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ValueError: Dimensions must be equal, but are 2 and 3799 for 'softmax_cross_entropy_with_logits_sg

I am developing a neural network model for classifying benign and malware apks.
I have tried using tf.squeeze() function but after using it I am unable to use optimizer
def neural_network_model(data):
l1 = tf.add(tf.matmul(data,hidden_1_layer['weight']), hidden_1_layer['bias'])
l1 = tf.nn.relu(l1)
l2 = tf.add(tf.matmul(l1,hidden_2_layer['weight']), hidden_2_layer['bias'])
l2 = tf.nn.relu(l2)
l3 = tf.add(tf.matmul(l2,hidden_3_layer['weight']), hidden_3_layer['bias'])
l3 = tf.nn.relu(l3)
output = tf.matmul(l3,output_layer['weight']) + output_layer['bias']
return output
def train_neural_network(x):
prediction = neural_network_model(x)
cost = tf.reduce_mean( tf.nn.softmax_cross_entropy_with_logits(logits=prediction, labels= y) )
optimizer = tf.train.AdamOptimizer(learning_rate=0.001).minimize(cost)
The shape of pred and y must be same however by running the code I am having different shape of pred is (3799,2) whereas the shape of y is (1,3799).

My remarks:
If your labels aren't one-hot encoded you can use tf.nn.sparse_softmax_cross_entropy_with_logits() without converting it to the one-hot encoded representation. Otherwise, tf.nn.softmax_cross_entropy_with_logits() accepts only one-hot encoded labels.
You can't pass numpy values as inputs to the loss function (or as inputs to anything except for feed_dict in session.run()) if you're writing code in a graph mode. Use placeholders instead.
Following is the example to illustrate how to use placeholders and feed numpy arrays of data.
import numpy as np
import tensorflow as tf
# Dummy data with 3 classes for illustration
n_classes =3
x_train = np.random.normal(size=(3799, 2)) # 3799 samples of size (2, ) each
y_train = np.random.randint(low=0, high=n_classes, size=(1, 3799))
# Define placeholders here
x = tf.placeholder(tf.float32, shape=(None, 2))
y = tf.placeholder(tf.int32, shape=(1, None))
# Define your network here
w = tf.Variable(tf.random_normal(shape=[2, n_classes]), dtype=tf.float32)
b = tf.Variable(tf.zeros([n_classes, ]), dtype=tf.float32)
logits = tf.matmul(x, w) + b
labels = tf.squeeze(y)
xentropy = tf.nn.sparse_softmax_cross_entropy_with_logits(logits=logits,
labels=labels)
cost = tf.reduce_mean(xentropy)
train_op = tf.train.AdamOptimizer(learning_rate=0.001).minimize(cost)
# Training
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
cost_val = sess.run(cost, feed_dict={x:x_train, y:y_train})
print(cost_val) # 1.8630761
sess.run(train_op, feed_dict={x:x_train, y:y_train}) # optimizer step
cost_val = sess.run(cost, feed_dict={x:x_train, y:y_train})
print(cost_val) # 1.8619089

