def compute_surprisal_loss(model, loss, updated_states, sample_probabilities,
surprisal_influence, mask):
"""
Compute penalization term on the average surprisal of the unread samples.
"""
if using_skip_rnn(model):
neg_updated_states = tf.subtract(
tf.ones(updated_states.get_shape(), dtype=tf.dtypes.float32),
updated_states)
surprisal_values = tf.multiply(
tf.multiply(tf.constant(-1.0), (tf.log(sample_probabilities))),
mask)
# printer_0 = tf.Print(neg_updated_states, [neg_updated_states], "Inverse of the updated states is ")
surprisals = tf.multiply(
neg_updated_states,
tf.where(tf.is_nan(surprisal_values),
tf.zeros_like(surprisal_values), surprisal_values))
tot_surprisal = tf.reduce_sum(surprisals)
# printer_1 = tf.Print(tot_surprisal, [tot_surprisal], "Total surprisal is ")
non_read_samples = tf.reduce_sum(tf.multiply(neg_updated_states, mask))
# printer_2 = tf.Print(non_read_samples, [non_read_samples], "Non read samples is ")
# with tf.control_dependencies([printer_0, printer_1, printer_2]):
average_surprisal = tf.div_no_nan(tot_surprisal, non_read_samples)
surprisal_loss = surprisal_influence * average_surprisal
# print = tf.cond(tf.math.is_nan(surprisal_loss),
# true_fn=lambda: tf.Print(surprisal_loss, [surprisal_loss], "Surprisal loss is null "),
# false_fn=lambda: tf.no_op())
# with tf.control_dependencies([print]):
return surprisal_loss
else:
return tf.zeros(loss.get_shape())
def metric_fn(per_example_loss, label_ids, logits, is_real_example):
"""Compute Matthew's correlations for STS-B."""
predictions = tf.argmax(logits, axis=-1, output_type=tf.int32)
# https://en.wikipedia.org/wiki/Matthews_correlation_coefficient
tp, tp_op = tf.metrics.true_positives(
predictions, label_ids, weights=is_real_example)
tn, tn_op = tf.metrics.true_negatives(
predictions, label_ids, weights=is_real_example)
fp, fp_op = tf.metrics.false_positives(
predictions, label_ids, weights=is_real_example)
fn, fn_op = tf.metrics.false_negatives(
predictions, label_ids, weights=is_real_example)
# Compute Matthew's correlation
mcc = tf.div_no_nan(
tp * tn - fp * fn,
tf.pow((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn), 0.5))
# Compute accuracy
accuracy = tf.metrics.accuracy(
labels=label_ids, predictions=predictions,
weights=is_real_example)
loss = tf.metrics.mean(
values=per_example_loss,
weights=is_real_example)
return {"matthew_corr": (mcc, tf.group(tp_op, tn_op, fp_op, fn_op)),
"eval_accuracy": accuracy, "eval_loss": loss,}
def embedding_lookup_sparse(embedding_params,
sparse_indices,
weights,
combiner,
name=None):
bs = tf.cast(sparse_indices.dense_shape[0], dtype=tf.int32)
if combiner != 'mean':
embedding_tensor_reduce = tf.nn.embedding_lookup_sparse(
embedding_params,
sparse_indices,
weights,
combiner=combiner,
name=name)
embedding_tensor_scatter = tf.pad(
embedding_tensor_reduce,
[[0, bs - tf.shape(embedding_tensor_reduce)[0]], [0, 0]],
'CONSTANT',
constant_values=0)
else:
embedding_tensor_reduce = tf.nn.embedding_lookup_sparse(
embedding_params, sparse_indices, weights, combiner='sum')
embedding_tensor_scatter = tf.pad(
embedding_tensor_reduce,
[[0, bs - tf.shape(embedding_tensor_reduce)[0]], [0, 0]],
'CONSTANT',
constant_values=0)
line_number = tf.cast(sparse_indices.indices[:, 0], tf.int32)
line_count = tf.expand_dims(
tf.math.bincount(line_number, minlength=bs, dtype=tf.float32), 1)
embedding_tensor_scatter = tf.div_no_nan(embedding_tensor_scatter,
line_count,
name=name)
return embedding_tensor_scatter
def encode(self, x, encode_params):
"""See base class."""
