def run_experiment_test(base_dir):
data_base_dir = base_dir #= r'C:\Users\ORI\Documents\Thesis\dataset_all'
all_subjects = [
"RSVP_Color116msVPicr.mat", "RSVP_Color116msVPpia.mat",
"RSVP_Color116msVPfat.mat", "RSVP_Color116msVPgcb.mat",
"RSVP_Color116msVPgcc.mat", "RSVP_Color116msVPgcd.mat",
"RSVP_Color116msVPgcf.mat", "RSVP_Color116msVPgcg.mat",
"RSVP_Color116msVPgch.mat", "RSVP_Color116msVPiay.mat",
"RSVP_Color116msVPicn.mat"
]
for subject in all_subjects:
# subject = "RSVP_Color116msVPgcd.mat"
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
data_generator = triplet_data_generator(
all_data_per_char_as_matrix[train_mode_per_block == 1],
target_per_char_as_matrix[train_mode_per_block == 1], 80)
testing_data, testing_tags = get_all_triplet_combinations_testing(
all_data_per_char_as_matrix, target_per_char_as_matrix,
train_mode_per_block)
valid_data = triplet_data_collection(
all_data_per_char_as_matrix[train_mode_per_block == 2],
target_per_char_as_matrix[train_mode_per_block == 2], 80)
total_number_of_char_in_training = all_data_per_char_as_matrix[
train_mode_per_block == 1].shape[0] / 10
# region Build the P300Net model
model = get_graph_lstm(3, 10, 25, 55)
# endregion
# region the P300Net identification model
P300IdentificationModel = get_item_lstm_subgraph(25, 55)
P300IdentificationModel.compile(loss='binary_crossentropy',
class_mode="binary",
optimizer='rmsprop')
# endregion
# region train the P300Net model
# model.fit_generator(data_generator, 2880, nb_epoch=10, validation_data=valid_data)
model.fit_generator(data_generator,
80 * 40,
nb_epoch=2,
validation_data=valid_data)
# endregion
# all_train_data = dict()
train_p300_model(
P300IdentificationModel,
all_data_per_char_as_matrix[train_mode_per_block == 1],
target_per_char_as_matrix[train_mode_per_block == 1])
final_model = get_item_lstm_subgraph(25, 55)
final_model_original_weights = final_model.get_weights()
final_model.compile(loss='binary_crossentropy',
class_mode="binary",
optimizer='sgd')
final_model.set_weights(
list(model.nodes['item_latent'].layer.get_weights()))
all_prediction_P300Net = predict_p300_model(
final_model,
all_data_per_char_as_matrix[train_mode_per_block != 1])
all_prediction_normal = predict_p300_model(
P300IdentificationModel,
all_data_per_char_as_matrix[train_mode_per_block != 1])
all_prediction_normal = all_prediction_P300Net
plt.subplot(1, 4, 1)
# plt.imshow(all_prediction, interpolation='none')
plt.subplot(1, 4, 2)
x = T.dmatrix('x')
import theano
softmax_res_func = theano.function([x], T.nnet.softmax(x))
#
# plt.imshow(softmax_res_func(all_prediction), interpolation='none')
# plt.subplot(1, 4, 3)
# plt.imshow(softmax_res_func(np.mean(all_prediction.reshape((-1, 10, 30)), axis=1)).astype(np.int),
# interpolation='none')
plt.subplot(1, 4, 3)
test_tags = target_per_char_as_matrix[
train_mode_per_block !=
1] # np.array([target_per_char[x][train_mode_per_block != 1] for x in range(30)]).T
# plt.imshow(np.mean(all_res.reshape((-1, 10, 30)), axis=1), interpolation='none')
all_res = test_tags
# plt.imshow(softmax_res_func(all_prediction_normal.reshape((-1, 30))), interpolation='none')
actual_untrained = np.argmax(softmax_res_func(
np.mean(all_prediction_normal.reshape((-1, 10, 30)), axis=1)),
axis=1)
# actual = np.where(np.round(softmax_res_func(np.mean(all_prediction.reshape((-1, 10, 30)), axis=1))) == 1)[0];
gt = np.argmax(np.mean(all_res.reshape((-1, 10, 30)), axis=1), axis=1)
# np.intersect1d(actual, gt)
# accuracy = len(np.intersect1d(actual, gt)) / float(len(gt))
plt.subplot(1, 2, 1)
plt.imshow(
