def run_tsgan(data_name, dir_data, ratios, tag):
## train gan
tf.reset_default_graph()
x_tr, y_tr, _, _, _ = ucr.load_ucr_flat(data_name, dir_data)
x = x_tr
x = np.reshape(x, x.shape + (1, 1))
conf = Config(x,
data_name,
tag,
x.shape[1],
x.shape[2],
x.shape[3],
state='train')
train.train(conf)
## classification
dir_gan = 'cache/{}'.format(tag)
feature_type = 'local-max'
norm_type = 'tanh'
model_name = 'LR'
model = base.StandardClassifierDic[model_name]
features_tr, y_tr, features_te, y_te, n_classes = encode(
data_name, dir_data, feature_type, norm_type, dir_gan)
res = {'ratio': [], 'distr': [], 'acc': [], 'acc_te': []}
for r in ratios:
features_tr_cur, y_tr_cur, _, _ = utils.split_stratified(
features_tr, y_tr, r)
acc, t = base.classify(model, features_tr_cur, y_tr_cur, features_te,
y_te)
res['ratio'].append(r)
res['distr'].append(utils.distribute_y_json(y_tr_cur))
res['acc'].append(acc[0])
res['acc_te'].append(acc[1])
df_res = pd.DataFrame(res)
return df_res
def encode(data_name, dir_data, feature_type, dir_gan):
tf.reset_default_graph()
## load data
x_tr_2d, y_tr, _, _, n_classes = ucr.load_ucr_flat(data_name, dir_data)
x_tr = np.reshape(x_tr_2d, x_tr_2d.shape + (1, 1))
## set up GAN
dir_checkpoint = os.path.join(dir_gan, data_name, 'checkpoint')
conf = Config(x_tr,
'',
'',
x_tr.shape[1],
x_tr.shape[2],
x_tr.shape[3],
state='test')
gan = TSGAN(conf.dim_z, conf.dim_h, conf.dim_w, conf.dim_c,
conf.random_seed, conf.g_lr, conf.d_lr, conf.g_beta1,
conf.d_beta1, conf.gf_dim, conf.df_dim)
## start to run
with tf.Session(config=tf_conf) as sess:
isload, counter = gan.load(sess, dir_checkpoint)
if not isload:
raise Exception("[!] Train a model first, then run test mode")
input_shape = [x_tr.shape[1], x_tr.shape[2], x_tr.shape[3]]
encoder = TSGANEncoder(gan, input_shape, type=feature_type)
layer1, layer2 = encode_on_batch(encoder, sess, x_tr, conf.batch_size)
return x_tr_2d, y_tr, layer1, layer2
def run_baselines(dir_data, data_name_list, dir_out_root):
dir_out = os.path.join(dir_out_root, 'raw')
n_runs = 3
for ir in range(n_runs):
dir_out_cur = os.path.join(dir_out, 'run{}'.format(ir))
make_dir(dir_out_cur)
for model_name, model in base.StandardClassifierDic.items():
print("******** processing model {}".format(model_name))
res = {
'dataset': [],
'acc': [],
'acc_te': [],
'time': [],
'time_te': []
}
for data_name in data_name_list:
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(
data_name, dir_data)
acc, t = base.classify(model, x_tr, y_tr, x_te, y_te)
res['dataset'].append(data_name)
res['acc'].append(acc[0])
res['acc_te'].append(acc[1])
res['time'].append(t[0])
res['time_te'].append(t[1])
print(model_name, data_name, acc, t)
df = pd.DataFrame(res)
df.to_csv(os.path.join(dir_out_cur, '{}.csv'.format(model_name)),
index=False)
def run_raw(data_name, dir_data, dir_out):
path_out = os.path.join(dir_out, data_name, 'raw')
if os.path.exists(path_out) is False:
os.makedirs(path_out)
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(data_name, dir_data)
np.savetxt(os.path.join(path_out, 'try'), y_tr, delimiter=',')
np.savetxt(os.path.join(path_out, 'tey'), y_te, delimiter=',')
run_manifold(x_tr, y_tr, x_te, y_te, path_out)
def run_standard(data_name, dir_data, ratios):
model_name = 'LR'
model = base.StandardClassifierDic[model_name]
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(data_name, dir_data)
res = {'ratio': [], 'distr': [], 'acc': [], 'acc_te': []}
for r in ratios:
x_tr_cur, y_tr_cur, _, _ = utils.split_stratified(x_tr, y_tr, r)
acc, t = base.classify(model, x_tr_cur, y_tr_cur, x_te, y_te)
res['ratio'].append(r)
res['distr'].append(utils.distribute_y_json(y_tr_cur))
res['acc'].append(acc[0])
res['acc_te'].append(acc[1])
df_res = pd.DataFrame(res)
return df_res
def run_fcn(data_name, dir_data, ratios):
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(data_name, dir_data)
x_tr = x_tr.reshape(x_tr.shape + (1, ))
x_te = x_te.reshape(x_te.shape + (1, ))
y_te_onehot = utils.dense_to_one_hot(y_te, n_classes)
n_epochs = 200
res = {'ratio': [], 'distr': [], 'acc': [], 'acc_te': []}
for r in ratios:
print("*** processing ratio={}".format(r))
x_tr_cur, y_tr_cur, _, _ = utils.split_stratified(x_tr, y_tr, r)
y_tr_cur_onehot = utils.dense_to_one_hot(y_tr_cur, n_classes)
model = FCN(x_tr_cur.shape[1:], n_classes)
df_metrics = model.fit(x_tr_cur, y_tr_cur_onehot, n_epochs=n_epochs)
acc_te = model.evaluate(x_te, y_te_onehot)
last = df_metrics.loc[df_metrics.shape[0] - 1, :]
res['ratio'].append(r)
res['distr'].append(utils.distribute_y_json(y_tr_cur))
res['acc'].append(last['acc'])
