def next_batch_test(self):
"""
returns:
a tuple(image, depths) where:
image is a float tensor with shape [batch size] + input_size
depth is a float tensor with shape [batch size] + depth_size
"""
filenames = self.test_file
dataset = tf.contrib.data.TFRecordDataset(filenames)
dataset = dataset.map(
self._parse_function) # Parse the record into tensors.
dataset = dataset.batch(self.config_dict["batch_size"])
iterator = dataset.make_initializable_iterator()
initializer = iterator.initializer
images_gt, depths = iterator.get_next()
# depths = tf.reshape(depths, [self.batch_size] + self.output_size)
# images = tf.reshape(images, [self.batch_size] + self.input_size)
images = simulator.applyTurbidity(images_gt, depths, self.c, self.binf,
self.range_array)
tf.summary.image("image_gt", images_gt)
tf.summary.image("image", images)
print(images.shape, images_gt.shape)
return images, images_gt, initializer
def next_batch_test(self):
"""
returns:
a tuple(image, transmissions) where:
image is a float tensor with shape [batch size] + input_size
transmissions is a float tensor with shape [batch size]
"""
filenames = self.test_file
dataset = tf.contrib.data.TFRecordDataset(filenames)
dataset = dataset.map(
self._parse_function) # Parse the record into tensors.
dataset = dataset.batch(self.config_dict["batch_size"])
iterator = dataset.make_initializable_iterator()
initializer = iterator.initializer
images = iterator.get_next()
size_x = self.config_dict['patch_size'][0]
size_y = self.config_dict['patch_size'][1]
offset_x = random.randint(0, self.input_size[0] - size_x - 1)
offset_y = random.randint(0, self.input_size[0] - size_y - 1)
images = images[:, offset_x:offset_x + size_x,
offset_y:offset_y + size_y]
# depths = tf.reshape(depths, [self.batch_size] + self.output_size)
# images = tf.reshape(images, [self.batch_size] + self.input_size)
transmissions = self.random_transmissions(self.batch_size)
images = simulator.applyTurbidityTransmission(images, self.binf,
transmissions)
tf.summary.image("image", images)
return images, transmissions, initializer
def next_batch_train(self, initial_step):
"""
returns:
a tuple(image, depths) where:
image is a float tensor with shape [batch size] + input_size
depth is a float tensor with shape [batch size] + depth_size
"""
filenames = self.train_file
dataset = tf.contrib.data.TFRecordDataset(filenames)
dataset = dataset.map(
self._parse_function) # Parse the record into tensors.
dataset = dataset.shuffle(buffer_size=3000)
dataset = dataset.batch(self.config_dict["batch_size"])
dataset = dataset.repeat(
self.config_dict["num_epochs"]) # Repeat the input.
dataset = dataset.skip(initial_step)
iterator = dataset.make_one_shot_iterator()
images, depths = iterator.get_next()
#depths = tf.reshape(depths, [None] + self.output_size)
#images = tf.reshape(images, [None] + self.input_size)
images = simulator.applyTurbidity(images, depths, self.c, self.binf,
self.range_array)
tf.summary.image("depth", depths)
tf.summary.image("image", images)
return images, depths
def input_fn(filenames, train=True, batch_size=16, buffer_size=512):
# Args:
# filenames: Filenames for the TFRecords files.
# train: Boolean whether training (True) or testing (False).
# batch_size: Return batches of this size.
# buffer_size: Read buffers of this size. The random shuffling
# is done on the buffer, so it must be big enough.
# Create a TensorFlow Dataset-object which has functionality
# for reading and shuffling data from TFRecords files.
dataset = tf.data.TFRecordDataset(filenames=filenames)
# Parse the serialized data in the TFRecords files.
# This returns TensorFlow tensors for the image and labels.
dataset = dataset.map(parse)
if train:
# If training then read a buffer of the given size and
# randomly shuffle it.
dataset = dataset.shuffle(buffer_size=buffer_size)
# Allow infinite reading of the data.
num_repeat = None
else:
# If testing then don't shuffle the data.
num_repeat = 1
# Repeat the dataset the given number of times.
dataset = dataset.repeat(num_repeat)
# Get a batch of data with the given size.
dataset = dataset.batch(batch_size)
# Create an iterator for the dataset and the above modifications.
iterator = dataset.make_one_shot_iterator()
# Get the next batch of images and labels, may take dimensionality info later but for now we set to _
images_batch, labels_batch, \
xdim_batch, ydim_batch, channels_batch = iterator.get_next()
if train:
images_batch = distort_batch(images_batch)
# The input-function must return a dict wrapping the images.
x = {'x': images_batch}
y = labels_batch
return x, y
def apply_augmentations(self, dataset: tf.data.Dataset) -> tf.data.Dataset: #x: tf.Tensor, label: tf.Tensor) -> tf.Tensor:
"""
Call this function to apply all of the augmentation in the order of specification
provided to the constructor __init__() of ImageAugmentor.
