def get_monitors(self, input_time_length):
monitors = [LossMonitor(), RuntimeMonitor()]
if self.cropped:
monitors.append(CroppedTrialMisclassMonitor(input_time_length))
else:
monitors.append(MisclassMonitor())
return monitors
def train(config):
cuda = True
model = config['model']
if model == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=2,
config=config).create_network()
to_dense_prediction_model(model)
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
dummy_input = np_to_var(train_set.X[:1, :, :, None])
if cuda:
dummy_input = dummy_input.cuda()
out = model(dummy_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
optimizer = optim.Adam(model.parameters())
iterator = CropsFromTrialsIterator(batch_size=60,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
stop_criterion = Or([MaxEpochs(20), NoDecrease('valid_misclass', 80)])
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length=input_time_length),
RuntimeMonitor()
]
model_constraint = MaxNormDefaultConstraint()
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2, keepdim=False), targets)
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
cuda=cuda)
exp.run()
print(exp.rememberer)
return exp.rememberer.lowest_val
def get_normal_settings():
if global_vars.get('problem') == 'regression':
loss_function = F.mse_loss
else:
loss_function = F.nll_loss
stop_criterion = Or([MaxEpochs(global_vars.get('max_epochs')),
NoIncreaseDecrease(f'valid_{global_vars.get("nn_objective")}', global_vars.get('max_increase_epochs'),
oper=get_oper_by_loss_function(loss_function))])
iterator = BalancedBatchSizeIterator(batch_size=global_vars.get('batch_size'))
monitors = [LossMonitor(), GenericMonitor('accuracy'), RuntimeMonitor()]
for metric in global_vars.get('evaluation_metrics'):
monitors.append(GenericMonitor(metric))
return stop_criterion, iterator, loss_function, monitors
def setUp(self):
args = parse_args(
['-e', 'tests', '-c', '../configurations/config.ini'])
init_config(args.config)
configs = get_configurations(args.experiment)
assert (len(configs) == 1)
global_vars.set_config(configs[0])
global_vars.set('eeg_chans', 22)
global_vars.set('num_subjects', 9)
global_vars.set('input_time_len', 1125)
global_vars.set('n_classes', 4)
set_params_by_dataset()
input_shape = (50, global_vars.get('eeg_chans'),
global_vars.get('input_time_len'))
class Dummy:
def __init__(self, X, y):
self.X = X
self.y = y
dummy_data = Dummy(X=np.ones(input_shape, dtype=np.float32),
y=np.ones(50, dtype=np.longlong))
self.iterator = BalancedBatchSizeIterator(
batch_size=global_vars.get('batch_size'))
self.loss_function = F.nll_loss
self.monitors = [
LossMonitor(),
MisclassMonitor(),
GenericMonitor('accuracy', acc_func),
RuntimeMonitor()
]
self.stop_criterion = Or([
MaxEpochs(global_vars.get('max_epochs')),
NoDecrease('valid_misclass',
global_vars.get('max_increase_epochs'))
])
self.naiveNAS = NaiveNAS(iterator=self.iterator,
exp_folder='../tests',
exp_name='',
train_set=dummy_data,
val_set=dummy_data,
test_set=dummy_data,
stop_criterion=self.stop_criterion,
monitors=self.monitors,
loss_function=self.loss_function,
config=global_vars.config,
subject_id=1,
fieldnames=None,
model_from_file=None)
def get_cropped_settings():
stop_criterion = Or([MaxEpochs(global_vars.get('max_epochs')),
NoIncreaseDecrease(f'valid_{global_vars.get("nn_objective")}', global_vars.get('max_increase_epochs'))])
iterator = CropsFromTrialsIterator(batch_size=global_vars.get('batch_size'),
input_time_length=global_vars.get('input_time_len'),
n_preds_per_input=global_vars.get('n_preds_per_input'))
loss_function = lambda preds, targets: F.nll_loss(torch.mean(preds, dim=2, keepdim=False), targets)
monitors = [LossMonitor(), GenericMonitor('accuracy', acc_func),
CroppedTrialGenericMonitor('accuracy', acc_func,
input_time_length=global_vars.get('input_time_len')), RuntimeMonitor()]
if global_vars.get('dataset') in ['NER15', 'Cho', 'SonarSub']:
monitors.append(CroppedTrialGenericMonitor('auc', auc_func,
input_time_length=global_vars.get('input_time_len')))
if global_vars.get('dataset') in ['BCI_IV_2b']:
monitors.append(CroppedGenericMonitorPerTimeStep('kappa', kappa_func,
input_time_length=global_vars.get('input_time_len')))
return stop_criterion, iterator, loss_function, monitors
def network_model(model, train_set, test_set, valid_set, n_chans, input_time_length, cuda):
max_epochs = 30
max_increase_epochs = 10
batch_size = 64
init_block_size = 1000
set_random_seeds(seed=20190629, cuda=cuda)
n_classes = 2
n_chans = n_chans
input_time_length = input_time_length
if model == 'deep':
model = Deep4Net(n_chans, n_classes, input_time_length=input_time_length,
final_conv_length='auto').create_network()
elif model == 'shallow':
model = ShallowFBCSPNet(n_chans, n_classes, input_time_length=input_time_length,
final_conv_length='auto').create_network()
if cuda:
model.cuda()
log.info("%s model: ".format(str(model)))
optimizer = AdamW(model.parameters(), lr=0.00625, weight_decay=0)
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or([MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)])
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = None
print(train_set.X.shape[0])
model_test = Experiment(model, train_set, valid_set, test_set, iterator=iterator,
loss_function=F.nll_loss, optimizer=optimizer,
model_constraint=model_constraint, monitors=monitors,
stop_criterion=stop_criterion, remember_best_column='valid_misclass',
run_after_early_stop=True, cuda=cuda)
model_test.run()
return model_test
def train_completetrials(train_set,
test_set,
n_classes,
max_epochs=100,
batch_size=60,
iterator=None,
cuda=True):
model = build_model(train_set.X.shape[2],
int(train_set.X.shape[1]),
n_classes,
cropped=False)
if iterator is None:
iterator = BalancedBatchSizeIterator(batch_size=batch_size,
seed=np.random.randint(9999999))
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
loss_function = F.nll_loss
return train(train_set, test_set, model, iterator, monitors, loss_function,
max_epochs, cuda)
def network_model(subject_id, model_type, data_type, cropped, cuda, parameters, hyp_params):
best_params = dict() # dictionary to store hyper-parameter values
#####Parameter passed to funciton#####
max_epochs = parameters['max_epochs']
max_increase_epochs = parameters['max_increase_epochs']
batch_size = parameters['batch_size']
#####Constant Parameters#####
best_loss = 100.0 # instatiate starting point for loss
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or([MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)])
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
epoch = 4096
#####Collect and format data#####
if data_type == 'words':
data, labels = format_data(data_type, subject_id, epoch)
data = data[:,:,768:1280] # within-trial window selected for classification
elif data_type == 'vowels':
data, labels = format_data(data_type, subject_id, epoch)
data = data[:,:,512:1024]
elif data_type == 'all_classes':
data, labels = format_data(data_type, subject_id, epoch)
data = data[:,:,768:1280]
x = lambda a: a * 1e6 # improves numerical stability
data = x(data)
data = normalize(data)
data, labels = balanced_subsample(data, labels) # downsampling the data to ensure equal classes
data, _, labels, _ = train_test_split(data, labels, test_size=0, random_state=42) # redundant shuffle of data/labels
#####model inputs#####
unique, counts = np.unique(labels, return_counts=True)
n_classes = len(unique)
n_chans = int(data.shape[1])
input_time_length = data.shape[2]
#####k-fold nested corss-validation#####
num_folds = 4
skf = StratifiedKFold(n_splits=num_folds, shuffle=True, random_state=10)
out_fold_num = 0 # outer-fold number
cv_scores = []
#####Outer=Fold#####
for inner_ind, outer_index in skf.split(data, labels):
inner_fold, outer_fold = data[inner_ind], data[outer_index]
inner_labels, outer_labels = labels[inner_ind], labels[outer_index]
out_fold_num += 1
# list for storing cross-validated scores
loss_with_params = dict()# for storing param values and losses
in_fold_num = 0 # inner-fold number
#####Inner-Fold#####
for train_idx, valid_idx in skf.split(inner_fold, inner_labels):
X_Train, X_val = inner_fold[train_idx], inner_fold[valid_idx]
y_train, y_val = inner_labels[train_idx], inner_labels[valid_idx]
in_fold_num += 1
train_set = SignalAndTarget(X_Train, y_train)
valid_set = SignalAndTarget(X_val, y_val)
loss_with_params[f"Fold_{in_fold_num}"] = dict()
####Nested cross-validation#####
for drop_prob in hyp_params['drop_prob']:
for loss_function in hyp_params['loss']:
for i in range(len(hyp_params['lr_adam'])):
model = None # ensure no duplication of models
# model, learning-rate and optimizer setup according to model_type
if model_type == 'shallow':
model = ShallowFBCSPNet(in_chans=n_chans, n_classes=n_classes, input_time_length=input_time_length,
n_filters_time=80, filter_time_length=40, n_filters_spat=80,
pool_time_length=75, pool_time_stride=25, final_conv_length='auto',
conv_nonlin=square, pool_mode='max', pool_nonlin=safe_log,
split_first_layer=True, batch_norm=True, batch_norm_alpha=0.1,
drop_prob=drop_prob).create_network()
lr = hyp_params['lr_ada'][i]
optimizer = optim.Adadelta(model.parameters(), lr=lr, rho=0.9, weight_decay=0.1, eps=1e-8)
elif model_type == 'deep':
model = Deep4Net(in_chans=n_chans, n_classes=n_classes, input_time_length=input_time_length,
final_conv_length='auto', n_filters_time=20, n_filters_spat=20, filter_time_length=10,
pool_time_length=3, pool_time_stride=3, n_filters_2=50, filter_length_2=15,
n_filters_3=100, filter_length_3=15, n_filters_4=400, filter_length_4=10,
first_nonlin=leaky_relu, first_pool_mode='max', first_pool_nonlin=safe_log, later_nonlin=leaky_relu,
later_pool_mode='max', later_pool_nonlin=safe_log, drop_prob=drop_prob,
double_time_convs=False, split_first_layer=False, batch_norm=True, batch_norm_alpha=0.1,
stride_before_pool=False).create_network() #filter_length_4 changed from 15 to 10
lr = hyp_params['lr_ada'][i]
optimizer = optim.Adadelta(model.parameters(), lr=lr, weight_decay=0.1, eps=1e-8)
elif model_type == 'eegnet':
model = EEGNetv4(in_chans=n_chans, n_classes=n_classes, final_conv_length='auto',
input_time_length=input_time_length, pool_mode='mean', F1=16, D=2, F2=32,
kernel_length=64, third_kernel_size=(8,4), drop_prob=drop_prob).create_network()
lr = hyp_params['lr_adam'][i]
optimizer = optim.Adam(model.parameters(), lr=lr, weight_decay=0, eps=1e-8, amsgrad=False)
set_random_seeds(seed=20190629, cuda=cuda)
if cuda:
model.cuda()
torch.backends.cudnn.deterministic = True
model = torch.nn.DataParallel(model)
log.info("%s model: ".format(str(model)))
loss_function = loss_function
model_loss_function = None
#####Setup to run the selected model#####
model_test = Experiment(model, train_set, valid_set, test_set=None, iterator=iterator,
loss_function=loss_function, optimizer=optimizer,
model_constraint=model_constraint, monitors=monitors,
stop_criterion=stop_criterion, remember_best_column='valid_misclass',
run_after_early_stop=True, model_loss_function=model_loss_function, cuda=cuda,
data_type=data_type, subject_id=subject_id, model_type=model_type,
cropped=cropped, model_number=str(out_fold_num))
model_test.run()
model_loss = model_test.epochs_df['valid_loss'].astype('float')
current_val_loss = current_loss(model_loss)
loss_with_params[f"Fold_{in_fold_num}"][f"{drop_prob}/{loss_function}/{lr}"] = current_val_loss
####Select and train optimized model#####
df = pd.DataFrame(loss_with_params)
df['mean'] = df.mean(axis=1) # compute mean loss across k-folds
writer_df = f"results_folder\\results\\S{subject_id}\\{model_type}_parameters.xlsx"
df.to_excel(writer_df)
best_dp, best_loss, best_lr = df.loc[df['mean'].idxmin()].__dict__['_name'].split("/") # extract best param values
if str(best_loss[10:13]) == 'nll':
best_loss = F.nll_loss
elif str(best_loss[10:13]) == 'cro':
best_loss = F.cross_entropy
print(f"Best parameters: dropout: {best_dp}, loss: {str(best_loss)[10:13]}, lr: {best_lr}")
#####Train model on entire inner fold set#####
torch.backends.cudnn.deterministic = True
model = None
#####Create outer-fold validation and test sets#####
X_valid, X_test, y_valid, y_test = train_test_split(outer_fold, outer_labels, test_size=0.5, random_state=42, stratify=outer_labels)
train_set = SignalAndTarget(inner_fold, inner_labels)
valid_set = SignalAndTarget(X_valid, y_valid)
test_set = SignalAndTarget(X_test, y_test)
if model_type == 'shallow':
model = ShallowFBCSPNet(in_chans=n_chans, n_classes=n_classes, input_time_length=input_time_length,
n_filters_time=60, filter_time_length=5, n_filters_spat=40,
pool_time_length=50, pool_time_stride=15, final_conv_length='auto',
conv_nonlin=relu6, pool_mode='mean', pool_nonlin=safe_log,
split_first_layer=True, batch_norm=True, batch_norm_alpha=0.1,
drop_prob=0.1).create_network() #50 works better than 75
optimizer = optim.Adadelta(model.parameters(), lr=2.0, rho=0.9, weight_decay=0.1, eps=1e-8)
elif model_type == 'deep':
model = Deep4Net(in_chans=n_chans, n_classes=n_classes, input_time_length=input_time_length,
final_conv_length='auto', n_filters_time=20, n_filters_spat=20, filter_time_length=5,
pool_time_length=3, pool_time_stride=3, n_filters_2=20, filter_length_2=5,
n_filters_3=40, filter_length_3=5, n_filters_4=1500, filter_length_4=10,
first_nonlin=leaky_relu, first_pool_mode='mean', first_pool_nonlin=safe_log, later_nonlin=leaky_relu,
later_pool_mode='mean', later_pool_nonlin=safe_log, drop_prob=0.1,
double_time_convs=False, split_first_layer=True, batch_norm=True, batch_norm_alpha=0.1,
stride_before_pool=False).create_network()
optimizer = AdamW(model.parameters(), lr=0.1, weight_decay=0)
elif model_type == 'eegnet':
model = EEGNetv4(in_chans=n_chans, n_classes=n_classes, final_conv_length='auto',
input_time_length=input_time_length, pool_mode='mean', F1=16, D=2, F2=32,
kernel_length=64, third_kernel_size=(8,4), drop_prob=0.1).create_network()
optimizer = optim.Adam(model.parameters(), lr=0.1, weight_decay=0, eps=1e-8, amsgrad=False)
if cuda:
model.cuda()
torch.backends.cudnn.deterministic = True
#model = torch.nn.DataParallel(model)
log.info("Optimized model")
model_loss_function=None
#####Setup to run the optimized model#####
optimized_model = op_exp(model, train_set, valid_set, test_set=test_set, iterator=iterator,
loss_function=best_loss, optimizer=optimizer,
model_constraint=model_constraint, monitors=monitors,
stop_criterion=stop_criterion, remember_best_column='valid_misclass',
run_after_early_stop=True, model_loss_function=model_loss_function, cuda=cuda,
data_type=data_type, subject_id=subject_id, model_type=model_type,
cropped=cropped, model_number=str(out_fold_num))
optimized_model.run()
log.info("Last 5 epochs")
log.info("\n" + str(optimized_model.epochs_df.iloc[-5:]))
writer = f"results_folder\\results\\S{subject_id}\\{data_type}_{model_type}_{str(out_fold_num)}.xlsx"
optimized_model.epochs_df.iloc[-30:].to_excel(writer)
accuracy = 1 - np.min(np.array(optimized_model.class_acc))
cv_scores.append(accuracy) # k accuracy scores for this param set.
