def main():
"""
"""
#a = mlfdb.mlfdb()
a = db.mlfdb()
io = _io.IO()
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
dst_dataset = options.dataset+'-validation'
logging.info('Splitting time range {} - {} from {} to {} as validation set'.format(starttime.strftime('%Y-%m-%d'), endtime.strftime('%Y-%m-%d'), options.dataset, dst_dataset))
_, param_names = io.read_parameters(options.parameters, drop=2)
param_names += ['count_flash', 'precipitation3h', 'precipitation6h']
meta_columns = ['loc_id', 'time', 'lon', 'lat']
count = 0
day_step = 1
hour_step = 0
start = starttime
end = start + timedelta(days=day_step, hours=hour_step)
if end > endtime: end = endtime
while end <= endtime:
logging.info('Processing time range {} - {}'.format(start.strftime('%Y-%m-%d %H:%M'), end.strftime('%Y-%m-%d %H:%M')))
try:
data = a.get_rows(options.dataset,
starttime=start,
endtime=end,
rowtype='feature',
return_type='pandas',
parameters=param_names)
except ValueError as e:
print(e)
start = end
end = start + timedelta(days=day_step, hours=hour_step)
continue
logging.debug(data.iloc[0:3])
#logging.debug('Features metadata shape: {} | Features shape: {}'.format(f_metadata.shape, f_data.shape))
logging.info('Processing {} rows...'.format(len(data)))
if len(data) > 0:
count += a.add_rows_from_df(df=data,
_type='feature',
dataset=dst_dataset
)
start = end
end = start + timedelta(days=day_step, hours=hour_step)
logging.info('Inserted {} rows into dataset {}'.format(count, options.dst_dataset))
def main():
"""
Get forecasted delay for every station
"""
io = _io.IO()
viz = _viz.Viz()
params, _ = io.read_parameters(options.parameters_filename)
model = io.load_scikit_model(options.model_file)
print(params)
print(len(params))
print(len(model.feature_importances_))
fname = 'results/manual/rfc_feature_importance.png'
viz.rfc_feature_importance(model.feature_importances_,
fname,
feature_names=params[2:] +
['precipitation3h', 'precipitation6h'],
fontsize=18)
def main():
"""
Main program
"""
local_device_protos = device_lib.list_local_devices()
logging.info(
[x.name for x in local_device_protos if x.device_type == 'GPU'])
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz(io)
starttime, endtime = io.get_dates(options)
#save_path = options.save_path+'/'+options.config_name
logging.info('Using dataset {}.{} and time range {} - {}'.format(
options.feature_dataset, options.feature_table,
starttime.strftime('%Y-%m-%d'), endtime.strftime('%Y-%m-%d')))
all_param_names = list(
set(options.label_params + options.feature_params +
options.meta_params))
aggs = io.get_aggs_from_param_names(options.feature_params)
logging.info('Reading data...')
bq.set_params(batch_size=2500000,
loc_col='trainstation',
project=options.project,
dataset=options.feature_dataset,
table=options.feature_table,
parameters=all_param_names,
only_winters=options.only_winters)
data = bq.get_rows(starttime, endtime)
data = io.filter_train_type(labels_df=data,
train_types=options.train_types,
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=[],
aggs=aggs)
if options.y_avg_hours is not None:
data = io.calc_running_delay_avg(data, options.y_avg_hours)
if options.y_avg:
data = io.calc_delay_avg(data)
data.sort_values(by=['time', 'trainstation'], inplace=True)
if options.month:
logging.info('Adding month to the dataset...')
data['month'] = data['time'].map(lambda x: x.month)
options.feature_params.append('month')
if options.normalize:
logging.info('Normalizing data...')
xscaler = StandardScaler()
yscaler = StandardScaler()
labels = data.loc[:, options.label_params].astype(
np.float32).values.reshape((-1, 1))
scaled_labels = pd.DataFrame(yscaler.fit_transform(labels),
columns=['delay'])
non_scaled_data = data.loc[:, options.meta_params + ['class']]
scaled_features = pd.DataFrame(xscaler.fit_transform(
data.loc[:, options.feature_params]),
columns=options.feature_params)
data = pd.concat([non_scaled_data, scaled_features, scaled_labels],
axis=1)
fname = options.save_path + '/xscaler.pkl'
io.save_scikit_model(xscaler, fname, fname)
fname = options.save_path + '/yscaler.pkl'
io.save_scikit_model(yscaler, fname, fname)
if options.pca:
logging.info('Doing PCA analyzis for the data...')
ipca = IncrementalPCA(n_components=options.pca_components,
whiten=options.whiten,
copy=False)
non_processed_data = data.loc[:, options.meta_params +
options.label_params]
processed_data = data.loc[:, options.feature_params]
ipca.fit(processed_data)
processed_features = pd.DataFrame(ipca.transform(processed_data))
data = pd.concat([non_processed_data, processed_data], axis=1)
fname = options.output_path + '/ipca_explained_variance.png'
viz.explained_variance(ipca, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
# Divide data to normal and delayed cases
data_test = data[(data.loc[:, 'class'] >= options.class_limit)]
data = data[(data.loc[:, 'class'] < options.class_limit)]
data_train, data_val = train_test_split(data, test_size=0.33)
data_train_x = data_train.loc[:, options.feature_params].values
data_train_y = data_train.loc[:, options.label_params].values
data_val_x = data_val.loc[:, options.feature_params].values
data_val_y = data_val.loc[:, options.label_params].values
# Initialization
logging.info('Building model...')
