Iterators - Loading data

In this tutorial, we focus on how to feed data into a training or inference program. Most training and inference modules in MXNet accept data iterators, which simplifies this procedure, especially when reading large datasets. Here we discuss the API conventions and several provided iterators.

Prerequisites

To complete this tutorial, we need:

$ pip install opencv-python requests matplotlib jupyter

MXNet Data Iterator

Data Iterators in MXNet are similar to Python iterator objects. In Python, the function iter allows fetching items sequentially by calling next() on iterable objects such as a Python list. Iterators provide an abstract interface for traversing various types of iterable collections without needing to expose details about the underlying data source.

In MXNet, data iterators return a batch of data as DataBatch on each call to next. A DataBatch often contains n training examples and their corresponding labels. Here n is the batch_size of the iterator. At the end of the data stream when there is no more data to read, the iterator raises StopIteration exception like Python iter. The structure of DataBatch is defined here.

Information such as name, shape, type and layout on each training example and their corresponding label can be provided as DataDesc data descriptor objects via the provide_data and provide_label properties in DataBatch. The structure of DataDesc is defined here.

All IO in MXNet is handled via mx.io.DataIter and its subclasses. In this tutorial, we’ll discuss a few commonly used iterators provided by MXNet.

Before diving into the details let’s setup the environment by importing some required packages:

import mxnet as mx
%matplotlib inline
import os
import sys
import subprocess
import numpy as np
import matplotlib.pyplot as plt
import tarfile

import warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)

Reading data in memory

When data is stored in memory, backed by either an NDArray or numpy ndarray, we can use the NDArrayIter to read data as below:

import numpy as np

# fix the seed
np.random.seed(42)
mx.random.seed(42)

data = np.random.rand(100,3)
label = np.random.randint(0, 10, (100,))
data_iter = mx.io.NDArrayIter(data=data, label=label, batch_size=30)
for batch in data_iter:
    print([batch.data, batch.label, batch.pad])

Reading data from CSV files

MXNet provides CSVIter to read from CSV files and can be used as below:

#lets save `data` into a csv file first and try reading it back
np.savetxt('data.csv', data, delimiter=',')
data_iter = mx.io.CSVIter(data_csv='data.csv', data_shape=(3,), batch_size=30)
for batch in data_iter:
    print([batch.data, batch.pad])

Custom Iterator

When the built-in iterators do not suit your application needs, you can create your own custom data iterator.

An iterator in MXNet should

  1. Implement next() in Python2 or __next()__ in Python3, returning a DataBatch or raising a StopIteration exception if at the end of the data stream.
  2. Implement the reset() method to restart reading from the beginning.
  3. Have a provide_data attribute, consisting of a list of DataDesc objects that store the name, shape, type and layout information of the data (more info here).
  4. Have a provide_label attribute consisting of a list of DataDesc objects that store the name, shape, type and layout information of the label.

When creating a new iterator, you can either start from scratch and define an iterator or reuse one of the existing iterators. For example, in the image captioning application, the input example is an image while the label is a sentence. Thus we can create a new iterator by:

  • creating a image_iter by using ImageRecordIter which provides multithreaded pre-fetch and augmentation.
  • creating a caption_iter by using NDArrayIter or the bucketing iterator provided in the rnn package.
  • next() returns the combined result of image_iter.next() and caption_iter.next()

The example below shows how to create a Simple iterator.

class SimpleIter(mx.io.DataIter):
    def __init__(self, data_names, data_shapes, data_gen,
                 label_names, label_shapes, label_gen, num_batches=10):
        self._provide_data = list(zip(data_names, data_shapes))
        self._provide_label = list(zip(label_names, label_shapes))
        self.num_batches = num_batches
        self.data_gen = data_gen
        self.label_gen = label_gen
        self.cur_batch = 0

    def __iter__(self):
        return self

    def reset(self):
        self.cur_batch = 0

    def __next__(self):
        return self.next()

    @property
    def provide_data(self):
        return self._provide_data

    @property
    def provide_label(self):
        return self._provide_label

    def next(self):
        if self.cur_batch < self.num_batches:
            self.cur_batch += 1
            data = [mx.nd.array(g(d[1])) for d,g in zip(self._provide_data, self.data_gen)]
            label = [mx.nd.array(g(d[1])) for d,g in zip(self._provide_label, self.label_gen)]
            return mx.io.DataBatch(data, label)
        else:
            raise StopIteration

We can use the above defined SimpleIter to train a simple MLP program below:

import mxnet as mx
num_classes = 10
net = mx.sym.Variable('data')
net = mx.sym.FullyConnected(data=net, name='fc1', num_hidden=64)
net = mx.sym.Activation(data=net, name='relu1', act_type="relu")
net = mx.sym.FullyConnected(data=net, name='fc2', num_hidden=num_classes)
net = mx.sym.SoftmaxOutput(data=net, name='softmax')
print(net.list_arguments())
print(net.list_outputs())

Here, there are four variables that are learnable parameters: the weights and biases of FullyConnected layers fc1 and fc2, two variables for input data: data for the training examples and softmax_label contains the respective labels and the softmax_output.

The data variables are called free variables in MXNet’s Symbol API. To execute a Symbol, they need to be bound with data. Click here learn more about Symbol.

