def set_tf_allow_growth(self):
import tensorflow as tf
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list="0"
set_session(tf.Session(config=config))
def __init__(self, root, noise):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.n_filters = 64
self.kernel_size = 3
self.batch_size = 32
self.n_conv_layers = 10
self.input_file_images_validation = "/net/duna/scratch1/aasensio/deepLearning/stars/database/database_validation.h5"
f = h5py.File(self.input_file_images_validation, 'r')
self.n_validation_orig, self.nx, self.ny, self.n_images = f.get("image").shape
f.close()
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def tf_allow_growth():
import tensorflow as tf
from keras.backend.tensorflow_backend import set_session
tf_config = tf.ConfigProto()
tf_config.gpu_options.allow_growth = True
sess = tf.Session(config=tf_config)
set_session(sess)
def check_session_cores(NUM_CORES):
import tensorflow as tf
import keras.backend.tensorflow_backend as KTF
sess = tf.Session(
config=tf.ConfigProto(inter_op_parallelism_threads=int(NUM_CORES),
intra_op_parallelism_threads=int(NUM_CORES)))
print(KTF)
KTF.set_session(sess)
print("Setting session to have {} cores".format(NUM_CORES))
def set_tf_allow_growth():
""" Allow TensorFlow to manage VRAM growth """
# pylint: disable=no-member
logger.debug("Setting Tensorflow 'allow_growth' option")
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list = "0"
set_session(tf.Session(config=config))
logger.debug("Set Tensorflow 'allow_growth' option")
def __init__(self, config):
tf_config = tf.ConfigProto()
tf_config.gpu_options.per_process_gpu_memory_fraction = config.gpu_memory_fraction
tf_config.gpu_options.visible_device_list = "0"
set_session(tf.Session(config=tf_config))
self.is_deploy = config.is_deploy
super(FullyConvolutionalModel, self).__init__(config)
def __init__(self, root, noise, option, lr, lr_multiplier, batch_size, nkernels):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.normalizations = np.load('normalization.npy')
self.root = root
self.option = option
self.noise = noise
self.n_filters = nkernels
self.lr = lr
self.lr_multiplier = lr_multiplier
self.batch_size = batch_size
self.input_training = "/net/viga/scratch1/deepLearning/doppler_imaging/database/training_stars.h5"
f = h5py.File(self.input_training, 'r')
self.n_training = len(f['modulus'])
f.close()
self.input_validation = "/net/viga/scratch1/deepLearning/doppler_imaging/database/validation_stars.h5"
f = h5py.File(self.input_validation, 'r')
self.n_validation = len(f['modulus'])
f.close()
self.batchs_per_epoch_training = int(self.n_training / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation / self.batch_size)
print("Original training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
if (self.n_training % self.batch_size != 0):
print("ALERT! Something wrong with the batch size")
# Normalization of alpha, beta, gamma
lmax = 3
k = 3.0
l = np.arange(lmax + 1)
cl = []
for l in range(lmax+1):
for i in range(2*l+1):
cl.append(np.sqrt(1.0 / (1.0+(l/1.0)**k)))
self.norm_spher_harm = np.array(cl)
def __init__(self, root, depth):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.nx = 700
self.ny = 700
self.depth = depth
def make_predictions_gpu(conf,shot_list,loader,custom_path=None):
loader.set_inference_mode(True)
if backend == 'tf' or backend == 'tensorflow':
first_time = "tensorflow" not in sys.modules
if first_time:
import tensorflow as tf
os.environ['KERAS_BACKEND'] = 'tensorflow'
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto(device_count={"GPU":1})
set_session(tf.Session(config=config))
else:
os.environ['THEANO_FLAGS'] = 'device=gpu,floatX=float32'
import theano
from keras.utils.generic_utils import Progbar
from plasma.models.builder import ModelBuilder
specific_builder = ModelBuilder(conf)
y_prime = []
y_gold = []
disruptive = []
model = specific_builder.build_model(True)
model.compile(optimizer=optimizer_class(),loss=conf['data']['target'].loss)
specific_builder.load_model_weights(model,custom_path)
model.reset_states()
pbar = Progbar(len(shot_list))
shot_sublists = shot_list.sublists(conf['model']['pred_batch_size'],do_shuffle=False,equal_size=True)
for (i,shot_sublist) in enumerate(shot_sublists):
X,y,shot_lengths,disr = loader.load_as_X_y_pred(shot_sublist)
#load data and fit on data
y_p = model.predict(X,
batch_size=conf['model']['pred_batch_size'])
model.reset_states()
y_p = loader.batch_output_to_array(y_p)
y = loader.batch_output_to_array(y)
#cut arrays back
y_p = [arr[:shot_lengths[j]] for (j,arr) in enumerate(y_p)]
y = [arr[:shot_lengths[j]] for (j,arr) in enumerate(y)]
pbar.add(1.0*len(shot_sublist))
loader.verbose=False#True during the first iteration
y_prime += y_p
y_gold += y
disruptive += disr
y_prime = y_prime[:len(shot_list)]
y_gold = y_gold[:len(shot_list)]
disruptive = disruptive[:len(shot_list)]
loader.set_inference_mode(False)
return y_prime,y_gold,disruptive
def __init__(self, root, noise, option, depth, network_type, activation, lr, lr_multiplier, batch_size, nkernels, n_inputs):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.option = option
self.noise = noise
self.depth = depth
self.n_filters = nkernels
self.network_type = network_type
self.activation = activation
self.lr = lr
self.lr_multiplier = lr_multiplier
self.batch_size = batch_size
self.n_inputs = n_inputs
self.median = np.loadtxt('/net/duna/scratch1/aasensio/deepLearning/mfbd/database/normalizations.txt')
# self.input_file_images_training = "/net/duna/scratch1/aasensio/deepLearning/mfbd/database/learning_hypercube.fits"
self.input_file_images_training = "/net/duna/scratch1/aasensio/deepLearning/mfbd/database/8542_learning_hypercube.fits"
f = fits.open(self.input_file_images_training, memmap=True)
self.n_training_orig, self.nx, self.ny, _ = f[0].data.shape
f.close()
# self.input_file_images_validation = "/net/duna/scratch1/aasensio/deepLearning/mfbd/database/validating_hypercube.fits"
self.input_file_images_validation = "/net/duna/scratch1/aasensio/deepLearning/mfbd/database/8542_validation_hypercube.fits"
f = fits.open(self.input_file_images_validation, memmap=True)
self.n_validation_orig, self.nx, self.ny, _ = f[0].data.shape
f.close()
self.batchs_per_epoch_training = int(self.n_training_orig / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_training = self.batchs_per_epoch_training * self.batch_size
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original training set size: {0}".format(self.n_training_orig))
print(" - Final training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def make_evaluations_gpu(conf,shot_list,loader):
loader.set_inference_mode(True)
if backend == 'tf' or backend == 'tensorflow':
first_time = "tensorflow" not in sys.modules
if first_time:
import tensorflow as tf
os.environ['KERAS_BACKEND'] = 'tensorflow'
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto(device_count={"GPU":1})
set_session(tf.Session(config=config))
else:
os.environ['THEANO_FLAGS'] = 'device=gpu,floatX=float32'
import theano
from keras.utils.generic_utils import Progbar
from plasma.models.builder import ModelBuilder
specific_builder = ModelBuilder(conf)
y_prime = []
y_gold = []
disruptive = []
batch_size = min(len(shot_list),conf['model']['pred_batch_size'])
pbar = Progbar(len(shot_list))
print('evaluating {} shots using batchsize {}'.format(len(shot_list),batch_size))
shot_sublists = shot_list.sublists(batch_size,equal_size=False)
all_metrics = []
all_weights = []
for (i,shot_sublist) in enumerate(shot_sublists):
batch_size = len(shot_sublist)
model = specific_builder.build_model(True,custom_batch_size=batch_size)
model.compile(optimizer=optimizer_class(),loss=conf['data']['target'].loss)
specific_builder.load_model_weights(model)
model.reset_states()
X,y,shot_lengths,disr = loader.load_as_X_y_pred(shot_sublist,custom_batch_size=batch_size)
#load data and fit on data
all_metrics.append(model.evaluate(X,y,batch_size=batch_size,verbose=False))
all_weights.append(batch_size)
model.reset_states()
pbar.add(1.0*len(shot_sublist))
loader.verbose=False#True during the first iteration
if len(all_metrics) > 1:
print('evaluations all: {}'.format(all_metrics))
loss = np.average(all_metrics,weights = all_weights)
print('Evaluation Loss: {}'.format(loss))
loader.set_inference_mode(False)
return loss
def __init__(self, networks, depths, filters_exit, activation, n_filters):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.networks = networks
self.activation = activation
self.n_filters = n_filters
self.depth = depths
self.filters_exit = filters_exit
def __init__(self, root, noise, option, depth, network_type, activation, lr, lr_multiplier, batch_size, nkernels):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.option = option
self.noise = noise
self.depth = depth
self.n_filters = nkernels
self.network_type = network_type
self.activation = activation
self.lr = lr
self.lr_multiplier = lr_multiplier
self.batch_size = batch_size
tmp = np.loadtxt('/net/vena/scratch/Dropbox/GIT/DeepLearning/hmi_super/training/normalization.txt')
self.median_HMI, self.median_SST = tmp[0], tmp[1]
self.input_file_images_training = "/net/viga/scratch1/cdiazbas/DATABASE/database_training_x2_PSF2.h5"
f = h5py.File(self.input_file_images_training, 'r')
self.n_training_orig, self.nx, self.ny, _ = f['imHMI'].shape
f.close()
self.input_file_images_validation = "/net/viga/scratch1/cdiazbas/DATABASE/database_validation_x2_PSF2.h5"
f = h5py.File(self.input_file_images_validation, 'r')
self.n_validation_orig, self.nx, self.ny, _ = f['imHMI'].shape
f.close()
self.batchs_per_epoch_training = int(self.n_training_orig / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_training = self.batchs_per_epoch_training * self.batch_size
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original training set size: {0}".format(self.n_training_orig))
print(" - Final training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def test(model_name, iter_num, gpu_id, vol_size=(160,192,224), nf_enc=[16,32,32,32], nf_dec=[32,32,32,32,32,16,16,3]):
"""
test
nf_enc and nf_dec
#nf_dec = [32,32,32,32,32,16,16,3]
