def main():
# tf flag
flags = tf.flags
flags.DEFINE_string("train_data_txt", "./train.txt", "train data txt")
flags.DEFINE_string("val_data_txt", "./val.txt", "validation data txt")
flags.DEFINE_string("outdir", "./output/", "outdir")
flags.DEFINE_float("beta", 1, "hyperparameter beta")
flags.DEFINE_integer("num_of_val", 600, "number of validation data")
flags.DEFINE_integer("batch_size", 30, "batch size")
flags.DEFINE_integer("num_iteration", 500001, "number of iteration")
flags.DEFINE_integer("save_loss_step", 200, "step of save loss")
flags.DEFINE_integer("save_model_step", 500,
"step of save model and validation")
flags.DEFINE_integer("shuffle_buffer_size", 1000, "buffer size of shuffle")
flags.DEFINE_integer("latent_dim", 6, "latent dim")
flags.DEFINE_list("image_size", [9 * 9 * 9], "image size")
flags.DEFINE_string("model", './model/model_{}', "pre training model1")
flags.DEFINE_string("model2", './model/model_{}', "pre training model2")
flags.DEFINE_boolean("is_n1_opt", True, "n1_opt")
FLAGS = flags.FLAGS
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard',
'train'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard', 'train'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard', 'val'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard', 'val'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard', 'rec'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard', 'rec'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard', 'kl'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard', 'kl'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
# read list
train_data_list = io.load_list(FLAGS.train_data_txt)
val_data_list = io.load_list(FLAGS.val_data_txt)
# shuffle list
random.shuffle(train_data_list)
# val step
val_step = FLAGS.num_of_val // FLAGS.batch_size
if FLAGS.num_of_val % FLAGS.batch_size != 0:
val_step += 1
# load train data and validation data
train_set = tf.data.Dataset.list_files(train_data_list)
train_set = train_set.apply(
tf.contrib.data.parallel_interleave(tf.data.TFRecordDataset,
cycle_length=6))
# train_set = tf.data.TFRecordDataset(train_data_list)
train_set = train_set.map(
lambda x: _parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
train_set = train_set.shuffle(buffer_size=FLAGS.shuffle_buffer_size)
train_set = train_set.repeat()
train_set = train_set.batch(FLAGS.batch_size)
train_iter = train_set.make_one_shot_iterator()
train_data = train_iter.get_next()
val_set = tf.data.Dataset.list_files(val_data_list)
val_set = val_set.apply(
tf.contrib.data.parallel_interleave(tf.data.TFRecordDataset,
cycle_length=os.cpu_count()))
# val_set = tf.data.TFRecordDataset(val_data_list)
val_set = val_set.map(
lambda x: _parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
val_set = val_set.repeat()
val_set = val_set.batch(FLAGS.batch_size)
val_iter = val_set.make_one_shot_iterator()
val_data = val_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config) as sess:
# with tf.Session() as sess:
# set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'beta': FLAGS.beta,
'latent_dim': FLAGS.latent_dim,
'batch_size': FLAGS.batch_size,
'image_size': FLAGS.image_size,
'encoder': encoder_mlp,
'decoder': decoder_mlp,
'is_res': False
}
VAE = Variational_Autoencoder(**kwargs)
kwargs_2 = {
'sess': sess,
'outdir': FLAGS.outdir,
'beta': FLAGS.beta,
'latent_dim': 8,
'batch_size': FLAGS.batch_size,
'image_size': FLAGS.image_size,
'encoder': encoder_mlp2,
'decoder': decoder_mlp_tanh,
'is_res': True,
'is_constraints': False,
# 'keep_prob': 0.5
}
VAE_2 = Variational_Autoencoder(**kwargs_2)
# print parmeters
utils.cal_parameter()
# prepare tensorboard
writer_train = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train'), sess.graph)
writer_val = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'val'))
writer_rec = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'rec'))
writer_kl = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'kl'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# use pre trained model
# ckpt_state = tf.train.get_checkpoint_state(FLAGS.model)
#
# if ckpt_state:
# restore_model = ckpt_state.model_checkpoint_path
# # VAE.restore_model(FLAGS.model+'model_{}'.format(FLAGS.itr))
VAE.restore_model(FLAGS.model)
if FLAGS.is_n1_opt == True:
VAE_2.restore_model(FLAGS.model2)
# training
tbar = tqdm(range(FLAGS.num_iteration), ascii=True)
for i in tbar:
train_data_batch = sess.run(train_data)
if FLAGS.is_n1_opt == True:
VAE.update(train_data_batch)
output1 = VAE.reconstruction_image(train_data_batch)
train_loss, rec_loss, kl_loss = VAE_2.update2(
train_data_batch, output1)
if i % FLAGS.save_loss_step is 0:
s = "Loss: {:.4f}, rec_loss: {:.4f}, kl_loss: {:.4f}".format(
train_loss, rec_loss, kl_loss)
tbar.set_description(s)
summary_train_loss = sess.run(merge_op,
{value_loss: train_loss})
writer_train.add_summary(summary_train_loss, i)
summary_rec_loss = sess.run(merge_op, {value_loss: rec_loss})
summary_kl_loss = sess.run(merge_op, {value_loss: kl_loss})
writer_rec.add_summary(summary_rec_loss, i)
writer_kl.add_summary(summary_kl_loss, i)
if i % FLAGS.save_model_step is 0:
# save model
VAE.save_model(i)
VAE_2.save_model2(i)
# validation
val_loss = 0.