model = convlstm.Autoencoder(data_train_x.shape[1]).get_model()
losses, val_losses, accs, val_accs, steps = [], [], [], [], []
boardcb = TensorBoard(log_dir=options.log_dir,
histogram_freq=0,
write_graph=True,
write_images=True)
logging.info('Data shape: {}'.format(
data_train.loc[:, options.feature_params].values.shape))
history = model.fit(data_train_x,
data_train_x,
validation_data=(data_val_x, data_val_x),
epochs=3,
callbacks=[boardcb]) #, batch_size=64)
history_fname = options.save_path + '/history.pkl'
io.save_keras_model(options.save_file, history_fname, model,
history.history)
# Reconstruction errors
logging.info('Plotting reconstruction errors...')
errors = {}
logging.info('Train:')
errors = get_reconst_error(model, data_train_x, data_train_y.ravel(),
errors, 'Train')
logging.info('Validation:')
errors = get_reconst_error(model, data_val_x, data_val_y.ravel(), errors,
'Validation')
logging.info('Test:')
data_test_x = data_test.loc[:, options.feature_params].values
data_test_y = data_test.loc[:, options.label_params].values
errors = get_reconst_error(model, data_test_x, data_test_y.ravel(), errors,
'Test')
for i in np.arange(4):
fname = options.output_path + '/reconstruction_error_{}.png'.format(i)
viz.reconstruction_error(errors, desired_class=i, filename=fname)
fname = options.output_path + '/reconstruction_error_all.png'.format(i)
viz.reconstruction_error(errors, filename=fname)
def main():
"""
Main program
"""
local_device_protos = device_lib.list_local_devices()
logging.info(
[x.name for x in local_device_protos if x.device_type == 'GPU'])
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
logging.info('Using dataset {} and time range {} - {}'.format(
options.feature_dataset, starttime.strftime('%Y-%m-%d'),
endtime.strftime('%Y-%m-%d')))
# In classification use always class as label param
option.label_params = 'class'
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
logging.info('Building model...')
model = convlstm.Classifier().get_model()
logging.info('Reading data...')
bq.set_params(starttime,
endtime,
batch_size=2500000,
loc_col='trainstation',
project=options.project,
dataset=options.feature_dataset,
table=options.feature_table,
parameters=all_param_names)
data = bq.get_rows()
data = io.filter_train_type(labels_df=data,
train_types=options.train_types,
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=['train_count', 'delay'],
aggs=aggs)
log_class_dist(data.loc[:, 'class'])
data.sort_values(by=['time', 'trainstation'], inplace=True)
if options.normalize:
logging.info('Normalizing data...')
xscaler = StandardScaler()
non_scaled_data = data.loc[:, options.meta_params + ['class']]
scaled_features = pd.DataFrame(xscaler.fit_transform(
data.loc[:, options.feature_params]),
columns=options.feature_params)
data = pd.concat([non_scaled_data, scaled_features], axis=1)
if options.pca:
logging.info('Doing PCA analyzis for the data...')
ipca = IncrementalPCA(n_components=options.pca_components,
whiten=options.whiten,
copy=False)
non_processed_data = data.loc[:, options.meta_params +
options.label_params]
processed_data = data.loc[:, options.feature_params]
ipca.fit(processed_data)
processed_features = pd.DataFrame(ipca.transform(processed_data))
data = pd.concat([non_processed_data, processed_data], axis=1)
fname = options.output_path + '/ipca_explained_variance.png'
viz.explained_variance(ipca, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
data_train, data_test = train_test_split(data, test_size=0.33)
# Define model
batch_size = io.get_batch_size(data_train,
options.pad_strategy,
quantile=options.quantile)
batch_size = 512
logging.info('Batch size: {}'.format(batch_size))
# Initialization
losses, val_losses, accs, val_accs, steps = [], [], [], [], []
boardcb = TensorBoard(log_dir=options.log_dir,
histogram_freq=0,
write_graph=True,
write_images=True)
logging.info('Data shape: {}'.format(
data_train.loc[:, options.feature_params].values.shape))
class_weights = class_weight.compute_class_weight(
'balanced', np.unique(data_train.loc[:, 'class'].values),
data_train.loc[:, 'class'].values)
weights = {}
i = 0
for w in class_weights:
weights[i] = w
i += 1
logging.info('Class weights: {}'.format(weights))
data_gen = TimeseriesGenerator(
data_train.loc[:, options.feature_params].values,
to_categorical(data_train.loc[:, 'class'].values),
length=24,
sampling_rate=1,
batch_size=batch_size)
data_test_gen = TimeseriesGenerator(
data_test.loc[:, options.feature_params].values,
to_categorical(data_test.loc[:, 'class'].values),
length=24,
sampling_rate=1,
batch_size=batch_size)
logging.info('X batch size: {}'.format(data_gen[0][0].shape))
logging.info('Y batch size: {}'.format(data_gen[1][0].shape))
history = model.fit_generator(data_gen,
validation_data=data_test_gen,
epochs=3,
class_weight=class_weights,
callbacks=[boardcb]) #, batch_size=64)
model_fname = options.save_path + '/model.json'
weights_fname = options.save_path + '/weights.h5'
history_fname = options.save_path + '/history.pkl'
io.save_model(model_fname, weights_fname, history_fname, model,
history.history)
scores = model.evaluate_generator(data_test_gen)
i = 0
error_data = {}
for name in model.metrics_names:
logging.info('{}: {:.4f}'.format(name, scores[i]))
error_data[name] = [scores[i]]
i += 1
fname = '{}/training_time_validation_errors.csv'.format(
options.output_path)
io.write_csv(error_data, filename=fname, ext_filename=fname)
pred_proba = model.predict_generator(data_test_gen)
pred = np.argmax(pred_proba, axis=1)
log_class_dist(pred)
#print(history.history)
fname = options.output_path + '/learning_over_time.png'
viz.plot_nn_perf(history.history,
metrics={
'[%]': {
'acc': 'Accuracy',
'F1': 'F1 Score',
'Precision': 'Precision',
'Recall': 'Recall'
}
},
filename=fname)
def main():
"""
Get data from db and save it as csv
"""
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
print('Using dataset {} and time range {} - {}'.format(
options.feature_dataset, starttime.strftime('%Y-%m-%d'),
endtime.strftime('%Y-%m-%d')))
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
if options.pca:
ipca = IncrementalPCA(n_components=options.pca_components,
whiten=options.whiten,
copy=False)
rmses, maes, r2s, vars, start_times, end_times, end_times_obj = [], [], [], [], [], [], []
start = starttime
end = endtime
print('Processing time range {} - {}'.format(
start.strftime('%Y-%m-%d %H:%M'), end.strftime('%Y-%m-%d %H:%M')))
try:
print('Reading data...')