softmax_res_func(
np.mean(all_prediction_normal.reshape((-1, 10, 30)), axis=1)))
plt.subplot(1, 2, 2)
plt.imshow(np.mean(all_res.reshape((-1, 10, 30)), axis=1))
plt.show()
accuracy = 0
accuracy_untrained = np.sum(actual_untrained == gt) / float(len(gt))
print "subject:{0} accu:{1} acc_untrained{2}".format(
subject, accuracy, accuracy_untrained)
args = parser.parse_args()
start_idx = args.start_sub_idx
end_idx = args.end_sub_idx
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
test_data_all_subject_with_noise = dict()
for experiment_counter, subject in enumerate(
all_subjects[start_idx:end_idx]):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
_, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
noise_data = dict()
noist_shifts = [-120, -80, -40, 0, 40, 80, 120]
for time_shift_noise in noist_shifts:
_, _, _, noise_data[
time_shift_noise], _ = create_data_rep_training(
file_name, (-200 + time_shift_noise),
(800 + time_shift_noise),
downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
help="first sub",
type=int,
default=len(all_subjects))
# parser.add_argument("start_sub_idx", help="first sub",
# type=int, default=len(all_subjects))
# parser.add_argument("last_sub_idx", help="last sub",
# type=int, default=len(all_subjects))
args = parser.parse_args()
start_idx = args.start_sub_idx
end_idx = args.end_sub_idx
for experiment_counter, subject in enumerate(
all_subjects[start_idx:end_idx]):
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
n_folds=4,
random_state=42,
shuffle=True))):
# seperate randomally
batch_size = 20
select = 1
train_as_p300 = False
train_indexes = train_mode_per_block == 1
def train_on_subjset(all_subjects, model_file_name):
print "start ----------{}-------".format(model_file_name)
parser = argparse.ArgumentParser()
parser.add_argument("-start_sub_idx",
help="first sub",
type=int,
default=0)
parser.add_argument("-end_sub_idx",
help="first sub",
type=int,
default=len(all_subjects))
args = parser.parse_args()
start_idx = args.start_sub_idx
end_idx = args.end_sub_idx
from experiments.P300_RSVP.model_left_out.load_left_out_model import load_left_out_model
only_p300_model_1 = load_left_out_model(model_file_name)
original_wights = only_p300_model_1.get_weights()
for experiment_counter, subject in enumerate(
all_subjects[start_idx:end_idx]):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
n_folds=4,
random_state=42,
shuffle=True))):
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
batch_size = 20
select = 1
train_as_p300 = False
train_indexes = train_mode_per_block == 1
validation_indexes = train_mode_per_block == 2
test_indexes = train_mode_per_block != 1
if train_as_p300:
data_generator_batch = triplet_data_generator_no_dict(
all_data_per_char_as_matrix[train_indexes],
target_per_char_as_matrix[train_indexes],
batch_size=batch_size,
select=select,
debug_mode=False)
else:
def flatten_repetitions(data_to_flatten):
return np.reshape(
np.reshape(data_to_flatten.T * 10,
(-1, 1)) + np.arange(10), (-1))
train_indexes = flatten_repetitions(
cross_validation_indexes[0])
test_indexes = flatten_repetitions(cross_validation_indexes[1])
train_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[train_indexes]).astype(
np.float32))
test_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[test_indexes]).astype(
np.float32))
train_tags_all_subject.append(
target_per_char_as_matrix[train_indexes])
test_tags_all_subject.append(
target_per_char_as_matrix[test_indexes])
eeg_sample_shape = (25, 55)
# keras.models.load_model(model_file_name) #
#
only_p300_model_1.set_weights(