for j in range(val_step):
val_data_batch = sess.run(val_data)
val_data_batch_output1 = VAE.reconstruction_image(
val_data_batch)
val_loss += VAE_2.validation2(val_data_batch,
val_data_batch_output1)
val_loss /= val_step
summary_val = sess.run(merge_op, {value_loss: val_loss})
writer_val.add_summary(summary_val, i)
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard')):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
if not os.path.exists(os.path.join(FLAGS.outdir, 'model')):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
# save flag file
FLAGS.flags_into_string()
FLAGS.append_flags_into_file(os.path.join(FLAGS.outdir, 'flagfile.txt'))
# get tfrecord list
train_data_list = glob.glob(FLAGS.indir + '/*')
# shuffle list
random.shuffle(train_data_list)
# load train data
train_set = tf.data.Dataset.list_files(train_data_list)
train_set = train_set.apply(
tf.data.experimental.parallel_interleave(
lambda x: tf.data.TFRecordDataset(x), cycle_length=os.cpu_count()))
train_set = train_set.map(
lambda x: utils._parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
train_set = train_set.shuffle(buffer_size=FLAGS.shuffle_buffer_size)
train_set = train_set.repeat()
train_set = train_set.batch(FLAGS.batch_size)
train_iter = train_set.make_one_shot_iterator()
train_data = train_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwargs = {
'sess': sess,
'latent_dim': FLAGS.latent_dim,
'scale_lambda': FLAGS.scale_lambda,
'scale_kappa': FLAGS.scale_kappa,
'scale_psi': FLAGS.scale_psi,
'k_size': FLAGS.k_size,
'image_size': FLAGS.image_size,
'points_num': FLAGS.points_num,
'encoder_layer': encoder_layer,
'points_encoder_layer': points_encoder_layer,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'code_discriminator_layer': code_discriminator_layer,
'lr': FLAGS.lr,
'is_training': True
}
Model = conditional_alphaGAN(**kwargs)
# print parameters
utils.cal_parameter()
# prepare tensorboard
writer_e_loss = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'e_loss'), sess.graph)
writer_g_loss = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'g_loss'))
writer_d_loss = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'd_loss'))
writer_c_loss = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'c_loss'))
# saving loss operation
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
step_e, step_g, step_d, step_c, = [], [], [], []
# training
tbar = tqdm(range(FLAGS.num_iteration), ascii=True)
for step in tbar:
for i in range(FLAGS.e_g_step):
train_image_batch, points_batch = sess.run(train_data)
noise = np.random.normal(
0., 1., size=[FLAGS.batch_size, FLAGS.latent_dim])
e_loss = Model.update_e(train_image_batch, points_batch)
g_loss = Model.update_g(train_image_batch, points_batch, noise)
for i in range(FLAGS.d_step):
d_loss = Model.update_d(train_image_batch, points_batch, noise)
c_loss = Model.update_c(train_image_batch, points_batch, noise)
step_e.append(e_loss)
step_g.append(g_loss)
step_d.append(d_loss)
step_c.append(c_loss)
if step % FLAGS.save_loss_step is 0:
s = "e_loss: {:.4f}, g_loss: {:.4f}, d_loss: {:.4f}, c_loss: {:.4f}".format(
np.mean(step_e), np.mean(step_g), np.mean(step_d),
np.mean(step_c))
tbar.set_description(s)
summary_e = sess.run(merge_op, {value_loss: np.mean(step_e)})
summary_g = sess.run(merge_op, {value_loss: np.mean(step_g)})
summary_d = sess.run(merge_op, {value_loss: np.mean(step_d)})
summary_c = sess.run(merge_op, {value_loss: np.mean(step_c)})
writer_e_loss.add_summary(summary_e, step)
writer_g_loss.add_summary(summary_g, step)
writer_d_loss.add_summary(summary_d, step)
writer_c_loss.add_summary(summary_c, step)
step_e.clear()
step_g.clear()
step_d.clear()
step_c.clear()
if step % FLAGS.save_model_step is 0:
# save model
Model.save_model(FLAGS.outdir, step)
def main():
# tf flag
flags = tf.flags
flags.DEFINE_string("data_path", "D:/M1_lecture/lecture/image_analysis/no_normalized_data.csv", "data path")
flags.DEFINE_string("outdir", "D:/M1_lecture/lecture/image_analysis/no_norm", "outdir path")
flags.DEFINE_string("gpu_index", "0", "GPU-index")
flags.DEFINE_integer("num_epoch", 1000, "number of iteration")
flags.DEFINE_integer("kfold", 10, "number of fold")
flags.DEFINE_list("input_size", [22], "input vector size")
flags.DEFINE_bool("cv", True, "if 10 fold CV or not")
FLAGS = flags.FLAGS
# load train data
data = np.loadtxt(FLAGS.data_path, delimiter=",").astype(np.float32)
feature = data[:, :data.shape[1]-1]
label = data[:, data.shape[1]-1]
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config = utils.config(index=FLAGS.gpu_index)) as sess:
# Resubstitution Method
if FLAGS.cv == False:
# set network
kwargs = {
'sess': sess,
'input_size': FLAGS.input_size,
'learning_rate': 1e-3
}
NN = neural_network(**kwargs)
# print parmeters
utils.cal_parameter()
# check floder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'R', 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'R', 'tensorboard'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'R', 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'R', 'model'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'R', 'predict'))):
os.makedirs(os.path.join(FLAGS.outdir, 'R', 'predict'))
# prepare tensorboard
writer_train = tf.summary.FileWriter(os.path.join(FLAGS.outdir, 'R', 'tensorboard', 'train'), sess.graph)
writer_test = tf.summary.FileWriter(os.path.join(FLAGS.outdir, 'R', 'tensorboard', 'test'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# training
tbar = tqdm(range(FLAGS.num_epoch), ascii=True)
for i in tbar:
train_step, train_data = utils.batch_iter(feature, label, batch_size=feature.shape[0], shuffle=True)
train_data_batch = next(train_data)
train_loss = NN.update(train_data_batch[0], np.reshape(train_data_batch[1] , (train_data_batch[1].shape[0],1)))
s = "Loss: {:.4f}".format(np.mean(train_loss))
tbar.set_description(s)
summary_train_loss = sess.run(merge_op, {value_loss: np.mean(train_loss)})
writer_train.add_summary(summary_train_loss, i+1)
NN.save_model(i+1, outdir=os.path.join(FLAGS.outdir, 'R'))
# test
test_loss_min = []
sess.run(init_op)
test_step, test_data = utils.batch_iter(feature, label, batch_size=feature.shape[0], shuffle=False)
tbar = tqdm(range(FLAGS.num_epoch), ascii=True)
for i in tbar:
NN.restore_model(os.path.join(FLAGS.outdir, 'R', 'model', 'model_{}'.format(i+1)))
test_data_batch = next(test_data)
test_loss, predict = NN.test(test_data_batch[0], np.reshape(test_data_batch[1], (test_data_batch[1].shape[0], 1)))
s = "Loss: {:.4f}".format(np.mean(test_loss))
tbar.set_description(s)
test_loss_min.append(np.mean(test_loss))
