def main():
logging.info("Calculating ISF")
data_16 = read_data(data_csv_path_16)
data_17 = read_data(data_csv_path_17)
data = pd.concat([data_16, data_17])
isf = eighteen_hundred_rule(data)
logging.info("ISF calculated by 1800 rule: {}".format(isf))
def test_convert_glucose(self):
data = readData.read_data(filename)
data = convertData.select_columns(data)
data = convertData.create_time_index(data)
self.assertIsInstance(data['glucoseAnnotation'][0], str)
data = convertData.convert_glucose_annotation(data)
self.assertIsInstance(data['glucoseAnnotation'][0], float)
def test_drop_dat_and_time(self):
data = readData.read_data(filename)
data = convertData.select_columns(data)
data = convertData.create_time_index(data)
self.assertEqual(7, data.shape[1])
data = convertData.drop_date_and_time(data)
self.assertEqual(5, data.shape[1])
def test_interpolate_cgm(self):
data = readData.read_data(filename)
data = convertData.select_columns(data)
data = convertData.create_time_index(data)
data = convertData.convert_glucose_annotation(data)
self.assertGreater(data['cgmValue'].isna().sum(), 10)
data = convertData.interpolate_cgm(data)
self.assertEqual(0, data['cgmValue'].isna().sum())
def load(self, filename):
# Read file as pandas Dataframe
logging.debug("read data...")
data_original = read_data(filename)
# Prepare Data
logging.debug("prepare data...")
data = prepare_data(data_original)
# Get Info from Profile.json
profile_reader = Profile_reader(filename)
# add data to tiny db
logging.debug("add data to database...")
count = add_to_db(data, self.db, profile_reader)
logging.info("added {} new items to DB".format(count))
def main():
logger.info("Start Main!")
# SELECT OPTIONS
run_autotune: bool = False # Select True if autotune should run. If data set has been run before, set to False to improve speed.
create_plots: bool = False # Select True if you want a plot for every prediction window
# SET USER DATA
user_data = UserData(bginitial = 100.0, cratio = 5, idur = 4, inputeeffect = None, sensf = 41, simlength = 13,
predictionlength = 180, stats = None)
# LOAD DATA
data = readData.read_data(filename)
# CLEAN UP DATA FRAME
data = convertData.convert(data)
# INTERPOLATE CGM MEASURES
data = convertData.interpolate_cgm(data)
# GET SENSITIVITY FACTOR AND CARBRATIO FOR EVERY DAY
logger.info("Run Autotune? " + str(run_autotune))
if run_autotune:
autotune_res = autotune.runAutotune(data)
else:
autotune_res = autotune.getAllSensAndCR(data)
# MAKE A ROLLING PREDICTION
logger.info("Start Prediciton")
prediction_result = rolling.rolling(data, pd.Timedelta('15 minutes'), user_data, autotune_res, create_plots)
logger.info("Finished prediction")
# ANALYSE PREDICTION RESULTS
summary, all_data = analyze.getSummary(prediction_result)
# CREATE PLOTS FOR ANALYSE SUMMARY
analyze.createErrorPlots(summary, all_data)
# CREATE A GIF OUT OF THE PREDICTION PLOTS
#if create_plots:
# gifmaker.makeGif(path + "results/plots/", data)
logger.info("Main finished!")
def main():
train_batch_sample, train_batch_label = readData.read_data(TRAIN_RECORDS,
batch_size=64)
train_batch_sample = tf.add(
train_batch_sample,
tf.random_normal(shape=tf.shape(train_batch_sample), stddev=0.1))
test_batch_sample, test_batch_label = readData.read_data(TEST_RECORDS,
batch_size=64)
train_batch_label_one_hot = tf.one_hot(train_batch_label,
depth=config_.NUM_CLASSES,
name="train_one_hot")
test_batch_label_one_hot = tf.one_hot(test_batch_label,
depth=config_.NUM_CLASSES)
# build TSCGAN
model = basic.TSCGAN()
d_loss, g_loss = model.graph(train_batch_sample, train_batch_label_one_hot)
train_top1, train_top5 = model.accuracy(model.logits_,
train_batch_label_one_hot)
d_train_op = model.get_opt(d_loss)
g_train_op = model.get_opt(g_loss, D_or_G='G')
# d for test
test_logits, _ = model.D(test_batch_sample, reuse=True, training=False)
###########################################################################
test_batch_label_ = tf.identity(test_batch_label, name="test_batch_label")
test_pred = tf.arg_max(test_logits, dimension=1, name="test_pred")
###########################################################################
test_top1, test_top5 = model.accuracy(test_logits,
test_batch_label_one_hot,
phrase='test')
d_var_list = tf.get_collection(
tf.GraphKeys.SAVEABLE_OBJECTS, scope="D") + tf.get_collection(
tf.GraphKeys.GLOBAL_VARIABLES, scope='D')
d_saver = tf.train.Saver(var_list=d_var_list)
with tf.Session() as sess:
writer = tf.summary.FileWriter(logdir='./ckpt', graph=sess.graph)
tf.local_variables_initializer().run()
tf.global_variables_initializer().run()
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
try:
while not coord.should_stop():
global GLOBAL_STEP
# Run training steps or whatever
train_num_iteration(sess=sess,
d_train_op=d_train_op,
g_train_op=g_train_op)
test_num_iteration(sess=sess, test_logits=test_logits)
d_saver.save(sess=sess,
save_path="ckpt/%s.ckpt" % DataSetName,
global_step=GLOBAL_STEP)
GLOBAL_STEP += 1
except tf.errors.OutOfRangeError:
print('Done training -- epoch limit reached')
except KeyboardInterrupt:
print('interrupted...')