data = bq.get_rows(start,
end,
loc_col='trainstation',
project=options.project,
dataset=options.feature_dataset,
table=options.feature_table,
parameters=all_param_names)
data = io.filter_train_type(labels_df=data,
train_types=options.train_types,
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=['delay'],
aggs=aggs)
if options.y_avg_hours is not None:
data = io.calc_running_delay_avg(data, options.y_avg_hours)
data.sort_values(by=['time', 'trainstation'], inplace=True)
if options.impute:
print('Imputing missing values...')
data.drop(columns=['train_type'], inplace=True)
data = imputer.fit_transform(data)
data.loc[:, 'train_type'] = None
if options.model == 'ard' and len(data) > options.n_samples:
print('Sampling {} values from data...'.format(options.n_samples))
data = data.sample(options.n_samples)
#l_data = data.loc[:,options.meta_params + options.label_params]
#f_data = data.loc[:,options.meta_params + options.feature_params]
except ValueError as e:
f_data, l_data = [], []
#f_data.rename(columns={'trainstation':'loc_name'}, inplace=True)
#logging.debug('Labels shape: {}'.format(l_data.shape))
print('Processing {} rows...'.format(len(data)))
#assert l_data.shape[0] == f_data.shape[0]
target = data.loc[:, options.label_params].astype(np.float32).values
#print(f_data.columns)
#features = f_data.drop(columns=['loc_name', 'time']).astype(np.float32).values
features = data.loc[:, options.feature_params].astype(np.float32).values
X_train, X_test, y_train, y_test = train_test_split(features,
target,
test_size=0.33)
logging.debug('Features shape: {}'.format(X_train.shape))
n_samples, n_dims = X_train.shape
if options.normalize:
print('Normalizing data...')
print(X_train)
scaler = StandardScaler()
X_train = scaler.fit_transform(X_train)
X_test = scaler.fit_transform(X_test)
if options.pca:
print('Doing PCA analyzis for the data...')
X_train = ipca.fit_transform(X_train)
fname = options.output_path + '/ipca_explained_variance.png'
viz.explained_variance(ipca, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
X_test = ipca.fit_transform(X_test)
logging.debug('Features shape after pre-processing: {}'.format(
X_train.shape))
print('Training...')
print(X_train.shape)
input_dim = X_train.shape[1]
#k1 = gpflow.kernels.Matern52(input_dim, lengthscales=0.3)
#k_seasonal = gpflow.kernels.Periodic(input_dim=input_dim, period=2190, name='k_seasonal')
#k_small = gpflow.kernels.Periodic(input_dim=input_dim, period=120, name='k_small')
k_weather = gpflow.kernels.RBF(input_dim=input_dim, ARD=True)
#k_noise = gpflow.kernels.White(input_dim=input_dim)
#k = k_seasonal + k_weather + k_noise
k = k_weather
Z = np.random.rand(150, input_dim)
if options.cv:
logging.info('Doing random search for hyper parameters...')
param_grid = {"length_scale": [0.1, 1, 2], "whiten": [True, False]}
model = GP(dim=input_dim, Z=Z)
random_search = RandomizedSearchCV(model,
param_distributions=param_grid,
n_iter=int(options.n_iter_search),
n_jobs=-1)
random_search.fit(X_train, y_train)
logging.info("RandomizedSearchCV done.")
sys.exit()
else:
model = GP(dim=input_dim, Z=Z)
model.fit(X_train.astype(np.float64),
y_train.reshape((-1, 1)).astype(np.float64))
model.save(options.save_file)
print('Training finished')
print(model.model)
# Z_list = options.z_list.split(',')
#for size in Z_list:
# with tf.Session() as sess:
#custom_config = gpflow.settings.get_settings()
#custom_config.verbosity.tf_compile_verb = True
#with gpflow.settings.temp_settings(custom_config), gpflow.session_manager.get_session().as_default():
#Z = X_train[::5].copy()
# Z = np.random.rand(int(size), 19)
# print('Training with inducing points: {}'.format(Z.shape))
#
# # model = gpflow.models.SVGP(X_train.astype(np.float64),
# # y_train.reshape((-1,1)).astype(np.float64),
# # kern=k,
# # likelihood=gpflow.likelihoods.Gaussian(),
# # Z=Z,
# # #Z=X_train.copy(),
# # minibatch_size=100,
# # whiten=options.normalize
# # )
# # #model.likelihood.variance = 0.01
# #
# # model.compile(session=sess)
# # opt = gpflow.train.ScipyOptimizer()
# # opt.minimize(model)
#
# model = GP(dim=19,
# Z=Z
# )
# model.fit(X_train.astype(np.float64),
# y_train.reshape((-1,1)).astype(np.float64))
#
# model.save(options.save_file)
#
# print('Training finished')
# print(model.model)
#fname=options.output_path+'/svga_performance.png'
#viz.plot_svga(model, fname)