original_wights
) #= get_only_P300_model_LSTM_CNN(eeg_sample_shape)
only_p300_model_1.summary()
from keras.optimizers import RMSprop
only_p300_model_1.compile(
optimizer=RMSprop(),
loss='binary_crossentropy',
metrics=['accuracy'],
)
model = only_p300_model_1
print "after compile"
# model = LDA()
train_data = stats.zscore(np.vstack(train_data_all_subject),
axis=1)
train_tags = np.vstack(train_tags_all_subject).flatten()
test_data = stats.zscore(np.vstack(test_data_all_subject), axis=1)
test_tags = np.vstack(test_tags_all_subject).flatten()
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
#
print "{} before train accuracy_test {}:{}, auc_score_test:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags)
print "{} before train accuracy_train {}:{}, auc_score_train:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
model.optimizer.lr.set_value(0.0001)
for i in range(1):
model.fit(train_data.reshape(
train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags,
verbose=1,
nb_epoch=30,
batch_size=600,
shuffle=True)
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
print "{} after train accuracy_test {}:{}, auc_score_test:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(
train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]), train_tags)
print "{} after train accuracy_train {}:{}, auc_score_train:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
# model.save(r"c:\temp\{}.h5".format(model_file_name,overwrite=True))
print "end ----------{}-------".format(file_name)
def train_on_subjset(all_subjects, file_name):
# all_subjects = ["RSVP_Color116msVPgcd.mat",
# "RSVP_Color116msVPgcc.mat",
# "RSVP_Color116msVPpia.mat",
# "RSVP_Color116msVPgcb.mat",
# "RSVP_Color116msVPgcf.mat",
# "RSVP_Color116msVPgcg.mat",
# "RSVP_Color116msVPgch.mat",
# # "RSVP_Color116msVPiay.mat",
# "RSVP_Color116msVPicn.mat",
# "RSVP_Color116msVPicr.mat",
# "RSVP_Color116msVPfat.mat",
#
# ];
#
#
# all_subjects = [
# "RSVP_Color116msVPiay.mat",
# ];
parser = argparse.ArgumentParser()
parser.add_argument("-start_sub_idx",
help="first sub",
type=int,
default=0)
parser.add_argument("-end_sub_idx",
help="first sub",
type=int,
default=len(all_subjects))
# parser.add_argument("start_sub_idx", help="first sub",
# type=int, default=len(all_subjects))
# parser.add_argument("last_sub_idx", help="last sub",
# type=int, default=len(all_subjects))
args = parser.parse_args()
start_idx = args.start_sub_idx
end_idx = args.end_sub_idx
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
for experiment_counter, subject in enumerate(
all_subjects[start_idx:end_idx]):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
n_folds=4,
random_state=42,
shuffle=True))):
batch_size = 20
select = 1
train_as_p300 = False
train_indexes = train_mode_per_block == 1
validation_indexes = train_mode_per_block == 2
test_indexes = train_mode_per_block != 1
if train_as_p300:
data_generator_batch = triplet_data_generator_no_dict(
all_data_per_char_as_matrix[train_indexes],
target_per_char_as_matrix[train_indexes],
batch_size=batch_size,
select=select,
debug_mode=False)
else:
# cross_validation_indexes = list(cross_validation.KFold(len(train_mode_per_block)/10, n_folds=4,
# random_state=42, shuffle=True))
def flatten_repetitions(data_to_flatten):
return np.reshape(
np.reshape(data_to_flatten.T * 10,
(-1, 1)) + np.arange(10), (-1))
train_indexes = flatten_repetitions(
cross_validation_indexes[0])
test_indexes = flatten_repetitions(cross_validation_indexes[1])