#####Print and store fold accuracies and mean accuracy#####
print(f"Class Accuracy: {np.mean(np.array(cv_scores))}")
results_df = pd.DataFrame(dict(cv_scores=cv_scores,
cv_mean=np.mean(np.array(cv_scores))))
writer2 = f"results_folder\\results\\S{subject_id}\\{data_type}_{model_type}_cvscores.xlsx"
results_df.to_excel(writer2)
return optimized_model, np.mean(np.array(cv_scores))
def run_exp(max_recording_mins, n_recordings, sec_to_cut,
duration_recording_mins, max_abs_val, max_min_threshold,
max_min_expected, shrink_val, max_min_remove, batch_set_zero_val,
batch_set_zero_test, sampling_freq, low_cut_hz, high_cut_hz,
exp_demean, exp_standardize, moving_demean, moving_standardize,
channel_demean, channel_standardize, divisor, n_folds, i_test_fold,
model_name, input_time_length, final_conv_length, batch_size,
max_epochs, only_return_exp):
cuda = True
preproc_functions = []
preproc_functions.append(lambda data, fs: (
data[:, int(sec_to_cut * fs):-int(sec_to_cut * fs)], fs))
preproc_functions.append(lambda data, fs: (data[:, :int(
duration_recording_mins * 60 * fs)], fs))
if max_abs_val is not None:
preproc_functions.append(
lambda data, fs: (np.clip(data, -max_abs_val, max_abs_val), fs))
if max_min_threshold is not None:
preproc_functions.append(lambda data, fs: (clean_jumps(
data, 200, max_min_threshold, max_min_expected, cuda), fs))
if max_min_remove is not None:
window_len = 200
preproc_functions.append(lambda data, fs: (set_jumps_to_zero(
data,
window_len=window_len,
threshold=max_min_remove,
cuda=cuda,
clip_min_max_to_zero=True), fs))
if shrink_val is not None:
preproc_functions.append(lambda data, fs: (shrink_spikes(
data,
shrink_val,
1,
9,
), fs))
preproc_functions.append(lambda data, fs: (resampy.resample(
data, fs, sampling_freq, axis=1, filter='kaiser_fast'), sampling_freq))
preproc_functions.append(lambda data, fs: (bandpass_cnt(
data, low_cut_hz, high_cut_hz, fs, filt_order=4, axis=1), fs))
if exp_demean:
preproc_functions.append(lambda data, fs: (exponential_running_demean(
data.T, factor_new=0.001, init_block_size=100).T, fs))
if exp_standardize:
preproc_functions.append(
lambda data, fs: (exponential_running_standardize(
data.T, factor_new=0.001, init_block_size=100).T, fs))
if moving_demean:
preproc_functions.append(lambda data, fs: (padded_moving_demean(
data, axis=1, n_window=201), fs))
if moving_standardize:
preproc_functions.append(lambda data, fs: (padded_moving_standardize(
data, axis=1, n_window=201), fs))
if channel_demean:
preproc_functions.append(lambda data, fs: (demean(data, axis=1), fs))
if channel_standardize:
preproc_functions.append(lambda data, fs:
(standardize(data, axis=1), fs))
if divisor is not None:
preproc_functions.append(lambda data, fs: (data / divisor, fs))
all_file_names, labels = get_all_sorted_file_names_and_labels()
lengths = np.load(
'/home/schirrmr/code/auto-diagnosis/sorted-recording-lengths.npy')
mask = lengths < max_recording_mins * 60
cleaned_file_names = np.array(all_file_names)[mask]
cleaned_labels = labels[mask]
diffs_per_rec = np.load(
'/home/schirrmr/code/auto-diagnosis/diffs_per_recording.npy')
def create_set(inds):
X = []
for i in inds:
log.info("Load {:s}".format(cleaned_file_names[i]))
x = load_data(cleaned_file_names[i], preproc_functions)
X.append(x)
y = cleaned_labels[inds].astype(np.int64)
return SignalAndTarget(X, y)
if not only_return_exp:
folds = get_balanced_batches(n_recordings,
None,
False,
n_batches=n_folds)
test_inds = folds[i_test_fold]
valid_inds = folds[i_test_fold - 1]
all_inds = list(range(n_recordings))
train_inds = np.setdiff1d(all_inds, np.union1d(test_inds, valid_inds))
rec_nr_sorted_by_diff = np.argsort(diffs_per_rec)[::-1]
train_inds = rec_nr_sorted_by_diff[train_inds]
valid_inds = rec_nr_sorted_by_diff[valid_inds]
test_inds = rec_nr_sorted_by_diff[test_inds]
train_set = create_set(train_inds)
valid_set = create_set(valid_inds)
test_set = create_set(test_inds)
else:
train_set = None
valid_set = None
test_set = None
set_random_seeds(seed=20170629, cuda=cuda)
# This will determine how many crops are processed in parallel
n_classes = 2
in_chans = 21
if model_name == 'shallow':
model = ShallowFBCSPNet(
in_chans=in_chans,
n_classes=n_classes,
input_time_length=input_time_length,
final_conv_length=final_conv_length).create_network()
elif model_name == 'deep':
model = Deep4Net(in_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=final_conv_length).create_network()
optimizer = optim.Adam(model.parameters())
to_dense_prediction_model(model)
log.info("Model:\n{:s}".format(str(model)))
if cuda:
model.cuda()
# determine output size
test_input = np_to_var(
np.ones((2, in_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
log.info("{:d} predictions per input/trial".format(n_preds_per_input))
iterator = CropsFromTrialsIterator(batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2)[:, :, 0], targets)
model_constraint = None
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length),
RuntimeMonitor(),
]
stop_criterion = MaxEpochs(max_epochs)
batch_modifier = None
if batch_set_zero_val is not None:
batch_modifier = RemoveMinMaxDiff(batch_set_zero_val,
clip_max_abs=True,
set_zero=True)
if (batch_set_zero_val is not None) and (batch_set_zero_test == True):
iterator = ModifiedIterator(
iterator,
batch_modifier,
)
batch_modifier = None
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
batch_modifier=batch_modifier,
cuda=cuda)
if not only_return_exp:
exp.run()
else:
exp.dataset = None
exp.splitter = None
return exp
def run_exp(data_folder, subject_id, low_cut_hz, model, cuda):
train_filename = 'A{:02d}T.gdf'.format(subject_id)
test_filename = 'A{:02d}E.gdf'.format(subject_id)
train_filepath = os.path.join(data_folder, train_filename)
test_filepath = os.path.join(data_folder, test_filename)
train_label_filepath = train_filepath.replace('.gdf', '.mat')
test_label_filepath = test_filepath.replace('.gdf', '.mat')
train_loader = BCICompetition4Set2A(train_filepath,
labels_filename=train_label_filepath)
test_loader = BCICompetition4Set2A(test_filepath,
labels_filename=test_label_filepath)
train_cnt = train_loader.load()
test_cnt = test_loader.load()
# Preprocessing
train_cnt = train_cnt.drop_channels(
['STI 014', 'EOG-left', 'EOG-central', 'EOG-right'])
assert len(train_cnt.ch_names) == 22
# lets convert to millvolt for numerical stability of next operations
train_cnt = mne_apply(lambda a: a * 1e6, train_cnt)
train_cnt = mne_apply(
lambda a: bandpass_cnt(
a, low_cut_hz, 38, train_cnt.info['sfreq'], filt_order=3, axis=1),
train_cnt)
train_cnt = mne_apply(
lambda a: exponential_running_standardize(
a.T, factor_new=1e-3, init_block_size=1000, eps=1e-4).T, train_cnt)
test_cnt = test_cnt.drop_channels(
['STI 014', 'EOG-left', 'EOG-central', 'EOG-right'])
assert len(test_cnt.ch_names) == 22
test_cnt = mne_apply(lambda a: a * 1e6, test_cnt)
test_cnt = mne_apply(
lambda a: bandpass_cnt(
a, low_cut_hz, 38, test_cnt.info['sfreq'], filt_order=3, axis=1),
test_cnt)
test_cnt = mne_apply(
lambda a: exponential_running_standardize(
a.T, factor_new=1e-3, init_block_size=1000, eps=1e-4).T, test_cnt)
marker_def = OrderedDict([('Left Hand', [1]), (
'Right Hand',
[2],
), ('Foot', [3]), ('Tongue', [4])])
ival = [-500, 4000]
train_set = create_signal_target_from_raw_mne(train_cnt, marker_def, ival)
test_set = create_signal_target_from_raw_mne(test_cnt, marker_def, ival)
train_set, valid_set = split_into_two_sets(train_set,
first_set_fraction=0.8)
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 4
n_chans = int(train_set.X.shape[1])
input_time_length = train_set.X.shape[2]
if model == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
elif model == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
optimizer = optim.Adam(model.parameters())
iterator = BalancedBatchSizeIterator(batch_size=60)
stop_criterion = Or([MaxEpochs(1600), NoDecrease('valid_misclass', 160)])
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=F.nll_loss,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
cuda=cuda)
exp.run()
return exp
def run_exp(max_epochs, only_return_exp):
from collections import OrderedDict
filenames = [
'data/robot-hall/NiRiNBD6.ds_1-1_500Hz.BBCI.mat',
'data/robot-hall/NiRiNBD8.ds_1-1_500Hz.BBCI.mat',
'data/robot-hall/NiRiNBD9.ds_1-1_500Hz.BBCI.mat',
'data/robot-hall/NiRiNBD10.ds_1-1_500Hz.BBCI.mat',
'data/robot-hall/NiRiNBD12_cursor_250Hz.BBCI.mat',
'data/robot-hall/NiRiNBD13_cursorS000R01_onlyFullRuns_250Hz.BBCI.mat',
'data/robot-hall/NiRiNBD14_cursor_250Hz.BBCI.mat',
'data/robot-hall/NiRiNBD15_cursor_250Hz.BBCI.mat'
]
sensor_names = [
'Fp1', 'Fpz', 'Fp2', 'AF7', 'AF3', 'AF4', 'AF8', 'F7', 'F5', 'F3',
'F1', 'Fz', 'F2', 'F4', 'F6', 'F8', 'FT7', 'FC5', 'FC3', 'FC1', 'FCz',
'FC2', 'FC4', 'FC6', 'FT8', 'M1', 'T7', 'C5', 'C3', 'C1', 'Cz', 'C2',
'C4', 'C6', 'T8', 'M2', 'TP7', 'CP5', 'CP3', 'CP1', 'CPz', 'CP2',
'CP4', 'CP6', 'TP8', 'P7', 'P5', 'P3', 'P1', 'Pz', 'P2', 'P4', 'P6',
'P8', 'PO7', 'PO5', 'PO3', 'POz', 'PO4', 'PO6', 'PO8', 'O1', 'Oz', 'O2'
]
name_to_start_codes = OrderedDict([('Right Hand', [1]), ('Feet', [2]),
('Rotation', [3]), ('Words', [4])])
name_to_stop_codes = OrderedDict([('Right Hand', [10]), ('Feet', [20]),
('Rotation', [30]), ('Words', [40])])
trial_ival = [500, 0]
min_break_length_ms = 6000
max_break_length_ms = 8000
break_ival = [1000, -500]
input_time_length = 700
filename_to_extra_args = {
'data/robot-hall/NiRiNBD12_cursor_250Hz.BBCI.mat':
dict(
name_to_start_codes=OrderedDict([('Right Hand', [1]),
('Feet', [2]), ('Rotation', [3]),
('Words', [4]), ('Rest', [5])]),
name_to_stop_codes=OrderedDict([('Right Hand', [10]),
('Feet', [20]), ('Rotation', [30]),
('Words', [40]), ('Rest', [50])]),
min_break_length_ms=3700,
max_break_length_ms=3900,
),
'data/robot-hall/NiRiNBD13_cursorS000R01_onlyFullRuns_250Hz.BBCI.mat':
dict(
name_to_start_codes=OrderedDict([('Right Hand', [1]),
('Feet', [2]), ('Rotation', [3]),
('Words', [4]), ('Rest', [5])]),
name_to_stop_codes=OrderedDict([('Right Hand', [10]),
('Feet', [20]), ('Rotation', [30]),
('Words', [40]), ('Rest', [50])]),
min_break_length_ms=3700,
max_break_length_ms=3900,
),
'data/robot-hall/NiRiNBD14_cursor_250Hz.BBCI.mat':
dict(
name_to_start_codes=OrderedDict([('Right Hand', [1]),
('Feet', [2]), ('Rotation', [3]),
('Words', [4]), ('Rest', [5])]),
name_to_stop_codes=OrderedDict([('Right Hand', [10]),
('Feet', [20]), ('Rotation', [30]),
('Words', [40]), ('Rest', [50])]),
min_break_length_ms=3700,
max_break_length_ms=3900,
),
'data/robot-hall/NiRiNBD15_cursor_250Hz.BBCI.mat':
dict(
name_to_start_codes=OrderedDict([('Right Hand', [1]),
('Feet', [2]), ('Rotation', [3]),
('Words', [4]), ('Rest', [5])]),
name_to_stop_codes=OrderedDict([('Right Hand', [10]),
('Feet', [20]), ('Rotation', [30]),
('Words', [40]), ('Rest', [50])]),
min_break_length_ms=3700,
max_break_length_ms=3900,
),
}
from braindecode.datautil.trial_segment import \
create_signal_target_with_breaks_from_mne
from copy import deepcopy
def load_data(filenames, sensor_names, name_to_start_codes,
name_to_stop_codes, trial_ival, break_ival,
min_break_length_ms, max_break_length_ms, input_time_length,
filename_to_extra_args):
all_sets = []
original_args = locals()
for filename in filenames:
kwargs = deepcopy(original_args)
if filename in filename_to_extra_args:
kwargs.update(filename_to_extra_args[filename])
log.info("Loading {:s}...".format(filename))
cnt = BBCIDataset(filename, load_sensor_names=sensor_names).load()
cnt = cnt.drop_channels(['STI 014'])
log.info("Resampling...")