x = self._validate_and_expand_encode_input(x)
dims = x.shape.as_list()
# Get static or dynamic leading dimension if static not available.
dim_0 = dims[0] if dims[0] else tf.shape(x)[0]
dim_1 = dims[1]
kashin_coefficients = tf.zeros([dim_0, self._get_pad_dim(dim_1)],
dtype=x.dtype)
clip_level = tf.norm(x, axis=1, keepdims=True) / tf.math.sqrt(
tf.cast(encode_params[self.DELTA_PARAMS_KEY], x.dtype) * dim_1)
last_iter_clip = self._last_iter_clip
residual = x
signs = self._random_signs(dim_1, encode_params[self.SEED_PARAMS_KEY],
x.dtype)
# Compute the Kashin coefficients.
for _ in range(self._num_iters - 1):
residual, kashin_coefficients = self._kashin_iter(
residual, kashin_coefficients, signs, clip_level)
clip_level *= tf.cast(encode_params[self.ETA_PARAMS_KEY], x.dtype)
# The last iteration can be with or without clipping.
kashin_coefficients += self._kashin_forward(residual, signs,
clip_level, last_iter_clip)
if last_iter_clip:
# If there is clipping in the last iteration, this can result in
# biased representation of smaller magnitude. We compensate for this
# by scaling such that the norm is preserved.
kashin_coefficients *= tf.div_no_nan(
tf.norm(x, axis=1, keepdims=True),
tf.norm(kashin_coefficients, axis=1, keepdims=True))
return {self.ENCODED_VALUES_KEY: kashin_coefficients}
def sparse_reduce(sparse_tensor, reduce_type):
bs = tf.cast(sparse_tensor.dense_shape[0], dtype=tf.int32)
if reduce_type == 'sum':
sparse_tensor_reduce = tf.sparse.reduce_sum(sparse_tensor,
axis=1,
keepdims=True)
elif reduce_type == 'max':
sparse_tensor_reduce = tf.sparse.reduce_max(sparse_tensor,
axis=1,
keepdims=True)
elif reduce_type == 'mean':
sparse_tensor_reduce = tf.sparse.reduce_sum(sparse_tensor,
axis=1,
keepdims=True)
indices = tf.cast(sparse_tensor.indices, tf.int32)
line_number_indices = indices[:, 0]
line_count = tf.expand_dims(
tf.math.bincount(line_number_indices,
minlength=bs,
dtype=tf.float32), 1)
sparse_tensor_reduce = tf.div_no_nan(sparse_tensor_reduce, line_count)
else:
assert False, "no this way"
sparse_tensor_scatter = tf.reshape(sparse_tensor_reduce, shape=[bs, 1])
return sparse_tensor_scatter
def forward(self, tensors, mode: str = None):
"""Computes Triplet Precision
Parameters
----------
tensors : Tuple[tf.Tensor]
- positives : shape = (batch, num_events)
- negatives : shape = (batch, num_events, num_negatives)
- mask : shape = (batch, num_events, num_negatives)
- weights : shape = (batch, num_events)
Returns
-------
tf.Tensor
BPR loss
"""
# Retrieve positives and negatives logits
positives, negatives, mask, weights = tensors
positives, negatives = make_same_shape([positives, negatives],
broadcast=False)
# One triplet precision per event
event_triplet = WeightedAverage()((tf.cast(
positives > negatives, tf.float32), tf.cast(mask, tf.float32)),
mode)
# Each event contributes according to its weight
event_weights = weights * tf.to_float(tf.reduce_any(mask, axis=-1))
return tf.div_no_nan(tf.reduce_sum(event_triplet * event_weights),
tf.reduce_sum(event_weights))
def __call__(self, tensors: Dict[str, tf.Tensor]) -> Dict[str, Tuple]:
# Retrieve tensors
logits = tensors[self.logits]
targets = tensors[self.targets]
ndims = len(targets.shape) - 1
# Set logits of inputs to -inf
if self.inputs is not None:
inputs = tensors[self.inputs]
logits = logits + tf.cast(inputs, tf.float32) * tf.float32.min
# Retrieve top k predictions
_, indices = tf.math.top_k(logits, k=self.k, sorted=True)
for _ in range(ndims):
indices = tf.expand_dims(indices, axis=-2)
equal_topk = tf.equal(tf.cast(indices, tf.int64), tf.expand_dims(targets, axis=-1))
# Discounted cumulative gain
pos_in_target = tf.reduce_sum(tf.cast(equal_topk, tf.float32), axis=-2)
discount = tf.math.log(2.0) / tf.math.log(tf.range(2, self.k + 2, dtype=tf.float32))
for _ in range(ndims + 1):
discount = tf.expand_dims(discount, axis=0)
dcg = tf.reduce_sum(discount * pos_in_target, axis=-1)
# Ideal discounted cumulative gain
num_targets = tf.reduce_sum(tf.cast(tf.not_equal(targets, -1), tf.int64), axis=-1)
num_targets = tf.math.minimum(num_targets, self.k)
all_in_target = tf.cast(tf.sequence_mask(num_targets, maxlen=self.k), tf.float32)
idcg = tf.reduce_sum(discount * all_in_target, axis=-1)
# Normalized DCG
ndcg = tf.div_no_nan(dcg, idcg)
return {self.name: tf.metrics.mean(ndcg)}
def get_IOU(y_true, y_pred):
# true box
true_halfwidth = y_true[..., 3] / 2.