finally:
print("cleaning...")
# When done, ask the threads to stop.
coord.request_stop()
# Wait for threads to finish.
coord.join(threads)
sess.close()
def test_select_columns(self):
data = readData.read_data(filename)
self.assertEqual(28, data.shape[1])
data = convertData.select_columns(data)
self.assertEqual(7, data.shape[1])
def test_create_time_index(self):
data = readData.read_data(filename)
data = convertData.select_columns(data)
self.assertEqual(type(data.index[0]), int)
data = convertData.create_time_index(data)
self.assertIsInstance(data.index[0], pd._libs.tslib.Timestamp)
def main():
train_batch_sample, train_batch_label = readData.read_data(TRAIN_RECORDS,
config=config_)
# train_batch_sample = tf.add(train_batch_sample,
# tf.random_normal(shape=tf.shape(train_batch_sample), stddev=0.1))
train_batch_label_one_hot = tf.one_hot(train_batch_label,
depth=config_.NUM_CLASSES,
name="train_one_hot")
########################## prepare test data
_, _, _, labels, features = bulid_record.build_dataset(
config_.TEST_RECORDS)
test_batch_sample = tf.Variable(features,
trainable=False,
dtype=tf.float32)
test_batch_label = tf.Variable(labels, trainable=False, dtype=tf.int64)
test_batch_label_one_hot = tf.one_hot(test_batch_label,
depth=config_.NUM_CLASSES)
############################################
# build TSCGAN
model = tsganv2.TSCGAN(config=config_)
logits, _ = model.D(train_batch_sample)
loss = tf.nn.softmax_cross_entropy_with_logits(
labels=train_batch_label_one_hot, logits=logits)
loss = tf.reduce_mean(loss, name='d_loss')
train_top1, train_top5 = model.accuracy(logits, train_batch_label_one_hot)
d_train_op = model.get_opt(loss, regulizer=False)
# g_train_op = model.get_opt(g_loss, D_or_G='G')
# d for test
test_logits, _ = model.D(test_batch_sample, reuse=True, training=False)
###########################################################################
test_batch_label_ = tf.identity(test_batch_label, name="test_batch_label")
test_pred = tf.arg_max(test_logits, dimension=1, name="test_pred")
###########################################################################
test_top1, test_top5 = model.accuracy(test_logits,
test_batch_label_one_hot,
phrase='test')
d_var_list = tf.get_collection(
tf.GraphKeys.SAVEABLE_OBJECTS, scope="D") + tf.get_collection(
tf.GraphKeys.GLOBAL_VARIABLES, scope='D')
d_saver = tf.train.Saver(var_list=d_var_list)
with tf.Session() as sess:
writer = tf.summary.FileWriter(logdir=os.path.join(
current_dir, 'ckpt_cnn'),
graph=sess.graph)
tf.local_variables_initializer().run()
tf.global_variables_initializer().run()
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
try:
while not coord.should_stop():
global GLOBAL_STEP
# Run training steps or whatever
train_accu, train_loss = train_num_iteration(
sess=sess,
d_train_op=d_train_op,
num_iteration=NUM_TRAIN_ITERATION)
model.decay_learning_rate()
test_accu = test_num_iteration(
sess=sess, model=model, num_iteration=NUM_TEST_ITERATION)
print(
"step %d, training loss %.6f , training accuracy %.6f , test accuracy %.6f."