# This needs to be changed. Ideally, we could just call load_model, and we wont have to
# specify the # of channels here, but the load_model is not working with the custom loss...
"""
gpu = '/gpu:' + str(gpu_id)
# Anatomical labels we want to evaluate
labels = sio.loadmat('../data/labels.mat')['labels'][0]
atlas = np.load('../data/atlas_norm.npz')
atlas_vol = atlas['vol']
atlas_seg = atlas['seg']
atlas_vol = np.reshape(atlas_vol, (1,)+atlas_vol.shape+(1,))
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
set_session(tf.Session(config=config))
# load weights of model
with tf.device(gpu):
net = networks.unet(vol_size, nf_enc, nf_dec)
net.load_weights('../models/' + model_name +
'/' + str(iter_num) + '.h5')
xx = np.arange(vol_size[1])
yy = np.arange(vol_size[0])
zz = np.arange(vol_size[2])
grid = np.rollaxis(np.array(np.meshgrid(xx, yy, zz)), 0, 4)
X_vol, X_seg = datagenerators.load_example_by_name('../data/test_vol.npz', '../data/test_seg.npz')
with tf.device(gpu):
pred = net.predict([X_vol, atlas_vol])
# Warp segments with flow
flow = pred[1][0, :, :, :, :]
sample = flow+grid
sample = np.stack((sample[:, :, :, 1], sample[:, :, :, 0], sample[:, :, :, 2]), 3)
warp_seg = interpn((yy, xx, zz), X_seg[0, :, :, :, 0], sample, method='nearest', bounds_error=False, fill_value=0)
vals, _ = dice(warp_seg, atlas_seg, labels=labels, nargout=2)
print(np.mean(vals), np.std(vals))
def __init__(self, root, depth, model, activation, n_filters):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.depth = depth
self.network_type = model
self.activation = activation
self.n_filters = n_filters
self.input_file_images_training = "/net/duna/scratch1/aasensio/deepLearning/mfbd/database/validating_hypercube.fits"
def __init__(self, root, noise, option):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.option = option
self.n_filters = 64
self.kernel_size = 3
self.batch_size = 32
self.n_conv_layers = 20
self.stride = 1
self.skip_frequency = 2
self.input_file_images_training = "/scratch1/aasensio/deepLearning/opticalFlow/database/database_images.h5"
self.input_file_velocity_training = "/scratch1/aasensio/deepLearning/opticalFlow/database/database_velocity.h5"
self.input_file_images_validation = "/scratch1/aasensio/deepLearning/opticalFlow/database/database_images_validation.h5"
self.input_file_velocity_validation = "/scratch1/aasensio/deepLearning/opticalFlow/database/database_velocity_validation.h5"
f = h5py.File(self.input_file_images_training, 'r')
self.n_training_orig, self.nx, self.ny, self.n_times = f.get("intensity").shape
f.close()
f = h5py.File(self.input_file_images_validation, 'r')
self.n_validation_orig, _, _, _ = f.get("intensity").shape
f.close()
self.batchs_per_epoch_training = int(self.n_training_orig / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_training = self.batchs_per_epoch_training * self.batch_size
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original training set size: {0}".format(self.n_training_orig))
print(" - Final training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def __init__(self, root, depth, model, activation, n_filters):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.depth = depth
self.network_type = model
self.activation = activation
self.n_filters = n_filters
self.input_file_images = "/net/viga/scratch1/cdiazbas/DATABASE/database_validation_x2.h5"
self.input_file_images_HMI = "/net/viga/scratch1/cdiazbas/DATABASE/database_prediction.h5"
def __init__(self, root, noise, option, depth, activation, lr, lr_multiplier, batch_size, nkernels):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.option = option
self.noise = noise
self.depth = depth
self.n_filters = nkernels
self.activation = activation
self.lr = lr
self.lr_multiplier = lr_multiplier
self.batch_size = batch_size
self.smooth = 1.0
self.input_file_images_training = "/net/viga/scratch1/deepLearning/mluna_segmentation/database/database.h5"
f = h5py.File(self.input_file_images_training, 'r')
self.n_training_orig, self.nx, self.ny, _ = f['halpha'].shape
f.close()
self.input_file_images_validation = "/net/viga/scratch1/deepLearning/mluna_segmentation/database/database_validation.h5"
f = h5py.File(self.input_file_images_validation, 'r')
self.n_validation_orig, self.nx, self.ny, _ = f['halpha'].shape
f.close()
self.batchs_per_epoch_training = int(self.n_training_orig / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_training = self.batchs_per_epoch_training * self.batch_size
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original training set size: {0}".format(self.n_training_orig))
print(" - Final training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def make_predictions(conf,shot_list,loader):
loader.set_inference_mode(True)
use_cores = max(1,mp.cpu_count()-2)
if backend == 'tf' or backend == 'tensorflow':
first_time = "tensorflow" not in sys.modules
if first_time:
import tensorflow as tf
os.environ['KERAS_BACKEND'] = 'tensorflow'
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto(device_count={"CPU":use_cores})
set_session(tf.Session(config=config))
else:
os.environ['THEANO_FLAGS'] = 'device=cpu'
import theano
from plasma.models.builder import ModelBuilder
specific_builder = ModelBuilder(conf)
y_prime = []
y_gold = []
disruptive = []
model = specific_builder.build_model(True)
model.compile(optimizer=optimizer_class(),loss=conf['data']['target'].loss)
specific_builder.load_model_weights(model)
model_save_path = specific_builder.get_latest_save_path()
start_time = time.time()
pool = mp.Pool(use_cores)
fn = partial(make_single_prediction,builder=specific_builder,loader=loader,model_save_path=model_save_path)
print('running in parallel on {} processes'.format(pool._processes))
for (i,(y_p,y,is_disruptive)) in enumerate(pool.imap(fn,shot_list)):
print('Shot {}/{}'.format(i,len(shot_list)))
sys.stdout.flush()
y_prime.append(y_p)
y_gold.append(y)
disruptive.append(is_disruptive)
pool.close()
pool.join()
print('Finished Predictions in {} seconds'.format(time.time()-start_time))
loader.set_inference_mode(False)
return y_prime,y_gold,disruptive
def __init__(self, root, output, name_of_variable):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.nx = 576
self.ny = 576
self.n_times = 2
self.n_filters = 64
self.batch_size = 1
self.n_conv_layers = 20
self.stride = 1
self.skip_frequency = 2
self.n_frames = 1
self.output = output
self.name_of_variable = name_of_variable
telescope_radius = 0.5 * 0.965 * u.meter
pixel_size = 0.02759 * u.arcsec / u.pixel
fov = 1152 * u.pixel
lambda0 = 500 * u.nm
imax = imax_degradation(telescope_radius, pixel_size, fov)
imax.compute_psf(lambda0)
res = io.readsav('/net/viga/scratch1/deepLearning/opticalFlow/mancha/c3d_1152_cont4_4bin_012000_continuum.sav')['continuum']
self.images = np.zeros((2,576,576), dtype='float32')
# 576 pixels are obtained by resampling 1152 pixels of 0.02759 "/px to 0.0545 "/px for IMaX
self.images[0,:,:] = congrid.resample(imax.apply_psf(res[0,:,:]), (576, 576))
self.images[1,:,:] = congrid.resample(imax.apply_psf(res[1,:,:]), (576, 576))
res = io.readsav('/net/viga/scratch1/deepLearning/opticalFlow/mancha/c3d_1152_cont4_4bin_012000.isotau.sav')
self.vx = np.zeros((3,576,576), dtype='float32')
self.vy = np.zeros((3,576,576), dtype='float32')
for i in range(3):
self.vx[i,:,:] = congrid.resample(imax.apply_psf(res['vx'][i,:,:]), (576, 576))
self.vy[i,:,:] = congrid.resample(imax.apply_psf(res['vy'][i,:,:]), (576, 576))