summary_test_loss = sess.run(merge_op, {value_loss: np.mean(test_loss)})
writer_test.add_summary(summary_test_loss, i+1)
predict_label = np.zeros((test_data_batch[0].shape[0], 2))
predict_label[:, 0] = test_data_batch[1]
predict_label[:, 1] = np.where(predict > 0.5, 1, 0)[:, 0]
np.savetxt(os.path.join(FLAGS.outdir, 'R', 'predict', 'result_{}.csv'.format(i + 1)),
predict_label.astype(np.int), delimiter=',', fmt="%d")
test_loss_min = np.argmin(np.asarray(test_loss_min))
np.savetxt(os.path.join(FLAGS.outdir, 'R' ,'min_loss_index.txt'), [test_loss_min+1], fmt="%d")
# Leave-one-out method (10-fold CV)
if FLAGS.cv == True:
kfold = StratifiedKFold(n_splits=FLAGS.kfold, shuffle=True, random_state=1)
fold_index = 0
# set network
kwargs = {
'sess': sess,
'input_size': FLAGS.input_size,
'learning_rate': 1e-3
}
NN = neural_network(**kwargs)
# print parmeters
utils.cal_parameter()
for train, test in kfold.split(feature, label):
fold_index += 1
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'L', str(fold_index) , 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'tensorboard'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'model'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'predict'))):
os.makedirs(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'predict'))
# prepare tensorboard
writer_train = tf.summary.FileWriter(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'tensorboard', 'train'),
sess.graph)
writer_test = tf.summary.FileWriter(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'tensorboard', 'test'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(tf.global_variables_initializer())
# training
tbar = tqdm(range(FLAGS.num_epoch), ascii=True)
for i in tbar:
train_step, train_data = utils.batch_iter(feature[train], label[train],
batch_size=feature[train].shape[0], shuffle=True)
train_data_batch = next(train_data)
train_loss = NN.update(train_data_batch[0],
np.reshape(train_data_batch[1], (train_data_batch[1].shape[0], 1)))
s = "Loss: {:.4f}".format(np.mean(train_loss))
tbar.set_description(s)
summary_train_loss = sess.run(merge_op, {value_loss: np.mean(train_loss)})
writer_train.add_summary(summary_train_loss, i + 1)
NN.save_model(i + 1, outdir=os.path.join(FLAGS.outdir, 'L', str(fold_index)))
# test
sess.run(init_op)
test_loss_min = []
test_step, test_data = utils.batch_iter(feature[test], label[test],
batch_size=feature[test].shape[0], shuffle=False)
tbar = tqdm(range(FLAGS.num_epoch), ascii=True)
for i in tbar:
NN.restore_model(os.path.join(FLAGS.outdir, 'L', str(fold_index) , 'model', 'model_{}'.format(i + 1)))
test_data_batch = next(test_data)
test_loss, predict = NN.test(test_data_batch[0],
np.reshape(test_data_batch[1], (test_data_batch[1].shape[0], 1)))
s = "Loss: {:.4f}".format(np.mean(test_loss))
tbar.set_description(s)
test_loss_min.append(np.mean(test_loss))
summary_test_loss = sess.run(merge_op, {value_loss: np.mean(test_loss)})
writer_test.add_summary(summary_test_loss, i + 1)
predict_label = np.zeros((test_data_batch[0].shape[0], 2))
predict_label[:, 0] = test_data_batch[1]
predict_label[:, 1] = np.where(predict > 0.5, 1, 0)[:,0]
np.savetxt(os.path.join(FLAGS.outdir, 'L', str(fold_index), 'predict', 'result_{}.csv'.format(i + 1)),
predict_label.astype(np.int), delimiter=',', fmt="%d")
test_loss_min = np.argmin(np.asarray(test_loss_min))
np.savetxt(os.path.join(FLAGS.outdir, 'L', str(fold_index),'min_loss_index.txt'), [test_loss_min+1], fmt="%d")
def main():
# tf flag
flags = tf.flags
flags.DEFINE_string(
"val_data_txt", 'F:/data_info/VAE_liver/set_5/TFrecord/fold_1/val.txt',
"validation data txt")
flags.DEFINE_string(
"model_dir",
'G:/experiment_result/liver/VAE/set_5/down/64/alpha_0.1/fold_1/beta_10/model',
"dir of model")
flags.DEFINE_string(
"outdir",
'G:/experiment_result/liver/VAE/set_5/down/64/alpha_0.1/fold_1/beta_10',
"outdir")
flags.DEFINE_string("gpu_index", "0", "GPU-index")
flags.DEFINE_float("beta", 1, "hyperparameter beta")
flags.DEFINE_integer("num_of_val", 76, "number of validation data")
flags.DEFINE_integer("train_iteration", 12001,
"number of training iteration")
flags.DEFINE_integer("batch_size", 1, "batch size")
flags.DEFINE_integer(
"num_per_val", 150,
"number per each validation(equal step of saving model)")
flags.DEFINE_integer("latent_dim", 4, "latent dim")
flags.DEFINE_list("image_size", [56, 72, 88, 1], "image size")
FLAGS = flags.FLAGS
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
# read list
val_data_list = io.load_list(FLAGS.val_data_txt)
# number of model
num_of_model = FLAGS.train_iteration // FLAGS.num_per_val
if FLAGS.train_iteration % FLAGS.num_per_val != 0:
num_of_model += 1
if FLAGS.train_iteration % FLAGS.num_per_val == 0:
num_of_model -= 1
# val_iter
num_val_iter = FLAGS.num_of_val // FLAGS.batch_size
if FLAGS.num_of_val % FLAGS.batch_size != 0:
num_val_iter += 1
# load validation data
val_set = tf.data.TFRecordDataset(val_data_list, compression_type='GZIP')
val_set = val_set.map(
lambda x: utils._parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
val_set = val_set.repeat()
val_set = val_set.batch(FLAGS.batch_size)
val_iter = val_set.make_one_shot_iterator()
val_data = val_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# # set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'beta': FLAGS.beta,
'latent_dim': FLAGS.latent_dim,
'batch_size': FLAGS.batch_size,
'image_size': FLAGS.image_size,
'encoder': encoder_resblock_bn,
'decoder': decoder_resblock_bn,
'downsampling': down_sampling,
'upsampling': up_sampling,
'is_training': False,
'is_down': False
}
VAE = Variational_Autoencoder(**kwargs)
# print parmeters
utils.cal_parameter()
# prepare tensorboard
writer_val = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'val'))
writer_val_rec = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'val_rec'))
writer_val_kl = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'val_kl'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# # validation
tbar = tqdm(range(num_of_model), ascii=True)
for i in tbar:
VAE.restore_model(FLAGS.model_dir +
'/model_{}'.format(i * FLAGS.num_per_val))
val_loss_all = []
val_rec_all = []
val_kl_all = []
for j in range(num_val_iter):
val_data_batch = sess.run(val_data)
val_loss, val_rec, val_kl = VAE.validation(val_data_batch)
val_loss_all.append(val_loss)
val_rec_all.append(val_rec)
val_kl_all.append(val_kl)
val_loss, val_rec, val_kl = np.mean(val_loss_all), np.mean(
val_rec_all), np.mean(val_kl_all)
s = "val: {:.4f}, val_rec: {:.4f}, val_kl: {:.4f} ".format(
val_loss, val_rec, val_kl)
tbar.set_description(s)
summary_val = sess.run(merge_op, {value_loss: val_loss})