% (GLOBAL_STEP * NUM_TRAIN_ITERATION, train_loss,
train_accu, test_accu))
d_saver.save(sess=sess,
save_path=os.path.join(
current_dir,
"ckpt_cnn/%s.ckpt" % DataSetName),
global_step=GLOBAL_STEP)
GLOBAL_STEP += 1
except tf.errors.OutOfRangeError:
print('Done training -- epoch limit reached')
except KeyboardInterrupt:
print('interrupted...')
finally:
# When done, ask the threads to stop.
coord.request_stop()
# Wait for threads to finish.
coord.join(threads)
sess.close()
print("all threads are closed! ")
def main():
train_batch_sample, train_batch_label = readData.read_data(TRAIN_RECORDS,
config=config_)
# train_batch_sample = tf.add(train_batch_sample,
# tf.random_normal(shape=tf.shape(train_batch_sample), stddev=0.1))
########################## prepare test data
_, _, _, labels, features = bulid_record.build_dataset(
config_.TEST_RECORDS)
test_batch_sample = tf.Variable(features,
trainable=False,
dtype=tf.float32)
test_batch_label = tf.Variable(labels, trainable=False, dtype=tf.int64)
############################################
# test_batch_sample, test_batch_label = readData.read_data(TEST_RECORDS, config=config_, is_training=False)
train_batch_label_one_hot = tf.one_hot(train_batch_label,
depth=config_.NUM_CLASSES,
name="train_one_hot")
test_batch_label_one_hot = tf.one_hot(test_batch_label,
depth=config_.NUM_CLASSES)
# build TSCGAN
model = tsganv2.TSCGAN(config=config_)
d_loss, g_loss = model.graph(train_batch_sample, train_batch_label_one_hot)
train_top1, train_top5 = model.accuracy(model.logits_,
train_batch_label_one_hot)
d_train_op = model.get_opt(d_loss, regulizer=False)
g_train_op = model.get_opt(g_loss, D_or_G='G', regulizer=False)
# g_train_op = model.get_opt(g_loss, D_or_G='G')
# d for test
test_logits, _ = model.D(test_batch_sample, reuse=True, training=False)
###########################################################################
test_batch_label_ = tf.identity(test_batch_label, name="test_batch_label")
test_pred = tf.arg_max(test_logits, dimension=1, name="test_pred")
###########################################################################
test_top1, test_top5 = model.accuracy(test_logits,
test_batch_label_one_hot,
phrase='test')
gpu_conf = tf.GPUOptions(allow_growth=True)
sess_conf = tf.ConfigProto(gpu_options=gpu_conf)
with tf.Session(config=sess_conf) as sess:
writer = tf.summary.FileWriter(logdir=os.path.join(
current_dir, 'ckpt'),
graph=sess.graph)
tf.local_variables_initializer().run()
tf.global_variables_initializer().run()
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
train_loss_track = []
test_loss_track = []
try:
while not coord.should_stop():
global GLOBAL_STEP
# Run training steps or whatever
train_accu, train_loss = train_num_iteration(
sess=sess,
d_train_op=d_train_op,
g_train_op=g_train_op,
num_iteration=NUM_TRAIN_ITERATION)
model.decay_learning_rate()
test_accu = test_num_iteration(sess=sess,
model=model,
num_iteration=1)
train_loss_track.append(train_accu)
test_loss_track.append(test_accu)
print(
"step %d, training loss %.6f , training accuracy %.6f , test accuracy %.6f."
% (GLOBAL_STEP * NUM_TRAIN_ITERATION, train_loss,
train_accu, test_accu))
if GLOBAL_STEP % 100 == 0:
model.save_ckpt(save_path=os.path.join(
current_dir, "ckpt/GAN%s.ckpt" % DataSetName),
global_step=GLOBAL_STEP)
GLOBAL_STEP += 1
except tf.errors.OutOfRangeError:
print('Done training -- epoch limit reached')
except KeyboardInterrupt:
print('Keyboard Interrupt')
finally:
print('saving accu curve.')
plt.plot(train_loss_track, label='train_accu')
plt.plot(test_loss_track, label='test_accu')
plt.legend(loc='lower right')
plt.savefig('%s_gan_train_test.jpg' % config_.DATASET_NAME)
print("max accu is ", max(test_loss_track))
# When done, ask the threads to stop.
coord.request_stop()
# Wait for threads to finish.
coord.join(threads)
sess.close()
print("all threads are closed! ")
def prep_csv():
data = read_data(filename)
data = convert(data)
data = interpolate_cgm(data)
cgm = data['cgmValue']
cgm.to_csv(path + 'data/csv/cgm_17_1-6.csv')