cnt = resample_cnt(cnt, 100)
log.info("Standardizing...")
cnt = mne_apply(
lambda a: exponential_running_standardize(
a.T, init_block_size=50).T, cnt)
log.info("Transform to set...")
full_set = (create_signal_target_with_breaks_from_mne(
cnt,
kwargs['name_to_start_codes'],
kwargs['trial_ival'],
kwargs['name_to_stop_codes'],
kwargs['min_break_length_ms'],
kwargs['max_break_length_ms'],
kwargs['break_ival'],
prepad_trials_to_n_samples=kwargs['input_time_length'],
))
all_sets.append(full_set)
return all_sets
sensor_names = [
'Fp1', 'Fpz', 'Fp2', 'AF7', 'AF3', 'AF4', 'AF8', 'F7', 'F5', 'F3',
'F1', 'Fz', 'F2', 'F4', 'F6', 'F8', 'FT7', 'FC5', 'FC3', 'FC1', 'FCz',
'FC2', 'FC4', 'FC6', 'FT8', 'M1', 'T7', 'C5', 'C3', 'C1', 'Cz', 'C2',
'C4', 'C6', 'T8', 'M2', 'TP7', 'CP5', 'CP3', 'CP1', 'CPz', 'CP2',
'CP4', 'CP6', 'TP8', 'P7', 'P5', 'P3', 'P1', 'Pz', 'P2', 'P4', 'P6',
'P8', 'PO7', 'PO5', 'PO3', 'POz', 'PO4', 'PO6', 'PO8', 'O1', 'Oz', 'O2'
]
#sensor_names = ['C3', 'C4']
n_chans = len(sensor_names)
if not only_return_exp:
all_sets = load_data(filenames, sensor_names, name_to_start_codes,
name_to_stop_codes, trial_ival, break_ival,
min_break_length_ms, max_break_length_ms,
input_time_length, filename_to_extra_args)
from braindecode.datautil.signal_target import SignalAndTarget
from braindecode.datautil.splitters import concatenate_sets
train_set = concatenate_sets(all_sets[:6])
valid_set = all_sets[6]
test_set = all_sets[7]
else:
train_set = None
valid_set = None
test_set = None
set_random_seeds(seed=20171017, cuda=True)
n_classes = 5
# final_conv_length determines the size of the receptive field of the ConvNet
model = ShallowFBCSPNet(in_chans=n_chans,
n_classes=n_classes,
input_time_length=input_time_length,
final_conv_length=30).create_network()
to_dense_prediction_model(model)
model.cuda()
from torch import optim
import numpy as np
optimizer = optim.Adam(model.parameters())
from braindecode.torch_ext.util import np_to_var
# determine output size
test_input = np_to_var(
np.ones((2, n_chans, input_time_length, 1), dtype=np.float32))
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
print("{:d} predictions per input/trial".format(n_preds_per_input))
from braindecode.datautil.iterators import CropsFromTrialsIterator
iterator = CropsFromTrialsIterator(batch_size=32,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
from braindecode.experiments.experiment import Experiment
from braindecode.experiments.monitors import RuntimeMonitor, LossMonitor, \
CroppedTrialMisclassMonitor, MisclassMonitor
from braindecode.experiments.stopcriteria import MaxEpochs
from braindecode.torch_ext.losses import log_categorical_crossentropy
import torch.nn.functional as F
import torch as th
from braindecode.torch_ext.modules import Expression
loss_function = log_categorical_crossentropy
model_constraint = MaxNormDefaultConstraint()
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length),
RuntimeMonitor(),
]
stop_criterion = MaxEpochs(max_epochs)
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_sample_misclass',
run_after_early_stop=True,
batch_modifier=None,
cuda=True)
if not only_return_exp:
exp.run()
return exp
def run_exp(
data_folders,
n_recordings,
sensor_types,
n_chans,
max_recording_mins,
sec_to_cut,
duration_recording_mins,
test_recording_mins,
max_abs_val,
sampling_freq,
divisor,
test_on_eval,
n_folds,
i_test_fold,
shuffle,
model_name,
n_start_chans,
n_chan_factor,
input_time_length,
final_conv_length,
model_constraint,
init_lr,
batch_size,
max_epochs,
cuda,
):
import torch.backends.cudnn as cudnn
cudnn.benchmark = True
preproc_functions = []
preproc_functions.append(lambda data, fs: (
data[:, int(sec_to_cut * fs):-int(sec_to_cut * fs)], fs))
preproc_functions.append(lambda data, fs: (data[:, :int(
duration_recording_mins * 60 * fs)], fs))
if max_abs_val is not None:
preproc_functions.append(
lambda data, fs: (np.clip(data, -max_abs_val, max_abs_val), fs))
preproc_functions.append(lambda data, fs: (resampy.resample(
data, fs, sampling_freq, axis=1, filter='kaiser_fast'), sampling_freq))
if divisor is not None:
preproc_functions.append(lambda data, fs: (data / divisor, fs))
dataset = DiagnosisSet(n_recordings=n_recordings,
max_recording_mins=max_recording_mins,
preproc_functions=preproc_functions,
data_folders=data_folders,
train_or_eval='train',
sensor_types=sensor_types)
if test_on_eval:
if test_recording_mins is None:
test_recording_mins = duration_recording_mins
test_preproc_functions = copy(preproc_functions)
test_preproc_functions[1] = lambda data, fs: (data[:, :int(
test_recording_mins * 60 * fs)], fs)
test_dataset = DiagnosisSet(n_recordings=n_recordings,
max_recording_mins=None,
preproc_functions=test_preproc_functions,
data_folders=data_folders,
train_or_eval='eval',
sensor_types=sensor_types)
X, y = dataset.load()
max_shape = np.max([list(x.shape) for x in X], axis=0)
assert max_shape[1] == int(duration_recording_mins * sampling_freq * 60)
if test_on_eval:
test_X, test_y = test_dataset.load()
max_shape = np.max([list(x.shape) for x in test_X], axis=0)
assert max_shape[1] == int(test_recording_mins * sampling_freq * 60)
if not test_on_eval:
splitter = TrainValidTestSplitter(n_folds,
i_test_fold,
shuffle=shuffle)
train_set, valid_set, test_set = splitter.split(X, y)
else:
splitter = TrainValidSplitter(n_folds,
i_valid_fold=i_test_fold,
shuffle=shuffle)
train_set, valid_set = splitter.split(X, y)
test_set = SignalAndTarget(test_X, test_y)
del test_X, test_y
del X, y # shouldn't be necessary, but just to make sure
set_random_seeds(seed=20170629, cuda=cuda)
n_classes = 2
if model_name == 'shallow':
model = ShallowFBCSPNet(
in_chans=n_chans,
n_classes=n_classes,
n_filters_time=n_start_chans,
n_filters_spat=n_start_chans,
input_time_length=input_time_length,
final_conv_length=final_conv_length).create_network()
elif model_name == 'deep':
model = Deep4Net(n_chans,
n_classes,
n_filters_time=n_start_chans,
n_filters_spat=n_start_chans,
input_time_length=input_time_length,
n_filters_2=int(n_start_chans * n_chan_factor),
n_filters_3=int(n_start_chans * (n_chan_factor**2.0)),
n_filters_4=int(n_start_chans * (n_chan_factor**3.0)),
final_conv_length=final_conv_length,
stride_before_pool=True).create_network()
elif (model_name == 'deep_smac'):
if model_name == 'deep_smac':
do_batch_norm = False
else:
assert model_name == 'deep_smac_bnorm'
do_batch_norm = True
double_time_convs = False
drop_prob = 0.244445
filter_length_2 = 12
filter_length_3 = 14
filter_length_4 = 12
filter_time_length = 21
final_conv_length = 1
first_nonlin = elu
first_pool_mode = 'mean'
first_pool_nonlin = identity
later_nonlin = elu
later_pool_mode = 'mean'
later_pool_nonlin = identity
n_filters_factor = 1.679066
n_filters_start = 32
pool_time_length = 1
pool_time_stride = 2
split_first_layer = True
n_chan_factor = n_filters_factor
n_start_chans = n_filters_start
model = Deep4Net(n_chans,
n_classes,
n_filters_time=n_start_chans,
n_filters_spat=n_start_chans,
input_time_length=input_time_length,
n_filters_2=int(n_start_chans * n_chan_factor),
n_filters_3=int(n_start_chans * (n_chan_factor**2.0)),
n_filters_4=int(n_start_chans * (n_chan_factor**3.0)),
final_conv_length=final_conv_length,
batch_norm=do_batch_norm,
double_time_convs=double_time_convs,
drop_prob=drop_prob,
filter_length_2=filter_length_2,
filter_length_3=filter_length_3,
filter_length_4=filter_length_4,
filter_time_length=filter_time_length,
first_nonlin=first_nonlin,
first_pool_mode=first_pool_mode,
first_pool_nonlin=first_pool_nonlin,
later_nonlin=later_nonlin,
later_pool_mode=later_pool_mode,
later_pool_nonlin=later_pool_nonlin,
pool_time_length=pool_time_length,
pool_time_stride=pool_time_stride,
split_first_layer=split_first_layer,
stride_before_pool=True).create_network()
elif model_name == 'shallow_smac':
conv_nonlin = identity
do_batch_norm = True
drop_prob = 0.328794
filter_time_length = 56
final_conv_length = 22
n_filters_spat = 73
n_filters_time = 24
pool_mode = 'max'
pool_nonlin = identity
pool_time_length = 84
pool_time_stride = 3
split_first_layer = True
model = ShallowFBCSPNet(
in_chans=n_chans,
n_classes=n_classes,
n_filters_time=n_filters_time,
n_filters_spat=n_filters_spat,
input_time_length=input_time_length,
final_conv_length=final_conv_length,
conv_nonlin=conv_nonlin,
batch_norm=do_batch_norm,
drop_prob=drop_prob,
filter_time_length=filter_time_length,
pool_mode=pool_mode,
pool_nonlin=pool_nonlin,
pool_time_length=pool_time_length,
pool_time_stride=pool_time_stride,
split_first_layer=split_first_layer,
).create_network()
elif model_name == 'linear':
model = nn.Sequential()
model.add_module("conv_classifier",
nn.Conv2d(n_chans, n_classes, (600, 1)))
model.add_module('softmax', nn.LogSoftmax())
model.add_module('squeeze', Expression(lambda x: x.squeeze(3)))
else:
assert False, "unknown model name {:s}".format(model_name)
to_dense_prediction_model(model)
log.info("Model:\n{:s}".format(str(model)))
if cuda:
model.cuda()
# determine output size
test_input = np_to_var(
np.ones((2, n_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
log.info("In shape: {:s}".format(str(test_input.cpu().data.numpy().shape)))
out = model(test_input)
log.info("Out shape: {:s}".format(str(out.cpu().data.numpy().shape)))
n_preds_per_input = out.cpu().data.numpy().shape[2]
log.info("{:d} predictions per input/trial".format(n_preds_per_input))
iterator = CropsFromTrialsIterator(batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
optimizer = optim.Adam(model.parameters(), lr=init_lr)
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2, keepdim=False), targets)
if model_constraint is not None:
assert model_constraint == 'defaultnorm'
model_constraint = MaxNormDefaultConstraint()
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedDiagnosisMonitor(input_time_length, n_preds_per_input),
RuntimeMonitor(),
]
stop_criterion = MaxEpochs(max_epochs)
batch_modifier = None
run_after_early_stop = True
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=run_after_early_stop,
batch_modifier=batch_modifier,
cuda=cuda)
exp.run()
return exp
samplingRate))
iterator = CropsFromTrialsIterator(
batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
# %% Loss function takes predictions as they come out of the network and the targets and returns a loss
loss_function = F.mse_loss
# Could be used to apply some constraint on the models, then should be object with apply method that accepts a module
model_constraint = None
# %% Monitors log the training progress
monitors = [
LossMonitor(),
CorrelationMonitor1d(input_time_length),
RuntimeMonitor(),
]
# %% Stop criterion determines when the first stop happens
stop_criterion = MaxEpochs(maxTrainEpochs)
# %% re-initialize model
model.load_state_dict(deepcopy(start_param_values))
if adam:
optimizer = optim.Adam(model.parameters())
else:
weight_decay = np.float32(2.0 * 0.001)
init_lr = np.float32((1 / 32.0) * 0.01)
def build_exp(model_name, cuda, data, batch_size, max_epochs, max_increase_epochs):
log.info("==============================")
log.info("Loading Data...")