Python - Low accuracy with low loss with tensorflow

I'm building a simple neural network that takes 3 values and gives 2 outputs.
I'm getting an accuracy of 67.5% and an average cost of 0.05
I have a training dataset of 1000 examples and 500 testing examples. I plan on making a larger dataset in the near future.
A little while ago I managed to get an accuracy of about 82% and sometimes a bit higher, but the cost was quite high.
I've been experimenting with adding another layer which is currently in the model and that is the reason I have got the loss under 1.0
I'm not sure what is going wrong, I'm new to Tensorflow and NNs in general.
Here is my code:
import tensorflow as tf
import numpy as np
import sys
sys.path.insert(0, '.../Dataset/Testing/')
sys.path.insert(0, '.../Dataset/Training/')
#other files
from TestDataNormaliser import *
from TrainDataNormaliser import *
learning_rate = 0.01
trainingIteration = 10
batchSize = 100
displayStep = 1
x = tf.placeholder("float", [None, 3])
y = tf.placeholder("float", [None, 2])
#layer 1
w1 = tf.Variable(tf.truncated_normal([3, 4], stddev=0.1))
b1 = tf.Variable(tf.zeros([4]))
y1 = tf.matmul(x, w1) + b1
#layer 2
w2 = tf.Variable(tf.truncated_normal([4, 4], stddev=0.1))
b2 = tf.Variable(tf.zeros([4]))
#y2 = tf.nn.sigmoid(tf.matmul(y1, w2) + b2)
y2 = tf.matmul(y1, w2) + b2
w3 = tf.Variable(tf.truncated_normal([4, 2], stddev=0.1))
b3 = tf.Variable(tf.zeros([2]))
y3 = tf.nn.sigmoid(tf.matmul(y2, w3) + b3) #sigmoid
#output
#wO = tf.Variable(tf.truncated_normal([2, 2], stddev=0.1))
#bO = tf.Variable(tf.zeros([2]))
a = y3 #tf.nn.softmax(tf.matmul(y2, wO) + bO) #y2
a_ = tf.placeholder("float", [None, 2])
#cost function
cross_entropy = tf.reduce_mean(-tf.reduce_sum(y * tf.log(a)))
#cross_entropy = -tf.reduce_sum(y*tf.log(a))
optimizer = tf.train.GradientDescentOptimizer(learning_rate).minimize(cross_entropy)
#training
init = tf.global_variables_initializer() #initialises tensorflow
with tf.Session() as sess:
sess.run(init) #runs the initialiser
writer = tf.summary.FileWriter(".../Logs")
writer.add_graph(sess.graph)
merged_summary = tf.summary.merge_all()
for iteration in range(trainingIteration):
avg_cost = 0
totalBatch = int(len(trainArrayValues)/batchSize) #1000/100
#totalBatch = 10
for i in range(batchSize):
start = i
end = i + batchSize #100
xBatch = trainArrayValues[start:end]
yBatch = trainArrayLabels[start:end]
#feeding training data
sess.run(optimizer, feed_dict={x: xBatch, y: yBatch})
i += batchSize
avg_cost += sess.run(cross_entropy, feed_dict={x: xBatch, y: yBatch})/totalBatch
if iteration % displayStep == 0:
print("Iteration:", '%04d' % (iteration + 1), "cost=", "{:.9f}".format(avg_cost))
#
print("Training complete")
predictions = tf.equal(tf.argmax(a, 1), tf.argmax(y, 1))
accuracy = tf.reduce_mean(tf.cast(predictions, "float"))
print("Accuracy:", accuracy.eval({x: testArrayValues, y: testArrayLabels}))