res['acc_te'].append(acc_te)
df_res = pd.DataFrame(res)
return df_res
def run_raw(data_name_list, dir_data, dir_out):
print("******** kmeans over raw data")
res = {'dataset': [], 'randIndex': [], 'time': []}
n_datasets = len(data_name_list)
for i, data_name in enumerate(data_name_list):
print("******** [{}/{}] processing {}".format(i, n_datasets,
data_name))
## load data
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(
data_name, dir_data)
x = np.vstack([x_tr, x_te])
y = np.hstack([y_tr, y_te])
## start to run
ri, t = kmeans(x, y, n_classes)
res['dataset'].append(data_name)
res['randIndex'].append(ri)
res['time'].append(t)
## save result
df = pd.DataFrame(res)
df.to_csv(os.path.join(dir_out, 'kmeans_raw.csv'), index=False)
return df
def start_training(data_name_list, dir_data_root, mode, tag):
n_datasets = len(data_name_list)
for i, data_name in enumerate(data_name_list):
print("******* [{}/{}] processing {}".format(i + 1, n_datasets,
data_name))
tf.reset_default_graph()
x_tr, _, x_te, _, _ = ucr.load_ucr_flat(data_name, dir_data_root)
x_tr = np.reshape(x_tr, x_tr.shape + (1, 1))
x_te = np.reshape(x_te, x_te.shape + (1, 1))
if mode == 'half':
x = x_tr
elif mode == 'all':
x = np.vstack([x_tr, x_te])
else:
raise ValueError("Can not find mode = {}".format(mode))
conf = Config(x,
data_name,
tag,
x.shape[1],
x.shape[2],
x.shape[3],
state='train')
train.train(conf)
def split_test2valid_stratified(
in_data_dir_root,
out_dir_parent,
out_dir_base='UCR_TS_Archive_2015_split-test-to-valid-stratified_valid-size-same-as-train'
):
""" Split the original test set to generate a validation set and the number samples of
each class in validation set is the same as the train set.
:param in_data_dir_root: this path shouldn't include Validation set.
:param out_dir_parent:
:param out_dir_base:
:param data_name_list:
:return:
"""
out_data_dir_root = os.path.join(out_dir_parent, out_dir_base)
data_name_list = get_dataset_testset_double_than_trainset_for_each_class(
in_data_dir_root)
print("This program will process {} data sets.".format(
len(data_name_list)))
print("They are: ", data_name_list)
print()
for fname in data_name_list:
print("processing data {}".format(fname))
# prepare data
X_train, y_train, X_test, y_test = ucr.load_ucr_flat(
fname, in_data_dir_root)
distr_train = utils.distribute_dataset(X_train, y_train)
distr_test = utils.distribute_dataset(X_test, y_test)
# split test set to validation set
X_valid, y_valid = [], []
X_test_new, y_test_new = [], []
for key in distr_train.keys():
num_tr = distr_train[key].shape[0]
inds_te = np.arange(distr_test[key].shape[0])
np.random.shuffle(inds_te)
X_valid_temp = distr_test[key][inds_te[:num_tr]]
X_valid.append(X_valid_temp)
y_valid.append(np.ones([X_valid_temp.shape[0], 1], int) * key)
X_test_new_temp = distr_test[key][inds_te[num_tr:]]
X_test_new.append(X_test_new_temp)
y_test_new.append(
np.ones([X_test_new_temp.shape[0], 1], int) * key)
X_valid = np.concatenate(X_valid, axis=0)
y_valid = np.concatenate(y_valid, axis=0)
X_test_new = np.concatenate(X_test_new, axis=0)
y_test_new = np.concatenate(y_test_new, axis=0)
# pack data set in UCR format
trainset = np.concatenate([y_train[:, np.newaxis], X_train], axis=1)
validset = np.concatenate([y_valid, X_valid], axis=1)
testset = np.concatenate([y_test_new, X_test_new], axis=1)
# make dir for specific data set
out_path = os.path.join(out_data_dir_root, fname)
if os.path.exists(out_path):
shutil.rmtree(out_path)
os.makedirs(out_path)
# output data to file
str_fmt = '%path,' + '%.4f,' * (X_train.shape[1])
str_fmt = str_fmt[:(len(str_fmt) - 1)]
np.savetxt(os.path.join(out_path, '{}_TRAIN'.format(fname)),
trainset,
fmt=str_fmt,
delimiter=',')
np.savetxt(os.path.join(out_path, '{}_TEST'.format(fname)),
testset,
fmt=str_fmt,
delimiter=',')
np.savetxt(os.path.join(out_path, '{}_VALID'.format(fname)),
validset,
fmt=str_fmt,
delimiter=',')
from data import ucr
import os
import numpy as np
import pandas as pd
if __name__ == '__main__':
dir_data = '../../dataset/UCR_TS_Archive_2015'
dir_out = 'result'
res = {'dataset': [], 'mean': [], 'std': []}
data_name_list = ucr.get_data_name_list(dir_data)
for data_name in data_name_list:
x_tr, y_tr, x_te, y_te, n_classes = ucr.load_ucr_flat(
data_name, dir_data)
x = np.vstack([x_tr, x_te])
mean = np.round(np.mean(np.mean(x, axis=1)), 2)
std = np.round(np.mean(np.std(x, axis=1)), 2)
res['dataset'].append(data_name)
res['mean'].append(mean)
res['std'].append(std)
df = pd.DataFrame(res)
df.to_csv(os.path.join(dir_out, 'check_znorm.csv'), index=False)