Why is the batch size None in the method call of a Keras layer? - tensorflow

I am implementing a custom layer in Keras. If I print the shape of the input passed to the call method, I get None as the first element. Why is that? Shouldn't the first element be the batch size?
def call(self, x):
print(x.shape) # (None, ...)
When I call model.fit, I am passing the batch size
batch_size = 50
model.fit(x_train, y_train, ..., batch_size=batch_size)
So, when is the method call actually called? And what is the recommended way of getting the batch size in the method call?

None means it is a dynamic shape. It can take any value depending on the batch size you choose.
When you define a model by default it is defined to support any batch size you can choose. This is what the None means. In TensorFlow 1.* the input to your model is an instance of tf.placeholder().
If you don't use the keras.InputLayer() with specified batch size you get the first dimension None by default:
import tensorflow as tf
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.Dense(units=2, input_shape=(2, )))
print(model.inputs[0].get_shape().as_list()) # [None, 2]
print(model.inputs[0].op.type == 'Placeholder') # True
When you do use keras.InputLayer() with specified batch size you can define the input placeholder with fixed batch size:
import tensorflow as tf
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.InputLayer((2,), batch_size=50))
model.add(tf.keras.layers.Dense(units=2, input_shape=(2, )))
print(model.inputs[0].get_shape().as_list()) # [50, 2]
print(model.inputs[0].op.type == 'Placeholder') # True
When you specify the batch size to the model.fit() method these input placeholders have already been defined and you cannot modify their shape. The batch size for model.fit() is used only to split the data you provided to batches.
If you define your input layer with batch size 2 and then you pass different value of a batch size to the model.fit() method you will get ValueError:
import tensorflow as tf
import numpy as np
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.InputLayer((2,), batch_size=2)) # <--batch_size==2
model.add(tf.keras.layers.Dense(units=2, input_shape=(2, )))
model.compile(optimizer=tf.keras.optimizers.Adam(),
loss='categorical_crossentropy')
x_train = np.random.normal(size=(10, 2))
y_train = np.array([[0, 1] for _ in range(10)])
model.fit(x_train, y_train, batch_size=3) # <--batch_size==3
This will raise:
ValueError: Thebatch_sizeargument value 3 is incompatible with the specified batch size of your Input Layer: 2

I faced the same issue and found that using tf.shape(your_variable) instead of your_variable.shape solved the problem. As tf.shape(your_variable) is dynamically evaluated later when the fit function is called.
reference
https://github.com/tensorflow/tensorflow/issues/36991#issuecomment-590448880
To get the value in integers consider output_shape variable.
Minimum working example
import tensorflow as tf
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.InputLayer((2,), batch_size=50))
model.add(tf.keras.layers.Dense(units=2, input_shape=(2, )))
print(model.output_shape)
print(type(model.output_shape[0]), type(model.output_shape[1]))
Output:
(50, 2)
<class 'int'> <class 'int'>

Related

"The Conv2D op currently only supports the NHWC tensor format on the CPU" Error despite NHWC Format (YOLO 3)

I am trying to get to run a bit of sample code from github in order to learn Working with Tensorflow 2 and the YOLO Framework. My Laptop has a M1000M Graphics Card and I installed the CUDA Platform from NVIDIA from here.
So the Code in question is this bit:
tf.compat.v1.disable_eager_execution()
_MODEL_SIZE = (416, 416)
_CLASS_NAMES_FILE = './data/labels/coco.names'
_MAX_OUTPUT_SIZE = 20
def main(type, iou_threshold, confidence_threshold, input_names):
class_names = load_class_names(_CLASS_NAMES_FILE)
n_classes = len(class_names)
model = Yolo_v3(n_classes=n_classes, model_size=_MODEL_SIZE,
max_output_size=_MAX_OUTPUT_SIZE,
iou_threshold=iou_threshold,
confidence_threshold=confidence_threshold)
if type == 'images':
batch_size = len(input_names)
batch = load_images(input_names, model_size=_MODEL_SIZE)
inputs = tf.compat.v1.placeholder(tf.float32, [batch_size, *_MODEL_SIZE, 3])
detections = model(inputs, training=False)
saver = tf.compat.v1.train.Saver(tf.compat.v1.global_variables(scope='yolo_v3_model'))
with tf.compat.v1.Session() as sess:
saver.restore(sess, './weights/model.ckpt')
detection_result = sess.run(detections, feed_dict={inputs: batch})
draw_boxes(input_names, detection_result, class_names, _MODEL_SIZE)
print('Detections have been saved successfully.')
While executing this (also wondering why starting the detection.py doesnt use GPU in the first place), I get the Error Message:
File "C:\SDKs etc\Python 3.8\lib\site-packages\tensorflow\python\client\session.py", line 1451, in _call_tf_sessionrun
return tf_session.TF_SessionRun_wrapper(self._session, options, feed_dict,
tensorflow.python.framework.errors_impl.UnimplementedError: The Conv2D op currently only supports the NHWC tensor format on the CPU. The op was given the format: NCHW
[[{{node yolo_v3_model/conv2d/Conv2D}}]]
Full Log see here.
If I am understanding this correctly, the format of inputs = tf.compat.v1.placeholder(tf.float32, [batch_size, *_MODEL_SIZE, 3]) is already NHWC (Model Size is a tuple of 2 Numbers) and I don't know how I need to change things in Code to get this running on CPU.
If I am understanding this correctly, the format of inputs =
tf.compat.v1.placeholder(tf.float32, [batch_size, *_MODEL_SIZE, 3]) is
already NHWC (Model Size is a tuple of 2 Numbers) and I don't know how
I need to change things in Code to get this running on CPU.
Yes you are. But look here:
def __init__(self, n_classes, model_size, max_output_size, iou_threshold,
confidence_threshold, data_format=None):
"""Creates the model.