summary_val_rec = sess.run(merge_op, {value_loss: val_rec})
summary_val_kl = sess.run(merge_op, {value_loss: val_kl})
writer_val.add_summary(summary_val, i * FLAGS.num_per_val)
writer_val_rec.add_summary(summary_val_rec, i * FLAGS.num_per_val)
writer_val_kl.add_summary(summary_val_kl, i * FLAGS.num_per_val)
val_loss_all.clear()
val_rec_all.clear()
val_kl_all.clear()
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
# load train data(cifar10, class: 10)
if FLAGS.problem == 'cifar10':
(x_train, y_train), (x_test,
y_test) = tf.keras.datasets.cifar10.load_data()
num_class = 10
# load train data(cifar100, class: 100)
if FLAGS.problem == 'cifar100':
(x_train, y_train), (x_test,
y_test) = tf.keras.datasets.cifar100.load_data(
label_mode='fine')
num_class = 100
# preprocess
train_gen = tf.keras.preprocessing.image.ImageDataGenerator(
rescale=1.0 / 255,
horizontal_flip=True,
width_shift_range=4.0 / 32.0,
height_shift_range=4.0 / 32.0)
test_gen = tf.keras.preprocessing.image.ImageDataGenerator(rescale=1.0 /
255)
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
if FLAGS.is_octconv:
network = octconv_resnet50
else:
network = normal_resnet50
# set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'input_size': FLAGS.image_size,
'alpha': FLAGS.alpha,
'network': network,
'num_class': num_class,
'is_training': True,
'learning_rate': 1e-3
}
Model = resnet_model(**kwargs)
utils.cal_parameter()
# prepare tensorboard
writer_train = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train'), sess.graph)
value_loss = tf.Variable(0.0)
tf.summary.scalar("train_loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
tbar = tqdm(range(FLAGS.epoch), ascii=True)
epoch_loss = []
for i in tbar:
train_data_shuffled = train_gen.flow(x_train,
y_train,
FLAGS.batch_size,
shuffle=True)
# one epoch
for iter in range(x_train.shape[0] // FLAGS.batch_size):
train_data_batch = next(train_data_shuffled)
label = tf.keras.utils.to_categorical(train_data_batch[1],
num_classes=num_class)
# training
train_loss = Model.update(train_data_batch[0], label)
epoch_loss.append(np.mean(train_loss))
s = "epoch:{}, step:{}, Loss: {:.4f}".format(
i, iter, np.mean(epoch_loss))
tbar.set_description(s)
summary_train_loss = sess.run(merge_op,
{value_loss: np.mean(epoch_loss)})
writer_train.add_summary(summary_train_loss, i)
epoch_loss.clear()
# save model
Model.save_model(i)
def main():
parser = argparse.ArgumentParser(description='py, train_data_txt, val_data_txt, outdir')
parser.add_argument('--train_data_txt', '-i1', default='', help='train data txt')
parser.add_argument('--val_data_txt', '-i2', default='', help='validation data txt')
parser.add_argument('--outdir', '-i3', default='./beta_0.1', help='outdir')
args = parser.parse_args()
# check folder
if not (os.path.exists(os.path.join(args.outdir, 'tensorboard', 'train'))):
os.makedirs(os.path.join(args.outdir, 'tensorboard', 'train'))
if not (os.path.exists(os.path.join(args.outdir, 'tensorboard', 'val'))):
os.makedirs(os.path.join(args.outdir, 'tensorboard', 'val'))
if not (os.path.exists(os.path.join(args.outdir, 'tensorboard', 'rec'))):
os.makedirs(os.path.join(args.outdir, 'tensorboard', 'rec'))
if not (os.path.exists(os.path.join(args.outdir, 'tensorboard', 'kl'))):
os.makedirs(os.path.join(args.outdir, 'tensorboard', 'kl'))
if not (os.path.exists(os.path.join(args.outdir, 'model'))):
os.makedirs(os.path.join(args.outdir, 'model'))
# tf flag
flags = tf.flags
flags.DEFINE_float("beta", 0.1, "hyperparameter beta")
flags.DEFINE_integer("num_of_val", 1000, "number of validation data")
flags.DEFINE_integer("batch_size", 30, "batch size")
flags.DEFINE_integer("num_iteration", 50001, "number of iteration")
flags.DEFINE_integer("save_loss_step", 50, "step of save loss")
flags.DEFINE_integer("save_model_step", 500, "step of save model and validation")
flags.DEFINE_integer("shuffle_buffer_size", 10000, "buffer size of shuffle")
flags.DEFINE_integer("latent_dim", 2, "latent dim")
flags.DEFINE_list("image_size", [512, 512, 1], "image size")
FLAGS = flags.FLAGS
# read list
train_data_list = io.load_list(args.train_data_txt)
val_data_list = io.load_list(args.val_data_txt)
# shuffle list
random.shuffle(train_data_list)
# val step
val_step = FLAGS.num_of_val // FLAGS.batch_size
if FLAGS.num_of_val % FLAGS.batch_size != 0:
val_step += 1
# load train data and validation data
train_set = tf.data.TFRecordDataset(train_data_list)
train_set = train_set.map(lambda x: _parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
train_set = train_set.shuffle(buffer_size=FLAGS.shuffle_buffer_size)
train_set = train_set.repeat()
train_set = train_set.batch(FLAGS.batch_size)
train_iter = train_set.make_one_shot_iterator()
train_data = train_iter.get_next()
val_set = tf.data.TFRecordDataset(val_data_list)
val_set = val_set.map(lambda x: _parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
val_set = val_set.repeat()
val_set = val_set.batch(FLAGS.batch_size)
val_iter = val_set.make_one_shot_iterator()
val_data = val_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config = utils.config) as sess:
# set network
kwargs = {
'sess': sess,
'outdir': args.outdir,
'beta': FLAGS.beta,
'latent_dim': FLAGS.latent_dim,
'batch_size': FLAGS.batch_size,
'image_size': FLAGS.image_size,
'encoder': cnn_encoder,
'decoder': cnn_decoder
}
VAE = Variational_Autoencoder(**kwargs)
# print parmeters
utils.cal_parameter()
# prepare tensorboard
writer_train = tf.summary.FileWriter(os.path.join(args.outdir, 'tensorboard', 'train'), sess.graph)
writer_val = tf.summary.FileWriter(os.path.join(args.outdir, 'tensorboard', 'val'))
writer_rec = tf.summary.FileWriter(os.path.join(args.outdir, 'tensorboard', 'rec'))
writer_kl = tf.summary.FileWriter(os.path.join(args.outdir, 'tensorboard', 'kl'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# training
tbar = tqdm(range(FLAGS.num_iteration), ascii=True)
for i in tbar:
train_data_batch = sess.run(train_data)
train_loss, rec_loss, kl_loss = VAE.update(train_data_batch)
if i % FLAGS.save_loss_step is 0:
s = "Loss: {:.4f}, rec_loss: {:.4f}, kl_loss: {:.4f}".format(train_loss, rec_loss, kl_loss)
tbar.set_description(s)
summary_train_loss = sess.run(merge_op, {value_loss: train_loss})
writer_train.add_summary(summary_train_loss, i)
summary_rec_loss = sess.run(merge_op, {value_loss: rec_loss})
summary_kl_loss = sess.run(merge_op, {value_loss: kl_loss})
writer_rec.add_summary(summary_rec_loss, i)
writer_kl.add_summary(summary_kl_loss, i)
if i % FLAGS.save_model_step is 0:
# save model
VAE.save_model(i)
# validation
val_loss = 0.