# data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes], shuffle_data=False)
#
# test_data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes],
# shuffle_data=False)
train_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[train_indexes]).astype(
np.float32))
test_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[test_indexes]).astype(
np.float32))
train_tags_all_subject.append(
target_per_char_as_matrix[train_indexes])
test_tags_all_subject.append(
target_per_char_as_matrix[test_indexes])
break
eeg_sample_shape = (25, 55)
only_p300_model_1 = get_only_P300_model_LSTM_CNN(eeg_sample_shape)
only_p300_model_1.summary()
from keras.optimizers import RMSprop
only_p300_model_1.compile(
optimizer=RMSprop(),
loss='binary_crossentropy',
metrics=['accuracy'],
)
model = only_p300_model_1
print "after compile"
# model = LDA()
train_data = stats.zscore(np.vstack(train_data_all_subject), axis=1)
train_tags = np.vstack(train_tags_all_subject).flatten()
test_data = stats.zscore(np.vstack(test_data_all_subject), axis=1)
test_tags = np.vstack(test_tags_all_subject).flatten()
for i in range(30):
model.fit(train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags,
verbose=1,
nb_epoch=1,
batch_size=600,
shuffle=True)
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
print "accuracy_test {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags)
print "accuracy_train {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
model.optimizer.lr.set_value(0.0001)
for i in range(30):
model.fit(train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags,
verbose=1,
nb_epoch=1,
batch_size=600,
shuffle=True)
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
print "accuracy_test {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags)
print "accuracy_train {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
model.save(r"c:\temp\single_subject_model.h5")
pass
def train_on_subjset(all_subjects, model_file_name):
print "start ----------{}-------".format(model_file_name)
# from experiments.P300_RSVP.model_left_out.load_left_out_model import load_left_out_model
model_file_name_full = os.path.join(os.path.dirname(LEFT_OUT_MODEL_FOLDER),
model_file_name)
# only_p300_model_1 = load_left_out_model(model_file_name)
# original_wights = only_p300_model_1.get_weights()
for experiment_counter, subject in enumerate(all_subjects):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
n_folds=4,
random_state=42,
shuffle=True))):
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
def flatten_repetitions(data_to_flatten):
return np.reshape(
np.reshape(data_to_flatten.T * 10,
(-1, 1)) + np.arange(10), (-1))
train_indexes = flatten_repetitions(cross_validation_indexes[0])
test_indexes = flatten_repetitions(cross_validation_indexes[1])
train_data_all_subject.append(
np.asarray(all_data_per_char_as_matrix[train_indexes]).astype(
np.float32))
test_data_all_subject.append(
np.asarray(all_data_per_char_as_matrix[test_indexes]).astype(
np.float32))
train_tags_all_subject.append(
target_per_char_as_matrix[train_indexes])
test_tags_all_subject.append(
target_per_char_as_matrix[test_indexes])
from keras.optimizers import RMSprop
print "after compile"
from sklearn.externals import joblib
model = joblib.load(model_file_name_full)
train_data = stats.zscore(np.vstack(train_data_all_subject),
axis=1)
train_tags = np.vstack(train_tags_all_subject).flatten()
test_data = stats.zscore(np.vstack(test_data_all_subject), axis=1)
test_tags = np.vstack(test_tags_all_subject).flatten()
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1], -1),
test_tags)
