From numpy ndarray to tfrecords

np_to_tfrecords.py

import numpy as np
import tensorflow as tf

__author__ = "Sangwoong Yoon"

def np_to_tfrecords(X, Y, file_path_prefix, verbose=True):
    """
    Converts a Numpy array (or two Numpy arrays) into a tfrecord file.
    For supervised learning, feed training inputs to X and training labels to Y.
    For unsupervised learning, only feed training inputs to X, and feed None to Y.
    The length of the first dimensions of X and Y should be the number of samples.
    
    Parameters
    ----------
    X : numpy.ndarray of rank 2
        Numpy array for training inputs. Its dtype should be float32, float64, or int64.
        If X has a higher rank, it should be rshape before fed to this function.
    Y : numpy.ndarray of rank 2 or None
        Numpy array for training labels. Its dtype should be float32, float64, or int64.
        None if there is no label array.
    file_path_prefix : str
        The path and name of the resulting tfrecord file to be generated, without '.tfrecords'
    verbose : bool
        If true, progress is reported.
    
    Raises
    ------
    ValueError
        If input type is not float (64 or 32) or int.
    
    """
    def _dtype_feature(ndarray):
        """match appropriate tf.train.Feature class with dtype of ndarray. """
        assert isinstance(ndarray, np.ndarray)
        dtype_ = ndarray.dtype
        if dtype_ == np.float64 or dtype_ == np.float32:
            return lambda array: tf.train.Feature(float_list=tf.train.FloatList(value=array))
        elif dtype_ == np.int64:
            return lambda array: tf.train.Feature(int64_list=tf.train.Int64List(value=array))
        else:  
            raise ValueError("The input should be numpy ndarray. \
                               Instaed got {}".format(ndarray.dtype))
            
    assert isinstance(X, np.ndarray)
    assert len(X.shape) == 2  # If X has a higher rank, 
                               # it should be rshape before fed to this function.
    assert isinstance(Y, np.ndarray) or Y is None
    
    # load appropriate tf.train.Feature class depending on dtype
    dtype_feature_x = _dtype_feature(X)
    if Y is not None:
        assert X.shape[0] == Y.shape[0]
        assert len(Y.shape) == 2
        dtype_feature_y = _dtype_feature(Y)            
    
    # Generate tfrecord writer
    result_tf_file = file_path_prefix + '.tfrecords'
    writer = tf.python_io.TFRecordWriter(result_tf_file)
    if verbose:
        print "Serializing {:d} examples into {}".format(X.shape[0], result_tf_file)
        
    # iterate over each sample,
    # and serialize it as ProtoBuf.
    for idx in range(X.shape[0]):
        x = X[idx]
        if Y is not None:
            y = Y[idx]
        
        d_feature = {}
        d_feature['X'] = dtype_feature_x(x)
        if Y is not None:
            d_feature['Y'] = dtype_feature_y(y)
            
        features = tf.train.Features(feature=d_feature)
        example = tf.train.Example(features=features)
        serialized = example.SerializeToString()
        writer.write(serialized)
    
    if verbose:
        print "Writing {} done!".format(result_tf_file)

        
#################################    
##      Test and Use Cases     ##
#################################

# 1-1. Saving a dataset with input and label (supervised learning)
xx = np.random.randn(10,5)
yy = np.random.randn(10,1)
np_to_tfrecords(xx, yy, 'test1', verbose=True)

# 1-2. Check if the data is stored correctly
# open the saved file and check the first entries
for serialized_example in tf.python_io.tf_record_iterator('test1.tfrecords'):
    example = tf.train.Example()
    example.ParseFromString(serialized_example)
    x_1 = np.array(example.features.feature['X'].float_list.value)
    y_1 = np.array(example.features.feature['Y'].float_list.value)
    break
    
# the numbers may be slightly different because of the floating point error.
print xx[0]
print x_1
print yy[0]
print y_1


# 2. Saving a dataset with only inputs (unsupervised learning)
xx = np.random.randn(100,100)
np_to_tfrecords(xx, None, 'test2', verbose=True)

Neat! Thank you. Thx from a beginner.

Thank you.

Might want to extend _dtype_feature to recognize unit8 which is a common image datatype. Then pass this as a bytes_list.

tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))

storing images in as uint8 will be 4x smaller than float32.

Very good code for tfrecord tutorial thank you

Thank you. I've been tearing my hair out trying to confirm that my data/labels were written to the record properly, and this made it so much easier.

Very useful code. Thank you!

Very useful code. not sure why returning a anonymous function from _dtype_feature works?

Thank you very much. But your code is very slow for huge datasets I think this is because you write the records one by one. I don't know if it is possible to write the whole data using tf.train.SequenceExample?

If someone is looking for a faster solution check my Kaggle kernel

If someone is looking for a faster solution check my Kaggle kernel

@tchaye56
Well that notebook(version 17) has an error.
But I'm glad that someone is working on a faster version :-)

Wait for 10 min I just sent a new commit

Thanks for this.

Please, after saving test1, how can I recover the whole array, i.e xx and not just x_1? Thanks in advance.

What about just using
tensor = tf.convert_to_tensor(array) result = tf.io.serialize_tensor(tensor)

How would 1-2 look like with the tf updates? tf_record_iterator does not work anymore, and I can't find out how to recover the file.

why is it important for len(X.shape) == 2?

thanks for your sharing! may i know what if i have X with higher dimenions? is that still possible to covert them to tfrecords? thanks!

It's been so long since I wrote this code and personally, I have moved to pytorch.
I have no idea if this would work for tensors with a higher rank.
My personal guess is it should probably work, if you comment out the assertions (L45, L53).
Could you try it? @songssssss

thanks for your reply! i tried to use tf.data.Dataset instead and it solved my memory issue