def __new__(cls):
with cls._lock:
# 初期設定(最初の呼び出しだけ)
if cls._instance is None:
cls.config = tf.ConfigProto()
cls.config.gpu_options.per_process_gpu_memory_fraction = 0.45
set_session(tf.Session(config=cls.config))
cls.voc_classes = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9', \
'p1', 'p2', 'p3', 'p4', 'p5', 'p6', 'p7', 'p8', 'p9', \
's1', 's2', 's3', 's4', 's5', 's6', 's7', 's8', 's9', \
'e', 's', 'w', 'n', 'haku', 'hatsu', 'chun']
cls.NUM_CLASSES = len(cls.voc_classes) + 1
cls.input_shape=(512, 512, 3)
cls.model = SSD512(cls.input_shape, num_classes=cls.NUM_CLASSES)
cls.model.load_weights(c['detection']['weight_path'], by_name=True)
cls.bbox_util = BBoxUtility(cls.NUM_CLASSES)
cls._instance = super().__new__(cls)
return cls._instance
def train(model,save_name, gpu_id, lr, n_iterations, reg_param, model_save_iter):
model_dir = '../models/' + save_name
if not os.path.isdir(model_dir):
os.mkdir(model_dir)
gpu = '/gpu:' + str(gpu_id)
os.environ["CUDA_VISIBLE_DEVICES"] = str(gpu_id)
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
set_session(tf.Session(config=config))
# UNET filters
nf_enc = [16,32,32,32]
if(model == 'vm1'):
nf_dec = [32,32,32,32,8,8,3]
else:
nf_dec = [32,32,32,32,32,16,16,3]
with tf.device(gpu):
model = networks.unet(vol_size, nf_enc, nf_dec)
model.compile(optimizer=Adam(lr=lr), loss=[
losses.cc3D(), losses.gradientLoss('l2')], loss_weights=[1.0, reg_param])
# model.load_weights('../models/udrnet2/udrnet1_1/120000.h5')
train_example_gen = datagenerators.example_gen(train_vol_names)
zero_flow = np.zeros((1, vol_size[0], vol_size[1], vol_size[2], 3))
for step in range(0, n_iterations):
X = train_example_gen.__next__()[0]
train_loss = model.train_on_batch(
[X, atlas_vol], [atlas_vol, zero_flow])
if not isinstance(train_loss, list):
train_loss = [train_loss]
printLoss(step, 1, train_loss)
if(step % model_save_iter == 0):
model.save(model_dir + '/' + str(step) + '.h5')
def __init__(self, root):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.nx = 700
self.ny = 700
self.n_times = 2
self.n_filters = 64
self.batch_size = 1
self.n_conv_layers = 16
self.stride = 1
self.skip_frequency = 2
self.n_diversity = 2
self.input_file_images_validation = "/net/duna/scratch1/aasensio/deepLearning/phaseDiv/database/database_images_validation.h5"
def __init__(self, root, noise, option, depth):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.option = option
self.noise = noise
self.depth = depth
self.batch_size = 128
self.input_file_images_training = "/net/duna/scratch1/aasensio/deepLearning/phaseDiv/database/database_images.h5"
self.input_file_images_validation = "/net/duna/scratch1/aasensio/deepLearning/phaseDiv/database/database_images_validation.h5"
f = h5py.File(self.input_file_images_training, 'r')
self.n_training_orig, self.nx, self.ny, _ = f.get("intensity").shape
f.close()
f = h5py.File(self.input_file_images_validation, 'r')
self.n_validation_orig, _, _, _ = f.get("intensity").shape
f.close()
self.batchs_per_epoch_training = int(self.n_training_orig / self.batch_size)
self.batchs_per_epoch_validation = int(self.n_validation_orig / self.batch_size)
self.n_training = self.batchs_per_epoch_training * self.batch_size
self.n_validation = self.batchs_per_epoch_validation * self.batch_size
print("Original training set size: {0}".format(self.n_training_orig))
print(" - Final training set size: {0}".format(self.n_training))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_training))
print("Original validation set size: {0}".format(self.n_validation_orig))
print(" - Final validation set size: {0}".format(self.n_validation))
print(" - Batch size: {0}".format(self.batch_size))
print(" - Batches per epoch: {0}".format(self.batchs_per_epoch_validation))
def __init__(self):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
K.set_session(session)
self.dropout = 0.4
self.depth = 64
self.batch_size = 32
self.zed = 100
(x_train, self.y_train), (self.x_test, self.y_test) = mnist.load_data(path='/net/vena/scratch/Dropbox/GIT/DeepLearning/GAN/mnist.dat')
self.n_train, self.nx, self.ny = x_train.shape
self.n_test, self.nx, self.ny = self.x_test.shape
self.x_train = np.zeros((self.n_train, self.nx, self.ny, 1), dtype='float32')
self.x_train[:,:,:,0] = x_train
def __init__(self):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = '../training/cnns/test'
self.batch_size = 32
self.fraction_training = 0.9
self.noise = 0.0
self.activation = 'relu'
self.depth = 5
self.n_kernels = 64
self.n_mixture = 8
self.c = 9 # Number of variables
self.l2_reg = 1e-7
self.lower = np.asarray([0.05, -5.0, 5.0, 0.0, 0.0, 0.0, -180.0, 0.0, -180.0])
self.upper = np.asarray([3.0, 5.0, 18.0, 0.5, 1000.0, 180.0, 180.0, 180.0, 180.0])
def __init__(self, root, observations, output, name_of_variable):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.nx = 800
self.ny = 800
self.n_times = 2
self.n_filters = 64
self.batch_size = 1
self.n_conv_layers = 20
self.stride = 1
self.skip_frequency = 2
self.n_frames = 57
self.observations = observations
self.output = output
self.name_of_variable = name_of_variable
def __init__(self, root):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = root
self.noise = 0.0
self.batch_size = 16
self.normalizations = np.load('../training/normalization.npy')
self.input_validation = "/net/viga/scratch1/deepLearning/doppler_imaging/database/validation_stars.h5"
f = h5py.File(self.input_validation, 'r')
self.n_validation = len(f['modulus'])
f.close()
self.batchs_per_epoch_validation = int(self.n_validation / self.batch_size)
def __init__(self, root):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
f = open('{0}_args.json'.format(root), 'r')
tmp = json.load(f)
f.close()
self.noise = float(tmp['noise'])
self.depth = int(tmp['depth'])
self.n_filters = int(tmp['kernels'])
self.activation = tmp['activation']
self.batch_size = int(tmp['batchsize'])
self.l2_reg = float(tmp['l2_regularization'])
self.root = root
self.noise = 0.0
self.batch_size = 16
self.nx = 500
self.ny = 500
def __init__(self, parsed):
# Only allocate needed memory
config = tf.ConfigProto()
config.gpu_options.allow_growth=True
session = tf.Session(config=config)
ktf.set_session(session)
self.root = parsed['output']
self.batch_size = int(parsed['batchsize'])
self.fraction_training = float(parsed['train_fraction'])
self.noise = float(parsed['noise'])
self.activation = parsed['activation']
self.depth = int(parsed['depth'])
self.n_kernels = int(parsed['kernels'])
self.lr = float(parsed['lr'])
self.l2_reg = float(parsed['l2_regularization'])
self.lr_multiplier = float(parsed['lr_multiplier'])
self.n_classes = int(parsed['classes'])
self.c = 9 # Number of variables
self.method = parsed['method']
self.lower = np.asarray([0.05, -5.0, 5.0, 0.0, 0.0, 0.0, -180.0, 0.0, -180.0])
self.upper = np.asarray([3.0, 5.0, 18.0, 0.5, 1000.0, 180.0, 180.0, 180.0, 180.0])
import time
import tensorflow as tf
from keras_frcnn import config
from keras import backend as K
from keras.layers import Input
from keras.models import Model
from keras.backend.tensorflow_backend import set_session
from keras_frcnn import roi_helpers
sys.setrecursionlimit(40000)
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.log_device_placement = True
sess = tf.Session(config=config)
set_session(sess)
parser = OptionParser()
parser.add_option("-p", "--path", dest="test_path", help="Path to test data.")