for j in range(val_step):
val_data_batch = sess.run(val_data)
val_loss += VAE.validation(val_data_batch)
val_loss /= val_step
summary_val = sess.run(merge_op, {value_loss: val_loss})
writer_val.add_summary(summary_val, i)
def main():
# tf flag
flags = tf.flags
flags.DEFINE_string(
"train_data_txt",
'F:/data_info/VAE_liver/set_5/TFrecord/fold_1/train.txt',
"train data txt")
flags.DEFINE_string(
"outdir",
'G:/experiment_result/liver/VAE/set_5/down/64/alpha_0.1/fold_1/beta_1',
"outdir")
flags.DEFINE_string("gpu_index", "0", "GPU-index")
flags.DEFINE_float("beta", 1, "hyperparameter beta")
flags.DEFINE_integer("batch_size", 12, "batch size")
flags.DEFINE_integer("num_iteration", 12001, "number of iteration")
flags.DEFINE_integer("save_loss_step", 150, "step of save loss")
flags.DEFINE_integer("save_model_step", 150,
"step of save model and validation")
flags.DEFINE_integer("shuffle_buffer_size", 200, "buffer size of shuffle")
flags.DEFINE_integer("latent_dim", 4, "latent dim")
flags.DEFINE_list("image_size", [56, 72, 88, 1], "image size")
FLAGS = flags.FLAGS
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
# read list
train_data_list = io.load_list(FLAGS.train_data_txt)
# shuffle list
random.shuffle(train_data_list)
# load train data
train_set = tf.data.Dataset.list_files(train_data_list)
train_set = train_set.apply(
tf.contrib.data.parallel_interleave(
lambda x: tf.data.TFRecordDataset(x, compression_type='GZIP'),
cycle_length=os.cpu_count()))
train_set = train_set.map(
lambda x: utils._parse_function(x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
# train_set = train_set.cache()
train_set = train_set.shuffle(buffer_size=FLAGS.shuffle_buffer_size)
train_set = train_set.repeat()
train_set = train_set.batch(FLAGS.batch_size)
train_iter = train_set.make_one_shot_iterator()
train_data = train_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# # set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'beta': FLAGS.beta,
'latent_dim': FLAGS.latent_dim,
'batch_size': FLAGS.batch_size,
'image_size': FLAGS.image_size,
'encoder': encoder_resblock_bn,
'decoder': decoder_resblock_bn,
'downsampling': down_sampling,
'upsampling': up_sampling,
'learning_rate': 1e-4,
'is_training': True,
'is_down': False
}
VAE = Variational_Autoencoder(**kwargs)
# print parmeters
utils.cal_parameter()
# prepare tensorboard
writer_train = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train'), sess.graph)
writer_rec = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train_rec'))
writer_kl = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train_kl'))
value_loss = tf.Variable(0.0)
tf.summary.scalar("loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# # training
tbar = tqdm(range(FLAGS.num_iteration), ascii=True)
epoch_train_loss = []
epoch_kl_loss = []
epoch_rec_loss = []
for i in tbar:
train_data_batch = sess.run(train_data)
train_loss, rec_loss, kl_loss = VAE.update(train_data_batch)
epoch_train_loss.append(train_loss)
epoch_kl_loss.append(kl_loss)
epoch_rec_loss.append(rec_loss)
if i % FLAGS.save_loss_step is 0:
s = "Loss: {:.4f}, kl_loss: {:.4f}, rec_loss: {:.4f}"\
.format(np.mean(epoch_train_loss), np.mean(epoch_kl_loss), np.mean(epoch_rec_loss))
tbar.set_description(s)
summary_train_loss = sess.run(merge_op,
{value_loss: train_loss})
summary_rec_loss = sess.run(merge_op, {value_loss: rec_loss})
summary_kl_loss = sess.run(merge_op, {value_loss: kl_loss})
writer_train.add_summary(summary_train_loss, i)
writer_rec.add_summary(summary_rec_loss, i)
writer_kl.add_summary(summary_kl_loss, i)
epoch_train_loss.clear()
epoch_kl_loss.clear()
epoch_rec_loss.clear()
if i % FLAGS.save_model_step is 0:
# save model
VAE.save_model(i)
def main(argv):
# turn off log message
tf.logging.set_verbosity(tf.logging.WARN)
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
# load train data(cifar10, class: 10)
if FLAGS.problem == 'cifar10':
(x_train, y_train), (x_test,
y_test) = tf.keras.datasets.cifar10.load_data()
num_class = 10
# load train data(cifar100, class: 100)
if FLAGS.problem == 'cifar100':
(x_train, y_train), (x_test,
y_test) = tf.keras.datasets.cifar100.load_data(
label_mode='fine')
num_class = 100
# preprocess
test_gen = tf.keras.preprocessing.image.ImageDataGenerator(rescale=1.0 /
255)
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
if FLAGS.is_octconv:
network = octconv_resnet50
else:
network = normal_resnet50
# set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'input_size': FLAGS.image_size,
'alpha': FLAGS.alpha,
'network': network,
'num_class': num_class,
'is_training': False,
'learning_rate': 1e-4
}
Model = resnet_model(**kwargs)
utils.cal_parameter()
# prepare tensorboard
writer_test = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'test'))
value_acc = tf.Variable(0.0)
tf.summary.scalar("test_accuracy", value_acc)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
tbar = tqdm(range(FLAGS.epoch), ascii=True)
epoch_acc = []
for i in tbar:
test_data = test_gen.flow(x_test,
y_test,
FLAGS.batch_size,
shuffle=False)
# one epoch
Model.restore_model(FLAGS.model_path + '/model_{}'.format(i))
for iter in range(x_test.shape[0] // FLAGS.batch_size):
train_data_batch = next(test_data)
label = tf.keras.utils.to_categorical(train_data_batch[1],
num_classes=num_class)
test_acc = Model.test(train_data_batch[0], label)
epoch_acc.append(np.mean(test_acc))
s = "epoch:{}, acc: {:.4f}".format(i, np.mean(epoch_acc))
tbar.set_description(s)
summary_test_acc = sess.run(merge_op,
{value_acc: np.mean(epoch_acc)})
writer_test.add_summary(summary_test_acc, i)
epoch_acc.clear()
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(FLAGS.dir):
raise Exception("model dirctory is not existed!")
if not os.path.exists(os.path.join(FLAGS.dir, 'dice')):
os.makedirs(os.path.join(FLAGS.dir, 'dice'))
# get ground truth list
ground_truth_list = io.load_list(FLAGS.ground_truth)
# load ground truth
ground_truth = io.load_data_from_path(ground_truth_list, dtype='int32')
# get tfrecord list
test_data_list = glob.glob(FLAGS.indir + '/*')
# load test data
test_set = tf.data.TFRecordDataset(test_data_list)
test_set = test_set.map(lambda x: utils._parse_function_val_test(
x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
test_set = test_set.repeat()
test_set = test_set.batch(FLAGS.batch_size)
test_iter = test_set.make_one_shot_iterator()
test_data = test_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwargs = {
'sess': sess,
'latent_dim': FLAGS.latent_dim,
'scale_lambda': FLAGS.scale_lambda,
'scale_kappa': FLAGS.scale_kappa,
'scale_psi': FLAGS.scale_psi,
'image_size': FLAGS.image_size,
'points_num': FLAGS.points_num,
'k_size': FLAGS.k_size,
'encoder_layer': encoder_layer,
'points_encoder_layer': points_encoder_layer,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'code_discriminator_layer': code_discriminator_layer,
'is_training': False
}
Model = conditional_alphaGAN(**kwargs)
sess.run(init_op)
# print parameters
utils.cal_parameter()
# test
dice_list = []
Model.restore_model(FLAGS.dir +
'/model/model_{}'.format(FLAGS.model_index))
for i in range(FLAGS.num_of_test):
_, test_points_batch, _ = sess.run(test_data)
np.random.seed(4)
tbar = tqdm(range(FLAGS.num_of_generate // FLAGS.batch_size),
ascii=True)
for j in tbar:
z = np.random.normal(0.,
1.,
size=[FLAGS.batch_size, FLAGS.latent_dim])
# z = utils.truncated_noise_sample(FLAGS.batch_size, FLAGS.latent_dim, truncation=2.0)
generate_batch = Model.generate_sample(z, test_points_batch)
# save logodds
generate_batch_ = np.asarray(generate_batch)
generate_batch_ = generate_batch_[0, :, :, :]
for image_index in range(generate_batch_.shape[0]):
gen = generate_batch_[image_index][:, :, :, 0]
io.write_mhd_and_raw(
gen,
'{}.mhd'.format(
os.path.join(
FLAGS.dir, 'dice', '{}'.format(i),
'{}'.format(j * FLAGS.batch_size +
image_index))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
if j is 0:
data = np.asarray(generate_batch)[0]
label = np.where(data > 0.5, 0, 1)
label = label.astype(np.int8)
pa = np.sum(label, axis=0)
else:
data = np.asarray(generate_batch)[0]
label_ = np.where(data > 0.5, 0, 1)
label_ = label_.astype(np.int8)
pa = pa + np.sum(label_, axis=0)
pa = pa / float(FLAGS.num_of_generate)
pa = pa.astype(np.float32)
# output image
io.write_mhd_and_raw(pa,
'{}_{}.mhd'.format(
os.path.join(FLAGS.dir, 'dice', 'PA'), i),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
# dice
gt = ground_truth[i]
gt = gt.astype(np.float32)
dice = utils.dice_coef(gt, pa)
dice_list.append([round(dice, 6)])
print(dice)
print('dice = %f' % np.mean(dice_list))
# write csv
io.write_csv(
dice_list,
os.path.join(FLAGS.dir, 'dice',
'dice_{}.csv'.format(FLAGS.model_index)), 'dice')
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(FLAGS.dir):
raise Exception("model dirctory is not existed!")