Args:
n_classes: Number of class labels.
model_size: The input size of the model.
max_output_size: Max number of boxes to be selected for each class.
iou_threshold: Threshold for the IOU.
confidence_threshold: Threshold for the confidence score.
data_format: The input format.
Returns:
None.
"""
if not data_format:
if tf.test.is_built_with_cuda():
data_format = 'channels_first'
else:
data_format = 'channels_last'
And later:
def __call__(self, inputs, training):
"""Add operations to detect boxes for a batch of input images.
Args:
inputs: A Tensor representing a batch of input images.
training: A boolean, whether to use in training or inference mode.
Returns:
A list containing class-to-boxes dictionaries
for each sample in the batch.
"""
with tf.compat.v1.variable_scope('yolo_v3_model'):
if self.data_format == 'channels_first':
inputs = tf.transpose(inputs, [0, 3, 1, 2])
Solution:
check tf.test.is_built_with_cuda() work as expected
if not - set order manually when create model:
model = Yolo_v3(n_classes=n_classes, model_size=_MODEL_SIZE,
max_output_size=_MAX_OUTPUT_SIZE,
iou_threshold=iou_threshold,
confidence_threshold=confidence_threshold,
data_format = 'channels_last')

how to initialize a Variable tensor for the weight matrix in a keras model?

I am trying to use tensors variables to use as weights in a keras layer..
I know that I can use numpy arrays instead but the reason I want to feed tensors is that I want my weight matrices to be of the type SparseTensor.
This is a small example that I have coded so far:
def model_keras(seed, new_hidden_size_list=None):
number_of_layers = 1
hidden_size = 512
hidden_size_list = [hidden_size] * number_of_layers
input_size = 784
output_size = 10
if new_hidden_size_list is not None:
hidden_size_list = new_hidden_size_list
weight_input = tf.Variable(tf.random.normal([784, 512], mean=0.0, stddev=1.0))
bias_input = tf.Variable(tf.random.normal([512], mean=0.0, stddev=1.0))
weight_output = tf.Variable(tf.random.normal([512, 10], mean=0.0, stddev=1.0))
# This gives me an error when trying to use in kernel_initializer and bias_initializer in the keras model
weight_initializer_input = tf.initializers.variables([weight_input])
bias_initializer_input = tf.initializers.variables([bias_input])
weight_initializer_output = tf.initializers.variables([weight_output])
# This works fine
#weight_initializer_input = tf.initializers.lecun_uniform(seed=None)
#bias_initializer_input = tf.initializers.lecun_uniform(seed=None)
#weight_initializer_output = tf.initializers.lecun_uniform(seed=None)
print(weight_initializer_input, bias_initializer_input, weight_initializer_output)
model = keras.models.Sequential()
for index in range(number_of_layers):
if index == 0:
# input layer
model.add(keras.layers.Dense(hidden_size_list[index], activation=nn.selu, use_bias=True,
kernel_initializer=weight_initializer_input,
bias_initializer=bias_initializer_input,
input_shape=(input_size,)))
else:
model.add(keras.layers.Dense(hidden_size_list[index], activation=nn.selu, use_bias=True,
kernel_initializer=weight_initializer_hidden,
bias_initializer=bias_initializer_hidden))
# output layer
model.add(keras.layers.Dense(output_size, use_bias=False, kernel_initializer=weight_initializer_output))
model.add(keras.layers.Activation(nn.softmax))
return model
I am using tensorflow 1.15.
Any idea how one can use custom (user defined) Tensor Variables as initializer instead of pre-set schemes (e.g. Glorot, Truncated Normal etc). Another approach that I could take is to explicitly define the computations instead of using the keras.Layer.
Many thanks
Your code works after enabling eager execution.
import tensorflow as tf
tf.compat.v1.enable_eager_execution()
Add this at the top of you file.
See this for working code.

Unable to save model with tensorflow 2.0.0 beta1

I have tried all the options described in the documentation but none of them allowed me to save my model in tensorflow 2.0.0 beta1. I've also tried to upgrade to the (also unstable) TF2-RC but that ruined even the code I had working in beta so I quickly rolled back for now to beta.
See a minimal reproduction code below.
What I have tried:
model.save("mymodel.h5")
NotImplementedError: Saving the model to HDF5 format requires the
model to be a Functional model or a Sequential model. It does not work
for subclassed models, because such models are defined via the body of
a Python method, which isn't safely serializable. Consider saving to
the Tensorflow SavedModel format (by setting save_format="tf") or
using save_weights.
model.save("mymodel", format='tf')
ValueError: Model <main.CVAE object at 0x7f1cac2e7c50> cannot be
saved because the input shapes have not been set. Usually, input
shapes are automatically determined from calling .fit() or .predict().
To manually set the shapes, call model._set_inputs(inputs).
3.
model._set_input(input_sample)
model.save("mymodel", format='tf')
AssertionError: tf.saved_model.save is not supported inside a traced
#tf.function. Move the call to the outer eagerly-executed context.
And this is where I am stuck now because it gives me no reasonable hint whatsoever. That's because I am NOT calling the save() function from a #tf.function, I'm already calling it from the outermost scope possible. In fact, I have no #tf.function at all in this minimal reproduction script below and still getting the same error.
So I really have no idea how to save my model, I've tried every options and they all throw errors and provide no hints.
The minimal reproduction example below works fine if you set save_model=False and it reproduces the error when save_model=True.
It may seem unnecessary in this simplified auto-encoder code example to use a subclassed model but I have lots of custom functions added to it in my original VAE code that I need it for.