#
print "{} before train accuracy_test {}:{}, auc_score_test:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(train_data.shape[0] * train_data.shape[1],
-1), train_tags)
print "{} before train accuracy_train {}:{}, auc_score_train:{} ".format(
subject, rep_per_sub, accuracy_train, auc_score_train)
print "end ----------{}-------".format(file_name)
def train_on_subjset(all_subjects, model_file_name):
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
for experiment_counter, subject in enumerate(all_subjects):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(
cross_validation.KFold(len(train_mode_per_block) / 10,
n_folds=4,
random_state=42,
shuffle=True))):
batch_size = 20
select = 1
train_as_p300 = False
train_indexes = train_mode_per_block == 1
validation_indexes = train_mode_per_block == 2
test_indexes = train_mode_per_block != 1
if train_as_p300:
data_generator_batch = triplet_data_generator_no_dict(
all_data_per_char_as_matrix[train_indexes],
target_per_char_as_matrix[train_indexes],
batch_size=batch_size,
select=select,
debug_mode=False)
else:
# cross_validation_indexes = list(cross_validation.KFold(len(train_mode_per_block)/10, n_folds=4,
# random_state=42, shuffle=True))
def flatten_repetitions(data_to_flatten):
return np.reshape(
np.reshape(data_to_flatten.T * 10,
(-1, 1)) + np.arange(10), (-1))
train_indexes = flatten_repetitions(
cross_validation_indexes[0])
test_indexes = flatten_repetitions(cross_validation_indexes[1])
# data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes], shuffle_data=False)
#
# test_data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes],
# shuffle_data=False)
train_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[train_indexes]).astype(
np.float32))
test_data_all_subject.append(
np.asarray(
all_data_per_char_as_matrix[test_indexes]).astype(
np.float32))
train_tags_all_subject.append(
target_per_char_as_matrix[train_indexes])
test_tags_all_subject.append(
target_per_char_as_matrix[test_indexes])
break
model = LDA()
from keras.optimizers import RMSprop
print "after compile"
train_data = stats.zscore(np.vstack(train_data_all_subject), axis=1)
train_tags = np.vstack(train_tags_all_subject).flatten()
test_data = stats.zscore(np.vstack(test_data_all_subject), axis=1)
test_tags = np.vstack(test_tags_all_subject).flatten()
model.fit(
train_data.reshape(train_data.shape[0] * train_data.shape[1], -1),
train_tags)
for i in range(1):
model.fit(
train_data.reshape(train_data.shape[0] * train_data.shape[1], -1),
train_tags)
accuracy_train, auc_score_train = predict_using_model(
model,
test_data.reshape(test_data.shape[0] * test_data.shape[1], -1),
test_tags)
print "accuracy_test {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(
model,
train_data.reshape(train_data.shape[0] * train_data.shape[1], -1),
train_tags)
print "accuracy_train {}:{}, auc_score_train:{} ".format(
i, accuracy_train, auc_score_train)
from sklearn.externals import joblib
joblib.dump(model, os.path.join(r"c:\temp", model_file_name + "_lda.plk"))
print "temp"
def train_on_subjset(all_subjects, model_file_name):
print "start ----------{}-------".format(model_file_name)
# all_subjects = ["RSVP_Color116msVPgcd.mat",
# "RSVP_Color116msVPgcc.mat",
# "RSVP_Color116msVPpia.mat",
# "RSVP_Color116msVPgcb.mat",
# "RSVP_Color116msVPgcf.mat",
# "RSVP_Color116msVPgcg.mat",
# "RSVP_Color116msVPgch.mat",
# # "RSVP_Color116msVPiay.mat",
# "RSVP_Color116msVPicn.mat",
# "RSVP_Color116msVPicr.mat",
# "RSVP_Color116msVPfat.mat",
#
# ];
#
#
# all_subjects = [
# "RSVP_Color116msVPiay.mat",
# ];
parser = argparse.ArgumentParser()