A few important notes:
You don't have non-linearities between your layers. This means you're training a network which is equivalent to a single-layer network, just with a lot of wasted computation. This is easily solved by adding a simple non-linearity, e.g. tf.nn.relu after each matmul/+ bias line, e.g. y2 = tf.nn.relu(y2) for all bar the last layer.
You are using a numerically unstable cross entropy implementation. I'd encourage you to use tf.nn.sigmoid_cross_entropy_with_logits, and removing your explicit sigmoid call (the input to your sigmoid function is what is generally referred to as the logits, or 'logistic units').
It seems you are not shuffling your dataset as you go. This could be particularly bad given your choice of optimizer, which leads us to...
Stochastic gradient descent is not great. For a boost without adding too much complication, consider using MomentumOptimizer instead. AdamOptimizer is my go-to, but play around with them.
When it comes to writing clean, maintainable code, I'd also encourage you to consider the following:
Use higher level APIs, e.g. tf.layers. It's good you know what's going on at a variable level, but it's easy to make a mistake with all that replicated code, and the default values with the layer implementations are generally pretty good
Consider using the tf.data.Dataset API for your data input. It's a bit scary at first, but it handles a lot of things like batching, shuffling, repeating epochs etc. very nicely
Consider using something like the tf.estimator.Estimator API for handling session runs, summary writing and evaluation.
With all those changes, you might have something that looks like the following (I've left your code in so you can roughly see the equivalent lines).
For graph construction:
def get_logits(features):
"""tf.layers API is cleaner and has better default values."""
# #layer 1
# w1 = tf.Variable(tf.truncated_normal([3, 4], stddev=0.1))
# b1 = tf.Variable(tf.zeros([4]))
# y1 = tf.matmul(x, w1) + b1
x = tf.layers.dense(features, 4, activation=tf.nn.relu)
# #layer 2
# w2 = tf.Variable(tf.truncated_normal([4, 4], stddev=0.1))
# b2 = tf.Variable(tf.zeros([4]))
# y2 = tf.matmul(y1, w2) + b2
x = tf.layers.dense(x, 4, activation=tf.nn.relu)
# w3 = tf.Variable(tf.truncated_normal([4, 2], stddev=0.1))
# b3 = tf.Variable(tf.zeros([2]))
# y3 = tf.nn.sigmoid(tf.matmul(y2, w3) + b3) #sigmoid
# N.B Don't take a non-linearity here.
logits = tf.layers.dense(x, 1, actiation=None)
# remove unnecessary final dimension, batch_size * 1 -> batch_size
logits = tf.squeeze(logits, axis=-1)
return logits
def get_loss(logits, labels):
"""tf.nn.sigmoid_cross_entropy_with_logits is numerically stable."""
# #cost function
# cross_entropy = tf.reduce_mean(-tf.reduce_sum(y * tf.log(a)))
return tf.nn.sigmoid_cross_entropy_with_logits(
logits=logits, labels=labels)
def get_train_op(loss):
"""There are better options than standard SGD. Try the following."""
learning_rate = 1e-3
# optimizer = tf.train.GradientDescentOptimizer(learning_rate)
optimizer = tf.train.MomentumOptimizer(learning_rate)
# optimizer = tf.train.AdamOptimizer(learning_rate)
return optimizer.minimize(loss)
def get_inputs(feature_data, label_data, batch_size, n_epochs=None,
shuffle=True):
"""
Get features and labels for training/evaluation.
Args:
feature_data: numpy array of feature data.
label_data: numpy array of label data
batch_size: size of batch to be returned
n_epochs: number of epochs to train for. None will result in repeating
forever/until stopped
shuffle: bool flag indicating whether or not to shuffle.
"""
dataset = tf.data.Dataset.from_tensor_slices(
(feature_data, label_data))
dataset = dataset.repeat(n_epochs)
if shuffle:
dataset = dataset.shuffle(len(feature_data))
dataset = dataset.batch(batch_size)
features, labels = dataset.make_one_shot_iterator().get_next()
return features, labels
For session running you could use this like you have (what I'd call 'the hard way')...
features, labels = get_inputs(
trainArrayValues, trainArrayLabels, batchSize, n_epochs, shuffle=True)
logits = get_logits(features)
loss = get_loss(logits, labels)
train_op = get_train_op(loss)
init = tf.global_variables_initializer()
# monitored sessions have the `should_stop` method, which works with datasets
with tf.train.MonitoredSession() as sess:
sess.run(init)
while not sess.should_stop():
# get both loss and optimizer step in the same session run
loss_val, _ = sess.run([loss, train_op])
print(loss_val)
# save variables etc, do evaluation in another graph with different inputs?
but I think you're better off using a tf.estimator.Estimator, though some people prefer tf.keras.Models.
def model_fn(features, labels, mode):
logits = get_logits(features)
loss = get_loss(logits, labels)
train_op = get_train_op(loss)
predictions = tf.greater(logits, 0)
accuracy = tf.metrics.accuracy(labels, predictions)
return tf.estimator.EstimatorSpec(
mode=mode, loss=loss, train_op=train_op,
eval_metric_ops={'accuracy': accuracy}, predictions=predictions)
def train_input_fn():
return get_inputs(trainArrayValues, trainArrayLabels, batchSize)
def eval_input_fn():
return get_inputs(
testArrayValues, testArrayLabels, batchSize, n_epochs=1, shuffle=False)
# Where variables and summaries will be saved to
model_dir = './model'
estimator = tf.estimator.Estimator(model_fn, model_dir)
estimator.train(train_input_fn, max_steps=max_steps)
estimator.evaluate(eval_input_fn)
Note if you use estimators the variables will be saved after training, so you won't need to re-train each time. If you want to reset, just delete the model_dir.

I see that you are using a softmax loss with sigmoidal activation functions in the last layer. Now let me explain the difference between softmax activations and sigmoidal.
You are now allowing the output of the network to be y=(0, 1), y=(1, 0), y=(0, 0) and y=(1, 1). This is because your sigmoidal activations "squish" each element in y between 0 and 1. Your loss function, however, assumes that your y vector sums to one.
What you need to do here is either to penalise the sigmoidal cross entropy function, which looks like this:
-tf.reduce_sum(y*tf.log(a))-tf.reduce_sum((1-y)*tf.log(1-a))
Or, if you want a to sum to one, you need to use softmax activations in your final layer (to get your a's) instead of sigmoids, which is implemented like this
exp_out = tf.exp(y3)
a = exp_out/tf reduce_sum(exp_out)
Ps. I'm using my phone on a train so please excuse typos