parser.add_option(
"-n",
"--num_rois",
type="int",
dest="num_rois",
help="Number of ROIs per iteration. Higher means more memory use.",
default=32)
parser.add_option(
"--config_filename",
dest="config_filename",
help=
config['system']['CUDA_VISIBLE_DEVICES'] = args.dev
exp_name = args.run_name
# Set path
model_path = os.path.join(config['log']['model_dir'], exp_name)
if not os.path.isdir(model_path):
os.makedirs(model_path)
result_basepath = os.path.join(config['log']['result_dir'], exp_name)
if not os.path.isdir(result_basepath):
os.makedirs(result_basepath)
# Env settings
os.environ["CUDA_VISIBLE_DEVICES"] = config['system']['CUDA_VISIBLE_DEVICES']
gpu_options = tf.compat.v1.GPUOptions(allow_growth=True)
sess_config = tf.compat.v1.ConfigProto(gpu_options=gpu_options)
set_session(tf.compat.v1.Session(config=sess_config))
# Split cases into train, val, test
with open(args.json + '.json', 'r') as reader:
case = json.loads(reader.read())
ntuh_partition, tcia_partition, msd_partition = case['partition']
tcia_partition['train'] = []
tcia_partition['validation'] = []
msd_partition['train'] = []
msd_partition['validation'] = []
# Get train patches
train_X, train_y, train_idx = get_patches(
config, [ntuh_partition, tcia_partition, msd_partition], mode='train')
train_X = np.array(train_X)
def __init__(self, on_sim):
## to force CPU mode
# import os
# os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
set_session(tf.Session(config=config))
self.img_height = 600 # 396 #300 # Height of the input images
self.img_width = 800 # 634 #480 # Width of the input images
self.img_channels = 3 # Number of color channels of the input images
intensity_mean = 127.5 # Set this to your preference (maybe `None`). The current settings transform the input pixel values to the interval `[-1,1]`.
intensity_range = 127.5 # Set this to your preference (maybe `None`). The current settings transform the input pixel values to the interval `[-1,1]`.
n_classes = 3 # 4 # Number of positive classes
scales = [
0.08, 0.16, 0.32, 0.64, 0.96
] # An explicit list of anchor box scaling factors. If this is passed, it will override `min_scale` and `max_scale`.
aspect_ratios = [0.5, 1.0,
2.0] # The list of aspect ratios for the anchor boxes
two_boxes_for_ar1 = True # Whether or not you want to generate two anchor boxes for aspect ratio 1
steps = None # In case you'd like to set the step sizes for the anchor box grids manually; not recommended
offsets = None # In case you'd like to set the offsets for the anchor box grids manually; not recommended
clip_boxes = False # Whether or not to clip the anchor boxes to lie entirely within the image boundaries
variances = [
1.0, 1.0, 1.0, 1.0
] # The list of variances by which the encoded target coordinates are scaled
self.normalize_coords = True # Whether or not the model is supposed to use coordinates relative to the image size
K.clear_session() # Clear previous
self.model = build_model(image_size=(self.img_height, self.img_width,
self.img_channels),
n_classes=n_classes,
mode='training',
l2_regularization=0.0005,
scales=scales,
aspect_ratios_global=aspect_ratios,
aspect_ratios_per_layer=None,
two_boxes_for_ar1=two_boxes_for_ar1,
steps=steps,
offsets=offsets,
clip_boxes=clip_boxes,
variances=variances,
normalize_coords=self.normalize_coords,
subtract_mean=intensity_mean,
divide_by_stddev=intensity_range)
weights_path = 'ssd7_epoch-14_loss-1.0911_val_loss-0.5348.h5'
if not on_sim:
weights_path = 'ssd7_4_epoch-18_loss-2.8798_val_loss-2.7147.h5'
rospy.loginfo("Loading SSD: %s", weights_path)
self.model.load_weights(weights_path, by_name=True)
global graph
graph = tf.get_default_graph()
adam = Adam(lr=0.001,
beta_1=0.9,
beta_2=0.999,
epsilon=1e-08,
decay=0.0)
ssd_loss = SSDLoss(neg_pos_ratio=3, alpha=1.0)
self.model.compile(optimizer=adam, loss=ssd_loss.compute_loss)
pass
# Now train the NN to predict 2d
dt = 1
# Time resolution From Alberto's TCAV axis conversion [um/pixel]
dE = 1
# Energy resolution [MeV/pix]
x = (np.arange(lpstrain.shape[1]) - np.round(lpstrain.shape[1] / 2)) * dt
y = (np.arange(lpstrain.shape[2]) - np.round(lpstrain.shape[2] / 2)) * dE
# Plot lps for a few random shots
for i in range(1):
plot_lps_vs_prediction_lucretia(lpstrain, lpstrain, x, y)
#%%# Set up the Tensorflow environment to use only one thread.
import tensorflow as tf
from keras.backend.tensorflow_backend import set_session
session_conf = tf.ConfigProto(intra_op_parallelism_threads=1,
inter_op_parallelism_threads=1)
set_session(tf.Session(config=session_conf))
# Build the MLP to train
model = Sequential()
model.add(
Dense(500, activation='relu', input_shape=(X_train_scaled.shape[1], )))
model.add(Dense(200, activation='relu'))
model.add(Dense(100, activation='relu'))
#model.add(LeakyReLU(100,alpha=0.05))
#model.add(Dense(500, activation='relu',input_shape = (X_train_scaled.shape[1],)))
#model.add(Dense(500, activation='relu'))
#model.add(Dense(200, activation='relu'))
#model.add(Dense(100, activation='relu'))
model.add(Dense(lpstrainreshaped.shape[1], activation='linear')
def set_tf_allow_growth():
""" Allow TensorFlow to manage VRAM growth """
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list = "0"
set_session(tf.Session(config=config))
load = args.load
train = args.train
mode = args.mode
suffix = args.suffix
people_id = int(args.test_people_id)
# filename prefix
prefix = mode
#if not train:
if True:
import tensorflow as tf
import keras.backend.tensorflow_backend as KTF
config = tf.ConfigProto()
config.gpu_options.per_process_gpu_memory_fraction = 0.45
sess = tf.Session(config=config)
KTF.set_session(sess)
if people_id > 140:
filename = 'test'
else:
filename = 'train'
print('Config: Load pretrained<-{}, suffix<-{}, epoch<-{}, lr<-{}'.format(
load, suffix, epoch, l_rate))
if mode == 'fusion_dr':
# dim of input vector
input_dim = 11510 * 9
# dim of per feature
feature_dim = 9
import os
import numpy as np
import cv2
import tensorflow as tf
from keras.utils import np_utils
from cnn_model_with_keras.darknet19_model import get_model
from keras.models import load_model
from keras.backend import tensorflow_backend as k
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
k.set_session(sess)
width = 224
height = 224
channels = 3
def read_img(path):
img = cv2.imread(path)
img = cv2.resize(img, (width, height))
# img = np.array(img)
return img
# 类别文件夹
folder_list = os.listdir("../flower/")
# 统计样本数
number = 0
for folder in folder_list:
img_list = os.listdir("../flower/" + folder)
import sys, os
sys.path.append(os.pardir)
from data_helpers import BPE
import numpy as np
import pandas as pd
import tensorflow as tf
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto()
# config.gpu_options.per_process_gpu_memory_fraction = 0.5
config.gpu_options.allow_growth = True # dynamically grow the memory used on the GPU
sess = tf.Session(config=config)
set_session(sess) # set this TensorFlow session as the default session for Keras.
bpe = BPE("../pre-trained-model/en.wiki.bpe.op25000.vocab")
# Build vocab, {token: index}
vocab = {}
for i, token in enumerate(bpe.words):
vocab[token] = i + 1
# Load preprocessed data from npz file
dataset = np.load('preprocessed_dataset.npz')
x_train = dataset['x_train']
y_train = dataset['y_train']
x_test = dataset['x_test']
y_test = dataset['y_test']
from gensim.models import KeyedVectors
def processFile(image):
aux = image.split("%")
action = int(aux[0])
reward = float(aux[1].split(".")[0].replace("_","."))
return action, reward
if __name__ == "__main__":
if len(sys.argv) != 5:
print("Usage: python3 ", sys.argv[0], " <batches> <n_epochs_per_batch> <frames_per_state> <reset_after>")
print()
print("Example: python3 ", sys.argv[0]," 15 10 1 50 # run 15 batches (with 10 instances per class in each) using 1 frame per state and reseting after 50 updatings")
sys.exit(1)
config = tf.ConfigProto(gpu_options=tf.GPUOptions(allow_growth=True))
session = tf.Session(config=config)
tensorflow_backend.set_session(session)
files = glob.glob("*.png")
files.sort()
batches = int(sys.argv[1])
n_epochs_per_batch = int(sys.argv[2])
frames_per_state = int(sys.argv[3])
reset_after = int(sys.argv[4])
test_inputs = getTestCNNInputs(files, frames_per_state)
models = None
for _ in range(batches):
for i in range(len(files) - 1):
right_images = []
left_images = []
for k in range(frames_per_state):
if i + k >= len(files):
import tensorflow as tf
from tensorflow import keras as tf_keras
from packaging import version as package_version
# prevent Keras from using up all gpu memory
if tf.executing_eagerly():
gpus = tf.config.experimental.list_physical_devices("GPU")
for gpu in gpus:
tf.config.experimental.set_memory_growth(gpu, True)
else:
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto()
config.gpu_options.per_process_gpu_memory_fraction = 0.5
set_session(tf.Session(config=config))
def pytest_generate_tests(metafunc):
# This function generates the list of tests for pytest, based
# on scenatios that will change the parameters in which the
# tests use to run.
# https://docs.pytest.org/en/latest/example/parametrize.html
idlist = []
argvalues = []
for scenario in metafunc.cls.scenarios:
idlist.append(scenario[0])
items = scenario[1].items()
argnames = [x[0] for x in items]
argvalues.append([x[1] for x in items])
metafunc.parametrize(argnames, argvalues, ids=idlist, scope="class")
def train(data_dir, model, model_dir, gpu_id, lr, nb_epochs, reg_param,
steps_per_epoch, load_model_file, data_loss, window_size,
batch_size):
"""
model training function
:param data_dir: folder with npz files for each subject.