true_halfheight = y_true[..., 4] / 2.
true_x1 = y_true[..., 1] - true_halfwidth
true_y1 = y_true[..., 2] - true_halfheight
true_x2 = y_true[..., 1] + true_halfwidth
true_y2 = y_true[..., 2] + true_halfheight
# pred box
pred_halfwidth = y_pred[..., 3] / 2.
pred_halfheight = y_pred[..., 4] / 2.
pred_x1 = y_pred[..., 1] - pred_halfwidth
pred_y1 = y_pred[..., 2] - pred_halfheight
pred_x2 = y_pred[..., 1] + pred_halfwidth
pred_y2 = y_pred[..., 2] + pred_halfheight
xA = tf.maximum(pred_x1, true_x1)
yA = tf.maximum(pred_y1, true_y1)
xB = tf.minimum(pred_x2, true_x2)
yB = tf.minimum(pred_y2, true_y2)
intersect = (tf.maximum(xB - xA, tf.zeros(tf.shape(xB))) *
tf.maximum(yB - yA, tf.zeros(tf.shape(yB))))
trueArea = y_true[..., 3] * y_true[..., 4]
predArea = y_pred[..., 3] * y_pred[..., 4]
union = trueArea + predArea - intersect
return tf.div_no_nan(intersect, union)
def forward(self, tensors, mode: str = None):
"""Forward method of the layer
Parameters
----------
tensors : Tuple[tf.Tensor]
- positives : shape = (batch, num_events)
- negatives : shape = (batch, num_events, num_negatives)
- mask : shape = (batch, num_events, num_negatives)
- weights : shape = (batch, num_events)
Returns
-------
tf.Tensor
BPR loss
"""
positives, negatives, mask, weights = tensors
positives, negatives = make_same_shape([positives, negatives],
broadcast=False)
# One score per negative : (batch, num_events, num_negatives)
scores = -tf.log_sigmoid(positives - negatives)
# One loss per event, average of scores : (batch, num_events)
event_scores = WeightedAverage()((scores, tf.to_float(mask)))
# Each event contributes according to its weight
event_weights = weights * tf.to_float(tf.reduce_any(mask, axis=-1))
event_losses = event_scores * event_weights
return tf.div_no_nan(tf.reduce_sum(event_losses),
tf.reduce_sum(event_weights))
def forward(self, tensors, mode: str = None):
"""Forward method of the layer
(details: https://arxiv.org/pdf/1706.03847.pdf)
Parameters
----------
tensors : Tuple[tf.Tensor]
- positives : shape = (batch, num_events)
- negatives : shape = (batch, num_events, num_negatives)
- mask : shape = (batch, num_events, num_negatives)
- weights : shape = (batch, num_events)
Returns
-------
tf.Tensor
TopOne Max loss
"""
positives, negatives, mask, weights = tensors
positives, negatives = make_same_shape([positives, negatives], broadcast=False)
softmax_scores = Softmax()((negatives, tf.to_float(mask)))
losses = tf.multiply(softmax_scores, tf.nn.sigmoid(negatives - positives) + tf.nn.sigmoid(tf.square(negatives)))
# One loss per event, average of scores : (batch, num_events)
event_scores = WeightedAverage()((losses, tf.to_float(mask)))
# Each event contributes according to its weight
event_weights = weights * tf.to_float(tf.reduce_any(mask, axis=-1))
event_losses = event_scores * event_weights
return tf.div_no_nan(tf.reduce_sum(event_losses), tf.reduce_sum(event_weights))
def encode(self, x, encode_params):
"""See base class."""
min_x = tf.reduce_min(x)
max_x = tf.reduce_max(x)
max_value = tf.cast(encode_params[self.MAX_INT_VALUE_PARAMS_KEY], x.dtype)
# Shift the values to range [0, max_value].
# In the case of min_x == max_x, this will return all zeros.
x = tf.div_no_nan(x - min_x, max_x - min_x) * max_value
# Randomized rounding.
floored_x = tf.floor(x)
random_seed = tf.random.uniform((2,), maxval=tf.int64.max, dtype=tf.int64)
num_elements = tf.reduce_prod(tf.shape(x))
rounding_floats = tf.reshape(
self._random_floats(num_elements, random_seed, x.dtype), tf.shape(x))
bernoulli = rounding_floats < (x - floored_x)
quantized_x = floored_x + tf.cast(bernoulli, x.dtype)
# Include the random seed in the encoded tensors so that it can be used to
# generate the same random sequence in the decode method.
encoded_tensors = {
self.ENCODED_VALUES_KEY: quantized_x,
self.SEED_PARAMS_KEY: random_seed,
self.MIN_MAX_VALUES_KEY: tf.stack([min_x, max_x])
}
return encoded_tensors
def UserEmbedding(tensors: tf.Tensor,
mode: str,
keep_prob: float,
reduce_mode: str = "average"):
"""Compute Weighted Sum (randomly masking inputs in TRAIN mode)."""