Generating MNIST numbers using LSTM-CGAN in TensorFlow

Inspired by this article, I'm trying to build a Conditional GAN which will use LSTM to generate MNIST numbers. I hope I'm using the same architecture as in the image below (except for the bidirectional RNN in discriminator, taken from this paper):
When I run this model, I've got very strange results. This image shows my model generating number 3 after each epoch. It should look more like this. It's really bad.
Loss of my discriminator network decreasing really fast up to close to zero. However, the loss of my generator network oscillates around some fixed point (maybe diverging slowly). I really don't know what's happening. Here is the most important part of my code (full code here):
timesteps = 28
X_dim = 28
Z_dim = 100
y_dim = 10
X = tf.placeholder(tf.float32, [None, timesteps, X_dim]) # reshaped MNIST image to 28x28
y = tf.placeholder(tf.float32, [None, y_dim]) # one-hot label
Z = tf.placeholder(tf.float32, [None, timesteps, Z_dim]) # numpy.random.uniform noise in range [-1; 1]
y_timesteps = tf.tile(tf.expand_dims(y, axis=1), [1, timesteps, 1]) # [None, timesteps, y_dim] - replicate y along axis=1
def discriminator(x, y):
with tf.variable_scope('discriminator', reuse=tf.AUTO_REUSE) as vs:
inputs = tf.concat([x, y], axis=2)
D_cell = tf.contrib.rnn.LSTMCell(64)
output, _ = tf.nn.dynamic_rnn(D_cell, inputs, dtype=tf.float32)
last_output = output[:, -1, :]
logit = tf.contrib.layers.fully_connected(last_output, 1, activation_fn=None)
pred = tf.nn.sigmoid(logit)
variables = [v for v in tf.all_variables() if v.name.startswith(vs.name)]
return variables, pred, logit
def generator(z, y):
with tf.variable_scope('generator', reuse=tf.AUTO_REUSE) as vs:
inputs = tf.concat([z, y], axis=2)
G_cell = tf.contrib.rnn.LSTMCell(64)
output, _ = tf.nn.dynamic_rnn(G_cell, inputs, dtype=tf.float32)
logit = tf.contrib.layers.fully_connected(output, X_dim, activation_fn=None)
pred = tf.nn.sigmoid(logit)
variables = [v for v in tf.all_variables() if v.name.startswith(vs.name)]
return variables, pred
G_vars, G_sample = run_generator(Z, y_timesteps)
D_vars, D_real, D_logit_real = run_discriminator(X, y_timesteps)
_, D_fake, D_logit_fake = run_discriminator(G_sample, y_timesteps)
D_loss = -tf.reduce_mean(tf.log(D_real) + tf.log(1. - D_fake))
G_loss = -tf.reduce_mean(tf.log(D_fake))
D_solver = tf.train.AdamOptimizer().minimize(D_loss, var_list=D_vars)
G_solver = tf.train.AdamOptimizer().minimize(G_loss, var_list=G_vars)
There is most likely something wrong with my model. Anyone could help me make the generator network converge?

There are a few things you can do to improve your network architecture and training phase.
Remove the tf.nn.sigmoid(logit) from both the generator and discriminator. Return just the pred.
Use a numerically stable function to calculate your loss functions and fix the loss functions:
D_loss = -tf.reduce_mean(tf.log(D_real) + tf.log(1. - D_fake))
G_loss = -tf.reduce_mean(tf.log(D_fake))
should be:
D_loss_real = tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_real,
labels=tf.ones_like(D_real))
D_loss_fake = tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_fake,
labels=tf.zeros_like(D_fake))
D_loss = -tf.reduce_mean(D_loss_real + D_loss_fake)
G_loss = -tf.reduce_mean(tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_real,
labels=tf.ones_like(D_real)))
Once you fixed the loss and used a numerically stable function, things will go better. Also, as a rule of thumb, if there's too much noise in the loss, reduce the learning rate (the default lr of ADAM is usually too high when training GANs).
Hope it helps

How to use an autoencoder to visualize dimensionality reduction? (Python | TensorFlow)