:param model: either vm1 or vm2 (based on CVPR 2018 paper)
:param model_dir: the model directory to save to
:param gpu_id: integer specifying the gpu to use
:param lr: learning rate
:param reg_param: the smoothness/reconstruction tradeoff parameter (lambda in CVPR paper)
:param steps_per_epoch: frequency with which to save models
:param batch_size: Optional, default of 1. can be larger, depends on GPU memory and volume size
:param load_model_file: optional h5 model file to initialize with
:param data_loss: data_loss: 'mse' or 'ncc'
"""
vol_size = [256, 256, 144] # (width, height, depth)
# set encoder, decoder feature number
nf_enc = [16, 32, 32, 32]
if model == 'vm1':
nf_dec = [32, 32, 32, 32, 8, 8]
elif model == 'vm2':
nf_dec = [32, 32, 32, 32, 32, 16, 16]
else: # 'vm2double':
nf_enc = [f * 2 for f in nf_enc]
nf_dec = [f * 2 for f in [32, 32, 32, 32, 32, 16, 16]]
# set loss function
# Mean Squared Error, Cross-Correlation, Negative Cross-Correlation
assert data_loss in [
'mse', 'cc', 'ncc'
], 'Loss should be one of mse or cc, found %s' % data_loss
if data_loss in ['ncc', 'cc']:
NCC = losses.NCC(win=window_size)
data_loss = NCC.loss
# prepare model folder
if not os.path.isdir(model_dir):
os.mkdir(model_dir)
# GPU handling
gpu = '/gpu:%d' % 0 # gpu_id
os.environ["CUDA_VISIBLE_DEVICES"] = gpu_id
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
set_session(tf.Session(config=config))
# prepare the model
with tf.device(gpu):
# in the CVPR layout, the model takes in [moving image, fixed image] and outputs [warped image, flow]
model = networks.cvpr2018_net(vol_size, nf_enc, nf_dec)
if load_model_file is not None:
model.load_weights(load_model_file)
# save first iteration
# model.save(os.path.join(model_dir, '%02d.h5' % initial_epoch))
# load data
# path = "../../dataset/urinary"
# vol_names = [filename for filename in os.listdir(data_dir) if (int(filename.split("_")[-1].split('.')[0]) < 206) and
# (int(filename.split("_")[-1].split('.')[0]) not in except_list)]
vol_names = [
filename for filename in os.listdir(data_dir)
if int(filename.split("_")[-1].split(".")[0]) in normal
]
# vol_names = [filename for filename in os.listdir(data_dir) if int(filename.split("_")[-1].split(".")[0]) in (9, 130, 128)]
vol_names.sort()
uro_gen = uro_generator(vol_names, data_dir, fixed='joyoungje')
# test_path = os.path.join(data_dir, 'test')
# test_vol_names = [filename for filename in os.listdir(test_path) if '.npz']
# test_gen = uro_generator(test_vol_names, test_path)
# fit
with tf.device(gpu):
mg_model = model
# compile
mg_model.compile(optimizer=Adam(lr=lr),
loss=[data_loss, losses.Grad('l2').loss],
loss_weights=[1.0, reg_param])
# fit
save_file_name = os.path.join(model_dir, '{epoch:04d}.h5')
save_callback = ModelCheckpoint(save_file_name)
mg_model.fit_generator(uro_gen,
epochs=nb_epochs,
verbose=1,
callbacks=[save_callback],
steps_per_epoch=steps_per_epoch)
monitor='val_acc',
verbose=1,
save_best_only=True,
save_weights_only=False,
mode='max',
period=1)
es_op = EarlyStopping(monitor='val_acc', patience=10, verbose=0, mode='max')
def get_session():
tf_config = tf.ConfigProto(allow_soft_placement=True)
#tf_config.gpu_options.allocator_type ='BFC'
return tf.Session(config=tf_config)
KTF.set_session(get_session())
from keras.engine import Input
from keras.models import Model
def get_model(embedding_matrix, max_length, n_class):
inputs = Input(shape=(max_length, ))
t_embed = K.placeholder(shape=(4, 300))
embedding_vec = Embedding(input_dim=embedding_matrix.shape[0],
output_dim=embedding_matrix.shape[1],
weights=[embedding_matrix],
trainable=False)(inputs)
logist = lea(embedding_vec, t_embed, n_class=n_class, l2_a=0)
model = Model(inputs=inputs, outputs=logist)
from config import albert_model_path, config_path, checkpoint_path, dict_path, model_save_path, log_dir, TERM_FREQUENCY_FILE
from bert4keras.bert import load_pretrained_model, set_gelu
from bert4keras.utils import SimpleTokenizer, load_vocab
from neo4j_search import search_entity
set_gelu('tanh') # 切换gelu版本
# 禁用GPU
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID" # see issue #152
os.environ["CUDA_VISIBLE_DEVICES"] = "0,1" # "0,1"
tf_config = tf.ConfigProto()
tf_config.gpu_options.allocator_type = 'BFC' #A "Best-fit with coalescing" algorithm, simplified from a version of dlmalloc.
tf_config.gpu_options.per_process_gpu_memory_fraction = 0.8
tf_config.gpu_options.allow_growth = True
set_session(tf.Session(config=tf_config))
# TAG_SCHEME = 'BIO'
TAG_SCHEME = 'BIOES'
model_save_path = './models_ner_classify_albert_tiny20191101_1356'
if TAG_SCHEME == 'BIO':
TRAIN_DATA_PATH = "./data/ner_rel_train.txt"
DEV_DATA_PATH = "./data/ner_rel_dev.txt"
TEST_DATA_PATH = "./data/ner_rel_test.txt"
# TRAIN_DATA_PATH = './data/ner_rel0_train_data.txt'
# DEV_DATA_PATH = './data/ner_rel0_dev_data.txt'
elif TAG_SCHEME == 'BIOES':
TRAIN_DATA_PATH = "./data/ner_rel_train_BIOES.txt"
DEV_DATA_PATH = "./data/ner_rel_dev_BIOES.txt"
# -*- coding:utf-8 -*-
from keras.backend import tensorflow_backend as K
import tensorflow as tf
config = tf.compat.v1.ConfigProto()
config.gpu_options.allow_growth = True
K.set_session(tf.compat.v1.Session(config=config))
l2 = tf.keras.regularizers.l2
def part_model(h, num_classes, weight_decay):
h = tf.keras.layers.ZeroPadding2D((3, 3))(h)
h = tf.keras.layers.Conv2D(filters=32,
kernel_size=7,
strides=1,
padding="valid",
use_bias=False,
kernel_regularizer=l2(weight_decay))(h)
h = tf.keras.layers.BatchNormalization()(h)
h = tf.keras.layers.LeakyReLU()(h)
h = tf.keras.layers.MaxPooling2D(pool_size=(3, 3),
strides=2,
padding="same")(h)
h = tf.keras.layers.ZeroPadding2D((3, 3))(h)
h = tf.keras.layers.Conv2D(filters=64,
kernel_size=7,
strides=1,
padding="valid",
import re
from PIL import Image
from dataset import data_gen
from matplotlib import pyplot as plt
import utils
import math
#from tensorflow.keras.preprocessing.image import ImageDataGenerator
from keras import callbacks
from tensorflow.python.keras.optimizers import Adam
from keras import regularizers
from metrics.miou import MeanIoU
from keras.models import Model
import keras.backend.tensorflow_backend as K
cfg = K.tf.ConfigProto(gpu_options={'allow_growth': True})
K.set_session(K.tf.Session(config=cfg))
"""
import tensorflow.keras.backend.tensorflow_backend as ktf
def get_session(gpu_fraction=0.333):
gpu_options = tf.GPUOptions(per_process_gpu_memory_fraction=gpu_fraction,
allow_growth=True)
return tf.Session(config=tf.ConfigProto(gpu_options=gpu_options))
ktf.set_session(get_session())
"""
config = tf.ConfigProto(device_count={'GPU': 1, 'CPU': 32})
sess = tf.Session(config=config)
keras.backend.set_session(sess)
#flags = tf.compat.v1.app.flags
import os
import time
import keras.backend.tensorflow_backend as K
import tensorflow as tf
from keras.callbacks import ReduceLROnPlateau, ModelCheckpoint, TensorBoard, CSVLogger
from keras.preprocessing.image import ImageDataGenerator
import dense_net_121
import hyperparameters
os.environ["CUDA_VISIBLE_DEVICES"] = "1"
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
K.set_session(sess)
h_params = hyperparameters.load_hyperparameters()
data_train_path = '../MURA_trainval_keras/'
data_valid_path = '../MURA_valid1_keras/'
pretrained_weights_path = '../pretrain_network_weights/densenet121_weights_tf.h5'
timestamp = int(time.time())
model_save_path = '../saved_models_' + str(timestamp) + '/'
tensorboard_path = '../tensorboard_' + str(timestamp) + '/'
os.makedirs(model_save_path, mode=0o700, exist_ok=True)
os.makedirs(tensorboard_path, mode=0o700, exist_ok=True)
data_train_generator = ImageDataGenerator(
horizontal_flip=True,
def convert(self, video_file, swap_model = False, duration = None, start_time = None, use_gan = False, face_filter = False, photos = True, crop_x = None, width = None, side_by_side = False):