# k_long_term = 66.0**2 * RBF(length_scale=67.0)
# k_seasonal = 2.4**2 * RBF(length_scale=90.0)* ExpSineSquared(length_scale=150, periodicity=1.0, periodicity_bounds=(0,10000))
# k_medium_term = 0.66**2 * RationalQuadratic(length_scale=1.2, alpha=0.78)
# k_noise = 0.18**2 * RBF(length_scale=0.134) + WhiteKernel(noise_level=0.19**2)
# #kernel_gpml = k_long_term + k_seasonal + k_medium_term + k_noise
# kernel_gpml = k_long_term + k_seasonal + k_medium_term + k_noise
#
# model = GaussianProcessRegressor(kernel=kernel_gpml, #alpha=0,
# optimizer=None, normalize_y=True)
# Metrics
y_pred, var = model.predict_f(X_test)
rmse = np.sqrt(mean_squared_error(y_test, y_pred))
mae = mean_absolute_error(y_test, y_pred)
r2 = r2_score(y_test, y_pred)
rmses.append(rmse)
maes.append(mae)
r2s.append(r2)
vars.append(var.mean())
start_times.append(start.strftime('%Y-%m-%dT%H:%M:%S'))
end_times.append(end.strftime('%Y-%m-%dT%H:%M:%S'))
end_times_obj.append(end)
print('RMSE: {:.2f}'.format(rmse))
print('MAE: {:.2f}'.format(mae))
print('Variance: {:.2f}-{:.2f}'.format(var.min(), var.max()))
print('R2 score: {:.2f}'.format(r2))
#io.save_scikit_model(model, filename=options.save_file, ext_filename=options.save_file)
if options.model == 'rf':
fname = options.output_path + '/rfc_feature_importance.png'
viz.rfc_feature_importance(model.feature_importances_, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
try:
fname = options.output_path + '/learning_over_time.png'
viz.plot_learning_over_time(end_times_obj,
rmses,
maes,
r2s,
filename=fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
except Exception as e:
logging.error(e)
error_data = {
'start_times': start_times,
'end_times': end_times,
'rmse': rmses,
'mae': maes,
'var': vars,
'r2': r2s
}
fname = '{}/training_time_validation_errors.csv'.format(
options.output_path)
io.write_csv(error_data, filename=fname, ext_filename=fname)
def main():
"""
Get data from db and save it as csv
"""
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
logging.info('Using dataset {} and time range {} - {}'.format(
options.feature_dataset, starttime.strftime('%Y-%m-%d'),
endtime.strftime('%Y-%m-%d')))
# Get params
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
io._download_from_bucket(options.save_file, options.save_file)
logging.info('Loadung model from {}...'.format(options.save_file))
predictor = io.load_scikit_model(options.save_file)
# Init error dicts
avg_delay = {}
avg_pred_delay = {}
station_count = 0
all_times = set()
station_rmse = {}
station_median_abs_err = {}
station_r2 = {}
# If stations are given as argument use them, else use all stations
logging.info('Loading stations from {}...'.format(options.stations_file))
stationList = io.get_train_stations(options.stations_file)
if options.stations is not None:
stations = options.stations.split(',')
else:
stations = stationList.keys()
# Get data
#stationName = '{} ({})'.format(stationList[station]['name'], station)
#logging.info('Processing station {}'.format(stationName))
# Read data and filter desired train types (ic and commuter)
logging.info('Loading data...')
data = bq.get_rows(starttime,
endtime,
loc_col='trainstation',
project=options.project,
dataset='trains_testset',
table='features_1',
parameters=all_param_names,
locations=stations)
data = io.filter_train_type(labels_df=data,
train_types=['K', 'L'],
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=['delay'],
aggs=aggs)
assert len(data) > 0, "Empty data"
if options.y_avg_hours is not None:
data = io.calc_running_delay_avg(data, options.y_avg_hours)
data.sort_values(by=['time', 'trainstation'], inplace=True)
logging.info('Processing {} rows...'.format(len(data)))
# Pick times for creating error time series
all_times = data.loc[:, 'time'].unique()
#station_count += 1
# Pick feature and label data from all data
l_data = data.loc[:, options.meta_params + options.label_params]
f_data = data.loc[:, options.meta_params + options.feature_params]
target = l_data['delay'].astype(np.float64).values.ravel()
features = f_data.drop(columns=['trainstation', 'time']).astype(
np.float64).values
# Get data
logging.info('Predicting...')
y_pred = predictor.predict(features)
# Calculate quantiles
logging.info('Calculating fractiles...')
groups, avg, pred = io.pred_fractiles(l_data, y_pred, stationList)
# Go through stations
for station in stations:
data = pred.loc[pred['trainstation'] == station, :]
times = data.loc[:, 'time']
if len(data) < 1:
continue
group = pred.loc[pred['trainstation'] == station, 'group'].values[0]
stationName = '{} ({} | Group {})'.format(stationList[station]['name'],
station, group)
logging.info('Processing station {} (having {} rows)...'.format(
station, len(data)))
logging.info('Calculating errors for given station...')
