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net.py
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net.py
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from __future__ import print_function
import time
import numpy as np
import tensorflow as tf # needs tf > 1.0
from tensorflow.contrib.tensorboard.plugins import projector # for 3d PCA/ t-SNE
from .tensorboard_util import *
print("tf.__version__:%s" % tf.__version__)
start = int(time.time())
gpu = True
# gpu = False
debug = False # summary.histogram : 'module' object has no attribute 'histogram' WTF
# debug = True # histogram_summary ...
# clear_tensorboard()
if debug:
set_tensorboard_run(auto_increment=True)
run_tensorboard(restart=False)
visualize_cluster = False # NOT YET: 'ProjectorConfig' object has no attribute 'embeddings'
weight_divider = 10.
default_learning_rate = 0.001 # mostly overwritten, so ignore it
decay_steps = 100000
decay_size = 0.1
save_step = 10000 # if you don't want to save snapshots, set to 0
checkpoint_dir = "checkpoints"
_cpu = '/cpu:0'
_gpu = '/GPU:0'
if not os.path.exists(checkpoint_dir):
os.makedirs(checkpoint_dir)
def nop(): return 0
def closest_unitary(A):
""" Calculate the unitary matrix U that is closest with respect to the operator norm distance to the general matrix A. """
try:
import scipy
V, __, Wh = scipy.linalg.svd(A)
return np.matrix(V.dot(Wh))
except:
return A
class net:
def __init__(self, model, input_width=0, output_width=0, input_shape=[], name=0, learning_rate=default_learning_rate):
self.fully_connected = self.dense # alias
device = _gpu if gpu else _cpu
device = None # auto
print("Using device ", device)
with tf.device(device):
self.session = tf.Session()
self.model = model
self.input_shape = input_shape or [input_width, input_width]
if not input_width: input_width, _ = self.get_data_shape()
self.input_width = input_width
self.last_width = self.input_width
self.last_shape = self.input_shape
self.output_width = output_width
self.num_classes = output_width
# self.batch_size=batch_size
self.layers = []
self.learning_rate = learning_rate
if isinstance(model, str):
self.name = model
self.restore()
return
self.name = model.__name__
if input_width == 0:
raise Exception("Please set input_width or input_shape")
if output_width == 0:
raise Exception("Please set number of classes via output_width")
self.generate_model(model)
def get_data_shape(self):
if self.input_shape:
if len(self.input_shape) == 1: return [self.input_shape[0], 0]
return self.input_shape[0], self.input_shape[1]
try:
return self.data.shape[0], self.data.shape[-1]
except:
raise Exception("Data does not have shape")
def generate_model(self, model, name=''):
if not model: return self
with tf.name_scope('state'):
self.keep_prob = tf.placeholder(tf.float32, name="dropout_keep_prob") # 1 for testing! else 1 - dropout
self.train_phase = tf.placeholder(tf.bool, name='train_phase')
with tf.device(_cpu): self.global_step = tf.Variable(0)
# dont set, feed or increment global_step, tensorflow will do it automatically
with tf.name_scope('data'):
if self.input_shape and len(self.input_shape) == 2:
shape_ = [None, self.input_shape[0], self.input_shape[1]] # batch:None
# todo [None, *self.input_shape]
self.x = x = self.input = tf.placeholder(tf.float32, shape_, name="input_x")
self.last_shape = x
elif self.input_width:
self.x = x = self.input = tf.placeholder(tf.float32, [None, self.input_width], name="input_x")
else:
raise Exception("need input_shape or input_width by now")
self.last_layer = self.x
tf.add_to_collection('inputs', self.x)
self.y = y = self.target = tf.placeholder(tf.float32, [None, self.output_width], name="target_y")
tf.add_to_collection('targets', self.target)
with tf.name_scope('model'):
model(self)
if (self.last_width != self.output_width):
self.classifier() # 10 classes auto
def dropout(self, keep_rate=0.6):
self.add(tf.nn.dropout(self.last_layer, keep_rate))
def add(self, layer):
self.layers.append(layer)
self.last_layer = layer
self.last_shape = layer.get_shape()
def reshape(self, shape):
self.last_layer = tf.reshape(self.last_layer, shape)
self.last_shape = shape
self.last_width = shape[-1]
# BN also serve as a stochastic regularizer and makes dropout regularization redundant! Furthermore dropout never really helped when inserted between convolution layers and was most useful between fully connected layers.