# Magic incantation to not have tensorflow blow up with an out of memory error.
import tensorflow as tf
import keras.backend.tensorflow_backend as K
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list="0"
K.set_session(tf.Session(config=config))
# Load model
model_name = "Original"
converter_name = "Masked"
if use_gan:
model_name = "GAN"
converter_name = "GAN"
model = PluginLoader.get_model(model_name)(Path(self._model_path(use_gan)))
if not model.load(swap_model):
print('model Not Found! A valid model must be provided to continue!')
exit(1)
# Load converter
converter = PluginLoader.get_converter(converter_name)
converter = converter(model.converter(False),
blur_size=8,
seamless_clone=True,
mask_type="facehullandrect",
erosion_kernel_size=None,
smooth_mask=True,
avg_color_adjust=True)
# Load face filter
filter_person = self._person_a
if swap_model:
filter_person = self._person_b
filter = FaceFilter(self._people[filter_person]['faces'])
# Define conversion method per frame
def _convert_frame(frame, convert_colors = True):
if convert_colors:
frame = cv2.cvtColor(frame, cv2.COLOR_BGR2RGB) # Swap RGB to BGR to work with OpenCV
for face in detect_faces(frame, "cnn"):
if (not face_filter) or (face_filter and filter.check(face)):
frame = converter.patch_image(frame, face)
frame = frame.astype(numpy.float32)
if convert_colors:
frame = cv2.cvtColor(frame, cv2.COLOR_BGR2RGB) # Swap RGB to BGR to work with OpenCV
return frame
def _convert_helper(get_frame, t):
return _convert_frame(get_frame(t))
media_path = self._video_path({ 'name' : video_file })
if not photos:
# Process video; start loading the video clip
video = VideoFileClip(media_path)
# If a duration is set, trim clip
if duration:
video = video.subclip(start_time, start_time + duration)
# Resize clip before processing
if width:
video = video.resize(width = width)
# Crop clip if desired
if crop_x:
video = video.fx(crop, x2 = video.w / 2)
# Kick off convert frames for each frame
new_video = video.fl(_convert_helper)
# Stack clips side by side
if side_by_side:
def add_caption(caption, clip):
text = (TextClip(caption, font='Amiri-regular', color='white', fontsize=80).
margin(40).
set_duration(clip.duration).
on_color(color=(0,0,0), col_opacity=0.6))
return CompositeVideoClip([clip, text])
video = add_caption("Original", video)
new_video = add_caption("Swapped", new_video)
final_video = clips_array([[video], [new_video]])
else:
final_video = new_video
# Resize clip after processing
#final_video = final_video.resize(width = (480 * 2))
# Write video
output_path = os.path.join(self.OUTPUT_PATH, video_file)
final_video.write_videofile(output_path, rewrite_audio = True)
# Clean up
del video
del new_video
del final_video
else:
# Process a directory of photos
for face_file in os.listdir(media_path):
face_path = os.path.join(media_path, face_file)
image = cv2.imread(face_path)
image = _convert_frame(image, convert_colors = False)
cv2.imwrite(os.path.join(self.OUTPUT_PATH, face_file), image)
num_classes = 1
save_model = True
epochs = int(config[dataset]["attack_epochs"])
user_epochs = int(config[dataset]["user_epochs"])
attack_epochs = int(config[dataset]["attack_shallow_model_epochs"])
batch_size = int(config[dataset]["defense_batch_size"])
defense_train_testing_ratio = float(config[dataset]["defense_training_ratio"])
result_folder = config[dataset]["result_folder"]
network_architecture = str(config[dataset]["network_architecture"])
fccnet = imp.load_source(str(config[dataset]["network_name"]),
network_architecture)
config_gpu = tf.ConfigProto()
config_gpu.gpu_options.per_process_gpu_memory_fraction = 0.5
config_gpu.gpu_options.visible_device_list = "0"
set_session(tf.Session(config=config_gpu))
#########loading defense data###################
(x_evaluate, y_evaluate,
l_evaluate) = input_data.input_data_attacker_evaluate()
evaluation_noise_filepath = result_folder + "/attack/" + "noise_data_evaluation.npz"
print(evaluation_noise_filepath)
if not os.path.isfile(evaluation_noise_filepath):
raise FileNotFoundError
npz_defense = np.load(evaluation_noise_filepath)
f_evaluate_noise = npz_defense['defense_output']
f_evaluate_origin = npz_defense['tc_output']
f_evaluate_defense = np.zeros(f_evaluate_noise.shape, dtype=np.float)
np.random.seed(100) #one time randomness, fix the seed
for i in np.arange(f_evaluate_defense.shape[0]):
0.1, # randomly shift images horizontally (fraction of total width)
height_shift_range=
0.1, # randomly shift images vertically (fraction of total height)
horizontal_flip=True, # randomly flip images
vertical_flip=True) # randomly flip images
#%% ------ CPU/GPU memory fix -------
import tensorflow as tf, keras.backend.tensorflow_backend as ktf
def get_session(gpu_fraction=0.25):
gpu_options = tf.GPUOptions(per_process_gpu_memory_fraction=gpu_fraction,
allow_growth=True)
return tf.Session(config=tf.ConfigProto(gpu_options=gpu_options))
ktf.set_session(get_session())
import psutil
def check_memusage():
process = psutil.Process(os.getpid())
pctused = 100 * process.memory_info().rss / psutil.virtual_memory().total
if pctused > 50:
print('**** High memory usage detected***')
print('Please check your code for memory leaks. Percent memory used: ',
pctused)
#%% Create demo data
def makedata(basepath):
def api_segmentLungAndLesion(dirModelLung,
dirModelLesion,
series,
ptrLogger=None,
shape4Lung=(256, 256, 64),
shape4Lesi=(512, 512, 256),
gpuMemUsage=0.4):
# (1) msg-helpers
def msgInfo(msg):
if ptrLogger is not None:
ptrLogger.info(msg)
else:
print(msg)
def msgErr(msg):
if ptrLogger is not None:
ptrLogger.error(msg)
else:
print(msg)
# (2.1) check data
if not series.isInitialized():
msgErr('Series is not initialized, skip .. [{0}]'.format(series))
return False
# if not series.isDownloaded():
# msgErr('Series data is not downloaded, skip .. [{0}]'.format(series))
# return False
if not series.isConverted():
msgErr(
'Series DICOM data is not converted to Nifti format, skip .. [{0}]'
.format(series))
return False
# (2.2) check existing files
pathNii = series.pathConvertedNifti(isRelative=False)
# pathSegmLungs = series.pathPostprocLungs(isRelative=False)
pathSegmLungs = series.pathPostprocLungs(isRelative=False)
pathSegmLesions = series.pathPostprocLesions2(isRelative=False)
if os.path.isfile(pathSegmLungs) and os.path.isfile(pathSegmLesions):
msgInfo('Series data is already segmented, skip task ... [{0}]'.format(
series))
return False
else:
# (2.3.0) TF GPU memory usage constraints
# FIXME:temporary fix, in future: apped memory usage parameter in application config
import tensorflow as tf
import keras.backend as K
from keras.backend.tensorflow_backend import set_session
if K.image_dim_ordering() == 'tf':
config = tf.ConfigProto()
config.gpu_options.per_process_gpu_memory_fraction = gpuMemUsage
set_session(tf.Session(config=config))
# (2.3.1) load and resize
try:
dataNii = nib.load(pathNii)
shapeOrig = dataNii.shape
niiResiz4Lung = resizeNii(dataNii, shape4Lung)
except Exception as err:
msgErr(
'Cant load and resize input nifti file [{0}] : {1}, for series [{2}]'
.format(pathNii, err, series))
return False
# (2.3.2) segment lungs
try:
if not os.path.isfile(pathSegmLungs):
K.clear_session()
lungMask = segmentLungs25D(
niiResiz4Lung,
dirWithModel=dirModelLung,
pathOutNii=None,
outSize=shapeOrig,
# outSize=shape4Lung,
threshold=0.5)
nib.save(lungMask, pathSegmLungs)
else:
pass
# lungMask = nib.load(pathSegmLungs)
except Exception as err:
msgErr('Cant segment lungs for file [{0}] : {1}, for series [{2}]'.