Code:
import tensorflow as tf
save_model = True
learning_rate = 1e-4
BATCH_SIZE = 100
TEST_BATCH_SIZE = 10
color_channels = 1
imsize = 28
(train_images, _), (test_images, _) = tf.keras.datasets.mnist.load_data()
train_images = train_images[:5000, ::]
test_images = train_images[:1000, ::]
train_images = train_images.reshape(-1, imsize, imsize, 1).astype('float32')
test_images = test_images.reshape(-1, imsize, imsize, 1).astype('float32')
train_images /= 255.
test_images /= 255.
train_dataset = tf.data.Dataset.from_tensor_slices(train_images).batch(BATCH_SIZE)
test_dataset = tf.data.Dataset.from_tensor_slices(test_images).batch(TEST_BATCH_SIZE)
class AE(tf.keras.Model):
def __init__(self):
super(AE, self).__init__()
self.network = tf.keras.Sequential([
tf.keras.layers.InputLayer(input_shape=(imsize, imsize, color_channels)),
tf.keras.layers.Flatten(),
tf.keras.layers.Dense(50),
tf.keras.layers.Dense(imsize**2 * color_channels),
tf.keras.layers.Reshape(target_shape=(imsize, imsize, color_channels)),
])
def decode(self, input):
logits = self.network(input)
return logits
optimizer = tf.keras.optimizers.Adam(learning_rate)
model = AE()
def compute_loss(data):
logits = model.decode(data)
loss = tf.reduce_mean(tf.losses.mean_squared_error(logits, data))
return loss
def train_step(data):
with tf.GradientTape() as tape:
loss = compute_loss(data)
gradients = tape.gradient(loss, model.trainable_variables)
optimizer.apply_gradients(zip(gradients, model.trainable_variables))
return loss, 0
def test_step(data):
loss = compute_loss(data)
return loss
input_shape_set = False
epoch = 0
epochs = 20
for epoch in range(epochs):
for train_x in train_dataset:
train_step(train_x)
if epoch % 1 == 0:
loss = 0.0
num_batches = 0
for test_x in test_dataset:
loss += test_step(test_x)
num_batches += 1
loss /= num_batches
print("Epoch: {}, Loss: {}".format(epoch, loss))
if save_model:
print("Saving model...")
if not input_shape_set:
# Note: Why set input shape manually and why here:
# 1. If I do not set input shape manually: ValueError: Model <main.CVAE object at 0x7f1cac2e7c50> cannot be saved because the input shapes have not been set. Usually, input shapes are automatically determined from calling .fit() or .predict(). To manually set the shapes, call model._set_inputs(inputs).
# 2. If I set input shape manually BEFORE the first actual train step, I get: RuntimeError: Attempting to capture an EagerTensor without building a function.
model._set_inputs(train_dataset.__iter__().next())
input_shape_set = True
# Note: Why choose tf format: model.save('MNIST/Models/model.h5') will return NotImplementedError: Saving the model to HDF5 format requires the model to be a Functional model or a Sequential model. It does not work for subclassed models, because such models are defined via the body of a Python method, which isn't safely serializable. Consider saving to the Tensorflow SavedModel format (by setting save_format="tf") or using save_weights.
model.save('MNIST/Models/model', save_format='tf')
I have tried the same minimal reproduction example in tensorflow-gpu 2.0.0-rc0 and the error was more revealing than what the beta version gave me. The error in RC says:
NotImplementedError: When subclassing the Model class, you should
implement a call method.
This got me read through https://www.tensorflow.org/beta/guide/keras/custom_layers_and_models where I found examples of how to do subclassing in TF2 in a way that allows saving. I was able to resolve the error and have the model saved by replacing my 'decode' method by 'call' in the above example (although this will be more complicated with my actual code where I had various methods defined for the class). This solved the error both in beta and in rc. Strangely, the training (or the saving) got also much faster in rc.
You should change two things:
Change the decode method to call, as you pointed out
As your model is of type Sequential, and not built inside the class, you want to call the save method on the self.network attribute of the model, i.e.,
model.network.save('mymodel.h5')
alternatively, to keep things more standard, you can implement this method inside the AE class, as follows:
def save(self, save_dir):
self.network.save(save_dir)
Cheers mate

How to get layer activation on batch during training

I'm using Keras (with tensorflow backend) and trying to get layers output(actual activation) on my training set during train time (using 'fit' function)
Is there any way to get the activations of last batch used for training as part of the on_batch_end Callback? or any other way to be able to access layers output?
I found this code below but it runs a forward pass again on a new data. I'm trying to utilize the fact that my network already did a forward pass as part of the training on batch itself and just pull the current activations, is that posible?
def get_activations(model, model_inputs, print_shape_only=False, layer_name=None):
print('----- activations -----')
activations = []
inp = model.input
model_multi_inputs_cond = True
if not isinstance(inp, list):
# only one input! let's wrap it in a list.
inp = [inp]
model_multi_inputs_cond = False
outputs = [layer.output for layer in model.layers if
layer.name == layer_name or layer_name is None] # all layer outputs
funcs = [K.function(inp + [K.learning_phase()], [out]) for out in outputs] # evaluation functions
if model_multi_inputs_cond:
list_inputs = []
list_inputs.extend(model_inputs)
list_inputs.append(0.)
else:
list_inputs = [model_inputs, 0.]
# Learning phase. 0 = Test mode (no dropout or batch normalization)
# layer_outputs = [func([model_inputs, 0.])[0] for func in funcs]
layer_outputs = [func(list_inputs)[0] for func in funcs]
for layer_activations in layer_outputs:
activations.append(layer_activations)
if print_shape_only:
print(layer_activations.shape)
else:
print(layer_activations)
return activations
You can write a custom Callback to obtain per-layer activations over the epochs. The answer here is helpful for understanding how to build the callback. I have added some lines for accessing the activations.
from keras.callbacks import LambdaCallback
from keras import backend as k
activation_list= []
def save_act(model):
# each object is an output tensor variable for a layer:
output_vars= [layer.output for layer in model.layers]
# get_output backend function for each layer
get_outputs_funcs= [k.function([model.input], [out]) for out in output_vars]
# fit the function for each layer, obtain the actual activations:
layers_acts= [f([X]) for f in get_outputs_funcs]
activation_list.append(layers_acts)
# Save activations for all layers for each epoch:
activations_callback= LambdaCallback(on_epoch_end=lambda epoch, logs: save_act(model))
model.fit(..., callbacks= [activations_callback], ...)