log.info("==============================")
train_set = data.train_set
valid_set = data.validation_set
test_set = data.test_set
log.info("==============================")
log.info("Setting Up Model...")
log.info("==============================")
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 4
n_chans = int(train_set.X.shape[1])
input_time_length = train_set.X.shape[2]
if model_name == "shallow":
model = NewShallowNet(
n_chans, n_classes, input_time_length, final_conv_length="auto"
)
# model = ShallowFBCSPNet(
# n_chans,
# n_classes,
# input_time_length=input_time_length,
# final_conv_length="auto",
# ).create_network()
elif model_name == "deep":
model = NewDeep4Net(n_chans, n_classes, input_time_length, "auto")
# model = Deep4Net(
# n_chans,
# n_classes,
# input_time_length=input_time_length,
# final_conv_length="auto",
# ).create_network()
elif model_name == "eegnet":
# model = EEGNet(n_chans, n_classes,
# input_time_length=input_time_length)
# model = EEGNetv4(n_chans, n_classes,
# input_time_length=input_time_length).create_network()
model = NewEEGNet(n_chans, n_classes, input_time_length=input_time_length)
if cuda:
model.cuda()
log.info("==============================")
log.info("Logging Model Architecture:")
log.info("==============================")
log.info("Model: \n{:s}".format(str(model)))
log.info("==============================")
log.info("Building Experiment:")
log.info("==============================")
optimizer = optim.Adam(model.parameters())
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or(
[MaxEpochs(max_epochs), NoDecrease("valid_misclass", max_increase_epochs)]
)
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
exp = Experiment(
model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=F.nll_loss,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column="valid_misclass",
run_after_early_stop=True,
cuda=cuda,
)
return exp
logging.basicConfig(format='%(asctime)s %(levelname)s : %(message)s',
level=logging.INFO, stream=sys.stdout)
WINDOW_LEN = 200
OVERLAP = 150
windows = windows_index(500,WINDOW_LEN,OVERLAP,250)
hyp_params = dict(window=windows[:2],
activation=["leaky_relu"],
structure= ["shallow"])
parameters = dict(best_loss = 100.0,
batch_size = 32,
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()],
model_constraint = MaxNormDefaultConstraint(),
max_increase_epochs = 0,
cuda = True,
epochs=1,
learning_rate_scheduler=StepLR,
lr_step=20, lr_gamma=0.9)
EEGSubNet_params = dict(n_filters_time=40, filter_time_length=5, n_filters_spat=40, n_filters_2=20, filter_length_2=20,
pool_time_length_1=5, pool_time_stride_1=2, pool_length_2=5, pool_stride_2=3, final_conv_length='auto',
conv_nonlin=th.nn.functional.leaky_relu, pool_mode='mean', pool_nonlin=safe_log,
split_first_layer=True, batch_norm=True, batch_norm_alpha=0.2,
drop_prob=0.1)
def test_experiment_class():
import mne
from mne.io import concatenate_raws
# 5,6,7,10,13,14 are codes for executed and imagined hands/feet
subject_id = 1
event_codes = [5, 6, 9, 10, 13, 14]
# This will download the files if you don't have them yet,
# and then return the paths to the files.
physionet_paths = mne.datasets.eegbci.load_data(subject_id, event_codes)
# Load each of the files
parts = [
mne.io.read_raw_edf(path,
preload=True,
stim_channel='auto',
verbose='WARNING') for path in physionet_paths
]
# Concatenate them
raw = concatenate_raws(parts)
# Find the events in this dataset
events = mne.find_events(raw, shortest_event=0, stim_channel='STI 014')
# Use only EEG channels
eeg_channel_inds = mne.pick_types(raw.info,
meg=False,
eeg=True,
stim=False,
eog=False,
exclude='bads')
# Extract trials, only using EEG channels
epoched = mne.Epochs(raw,
events,
dict(hands=2, feet=3),
tmin=1,
tmax=4.1,
proj=False,
picks=eeg_channel_inds,
baseline=None,
preload=True)
import numpy as np
from braindecode.datautil.signal_target import SignalAndTarget
from braindecode.datautil.splitters import split_into_two_sets
# Convert data from volt to millivolt
# Pytorch expects float32 for input and int64 for labels.
X = (epoched.get_data() * 1e6).astype(np.float32)
y = (epoched.events[:, 2] - 2).astype(np.int64) # 2,3 -> 0,1
train_set = SignalAndTarget(X[:60], y=y[:60])
test_set = SignalAndTarget(X[60:], y=y[60:])
train_set, valid_set = split_into_two_sets(train_set,
first_set_fraction=0.8)
from braindecode.models.shallow_fbcsp import ShallowFBCSPNet
from torch import nn
from braindecode.torch_ext.util import set_random_seeds
from braindecode.models.util import to_dense_prediction_model
# Set if you want to use GPU
# You can also use torch.cuda.is_available() to determine if cuda is available on your machine.
cuda = False
set_random_seeds(seed=20170629, cuda=cuda)
# This will determine how many crops are processed in parallel
input_time_length = 450
n_classes = 2
in_chans = train_set.X.shape[1]
# final_conv_length determines the size of the receptive field of the ConvNet
model = ShallowFBCSPNet(in_chans=in_chans,
n_classes=n_classes,
input_time_length=input_time_length,
final_conv_length=12).create_network()
to_dense_prediction_model(model)
if cuda:
model.cuda()
from torch import optim
optimizer = optim.Adam(model.parameters())
from braindecode.torch_ext.util import np_to_var
# determine output size
test_input = np_to_var(
np.ones((2, in_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
print("{:d} predictions per input/trial".format(n_preds_per_input))
from braindecode.experiments.experiment import Experiment
from braindecode.datautil.iterators import CropsFromTrialsIterator
from braindecode.experiments.monitors import RuntimeMonitor, LossMonitor, \
CroppedTrialMisclassMonitor, MisclassMonitor
from braindecode.experiments.stopcriteria import MaxEpochs
import torch.nn.functional as F
import torch as th
from braindecode.torch_ext.modules import Expression
# Iterator is used to iterate over datasets both for training
# and evaluation
iterator = CropsFromTrialsIterator(batch_size=32,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
# Loss function takes predictions as they come out of the network and the targets
# and returns a loss
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2, keepdim=False), targets)
# Could be used to apply some constraint on the models, then should be object
# with apply method that accepts a module
model_constraint = None
# Monitors log the training progress
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length),
RuntimeMonitor(),
]
# Stop criterion determines when the first stop happens
stop_criterion = MaxEpochs(4)
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
batch_modifier=None,
cuda=cuda)
# need to setup python logging before to be able to see anything
import logging
import sys
logging.basicConfig(format='%(asctime)s %(levelname)s : %(message)s',
level=logging.DEBUG,
stream=sys.stdout)
exp.run()
import pandas as pd
from io import StringIO
compare_df = pd.read_csv(
StringIO(
u'train_loss,valid_loss,test_loss,train_sample_misclass,valid_sample_misclass,'
'test_sample_misclass,train_misclass,valid_misclass,test_misclass\n'
'0,0.8692976435025532,0.7483791708946228,0.6975634694099426,'
'0.5389371657754011,0.47103386809269165,0.4425133689839572,'
'0.6041666666666667,0.5,0.4\n1,2.3362590074539185,'
'2.317707061767578,2.1407743096351624,0.4827874331550802,'
'0.5,0.4666666666666667,0.5,0.5,0.4666666666666667\n'
'2,0.5981490015983582,0.785034716129303,0.7005959153175354,'
'0.3391822638146168,0.47994652406417115,0.41996434937611404,'
'0.22916666666666663,0.41666666666666663,0.43333333333333335\n'
'3,0.6355261653661728,0.785034716129303,'
'0.7005959153175354,0.3673351158645276,0.47994652406417115,'
'0.41996434937611404,0.2666666666666667,0.41666666666666663,'
'0.43333333333333335\n4,0.625280424952507,'
'0.802731990814209,0.7048938572406769,0.3367201426024955,'
'0.43137254901960786,0.4229946524064171,0.3666666666666667,'
'0.5833333333333333,0.33333333333333337\n'))
for col in compare_df:
np.testing.assert_allclose(np.array(compare_df[col]),
exp.epochs_df[col],
rtol=1e-4,
atol=1e-5)
def test_experiment_class():
import mne
from mne.io import concatenate_raws
# 5,6,7,10,13,14 are codes for executed and imagined hands/feet
subject_id = 1
event_codes = [5, 6, 9, 10, 13, 14]
# This will download the files if you don't have them yet,
# and then return the paths to the files.
physionet_paths = mne.datasets.eegbci.load_data(subject_id, event_codes)
# Load each of the files
parts = [mne.io.read_raw_edf(path, preload=True, stim_channel='auto',
verbose='WARNING')
for path in physionet_paths]
# Concatenate them
raw = concatenate_raws(parts)
# Find the events in this dataset
events, _ = mne.events_from_annotations(raw)
# Use only EEG channels
eeg_channel_inds = mne.pick_types(raw.info, meg=False, eeg=True, stim=False,
eog=False,
exclude='bads')
# Extract trials, only using EEG channels
epoched = mne.Epochs(raw, events, dict(hands=2, feet=3), tmin=1, tmax=4.1,
proj=False, picks=eeg_channel_inds,
baseline=None, preload=True)