embeddings, mask = tensors
# Drop entries without re-scaling (not classical dropout)
if mode == deepr.TRAIN:
LOGGER.info("Applying random mask to inputs (TRAIN only)")
mask_random = tf.random.uniform(tf.shape(mask)) <= keep_prob
mask = tf.logical_and(mask, mask_random)
weights = tf.cast(mask, tf.float32)
# Scale the weights depending on the reduce mode
if reduce_mode == "l2":
weights = tf.nn.l2_normalize(weights, axis=-1)
elif reduce_mode == "average":
weights = tf.div_no_nan(weights,
tf.reduce_sum(weights, axis=-1, keepdims=True))
elif reduce_mode == "sum":
pass
else:
raise ValueError(
f"Reduce mode {reduce_mode} unknown (must be 'l2', 'average' or 'sum')"
)
return tf.reduce_sum(embeddings * tf.expand_dims(weights, axis=-1),
axis=-2)
def encode(self, x, encode_params):
"""See base class."""
dim = tf.shape(x)[-1]
x = tf.reshape(x, [-1, dim])
# Per-channel min and max.
min_x = tf.reduce_min(x, axis=0)
max_x = tf.reduce_max(x, axis=0)
max_value = tf.cast(encode_params[self.MAX_INT_VALUE_PARAMS_KEY], x.dtype)
# Shift the values to range [0, max_value].
# In the case of min_x == max_x, this will return all zeros.
x = tf.div_no_nan(x - min_x, max_x - min_x) * max_value
if self._stochastic: # Randomized rounding.
floored_x = tf.floor(x)
bernoulli = tf.random_uniform(tf.shape(x), dtype=x.dtype)
bernoulli = bernoulli < (x - floored_x)
quantized_x = floored_x + tf.cast(bernoulli, x.dtype)
else: # Deterministic rounding.
quantized_x = tf.round(x)
encoded_tensors = {
self.ENCODED_VALUES_KEY: quantized_x,
self.MIN_MAX_VALUES_KEY: tf.stack([min_x, max_x])
}
return encoded_tensors
def masked_softmax_cross_entropy_with_logit(y_true, y_pred):
"""
Masks elements that is not equal to -1 in y_true and
averages alive-elements.
Sample weight and the standard mask of layers should not be enabled.
If they work averaging will be done twice time.
Standard mask system of Kreras does not seem to work correctly on TPU
So this loss is a temporary measure.
"""
if len(y_true.shape)+1 != len(y_pred.shape):
y_true = tf.squeeze(y_true, axis=[-1])
mask = tf.not_equal(y_true, -1)
safe_y_true = tf.where(mask, y_true, tf.zeros_like(y_true))
safe_y_true = tf.cast(safe_y_true, dtype=tf.int32)
cross_entropy = tf.nn.sparse_softmax_cross_entropy_with_logits(
labels=safe_y_true,
logits=y_pred,
)
mask = tf.cast(mask, tf.float32)
sum_cross_entropy = tf.reduce_sum(cross_entropy*mask)
sum_mask = tf.reduce_sum(mask)
averaged_loss = tf.div_no_nan(sum_cross_entropy, sum_mask)
return averaged_loss
def height_normal_consistency_loss(depth, normal, mask3,
consistency_loss_factor: float,
imgSize: int, max_outputs: int):
near = uncompressDepth(1)
far = uncompressDepth(0)
d = uncompressDepth(depth)
h = tf.div_no_nan(d - near, far - near)
sobel = tf.image.sobel_edges(
h) # b,h,w,1,[dy,dx] - 1 because height has 1 channel
dx = sobel[:, :, :, :, 1] # b,h,w,1
dy = -sobel[:, :, :, :, 0]
# We're using a depth map instead of a height. Which means bright
# values are at a greater depth. Thus, we need to invert the gradient
texelSize = 1 / imgSize
dz = tf.ones_like(dx) * texelSize * 2
cn = tf.nn.l2_normalize(tf.concat([dx, dy, dz], axis=-1), axis=-1)
cn = cn * 0.5 + 0.5
cl = masked_loss(l1_loss(cn, normal), mask3)
clr = tf.reduce_mean(cl, name="consistency_loss") * consistency_loss_factor
add_moving_summary(clr)
tf.losses.add_loss(clr, tf.GraphKeys.LOSSES)
repeat = [1 for _ in range(len(depth.shape))]