format(pathNii, err, series))
return False
# (2.3.3) segment lesions
try:
if not os.path.isfile(pathSegmLesions):
# lesionMask = segmentLesions3D(niiResiz4Lesi,
# dirWithModel=dirModelLesion,
# pathOutNii=None,
# outSize=shapeOrig,
# # outSize=shape4Lung,
# threshold=None)
K.clear_session()
shape_lesions = [512, 512, 256]
nii_lung_resiz4lesion = resizeNii(pathSegmLungs,
shape_lesions,
parOrder=0)
nii_data_resiz4lesion = resizeNii(dataNii,
shape_lesions,
parOrder=1)
lesionMask, lesionMaskVal = segmentLesions3Dv3(
nii_data_resiz4lesion,
dir_with_model=dirModelLesion,
nii_lings=nii_lung_resiz4lesion,
path_out_nii=None,
# outSize=shapeOrig,
# outSize=shape4Lung,
threshold=None)
# lesionMask = segmentLesions3Dv2(niiResiz4Lesi,
# dirWithModel=dirModelLesion,
# pathOutNii=None,
# outSize=shapeOrig,
# # outSize=shape4Lung,
# threshold=None,
# path_lungs=pathSegmLungs)
# (2.3.4) save results
try:
lesionMask = resizeNii(lesionMask, shapeOrig, parOrder=0)
nib.save(lesionMask, pathSegmLesions)
except Exception as err:
msgErr(
'Cant save segmentation results to file [{0}] : {1}, for series [{2}]'
.format(pathSegmLesions, err, series))
return False
except Exception as err:
msgErr(
'Cant segment lesions for file [{0}] : {1}, for series [{2}]'.
format(pathNii, err, series))
return False
return True
"embeddings_size": 32,
"use_full_tags": True,
"callbacks": {
"EarlyStopping": {
"patience": 5,
"monitor": "val_loss"
}
}
}
KEYS = ["labels", "feats", "reverse", "bigrams"]
if __name__ == "__main__":
config = tf.ConfigProto()
config.gpu_options.per_process_gpu_memory_fraction = 0.3
kbt.set_session(tf.Session(config=config))
languages = ["belarusian"]
corr_dir = os.path.join("conll2018", "task1", "all")
use_label, use_bigram_loss, reverse = True, True, True
for language in languages:
infile = os.path.join(corr_dir, "{}-train-{}".format(language, mode))
data = read_infile(infile, for_lm=True)
dev_file = os.path.join(corr_dir, "{}-dev".format(language, mode))
dev_data = read_infile(dev_file, for_lm=True)
for (use_bigram_loss, use_feats) in itertools.product([False, True],
[False, True]):
model = NeuralLM(use_bigram_loss=use_bigram_loss,
use_label=use_label,
use_feats=use_feats,
nepochs=30,
from keras import layers
from keras import Model, Input
from image_data import *
import tensorflow as tf
from keras import optimizers
from keras.backend.tensorflow_backend import set_session
config = tf.ConfigProto(
gpu_options=tf.GPUOptions(per_process_gpu_memory_fraction=0.8)
# device_count = {'GPU': 1}
)
config.gpu_options.allow_growth = True
session = tf.Session(config=config)
set_session(session)
import matplotlib.pyplot as plt
# audio net
input_image = Input(shape=(224, 224, 3), name='image')
image_conv1_1 = layers.Conv2D(64, (3, 3))(input_image)
x = layers.BatchNormalization()(image_conv1_1)
x = layers.ReLU()(x)
x = layers.ZeroPadding2D((1, 1))(x)
x = layers.Conv2D(64, (3, 3))(x)
x = layers.BatchNormalization()(x)
x = layers.ReLU()(x)
x = layers.ZeroPadding2D((1, 1))(x)
image_pool1 = layers.MaxPooling2D((2, 2), strides=(2, 2))(x)
x = layers.Conv2D(128, (3, 3))(image_pool1)
x = layers.BatchNormalization()(x)
x = layers.ReLU()(x)
PATH = '../' + KEYWORD
################# Parameter Setting #######################
###########################Reproducible#############################
import random
np.random.seed(100)
random.seed(100)
os.environ['PYTHONHASHSEED'] = '0' # necessary for py3
import tensorflow as tf
from keras.backend.tensorflow_backend import set_session
tf.set_random_seed(100)
config = tf.ConfigProto(intra_op_parallelism_threads=1, inter_op_parallelism_threads=1)
config.gpu_options.per_process_gpu_memory_fraction = 0.3
config.gpu_options.visible_device_list = '2'
set_session(tf.Session(graph=tf.get_default_graph(), config=config))
###################################################################
def main():
if not os.path.exists(PATH):
os.makedirs(PATH)
currentPython = sys.argv[0]
shutil.copy2(currentPython, PATH)
shutil.copy2('Param.py', PATH)
shutil.copy2('Param_STResNet.py', PATH)
data, timestamps = load_data(dataFile_lst, timeFile)
data_norm = [x / MAX_FLOWIO for x in data]
print(KEYWORD, 'training started', time.ctime())
trainModel(MODELNAME, data_norm, timestamps)
def handle_requests(ctx, socket):
# Load SSD model
ssd_model = load_SSD_model()
# Load trained tensorflow car classifier and set tensorflow configs
tf_config = K.tf.ConfigProto()
tf_config.gpu_options.per_process_gpu_memory_fraction = CarConfig.crcl[
"classifier_gpu_memory_frac"]
K.set_session(K.tf.Session(config=tf_config))
init = K.tf.global_variables_initializer()
sess = K.get_session()
sess.run(init)
# Define a concurrent future and an executor to be used in case plate recognition is enabled
future1 = None
executor = None
is_initialized = False
use_plate_recognition = CarConfig.crcl["enable_plate_recognition"]
if use_plate_recognition:
# Initialize process executor once
executor = ProcessPoolExecutor(max_workers=1)
# Load model once
car_classifier_model, car_classifier_loaded_model_json = load_model_and_json(
)
print('Loaded both models successfully, ready to roll.')
print('Server is started on:', tcp_address)
while True:
try:
request = socket.recv()
image = zmq_comm.decode_request(request)
found_objects = []
with isess.as_default():
found_objects = extract_objects(ssd_model, image)
clasifications = []
with sess.as_default():
for o in found_objects:
# Crop image according to empirical margin values
cropped, cropped_wo_margin = crop_image(
image, o['topleft'], o['bottomright'],
float(o['confidence']))
if cropped is None or cropped_wo_margin is None:
continue
found_plate = ""
predictions = []
filtered_candidates = []
# Run plate recognition in parallel while the main thread continues
# Note that, if you call 'future.result()' here, it just waits for process to end
# Also notice that, we are sending the original cropped image to plate extraction (a.k.a. no margins)
if use_plate_recognition:
future1 = executor.submit(extract_plate,
cropped_wo_margin,
is_initialized)
# Preprocess the image
cropped = cropped * 1. / 255
cropped = cv2.resize(cropped, (299, 299))
cropped = cropped.reshape((1, ) + cropped.shape)
# Feed image to classifier
preds = car_classifier_model.predict(cropped)[0]
predict_list = classifyIndices(
car_classifier_loaded_model_json, preds,
CarConfig.crcl["n"])
predictions = []
tags = ["model", "score"]
for index, p in enumerate(predict_list):
predictions.append(
dict(zip(tags, [p.name, str(p.score)])))
# Wait for plate recognition to finish its job
if use_plate_recognition and future1 is not None:
try:
found_plate, is_initialized = future1.result(
timeout=CarConfig.crcl["plate_service_timeout"]
)
except TimeoutError as e:
print(
"Could not get any respond from plate service. Timeout."