if not os.path.exists(os.path.join(FLAGS.dir, 'generalization')):
os.makedirs(os.path.join(FLAGS.dir, 'generalization'))
# get tfrecord list
test_data_list = glob.glob(FLAGS.indir + '/*')
# test step
test_step = FLAGS.num_of_test // FLAGS.batch_size
if FLAGS.num_of_test % FLAGS.batch_size != 0:
test_step += 1
# load test data
test_set = tf.data.TFRecordDataset(test_data_list)
test_set = test_set.map(lambda x: utils._parse_function_val_test(
x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
test_set = test_set.batch(FLAGS.batch_size)
test_iter = test_set.make_one_shot_iterator()
test_data = test_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwargs = {
'sess': sess,
'latent_dim': FLAGS.latent_dim,
'scale_lambda': FLAGS.scale_lambda,
'scale_kappa': FLAGS.scale_kappa,
'scale_psi': FLAGS.scale_psi,
'image_size': FLAGS.image_size,
'points_num': FLAGS.points_num,
'k_size': FLAGS.k_size,
'encoder_layer': encoder_layer,
'points_encoder_layer': points_encoder_layer,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'code_discriminator_layer': code_discriminator_layer,
'is_training': False
}
Model = conditional_alphaGAN(**kwargs)
sess.run(init_op)
# print parameters
utils.cal_parameter()
# test
Model.restore_model(FLAGS.dir +
'/model/model_{}'.format(FLAGS.model_index))
tbar = tqdm(range(test_step), ascii=True)
for i in tbar:
test_image_batch, test_points_batch, test_label_batch = sess.run(
test_data)
reconstruction_batch = Model.reconstruction(
test_image_batch, test_points_batch)
# dilation of points
test_points_batch = tf.keras.layers.MaxPooling3D(
pool_size=5, strides=1, padding='same')(test_points_batch)
test_points_batch = test_points_batch.eval()
test_points_batch = test_points_batch * 2 # scaling
if i is 0:
test_label = np.asarray(test_label_batch)
reconstruction = np.asarray(reconstruction_batch)[0]
points = np.asarray(test_points_batch)
else:
test_label = np.concatenate(
(test_label, np.asarray(test_label_batch)), axis=0)
reconstruction = np.concatenate(
(reconstruction, np.asarray(reconstruction_batch)[0]),
axis=0)
points = np.concatenate((points, np.array(test_points_batch)),
axis=0)
# calculate Jaccard Index and output images
generalization = []
tbar = tqdm(range(reconstruction.shape[0]), ascii=True)
for i in tbar:
test_label_single = test_label[i][:, :, :, 0]
reconstruction_single = reconstruction[i][:, :, :, 0]
points_single = points[i][:, :, :, 0]
# label
rec_label = np.where(reconstruction_single > 0.5, 0, 1)
rec_label = rec_label.astype(np.int8)
# calculate ji
generalization.append(
[utils.jaccard(rec_label, test_label_single)])
# label and points
label_and_points = rec_label + points_single
rec_label = rec_label.astype(np.int8)
label_and_points = label_and_points.astype(np.int8)
# output image
io.write_mhd_and_raw(reconstruction_single,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'generalization',
'logodds',
'generate_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
io.write_mhd_and_raw(rec_label,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'generalization',
'predict',
'recon_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
io.write_mhd_and_raw(label_and_points,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'generalization',
'label_and_points',
'generate_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
print('generalization = %f' % np.mean(generalization))
# write csv
io.write_csv(
generalization,
os.path.join(FLAGS.dir, 'generalization',
'generalization_val_{}.csv'.format(
FLAGS.model_index)), 'generalization')
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(FLAGS.dir):
raise Exception("model dirctory is not existed!")
if not os.path.exists(os.path.join(FLAGS.dir, 'specificity')):
os.makedirs(os.path.join(FLAGS.dir, 'specificity'))
# load ground truth
ground_truth_list = glob.glob(FLAGS.ground_truth + '/*.mhd')
ground_truth = io.load_data_from_path(ground_truth_list, dtype='int32')
# get tfrecord list
test_data_list = glob.glob(FLAGS.indir + '/*')
# load test data
test_set = tf.data.TFRecordDataset(test_data_list)
test_set = test_set.map(lambda x: utils._parse_function_val_test(
x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
# test_set = test_set.shuffle(buffer_size=FLAGS.num_of_test)
test_set = test_set.repeat()
test_set = test_set.batch(FLAGS.batch_size)
test_iter = test_set.make_one_shot_iterator()
test_data = test_iter.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwargs = {
'sess': sess,
'latent_dim': FLAGS.latent_dim,
'scale_lambda': FLAGS.scale_lambda,
'scale_kappa': FLAGS.scale_kappa,
'scale_psi': FLAGS.scale_psi,
'image_size': FLAGS.image_size,
'points_num': FLAGS.points_num,
'k_size': FLAGS.k_size,
'encoder_layer': encoder_layer,
'points_encoder_layer': points_encoder_layer,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'code_discriminator_layer': code_discriminator_layer,
'is_training': False
}
Model = conditional_alphaGAN(**kwargs)
sess.run(init_op)
# print parameters
utils.cal_parameter()
# test
Model.restore_model(FLAGS.dir +
'/model/model_{}'.format(FLAGS.model_index))
tbar = tqdm(range(FLAGS.num_of_generate // FLAGS.batch_size),
ascii=True)
for i in tbar:
np.random.seed(4)
z = np.random.normal(0.,
1.,
size=[FLAGS.batch_size, FLAGS.latent_dim])
_, test_points_batch, _ = sess.run(test_data)
generate_batch = Model.generate_sample(z, test_points_batch)
# dilation of points
test_points_dilate = tf.keras.layers.MaxPooling3D(
pool_size=3, strides=1, padding='same')(test_points_batch)
test_points_dilate = test_points_dilate.eval()
test_points_dilate = test_points_dilate * 2 # scaling
if i is 0:
samples = np.asarray(generate_batch)[0]
points = np.asarray(test_points_dilate)
else:
samples = np.concatenate(
(samples, np.asarray(generate_batch)[0]), axis=0)
points = np.concatenate(
(points, np.asarray(test_points_dilate)), axis=0)
# calculate Jaccard Index and output images
specificity = []
tbar = tqdm(range(samples.shape[0]), ascii=True)
for i in tbar:
gen = samples[i][:, :, :, 0]
points_single = points[i][:, :, :, 0]
# label
gen_label = np.where(gen > 0.5, 0, 1)
# calculate ji
case_max_ji = 0.