import numpy as np
from braindecode.datautil.signal_target import SignalAndTarget
from braindecode.datautil.splitters import split_into_two_sets
# Convert data from volt to millivolt
# Pytorch expects float32 for input and int64 for labels.
X = (epoched.get_data() * 1e6).astype(np.float32)
y = (epoched.events[:, 2] - 2).astype(np.int64) # 2,3 -> 0,1
train_set = SignalAndTarget(X[:60], y=y[:60])
test_set = SignalAndTarget(X[60:], y=y[60:])
train_set, valid_set = split_into_two_sets(train_set,
first_set_fraction=0.8)
from braindecode.models.shallow_fbcsp import ShallowFBCSPNet
from torch import nn
from braindecode.torch_ext.util import set_random_seeds
from braindecode.models.util import to_dense_prediction_model
# Set if you want to use GPU
# You can also use torch.cuda.is_available() to determine if cuda is available on your machine.
cuda = False
set_random_seeds(seed=20170629, cuda=cuda)
# This will determine how many crops are processed in parallel
input_time_length = 450
n_classes = 2
in_chans = train_set.X.shape[1]
# final_conv_length determines the size of the receptive field of the ConvNet
model = ShallowFBCSPNet(in_chans=in_chans, n_classes=n_classes,
input_time_length=input_time_length,
final_conv_length=12).create_network()
to_dense_prediction_model(model)
if cuda:
model.cuda()
from torch import optim
optimizer = optim.Adam(model.parameters())
from braindecode.torch_ext.util import np_to_var
# determine output size
test_input = np_to_var(
np.ones((2, in_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
print("{:d} predictions per input/trial".format(n_preds_per_input))
from braindecode.experiments.experiment import Experiment
from braindecode.datautil.iterators import CropsFromTrialsIterator
from braindecode.experiments.monitors import RuntimeMonitor, LossMonitor, \
CroppedTrialMisclassMonitor, MisclassMonitor
from braindecode.experiments.stopcriteria import MaxEpochs
import torch.nn.functional as F
import torch as th
from braindecode.torch_ext.modules import Expression
# Iterator is used to iterate over datasets both for training
# and evaluation
iterator = CropsFromTrialsIterator(batch_size=32,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
# Loss function takes predictions as they come out of the network and the targets
# and returns a loss
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2, keepdim=False), targets)
# Could be used to apply some constraint on the models, then should be object
# with apply method that accepts a module
model_constraint = None
# Monitors log the training progress
monitors = [LossMonitor(), MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length),
RuntimeMonitor(), ]
# Stop criterion determines when the first stop happens
stop_criterion = MaxEpochs(4)
exp = Experiment(model, train_set, valid_set, test_set, iterator,
loss_function, optimizer, model_constraint,
monitors, stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True, batch_modifier=None, cuda=cuda)
# need to setup python logging before to be able to see anything
import logging
import sys
logging.basicConfig(format='%(asctime)s %(levelname)s : %(message)s',
level=logging.DEBUG, stream=sys.stdout)
exp.run()
import pandas as pd
from io import StringIO
compare_df = pd.read_csv(StringIO(
'train_loss,valid_loss,test_loss,train_sample_misclass,valid_sample_misclass,'
'test_sample_misclass,train_misclass,valid_misclass,test_misclass\n'
'14.167170524597168,13.910758018493652,15.945781707763672,0.5,0.5,'
'0.5333333333333333,0.5,0.5,0.5333333333333333\n'
'1.1735659837722778,1.4342904090881348,1.8664429187774658,0.4629567736185384,'
'0.5120320855614973,0.5336007130124778,0.5,0.5,0.5333333333333333\n'
'1.3168460130691528,1.60431969165802,1.9181344509124756,0.49298128342245995,'
'0.5109180035650625,0.531729055258467,0.5,0.5,0.5333333333333333\n'
'0.8465543389320374,1.280307412147522,1.439755916595459,0.4413435828877005,'
'0.5461229946524064,0.5283422459893048,0.47916666666666663,0.5,'
'0.5333333333333333\n0.6977059841156006,1.1762590408325195,1.2779350280761719,'
'0.40290775401069523,0.588903743315508,0.5307486631016043,0.5,0.5,0.5\n'
'0.7934166193008423,1.1762590408325195,1.2779350280761719,0.4401069518716577,'
'0.588903743315508,0.5307486631016043,0.5,0.5,0.5\n0.5982189178466797,'
'0.8581563830375671,0.9598925113677979,0.32032085561497325,0.47660427807486627,'
'0.4672905525846702,0.31666666666666665,0.5,0.4666666666666667\n0.5044312477111816,'
'0.7133197784423828,0.8164243102073669,0.2591354723707665,0.45699643493761144,'
'0.4393048128342246,0.16666666666666663,0.41666666666666663,0.43333333333333335\n'
'0.4815250039100647,0.6736412644386292,0.8016976714134216,0.23413547237076648,'
'0.39505347593582885,0.42932263814616756,0.15000000000000002,0.41666666666666663,0.5\n'))
for col in compare_df:
np.testing.assert_allclose(np.array(compare_df[col]),
exp.epochs_df[col],
rtol=1e-3, atol=1e-4)
def run_experiment(train_set, valid_set, test_set, model_name, optimizer_name,
init_lr, scheduler_name, use_norm_constraint, weight_decay,
schedule_weight_decay, restarts, max_epochs,
max_increase_epochs, np_th_seed):
set_random_seeds(np_th_seed, cuda=True)
#torch.backends.cudnn.benchmark = True# sometimes crashes?
if valid_set is not None:
assert max_increase_epochs is not None
assert (max_epochs is None) != (restarts is None)
if max_epochs is None:
max_epochs = np.sum(restarts)
n_classes = int(np.max(train_set.y) + 1)
n_chans = int(train_set.X.shape[1])
input_time_length = 1000
if model_name == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=2).create_network()
elif model_name == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=30).create_network()
elif model_name in [
'resnet-he-uniform', 'resnet-he-normal', 'resnet-xavier-normal',
'resnet-xavier-uniform'
]:
init_name = model_name.lstrip('resnet-')
from torch.nn import init
init_fn = {
'he-uniform': lambda w: init.kaiming_uniform(w, a=0),
'he-normal': lambda w: init.kaiming_normal(w, a=0),
'xavier-uniform': lambda w: init.xavier_uniform(w, gain=1),
'xavier-normal': lambda w: init.xavier_normal(w, gain=1)
}[init_name]
model = EEGResNet(in_chans=n_chans,
n_classes=n_classes,
input_time_length=input_time_length,
final_pool_length=10,
n_first_filters=48,
conv_weight_init_fn=init_fn).create_network()
else:
raise ValueError("Unknown model name {:s}".format(model_name))
if 'resnet' not in model_name:
to_dense_prediction_model(model)
model.cuda()
model.eval()
out = model(np_to_var(train_set.X[:1, :, :input_time_length, None]).cuda())
n_preds_per_input = out.cpu().data.numpy().shape[2]
if optimizer_name == 'adam':
optimizer = optim.Adam(model.parameters(),
weight_decay=weight_decay,
lr=init_lr)
elif optimizer_name == 'adamw':
optimizer = AdamW(model.parameters(),
weight_decay=weight_decay,
lr=init_lr)
iterator = CropsFromTrialsIterator(batch_size=60,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input,
seed=np_th_seed)
if scheduler_name is not None:
assert schedule_weight_decay == (optimizer_name == 'adamw')
if scheduler_name == 'cosine':
n_updates_per_epoch = sum(
[1 for _ in iterator.get_batches(train_set, shuffle=True)])
if restarts is None:
n_updates_per_period = n_updates_per_epoch * max_epochs
else:
n_updates_per_period = np.array(restarts) * n_updates_per_epoch
scheduler = CosineAnnealing(n_updates_per_period)
optimizer = ScheduledOptimizer(
scheduler,
optimizer,
schedule_weight_decay=schedule_weight_decay)
elif scheduler_name == 'cut_cosine':
# TODO: integrate with if clause before, now just separate
# to avoid messing with code
n_updates_per_epoch = sum(
[1 for _ in iterator.get_batches(train_set, shuffle=True)])
if restarts is None:
n_updates_per_period = n_updates_per_epoch * max_epochs
else:
n_updates_per_period = np.array(restarts) * n_updates_per_epoch
scheduler = CutCosineAnnealing(n_updates_per_period)
optimizer = ScheduledOptimizer(
scheduler,
optimizer,
schedule_weight_decay=schedule_weight_decay)
else:
raise ValueError("Unknown scheduler")
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length=input_time_length),
RuntimeMonitor()
]
if use_norm_constraint:
model_constraint = MaxNormDefaultConstraint()
else:
model_constraint = None
# change here this cell
loss_function = lambda preds, targets: F.nll_loss(th.mean(preds, dim=2),
targets)
if valid_set is not None:
run_after_early_stop = True
do_early_stop = True
remember_best_column = 'valid_misclass'
stop_criterion = Or([
MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)
])
else:
run_after_early_stop = False
do_early_stop = False
remember_best_column = None
stop_criterion = MaxEpochs(max_epochs)
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column=remember_best_column,
run_after_early_stop=run_after_early_stop,
cuda=True,
do_early_stop=do_early_stop)
exp.run()
return exp
from utils import load_subject, format_data, timer, windows, get_model_loss_and_acc
from braindecode.datautil.signal_target import SignalAndTarget
from sklearn.model_selection import StratifiedKFold
from braindecode.experiments.stopcriteria import MaxEpochs, NoDecrease, Or
from braindecode.experiments.monitors import LossMonitor, MisclassMonitor, RuntimeMonitor
from braindecode.torch_ext.constraints import MaxNormDefaultConstraint
import numpy as np
import pandas as pd
import warnings
warnings.filterwarnings('ignore', category=FutureWarning)
hyp_params = dict(activation=["elu", "relu"], lr=[0.001], epochs=[1, 2])
parameters = dict(
best_loss=100.0,
batch_size=64,
monitors=[LossMonitor(),
MisclassMonitor(),
RuntimeMonitor()],
model_constraint=MaxNormDefaultConstraint(),
max_increase_epochs=1,
cuda=False)
@timer
def trainNestedCV(direct, subject, session, filename, hyp_params, parameters):
subj = load_subject(direct, subject, 1, filename)["subject"]
#
# data = subj.data3D.astype(np.float32) # convert data to 3d for deep learning
# labels = subj.labels.astype(np.int64)
# labels[:] = [x - 1 for x in labels]
def fit(self,
train_X,
train_y,
epochs,
batch_size,
input_time_length=None,
validation_data=None,
model_constraint=None,
remember_best_column=None,
scheduler=None):
if not self.compiled:
raise ValueError(
"Compile the model first by calling model.compile(loss, optimizer, metrics)"
)
if self.cropped and input_time_length is None:
raise ValueError(
"In cropped mode, need to specify input_time_length,"
"which is the number of timesteps that will be pushed through"
"the network in a single pass.")
if self.cropped:
test_input = np_to_var(train_X[0:1], dtype=np.float32)
while len(test_input.size()) < 4:
test_input = test_input.unsqueeze(-1)
if self.cuda:
test_input = test_input.cuda()
out = self.network(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
iterator = CropsFromTrialsIterator(
batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input,
seed=self.seed_rng.randint(0, 4294967295))
else:
iterator = BalancedBatchSizeIterator(batch_size=batch_size,
seed=self.seed_rng.randint(
0, 4294967295))
stop_criterion = MaxEpochs(
epochs - 1
) # -1 since we dont print 0 epoch, which matters for this stop criterion
train_set = SignalAndTarget(train_X, train_y)
optimizer = self.optimizer
if scheduler is not None:
assert scheduler == 'cosine'
n_updates_per_epoch = sum(
[1 for _ in iterator.get_batches(train_set, shuffle=True)])
n_updates_per_period = n_updates_per_epoch * epochs
if scheduler == 'cosine':
scheduler = CosineAnnealing(n_updates_per_period)
schedule_weight_decay = False
if optimizer.__class__.__name__ == 'AdamW':
schedule_weight_decay = True
optimizer = ScheduledOptimizer(
scheduler,
self.optimizer,
schedule_weight_decay=schedule_weight_decay)
loss_function = self.loss
if self.cropped:
loss_function = lambda outputs, targets:\
self.loss(th.mean(outputs, dim=2), targets)
if validation_data is not None:
valid_set = SignalAndTarget(validation_data[0], validation_data[1])
else:
valid_set = None
test_set = None
if self.cropped:
monitor_dict = {
'acc': lambda: CroppedTrialMisclassMonitor(input_time_length)
}
else:
monitor_dict = {'acc': MisclassMonitor}
self.monitors = [LossMonitor()]
extra_monitors = [monitor_dict[m]() for m in self.metrics]
self.monitors += extra_monitors
self.monitors += [RuntimeMonitor()]
exp = Experiment(self.network,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=self.monitors,
stop_criterion=stop_criterion,
remember_best_column=remember_best_column,
run_after_early_stop=False,
cuda=self.cuda,
print_0_epoch=False,
do_early_stop=(remember_best_column is not None))
exp.run()
self.epochs_df = exp.epochs_df
return exp
def fit(
self,
train_X,
train_y,
epochs,
batch_size,
input_time_length=None,
validation_data=None,
model_constraint=None,
remember_best_column=None,
scheduler=None,
log_0_epoch=True,
):
"""
Fit the model using the given training data.
Will set `epochs_df` variable with a pandas dataframe to the history
of the training process.
Parameters
----------
train_X: ndarray
Training input data
train_y: 1darray
Training labels
epochs: int
Number of epochs to train
batch_size: int
input_time_length: int, optional
Super crop size, what temporal size is pushed forward through
the network, see cropped decoding tuturial.
validation_data: (ndarray, 1darray), optional
X and y for validation set if wanted
model_constraint: object, optional
You can supply :class:`.MaxNormDefaultConstraint` if wanted.
remember_best_column: string, optional
In case you want to do an early stopping/reset parameters to some
"best" epoch, define here the monitored value whose minimum
determines the best epoch.
scheduler: 'cosine' or None, optional
Whether to use cosine annealing (:class:`.CosineAnnealing`).
log_0_epoch: bool
Whether to compute the metrics once before training as well.