repeat[-1] = 3
tbutil.four_side_by_side(tf.tile(depth, repeat), cn, normal, cl,
"consistency", max_outputs)
def __call__(self, tensors: Dict[str, tf.Tensor]) -> Dict[str, Tuple]:
# Retrieve tensors
logits = tensors[self.logits] # (batch, num_classes)
targets = tensors[self.targets] # (batch, ..., num_targets)
ndims = len(targets.shape) - 1
# Set logits of inputs to -inf
if self.inputs is not None:
inputs = tensors[self.inputs] # (batch, num_classes)
logits = logits + tf.cast(inputs, tf.float32) * tf.float32.min
# Retrieve top k predictions, shape = (batch, k)
_, indices = tf.math.top_k(logits, k=self.k, sorted=True)
# shape = (batch, ..., 1, k)
for _ in range(ndims):
indices = tf.expand_dims(indices, axis=-2)
# shape = (batch, ..., num_targets, k)
equal_topk = tf.equal(tf.cast(indices, tf.int64), tf.expand_dims(targets, axis=-1))
# Compute number of items in top k
num_in_topk = tf.reduce_sum(tf.reduce_sum(tf.cast(equal_topk, tf.int64), axis=-1), axis=-1)
num_targets = tf.reduce_sum(tf.cast(tf.not_equal(targets, -1), tf.int64), axis=-1)
num_targets = tf.math.minimum(num_targets, self.k)
recall_at_k = tf.div_no_nan(tf.cast(num_in_topk, tf.float32), tf.cast(num_targets, tf.float32))
return {self.name: tf.metrics.mean(recall_at_k)}
def reduce_mean_masked(input_tensor,
is_valid,
axis=None,
keepdims=False,
try_fast=True):
"""Compute the mean of elements across dimensions of a tensor, ignoring elements if
the corresponding element in `mask` is False.
In general, `K = dim(mask) <= dim(input_tensor) = L`, and `mask`'s shape must match
the first K dimensions of `tensor`'s shape. Then `input_tensor[i1,...,iK,...iL]` is
ignored iff `mask[i1,...,iK]` is False.
"""
if try_fast:
return tf.cond(
tf.reduce_all(is_valid),
lambda: tf.reduce_mean(input_tensor, axis=axis, keepdims=keepdims),
lambda: reduce_mean_masked(
input_tensor, is_valid, axis, keepdims, try_fast=False))
if axis is None and not keepdims:
return tf.reduce_mean(tf.boolean_mask(input_tensor, is_valid))
n_new_dims = input_tensor.get_shape().ndims - is_valid.get_shape().ndims
is_valid = expand_dims(is_valid, [-1] * n_new_dims)
is_valid = broadcast_like(is_valid, input_tensor)
replaced = tf.where(is_valid, input_tensor, tf.zeros_like(input_tensor))
sum_valid = tf.reduce_sum(replaced, axis=axis, keepdims=keepdims)
n_valid = tf.count_nonzero(is_valid,
axis=axis,
keepdims=keepdims,
dtype=input_tensor.dtype)
return tf.div_no_nan(sum_valid, n_valid)
def forward(self, tensors, mode: str = None):
"""Forward method of the layer
Parameters
----------
tensors : Tuple[tf.Tensor]
- positives : shape = (batch, num_events)
- negatives : shape = (batch, num_events, num_negatives)
- mask : shape = (batch, num_events, num_negatives)
- weights : shape = (batch, num_events)
Returns
-------
tf.Tensor
Negative Sampling loss
"""
positives, negatives, mask, weights = tensors
true_losses = tf.nn.sigmoid_cross_entropy_with_logits(
labels=tf.ones_like(positives), logits=positives)
sampled_losses = tf.nn.sigmoid_cross_entropy_with_logits(
labels=tf.zeros_like(negatives), logits=negatives)
event_scores = true_losses + WeightedAverage()(
(sampled_losses, tf.to_float(mask)))
event_weights = weights * tf.to_float(tf.reduce_any(mask, axis=-1))
return tf.div_no_nan(tf.reduce_sum(event_scores * event_weights),
tf.reduce_sum(event_weights))
def encode(self, x, encode_params):
"""See base class."""