for image_index in range(ground_truth.shape[0]):
ji = utils.jaccard(gen_label, ground_truth[image_index])
if ji > case_max_ji:
case_max_ji = ji
specificity.append([case_max_ji])
# label and points
label_and_points = gen_label + points_single
gen_label = gen_label.astype(np.int8)
label_and_points = label_and_points.astype(np.int8)
# output image
io.write_mhd_and_raw(gen,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'specificity',
'logodds',
'generate_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
io.write_mhd_and_raw(gen_label,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'specificity',
'label',
'generate_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
io.write_mhd_and_raw(label_and_points,
'{}.mhd'.format(
os.path.join(FLAGS.dir, 'specificity',
'label_and_points',
'generate_{}'.format(i))),
spacing=[1, 1, 1],
origin=[0, 0, 0],
compress=True)
#
print('specificity = %f' % np.mean(specificity))
# write csv
io.write_csv(
specificity,
os.path.join(FLAGS.dir, 'specificity_shape',
'specificity_{}.csv'.format(FLAGS.model_index)),
'specificity')
def main(argv):
# check folder
if not (os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard'))):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
if not (os.path.exists(os.path.join(FLAGS.outdir, 'model'))):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
# get file list
train_data_list = glob.glob(FLAGS.indir + '/*')
# shuffle list
random.shuffle(train_data_list)
# load train data
train_set = tf.data.Dataset.list_files(train_data_list)
train_set = train_set.apply(
tf.contrib.data.parallel_interleave(
lambda x: tf.data.TFRecordDataset(x), cycle_length=os.cpu_count()))
train_set = train_set.map(utils._parse_function,
num_parallel_calls=os.cpu_count())
train_set = train_set.shuffle(buffer_size=FLAGS.shuffle_buffer_size)
train_set = train_set.repeat()
train_set = train_set.batch(FLAGS.batch_size)
train_set = train_set.prefetch(1)
train_iter = train_set.make_one_shot_iterator()
train_data = train_iter.get_next()
# step of each epoch
if FLAGS.num_data % FLAGS.batch_size == 0:
step_of_epoch = FLAGS.num_data / FLAGS.batch_size
else:
step_of_epoch = FLAGS.num_data // FLAGS.batch_size + 1
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
if FLAGS.is_octconv:
network = octconv_resnet50
else:
network = normal_resnet50
# set network
kwargs = {
'sess': sess,
'outdir': FLAGS.outdir,
'input_size': FLAGS.image_size,
'alpha': FLAGS.alpha,
'network': network,
'is_training': True,
'learning_rate': 1e-4
}
Model = resnet_model(**kwargs)
utils.cal_parameter()
# prepare tensorboard
writer_train = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train'), sess.graph)
value_loss = tf.Variable(0.0)
tf.summary.scalar("train_loss", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
tbar = tqdm(range(FLAGS.epoch), ascii=True)
epoch_loss = []
for i in tbar:
# one epoch
for step in range(step_of_epoch):
train_data_batch, train_label_batch = sess.run(train_data)
train_loss = Model.update(train_data_batch, train_label_batch)
epoch_loss.append(train_loss)
s = "epoch:{}, step:{}, Loss: {:.4f}".format(
i, step, np.mean(epoch_loss))
tbar.set_description(s)
summary_train_loss = sess.run(merge_op,
{value_loss: np.mean(epoch_loss)})
writer_train.add_summary(summary_train_loss, i)
epoch_loss.clear()
# save model
Model.save_model(i)
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(os.path.join(FLAGS.outdir, 'tensorboard')):
os.makedirs(os.path.join(FLAGS.outdir, 'tensorboard'))
if not os.path.exists(os.path.join(FLAGS.outdir, 'model')):
os.makedirs(os.path.join(FLAGS.outdir, 'model'))
(x_train, _), (_, _) = tf.keras.datasets.mnist.load_data()
x_train = np.expand_dims(x_train, axis=-1)
# preprocess
train_gen = tf.keras.preprocessing.image.ImageDataGenerator(rescale=1.0 /
255.)
# tensorboard variable
loss_value = tf.Variable(0.)
tf.summary.scalar("loss", loss_value)
merge_op = tf.summary.merge_all()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwars = {
'sess': sess,
'noise_dim': FLAGS.noise_dim,
'image_size': FLAGS.image_size,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'is_training': True
}
Model = DCGAN(**kwars)
utils.cal_parameter()
# prepare tensorboard
writer_train_g = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train_g'), sess.graph)
writer_train_d = tf.summary.FileWriter(
os.path.join(FLAGS.outdir, 'tensorboard', 'train_d'))
# initialize
sess.run(init_op)
tbar = tqdm(range(FLAGS.epoch), ascii=True)
epoch_loss_g = []
epoch_loss_d = []
for step in tbar:
train_data_shuffled = train_gen.flow(x_train,
y=None,
batch_size=FLAGS.batch_size,
shuffle=True)
# one epoch
for iter in range(x_train.shape[0] // FLAGS.batch_size):
train_data_batch = next(train_data_shuffled)
noise = np.random.uniform(
-1., 1., size=[FLAGS.batch_size, FLAGS.noise_dim])
# training
d_loss = Model.update_d(noise, train_data_batch)
g_loss = Model.update_g(noise)
epoch_loss_d.append(d_loss)
epoch_loss_g.append(g_loss)
s = "epoch:{}, loss_d:{:.4f}, loss_g:{:.4f}".format(
step + 1, np.mean(epoch_loss_d), np.mean(epoch_loss_g))
tbar.set_description(s)
sum_d_loss = sess.run(merge_op,
{loss_value: np.mean(epoch_loss_d)})
sum_g_loss = sess.run(merge_op,
{loss_value: np.mean(epoch_loss_g)})
writer_train_d.add_summary(sum_d_loss, step)
writer_train_g.add_summary(sum_g_loss, step)
epoch_loss_d.clear()
epoch_loss_g.clear()
# save model
Model.save_model(FLAGS.outdir, step)
def main(argv):
# turn off log message
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.FATAL)
# check folder
if not os.path.exists(os.path.join(FLAGS.dir, 'tensorboard')):
os.makedirs(os.path.join(FLAGS.dir, 'tensorboard'))
if not os.path.exists(FLAGS.dir):
raise Exception("model dirctory is not existed!")