rmse = math.sqrt(
metrics.mean_squared_error(data.loc[:, 'delay'],
data.loc[:, 'pred_delay']))
median_abs_err = metrics.median_absolute_error(
data.loc[:, 'delay'], data.loc[:, 'pred_delay'])
r2 = metrics.r2_score(data.loc[:, 'delay'], data.loc[:, 'pred_delay'])
# Put errors to timeseries
station_rmse[station] = rmse
station_median_abs_err[station] = median_abs_err
station_r2[station] = r2
logging.info('RMSE for station {}: {}'.format(stationName, rmse))
logging.info('Mean absolute error for station {}: {}'.format(
stationName, median_abs_err))
logging.info('R2 score for station {}: {}'.format(stationName, r2))
# Create csv and upload it to pucket
times_formatted = [t.strftime('%Y-%m-%dT%H:%M:%S') for t in times]
delay_data = {
'times': times_formatted,
'delay': data.loc[:, 'delay'].values,
'predicted delay': data.loc[:, 'pred_delay'].values,
'low': data.loc[:, 'pred_delay_low'].values,
'high': data.loc[:, 'pred_delay_high'].values
}
fname = '{}/delays_{}.csv'.format(options.vis_path, station)
io.write_csv(delay_data, fname, fname)
# Draw visualisation
fname = '{}/{}.png'.format(options.vis_path, station)
viz.plot_delay(times, data.loc[:, 'delay'].values,
data.loc[:, 'pred_delay'].values,
'Delay for station {}'.format(stationName), fname,
data.loc[:, 'pred_delay_low'].values,
data.loc[:, 'pred_delay_high'].values)
io._upload_to_bucket(filename=fname, ext_filename=fname)
# Save all station related results to csv and upload them to bucket
fname = '{}/station_rmse.csv'.format(options.vis_path)
io.dict_to_csv(station_rmse, fname, fname)
fname = '{}/station_median_absolute_error.csv'.format(options.vis_path)
io.dict_to_csv(station_median_abs_err, fname, fname)
fname = '{}/station_r2.csv'.format(options.vis_path)
io.dict_to_csv(station_r2, fname, fname)
# Create timeseries of avg actual delay and predicted delay
all_times = sorted(list(all_times))
avg_delay = avg.loc[:, 'avg_delay'].dropna().values.ravel()
avg_pred_delay = avg.loc[:, 'avg_pred_delay'].dropna().values.ravel()
# Calculate average over all times and stations
rmse = math.sqrt(metrics.mean_squared_error(avg_delay, avg_pred_delay))
median_abs_err = metrics.median_absolute_error(avg_delay, avg_pred_delay)
r2 = metrics.r2_score(avg_delay, avg_pred_delay)
logging.info('RMSE for average delay over all stations: {}'.format(rmse))
logging.info(
'Mean absolute error for average delay over all stations: {}'.format(
median_abs_err))
logging.info('R2 score for average delay over all stations: {}'.format(r2))
# Write average data into file
avg_errors = {
'rmse': rmse,
'mae': median_abs_err,
'r2': r2,
'nro_of_samples': len(avg_delay)
}
fname = '{}/avg_erros.csv'.format(options.vis_path)
io.dict_to_csv(avg_errors, fname, fname)
# Create timeseries of average delay and predicted delays over all stations
all_times_formatted = [t.strftime('%Y-%m-%dT%H:%M:%S') for t in all_times]
delay_data = {
'times': all_times_formatted,
'delay': avg_delay,
'predicted delay': avg_pred_delay
}
# write csv
fname = '{}/avg_delays_all_stations.csv'.format(options.vis_path)
io.write_csv(delay_data, fname, fname)
for i in np.arange(0, 3):
fname = '{}/avg_group_{}.png'.format(options.vis_path, (i + 1))
times = groups[i].index.values
if len(times) < 2:
continue
g_avg_delay = groups[i].loc[:, 'avg_delay'].values.ravel()
g_avg_pred_delay = groups[i].loc[:, 'avg_pred_delay'].values.ravel()
g_avg_pred_delay_low = groups[
i].loc[:, 'avg_pred_delay_low'].values.ravel()
g_avg_pred_delay_high = groups[
i].loc[:, 'avg_pred_delay_high'].values.ravel()
viz.plot_delay(times, g_avg_delay, g_avg_pred_delay,
'Average delay for group {}'.format(i + 1), fname,
g_avg_pred_delay_low, g_avg_pred_delay_high)
io._upload_to_bucket(filename=fname, ext_filename=fname)
# visualise
fname = '{}/avg_all_stations.png'.format(options.vis_path)
viz.plot_delay(all_times, avg_delay, avg_pred_delay,
'Average delay for all station', fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
options = Options()
options.starttime = '2010-01-01'
options.endtime = '2018-01-01'
options.config_filename = 'cnf/rf.ini'
options.config_name = 'all_params_1'
options.stations_file = 'cnf/stations.json'
options.stations = None #'PSL,OL,TPE,OV,PM,II,KEM,HKI'
options.gs_bucket = 'trains-data'
_config.read(options)
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
# Get params
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
print('Loading stations from {}...'.format(options.stations_file))
stationList = io.get_train_stations(options.stations_file)
if options.stations is not None:
stations = options.stations.split(',')
else:
stations = stationList.keys()
print('Loading data...')
def main():
"""
Get data from db and save it as csv
"""
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz(io)
starttime, endtime = io.get_dates(options)
logging.info('Using dataset {} and time range {} - {}'.format(options.feature_dataset,
starttime.strftime('%Y-%m-%d'),
endtime.strftime('%Y-%m-%d')))
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
if options.model == 'bgm':
model = BayesianGaussianMixture(weight_concentration_prior_type="dirichlet_process",
n_components=options.n_components)
elif options.model == 'rfc':
model = RandomForestClassifier(n_jobs=-1)
else:
raise('Model not specificied or wrong. Add "model: bgm" to config file.')
if options.pca:
ipca = IncrementalPCA(n_components=options.pca_components,
whiten = options.whiten,
copy = False)
sum_columns = []
if options.reason_code_table is not None:
sum_columns = ['count']
logging.info('Processing time range {} - {}'.format(starttime.strftime('%Y-%m-%d %H:%M'),
endtime.strftime('%Y-%m-%d %H:%M')))
logging.info('Reading data...')
data = bq.get_rows(starttime,
endtime,
loc_col='trainstation',
project=options.project,
dataset=options.feature_dataset,
table=options.feature_table,
parameters=all_param_names,
reason_code_table=options.reason_code_table)
data = io.filter_train_type(labels_df=data,
train_types=options.train_types,
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=sum_columns,
aggs=aggs)
data.sort_values(by=['time', 'trainstation'], inplace=True)
logging.info('Processing {} rows...'.format(len(data)))
if options.month:
logging.info('Adding month to the dataset...')