I'm trying to adapt Aymeric Damien's code to visualize the dimensionality reduction performed by an autoencoder implemented in TensorFlow. All of the examples I have seen work on the mnist digits dataset but I wanted to use this method to visualize the iris dataset in 2 dimensions as a toy example so I can figure out how to tweak it for my real-world datasets.
My question is: How can one get the sample-specific 2 dimensional embeddings to visualize?
For example, the iris dataset has 150 samples with 4 attributes. I added 4 noise attributes to get a total of 8 attributes. The encoding/decoding follows: [8, 4, 2, 4, 8] but I'm not sure how to extract an array of shape (150, 2) to visualize the embeddings. I haven't found any tutorials on how to visualize the dimensionality reduction using TensorFlow.
from sklearn.datasets import load_iris
from sklearn.decomposition import PCA
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
%matplotlib inline
# Set random seeds
np.random.seed(0)
tf.set_random_seed(0)
# Load data
iris = load_iris()
# Original Iris : (150,4)
X_iris = iris.data
# Iris with noise : (150,8)
X_iris_with_noise = np.concatenate([X_iris, np.random.random(size=X_iris.shape)], axis=1).astype(np.float32)
y_iris = iris.target
# PCA
pca_xy = PCA(n_components=2).fit_transform(X_iris_with_noise)
with plt.style.context("seaborn-white"):
fig, ax = plt.subplots()
ax.scatter(pca_xy[:,0], pca_xy[:,1], c=y_iris, cmap=plt.cm.Set2)
ax.set_title("PCA | Iris with noise")
# Training Parameters
learning_rate = 0.01
num_steps = 1000
batch_size = 10
display_step = 250
examples_to_show = 10
# Network Parameters
num_hidden_1 = 4 # 1st layer num features
num_hidden_2 = 2 # 2nd layer num features (the latent dim)
num_input = 8 # Iris data input
# tf Graph input
X = tf.placeholder(tf.float32, [None, num_input], name="input")
weights = {
'encoder_h1': tf.Variable(tf.random_normal([num_input, num_hidden_1]), dtype=tf.float32, name="encoder_h1"),
'encoder_h2': tf.Variable(tf.random_normal([num_hidden_1, num_hidden_2]), dtype=tf.float32, name="encoder_h2"),
'decoder_h1': tf.Variable(tf.random_normal([num_hidden_2, num_hidden_1]), dtype=tf.float32, name="decoder_h1"),
'decoder_h2': tf.Variable(tf.random_normal([num_hidden_1, num_input]), dtype=tf.float32, name="decoder_h2"),
}
biases = {
'encoder_b1': tf.Variable(tf.random_normal([num_hidden_1]), dtype=tf.float32, name="encoder_b1"),
'encoder_b2': tf.Variable(tf.random_normal([num_hidden_2]), dtype=tf.float32, name="encoder_b2"),
'decoder_b1': tf.Variable(tf.random_normal([num_hidden_1]), dtype=tf.float32, name="decoder_b1"),
'decoder_b2': tf.Variable(tf.random_normal([num_input]), dtype=tf.float32, name="decoder_b2"),
}
# Building the encoder
def encoder(x):
# Encoder Hidden layer with sigmoid activation #1
layer_1 = tf.nn.sigmoid(tf.add(tf.matmul(x, weights['encoder_h1']),
biases['encoder_b1']))
# Encoder Hidden layer with sigmoid activation #2
layer_2 = tf.nn.sigmoid(tf.add(tf.matmul(layer_1, weights['encoder_h2']),
biases['encoder_b2']))
return layer_2
# Building the decoder
def decoder(x):
# Decoder Hidden layer with sigmoid activation #1
layer_1 = tf.nn.sigmoid(tf.add(tf.matmul(x, weights['decoder_h1']),
biases['decoder_b1']))
# Decoder Hidden layer with sigmoid activation #2
layer_2 = tf.nn.sigmoid(tf.add(tf.matmul(layer_1, weights['decoder_h2']),
biases['decoder_b2']))
return layer_2
# Construct model
encoder_op = encoder(X)
decoder_op = decoder(encoder_op)
# Prediction
y_pred = decoder_op
# Targets (Labels) are the input data.
y_true = X
# Define loss and optimizer, minimize the squared error
loss = tf.reduce_mean(tf.pow(y_true - y_pred, 2))
optimizer = tf.train.RMSPropOptimizer(learning_rate).minimize(loss)
# Initialize the variables (i.e. assign their default value)
init = tf.global_variables_initializer()
# Start Training
# Start a new TF session
with tf.Session() as sess:
# Run the initializer
sess.run(init)
# Training
for i in range(1, num_steps+1):
# Prepare Data
# Get the next batch of Iris data
idx_train = np.random.RandomState(i).choice(np.arange(X_iris_with_noise.shape[0]), size=batch_size)
batch_x = X_iris_with_noise[idx_train,:]
# Run optimization op (backprop) and cost op (to get loss value)
_, l = sess.run([optimizer, loss], feed_dict={X: batch_x})
# Display logs per step
if i % display_step == 0 or i == 1:
print('Step %i: Minibatch Loss: %f' % (i, l))

