python - ValueError: Can not squeeze dim[1], expected a dimension of 1, got 3 for 'sparse_softmax_cross_entropy_loss

Question

I tried to replace the training and validation data with local images. But when running the training code, it came up with the error :

ValueError: Can not squeeze dim[1], expected a dimension of 1, got 3 for 'sparse_softmax_cross_entropy_loss/remove_squeezable_dimensions/Squeeze' (op: 'Squeeze') with input shapes: [100,3].

I don't know how to fix it up. There is no visible variable in the model definition code. The code was modified from TensorFlow tutorial. The images are jpgs.

Here is the detail Error message:

INFO:tensorflow:Using default config.
INFO:tensorflow:Using config: {'_log_step_count_steps': 100, '_is_chief': True, '_model_dir': '/tmp/mnist_convnet_model', '_tf_random_seed': None, '_session_config': None, '_save_checkpoints_secs': 600, '_num_worker_replicas': 1, '_save_checkpoints_steps': None, '_service': None, '_keep_checkpoint_max': 5, '_cluster_spec': <tensorflow.python.training.server_lib.ClusterSpec object at 0x00000288088D50F0>, '_keep_checkpoint_every_n_hours': 10000, '_task_type': 'worker', '_master': '', '_save_summary_steps': 100, '_num_ps_replicas': 0, '_task_id': 0}
Traceback (most recent call last):
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkcommon_shapes.py", line 686, in _call_cpp_shape_fn_impl
    input_tensors_as_shapes, status)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkerrors_impl.py", line 473, in __exit__
    c_api.TF_GetCode(self.status.status))
tensorflow.python.framework.errors_impl.InvalidArgumentError: Can not squeeze dim[1], expected a dimension of 1, got 3 for 'sparse_softmax_cross_entropy_loss/remove_squeezable_dimensions/Squeeze' (op: 'Squeeze') with input shapes: [100,3].

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "D:f_exe_5_make_image_lablescnn_mnist.py", line 214, in <module>
    tf.app.run()
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonplatformapp.py", line 124, in run
    _sys.exit(main(argv))
  File "D:f_exe_5_make_image_lablescnn_mnist.py", line 203, in main
    hooks=[logging_hook])
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonestimatorestimator.py", line 314, in train
    loss = self._train_model(input_fn, hooks, saving_listeners)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonestimatorestimator.py", line 743, in _train_model
    features, labels, model_fn_lib.ModeKeys.TRAIN, self.config)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonestimatorestimator.py", line 725, in _call_model_fn
    model_fn_results = self._model_fn(features=features, **kwargs)
  File "D:f_exe_5_make_image_lablescnn_mnist.py", line 67, in cnn_model_fn
    loss = tf.losses.sparse_softmax_cross_entropy(labels=labels, logits=logits)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonopslosseslosses_impl.py", line 790, in sparse_softmax_cross_entropy
    labels, logits, weights, expected_rank_diff=1)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonopslosseslosses_impl.py", line 720, in _remove_squeezable_dimensions
    labels, predictions, expected_rank_diff=expected_rank_diff)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonopsconfusion_matrix.py", line 76, in remove_squeezable_dimensions
    labels = array_ops.squeeze(labels, [-1])
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonopsarray_ops.py", line 2490, in squeeze
    return gen_array_ops._squeeze(input, axis, name)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonopsgen_array_ops.py", line 7049, in _squeeze
    "Squeeze", input=input, squeeze_dims=axis, name=name)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkop_def_library.py", line 787, in _apply_op_helper
    op_def=op_def)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkops.py", line 3162, in create_op
    compute_device=compute_device)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkops.py", line 3208, in _create_op_helper
    set_shapes_for_outputs(op)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkops.py", line 2427, in set_shapes_for_outputs
    return _set_shapes_for_outputs(op)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkops.py", line 2400, in _set_shapes_for_outputs
    shapes = shape_func(op)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkops.py", line 2330, in call_with_requiring
    return call_cpp_shape_fn(op, require_shape_fn=True)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkcommon_shapes.py", line 627, in call_cpp_shape_fn
    require_shape_fn)
  File "C:UsersASUSAppDataLocalProgramsPythonPython35libsite-packagesensorflowpythonframeworkcommon_shapes.py", line 691, in _call_cpp_shape_fn_impl
    raise ValueError(err.message)
ValueError: Can not squeeze dim[1], expected a dimension of 1, got 3 for 'sparse_softmax_cross_entropy_loss/remove_squeezable_dimensions/Squeeze' (op: 'Squeeze') with input shapes: [100,3].
>>> 