# when applying batchnorm you can drop biases [redundant: BN(x)=ax+b] and must increase learning rate!! ++
def batchnorm(self, input=None, center=False): # for conv2d and fully_connected [only!?]
if input is None: input = self.last_layer
from tensorflow.contrib.layers.python.layers import batch_norm as batch_norm
with tf.name_scope('batchnorm') as scope:
# mean, var = tf.nn.moments(input, axes=[0, 1, 2])
# self.batch_norm = tf.nn.batch_normalization(input, mean, var, offset=1, scale=1, variance_epsilon=1e-6)
# self.last_layer=self.batch_norm
# activation_fn all in one go! sigmoid: center=true! relu:center=False?
# is_training why not automatic?? bad implementation: placeholder -> needs_moments
# vs low level nn.batch_normalization(inputs, mean, variance, beta, gamma, epsilon) # nn.fused_batch_norm
# data_format: A string. `NHWC` vs NCHW WHY NOT AUTO??
# activation_fn inline
train_op = batch_norm(input, is_training=True, center=center, updates_collections=None, scope=scope)
test_op = batch_norm(input, is_training=False, updates_collections=None, center=False, scope=scope, reuse=True)
output = tf.cond(self.train_phase, lambda: train_op, lambda: test_op)
# output=self.debug_print(output)
self.add(output)
return output
def addLayer(self, nChannels, nOutChannels, do_dropout):
ident = self.last_layer
self.batchnorm()
# self.add(tf.nn.relu(ident)) # nChannels ?
self.conv([3, 3, nChannels, nOutChannels], pool=False, dropout=do_dropout, norm=tf.nn.relu) # None
concat = tf.concat(axis=3, values=[ident, self.last_layer])
print("concat ", concat.get_shape())
self.add(concat)
def addTransition(self, nChannels, nOutChannels, do_dropout):
self.batchnorm()
self.add(tf.nn.relu(self.last_layer))
self.conv([1, 1, nChannels, nOutChannels], pool=True, dropout=do_dropout, norm=None) # pool (2, 2)
# self.add(tf.nn.SpatialConvolution(nChannels, nOutChannels, 1, 1, 1, 1, 0, 0))
# Fully connected 'pyramid' layer, allows very high learning_rate >0.1 (but don't abuse)
# NOT TO BE CONFUSED with buildDenseConv below!
def fullDenseNet(self, hidden=20, depth=3, act=tf.nn.tanh, dropout=True, norm=None): #
if hidden > 100: print("WARNING: denseNet uses O(n^2) quadratic memory for " + str(hidden)) + " hidden units"
if depth < 3: print(
"WARNING: did you mean to use Fully connected layer 'dense'? Expecting depth>3 vs " + str(depth))
inputs = self.last_layer
inputs_width = self.last_width
width = hidden
while depth > 0:
with tf.name_scope('DenNet_{:d}'.format(width)) as scope:
print("dense width ", inputs_width, "x", width)
nr = len(self.layers)
weights = tf.Variable(tf.random_uniform([inputs_width, width], minval=-1. / width, maxval=1. / width),
name="weights")
bias = tf.Variable(tf.random_uniform([width], minval=-1. / width, maxval=1. / width),
name="bias") # auto nr + context
dense1 = tf.matmul(inputs, weights, name='dense_' + str(nr)) + bias
tf.summary.histogram('dense_' + str(nr), dense1)
tf.summary.histogram('dense_' + str(nr) + '/sparsity', tf.nn.zero_fraction(dense1))
tf.summary.histogram('weights_' + str(nr), weights)
tf.summary.histogram('weights_' + str(nr) + '/sparsity', tf.nn.zero_fraction(weights))
tf.summary.histogram('bias_' + str(nr), bias)
if act: dense1 = act(dense1)
if norm: dense1 = self.norm(dense1, lsize=1) # SHAPE!
if dropout: dense1 = tf.nn.dropout(dense1, self.keep_prob)
self.add(dense1)
self.last_width = width
inputs = tf.concat(axis=1, values=[inputs, dense1])
inputs_width += width
depth = depth - 1
self.last_width = width
# Densely Connected Convolutional Networks https://arxiv.org/abs/1608.06993
def buildDenseConv(self, nBlocks=3, nChannels=64, magic_factor=0):
if magic_factor: print("magic_factor DEPRECATED!")