data['month'] = data['time'].map(lambda x: x.month)
options.feature_params.append('month')
if options.balance:
logging.info('Balancing data...')
count = data.groupby('class').size().min()
data = pd.concat([data.loc[data['class'] == 0].sample(n=count),
data.loc[data['class'] == 1].sample(n=count),
data.loc[data['class'] == 2].sample(n=count),
data.loc[data['class'] == 3].sample(n=count)])
target = data.loc[:,options.label_params].astype(np.int32).values.ravel()
features = data.loc[:,options.feature_params].astype(np.float32).values
X_train, X_test, y_train, y_test = train_test_split(features, target, test_size=0.10)
logging.debug('Features shape: {}'.format(X_train.shape))
io.log_class_dist(y_train, np.arange(4))
n_samples, n_dims = X_train.shape
if options.normalize:
logging.info('Normalizing data...')
scaler = StandardScaler()
X_train = scaler.fit_transform(X_train)
X_test = scaler.fit_transform(X_test)
if options.pca:
logging.info('Doing PCA analyzis for the data...')
X_train = ipca.fit_transform(X_train)
fname = options.output_path+'/ipca_explained_variance.png'
viz.explained_variance(ipca, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
X_test = ipca.fit_transform(X_test)
logging.debug('Features shape after pre-processing: {}'.format(X_train.shape))
if options.cv:
logging.info('Doing random search for hyper parameters...')
if options.model == 'bgm':
param_grid = {"n_components": [1, 2, 4, 8, 16],
"covariance_type": ['full', 'tied', 'diag', 'spherical'],
"init_params": ['kmeans', 'random']
}
elif options.model == 'rfc':
raise("Not implemented. Get back to work!")
else:
raise("No param_grid set for given model ({})".format(options.model))
random_search = RandomizedSearchCV(model,
param_distributions=param_grid,
n_iter=int(options.n_iter_search),
n_jobs=-1)
random_search.fit(X_train, y_train)
logging.info("RandomizedSearchCV done.")
fname = options.output_path+'/random_search_cv_results.txt'
report_cv_results(random_search.cv_results_, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
sys.exit()
else:
logging.info('Training...')
model.fit(X_train, y_train)
# Metrics
y_pred = model.predict(X_test)
acc = accuracy_score(y_test, y_pred)
logging.info('Accuracy: {}'.format(acc))
io.save_scikit_model(model, filename=options.save_file, ext_filename=options.save_file)
# Performance
y_pred = model.predict(X_test)
acc = accuracy_score(y_test, y_pred)
precision = precision_score(y_test, y_pred, average='micro')
recall = recall_score(y_test, y_pred, average='micro')
f1 = f1_score(y_test, y_pred, average='micro')
logging.info('Accuracy: {}'.format(acc))
logging.info('Precision: {}'.format(precision))
logging.info('Recall: {}'.format(recall))
logging.info('F1 score: {}'.format(f1))
io.log_class_dist(y_pred, labels=np.arange(4))
error_data = {'acc': [acc],
'precision': [precision],
'recall': [recall],
'f1': [f1]}
fname = '{}/training_time_validation_errors.csv'.format(options.output_path)
io.write_csv(error_data, filename=fname, ext_filename=fname)
# Confusion matrices
fname = '{}/confusion_matrix_validation.png'.format(options.output_path)
viz.plot_confusion_matrix(y_test, y_pred, np.arange(4), filename=fname)
fname = '{}/confusion_matrix_validation_normalised.png'.format(options.output_path)
viz.plot_confusion_matrix(y_test, y_pred, np.arange(4), True, filename=fname)
# Save models
io.save_scikit_model(model, filename=options.save_file, ext_filename=options.save_file)
if options.normalize:
fname=options.save_path+'/xscaler.pkl'
io.save_scikit_model(scaler, filename=fname, ext_filename=fname)
if options.model == 'rfc':
fname = options.output_path+'/rfc_feature_importance.png'
viz.rfc_feature_importance(model.feature_importances_, fname, feature_names=options.feature_params)
def main():
"""
Get data from db and save it as csv
"""
#a = mlfdb.mlfdb()
a = _bq.BQHandler()
io = _io.IO(gs_bucket='trains-data')
viz = _viz.Viz()
if not os.path.exists(options.save_path):
os.makedirs(options.save_path)
starttime, endtime = io.get_dates(options)
logging.debug(options.what)
what = options.what.split(',')
logging.debug(what)
all_param_names = [
'time', 'trainstation', 'train_type', 'train_count', 'total_delay',
'delay', 'name', 'lat', 'lon'
]
logging.info('Loading classification dataset from db')
logging.info('Using time range {} - {}'.format(
starttime.strftime('%Y-%m-%d'), endtime.strftime('%Y-%m-%d')))
# Read data and filter desired train_types (ic and commuter)
l_data = a.get_rows(starttime,
endtime,
loc_col='trainstation',
project='trains-197305',
dataset='trains_2009_18',
table='features',
parameters=all_param_names)
# data = io.filter_train_type(labels_df=data,
# train_types=['K','L'],
# sum_types=True,
# train_type_column='train_type',
# location_column='trainstation',
# time_column='time',
# sum_columns=['delay'],
# aggs=aggs)
# l_data.rename(columns={0: 'trainstation', 1:'time', 2: 'lon', 3: 'lat', 4: 'train type', 5: 'delay', 6: 'train count', 7: 'total delay'}, inplace=True)
#l_data.set_index(pd.DatetimeIndex(pd.to_datetime(l_data.loc[:,'time'].astype(int), unit='s')), inplace=True)
#l_data.set_index('time', drop=False, inplace=True)
passangers = io.filter_train_type(labels_df=l_data,
train_types=['L', 'K'],
sum_types=True)
l_data.set_index(pd.to_datetime(l_data.loc[:, 'time']), inplace=True)
#passangers.set_index(pd.to_datetime(passangers.loc[:,'time']), inplace=True)