Here is my code:

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

#imports
import numpy as np
import tensorflow as tf
import glob
import cv2
import random
import matplotlib.pylab as plt
import pandas as pd
import sys as system
from mlxtend.preprocessing import one_hot
from sklearn import preprocessing
from sklearn.preprocessing import LabelEncoder
from sklearn.preprocessing import OneHotEncoder


tf.logging.set_verbosity(tf.logging.INFO)

def cnn_model_fn(features, labels, mode):
    """Model function for CNN"""
    #Input Layer
    input_layer = tf.reshape(features["x"], [-1,320,320,3])
    #Convolutional Layer #1
    conv1 = tf.layers.conv2d(
        inputs = input_layer,
        filters = 32,
        kernel_size=[5,5],
        padding = "same",
        activation=tf.nn.relu)

    #Pooling Layer #1
    pool1 = tf.layers.max_pooling2d(inputs=conv1, pool_size=[2,2], strides=2)

    #Convolutional Layer #2 and Pooling Layer #2
    conv2 = tf.layers.conv2d(
        inputs=pool1,
        filters=64,
        kernel_size=[5,5],
        padding="same",
        activation=tf.nn.relu)
    pool2 = tf.layers.max_pooling2d(inputs=conv2, pool_size=[2,2], strides=2)

    #Dense Layer
    pool2_flat = tf.reshape(pool2, [-1,80*80*64])
    dense = tf.layers.dense(inputs=pool2_flat, units=1024, activation=tf.nn.relu)
    dropout = tf.layers.dropout(
        inputs=dense, rate=0.4, training=mode == tf.estimator.ModeKeys.TRAIN)

    #Logits Layer
    logits = tf.layers.dense(inputs=dropout, units=3)

    predictions = {
        #Generate predictions (for PREDICT and EVAL mode)
        "classes": tf.argmax(input=logits, axis=1),
        #Add 'softmax_tensor' to the graph. It is used for PREDICT and by the
        #'logging_hook'
        "probabilities": tf.nn.softmax(logits, name="softmax_tensor")
    }

    if mode == tf.estimator.ModeKeys.PREDICT:
        return tf.estimator.EstimatorSpec(mode=mode, predictions=predictions)

    # Calculate Loss (for both TRAIN and EVAL modes
    loss = tf.losses.sparse_softmax_cross_entropy(labels=labels, logits=logits)


# Configure the Training Op (for TRAIN mode)
    if mode == tf.estimator.ModeKeys.TRAIN:
        optimizer = tf.train.GradientDescentOptimizer(learning_rate=0.001)
        train_op = optimizer.minimize(
            loss=loss,
            global_step=tf.train.get_global_step())
        return tf.estimator.EstimatorSpec(mode=mode, loss=loss, train_op=train_op)

    # Add evaluation metrics (for EVAL mode)
    eval_metric_ops = {
        "accuracy": tf.metrics.accuracy(
            labels=labels, predictions=predictions["classes"])}
    return tf.estimator.EstimatorSpec(
        mode=mode, loss=loss,eval_metric_ops=eval_metric_ops)

def main(unused_argv):
    '''
    #Load training and eval data
    mnist = tf.contrib.learn.datasets.load_dataset("mnist")
    train_data = mnist.train.images
    train_labels = np.asarray(mnist.train.labels, dtype=np.int32)
    eval_data = mnist.test.images
    eval_labels = np.asarray(mnist.test.labels, dtype=np.int32)
    '''
    #Load cats, dogs and cars image in local folder
    X_data = []
    files = glob.glob("data/cats/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data.append(imgNR)

    files = glob.glob("data/dogs/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data.append(imgNR)

    files = glob.glob ("data/cars/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data.append (imgNR)
    #print('X_data count:', len(X_data))