depth = 3 * nBlocks + 4
if (depth - 4) % 3: raise Exception("Depth must be 3N + 4! (4,7,10,...) ") # # layers in each denseblock
N = (depth - 4) // 3
print("N=%d" % N)
do_dropout = True # None nil to disable dropout, non - zero number to enable dropout and set drop rate
# dropRate = self.keep_prob # nil to disable dropout, non - zero number to enable dropout and set drop rate
# channels before entering the first denseblock ??
# set it to be comparable with growth rate ??
growthRate = 12
self.conv([3, 3, 1, nChannels]) # why this
# self.conv([1, 3, 3, nChannels]) # and not this?
# self.add(tf.nn.SpatialConvolution(3, nChannels, 3, 3, 1, 1, 1, 1))
for i in range(N):
self.addLayer(nChannels, growthRate, do_dropout)
nChannels += growthRate
self.addTransition(nChannels, nChannels, do_dropout)
for i in range(N):
self.addLayer(nChannels, growthRate, do_dropout)
nChannels += growthRate
self.addTransition(nChannels, nChannels, do_dropout)
for i in range(N):
self.addLayer(nChannels, growthRate, do_dropout)
nChannels += growthRate
self.batchnorm()
self.add(tf.nn.relu(self.last_layer))
# self.add(tf.nn.max_pool(self.last_layer, ksize=[1, 8, 8, 1], strides=[1, 2, 2, 1], padding='SAME'))
# self.add(tf.nn.max_pool(self.last_layer, ksize=[1, 8, 8, 1], strides=[1, 1, 1, 1], padding='SAME'))
# self.add(tf.nn.max_pool(self.last_layer, ksize=[1, 4, 4, 1], strides=[1, 1, 1, 1], padding='SAME'))
self.add(tf.nn.max_pool(self.last_layer, ksize=[1, 4, 4, 1], strides=[1, 2, 2, 1], padding='SAME'))
# self.add(tf.nn.SpatialAveragePooling(8, 8)).add(nn.Reshape(nChannels))
shape = self.last_layer.get_shape()
nBytes = shape[1] * shape[2] * shape[3]
self.reshape([-1, int(nBytes)]) # ready for classification
# Today's most performant vision models don't use fully connected layers anymore (they use convolutional blocks till the end and then some parameterless global averaging layer).
# Fully connected layer
def dense(self, hidden=1024, depth=1, activation=tf.nn.tanh, dropout=False, parent=-1, bn=False): #
if parent == -1: parent = self.last_layer
if bn:
print("dropout = False while using batchnorm")
dropout = False
shape = self.last_layer.get_shape()
if shape and len(shape) > 2:
if len(shape) == 3:
self.last_width = int(shape[1] * shape[2])
else:
self.last_width = int(shape[1] * shape[2] * shape[3])
if self.last_width == 0:
raise Exception("self.last_width Must not be zero")
print("reshaping ", shape, "to", self.last_width)
parent = tf.reshape(parent, [-1, self.last_width])
width = hidden
while depth > 0:
with tf.name_scope('Dense_{:d}'.format(hidden)) as scope:
print("Dense ", self.last_width, width)
nr = len(self.layers)
U = tf.random_uniform([self.last_width, width], minval=-1. / width, maxval=1. / width)
# U = np.random.rand(self.last_width, width) / (self.last_width + width)
if self.last_width == width:
U = closest_unitary(U / weight_divider)
weights = tf.Variable(U, name="weights_dense_" + str(nr), dtype=tf.float32)
bias = tf.Variable(tf.random_uniform([width], minval=-1. / width, maxval=1. / width), name="bias_dense")
dense1 = tf.matmul(parent, weights, name='dense_' + str(nr)) + bias
tf.summary.histogram('dense_' + str(nr), dense1)
tf.summary.histogram('weights_' + str(nr), weights)
tf.summary.histogram('bias_' + str(nr), bias)