parser.add_argument("-start_sub_idx", help="first sub",
type=int, default=0)
parser.add_argument("-end_sub_idx", help="first sub",
type=int, default=len(all_subjects))
# parser.add_argument("start_sub_idx", help="first sub",
# type=int, default=len(all_subjects))
# parser.add_argument("last_sub_idx", help="last sub",
# type=int, default=len(all_subjects))
args = parser.parse_args()
start_idx = args.start_sub_idx
end_idx = args.end_sub_idx
train_data_all_subject = []
test_data_all_subject = []
train_tags_all_subject = []
test_tags_all_subject = []
for experiment_counter, subject in enumerate(all_subjects[start_idx:end_idx]):
print "start subject:{}".format(subject)
file_name = os.path.join(data_base_dir, subject)
all_data_per_char, target_per_char, train_mode_per_block, all_data_per_char_as_matrix, target_per_char_as_matrix = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for noise_jump in range(-40*3,40*3,40):
all_data_per_char_noise, _, _, all_data_per_char_as_matrix_noise, _ = create_data_rep_training(
file_name, -200, 800, downsampe_params=8)
for rep_per_sub, cross_validation_indexes in enumerate(
list(cross_validation.KFold(len(train_mode_per_block) / 10, n_folds=4,
random_state=42, shuffle=True))):
batch_size = 20
select = 1
train_as_p300 = False
train_indexes = train_mode_per_block == 1
validation_indexes = train_mode_per_block == 2
test_indexes = train_mode_per_block != 1
if train_as_p300:
data_generator_batch = triplet_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
target_per_char_as_matrix[train_indexes],
batch_size=batch_size, select=select,
debug_mode=False)
else:
# cross_validation_indexes = list(cross_validation.KFold(len(train_mode_per_block)/10, n_folds=4,
# random_state=42, shuffle=True))
def flatten_repetitions(data_to_flatten):
return np.reshape(np.reshape(data_to_flatten.T * 10, (-1, 1)) + np.arange(10), (-1))
train_indexes = flatten_repetitions(cross_validation_indexes[0])
test_indexes = flatten_repetitions(cross_validation_indexes[1])
# data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes], shuffle_data=False)
#
# test_data_generator_batch = simple_data_generator_no_dict(all_data_per_char_as_matrix[train_indexes],
# target_per_char_as_matrix[train_indexes],
# shuffle_data=False)
train_data_all_subject.append(np.asarray(all_data_per_char_as_matrix[train_indexes]).astype(np.float32))
test_data_all_subject.append(np.asarray(all_data_per_char_as_matrix[test_indexes]).astype(np.float32))
train_tags_all_subject.append(target_per_char_as_matrix[train_indexes])
test_tags_all_subject.append(target_per_char_as_matrix[test_indexes])
break
eeg_sample_shape = (25, 55)
only_p300_model_1 = get_only_P300_model_LSTM_CNN(eeg_sample_shape)
only_p300_model_1.summary()
from keras.optimizers import RMSprop
only_p300_model_1.compile(optimizer=RMSprop(), loss='binary_crossentropy', metrics=['accuracy'], )
model = only_p300_model_1
print "after compile"
# model = LDA()
train_data = stats.zscore(np.vstack(train_data_all_subject), axis=1)
train_tags = np.vstack(train_tags_all_subject).flatten()
test_data = stats.zscore(np.vstack(test_data_all_subject), axis=1)
test_tags = np.vstack(test_tags_all_subject).flatten()
for i in range(1):
model.fit(train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]), train_tags,
verbose=1, nb_epoch=30, batch_size=600, shuffle=True)
accuracy_train, auc_score_train = predict_using_model(model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
print "accuracy_test {}:{}, auc_score_train:{} ".format(i, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(model,