# The dimensionality of the activation object: [epoch][layer][0][input][unit]
# I usually use the mean activations for each hidden layer over the epochs (to visualise and check for signs of saturation):
n_layers= 2; n_epochs =100
layer_sizes= [10,10,10]; input_size= X.shape[0]
act_layers= np.zeros((n_layers, n_epochs))
for ep in range(n_epochs):
for layer in range(n_layers):
layer_outs_wrt_inputs= np.zeros((layer_sizes[layer], input_size))
for i in range(input_size):
perlayer_outs= activation_list[ep][layer][0][i]
layer_outs_wrt_inputs[layer, i]= np.mean(perlayer_outs)
ave_over_inputs= np.mean(layer_outs_wrt_inputs)
act_layers[layer, ep]= ave_over_inputs
acts_L1= act_layers[0]; acts_L2= act_layers[1]
plt.plot(epochs, acts_L1, linestyle= 'dotted', color= 'red', label= 'layer 1')
plt.plot(epochs, acts_L2, linestyle= 'dotted', color= 'blue', label= 'layer 2')
plt.legend()
plt.show()

Create keras callback to save model predictions and targets for each batch during training

I am building a simple Sequential model in Keras (tensorflow backend). During training I want to inspect the individual training batches and model predictions. Therefore, I am trying to create a custom Callback that saves the model predictions and targets for each training batch. However, the model is not using the current batch for prediction, but the entire training data.
How can I hand over only the current training batch to the Callback?
And how can I access the batches and targets that the Callback saves in self.predhis and self.targets?
My current version looks as follows:
callback_list = [prediction_history((self.x_train, self.y_train))]
self.model.fit(self.x_train, self.y_train, batch_size=self.batch_size, epochs=self.n_epochs, validation_data=(self.x_val, self.y_val), callbacks=callback_list)
class prediction_history(keras.callbacks.Callback):
def __init__(self, train_data):
self.train_data = train_data
self.predhis = []
self.targets = []
def on_batch_end(self, epoch, logs={}):
x_train, y_train = self.train_data
self.targets.append(y_train)
prediction = self.model.predict(x_train)
self.predhis.append(prediction)
tf.logging.info("Prediction shape: {}".format(prediction.shape))
tf.logging.info("Targets shape: {}".format(y_train.shape))
NOTE: this answer is outdated and only works with TF1. Check #bers's answer for a solution tested on TF2.
After model compilation, the placeholder tensor for y_true is in model.targets and y_pred is in model.outputs.
To save the values of these placeholders at each batch, you can:
First copy the values of these tensors into variables.
Evaluate these variables in on_batch_end, and store the resulting arrays.
Now step 1 is a bit involved because you'll have to add an tf.assign op to the training function model.train_function. Using current Keras API, this can be done by providing a fetches argument to K.function() when the training function is constructed.
In model._make_train_function(), there's a line:
self.train_function = K.function(inputs,
[self.total_loss] + self.metrics_tensors,
updates=updates,
name='train_function',
**self._function_kwargs)
The fetches argument containing the tf.assign ops can be provided via model._function_kwargs (only works after Keras 2.1.0).
As an example:
from keras.layers import Dense
from keras.models import Sequential
from keras.callbacks import Callback
from keras import backend as K
import tensorflow as tf
import numpy as np
class CollectOutputAndTarget(Callback):
def __init__(self):
super(CollectOutputAndTarget, self).__init__()
self.targets = [] # collect y_true batches
self.outputs = [] # collect y_pred batches
# the shape of these 2 variables will change according to batch shape
# to handle the "last batch", specify `validate_shape=False`
self.var_y_true = tf.Variable(0., validate_shape=False)
self.var_y_pred = tf.Variable(0., validate_shape=False)
def on_batch_end(self, batch, logs=None):
# evaluate the variables and save them into lists
self.targets.append(K.eval(self.var_y_true))
self.outputs.append(K.eval(self.var_y_pred))
# build a simple model
# have to compile first for model.targets and model.outputs to be prepared
model = Sequential([Dense(5, input_shape=(10,))])
model.compile(loss='mse', optimizer='adam')
# initialize the variables and the `tf.assign` ops
cbk = CollectOutputAndTarget()
fetches = [tf.assign(cbk.var_y_true, model.targets[0], validate_shape=False),
tf.assign(cbk.var_y_pred, model.outputs[0], validate_shape=False)]
model._function_kwargs = {'fetches': fetches} # use `model._function_kwargs` if using `Model` instead of `Sequential`
# fit the model and check results
X = np.random.rand(10, 10)
Y = np.random.rand(10, 5)
model.fit(X, Y, batch_size=8, callbacks=[cbk])
Unless the number of samples can be divided by the batch size, the final batch will have a different size than other batches. So K.variable() and K.update() can't be used in this case. You'll have to use tf.Variable(..., validate_shape=False) and tf.assign(..., validate_shape=False) instead.