Returns
-------
exp:
Underlying braindecode :class:`.Experiment`
"""
if (not hasattr(self, "compiled")) or (not self.compiled):
raise ValueError(
"Compile the model first by calling model.compile(loss, optimizer, metrics)"
)
if self.cropped and input_time_length is None:
raise ValueError(
"In cropped mode, need to specify input_time_length,"
"which is the number of timesteps that will be pushed through"
"the network in a single pass.")
train_X = _ensure_float32(train_X)
if self.cropped:
self.network.eval()
test_input = np_to_var(
np.ones(
(1, train_X[0].shape[0], input_time_length) +
train_X[0].shape[2:],
dtype=np.float32,
))
while len(test_input.size()) < 4:
test_input = test_input.unsqueeze(-1)
if self.is_cuda:
test_input = test_input.cuda()
out = self.network(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
self.iterator = CropsFromTrialsIterator(
batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input,
seed=self.seed_rng.randint(0,
np.iinfo(np.int32).max - 1),
)
else:
self.iterator = BalancedBatchSizeIterator(
batch_size=batch_size,
seed=self.seed_rng.randint(0,
np.iinfo(np.int32).max - 1),
)
if log_0_epoch:
stop_criterion = MaxEpochs(epochs)
else:
stop_criterion = MaxEpochs(epochs - 1)
train_set = SignalAndTarget(train_X, train_y)
optimizer = self.optimizer
if scheduler is not None:
assert (scheduler == "cosine"
), "Supply either 'cosine' or None as scheduler."
n_updates_per_epoch = sum([
1 for _ in self.iterator.get_batches(train_set, shuffle=True)
])
n_updates_per_period = n_updates_per_epoch * epochs
if scheduler == "cosine":
scheduler = CosineAnnealing(n_updates_per_period)
schedule_weight_decay = False
if optimizer.__class__.__name__ == "AdamW":
schedule_weight_decay = True
optimizer = ScheduledOptimizer(
scheduler,
self.optimizer,
schedule_weight_decay=schedule_weight_decay,
)
loss_function = self.loss
if self.cropped:
loss_function = lambda outputs, targets: self.loss(
th.mean(outputs, dim=2), targets)
if validation_data is not None:
valid_X = _ensure_float32(validation_data[0])
valid_y = validation_data[1]
valid_set = SignalAndTarget(valid_X, valid_y)
else:
valid_set = None
test_set = None
self.monitors = [LossMonitor()]
if self.cropped:
self.monitors.append(
CroppedTrialMisclassMonitor(input_time_length))
else:
self.monitors.append(MisclassMonitor())
if self.extra_monitors is not None:
self.monitors.extend(self.extra_monitors)
self.monitors.append(RuntimeMonitor())
exp = Experiment(
self.network,
train_set,
valid_set,
test_set,
iterator=self.iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=self.monitors,
stop_criterion=stop_criterion,
remember_best_column=remember_best_column,
run_after_early_stop=False,
cuda=self.is_cuda,
log_0_epoch=log_0_epoch,
do_early_stop=(remember_best_column is not None),
)
exp.run()
self.epochs_df = exp.epochs_df
return exp
def get_monitors(self, input_time_length):
return [LossMonitor(), PearsonMonitor(), RuntimeMonitor()]
def run_exp(epoches, batch_size, subject_num, model_type, cuda, single_subject,
single_subject_num):
# ival = [-500, 4000]
max_increase_epochs = 160
# Preprocessing
X, y = loadSubjects(subject_num, single_subject, single_subject_num)
X = X.astype(np.float32)
y = y.astype(np.int64)
X, y = shuffle(X, y)
trial_length = X.shape[2]
print("trial_length " + str(trial_length))
print("trying to run with {} sec trials ".format((trial_length - 1) / 256))
print("y")
print(y)
trainingSampleSize = int(len(X) * 0.6)
valudationSampleSize = int(len(X) * 0.2)
testSampleSize = int(len(X) * 0.2)
print("INFO : Training sample size: {}".format(trainingSampleSize))
print("INFO : Validation sample size: {}".format(valudationSampleSize))
print("INFO : Test sample size: {}".format(testSampleSize))
train_set = SignalAndTarget(X[:trainingSampleSize],
y=y[:trainingSampleSize])
valid_set = SignalAndTarget(
X[trainingSampleSize:(trainingSampleSize + valudationSampleSize)],
y=y[trainingSampleSize:(trainingSampleSize + valudationSampleSize)])
test_set = SignalAndTarget(X[(trainingSampleSize + valudationSampleSize):],
y=y[(trainingSampleSize +
valudationSampleSize):])
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 3
n_chans = int(train_set.X.shape[1])
input_time_length = train_set.X.shape[2]
if model_type == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
elif model_type == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
elif model_type == 'eegnet':
model = EEGNetv4(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
optimizer = optim.Adam(model.parameters())
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or([
MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)
])
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=F.nll_loss,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
cuda=cuda)
exp.run()
# th.save(model, "models\{}-cropped-singleSubjectNum{}-{}sec-{}epoches-torch_model".format(model_type, single_subject_num, ((trial_length - 1) / 256), epoches))
return exp
def run_exp(data_folder, subject_id, low_cut_hz, model, cuda):
ival = [-500, 4000]
max_epochs = 1600
max_increase_epochs = 160
batch_size = 60
high_cut_hz = 38
factor_new = 1e-3
init_block_size = 1000
valid_set_fraction = 0.2
train_filename = "A{:02d}T.gdf".format(subject_id)
test_filename = "A{:02d}E.gdf".format(subject_id)
train_filepath = os.path.join(data_folder, train_filename)
test_filepath = os.path.join(data_folder, test_filename)
train_label_filepath = train_filepath.replace(".gdf", ".mat")
test_label_filepath = test_filepath.replace(".gdf", ".mat")
train_loader = BCICompetition4Set2A(
train_filepath, labels_filename=train_label_filepath
)
test_loader = BCICompetition4Set2A(
test_filepath, labels_filename=test_label_filepath
)
train_cnt = train_loader.load()
test_cnt = test_loader.load()
# Preprocessing
train_cnt = train_cnt.drop_channels(
["EOG-left", "EOG-central", "EOG-right"]
)
assert len(train_cnt.ch_names) == 22
# lets convert to millvolt for numerical stability of next operations
train_cnt = mne_apply(lambda a: a * 1e6, train_cnt)
train_cnt = mne_apply(
lambda a: bandpass_cnt(
a,
low_cut_hz,
high_cut_hz,
train_cnt.info["sfreq"],
filt_order=3,
axis=1,
),
train_cnt,
)
train_cnt = mne_apply(
lambda a: exponential_running_standardize(
a.T,
factor_new=factor_new,
init_block_size=init_block_size,
eps=1e-4,
).T,
train_cnt,
)
test_cnt = test_cnt.drop_channels(["EOG-left", "EOG-central", "EOG-right"])
assert len(test_cnt.ch_names) == 22
test_cnt = mne_apply(lambda a: a * 1e6, test_cnt)
test_cnt = mne_apply(
lambda a: bandpass_cnt(
a,
low_cut_hz,
high_cut_hz,
test_cnt.info["sfreq"],
filt_order=3,
axis=1,
),
test_cnt,
)
test_cnt = mne_apply(
lambda a: exponential_running_standardize(
a.T,
factor_new=factor_new,
init_block_size=init_block_size,
eps=1e-4,
).T,
test_cnt,
)
marker_def = OrderedDict(
[
("Left Hand", [1]),
("Right Hand", [2]),
("Foot", [3]),
("Tongue", [4]),
]
)
train_set = create_signal_target_from_raw_mne(train_cnt, marker_def, ival)
test_set = create_signal_target_from_raw_mne(test_cnt, marker_def, ival)
train_set, valid_set = split_into_two_sets(
train_set, first_set_fraction=1 - valid_set_fraction
)
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 4
n_chans = int(train_set.X.shape[1])
input_time_length = train_set.X.shape[2]
if model == "shallow":
model = ShallowFBCSPNet(
n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length="auto",
).create_network()
elif model == "deep":
model = Deep4Net(
n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length="auto",
).create_network()
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
optimizer = optim.Adam(model.parameters())
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or(
[
MaxEpochs(max_epochs),
NoDecrease("valid_misclass", max_increase_epochs),
]
)
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
exp = Experiment(
model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=F.nll_loss,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column="valid_misclass",
run_after_early_stop=True,
cuda=cuda,
)
exp.run()
return exp
def run_exp(max_recording_mins, n_recordings, sec_to_cut,
duration_recording_mins, max_abs_val, max_min_threshold,
max_min_expected, shrink_val, max_min_remove, batch_set_zero_val,
batch_set_zero_test, sampling_freq, low_cut_hz, high_cut_hz,
exp_demean, exp_standardize, moving_demean, moving_standardize,
channel_demean, channel_standardize, divisor, n_folds, i_test_fold,
input_time_length, final_conv_length, pool_stride, n_blocks_to_add,
sigmoid, model_constraint, batch_size, max_epochs,
only_return_exp):
cuda = True
preproc_functions = []
preproc_functions.append(lambda data, fs: (
data[:, int(sec_to_cut * fs):-int(sec_to_cut * fs)], fs))
preproc_functions.append(lambda data, fs: (data[:, :int(
duration_recording_mins * 60 * fs)], fs))
if max_abs_val is not None:
preproc_functions.append(
lambda data, fs: (np.clip(data, -max_abs_val, max_abs_val), fs))
if max_min_threshold is not None:
preproc_functions.append(lambda data, fs: (clean_jumps(
data, 200, max_min_threshold, max_min_expected, cuda), fs))
if max_min_remove is not None:
window_len = 200
preproc_functions.append(lambda data, fs: (set_jumps_to_zero(
data,
window_len=window_len,
threshold=max_min_remove,
cuda=cuda,
clip_min_max_to_zero=True), fs))
if shrink_val is not None:
preproc_functions.append(lambda data, fs: (shrink_spikes(
data,
shrink_val,
1,
9,
), fs))
preproc_functions.append(lambda data, fs: (resampy.resample(
data, fs, sampling_freq, axis=1, filter='kaiser_fast'), sampling_freq))
preproc_functions.append(lambda data, fs: (bandpass_cnt(
data, low_cut_hz, high_cut_hz, fs, filt_order=4, axis=1), fs))
if exp_demean:
preproc_functions.append(lambda data, fs: (exponential_running_demean(
data.T, factor_new=0.001, init_block_size=100).T, fs))
if exp_standardize:
preproc_functions.append(
lambda data, fs: (exponential_running_standardize(
data.T, factor_new=0.001, init_block_size=100).T, fs))
if moving_demean:
preproc_functions.append(lambda data, fs: (padded_moving_demean(
data, axis=1, n_window=201), fs))
if moving_standardize:
preproc_functions.append(lambda data, fs: (padded_moving_standardize(
data, axis=1, n_window=201), fs))
if channel_demean:
preproc_functions.append(lambda data, fs: (demean(data, axis=1), fs))
if channel_standardize:
preproc_functions.append(lambda data, fs:
(standardize(data, axis=1), fs))
if divisor is not None:
preproc_functions.append(lambda data, fs: (data / divisor, fs))
dataset = DiagnosisSet(n_recordings=n_recordings,
max_recording_mins=max_recording_mins,
preproc_functions=preproc_functions)
if not only_return_exp:
X, y = dataset.load()
splitter = Splitter(
n_folds,
i_test_fold,
)
if not only_return_exp:
train_set, valid_set, test_set = splitter.split(X, y)
del X, y # shouldn't be necessary, but just to make sure
else:
train_set = None
valid_set = None
test_set = None
set_random_seeds(seed=20170629, cuda=cuda)
if sigmoid:
n_classes = 1
else:
n_classes = 2
in_chans = 21
net = Deep4Net(
in_chans=in_chans,
n_classes=n_classes,
input_time_length=input_time_length,
final_conv_length=final_conv_length,
pool_time_length=pool_stride,
pool_time_stride=pool_stride,
n_filters_2=50,
n_filters_3=80,
n_filters_4=120,
)
model = net_with_more_layers(net, n_blocks_to_add, nn.MaxPool2d)
if sigmoid:
model = to_linear_plus_minus_net(model)
optimizer = optim.Adam(model.parameters())
to_dense_prediction_model(model)
log.info("Model:\n{:s}".format(str(model)))
if cuda:
model.cuda()
# determine output size
test_input = np_to_var(
np.ones((2, in_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
log.info("{:d} predictions per input/trial".format(n_preds_per_input))
iterator = CropsFromTrialsIterator(batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
if sigmoid:
loss_function = lambda preds, targets: binary_cross_entropy_with_logits(
th.mean(preds, dim=2)[:, 1, 0], targets.type_as(preds))
else:
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2)[:, :, 0], targets)
if model_constraint is not None:
model_constraint = MaxNormDefaultConstraint()
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length),
RuntimeMonitor(),
]
stop_criterion = MaxEpochs(max_epochs)
batch_modifier = None
if batch_set_zero_val is not None:
batch_modifier = RemoveMinMaxDiff(batch_set_zero_val,
clip_max_abs=True,
set_zero=True)
if (batch_set_zero_val is not None) and (batch_set_zero_test == True):
iterator = ModifiedIterator(
iterator,
batch_modifier,
)
batch_modifier = None
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
batch_modifier=batch_modifier,
cuda=cuda)
if not only_return_exp:
exp.run()
else:
exp.dataset = dataset
exp.splitter = splitter
return exp
def run_exp_on_high_gamma_dataset(train_filename, test_filename, low_cut_hz,
model_name, max_epochs, max_increase_epochs,
np_th_seed, debug):
train_set, valid_set, test_set = load_train_valid_test(
train_filename=train_filename,
test_filename=test_filename,
low_cut_hz=low_cut_hz,
debug=debug)
if debug:
max_epochs = 4
set_random_seeds(np_th_seed, cuda=True)
#torch.backends.cudnn.benchmark = True# sometimes crashes?