Your embedding is accessible with h = encoder(X). Then, for each batch you can get the value as follow:
_, l, embedding = sess.run([optimizer, loss, h], feed_dict={X: batch_x})
There is an even nicer solution with TensorBoard using Embeddings Visualization (https://www.tensorflow.org/programmers_guide/embedding):
from tensorflow.contrib.tensorboard.plugins import projector
config = projector.ProjectorConfig()
embedding = config.embeddings.add()
embedding.tensor_name = h.name
# Use the same LOG_DIR where you stored your checkpoint.
summary_writer = tf.summary.FileWriter(LOG_DIR)
projector.visualize_embeddings(summary_writer, config)

How to test tensorflow cifar10 cnn tutorial model

I am relatively new to machine-learning and currently have almost no experiencing in developing it.
So my Question is: after training and evaluating the cifar10 dataset from the tensorflow tutorial I was wondering how could one test it with sample images?
I could train and evaluate the Imagenet tutorial from the caffe machine-learning framework and it was relatively easy to use the trained model on custom applications using the python API.
Any help would be very appreciated!

This isn't 100% the answer to the question, but it's a similar way of solving it, based on a MNIST NN training example suggested in the comments to the question.
Based on the TensorFlow begginer MNIST tutorial, and thanks to this tutorial, this is a way of training and using your Neural Network with custom data.
Please note that similar should be done for tutorials such as the CIFAR10, as #Yaroslav Bulatov mentioned in the comments.
import input_data
import datetime
import numpy as np
import tensorflow as tf
import cv2
from matplotlib import pyplot as plt
import matplotlib.image as mpimg
from random import randint
mnist = input_data.read_data_sets("MNIST_data/", one_hot=True)
x = tf.placeholder("float", [None, 784])
W = tf.Variable(tf.zeros([784,10]))
b = tf.Variable(tf.zeros([10]))
y = tf.nn.softmax(tf.matmul(x,W) + b)
y_ = tf.placeholder("float", [None,10])
cross_entropy = -tf.reduce_sum(y_*tf.log(y))
train_step = tf.train.GradientDescentOptimizer(0.01).minimize(cross_entropy)
init = tf.initialize_all_variables()
sess = tf.Session()
sess.run(init)
#Train our model
iter = 1000
for i in range(iter):
batch_xs, batch_ys = mnist.train.next_batch(100)
sess.run(train_step, feed_dict={x: batch_xs, y_: batch_ys})
#Evaluationg our model:
correct_prediction=tf.equal(tf.argmax(y,1), tf.argmax(y_,1))
accuracy=tf.reduce_mean(tf.cast(correct_prediction,"float"))
print "Accuracy: ", sess.run(accuracy, feed_dict={x: mnist.test.images, y_: mnist.test.labels})
#1: Using our model to classify a random MNIST image from the original test set:
num = randint(0, mnist.test.images.shape[0])
img = mnist.test.images[num]
classification = sess.run(tf.argmax(y, 1), feed_dict={x: [img]})
'''
#Uncomment this part if you want to plot the classified image.
plt.imshow(img.reshape(28, 28), cmap=plt.cm.binary)
plt.show()
'''
print 'Neural Network predicted', classification[0]
print 'Real label is:', np.argmax(mnist.test.labels[num])
#2: Using our model to classify MNIST digit from a custom image:
# create an an array where we can store 1 picture
images = np.zeros((1,784))
# and the correct values
correct_vals = np.zeros((1,10))
# read the image
gray = cv2.imread("my_digit.png", 0 ) #0=cv2.CV_LOAD_IMAGE_GRAYSCALE #must be .png!
# rescale it
gray = cv2.resize(255-gray, (28, 28))
# save the processed images
cv2.imwrite("my_grayscale_digit.png", gray)
"""
all images in the training set have an range from 0-1
and not from 0-255 so we divide our flatten images
(a one dimensional vector with our 784 pixels)
to use the same 0-1 based range
"""
flatten = gray.flatten() / 255.0
"""
we need to store the flatten image and generate
the correct_vals array
correct_val for a digit (9) would be
[0,0,0,0,0,0,0,0,0,1]
"""
images[0] = flatten
my_classification = sess.run(tf.argmax(y, 1), feed_dict={x: [images[0]]})
"""
we want to run the prediction and the accuracy function
using our generated arrays (images and correct_vals)
"""
print 'Neural Network predicted', my_classification[0], "for your digit"
For further image conditioning (digits should be completely dark in a white background) and better NN training (accuracy>91%) please check the Advanced MNIST tutorial from TensorFlow or the 2nd tutorial i've mentioned.