if self.MIN_MAX_VALUES_KEY in encode_params:
min_max = tf.cast(encode_params[self.MIN_MAX_VALUES_KEY], x.dtype)
min_x, max_x = min_max[0], min_max[1]
x = tf.clip_by_value(x, min_x, max_x)
else:
min_x = tf.reduce_min(x)
max_x = tf.reduce_max(x)
max_value = tf.cast(encode_params[self.MAX_INT_VALUE_PARAMS_KEY],
x.dtype)
# Shift the values to range [0, max_value].
# In the case of min_x == max_x, this will return all zeros.
x = tf.div_no_nan(x - min_x, max_x - min_x) * max_value
if self._stochastic: # Randomized rounding.
floored_x = tf.floor(x)
bernoulli = tf.random_uniform(tf.shape(x), dtype=x.dtype)
bernoulli = bernoulli < (x - floored_x)
quantized_x = floored_x + tf.cast(bernoulli, x.dtype)
else: # Deterministic rounding.
quantized_x = tf.round(x)
encoded_tensors = {self.ENCODED_VALUES_KEY: quantized_x}
if self.MIN_MAX_VALUES_KEY not in encode_params:
encoded_tensors[self.MIN_MAX_VALUES_KEY] = tf.stack([min_x, max_x])
return encoded_tensors
def apply_embed_on_doc_id(self):
"""Applies embedding lookup and averaging for doc id features
:return Tensor Shape=[batch_size, max_group_size, num_doc_id_fields, num_units_for_id_ftr]
"""
hparams = self._hparams
doc_ftrs = []
for i, doc_field in enumerate(self._doc_id_fields):
seq_mask = tf.cast(
tf.not_equal(doc_field, hparams.pad_id_for_id_ftr),
dtype=tf.float32) # [batch_size, max_group_size, num_doc_id]
seq_mask = tf.expand_dims(
seq_mask,
axis=-1) # [batch_size, max_group_size, num_doc_id, 1]
seq_length = tf.reduce_sum(
seq_mask,
axis=-2,
) # [batch_size, max_group_size, 1]
doc_id_embeddings = tf.nn.embedding_lookup(
self.embedding,
doc_field,
) # [batch_size, max_group_size, num_doc_id, num_units_for_id_ftr]
sum_doc_id_embedding = tf.reduce_sum(
doc_id_embeddings * seq_mask,
axis=2) # [batch_size, max_group_size, num_units_for_id_ftr]
doc_id_avg_embedding = tf.div_no_nan(
sum_doc_id_embedding, seq_length
) # [batch_size, max_group_size, num_units_for_id_ftr]
doc_ftrs.append(doc_id_avg_embedding)
return tf.stack(doc_ftrs, axis=2)
def spec(
self,
ndl: tf.Tensor,
ndv: tf.Tensor,
ndh: tf.Tensor,
ldh: tf.Tensor,
vdh: tf.Tensor,
F0: tf.Tensor,
roughness: tf.Tensor,
) -> tf.Tensor:
with tf.variable_scope("Specular"):
alpha = saturate(roughness * roughness, 1e-3)
F = self.F(F0, ldh)
G = self.G(alpha, ndl, ndv)
D = self.D(alpha, ndh)
ret = tf.div_no_nan(F * G * D, 4.0 * ndl)
ret = tf.where(tf.math.less(self._to_vec3(ndh), EPS),
tf.zeros_like(ret), ret)
ret = tf.where(tf.math.less(self._to_vec3(ldh * ndl), EPS),
tf.zeros_like(ret), ret)
ret = tf.where(tf.math.less(self._to_vec3(vdh * ndv), EPS),
tf.zeros_like(ret), ret)
return ret
def divide_no_nan(self, x, y):
if version.parse(tf.__version__) >= version.parse('1.11.0'):
return tf.div_no_nan(x, y)
else:
result = x / y
return tf.where(tf.is_finite(result), result,
tf.zeros_like(result))
def forward(self, tensors, mode: str = None):
"""Forward method of the layer"""
values, weights = tensors
# Values and weights need to have the same shape up to axis
# and compatible after axis
axis = len(weights.shape) - 1
weights = tf.broadcast_to(
weights,
tf.maximum(tf.shape(weights),
tf.shape(values)[:len(weights.shape)]))
values, weights = make_same_shape([values, weights], broadcast=False)
# Reduce weighted values and weights
weighted_values = tf.reduce_sum(values * weights, axis=axis)
sum_weights = tf.reduce_sum(weights, axis=axis)
# Average values and weights, take care of all weights zeros
if self.default is None:
return weighted_values / sum_weights
elif self.default == 0:
weighted_average = tf.div_no_nan(weighted_values, sum_weights)
else:
weighted_average = tf.where(
tf.equal(sum_weights, 0),
self.default * tf.ones_like(weighted_values),
weighted_values / sum_weights)
return weighted_average
def D(self, alpha: tf.Tensor, ndh: tf.Tensor) -> tf.Tensor:
with tf.variable_scope("Distribution"):
a2 = alpha * alpha
denom = (ndh * ndh) * (a2 - 1) + 1.0
denom2 = denom * denom
return tf.div_no_nan(a2, np.pi * denom2)
def uncompressDepth(d: tf.Tensor,
sigma: float = 2.5,
epsilon: float = 0.7) -> tf.Tensor:
"""From 0-1 values to full depth range. The possible depth range
is modelled by sigma and epsilon and with sigma=2.5 and epsilon=0.7
it is between 0.17 and 1.4.
