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dsb_a9_c3_s2_p8a1.py
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dsb_a9_c3_s2_p8a1.py
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import numpy as np
import data_transforms
import data_iterators
import pathfinder
import lasagne as nn
from collections import namedtuple
from functools import partial
import lasagne.layers.dnn as dnn
import theano.tensor as T
import utils
import utils_lung
# TODO: import correct config here
candidates_config = 'dsb_c3_s2_p8a1'
restart_from_save = None
rng = np.random.RandomState(42)
predictions_dir = utils.get_dir_path('model-predictions', pathfinder.METADATA_PATH)
candidates_path = predictions_dir + '/%s' % candidates_config
id2candidates_path = utils_lung.get_candidates_paths(candidates_path)
# transformations
p_transform = {'patch_size': (48, 48, 48),
'mm_patch_size': (48, 48, 48),
'pixel_spacing': (1., 1., 1.)
}
n_candidates_per_patient = 2
def data_prep_function(data, patch_centers, pixel_spacing, p_transform,
p_transform_augment, **kwargs):
x = data_transforms.transform_dsb_candidates(data=data,
patch_centers=patch_centers,
p_transform=p_transform,
p_transform_augment=p_transform_augment,
pixel_spacing=pixel_spacing)
x = data_transforms.pixelnormHU(x)
return x
data_prep_function_train = partial(data_prep_function, p_transform_augment=None,
p_transform=p_transform)
data_prep_function_valid = partial(data_prep_function, p_transform_augment=None,
p_transform=p_transform)
# data iterators
batch_size = 4
train_valid_ids = utils.load_pkl(pathfinder.VALIDATION_SPLIT_PATH)
train_pids, valid_pids = train_valid_ids['training'], train_valid_ids['validation']
print 'n train', len(train_pids)
print 'n valid', len(valid_pids)
train_data_iterator = data_iterators.DSBPatientsDataGenerator(data_path=pathfinder.DATA_PATH,
batch_size=batch_size,
transform_params=p_transform,
n_candidates_per_patient=n_candidates_per_patient,
data_prep_fun=data_prep_function_train,
id2candidates_path=id2candidates_path,
rng=rng,
patient_ids=train_pids,
random=True, infinite=True)
valid_data_iterator = data_iterators.DSBPatientsDataGenerator(data_path=pathfinder.DATA_PATH,
batch_size=1,
transform_params=p_transform,
n_candidates_per_patient=n_candidates_per_patient,
data_prep_fun=data_prep_function_valid,
id2candidates_path=id2candidates_path,
rng=rng,
patient_ids=valid_pids,
random=False, infinite=False)
nchunks_per_epoch = train_data_iterator.nsamples / batch_size
max_nchunks = nchunks_per_epoch * 10
validate_every = int(0.5 * nchunks_per_epoch)
save_every = int(0.25 * nchunks_per_epoch)
learning_rate_schedule = {
0: 1e-5,
int(5 * nchunks_per_epoch): 2e-6,
int(6 * nchunks_per_epoch): 1e-6,
int(7 * nchunks_per_epoch): 5e-7,
int(9 * nchunks_per_epoch): 2e-7
}
# model
conv3 = partial(dnn.Conv3DDNNLayer,
pad="valid",
filter_size=3,
nonlinearity=nn.nonlinearities.rectify,
b=nn.init.Constant(0.1),
W=nn.init.Orthogonal("relu"))
max_pool = partial(dnn.MaxPool3DDNNLayer,
pool_size=2)
def dense_prelu_layer(l_in, num_units):
l = nn.layers.DenseLayer(l_in, num_units=num_units, W=nn.init.Orthogonal(),
nonlinearity=nn.nonlinearities.linear)
l = nn.layers.ParametricRectifierLayer(l)
return l
def build_model():
l_in = nn.layers.InputLayer((None, n_candidates_per_patient, 1,) + p_transform['patch_size'])
l_in_rshp = nn.layers.ReshapeLayer(l_in, (-1, 1,) + p_transform['patch_size'])
l_target = nn.layers.InputLayer((batch_size,))
l = conv3(l_in_rshp, num_filters=128)
l = conv3(l, num_filters=128)
l = max_pool(l)
l = conv3(l, num_filters=128)
l = conv3(l, num_filters=128)
l = max_pool(l)
l = conv3(l, num_filters=256)
l = conv3(l, num_filters=256)
l = conv3(l, num_filters=256)
num_units_dense = 512
l_d01 = dense_prelu_layer(l, num_units=512)
l_d01 = nn.layers.ReshapeLayer(l_d01, (-1, n_candidates_per_patient, num_units_dense))
l_d02 = dense_prelu_layer(nn.layers.dropout(l_d01), num_units=512)
l_out = nn.layers.DenseLayer(l_d02, num_units=2,
W=nn.init.Constant(0.),
b=np.array([np.log((1397. - 362) / 1398), np.log(362. / 1397)], dtype='float32'),
nonlinearity=nn.nonlinearities.softmax)
return namedtuple('Model', ['l_in', 'l_out', 'l_target'])(l_in, l_out, l_target)
def build_objective(model, deterministic=False, epsilon=1e-12):
predictions = nn.layers.get_output(model.l_out, deterministic=deterministic)
targets = T.cast(T.flatten(nn.layers.get_output(model.l_target)), 'int32')
p = predictions[T.arange(predictions.shape[0]), targets]
p = T.clip(p, epsilon, 1.)
loss = T.mean(T.log(p))
return -loss
def build_updates(train_loss, model, learning_rate):
updates = nn.updates.adam(train_loss, nn.layers.get_all_params(model.l_out, trainable=True), learning_rate)
return updates