n_classes = int(np.max(train_set.y) + 1)
n_chans = int(train_set.X.shape[1])
input_time_length = 1000
if model_name == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=2).create_network()
elif model_name == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=30).create_network()
to_dense_prediction_model(model)
model.cuda()
model.eval()
out = model(np_to_var(train_set.X[:1, :, :input_time_length, None]).cuda())
n_preds_per_input = out.cpu().data.numpy().shape[2]
optimizer = optim.Adam(model.parameters(), weight_decay=0, lr=1e-3)
iterator = CropsFromTrialsIterator(batch_size=60,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input,
seed=np_th_seed)
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length=input_time_length),
RuntimeMonitor()
]
model_constraint = MaxNormDefaultConstraint()
loss_function = lambda preds, targets: F.nll_loss(th.mean(preds, dim=2),
targets)
run_after_early_stop = True
do_early_stop = True
remember_best_column = 'valid_misclass'
stop_criterion = Or([
MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)
])
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column=remember_best_column,
run_after_early_stop=run_after_early_stop,
cuda=True,
do_early_stop=do_early_stop)
exp.run()
return exp
def run_exp(data_folder, session_id, subject_id, low_cut_hz, model, cuda):
ival = [-500, 4000]
max_epochs = 1600
max_increase_epochs = 160
batch_size = 10
high_cut_hz = 38
factor_new = 1e-3
init_block_size = 1000
valid_set_fraction = .2
''' # BCIcompetition
train_filename = 'A{:02d}T.gdf'.format(subject_id)
test_filename = 'A{:02d}E.gdf'.format(subject_id)
train_filepath = os.path.join(data_folder, train_filename)
test_filepath = os.path.join(data_folder, test_filename)
train_label_filepath = train_filepath.replace('.gdf', '.mat')
test_label_filepath = test_filepath.replace('.gdf', '.mat')
train_loader = BCICompetition4Set2A(
train_filepath, labels_filename=train_label_filepath)
test_loader = BCICompetition4Set2A(
test_filepath, labels_filename=test_label_filepath)
train_cnt = train_loader.load()
test_cnt = test_loader.load()
'''
# GIGAscience
filename = 'sess{:02d}_subj{:02d}_EEG_MI.mat'.format(
session_id, subject_id)
filepath = os.path.join(data_folder, filename)
train_variable = 'EEG_MI_train'
test_variable = 'EEG_MI_test'
train_loader = GIGAscience(filepath, train_variable)
test_loader = GIGAscience(filepath, test_variable)
train_cnt = train_loader.load()
test_cnt = test_loader.load()
# Preprocessing
''' channel
['Fp1', 'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FC2', 'FC6', 'T7', 'C3', 'Cz', 'C4', 'T8', 'TP9', 'CP5',
'CP1', 'CP2', 'CP6', 'TP10', 'P7', 'P3', 'Pz', 'P4', 'P8', 'PO9', 'O1', 'Oz', 'O2', 'PO10', 'FC3', 'FC4', 'C5',
'C1', 'C2', 'C6', 'CP3', 'CPz', 'CP4', 'P1', 'P2', 'POz', 'FT9', 'FTT9h', 'TTP7h', 'TP7', 'TPP9h', 'FT10',
'FTT10h', 'TPP8h', 'TP8', 'TPP10h', 'F9', 'F10', 'AF7', 'AF3', 'AF4', 'AF8', 'PO3', 'PO4']
'''
train_cnt = train_cnt.pick_channels([
'FC5', 'FC3', 'FC1', 'Fz', 'FC2', 'FC4', 'FC6', 'C5', 'C3', 'C1', 'Cz',
'C2', 'C4', 'C6', 'CP5', 'CP3', 'CP1', 'CPz', 'CP2', 'CP4', 'CP6', 'Pz'
])
train_cnt, train_cnt.info['events'] = train_cnt.copy().resample(
250, npad='auto', events=train_cnt.info['events'])
assert len(train_cnt.ch_names) == 22
# lets convert to millvolt for numerical stability of next operations
train_cnt = mne_apply(lambda a: a * 1e6, train_cnt)
train_cnt = mne_apply(
lambda a: bandpass_cnt(a,
low_cut_hz,
high_cut_hz,
train_cnt.info['sfreq'],
filt_order=3,
axis=1), train_cnt)
train_cnt = mne_apply(
lambda a: exponential_running_standardize(a.T,
factor_new=factor_new,
init_block_size=
init_block_size,
eps=1e-4).T, train_cnt)
test_cnt = test_cnt.pick_channels([
'FC5', 'FC3', 'FC1', 'Fz', 'FC2', 'FC4', 'FC6', 'C5', 'C3', 'C1', 'Cz',
'C2', 'C4', 'C6', 'CP5', 'CP3', 'CP1', 'CPz', 'CP2', 'CP4', 'CP6', 'Pz'
])
test_cnt, test_cnt.info['events'] = test_cnt.copy().resample(
250, npad='auto', events=test_cnt.info['events'])
assert len(test_cnt.ch_names) == 22
test_cnt = mne_apply(lambda a: a * 1e6, test_cnt)
test_cnt = mne_apply(
lambda a: bandpass_cnt(a,
low_cut_hz,
high_cut_hz,
test_cnt.info['sfreq'],
filt_order=3,
axis=1), test_cnt)
test_cnt = mne_apply(
lambda a: exponential_running_standardize(a.T,
factor_new=factor_new,
init_block_size=
init_block_size,
eps=1e-4).T, test_cnt)
marker_def = OrderedDict([('Right Hand', [1]), ('Left Hand', [2])])
train_set = create_signal_target_from_raw_mne(train_cnt, marker_def, ival)
test_set = create_signal_target_from_raw_mne(test_cnt, marker_def, ival)
train_set, valid_set = split_into_two_sets(train_set,
first_set_fraction=1 -
valid_set_fraction)
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 2
n_chans = int(train_set.X.shape[1])
input_time_length = train_set.X.shape[2]
if model == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
elif model == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length='auto').create_network()
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
optimizer = optim.Adam(model.parameters())
iterator = BalancedBatchSizeIterator(batch_size=batch_size)
stop_criterion = Or([
MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)
])
monitors = [LossMonitor(), MisclassMonitor(), RuntimeMonitor()]
model_constraint = MaxNormDefaultConstraint()
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=F.nll_loss,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
cuda=cuda)
exp.run()
return exp
def run_exp(data_folder, subject_id, low_cut_hz, model, cuda):
ival = [-500, 4000]
input_time_length = 1000
max_epochs = 800
max_increase_epochs = 80
batch_size = 60
high_cut_hz = 38
factor_new = 1e-3
init_block_size = 1000
valid_set_fraction = 0.2
train_filename = 'A{:02d}T.gdf'.format(subject_id)
test_filename = 'A{:02d}E.gdf'.format(subject_id)
train_filepath = os.path.join(data_folder, train_filename)
test_filepath = os.path.join(data_folder, test_filename)
train_label_filepath = train_filepath.replace('.gdf', '.mat')
test_label_filepath = test_filepath.replace('.gdf', '.mat')
train_loader = BCICompetition4Set2A(train_filepath,
labels_filename=train_label_filepath)
test_loader = BCICompetition4Set2A(test_filepath,
labels_filename=test_label_filepath)
train_cnt = train_loader.load()
test_cnt = test_loader.load()
# Preprocessing
train_cnt = train_cnt.drop_channels(
['STI 014', 'EOG-left', 'EOG-central', 'EOG-right'])
assert len(train_cnt.ch_names) == 22
# lets convert to millvolt for numerical stability of next operations
train_cnt = mne_apply(lambda a: a * 1e6, train_cnt)
train_cnt = mne_apply(
lambda a: bandpass_cnt(a,
low_cut_hz,
high_cut_hz,
train_cnt.info['sfreq'],
filt_order=3,
axis=1), train_cnt)
train_cnt = mne_apply(
lambda a: exponential_running_standardize(a.T,
factor_new=factor_new,
init_block_size=
init_block_size,
eps=1e-4).T, train_cnt)
test_cnt = test_cnt.drop_channels(
['STI 014', 'EOG-left', 'EOG-central', 'EOG-right'])
assert len(test_cnt.ch_names) == 22
test_cnt = mne_apply(lambda a: a * 1e6, test_cnt)
test_cnt = mne_apply(
lambda a: bandpass_cnt(a,
low_cut_hz,
high_cut_hz,
test_cnt.info['sfreq'],
filt_order=3,
axis=1), test_cnt)
test_cnt = mne_apply(
lambda a: exponential_running_standardize(a.T,
factor_new=factor_new,
init_block_size=
init_block_size,
eps=1e-4).T, test_cnt)
marker_def = OrderedDict([('Left Hand', [1]), (
'Right Hand',
[2],
), ('Foot', [3]), ('Tongue', [4])])
train_set = create_signal_target_from_raw_mne(train_cnt, marker_def, ival)
test_set = create_signal_target_from_raw_mne(test_cnt, marker_def, ival)
train_set, valid_set = split_into_two_sets(train_set,
first_set_fraction=1 -
valid_set_fraction)
set_random_seeds(seed=20190706, cuda=cuda)
n_classes = 4
n_chans = int(train_set.X.shape[1])
if model == 'shallow':
model = ShallowFBCSPNet(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=30).create_network()
elif model == 'deep':
model = Deep4Net(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=2).create_network()
to_dense_prediction_model(model)
if cuda:
model.cuda()
log.info("Model: \n{:s}".format(str(model)))
dummy_input = np_to_var(train_set.X[:1, :, :, None])
if cuda:
dummy_input = dummy_input.cuda()
out = model(dummy_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
optimizer = optim.Adam(model.parameters())
iterator = CropsFromTrialsIterator(batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input)
stop_criterion = Or([
MaxEpochs(max_epochs),
NoDecrease('valid_misclass', max_increase_epochs)
])
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedTrialMisclassMonitor(input_time_length=input_time_length),
RuntimeMonitor()
]
model_constraint = MaxNormDefaultConstraint()
loss_function = lambda preds, targets: F.nll_loss(
th.mean(preds, dim=2, keepdim=False), targets)
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
cuda=cuda)
exp.run()
return exp
def run_exp(max_recording_mins,
n_recordings,
sec_to_cut_at_start,
sec_to_cut_at_end,
duration_recording_mins,
max_abs_val,
clip_before_resample,
sampling_freq,
divisor,
n_folds,
i_test_fold,
shuffle,
merge_train_valid,
model,
input_time_length,
optimizer,
learning_rate,
weight_decay,
scheduler,
model_constraint,
batch_size,
max_epochs,
only_return_exp,
time_cut_off_sec,
start_time,
test_on_eval,
test_recording_mins,
sensor_types,
log_dir,
np_th_seed,
cuda=True):
import torch.backends.cudnn as cudnn
cudnn.benchmark = True
if optimizer == 'adam':
assert merge_train_valid == False
else:
assert optimizer == 'adamw'
assert merge_train_valid == True
preproc_functions = create_preproc_functions(
sec_to_cut_at_start=sec_to_cut_at_start,
sec_to_cut_at_end=sec_to_cut_at_end,
duration_recording_mins=duration_recording_mins,
max_abs_val=max_abs_val,
clip_before_resample=clip_before_resample,
sampling_freq=sampling_freq,
divisor=divisor)
dataset = DiagnosisSet(n_recordings=n_recordings,
max_recording_mins=max_recording_mins,
preproc_functions=preproc_functions,
train_or_eval='train',
sensor_types=sensor_types)
if test_on_eval:
if test_recording_mins is None:
test_recording_mins = duration_recording_mins
test_preproc_functions = create_preproc_functions(
sec_to_cut_at_start=sec_to_cut_at_start,
sec_to_cut_at_end=sec_to_cut_at_end,
duration_recording_mins=test_recording_mins,
max_abs_val=max_abs_val,
clip_before_resample=clip_before_resample,
sampling_freq=sampling_freq,
divisor=divisor)
test_dataset = DiagnosisSet(n_recordings=n_recordings,
max_recording_mins=None,
preproc_functions=test_preproc_functions,
train_or_eval='eval',
sensor_types=sensor_types)
if not only_return_exp:
X, y = dataset.load()
max_shape = np.max([list(x.shape) for x in X], axis=0)
assert max_shape[1] == int(duration_recording_mins * sampling_freq *
60)
if test_on_eval:
test_X, test_y = test_dataset.load()
max_shape = np.max([list(x.shape) for x in test_X], axis=0)
assert max_shape[1] == int(test_recording_mins * sampling_freq *
60)
if not test_on_eval:
splitter = TrainValidTestSplitter(n_folds,
i_test_fold,
shuffle=shuffle)
else:
splitter = TrainValidSplitter(n_folds,
i_valid_fold=i_test_fold,
shuffle=shuffle)
if not only_return_exp:
if not test_on_eval:
train_set, valid_set, test_set = splitter.split(X, y)
else:
train_set, valid_set = splitter.split(X, y)
test_set = SignalAndTarget(test_X, test_y)
del test_X, test_y
del X, y # shouldn't be necessary, but just to make sure
if merge_train_valid:
train_set = concatenate_sets([train_set, valid_set])
# just reduce valid for faster computations
valid_set.X = valid_set.X[:8]
valid_set.y = valid_set.y[:8]
