_grad = True |
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# Only optimize parameters that requires gradient. |
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optimizer = AdamW(filter(lambda p: p.requires_grad, model.network.parameters()), |
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lr=lr, weight_decay=0.5*0.001) |
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model.compile(loss=F.nll_loss, optimizer=optimizer, |
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iterator_seed=20200205, ) |
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cutoff = int(rate * 200 / 100) |
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# Use only session 1 data for training |
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assert(cutoff <= 200) |
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for fold, subj in enumerate(subjs): |
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suffix = '_s' + str(subj) + '_f' + str(fold) |
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checkpoint = torch.load(pjoin(modelpath, 'model_f' + str(fold) + '.pt'), |
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map_location='cuda:' + str(args.gpu)) |
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reset_model(checkpoint) |
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X, Y = get_data(subj) |
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X_train, Y_train = X[:cutoff], Y[:cutoff] |
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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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model.fit(X_train, Y_train, epochs=TRAIN_EPOCH, |
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batch_size=BATCH_SIZE, scheduler='cosine', |
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validation_data=(X_val, Y_val), remember_best_column='valid_loss') |
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model.epochs_df.to_csv(pjoin(outpath, 'epochs' + suffix + '.csv')) |
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test_loss = model.evaluate(X_test, Y_test) |
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with open(pjoin(outpath, 'test' + suffix + '.json'), 'w') as f: |
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json.dump(test_loss, f) |
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dfile.close() |