"""
return tf.div_no_nan(1.0, 2.0 * sigma * d + epsilon)
def bbox_iou_circle(self, boxes1, boxes2):
boxes1_area = boxes1[..., 2] * boxes1[..., 3]
boxes2_area = boxes2[..., 2] * boxes2[..., 3]
# boxes [...,0:2] x0,y0; [...,2:4] x1,y1
boxes1 = tf.concat([boxes1[..., :2] - boxes1[..., 2:] * 0.5,
boxes1[..., :2] + boxes1[..., 2:] * 0.5], axis=-1)
boxes2 = tf.concat([boxes2[..., :2] - boxes2[..., 2:] * 0.5,
boxes2[..., :2] + boxes2[..., 2:] * 0.5], axis=-1)
# constant pi / 4
C = tf.constant(math.pi/4.)
# three cases: pred enclose GT; GT enclose pred; neither
pred_enc_GT_mask = tf.cast(boxes1[...,0]<boxes2[...,0], tf.float32) *\
tf.cast(boxes1[...,1]<boxes2[...,1], tf.float32) *\
tf.cast(boxes1[...,2]>boxes2[...,2], tf.float32) *\
tf.cast(boxes1[...,3]>boxes2[...,3], tf.float32)
GT_enc_pred_mask = tf.cast(boxes1[...,0]>boxes2[...,0], tf.float32) *\
tf.cast(boxes1[...,1]>boxes2[...,1], tf.float32) *\
tf.cast(boxes1[...,2]<boxes2[...,2], tf.float32) *\
tf.cast(boxes1[...,3]<boxes2[...,3], tf.float32)
part_intersect_mask = 1.0 - GT_enc_pred_mask - pred_enc_GT_mask
left_up = tf.maximum(boxes1[..., :2], boxes2[..., :2])
right_down = tf.minimum(boxes1[..., 2:], boxes2[..., 2:])
inter_section = tf.maximum(right_down - left_up, 0.0)
inter_area = inter_section[..., 0] * inter_section[..., 1]
union_area = boxes1_area + boxes2_area - inter_area
# case 1 IOU:
pred_enc_GT_iou = pred_enc_GT_mask * tf.div_no_nan(inter_area, C * union_area)
# case 2 IOU:
GT_enc_pred_iou = GT_enc_pred_mask * tf.div_no_nan(C * inter_area, union_area)
# case 3 IOU
part_intersect_iou = part_intersect_mask * tf.div_no_nan(C * inter_area, \
(C * boxes1_area + boxes2_area - C * inter_area))
#iou = 1.0 * tf.div_no_nan(inter_area, union_area)
iou_circle = pred_enc_GT_iou + GT_enc_pred_iou + part_intersect_iou
return iou_circle
def loss(self, y_true, y_pred):
ndims = len(y_pred.get_shape().as_list()) - 2
vol_axes = list(range(1, ndims+1))
top = 2 * tf.reduce_sum(y_true * y_pred, vol_axes)
bottom = tf.reduce_sum(y_true + y_pred, vol_axes)
dice = tf.reduce_mean(tf.div_no_nan(top, bottom))
return -dice
def __call__(self) -> Image:
declare_eager_execution()
if self.emap is None:
self.generate_emap()
if self.atten_corr is not None:
listmode_ = self.atten_corr(self.listmode)
else:
listmode_ = self.listmode
x_tf = Image(data=tf.Variable(
np.ones(self.image_config.shape, dtype=np.float32)),
center=self.image_config.center,
size=self.image_config.size)
emap_data_n0_zero = copy(self.emap.data)
emap_data_n0_zero[emap_data_n0_zero == 0.0] = 1e8
emap_tf = self.emap.update(data=tf.constant(emap_data_n0_zero))
lors_tf = self.listmode.lors.update(
data=tf.constant(self.listmode.lors.data))
listmode_tf = self.listmode.update(data=tf.constant(listmode_.data),
lors=lors_tf)
for _ in tqdm(range(self.n_iter)):
_listmode_tf = Project('tf-eager')(x_tf, lors_tf)
listmode_div = tf.div_no_nan(listmode_tf.data, _listmode_tf.data)
_bp = BackProject('tf-eager')(
listmode_tf.update(data=listmode_div), emap_tf)
x_tf = x_tf * _bp / emap_tf
x = x_tf.update(data=x_tf.data.numpy())