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/train_X.npy', train_set.X)
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/train_y.npy', train_set.y)
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/valid_X.npy', valid_set.X)
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/valid_y.npy', valid_set.y)
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/test_X.npy', test_set.X)
# np.save('/data/schirrmr/schirrmr/auto-diag/lukasrepr/compare/mne-0-16-2/test_y.npy', test_set.y)
else:
train_set = None
valid_set = None
test_set = None
log.info("Model:\n{:s}".format(str(model)))
if cuda:
model.cuda()
model.eval()
in_chans = 21
# determine output size
test_input = np_to_var(
np.ones((2, in_chans, input_time_length, 1), dtype=np.float32))
if cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
log.info("{:d} predictions per input/trial".format(n_preds_per_input))
iterator = CropsFromTrialsIterator(batch_size=batch_size,
input_time_length=input_time_length,
n_preds_per_input=n_preds_per_input,
seed=np_th_seed)
assert optimizer in ['adam', 'adamw'], ("Expect optimizer to be either "
"adam or adamw")
schedule_weight_decay = optimizer == 'adamw'
if optimizer == 'adam':
optim_class = optim.Adam
assert schedule_weight_decay == False
assert merge_train_valid == False
else:
optim_class = AdamW
assert schedule_weight_decay == True
assert merge_train_valid == True
optimizer = optim_class(model.parameters(),
lr=learning_rate,
weight_decay=weight_decay)
if scheduler is not None:
assert scheduler == 'cosine'
n_updates_per_epoch = sum(
[1 for _ in iterator.get_batches(train_set, shuffle=True)])
# Adapt if you have a different number of epochs
n_updates_per_period = n_updates_per_epoch * max_epochs
scheduler = CosineAnnealing(n_updates_per_period)
optimizer = ScheduledOptimizer(
scheduler, optimizer, schedule_weight_decay=schedule_weight_decay)
loss_function = nll_loss_on_mean
if model_constraint is not None:
assert model_constraint == 'defaultnorm'
model_constraint = MaxNormDefaultConstraint()
monitors = [
LossMonitor(),
MisclassMonitor(col_suffix='sample_misclass'),
CroppedDiagnosisMonitor(input_time_length, n_preds_per_input),
RuntimeMonitor(),
]
stop_criterion = MaxEpochs(max_epochs)
loggers = [Printer(), TensorboardWriter(log_dir)]
batch_modifier = None
exp = Experiment(model,
train_set,
valid_set,
test_set,
iterator,
loss_function,
optimizer,
model_constraint,
monitors,
stop_criterion,
remember_best_column='valid_misclass',
run_after_early_stop=True,
batch_modifier=batch_modifier,
cuda=cuda,
loggers=loggers)
if not only_return_exp:
# Until first stop
exp.setup_training()
exp.monitor_epoch(exp.datasets)
exp.log_epoch()
exp.rememberer.remember_epoch(exp.epochs_df, exp.model, exp.optimizer)
exp.iterator.reset_rng()
while not exp.stop_criterion.should_stop(exp.epochs_df):
if (time.time() - start_time) > time_cut_off_sec:
log.info(
"Ran out of time after {:.2f} sec.".format(time.time() -
start_time))
return exp
log.info("Still in time after {:.2f} sec.".format(time.time() -
start_time))
exp.run_one_epoch(exp.datasets, remember_best=True)
if (time.time() - start_time) > time_cut_off_sec:
log.info("Ran out of time after {:.2f} sec.".format(time.time() -
start_time))
return exp
if not merge_train_valid:
exp.setup_after_stop_training()
# Run until second stop
datasets = exp.datasets
datasets['train'] = concatenate_sets(
[datasets['train'], datasets['valid']])
exp.monitor_epoch(datasets)
exp.log_epoch()
exp.iterator.reset_rng()
while not exp.stop_criterion.should_stop(exp.epochs_df):
if (time.time() - start_time) > time_cut_off_sec:
log.info("Ran out of time after {:.2f} sec.".format(
time.time() - start_time))
return exp
log.info("Still in time after {:.2f} sec.".format(time.time() -
start_time))
exp.run_one_epoch(datasets, remember_best=False)
else:
exp.dataset = dataset
exp.splitter = splitter
if test_on_eval:
exp.test_dataset = test_dataset
return exp
def setup_exp(
train_folder,
n_recordings,
n_chans,
model_name,
n_start_chans,
n_chan_factor,
input_time_length,
final_conv_length,
model_constraint,
stride_before_pool,
init_lr,
batch_size,
max_epochs,
cuda,
num_workers,
task,
weight_decay,
n_folds,
shuffle_folds,
lazy_loading,
eval_folder,
result_folder,
run_on_normals,
run_on_abnormals,
seed,
l2_decay,
gradient_clip,
):
info_msg = "using {}, {}".format(
os.environ["SLURM_JOB_PARTITION"],
os.environ["SLURMD_NODENAME"],
)
info_msg += ", gpu {}".format(os.environ["CUDA_VISIBLE_DEVICES"])
logging.info(info_msg)
logging.info("Targets for this task: <{}>".format(task))
import torch.backends.cudnn as cudnn
cudnn.benchmark = True
if task == "age":
loss_function = mse_loss_on_mean
remember_best_column = "valid_rmse"
n_classes = 1
else:
loss_function = nll_loss_on_mean
remember_best_column = "valid_misclass"
n_classes = 2
if model_constraint is not None:
assert model_constraint == 'defaultnorm'
model_constraint = MaxNormDefaultConstraint()
stop_criterion = MaxEpochs(max_epochs)
set_random_seeds(seed=seed, cuda=cuda)
if model_name == 'shallow':
model = ShallowFBCSPNet(
in_chans=n_chans,
n_classes=n_classes,
n_filters_time=n_start_chans,
n_filters_spat=n_start_chans,
input_time_length=input_time_length,
final_conv_length=final_conv_length).create_network()
elif model_name == 'deep':
model = Deep4Net(
n_chans,
n_classes,
n_filters_time=n_start_chans,
n_filters_spat=n_start_chans,
input_time_length=input_time_length,
n_filters_2=int(n_start_chans * n_chan_factor),
n_filters_3=int(n_start_chans * (n_chan_factor**2.0)),
n_filters_4=int(n_start_chans * (n_chan_factor**3.0)),
final_conv_length=final_conv_length,
stride_before_pool=stride_before_pool).create_network()
elif model_name == 'eegnet':
model = EEGNetv4(n_chans,
n_classes,
input_time_length=input_time_length,
final_conv_length=final_conv_length).create_network()
elif model_name == "tcn":
assert task != "age", "what to change to do regression with tcn?!"
model = TemporalConvNet(input_size=n_chans,
output_size=n_classes,
context_size=0,
num_channels=55,
num_levels=5,
kernel_size=16,
dropout=0.05270154233150525,
skip_mode=None,
use_context=0,
lasso_selection=0.0,
rnn_normalization=None)
else:
assert False, "unknown model name {:s}".format(model_name)
if task == "age":
# remove softmax layer, set n_classes to 1
model.n_classes = 1
new_model = nn.Sequential()
for name, module_ in model.named_children():
if name == "softmax":
continue
new_model.add_module(name, module_)
model = new_model
# maybe check if this works and wait / re-try after some time?
# in case of all cuda devices are busy
if cuda:
model.cuda()
if model_name != "tcn":
to_dense_prediction_model(model)
logging.info("Model:\n{:s}".format(str(model)))
test_input = np_to_var(
np.ones((2, n_chans, input_time_length, 1), dtype=np.float32))
if list(model.parameters())[0].is_cuda:
test_input = test_input.cuda()
out = model(test_input)
n_preds_per_input = out.cpu().data.numpy().shape[2]
if eval_folder is None:
logging.info("will do validation")
if lazy_loading:
logging.info(
"using lazy loading to load {} recs".format(n_recordings))
dataset = TuhLazy(train_folder,
target=task,
n_recordings=n_recordings)
else:
logging.info("using traditional loading to load {} recs".format(
n_recordings))
dataset = Tuh(train_folder, n_recordings=n_recordings, target=task)
assert not (run_on_normals and run_on_abnormals), (
"decide whether to run on normal or abnormal subjects")
# only run on normal subjects
if run_on_normals:
ids = [
i for i in range(len(dataset)) if dataset.pathologicals[i] == 0
] # 0 is non-pathological
dataset = TuhSubset(dataset, ids)
logging.info("only using {} normal subjects".format(len(dataset)))
if run_on_abnormals:
ids = [
i for i in range(len(dataset)) if dataset.pathologicals[i] == 1
] # 1 is pathological
dataset = TuhSubset(dataset, ids)
logging.info("only using {} abnormal subjects".format(
len(dataset)))
indices = np.arange(len(dataset))
kf = KFold(n_splits=n_folds, shuffle=shuffle_folds)
for i, (train_ind, test_ind) in enumerate(kf.split(indices)):
assert len(np.intersect1d(
train_ind, test_ind)) == 0, ("train and test set overlap!")
# seed is in range of number of folds and was set by submit script
if i == seed:
break
if lazy_loading:
test_subset = TuhLazySubset(dataset, test_ind)
train_subset = TuhLazySubset(dataset, train_ind)
else:
test_subset = TuhSubset(dataset, test_ind)
train_subset = TuhSubset(dataset, train_ind)
else:
logging.info("will do final evaluation")
if lazy_loading:
train_subset = TuhLazy(train_folder, target=task)
test_subset = TuhLazy(eval_folder, target=task)
else:
train_subset = Tuh(train_folder, target=task)
test_subset = Tuh(eval_folder, target=task)
# remove rec:
# train/abnormal/01_tcp_ar/081/00008184/s001_2011_09_21/00008184_s001_t001
# since it contains no crop without outliers (channels A1, A2 broken)
subjects = [f.split("/")[-3] for f in train_subset.file_paths]
if "00008184" in subjects:
bad_id = subjects.index("00008184")
train_subset = remove_file_from_dataset(
train_subset,
file_id=bad_id,
file=("train/abnormal/01_tcp_ar/081/00008184/s001_2011_09_21/"
"00008184_s001_t001"))
subjects = [f.split("/")[-3] for f in test_subset.file_paths]
if "00008184" in subjects:
bad_id = subjects.index("00008184")
test_subset = remove_file_from_dataset(
test_subset,
file_id=bad_id,
file=("train/abnormal/01_tcp_ar/081/00008184/s001_2011_09_21/"
"00008184_s001_t001"))
if task == "age":
# standardize ages based on train set
y_train = train_subset.y
y_train_mean = np.mean(y_train)
y_train_std = np.std(y_train)
train_subset.y = (y_train - y_train_mean) / y_train_std
y_test = test_subset.y
test_subset.y = (y_test - y_train_mean) / y_train_std
if lazy_loading:
iterator = LazyCropsFromTrialsIterator(
input_time_length,
n_preds_per_input,
batch_size,
seed=seed,
num_workers=num_workers,
reset_rng_after_each_batch=False,
check_preds_smaller_trial_len=False) # True!
else:
iterator = CropsFromTrialsIterator(batch_size, input_time_length,
n_preds_per_input, seed)
monitors = []
monitors.append(LossMonitor())
monitors.append(RAMMonitor())
monitors.append(RuntimeMonitor())
if task == "age":
monitors.append(
RMSEMonitor(input_time_length,
n_preds_per_input,
mean=y_train_mean,
std=y_train_std))
else:
monitors.append(
CroppedDiagnosisMonitor(input_time_length, n_preds_per_input))
monitors.append(LazyMisclassMonitor(col_suffix='sample_misclass'))
if lazy_loading:
n_updates_per_epoch = len(
iterator.get_batches(train_subset, shuffle=False))
else:
n_updates_per_epoch = sum(
[1 for _ in iterator.get_batches(train_subset, shuffle=False)])
n_updates_per_period = n_updates_per_epoch * max_epochs
logging.info("there are {} updates per epoch".format(n_updates_per_epoch))
if model_name == "tcn":
adamw = ExtendedAdam(model.parameters(),
lr=init_lr,
weight_decay=weight_decay,
l2_decay=l2_decay,
gradient_clip=gradient_clip)
else:
adamw = AdamWWithTracking(model.parameters(),
init_lr,
weight_decay=weight_decay)
scheduler = CosineAnnealing(n_updates_per_period)
optimizer = ScheduledOptimizer(scheduler,
adamw,
schedule_weight_decay=True)
exp = Experiment(model=model,
train_set=train_subset,
valid_set=None,
test_set=test_subset,
iterator=iterator,
loss_function=loss_function,
optimizer=optimizer,
model_constraint=model_constraint,
monitors=monitors,
stop_criterion=stop_criterion,
remember_best_column=remember_best_column,
run_after_early_stop=False,
batch_modifier=None,
cuda=cuda,
do_early_stop=False,
reset_after_second_run=False)
return exp