# get tfrecord list
val_data_list = glob.glob(FLAGS.indir + '/*')
# get ground truth list
ground_truth_list = glob.glob(FLAGS.ground_truth + '/*.mhd')
# load ground truth
ground_truth = io.load_data_from_path(ground_truth_list, dtype='int32')
# number of model
num_of_model = FLAGS.train_iteration // FLAGS.save_model_step
num_of_model = num_of_model + 1 if FLAGS.train_iteration % FLAGS.save_model_step is not 0 else num_of_model - 1
# val_iter
num_val_iter = FLAGS.num_of_val // FLAGS.batch_size
if FLAGS.num_of_val % FLAGS.batch_size != 0:
num_val_iter += 1
# load val data
val_set = tf.data.Dataset.list_files(val_data_list)
val_set = val_set.apply(
tf.data.experimental.parallel_interleave(
lambda x: tf.data.TFRecordDataset(x), cycle_length=os.cpu_count()))
val_set = val_set.map(lambda x: utils._parse_function_val_test(
x, image_size=FLAGS.image_size),
num_parallel_calls=os.cpu_count())
val_set = val_set.repeat()
val_set = val_set.batch(FLAGS.batch_size)
val_set = val_set.make_one_shot_iterator()
val_data = val_set.get_next()
# initializer
init_op = tf.group(tf.initializers.global_variables(),
tf.initializers.local_variables())
with tf.Session(config=utils.config(index=FLAGS.gpu_index)) as sess:
# set network
kwargs = {
'sess': sess,
'latent_dim': FLAGS.latent_dim,
'scale_lambda': FLAGS.scale_lambda,
'scale_kappa': FLAGS.scale_kappa,
'scale_psi': FLAGS.scale_psi,
'image_size': FLAGS.image_size,
'points_num': FLAGS.points_num,
'k_size': FLAGS.k_size,
'encoder_layer': encoder_layer,
'points_encoder_layer': points_encoder_layer,
'generator_layer': generator_layer,
'discriminator_layer': discriminator_layer,
'code_discriminator_layer': code_discriminator_layer,
'is_training': False
}
Model = conditional_alphaGAN(**kwargs)
# print parameters
utils.cal_parameter()
# prepare tensorboard
writer_gen = tf.summary.FileWriter(
os.path.join(FLAGS.dir, 'tensorboard', 'val_generalization'))
writer_spe = tf.summary.FileWriter(
os.path.join(FLAGS.dir, 'tensorboard', 'val_specificity'))
writer_val_ls = tf.summary.FileWriter(
os.path.join(FLAGS.dir, 'tensorboard', 'val_ls'))
writer_val_eikonal = tf.summary.FileWriter(
os.path.join(FLAGS.dir, 'tensorboard', 'val_eikonal'))
writer_all = tf.summary.FileWriter(
os.path.join(FLAGS.dir, 'tensorboard',
'val_all')) # mean of generalization and specificity
# saving loss operation
value_loss = tf.Variable(0.0)
tf.summary.scalar("evaluation", value_loss)
merge_op = tf.summary.merge_all()
# initialize
sess.run(init_op)
# validation
tbar = tqdm(range(num_of_model), ascii=True)
for step in tbar:
Model.restore_model(
FLAGS.dir +
'/model/model_{}'.format(step * FLAGS.save_model_step))
generalization, specificity, val_ls, val_eikonal = [], [], [], []
points = []
real_image = []
# reconstruction
for i in range(num_val_iter):
val_image_batch, val_points_batch, val_label_batch = sess.run(
val_data)
points.append(val_points_batch)
real_image.append(val_image_batch)
reconstruction_batch = Model.reconstruction(
val_image_batch, val_points_batch)
if i is 0:
val_label = np.asarray(val_label_batch)
reconstruction = np.asarray(reconstruction_batch)[0]
else:
val_label = np.concatenate(
(val_label, np.asarray(val_label_batch)), axis=0)
reconstruction = np.concatenate(
(reconstruction, np.asarray(reconstruction_batch)[0]),
axis=0)
# calculate generalization
for i in range(reconstruction.shape[0]):
val_label_single = val_label[i][:, :, :, 0]
reconstruction_single = reconstruction[i][:, :, :, 0]
# label
rec_label = np.where(reconstruction_single > 0.5, 0, 1)
# calculate ji
generalization.append(
[utils.jaccard(rec_label, val_label_single)])
# samples from latent space
points_ls = np.ones_like(points) * 0.5
for i in range(FLAGS.num_of_generate // FLAGS.batch_size):
shuffle_fun(points_ls, points)
z = np.random.normal(0.,
1.,
size=[FLAGS.batch_size, FLAGS.latent_dim])
generate_batch, level_set_loss, eikonal_loss = Model.validation_specificity(
points_ls[random.randint(0, num_val_iter - 1)], z,
points[random.randint(0, num_val_iter - 1)])
val_ls.append(level_set_loss)
val_eikonal.append(eikonal_loss)
if i is 0:
samples = np.asarray(generate_batch)
else:
samples = np.concatenate(
(samples, np.asarray(generate_batch)), axis=0)
# calculate specificity
for i in range(samples.shape[0]):
gen = samples[i][:, :, :, 0]
# label
gen_label = np.where(gen > 0.5, 0, 1)
# calculate ji
case_max_ji = 0.
for image_index in range(ground_truth.shape[0]):
ji = utils.jaccard(gen_label, ground_truth[image_index])
if ji > case_max_ji:
case_max_ji = ji
specificity.append([case_max_ji])
s = "val_generalization: {:.4f}, val_specificity: {:.4f}, ls: {:.4f}, eikonal: {:.4f}, mean: {:.4f}".format(
np.mean(generalization), np.mean(specificity), np.mean(val_ls),
np.mean(val_eikonal),
(np.mean(generalization) + np.mean(specificity)) / 2.)
tbar.set_description(s)
summary_gen = sess.run(merge_op,
{value_loss: np.mean(generalization)})
summary_spe = sess.run(merge_op,
{value_loss: np.mean(specificity)})
summary_ls = sess.run(merge_op, {value_loss: np.mean(val_ls)})
summary_eikonal = sess.run(merge_op,
{value_loss: np.mean(val_eikonal)})
summary_all = sess.run(merge_op, {
value_loss:
(np.mean(generalization) + np.mean(specificity)) / 2.
})
writer_gen.add_summary(summary_gen, step * FLAGS.save_model_step)
writer_spe.add_summary(summary_spe, step * FLAGS.save_model_step)
writer_val_ls.add_summary(summary_ls, step * FLAGS.save_model_step)
writer_val_eikonal.add_summary(summary_eikonal,
step * FLAGS.save_model_step)
writer_all.add_summary(summary_all, step * FLAGS.save_model_step)
generalization.clear()
specificity.clear()
val_ls.clear()
val_eikonal.clear()
points.clear()
real_image.clear()