Args:
dataset, tf.data.Dataset: must yield individual examples of form (x, y)
Returns:
Augmented dataset
"""
for f in self.augmentations:
# Apply an augmentation only in 25% of the cases.000000
aug = self.maps[f]
dataset = dataset.map(lambda x,y: tf.cond(tf.random_uniform([], 0, 1) > (1 - self.p)), lambda: (aug(x),y), lambda: (x,y), num_parallel_calls=4)
return dataset
def next_batch_train(self, initial_step):
"""
args:
batch_size:
number of examples per returned batch
num_epochs:
number of time to read the input data
returns:
a tuple(image, transmissions) where:
image is a float tensor with shape [batch size] + patch_size
transmissions is a float tensor with shape [batch size]
"""
filenames = self.train_file
dataset = tf.contrib.data.TFRecordDataset(filenames)
dataset = dataset.map(
self._parse_function) # Parse the record into tensors.
dataset = dataset.shuffle(buffer_size=3000)
dataset = dataset.batch(self.config_dict["batch_size"])
dataset = dataset.repeat(
self.config_dict["num_epochs"]) # Repeat the input.
dataset = dataset.skip(initial_step)
iterator = dataset.make_one_shot_iterator()
images = iterator.get_next()
size_x = self.config_dict['patch_size'][0]
size_y = self.config_dict['patch_size'][1]
offset_x = random.randint(0, self.input_size[0] - size_x - 1)
offset_y = random.randint(0, self.input_size[0] - size_y - 1)
images = images[:, offset_x:offset_x + size_x,
offset_y:offset_y + size_y]
transmissions = self.random_transmissions(self.batch_size)
images = simulator.applyTurbidityTransmission(images, self.binf,
transmissions)
tf.summary.image("image", images)
return images, transmissions
def next_batch_train(self, initial_step, sess):
"""
returns:
a tuple(image, depths) where:
image is a float tensor with shape [batch size] + input_size
depth is a float tensor with shape [batch size] + depth_size
"""
filenames = self.train_file
dataset = tf.contrib.data.TFRecordDataset(filenames)
dataset = dataset.map(
self._parse_function) # Parse the record into tensors.
dataset = dataset.shuffle(buffer_size=3000)
dataset = dataset.batch(self.config_dict["batch_size"])
dataset = dataset.repeat(
self.config_dict["num_epochs"]) # Repeat the input.
dataset = dataset.skip(initial_step)
iterator = dataset.make_one_shot_iterator()
images_gt, depths = iterator.get_next()
#print (depths.eval(session=sess))
#depths = tf.reshape(depths, [None] + self.output_size)
#images = tf.reshape(images, [None] + self.input_size)
images = simulator.applyTurbidity(images_gt, depths, self.c, self.binf,
self.range_array)
tf.summary.image("image_gt", images_gt)
tf.summary.image("depth", depths)
tf.summary.image("image", images)
# sess = tf.Session()
# d, im = sess.run([depths[0], images_gt[0]])
# print (im.dtype)
# pic = Image.fromarray(img_as_ubyte(im))
# print("depths[0]", np.min(d), np.max(d), np.mean(d))
# pic.show()
return images, images_gt
def train():
training_filename = [
"/home/szaman5/Phytoplankton_Classifier/test_data/train.tfrecords"
]
validation_filename = [
"/home/szaman5/Phytoplankton_Classifier/test_data/validation.tfrecords"
]
filename = tf.placeholder(tf.string, shape=[None])
dataset = tf.data.TFRecordDataset(filename)
dataset = dataset.map(_parser, num_parallel_calls=40)
dataset = dataset.shuffle(buffer_size=int(sys.argv[1]))
dataset = dataset.batch(int(sys.argv[2]))
dataset = dataset.prefetch(buffer_size=int(sys.argv[2]) * 100)
iterator = dataset.make_initializable_iterator()
next_element = iterator.get_next()
counter = 0
NUM_EPOCHS = 40
val_acc = 0
acc = 0
count = 0
for epoch in range(NUM_EPOCHS):
session.run(iterator.initializer,
feed_dict={filename: training_filename})
#x_batch, y_true_batch = data.train.next_batch(batch_size)
while True:
try:
t = time()
x_batch, y_true_batch = session.run(next_element)
#print("Load time is",time()-t)
feed_dict_tr = {
x: x_batch,
y_true: y_true_batch,
keep_prob: 0.3
}
_, acc = session.run([optimizer, accuracy],
feed_dict=feed_dict_tr)
#acc = session.run(accuracy,feed_dict= feed_dict_tr)
#print(time()-t)
count += 1