train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]),
train_tags)
print "accuracy_train {}:{}, auc_score_train:{} ".format(i, accuracy_train, auc_score_train)
model.optimizer.lr.set_value(0.0001)
for i in range(1):
model.fit(train_data.reshape(train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]), train_tags,
verbose=1, nb_epoch=30, batch_size=600, shuffle=True)
accuracy_train, auc_score_train = predict_using_model(model,
test_data.reshape(test_data.shape[0] * test_data.shape[1],
test_data.shape[2], test_data.shape[3]),
test_tags)
print "accuracy_test {}:{}, auc_score_train:{} ".format(i, accuracy_train, auc_score_train)
accuracy_train, auc_score_train = predict_using_model(model,
train_data.reshape(
train_data.shape[0] * train_data.shape[1],
train_data.shape[2], train_data.shape[3]), train_tags)
print "accuracy_train {}:{}, auc_score_train:{} ".format(i, accuracy_train, auc_score_train)
model.save(r"c:\temp\{}.h5".format(model_file_name,overwrite=True))
print "end ----------{}-------".format(file_name)
pass
# from keras.models import Sequential
#
# from keras.layers import merge, Input, Dense, Flatten, Activation, Lambda, LSTM, noise
#
# eeg_sample_shape = (25, 55)
# only_p300_model_1 = get_only_P300_model_LSTM(eeg_sample_shape)
#
# use_p300net = False
# if use_p300net:
# model = get_P300_model(only_p300_model_1, select=select)
# else:
#
# only_p300_model_1.compile(optimizer = 'rmsprop',loss = 'binary_crossentropy', metrics=['accuracy'], )
# model= only_p300_model_1
# print "after compile"
#
#
#
#
# test_tags = target_per_char_as_matrix[test_indexes]
#
# test_data = all_data_per_char_as_matrix[test_indexes].reshape(-1,all_data_per_char_as_matrix.shape[2],all_data_per_char_as_matrix.shape[3])
#
# validation_tags = target_per_char_as_matrix[validation_indexes]
# vaidation_data = all_data_per_char_as_matrix[validation_indexes].reshape(-1,all_data_per_char_as_matrix.shape[2],all_data_per_char_as_matrix.shape[3])
#
#
# train_for_inspecting_tag = target_per_char_as_matrix[train_indexes]
# train_for_inspecting_data = all_data_per_char_as_matrix[train_indexes].reshape(-1,
# all_data_per_char_as_matrix.shape[2],
# all_data_per_char_as_matrix.shape[3])
# np.save(os.path.join(experiments_dir, RESULTS_DIR,
# subject[-7:-4] + "test_data_{}_".format(rep_per_sub) + ".npy"),test_data)
#
# np.save(os.path.join(experiments_dir, RESULTS_DIR,
# subject[-7:-4] + "train_for_inspecting_data_{}_".format(rep_per_sub) + ".npy"), train_for_inspecting_data)
#
# np.save(os.path.join(experiments_dir, RESULTS_DIR,
# subject[-7:-4] + "train_for_inspecting_tag_{}_".format(rep_per_sub) + ".npy"),
# train_for_inspecting_tag)
#
# np.save(os.path.join(experiments_dir, RESULTS_DIR,
# subject[-7:-4] + "test_tags_{}_".format(rep_per_sub) + ".npy"),
# test_tags)
# class LossHistory(keras.callbacks.Callback):
#
# def on_epoch_end(self, epoch, logs={}):
# from sklearn.metrics import roc_auc_score
# if epoch in [0,11, 12, 13]:
# save_path = os.path.join(experiments_dir, RESULTS_DIR,
# subject[-7:-4] + "weight_{}_{}_".format(rep_per_sub, epoch) + ".h5")
# self.model.save(save_path)
# # os.path.join( experiments_dir, RESULTS_DIR, subject[-7:-4] + "_{}_".format(rep_per_sub) + ".npy")
# # self.save('')
# all_prediction_P300Net = model.predict(stats.zscore(test_data, axis=1).astype(np.float32))
# actual = np.argmax(np.mean(all_prediction_P300Net.reshape((-1, 10, 30)), axis=1), axis=1);
# gt = np.argmax(np.mean(test_tags.reshape((-1, 10, 30)), axis=1), axis=1)
# tests_accuracy = np.sum(actual == gt) / float(len(gt))
# auc_score_test = roc_auc_score(test_tags.flatten(), all_prediction_P300Net)
#
#
# # all_prediction_P300Net = model.predict(stats.zscore(vaidation_data, axis=1).astype(np.float32))
# # actual = np.argmax(np.mean(all_prediction_P300Net.reshape((-1, 10, 30)), axis=1), axis=1);
# # gt = np.argmax(np.mean(validation_tags.reshape((-1, 10, 30)), axis=1), axis=1)
# # validation_accuracy = np.sum(actual == gt) / float(len(gt))
# # auc_score_validation = roc_auc_score(validation_tags.flatten(), all_prediction_P300Net)
#
# all_prediction_P300Net = model.predict(stats.zscore(train_for_inspecting_data, axis=1).astype(np.float32))
# actual = np.argmax(np.mean(all_prediction_P300Net.reshape((-1, 10, 30)), axis=1), axis=1);
# gt = np.argmax(np.mean(train_for_inspecting_tag.reshape((-1, 10, 30)), axis=1), axis=1)
# train_accuracy = np.sum(actual == gt) / float(len(gt))
# auc_score_train = roc_auc_score(train_for_inspecting_tag.flatten(), all_prediction_P300Net)
# from keras.callbacks import ModelCheckpoint
#
# logs['tests_accuracy'] = tests_accuracy
# logs['accuracy_train'] = train_accuracy
# logs['validation_accuracy'] = train_accuracy
# logs['auc_score_train'] = auc_score_train
# logs['auc_score_test'] = auc_score_test
# logs['auc_score_validation'] = auc_score_test
# logs['subject'] = subject
#
#
#
#
# print "\n*{} epoch:{} mid****accuracy*: {} *accuracy_train*:{} auc_score_train:{} auc_score_test:{} \n"\
# .format(subject,epoch,tests_accuracy,train_accuracy, auc_score_train, auc_score_test)
#
#
#
# history = LossHistory()
#
# # model.fit_generator(data_generator_batch, 7200, 20, callbacks=[history],nb_worker=1,max_q_size=1)
#
# use_generator = False
# if use_generator:
# log_history = model.fit_generator(data_generator_batch, 7200, 20, callbacks=[history], nb_worker=1, max_q_size=1)
# else:
# samples_weight = np.ones_like(data_generator_batch[1])
# samples_weight[samples_weight == 1] = 30
# log_history = model.fit(data_generator_batch[0], data_generator_batch[1], nb_epoch=21, batch_size=900,verbose=1,
# callbacks=[history], shuffle=False, validation_split=0.1,sample_weight=samples_weight)
#
# results_directory =os.path.join(experiments_dir, RESULTS_DIR)
# if not os.path.exists(results_directory):
# os.makedirs(results_directory)
#
# #np.save(os.path.join(experiments_dir, RESULTS_DIR, subject[-7:-4]+"_{}_".format(rep_per_sub)+".npy"), log_history.history)
#
# all_prediction_P300Net = model.predict(stats.zscore(test_data,axis=1).astype(np.float32))
# import theano
# import theano.tensor as T
#
# x = T.dmatrix('x')
# softmax_res_func = theano.function([x], T.nnet.softmax(x))
#
#
# actual = np.argmax(np.mean(all_prediction_P300Net.reshape((-1, 10, 30)), axis=1), axis=1);
# gt = np.argmax(np.mean(test_tags.reshape((-1, 10, 30)), axis=1), axis=1)
# accuracy = np.sum(actual == gt) / float(len(gt))
# print "subject:{}, accuracy: {}".format(subject, accuracy)
# break
# count False positive
# print ("temp")
if __name__ == "__main__":
all_subjects = ["RSVP_Color116msVPgcd.mat",
"RSVP_Color116msVPgcc.mat",
"RSVP_Color116msVPpia.mat",
"RSVP_Color116msVPgcb.mat",
"RSVP_Color116msVPgcf.mat",
"RSVP_Color116msVPgcg.mat",
"RSVP_Color116msVPgch.mat",
"RSVP_Color116msVPiay.mat",
"RSVP_Color116msVPicn.mat",
"RSVP_Color116msVPicr.mat",
"RSVP_Color116msVPfat.mat",
];
for left_out_subject in all_subjects[3:]:
training_set = list(set(all_subjects).difference(set([left_out_subject])))
model_file_name = os.path.basename(left_out_subject).split(".")[0]
train_on_subjset(training_set, model_file_name)
print "stam"