# if self.scatter_corr is not None:
# if self.atten_corr is not None:
# listmode_ = self.scatter_corr(x, self.atten_corr.u_map, self.scanner, self.listmode)
# x_tf = Image(data = tf.Variable(np.ones(self.image_config.shape, dtype = np.float32)),
# center = self.image_config.center,
# size = self.image_config.size)
# emap_data_n0_zero = copy(self.emap.data)
# emap_data_n0_zero[emap_data_n0_zero == 0.0] = 1e8
# emap_tf = self.emap.update(data = tf.constant(emap_data_n0_zero))
# lors_tf = self.listmode.lors.update(data = tf.constant(self.listmode.lors.data))
# listmode_tf = self.listmode.update(data = tf.constant(listmode_.data), lors = lors_tf)
# for _ in tqdm(range(self.n_iter)):
# _listmode_tf = Project('tf-eager')(x_tf, lors_tf)
# listmode_div = tf.div_no_nan(listmode_tf.data, _listmode_tf.data)
# _bp = BackProject('tf-eager')(listmode_tf.update(data = listmode_div), emap_tf)
# x_tf = x_tf * _bp / emap_tf
# x = x_tf.update(data = x_tf.data.numpy())
if self.psf_corr is not None:
image_ = self.psf_corr(x)
else:
image_ = x
return image_
def nonzero_reduce_mean(emb): # nonzero-mean-pooling
axis_2_sum = tf.reduce_sum(emb, axis=2)
multi_cate_nonzero = tf.count_nonzero(axis_2_sum,
1,
keepdims=True,
dtype=float)
multi_cate_sum = tf.reduce_sum(emb, axis=1)
reduce_mean_emb = tf.div_no_nan(multi_cate_sum, multi_cate_nonzero)
return reduce_mean_emb
def batch_semi_hard(labels, embeddings):
"""Computes the triplet loss with semi-hard negative mining.
The loss encourages the positive distances (between a pair of embeddings with
the same labels) to be smaller than the minimum negative distance among
which are at least greater than the positive distance plus the margin constant
(called semi-hard negative) in the mini-batch. If no such negative exists,
uses the largest negative distance instead.
See: https://arxiv.org/abs/1503.03832.
:param labels: 1-D tf.int32 `Tensor` with shape [batch_size] of multiclass integer labels.
:param embeddings: 2-D float `Tensor` of embedding vectors. Embeddings should be l2 normalized.
:return loss: tf.float32 scalar.
"""
labels = tf.reshape(labels, [-1, 1])
batch_size = tf.size(labels)
# Build pairwise squared distance matrix.
dist = euclidean_distance(embeddings, squared=True)
# Build pairwise binary adjacency matrix (equal label mask).
adjacency = tf.equal(labels, tf.transpose(labels))
# Invert so we can select negatives only.
adjacency_not = tf.logical_not(adjacency)
# Compute the mask.
dist_tile = tf.tile(
dist,
[batch_size, 1]) # stack dist matrix batch_size times, axis=0
mask = tf.logical_and(tf.tile(adjacency_not, [batch_size, 1]),
tf.greater(dist_tile, tf.reshape(dist, [-1, 1])))
mask = tf.cast(mask, dtype=tf.float32)
is_negatives_outside = tf.reshape(
tf.greater(tf.reduce_sum(mask, axis=1, keepdims=True), 0.0),
[batch_size, batch_size])
is_negatives_outside = tf.transpose(is_negatives_outside)
# negatives_outside: smallest D_an where D_an > D_ap.
negatives_outside = tf.reshape(masked_minimum(dist_tile, mask),
[batch_size, batch_size])
negatives_outside = tf.transpose(negatives_outside)
# negatives_inside: largest D_an.
adjacency_not = tf.cast(adjacency_not, dtype=tf.float32)
negatives_inside = tf.tile(masked_maximum(dist, adjacency_not),
[1, batch_size])
semi_hard_negatives = tf.where(is_negatives_outside, negatives_outside,
negatives_inside)
# In lifted-struct, the authors multiply 0.5 for upper triangular
# in semihard, they take all positive pairs except the diagonal.
mask_positives = tf.cast(adjacency, dtype=tf.float32) - tf.diag(
tf.ones([batch_size]))
n_positives = tf.reduce_sum(mask_positives)
loss_mat = get_loss_tensor(dist, semi_hard_negatives)
loss = tf.div_no_nan(
tf.reduce_sum(tf.multiply(loss_mat, mask_positives)), n_positives)
return loss