    X_data_Val = []
    files = glob.glob ("data/Validation/cats/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data_Val.append (imgNR)

    files = glob.glob ("data/Validation/dogs/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data_Val.append (imgNR)

    files = glob.glob ("data/Validation/cars/*.jpg")
    for myFile in files:
        image = cv2.imread (myFile)
        imgR = cv2.resize(image, (320, 320))
        imgNR = imgR/255
        X_data_Val.append (imgNR)


    #Feed One hot lables
    Y_Label = np.zeros(shape=(300,1))
    for el in range(0,100):
        Y_Label[el]=[0]
    for el in range(101,200):
        Y_Label[el]=[1]
    for el in range(201,300):
        Y_Label[el]=[2]
    onehot_encoder = OneHotEncoder(sparse=False)
    #Y_Label_RS = Y_Label.reshape(len(Y_Label), 1)
    Y_Label_Encode = onehot_encoder.fit_transform(Y_Label)

    #print('Y_Label_Encode shape:', Y_Label_Encode.shape)


    Y_Label_Val = np.zeros(shape=(30,1))
    for el in range(0, 10):
        Y_Label_Val[el]=[0]
    for el in range(11, 20):
        Y_Label_Val[el]=[1]
    for el in range(21, 30):
        Y_Label_Val[el]=[2]

    #Y_Label_Val_RS = Y_Label_Val.reshape(len(Y_Label_Val), 1)
    Y_Label_Val_Encode = onehot_encoder.fit_transform(Y_Label_Val)

    #print('Y_Label_Val_Encode shape:', Y_Label_Val_Encode.shape)

    train_data = np.array(X_data)
    train_data = train_data.astype(np.float32)
    train_labels = np.asarray(Y_Label_Encode, dtype=np.int32)

    eval_data = np.array(X_data_Val)
    eval_data = eval_data.astype(np.float32)
    eval_labels = np.asarray(Y_Label_Val_Encode, dtype=np.int32)

    print(train_data.shape)
    print(train_labels.shape)

    #Create the Estimator
    mnist_classifier = tf.estimator.Estimator(
        model_fn=cnn_model_fn, model_dir="/tmp/mnist_convnet_model")
    # Set up logging for predictions
    tensor_to_log = {"probabilities": "softmax_tensor"}
    logging_hook = tf.train.LoggingTensorHook(
        tensors=tensor_to_log, every_n_iter=50)


    # Train the model
    train_input_fn = tf.estimator.inputs.n

Answer 1

The error here is from tf.losses.sparse_softmax_cross_entropy(labels=labels, logits=logits).

The TensorFlow documentation clearly states that "labels vector must provide a single specific index for the true class for each row of logits". So your labels vector must include only class-indices like 0,1,2 and not their respective one-hot-encodings like [1,0,0], [0,1,0], [0,0,1].

Reproducing the error to explain further:

import numpy as np
import tensorflow as tf

# Create random-array and assign as logits tensor
np.random.seed(12345)
logits = tf.convert_to_tensor(np.random.sample((4,4)))
print logits.get_shape() #[4,4]

# Create random-labels (Assuming only 4 classes)
labels = tf.convert_to_tensor(np.array([2, 2, 0, 1]))

loss_1 = tf.losses.sparse_softmax_cross_entropy(labels, logits)

sess = tf.Session()
sess.run(tf.global_variables_initializer())

print 'Loss: {}'.format(sess.run(loss_1)) # 1.44836854

# Now giving one-hot-encodings in place of class-indices for labels
wrong_labels = tf.convert_to_tensor(np.array([[0,0,1,0], [0,0,1,0], [1,0,0,0],[0,1,0,0]]))
loss_2 = tf.losses.sparse_softmax_cross_entropy(wrong_labels, logits)

# This should give you a similar error as soon as you define it

So try giving class-indices instead of one-hot encodings in your Y_Labels vector. Hope this clears your doubt.