# ################################################################################
if 'histograms' in what:
# All delays
filename = options.save_path + '/hist_all_delays_all.png'
viz.hist_all_delays(
l_data.loc[:,
['train_type', 'train_count', 'delay', 'total_delay']],
filename)
# Different train types
for name, t in train_types.items():
filename = options.save_path + '/hist_all_delays_{}.png'.format(
name)
df = l_data[l_data.loc[:, 'train_type'].isin([t])]
viz.hist_all_delays(df.loc[:, statlist], filename)
# All passanger trains
filename = options.save_path + '/hist_all_delays_passanger.png'
viz.hist_all_delays(passangers.loc[:, statlist], filename)
# all parameters
passangers.replace(-99, np.nan, inplace=True)
delayed_data = passangers[passangers.loc[:, 'delay'] > 50]
d = {'A': passangers, 'B': delayed_data}
comp_data = pd.concat(d.values(), axis=1, keys=d.keys())
filename = options.save_path + '/histograms_compare.png'
viz.all_hist(comp_data, filename=filename)
# ################################################################################
if 'history' in what:
# Mean delays over time
# All trains
filename = options.save_path + '/mean_delays_over_time_all.png'
s = l_data.groupby(l_data.index)[statlist].mean()
viz.plot_delays(s, filename)
# for passanger trains
filename = options.save_path + '/mean_delays_over_time_passanger.png'
s = passangers.groupby(passangers.index)[statlist].mean()
viz.plot_delays(s, filename)
# for different train_types
for name, t in train_types.items():
filename = options.save_path + '/mean_delays_over_time_{}.png'.format(
name)
df = l_data[l_data.loc[:, 'train_type'].isin([t])]
s = df.groupby(df.index)[statlist].mean()
viz.plot_delays(s, filename)
# Median delays over time
# All trains
filename = options.save_path + '/median_delays_over_time_all.png'
s = l_data.groupby(l_data.index)[statlist].median()
viz.plot_delays(s, filename)
# for passanger trains
filename = options.save_path + '/median_delays_over_time_passanger.png'
s = passangers.groupby(passangers.index)[statlist].median()
viz.plot_delays(s, filename)
# for different train_types
for name, t in train_types.items():
filename = options.save_path + '/median_delays_over_time_{}.png'.format(
name)
df = l_data[l_data.loc[:, 'train_type'].isin([t])]
s = df.groupby(df.index)[statlist].median()
viz.plot_delays(s, filename)
# ################################################################################
if 'heatmap' in what:
# locs = a.get_locations_by_dataset(options.dataset,
# starttime=starttime,
# endtime=endtime,
# rettype='dict')
# # Heatmap bad some stations
#locs = l_data.loc[:, 'trainstation'].unique().values.ravel()
locs = io.get_train_stations('cnf/stations.json')
#print(locs)
if not os.path.exists(options.save_path + '/heatmap'):
os.makedirs(options.save_path + '/heatmap')
heatmap_year(l_data, passangers, 2018, locs)
for year in np.arange(2010, 2019, 1):
heatmap_year(l_data, passangers, year, locs)
# ################################################################################
if 'detailed_heatmap' in what:
locs = a.get_locations_by_dataset(options.dataset,
starttime=starttime,
endtime=endtime,
rettype='dict')
# Heatmap bad some stations
if not os.path.exists(options.save_path + '/detailed_heatmap'):
os.makedirs(options.save_path + '/detailed_heatmap')
d = starttime
while d < endtime:
heatmap_day(l_data, passangers, d, locs)
d += dt.timedelta(days=1)
def main():
"""
Main program
"""
local_device_protos = device_lib.list_local_devices()
logging.info(
[x.name for x in local_device_protos if x.device_type == 'GPU'])
bq = _bq.BQHandler()
io = _io.IO(gs_bucket=options.gs_bucket)
viz = _viz.Viz()
starttime, endtime = io.get_dates(options)
#save_path = options.save_path+'/'+options.config_name
logging.info('Using dataset {} and time range {} - {}'.format(
options.feature_dataset, starttime.strftime('%Y-%m-%d'),
endtime.strftime('%Y-%m-%d')))
all_param_names = options.label_params + options.feature_params + options.meta_params
aggs = io.get_aggs_from_param_names(options.feature_params)
logging.info('Reading data...')
bq.set_params(starttime,
endtime,
batch_size=2500000,
loc_col='trainstation',
project=options.project,
dataset=options.feature_dataset,
table=options.feature_table,
parameters=all_param_names,
only_winters=options.only_winters)
data = bq.get_rows()
data = io.filter_train_type(labels_df=data,
train_types=options.train_types,
sum_types=True,
train_type_column='train_type',
location_column='trainstation',
time_column='time',
sum_columns=['train_count', 'delay'],
aggs=aggs)
if options.y_avg_hours is not None:
data = io.calc_running_delay_avg(data, options.y_avg_hours)
if options.y_avg:
data = io.calc_delay_avg(data)
data.sort_values(by=['time', 'trainstation'], inplace=True)
if options.normalize:
logging.info('Normalizing data...')
xscaler = StandardScaler()
yscaler = StandardScaler()
non_scaled_data = data.loc[:, options.meta_params]
labels = data.loc[:, options.label_params].astype(
np.float32).values.reshape((-1, 1))
yscaler.fit(labels)
scaled_labels = pd.DataFrame(yscaler.transform(labels),
columns=['delay'])
scaled_features = pd.DataFrame(xscaler.fit_transform(
data.loc[:, options.feature_params].astype(np.float32)),
columns=options.feature_params)
data = pd.concat([non_scaled_data, scaled_features, scaled_labels],
axis=1)
if options.pca:
logging.info('Doing PCA analyzis for the data...')