tf.summary.histogram('dense_' + str(nr) + '/sparsity', tf.nn.zero_fraction(dense1))
tf.summary.histogram('weights_' + str(nr) + '/sparsity', tf.nn.zero_fraction(weights))
if bn: dense1 = self.batchnorm(dense1, center=True)
if activation: dense1 = activation(dense1)
if dropout: dense1 = tf.nn.dropout(dense1, self.keep_prob)
self.layers.append(dense1)
self.last_layer = parent = dense1
self.last_width = width
depth = depth - 1
self.last_shape = [-1, width] # dense
def conv2(self, shape, act=tf.nn.relu, pool=True, dropout=False, norm=True, name=None):
with tf.name_scope('conv'):
print("input shape ", self.last_shape)
print("conv shape ", shape)
# padding='VALID'
conv = slim.conv2d(self.last_layer, shape[-1], [shape[1], shape[2]], 3, padding='SAME', scope=name)
# if pool: conv = tf.nn.max_pool(conv, ksize=[1, 2, 2, 1], strides=[1, 2, 2, 1], padding='SAME')
# if(pool): conv = slim.max_pool2d(conv, [2, 2], 1, scope='pool1')
# if(pool): conv = slim.max_pool2d(conv, [3, 3], 2, scope='pool1')
self.add(conv)
# Convolution Layer
def conv(self, shape, act=tf.nn.relu, pool=True, dropout=False, norm=True,
name=None): # True why dropout bad in tensorflow??
with tf.name_scope('conv'):
print("input shape ", self.last_shape)
print("conv shape ", shape)
width = shape[-1]
filters = tf.Variable(tf.random_normal(shape), name="filters")
# filters = tf.Variable(tf.random_uniform(shape, minval=-1. / width, maxval=1. / width), name="filters")
_bias = tf.Variable(tf.random_normal([shape[-1]]), name="bias")
# # conv1 = conv2d('conv', _X, _weights, _bias)
conv1 = tf.nn.bias_add(tf.nn.conv2d(self.last_layer, filter=filters, strides=[1, 1, 1, 1], padding='SAME'), _bias)
if debug: tf.summary.histogram('conv_' + str(len(self.layers)), conv1)
if act: conv1 = act(conv1)
if pool: conv1 = tf.nn.max_pool(conv1, ksize=[1, 2, 2, 1], strides=[1, 2, 2, 1], padding='SAME')
if norm: conv1 = tf.nn.lrn(conv1, depth_radius=4, bias=1.0, alpha=0.001 / 9.0, beta=0.75)
if debug: tf.summary.histogram('norm_' + str(len(self.layers)), conv1)
if dropout: conv1 = tf.nn.dropout(conv1, self.keep_prob)
print("output shape ", conv1.get_shape())
self.add(conv1)
def rnn(self, num_hidden=42):
# tf.contrib.rnn.BasicLSTMCell() OLD
# tensorflow.python.ops.rnn_cell.BasicLSTMCell()
# tensorflow.models.rnn.BasicLSTMCell()
cell = tf.nn.rnn_cell.LSTMCell(num_hidden)
val, _ = tf.nn.dynamic_rnn(cell, self.last_layer, dtype=tf.float32)
# Dropout does actually work quite well between recurrent units if you tie the dropout masks across time
# val = tf.nn.dropout(val,self.keep_prob) # deprecated by batchnorm
val = tf.transpose(val, [1, 0, 2])
self.last = tf.gather(val, int(val.get_shape()[0]) - 1)
def classifier(self, classes=0): # Define loss and optimizer
if not classes: classes = self.num_classes
if not classes: raise Exception("Please specify num_classes")
with tf.name_scope('prediction'): # prediction
if self.last_width != classes:
# print("Automatically adding dense prediction")
self.dense(hidden=classes, activation=None, dropout=False)
# cross_entropy = -tf.reduce_sum(y_*y)
with tf.name_scope('classifier'):
y_ = self.target
manual = False # True
if classes > 100:
print("using sampled_softmax_loss")
y = prediction = self.last_layer
self.cost = tf.reduce_mean(tf.nn.sampled_softmax_loss(y, y_)) # for big vocab
elif manual:
# prediction = y =self.last_layer=tf.nn.softmax(self.last_layer)
# self.cost = cross_entropy = -tf.reduce_sum(y_ * tf.log(y+ 1e-10)) # against NaN!
prediction = y = tf.nn.log_softmax(self.last_layer)
self.cost = cross_entropy = -tf.reduce_sum(y_ * y)
else:
self.output = y = prediction = self.last_layer
self.cost = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=y, labels=y_)) # prediction, target
tf.add_to_collection('outputs', self.output)
# if not gpu:
with tf.device(_cpu):
tf.summary.scalar('cost', self.cost)
# self.cost = tf.Print(self.cost , [self.cost ], "debug cost : ")
# learning_scheme=self.learning_rate
learning_scheme = tf.train.exponential_decay(self.learning_rate, self.global_step, decay_steps, decay_size,
staircase=True)
with tf.device(_cpu):
tf.summary.scalar('learning_rate', learning_scheme)
self.optimize = tf.train.AdamOptimizer(learning_scheme).minimize(self.cost)
# self.optimizer = NeuralOptimizer(data=None, learning_rate=0.01, shared_loss=self.cost).minimize(self.cost) No good
# Evaluate model
correct_pred = tf.equal(tf.argmax(prediction, 1), tf.argmax(self.target, 1))
self.accuracy = tf.reduce_mean(tf.cast(correct_pred, tf.float32))
# if not gpu:
tf.summary.scalar('accuracy', self.accuracy)
# Launch the graph
# noinspection PyAttributeOutsideInit
def regression(self, dimensions, tolerance=3.):
# self.dense(100)
with tf.name_scope("regression"):
self.dense(dimensions)
self.y = tf.placeholder(tf.float32, [None, dimensions], name="target_y") # self.batch_size
print("REGRESSION 'accuracy' might not be indicative, watch loss")
with tf.name_scope("train"):
# self.learning_rate = tf.Variable(0.5, trainable=False)
self.cost = tf.reduce_mean(tf.pow(self.y - self.last_layer, 2))
self.optimize = tf.train.AdamOptimizer(self.learning_rate).minimize(self.cost)
self.accuracy = tf.maximum(0., 100 - tf.sqrt(self.cost)/tolerance)
# self.accuracy = 1 - abs(self.y - self.last_layer)
tf.add_to_collection('train_ops', [self.learning_rate, self.cost, self.optimize, self.accuracy])
def debug_print(self, throughput, to_print=[]):
return tf.cond(self.train_phase, lambda: throughput, lambda: tf.Print(throughput, to_print + [nop()], "OK!"))
def next_batch(self, batch_size, session, test=False):
# self.data either a generator or a data struct with properties .train/test.images/labels
try:
if test:
test_images = self.data.test.images[:batch_size]
test_labels = self.data.test.labels[:batch_size]
return test_images, test_labels
return self.data.train.next_batch(batch_size)
except:
try:
return next(self.data)
except:
return next(self.data.train)
def train(self, data=0, steps=-1, dropout=None, display_step=10, test_step=100, batch_size=10,
resume=save_step): # epochs=-1,
print("learning_rate: %f" % self.learning_rate)
if data: self.data = data
steps = 9999999 if steps < 0 else steps
session = self.session
# with tf.device(_cpu):
# t = tf.verify_tensor_all_finite(t, msg)
tf.add_check_numerics_ops()
self.summaries = tf.summary.merge_all()
self.summary_writer = tf.summary.FileWriter(current_logdir(), session.graph)
if not dropout: dropout = 1. # keep all
x = self.x
y = self.y
keep_prob = self.keep_prob
if not resume or not self.resume(session):
session.run([tf.global_variables_initializer()])
saver = tf.train.Saver(tf.global_variables())
snapshot = self.name + str(get_last_tensorboard_run_nr())
step = 0 # show first
while step < steps:
batch_xs, batch_ys = self.next_batch(batch_size, session)
# batch_xs=np.array(batch_xs).reshape([-1]+self.input_shape)
# print("step %d \r" % step)# end=' ')
# tf.train.shuffle_batch_join(example_list, batch_size, capacity=min_queue_size + batch_size * 16, min_queue_size)
# Fit training using batch data
feed_dict = {x: batch_xs, y: batch_ys, keep_prob: dropout, self.train_phase: True}
loss, _ = session.run([self.cost, self.optimize], feed_dict=feed_dict)
if step % display_step == 0:
seconds = int(time.time()) - start
# Calculate batch accuracy, loss
feed = {x: batch_xs, y: batch_ys, keep_prob: 1., self.train_phase: False}
acc, summary = session.run([self.accuracy, self.summaries], feed_dict=feed)
# self.summary_writer.add_summary(summary, step) # only test summaries for smoother curve
print("\rStep {:d} Loss= {:.6f} Accuracy= {:.3f} Time= {:d}s".format(step, loss, acc, seconds), end=' ')
if str(loss) == "nan": return print("\nLoss gradiant explosion, exiting!") # restore!