#print("Batch %d complete",count)
except tf.errors.OutOfRangeError as e:
break
#print("Training complete. Starting Test set")
session.run(iterator.initializer,
feed_dict={filename: validation_filename})
val_b = 0
while True:
try:
x_valid_batch, y_valid_batch = session.run(next_element)
feed_dict_val = {
x: x_valid_batch,
y_true: y_valid_batch,
keep_prob: 1
}
#val_loss = session.run(cost,feed_dict=feed_dict_val)
val_loss, val_acc, valacc3 = session.run(
[cost, accuracy2, accuracy3], feed_dict=feed_dict_val)
#summary,val_acc = session.run([merged,accuracy],feed_dict=feed_dict_val)
#print("Batch Accuracy: ",epoch,val_acc)
val_acc3 = session.run(accuracy3, feed_dict=feed_dict_val)
print(val_acc, val_acc3)
val_b += 1
#writer.add_summary(summary,epoch)
#print("Validation bath:",val_b)
except tf.errors.OutOfRangeError as e:
show_progress(epoch, acc, val_acc, val_loss)
saver.save(
session,
"/home/szaman5/Phytoplankton_Classifier/trained_model/")
break
def main(_):
tf_record_base = '/home/westwell/Desktop/dolores_storage/humpback_whale_identification/' \
'data/all/tfrecord_single_image/'
os.environ['CUDA_VISIBLE_DEVICES'] = FLAGS.gpu
if FLAGS.cfg_file is None:
raise ValueError('You must supply the cfg file !')
cfg = _cfg_from_file(FLAGS.cfg_file)
train_cfg = cfg['train']
# print all configs
print('############################ cfg ############################')
for k in cfg:
print('%s: %s' % (k, cfg[k]))
tf.logging.set_verbosity(tf.logging.INFO)
#######################################################################
############## sigle GPU version ##############
#######################################################################
#### get features ####
input_image = tf.placeholder(tf.uint8,
shape=[None, None, 3],
name='input_image')
image = resize_to_range(input_image, cfg['min_resize_value'],
cfg['max_resize_value'])
image = corp_image(image, cfg['corp_size'], random_crop=False)
image = tf.expand_dims(image, axis=0)
feature_for_dst, _ = feature_extractor.extract_features(
images=image,
num_classes=None,
output_stride=cfg['output_stride'],
global_pool=True,
model_variant=cfg['model_variant'],
weight_decay=0.0,
dropout_keep_prob=1.0,
regularize_depthwise=False,
reuse=tf.AUTO_REUSE,
is_training=False,
fine_tune_batch_norm=False,
cfg=cfg)
if len(feature_for_dst.shape) == 4:
feature_for_dst = tf.squeeze(feature_for_dst,
axis=[1, 2],
name='features_for_dst')
elif len(feature_for_dst.shape) == 2:
feature_for_dst = tf.identity(feature_for_dst, name='features_for_dst')
else:
raise Exception('feature_for_dst shape not right, got %s' %
(feature_for_dst.shape))
#### get similarity probs of two features ####
ref_features = tf.placeholder(tf.float32,
shape=[None, feature_for_dst.shape[-1]],
name='ref_features')
dut_feature = tf.placeholder(tf.float32,
shape=[1, feature_for_dst.shape[-1]],
name='dut_features')
prob_same_ids = similarity_prob_for_one_query(
ref_features=ref_features,
dut_feature=dut_feature,
d_cfg=cfg['distance_config'],
scope='similarity_prob_for_one_query')
#### set up session config ####
# session config:
sess_cfg = tf.ConfigProto(allow_soft_placement=True,
log_device_placement=False)
sess_cfg.gpu_options.allow_growth = True
#### do test the model ####
with tf.Session(config=sess_cfg) as sess:
# init
#sess.run(tf.global_variables_initializer())
#sess.run(tf.local_variables_initializer())
# restore vars from pretrained ckpt:
vars_to_restore = _var_to_restore(None)
for v in vars_to_restore:
print(v.op.name)
restor_saver = tf.train.Saver(var_list=vars_to_restore)
restor_saver.restore(sess,
tf.train.latest_checkpoint(FLAGS.output_dir))
# forward all ref images
filenames = _get_tfrecord_names(tf_record_base, FLAGS.ref_images_set)
dataset = tf.data.TFRecordDataset(filenames)
dataset = dataset.map(
lambda record: _parser_humpback_whale(record, 'eval'))
dataset.batch(batch_size=1)
iterator = dataset.make_one_shot_iterator()
ref_image, _, ref_image_name, ref_class_name, _, _ = iterator.get_next(
)
all_ref_features = None
all_ref_cls_name = []