To verify the correctness of the saved arrays, you can add one line in training.py to print out the shuffled index array:
if shuffle == 'batch':
index_array = _batch_shuffle(index_array, batch_size)
elif shuffle:
np.random.shuffle(index_array)
print('Index array:', repr(index_array)) # Add this line
batches = _make_batches(num_train_samples, batch_size)
The shuffled index array should be printed out during fitting:
Epoch 1/1
Index array: array([8, 9, 3, 5, 4, 7, 1, 0, 6, 2])
10/10 [==============================] - 0s 23ms/step - loss: 0.5670
And you can check if cbk.targets is the same as Y[index_array]:
index_array = np.array([8, 9, 3, 5, 4, 7, 1, 0, 6, 2])
print(Y[index_array])
[[ 0.75325592 0.64857277 0.1926653 0.7642865 0.38901153]
[ 0.77567689 0.13573623 0.4902501 0.42897559 0.55825652]
[ 0.33760938 0.68195038 0.12303088 0.83509441 0.20991668]
[ 0.98367778 0.61325065 0.28973401 0.28734073 0.93399794]
[ 0.26097574 0.88219054 0.87951941 0.64887846 0.41996446]
[ 0.97794604 0.91307569 0.93816428 0.2125808 0.94381495]
[ 0.74813435 0.08036688 0.38094272 0.83178364 0.16713736]
[ 0.52609421 0.39218962 0.21022047 0.58569125 0.08012982]
[ 0.61276627 0.20679494 0.24124858 0.01262245 0.0994412 ]
[ 0.6026137 0.25620512 0.7398164 0.52558182 0.09955769]]
print(cbk.targets)
[array([[ 0.7532559 , 0.64857274, 0.19266529, 0.76428652, 0.38901153],
[ 0.77567691, 0.13573623, 0.49025011, 0.42897558, 0.55825651],
[ 0.33760938, 0.68195039, 0.12303089, 0.83509439, 0.20991668],
[ 0.9836778 , 0.61325067, 0.28973401, 0.28734073, 0.93399793],
[ 0.26097575, 0.88219053, 0.8795194 , 0.64887846, 0.41996446],
[ 0.97794604, 0.91307569, 0.93816429, 0.2125808 , 0.94381493],
[ 0.74813437, 0.08036689, 0.38094273, 0.83178365, 0.16713737],
[ 0.5260942 , 0.39218962, 0.21022047, 0.58569127, 0.08012982]], dtype=float32),
array([[ 0.61276627, 0.20679495, 0.24124858, 0.01262245, 0.0994412 ],
[ 0.60261369, 0.25620511, 0.73981643, 0.52558184, 0.09955769]], dtype=float32)]
As you can see, there are two batches in cbk.targets (one "full batch" of size 8 and the final batch of size 2), and the row order is the same as Y[index_array].
Long edit (almost a new answer) for the following reasons:
Yu-Yang's 2017 answer relies on the private _make_train_function and _function_kwargs APIs, which work only in TF1 (and maybe in TF1 compatibility, so-called non-eager mode).
Similarly, Binyan Hu's 2020 answer relies on _make_test_function and does not work in TF2 by default (requiring non-eager mode as well).
My own Jan 2020 answer, which was already subject to several required configuration settings, seems to have stopped working with (or before) TF 2.5, and I was not able to make model.inputs or model.outputs work any longer.
Finally, the earlier version of this answer requires potentially expensive model evaluation to obtain the predictions for each batch. A similar solution to obtain activation histograms even led to OOM issues with repeated training of different models.
So I set out find a way to obtain all possible quantities (inputs, targets, predictions, activations), batch-wise, without using any private APIs. The aim was to be able to call .numpy() on the intended quantities, so Keras callbacks can run ordinary Python code to ease debugging (I suppose that is what this question is mainly about - for maximum performance, one would probably try to integrate as many computations as possible into TensorFlow's graph operations anyway).
This is the common base model for all solutions:
"""Demonstrate batch data access."""
import tensorflow as tf
from tensorflow import keras
class DataCallback(keras.callbacks.Callback):
"""This class is where all implementations differ."""
def tf_nan(dtype):
"""Create NaN variable of proper dtype and variable shape for assign()."""
return tf.Variable(float("nan"), dtype=dtype, shape=tf.TensorShape(None))
def main():
"""Run main."""
model = keras.Sequential([keras.layers.Dense(1, input_shape=(2,))])
callback = DataCallback()
model.compile(loss="mse", optimizer="adam")
model.fit(
x=tf.transpose(tf.range(7.0) + [[0.2], [0.4]]),
y=tf.transpose(tf.range(7.0) + 10 + [[0.5]]),
validation_data=(
tf.transpose(tf.range(11.0) + 30 + [[0.6], [0.7]]),
tf.transpose(tf.range(11.0) + 40 + [[0.9]]),
),
shuffle=False,
batch_size=3,
epochs=2,
verbose=0,
callbacks=[callback],
)
model.save("tmp.tf")
if __name__ == "__main__":
main()
The following three snippets show one possible solution each, each with their own pros and cons. The core trick is always the same: allocate a tf.Variable and use tf.Variable.assign to export the intended quantity, from some Keras code run in graph mode, into the callback. The methods differ slightly in callback initialization and (in one case) model compilation, and most importantly, in the quantities they can access, which is why I summarize them above each snippet.
Custom metric
Using a custom (fake) metric (similar to my Jan 2020 answer), while we cannot seem to access model.inputs nor model.outputs any more (and model.(_)targets does not even exist any longer), we can access y_true and y_pred, which represent the model targets and outputs:
[ ] Inputs/Samples (x)
[ ] Weights (w)
[+] Targets/Labels (y_true)
[+] Outputs/Predictions (y_pred)
[ ] All layers (or only final input/output layers)
"""Demonstrate batch data access using a custom metric."""
import tensorflow as tf
from tensorflow import keras
class DataCallback(keras.callbacks.Callback): # diff
"""Callback to operate on batch data from metric."""
def __init__(self):
"""Offer a metric to access batch data."""
super().__init__()
self.y_true = None
self.y_pred = None
def set_model(self, model):
"""Initialize variables when model is set."""
self.y_true = tf_nan(model.output.dtype)
self.y_pred = tf_nan(model.output.dtype)
def metric(self, y_true, y_pred):
"""Fake metric."""
self.y_true.assign(y_true)
self.y_pred.assign(y_pred)
return 0
def on_train_batch_end(self, _batch, _logs=None):
"""See keras.callbacks.Callback.on_train_batch_end."""
print("y_true =", self.y_true.numpy())
print("y_pred =", self.y_pred.numpy())
def on_train_end(self, _logs=None):
"""Clean up."""