)
cl = {
'label': o['label'],
'confidence': o['confidence'],
'topleft': o['topleft'],
'bottomright': o['bottomright'],
'predictions': predictions,
'plate': found_plate
}
clasifications.append(cl)
result_dict = {}
result_dict["result"] = clasifications
result_dict["message"] = "OK"
# print(result_dict)
socket.send_json(result_dict)
except Exception as e:
result_dict = {}
result_dict["result"] = []
result_dict["message"] = str(e)
socket.send_json(result_dict)
finally:
#TODO: Implement this
pass
from keras.layers import GRU, Input, Dense
from keras import losses
from keras.optimizers import Adam
from keras.regularizers import l2
from keras.models import load_model
#from keras.callbacks import EarlyStopping, ModelCheckpoint
import tensorflow as tf
import keras.backend.tensorflow_backend as KTF
from sklearn.utils import class_weight
from sklearn.metrics import classification_report
KTF.set_session(
tf.Session(config=tf.ConfigProto(device_count={
'CPU': 1,
'GPU': 1
})))
datapath = ''
modelpath = ''
############################# HYPERPARAMETERS ##########################################
ntr = 3
nte = 3
nva = 5 #duration of one utterance 'in seconds' for - training, validation and testing files
EPOCHS = 40
DROP = 0.2
REC_DROP = 0.2
BATCH_SIZE = 64
#VAL_SPLIT = 0.2
def train(data_dir,
atlas_file,
model_dir,
model_dir_intermediate,
gpu_id,
lr,
nb_epochs,
prior_lambda,
image_sigma,
steps_per_epoch,
batch_size,
load_model_file,
bidir,
initial_epoch=0):
"""
model training function
:param data_dir: folder with npz files for each subject.
:param atlas_file: atlas filename. So far we support npz file with a 'vol' variable
:param model_dir: model folder to save to
:param gpu_id: integer specifying the gpu to use
:param lr: learning rate
:param nb_epochs: number of training iterations
:param prior_lambda: the prior_lambda, the scalar in front of the smoothing laplacian, in MICCAI paper
:param image_sigma: the image sigma in MICCAI paper
:param steps_per_epoch: frequency with which to save models
:param batch_size: Optional, default of 1. can be larger, depends on GPU memory and volume size
:param load_model_file: optional h5 model file to initialize with
:param bidir: logical whether to use bidirectional cost function
"""
# load atlas from provided files. The atlas we used is 160x192x224.
atlas_vol = np.load(atlas_file)['vol'][np.newaxis, ..., np.newaxis]
vol_size = atlas_vol.shape[1:-1]
# prepare data files
# for the CVPR and MICCAI papers, we have data arranged in train/validate/test folders
# inside each folder is a /vols/ and a /asegs/ folder with the volumes
# and segmentations. All of our papers use npz formated data.
train_vol_names = glob.glob(os.path.join(data_dir, '*.npz'))
random.shuffle(train_vol_names) # shuffle volume list
assert len(train_vol_names) > 0, "Could not find any training data"
# Diffeomorphic network architecture used in MICCAI 2018 paper
nf_enc = [16, 32, 32, 32]
nf_dec = [32, 32, 32, 32, 16, 3]
# prepare model folder
if not os.path.isdir(model_dir):
os.mkdir(model_dir)
# gpu handling
debug_cpu = False
if debug_cpu: # if you memory errors at home and just wanna test this before sending the job to DGX-1
print(
'\n==============\nYou are now training with CPU in the debug mode! Was this desired?\n==============\n'
)
dev = '/cpu:%d' % 0 # gpu_id
os.environ["CUDA_VISIBLE_DEVICES"] = ''
nb_gpus = 1
else:
print('Training with GPU')
dev = '/gpu:%d' % 0 # gpu_id
os.environ["CUDA_VISIBLE_DEVICES"] = gpu_id
nb_gpus = len(gpu_id.split(','))
assert np.mod(batch_size, nb_gpus) == 0, \
'batch_size should be a multiple of the nr. of gpus. ' + \
'Got batch_size %d, %d gpus' % (batch_size, nb_gpus)
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
set_session(tf.Session(config=config))
# prepare the model
with tf.device(dev):
# the MICCAI201 model takes in [image_1, image_2] and outputs [warped_image_1, velocity_stats]
# in these experiments, we use image_2 as atlas
model = networks.miccai2018_net(vol_size, nf_enc, nf_dec, bidir=bidir)
# load initial weights
if load_model_file is not None and load_model_file != "":
print('Load initial weights from {}'.format(load_model_file))
model.load_weights(load_model_file)
else:
print('No pre-trained model given to load initial weights from')
# save first iteration
model.save(os.path.join(model_dir, '%02d.h5' % initial_epoch))
# compile
# note: best to supply vol_shape here than to let tf figure it out.
flow_vol_shape = model.outputs[-1].shape[1:-1]
loss_class = losses.Miccai2018(image_sigma,
prior_lambda,
flow_vol_shape=flow_vol_shape)
if bidir:
model_losses = [
loss_class.recon_loss, loss_class.recon_loss,
loss_class.kl_loss
]
loss_weights = [0.5, 0.5, 1]
else:
model_losses = [loss_class.recon_loss, loss_class.kl_loss]
loss_weights = [1, 1]
# data generator
train_example_gen = datagenerators.example_gen(train_vol_names,
batch_size=batch_size)
atlas_vol_bs = np.repeat(atlas_vol, batch_size, axis=0)
miccai2018_gen = datagenerators.miccai2018_gen(train_example_gen,
atlas_vol_bs,
batch_size=batch_size,
bidir=bidir)
# prepare callbacks
save_file_name = os.path.join(model_dir_intermediate, '{epoch:02d}.h5')
# fit generator
with tf.device(dev):
# multi-gpu support
if nb_gpus > 1:
save_callback = nrn_gen.ModelCheckpointParallel(save_file_name)
mg_model = multi_gpu_model(model, gpus=nb_gpus)
# single gpu
else:
save_callback = ModelCheckpoint(save_file_name)
mg_model = model
# TODO! Add LR scheduler here
model.compile(optimizer=Adam(lr=lr),
loss=model_losses,
loss_weights=loss_weights)
model.fit_generator(miccai2018_gen,
initial_epoch=initial_epoch,
epochs=nb_epochs,
callbacks=[save_callback],
steps_per_epoch=steps_per_epoch,
verbose=1)
def set_keras_gpu_use(percentage):
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
KTF.set_session(sess)
from keras.models import load_model
from keras.layers import Conv2D, MaxPooling2D, Dropout, Flatten, Dense
from keras.callbacks import EarlyStopping, ModelCheckpoint
from keras.optimizers import Adagrad
from keras.backend import tensorflow_backend as tback
from keras.utils import multi_gpu_model
FLAGS = None
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
tback.set_session(tf.Session(config = config))
colorindex = np.array(
[[0, 0, 0, 255],
[0, 0, 255, 0],
[0, 255, 0, 0],
[255, 0, 0, 0]],
dtype = np.float32)
datafile = h5py.File('/home/pangaofeng/share/label/testn.mat', 'r');
data = datafile['testxdata'];
label = datafile['testdata'];
print(label.shape)
with h5py.File('oauc.mat', 'r') as oauc_file:
from keras.layers import Conv2D, MaxPooling2D
from keras.callbacks import TensorBoard
import numpy as np
import os
import random
import cv2
import time
# Returns the TF session to be used by the backend.
def get_session(gpu_fraction=0.85):
gpu_options = tf.GPUOptions(per_process_gpu_memory_fraction=gpu_fraction)
return tf.Session(config=tf.ConfigProto(gpu_options=gpu_options))
backend.set_session(get_session())
model = Sequential()
model.add(
Conv2D(32, (7, 7),
padding='same',
input_shape=(176, 200, 1),
activation='relu'))
model.add(Conv2D(32, (3, 3), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Dropout(0.2))
model.add(Conv2D(64, (3, 3), padding='same', activation='relu'))
model.add(Conv2D(64, (3, 3), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Dropout(0.2))
import sys
import random
import keras
import tensorflow as tf
import keras.backend as K
from keras.models import Model
from keras.callbacks import EarlyStopping, ModelCheckpoint, ReduceLROnPlateau, TensorBoard
from model import build_model
from transform import trainAug, valAug
from dataloader import DataGenerator
from keras.losses import binary_crossentropy
import keras.backend.tensorflow_backend as KTF
from keras import optimizers
KTF.set_session(tf.Session(config=tf.ConfigProto(device_count={'gpu': 0})))
class ViolenceNet:
def __init__(self):
self.epoch = 150
self.lr = 0.005
self.lr_drop = 5
self.batch_size = 1
self.model = build_model()
self.trainLoader = DataGenerator('./data/rgb_train.txt',
batch_size=self.batch_size,
random_shift=True,
transform=trainAug())
self.valLoader = DataGenerator('./data/rgb_val.txt',