if step % test_step == 0: self.test(step)
if step % save_step == 0 and step > 0:
print("SAVING snapshot %s" % snapshot)
saver.save(session, checkpoint_dir + "/" + snapshot + ".ckpt", self.global_step)
step += 1
print("\nOptimization Finished!")
self.test(step, number=10000) # final test
def test(self, step, number=400): # 256 self.batch_size
session = sess = self.session
config = projector.ProjectorConfig()
if visualize_cluster: # EMBEDDINGs ++ https://github.com/tensorflow/tensorflow/issues/6322
embedding = config.embeddings.add() # You can add multiple embeddings. Here just one.
run_metadata = tf.RunMetadata()
run_options = tf.RunOptions(trace_level=tf.RunOptions.FULL_TRACE)
# Calculate accuracy for 256 mnist test images
test_images, test_labels = self.next_batch(number, session, test=True)
# test_images = np.array(test_images).reshape([-1] + self.input_shape)
feed_dict = {self.x: test_images, self.y: test_labels, self.keep_prob: 1., self.train_phase: False}
# accuracy,summary= self.session.run([self.accuracy, self.summaries], feed_dict=feed_dict)
accuracy, summary = session.run([self.accuracy, self.summaries], feed_dict, run_options, run_metadata)
print('\t' * 3 + "Test Accuracy: {:.2f}".format( accuracy))
self.summary_writer.add_run_metadata(run_metadata, 'step #%03d' % step)
self.summary_writer.add_summary(summary, global_step=step)
if accuracy == 1.0:
print("OVERFIT OK. Early stopping")
exit(0)
def resume(self, session):
checkpoint = tf.train.latest_checkpoint(checkpoint_dir)
if checkpoint:
if self.name and not self.name in checkpoint:
print("IGNORING checkpoint of other run : " + checkpoint + " !")
checkpoint = None
else:
print("NO checkpoint, nothing to resume")
if checkpoint:
print("LOADING " + checkpoint + " !")
try:
persister = tf.train.Saver(tf.global_variables())
persister.restore(session, checkpoint)
print("resume checkpoint successful!")
return True
except Exception as ex:
print(ex)
print("CANNOT LOAD checkpoint %s !" % checkpoint)
return False
def restore(self): # name
# if not session: session= tf.Session()
self.session = tf.Session()
checkpoint = tf.train.get_checkpoint_state(checkpoint_dir)
if checkpoint and checkpoint.model_checkpoint_path:
print("Restoring old model from meta graph")
loader = tf.train.import_meta_graph(checkpoint.model_checkpoint_path + ".meta")
else:
print("No model from meta graph, nothing to restore")
return self
self.session.run(tf.global_variables_initializer())
print("loading checkpoint %s" % checkpoint.model_checkpoint_path)
try:
loader.restore(self.session, tf.train.latest_checkpoint(checkpoint_dir))
except:
pass
# loader.restore(self.session , checkpoint) #Unable to get element from the feed as bytes! HUH??
self.input = self.x = tf.get_collection('inputs')[0]
self.target = self.y = tf.get_collection('targets')[0]
self.output = self.last_layer = tf.get_collection('outputs')[0]
self.dropout_keep_prob = self.session.graph.get_tensor_by_name("state/dropout_keep_prob:0") # :0 WTF!?!?!
self.train_phase = self.session.graph.get_tensor_by_name(name='state/train_phase:0')
return self
def predict(self, eval_data=None, model=None):
if eval_data is None:
eval_data = np.random.random(self.input_shape)
feed_dict = {self.x: [eval_data], self.dropout_keep_prob: 1.0, self.train_phase: False}
result = self.session.run([self.output], feed_dict)
best = np.argmax(result)
# print("prediction: %s" % result)
print("predicted: %s" % best)
return best