del self.y_true, self.y_pred
def tf_nan(dtype):
"""Create NaN variable of proper dtype and variable shape for assign()."""
return tf.Variable(float("nan"), dtype=dtype, shape=tf.TensorShape(None))
def main():
"""Run main."""
model = keras.Sequential([keras.layers.Dense(1, input_shape=(2,))])
callback = DataCallback()
model.compile(loss="mse", optimizer="adam", metrics=[callback.metric]) # diff
model.fit(
x=tf.transpose(tf.range(7.0) + [[0.2], [0.4]]),
y=tf.transpose(tf.range(7.0) + 10 + [[0.5]]),
validation_data=(
tf.transpose(tf.range(11.0) + 30 + [[0.6], [0.7]]),
tf.transpose(tf.range(11.0) + 40 + [[0.9]]),
),
shuffle=False,
batch_size=3,
epochs=2,
verbose=0,
callbacks=[callback],
)
model.save("tmp.tf")
if __name__ == "__main__":
main()
Custom training step
A custom training step is what I used in an earlier version of this answer. The idea still works in principle, but y_pred can be expensive and it might make sense to use a custom metric (see above) if that is required.
[+] Inputs/Samples (x)
[+] Weights (w)
[+] Targets/Labels (y_true)
[~] Outputs/Predictions (y_pred) [expensive!]
[ ] All layers (or only final input/output layers)
"""Demonstrate batch data access using a custom training step."""
import tensorflow as tf
from tensorflow import keras
class DataCallback(keras.callbacks.Callback): # diff
"""Callback to operate on batch data from training step."""
def __init__(self):
"""Initialize tf.Variables."""
super().__init__()
self.x = None
self.w = None
self.y_true = None
self.y_pred = None
def set_model(self, model):
"""Wrap the model.train_step function to access training batch data."""
self.x = tf_nan(model.input.dtype)
# pylint:disable=protected-access (replace by proper dtype if you know it)
if model.compiled_loss._user_loss_weights is not None:
self.w = tf_nan(model.compiled_loss._user_loss_weights.dtype)
self.y_true = tf_nan(model.output.dtype)
self.y_pred = tf_nan(model.output.dtype)
model_train_step = model.train_step
def outer_train_step(data):
# https://github.com/keras-team/keras/blob/v2.7.0/keras/engine/training.py
x, y_true, w = keras.utils.unpack_x_y_sample_weight(data)
self.x.assign(x)
if w is not None:
self.w.assign(w)
self.y_true.assign(y_true)
result = model_train_step(data)
y_pred = model(x)
self.y_pred.assign(y_pred)
return result
model.train_step = outer_train_step
def on_train_batch_end(self, _batch, _logs=None):
"""See keras.callbacks.Callback.on_train_batch_end."""
print("x =", self.x.numpy())
if self.w is not None:
print("w =", self.w.numpy())
print("y_true =", self.y_true.numpy())
print("y_pred =", self.y_pred.numpy())
def on_train_end(self, _logs=None):
"""Clean up."""
del self.x, self.w, self.y_true, self.y_pred
def tf_nan(dtype):
"""Create NaN variable of proper dtype and variable shape for assign()."""
return tf.Variable(float("nan"), dtype=dtype, shape=tf.TensorShape(None))
def main():
"""Run main."""
model = keras.Sequential([keras.layers.Dense(1, input_shape=(2,))])
callback = DataCallback()
model.compile(loss="mse", optimizer="adam")
model.fit(
x=tf.transpose(tf.range(7.0) + [[0.2], [0.4]]),
y=tf.transpose(tf.range(7.0) + 10 + [[0.5]]),
validation_data=(
tf.transpose(tf.range(11.0) + 30 + [[0.6], [0.7]]),
tf.transpose(tf.range(11.0) + 40 + [[0.9]]),
),
shuffle=False,
batch_size=3,
epochs=2,
verbose=0,
callbacks=[callback],
)
model.save("tmp.tf")
if __name__ == "__main__":
main()
Custom layer call
A custom layer call is a super-flexible way of accessing each layer's inputs and outputs. The callback handles patching of the call functions for a list of layers. While we cannot access weights and targets (as these quantitities do not make sense at the level of individual layers), it allows us to access individual layer activations, which can be handy for questions such as How does one log activations using `tf.keras.callbacks.TensorBoard`?.
[+] Inputs/Samples (x)
[ ] Weights (w)
[ ] Targets/Labels (y_true)
[+] Outputs/Predictions (y_pred)
[+] All layers (or only final input/output layers)
"""Demonstrate batch data access using custom layer calls."""
import tensorflow as tf
from tensorflow import keras
class DataCallback(keras.callbacks.Callback): # diff
"""Callback to operate on batch data from selected (to be wrapped) layers."""
def __init__(self, layers):
"""Wrap the calls of an iterable of model layers to access layer batch data."""
super().__init__()
self.data = {}
self.inner_calls = {}
self.outer_calls = {}
for layer in layers:
self.data[layer] = {
"inputs": tf_nan(layer.input.dtype),
"outputs": tf_nan(layer.output.dtype),
}
self.inner_calls[layer] = layer.call
def outer_call(inputs, layer=layer, layer_call=layer.call):
self.data[layer]["inputs"].assign(inputs)
outputs = layer_call(inputs)
self.data[layer]["outputs"].assign(outputs)
return outputs
self.outer_calls[layer] = outer_call
def on_train_batch_begin(self, _epoch, _logs=None):
"""Wrap layer calls during each batch."""
for layer, call in self.outer_calls.items():
layer.call = call
def on_train_batch_end(self, _epoch, _logs=None):
"""Restore original layer calls for ModelCheckpoint, model.save, ..."""