all_ref_images_name = []
i = 0
while True:
try:
one_ref_image, one_ref_image_name, one_ref_class_name = sess.run(
[ref_image, ref_image_name, ref_class_name])
if i % 100 == 0:
print(i, one_ref_class_name)
all_ref_cls_name.append(one_ref_class_name)
all_ref_images_name.append(one_ref_image_name)
one_ref_feature = sess.run(
tf.get_default_graph().get_tensor_by_name(
'features_for_dst:0'),
feed_dict={'input_image:0': one_ref_image})
if all_ref_features is None:
all_ref_features = one_ref_feature
else:
all_ref_features = np.concatenate(
(all_ref_features, one_ref_feature), axis=0)
i += 1
except tf.errors.OutOfRangeError:
tf.logging.info('End of forward ref images')
break
if FLAGS.save_features:
ref_concated = np.concatenate(
(all_ref_features, np.array(all_ref_images_name).reshape(
(all_ref_features.shape[0], 1)),
np.array(all_ref_cls_name).reshape(
(all_ref_features.shape[0], 1))),
axis=1)
np.save(
os.path.join(FLAGS.output_dir, '..',
'ref_concated_%s.npy' % (FLAGS.ref_images_set)),
ref_concated)
all_ref_cls_name.append('new_whale'.encode(encoding='utf-8'))
# forward all test images
filenames = _get_tfrecord_names(tf_record_base, FLAGS.dut_images_set)
dataset = tf.data.TFRecordDataset(filenames)
dataset = dataset.map(
lambda record: _parser_humpback_whale(record, 'eval'))
dataset.batch(batch_size=1)
iterator = dataset.make_one_shot_iterator()
dut_image, _, dut_image_name, dut_class_name, _, _ = iterator.get_next(
)
all_dut_featurs = None
all_dut_cls_name = []
all_dut_image_names = []
i = 0
while True:
try:
one_dut_image, one_dut_image_name, one_dut_class_name = sess.run(
[dut_image, dut_image_name, dut_class_name])
if i % 100 == 0:
print(i, one_dut_image_name)
all_dut_cls_name.append(one_dut_class_name)
all_dut_image_names.append(one_dut_image_name)
one_dut_feature = sess.run(
tf.get_default_graph().get_tensor_by_name(
'features_for_dst:0'),
feed_dict={'input_image:0': one_dut_image})
if all_dut_featurs is None:
all_dut_featurs = one_dut_feature
else:
all_dut_featurs = np.concatenate(
(all_dut_featurs, one_dut_feature), axis=0)
i += 1
except tf.errors.OutOfRangeError:
tf.logging.info('End of forward dut images')
break
if FLAGS.save_features:
dut_concated = np.concatenate(
(all_dut_featurs, np.array(all_dut_image_names).reshape(
(all_dut_featurs.shape[0], 1)),
np.array(all_dut_cls_name).reshape(
(all_dut_featurs.shape[0], 1))),
axis=1)
np.save(
os.path.join(FLAGS.output_dir, '..',
'dut_concated_%s.npy' % (FLAGS.dut_images_set)),
dut_concated)
# got prob_same_id for every test image and write result
# submission file
for nw_prob in FLAGS.new_whale_prob:
output_file_path = os.path.join(
FLAGS.output_dir, '..',
'submission_%s_%s.csv' % (nw_prob, time.time()))
if os.path.isfile(output_file_path):
raise Exception("submission file exists!! : %s" %
(output_file_path))
with open(output_file_path, 'w') as f:
f.write('Image,Id\n')
for i in range(len(all_dut_image_names)):
one_prob_same_ids = sess.run(
tf.get_default_graph().get_tensor_by_name(
'similarity_prob_for_one_query/prob_same_ids:0'),
feed_dict={
'ref_features:0':
all_ref_features,
'dut_features:0':
np.expand_dims(all_dut_featurs[i], axis=0)
})
one_prob_same_ids = np.concatenate(
(np.squeeze(one_prob_same_ids), [nw_prob]), axis=0)
if i % 100 == 0:
print('compare with: %f' % (nw_prob), i,
all_dut_image_names[i], one_prob_same_ids.min(),
one_prob_same_ids.max())
one_order = np.argsort(one_prob_same_ids)[::-1] # prob index
one_order = one_order.tolist()
one_predictions = []
for idx in one_order:
tmp_prediction = all_ref_cls_name[idx]
if tmp_prediction not in one_predictions:
one_predictions.append(tmp_prediction)
if len(one_predictions) == 5: # write one result
with open(output_file_path, 'a') as f:
content = os.path.basename(
all_dut_image_names[i].decode()) + ','
for j in range(len(one_predictions)):
if j == 0:
content = content + one_predictions[
j].decode()
else:
content = content + ' ' + one_predictions[
j].decode()
content = content + '\n'
f.write(content)
break # finish on dut image
i += 1