ipca = IncrementalPCA(n_components=options.pca_components,
whiten=options.whiten,
copy=False)
non_processed_data = data.loc[:, options.meta_params +
options.label_params]
processed_data = data.loc[:, options.feature_params]
ipca.fit(processed_data)
processed_features = pd.DataFrame(ipca.transform(processed_data))
data = pd.concat([non_processed_data, processed_data], axis=1)
fname = options.output_path + '/ipca_explained_variance.png'
viz.explained_variance(ipca, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
data_train, data_test = train_test_split(data, test_size=0.33)
X_test, y_test = io.extract_batch(data_test,
options.time_steps,
batch_size=None,
pad_strategy=options.pad_strategy,
quantile=options.quantile,
label_params=options.label_params,
feature_params=options.feature_params)
# Define model
batch_size = io.get_batch_size(data_train,
options.pad_strategy,
quantile=options.quantile)
logging.info('Batch size: {}'.format(batch_size))
model = LSTM.LSTM(options.time_steps,
len(options.feature_params),
1,
options.n_hidden,
options.lr,
options.p_drop,
batch_size=batch_size)
# Initialization
rmses, mses, maes, steps, train_mse = [], [], [], [], []
saver = tf.train.Saver()
sess = tf.Session()
init = tf.global_variables_initializer()
sess.run(init)
summary_writer = tf.summary.FileWriter(options.log_dir,
graph=tf.get_default_graph())
#tf.summary.scalar('Training MSE', model.loss)
tf.summary.scalar('Validation_MSE', model.mse)
tf.summary.scalar('Validation_RMSE', model.rmse)
tf.summary.scalar('Validation_MAE', model.mae)
tf.summary.histogram('y_pred_hist', model.y_pred)
merged_summary_op = tf.summary.merge_all()
train_summary_op = tf.summary.scalar('Training_MSE', model.loss)
train_step = 0
start = 0
while True:
# If slow is set, go forward one time step at time,
# else proceed whole batch size
if options.slow:
X_train, y_train = io.extract_batch(
data_train,
options.time_steps,
start=start,
pad_strategy=options.pad_strategy,
quantile=options.quantile,
label_params=options.label_params,
feature_params=options.feature_params)
else:
X_train, y_train = io.extract_batch(
data_train,
options.time_steps,
train_step,
pad_strategy=options.pad_strategy,
quantile=options.quantile,
label_params=options.label_params,
feature_params=options.feature_params)
if (len(X_train) < options.time_steps):
break
if options.cv:
logging.info('Doing random search for hyper parameters...')
param_grid = {
"C": [0.001, 0.01, 0.1, 1, 10],
"epsilon": [0.01, 0.1, 0.5],
"kernel": ['rbf', 'linear', 'poly', 'sigmoid', 'precomputed'],
"degree": [2, 3, 4],
"shrinking": [True, False],
"gamma": [0.001, 0.01, 0.1],
"coef0": [0, 0.1, 1]
}
random_search = RandomizedSearchCV(model,
param_distributions=param_grid,
n_iter=int(
options.n_iter_search),
n_jobs=-1)
random_search.fit(X_train, y_train)
logging.info("RandomizedSearchCV done.")
fname = options.output_path + '/random_search_cv_results.txt'
report_cv_results(random_search.cv_results_, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
sys.exit()
else:
if train_step == 0:
logging.info('Training...')
feed_dict = {model.X: X_train, model.y: y_train}
_, loss, train_summary = sess.run(
[model.train_op, model.loss, train_summary_op],
feed_dict=feed_dict)
summary_writer.add_summary(train_summary, train_step * batch_size)
# Metrics
feed_dict = {model.X: X_test, model.y: y_test}
#model.cell_init_state: state}
val_loss, rmse, mse, mae, y_pred, summary = sess.run(
[
model.loss, model.rmse, model.mse, model.mae, model.y_pred,
merged_summary_op
],
feed_dict=feed_dict)
train_mse.append(loss)
mses.append(mse)
rmses.append(rmse)
maes.append(mae)
steps.append(train_step)
summary_writer.add_summary(summary, train_step * batch_size)
if train_step % 50 == 0:
logging.info("Step {}:".format(train_step))
logging.info("Training loss: {:.4f}".format(loss))
logging.info("Validation MSE: {:.4f}".format(val_loss))
logging.info('Validation RMSE: {}'.format(rmse))
logging.info('Validation MAE: {}'.format(mae))
logging.info('................')
saver.save(sess, options.save_file)
train_step += 1
start += 1
# <-- while True:
saver.save(sess, options.save_file)
if options.normalize:
fname = options.save_path + '/yscaler.pkl'
io.save_scikit_model(yscaler, fname, fname)
io._upload_dir_to_bucket(options.save_path, options.save_path)
try:
fname = options.output_path + '/learning_over_time.png'
metrics = [{
'metrics': [{
'values': mses,
'label': 'Validation MSE'
}, {
'values': train_mse,
'label': 'Train MSE'
}],
'y_label':
'MSE'
}, {
'metrics': [{
'values': rmses,
'label': 'Validation RMSE'
}],
'y_label': 'RMSE'
}, {
'metrics': [{
'values': maes,
'label': 'Validation MAE'
}],
'y_label': 'MAE'
}]
viz.plot_learning(metrics, fname)
io._upload_to_bucket(filename=fname, ext_filename=fname)
except Exception as e:
logging.error(e)
error_data = {
'steps': steps,
'mse': mses,
'rmse': rmses,
'mae': maes,
'train_mse': train_mse
}
fname = '{}/training_time_validation_errors.csv'.format(
options.output_path)
io.write_csv(error_data, filename=fname, ext_filename=fname)