for layer, call in self.inner_calls.items():
layer.call = call
for layer, data in self.data.items():
print("Layer =", layer)
print("Inputs =", data["inputs"].numpy())
print("Outputs =", data["outputs"].numpy())
def tf_nan(dtype):
"""Create NaN variable of proper dtype and variable shape for assign()."""
return tf.Variable(float("nan"), dtype=dtype, shape=tf.TensorShape(None))
def main():
"""Run main."""
model = keras.Sequential([keras.layers.Dense(1, input_shape=(2,))])
callback = DataCallback(model.layers) # diff
model.compile(loss="mse", optimizer="adam")
model.fit(
x=tf.transpose(tf.range(7.0) + [[0.2], [0.4]]),
y=tf.transpose(tf.range(7.0) + 10 + [[0.5]]),
validation_data=(
tf.transpose(tf.range(11.0) + 30 + [[0.6], [0.7]]),
tf.transpose(tf.range(11.0) + 40 + [[0.9]]),
),
shuffle=False,
batch_size=3,
epochs=2,
verbose=0,
callbacks=[callback],
)
model.save("tmp.tf")
if __name__ == "__main__":
main()
When to use which and open to-dos
I think the snippets above each solution nicely summarize what each approach is capable of. Generally,
a custom training step will be ideal to access the model input, such as batched dataset generators, effects of shuffling, etc;
a custom layer call is ideal to access the in-betweens of the model; and
a custom metric is ideal to access the outputs of the model.
I am fairly certain (but have not tried) that one can combine all approaches to be able to access all batch quantities simultaneously. I have not tested anything but training mode - each method can have further pros and cons relating to their usefulness in testing or prediction mode. Finally, I assume, but have not tested either, that their should be only minor differences between tf.keras and keras. Having tested this code on TF2.8.rc1 and Keras 2.8.0, which has moved the tf.keras code back into the keras pip package, and not using any private APIs, I believe this assumption is justified.
It would be great if this approach could be extended to access model.inputs and model.outputs again. Currently, I am getting errors such as this one:
TypeError: You are passing KerasTensor(...), an intermediate Keras symbolic input/output, to a TF API that does not allow registering custom dispatchers, such as tf.cond, tf.function, gradient tapes, or tf.map_fn. Keras Functional model construction only supports TF API calls that do support dispatching, such as tf.math.add or tf.reshape. Other APIs cannot be called directly on symbolic Kerasinputs/outputs. You can work around this limitation by putting the operation in a custom Keras layer call and calling that layer on this symbolic input/output.
Previous answer
From TF 2.2 on, you can use custom training steps rather than callbacks to achieve what you want. Here's a demo that works with tensorflow==2.2.0rc1, using inheritance to improve the keras.Sequential model. Performance-wise, this is not ideal as predictions are made twice, once in self(x, training=True) and once in super().train_step(data). But you get the idea.
This works in eager mode and does not use private APIs, so it should be pretty stable. One caveat is that you have to use tf.keras (standalone keras does not support Model.train_step), but I feel standalone keras is becoming more and more deprecated anyway. (In fact, tf.keras migrates to keras in TF2.8.)
"""Demonstrate access to Keras batch tensors in a tf.keras custom training step."""
import numpy as np
from tensorflow import keras
from tensorflow.keras import backend as K
from tensorflow.python.keras.engine import data_adapter
in_shape = (2,)
out_shape = (1,)
batch_size = 3
n_samples = 7
class SequentialWithPrint(keras.Sequential):
def train_step(self, original_data):
# Basically copied one-to-one from https://git.io/JvDTv
data = data_adapter.expand_1d(original_data)
x, y_true, w = data_adapter.unpack_x_y_sample_weight(data)
y_pred = self(x, training=True)
# this is pretty much like on_train_batch_begin
K.print_tensor(w, "Sample weight (w) =")
K.print_tensor(x, "Batch input (x) =")
K.print_tensor(y_true, "Batch output (y_true) =")
K.print_tensor(y_pred, "Prediction (y_pred) =")
result = super().train_step(original_data)
# add anything here for on_train_batch_end-like behavior
return result
# Model
model = SequentialWithPrint([keras.layers.Dense(out_shape[0], input_shape=in_shape)])
model.compile(loss="mse", optimizer="adam")
# Example data
X = np.random.rand(n_samples, *in_shape)
Y = np.random.rand(n_samples, *out_shape)
model.fit(X, Y, batch_size=batch_size)
print("X: ", X)
print("Y: ", Y)
Finally, here is a simpler example without inheritance:
"""Demonstrate access to Keras batch tensors in a tf.keras custom training step."""
import tensorflow as tf
IN_SHAPE = (2,)
OUT_SHAPE = (1,)
BATCH_SIZE = 3
N_SAMPLES = 7
def make_print_data_and_train_step(keras_model):
"""Return a train_step function that prints data batches."""
original_train_step = keras_model.train_step
def print_data_and_train_step(data):
# Adapted from https://git.io/JvDTv, skipping data_adapter.expand_1d
x, y_true, w = tf.keras.utils.unpack_x_y_sample_weight(data)
y_pred = keras_model(x, training=True)
# this is pretty much like on_train_batch_begin
tf.keras.backend.print_tensor(w, "Sample weight (w) =")
tf.keras.backend.print_tensor(x, "Batch input (x) =")
tf.keras.backend.print_tensor(y_true, "Batch output (y_true) =")
tf.keras.backend.print_tensor(y_pred, "Prediction (y_pred) =")
result = original_train_step(data)
# add anything here for on_train_batch_end-like behavior
return result
return print_data_and_train_step
# Model
model = tf.keras.Sequential([tf.keras.layers.Dense(OUT_SHAPE[0], input_shape=IN_SHAPE)])
model.train_step = make_print_data_and_train_step(model)
model.compile(loss="mse", optimizer="adam")
# Example data
X = tf.random.normal((N_SAMPLES, *IN_SHAPE))
Y = tf.random.normal((N_SAMPLES, *OUT_SHAPE))
model.fit(X, Y, batch_size=BATCH_SIZE)
print("X: ", X)
print("Y: ", Y)
Update: This approach has stopped working. See my other answer a number of solutions compatible with TF2.8 (and hopefully beyond).