The below example is not for the mnist tutorial, but a simple XOR example. Note the train() and test() methods. All that we declare & keep globally are the weights, biases, and session. In the test method we redefine the shape of the input and reuse the same weights & biases (and session) that we refined in training.
import tensorflow as tf
#parameters for the net
w1 = tf.Variable(tf.random_uniform(shape=[2,2], minval=-1, maxval=1, name='weights1'))
w2 = tf.Variable(tf.random_uniform(shape=[2,1], minval=-1, maxval=1, name='weights2'))
#biases
b1 = tf.Variable(tf.zeros([2]), name='bias1')
b2 = tf.Variable(tf.zeros([1]), name='bias2')
#tensorflow session
sess = tf.Session()
def train():
#placeholders for the traning inputs (4 inputs with 2 features each) and outputs (4 outputs which have a value of 0 or 1)
x = tf.placeholder(tf.float32, [4, 2], name='x-inputs')
y = tf.placeholder(tf.float32, [4, 1], name='y-inputs')
#set up the model calculations
temp = tf.sigmoid(tf.matmul(x, w1) + b1)
output = tf.sigmoid(tf.matmul(temp, w2) + b2)
#cost function is avg error over training samples
cost = tf.reduce_mean(((y * tf.log(output)) + ((1 - y) * tf.log(1.0 - output))) * -1)
#training step is gradient descent
train_step = tf.train.GradientDescentOptimizer(learning_rate=0.01).minimize(cost)
#declare training data
training_x = [[0,1], [0,0], [1,0], [1,1]]
training_y = [[1], [0], [1], [0]]
#init session
init = tf.initialize_all_variables()
sess.run(init)
#training
for i in range(100000):
sess.run(train_step, feed_dict={x:training_x, y:training_y})
if i % 1000 == 0:
print (i, sess.run(cost, feed_dict={x:training_x, y:training_y}))
print '\ntraining done\n'
def test(inputs):
#redefine the shape of the input to a single unit with 2 features
xtest = tf.placeholder(tf.float32, [1, 2], name='x-inputs')
#redefine the model in terms of that new input shape
temp = tf.sigmoid(tf.matmul(xtest, w1) + b1)
output = tf.sigmoid(tf.matmul(temp, w2) + b2)
print (inputs, sess.run(output, feed_dict={xtest:[inputs]})[0, 0] >= 0.5)
train()
test([0,1])
test([0,0])
test([1,1])
test([1,0])

I recommend taking a look at the basic MNIST tutorial on the TensorFlow website. It looks like you define some function that generates the type of output that you want, and then run your session, passing it this evaluation function (correct_prediction below), and a dictionary containing whatever arguments you require (x and y_ below).
If you have defined and trained some network that takes an input x, generates a response y based on your inputs, and you know your expected responses for your testing set y_, you may be able to print out every response to your testing set with something like:
correct_prediction = tf.equal(y, y_) % Check whether your prediction is correct
print(sess.run(correct_prediction, feed_dict={x: test_images, y_: test_labels}))
This is just a modification of what is done in the tutorial, where instead of trying to print each response, they determine the percent of correct responses. Also note that the tutorial uses one-hot vectors for the prediction y and actual value y_, so in order to return the associated numeral, they have to find which index of these vectors are equal to one with tf.argmax(y, 1).
Edit
In general, if you define something in your graph, you can output it later when you run your graph. Say you define something that determines the result of the softmax function on your output logits as:
graph = tf.Graph()
with graph.as_default():
...
prediction = tf.nn.softmax(logits)
...
then you can output this at run time with:
with tf.Session(graph=graph) as sess:
...
feed_dict = { ... } # define your feed dictionary
pred = sess.run([prediction], feed_dict=feed_dict)
# do stuff with your prediction vector