One problem with #Yu-Yang's solution is that it relies on model._function_kwargs, which is not guaranteed to work as it is not part of the API. In particular, in TF2 with eager execution, session kwargs seem to be either not accepted at all or run preemptively due to eager mode.
Therefore, here is my solution tested on tensorflow==2.1.0. The trick is to replace fetches by a Keras metric, in which the assignment operations from fetches are made during training.
This even enables a Keras-only solution if the batch size divides the number of samples; otherwise, another trick has to be applied when initializing TensorFlow variables with a None shape, similar to validate_shape=False in earlier solutions (compare https://github.com/tensorflow/tensorflow/issues/35667).
Importantly, tf.keras behaves differently from keras (sometimes just ignoring assignments, or seeing variables as Keras symbolic tensors), so this updated solution takes care of both implementations (Keras==2.3.1 and tensorflow==2.1.0).
"""Demonstrate access to Keras symbolic tensors in a (tf.)keras.Callback."""
import numpy as np
import tensorflow as tf
use_tf_keras = True
if use_tf_keras:
from tensorflow import keras
from tensorflow.keras import backend as K
tf.config.experimental_run_functions_eagerly(False)
compile_kwargs = {"run_eagerly": False, "experimental_run_tf_function": False}
else:
import keras
from keras import backend as K
compile_kwargs = {}
in_shape = (2,)
out_shape = (1,)
batch_size = 3
n_samples = 7
class CollectKerasSymbolicTensorsCallback(keras.callbacks.Callback):
"""Collect Keras symbolic tensors."""
def __init__(self):
"""Initialize intermediate variables for batches and lists."""
super().__init__()
# Collect batches here
self.inputs = []
self.targets = []
self.outputs = []
# # For a pure Keras solution, we need to know the shapes beforehand;
# # in particular, batch_size must divide n_samples:
# self.input = K.variable(np.empty((batch_size, *in_shape)))
# self.target = K.variable(np.empty((batch_size, *out_shape)))
# self.output = K.variable(np.empty((batch_size, *out_shape)))
# If the shape of these variables will change (e.g., last batch), initialize
# arbitrarily and specify `shape=tf.TensorShape(None)`:
self.input = tf.Variable(0.0, shape=tf.TensorShape(None))
self.target = tf.Variable(0.0, shape=tf.TensorShape(None))
self.output = tf.Variable(0.0, shape=tf.TensorShape(None))
def on_batch_end(self, batch, logs=None):
"""Evaluate the variables and save them into lists."""
self.inputs.append(K.eval(self.input))
self.targets.append(K.eval(self.target))
self.outputs.append(K.eval(self.output))
def on_train_end(self, logs=None):
"""Print all variables."""
print("Inputs: ", *self.inputs)
print("Targets: ", *self.targets)
print("Outputs: ", *self.outputs)
#tf.function
def assign_keras_symbolic_tensors_metric(_foo, _bar):
"""
Return the assignment operations as a metric to have them evaluated by Keras.
This replaces `fetches` from the TF1/non-eager-execution solution.
"""
# Collect assignments as list of (dest, src)
assignments = (
(callback.input, model.inputs[0]),
(callback.target, model._targets[0] if use_tf_keras else model.targets[0]),
(callback.output, model.outputs[0]),
)
for (dest, src) in assignments:
dest.assign(src)
return 0
callback = CollectKerasSymbolicTensorsCallback()
metrics = [assign_keras_symbolic_tensors_metric]
# Example model
model = keras.Sequential([keras.layers.Dense(out_shape[0], input_shape=in_shape)])
model.compile(loss="mse", optimizer="adam", metrics=metrics, **compile_kwargs)
# Example data
X = np.random.rand(n_samples, *in_shape)
Y = np.random.rand(n_samples, *out_shape)
model.fit(X, Y, batch_size=batch_size, callbacks=[callback])
print("X: ", X)
print("Y: ", Y)
Inspired by the way tf.keras.callbacks.TesnsorBoard saves v1 (graph) summaries.
No variable assignments and no redundant metrics.
For use with tensorflow>=2.0.0, graph (disable eager) mode during evaluating.
Extensive operations on the numpy predictions can be implemented by overriding SavePrediction._pred_callback.
import numpy as np
import tensorflow as tf
from tensorflow import keras
tf.compat.v1.disable_eager_execution()
in_shape = (2,)
out_shape = (1,)
batch_size = 2
n_samples = 32
class SavePrediction(keras.callbacks.Callback):
def __init__(self):
super().__init__()
self._get_pred = None
self.preds = []
def _pred_callback(self, preds):
self.preds.append(preds)
def set_model(self, model):
super().set_model(model)
if self._get_pred is None:
self._get_pred = self.model.outputs[0]
def on_test_begin(self, logs):
# pylint: disable=protected-access
self.model._make_test_function()
# pylint: enable=protected-access
if self._get_pred not in self.model.test_function.fetches:
self.model.test_function.fetches.append(self._get_pred)
self.model.test_function.fetch_callbacks[self._get_pred] = self._pred_callback
def on_test_end(self, logs):
if self._get_pred in self.model.test_function.fetches:
self.model.test_function.fetches.remove(self._get_pred)
if self._get_pred in self.model.test_function.fetch_callbacks:
self.model.test_function.fetch_callbacks.pop(self._get_pred)
print(self.preds)
model = keras.Sequential([
keras.layers.Dense(out_shape[0], input_shape=in_shape)
])
model.compile(loss="mse", optimizer="adam")
X = np.random.rand(n_samples, *in_shape)
Y = np.random.rand(n_samples, *out_shape)
model.evaluate(X, Y,
batch_size=batch_size,
callbacks=[SavePrediction()])