We use the data iterator to feed examples to a neural network via MXNet’s module API. Click here to learn more about Module.

import logging
logging.basicConfig(level=logging.INFO)

n = 32
data_iter = SimpleIter(['data'], [(n, 100)],
                  [lambda s: np.random.uniform(-1, 1, s)],
                  ['softmax_label'], [(n,)],
                  [lambda s: np.random.randint(0, num_classes, s)])

mod = mx.mod.Module(symbol=net)
mod.fit(data_iter, num_epoch=5)

A note on python 3 usage: Lot of the methods in mxnet use string for python2 and bytes for python3. In order to keep this tutorial readable, we are going to define a utility function that converts string to bytes in python 3 environment

def str_or_bytes(str):
    """
    A utility function for this tutorial that helps us convert string 
    to bytes if we are using python3.

    Parameters
    ----------
    str : string

    Returns
    -------
    string (python2) or bytes (python3)
    """
    if sys.version_info[0] < 3:
        return str
    else:
        return bytes(str, 'utf-8')

Record IO

Record IO is a file format used by MXNet for data IO. It compactly packs the data for efficient read and writes from distributed file system like Hadoop HDFS and AWS S3. You can learn more about the design of RecordIO here.

MXNet provides MXRecordIO and MXIndexedRecordIO for sequential access of data and random access of the data.

MXRecordIO

First, let’s look at an example on how to read and write sequentially using MXRecordIO. The files are named with a .rec extension.

record = mx.recordio.MXRecordIO('tmp.rec', 'w')
for i in range(5):
    record.write(str_or_bytes('record_%d'%i))

record.close()

We can read the data back by opening the file with an option r as below:

record = mx.recordio.MXRecordIO('tmp.rec', 'r')
while True:
    item = record.read()
    if not item:
        break
    print (item)
record.close()

MXIndexedRecordIO

MXIndexedRecordIO supports random or indexed access to the data. We will create an indexed record file and a corresponding index file as below:

record = mx.recordio.MXIndexedRecordIO('tmp.idx', 'tmp.rec', 'w')
for i in range(5):
    record.write_idx(i, str_or_bytes('record_%d'%i))

record.close()

Now, we can access the individual records using the keys

record = mx.recordio.MXIndexedRecordIO('tmp.idx', 'tmp.rec', 'r')
record.read_idx(3)

You can also list all the keys in the file.

record.keys

Packing and Unpacking data

Each record in a .rec file can contain arbitrary binary data. However, most deep learning tasks require data to be input in label/data format. The mx.recordio package provides a few utility functions for such operations, namely: pack, unpack, pack_img, and unpack_img.

Packing/Unpacking Binary Data

pack and unpack are used for storing float (or 1d array of float) label and binary data. The data is packed along with a header. The header structure is defined here.

# pack
data = 'data'
label1 = 1.0
header1 = mx.recordio.IRHeader(flag=0, label=label1, id=1, id2=0)
s1 = mx.recordio.pack(header1, str_or_bytes(data))

label2 = [1.0, 2.0, 3.0]
header2 = mx.recordio.IRHeader(flag=3, label=label2, id=2, id2=0)
s2 = mx.recordio.pack(header2, str_or_bytes(data))

# unpack
print(mx.recordio.unpack(s1))
print(mx.recordio.unpack(s2))

Packing/Unpacking Image Data

MXNet provides pack_img and unpack_img to pack/unpack image data. Records packed by pack_img can be loaded by mx.io.ImageRecordIter.

data = np.ones((3,3,1), dtype=np.uint8)
label = 1.0
header = mx.recordio.IRHeader(flag=0, label=label, id=0, id2=0)
s = mx.recordio.pack_img(header, data, quality=100, img_fmt='.jpg')

# unpack_img
print(mx.recordio.unpack_img(s))

Using tools/im2rec.py

You can also convert raw images into RecordIO format using the im2rec.py utility script that is provided in the MXNet src/tools folder. An example of how to use the script for converting to RecordIO format is shown in the Image IO section below.

Image IO

In this section, we will learn how to preprocess and load image data in MXNet.

There are 4 ways of loading image data in MXNet.

  1. Using mx.image.imdecode to load raw image files.
  2. Using mx.img.ImageIter implemented in Python which is very flexible to customization. It can read from .rec(RecordIO) files and raw image files.
  3. Using mx.io.ImageRecordIter implemented on the MXNet backend in C++. This is less flexible to customization but provides various language bindings.
  4. Creating a Custom iterator inheriting mx.io.DataIter

Preprocessing Images

Images can be preprocessed in different ways. We list some of them below:

  • Using mx.io.ImageRecordIter which is fast but not very flexible. It is great for simple tasks like image recognition but won’t work for more complex tasks like detection and segmentation.
  • Using mx.recordio.unpack_img (or cv2.imread, skimage, etc) + numpy is flexible but slow due to Python Global Interpreter Lock (GIL).
  • Using MXNet provided mx.image package. It stores images in NDArray format and leverages MXNet’s dependency engine to automatically parallelize processing and circumvent GIL.

Below, we demonstrate some of the frequently used preprocessing routines provided by the mx.image package.

Let’s download sample images that we can work with.

fname = mx.test_utils.download(url='http://data.mxnet.io/data/test_images.tar.gz', dirname='data', overwrite=False)
tar = tarfile.open(fname)
tar.extractall(path=os.path.join('.','data'))
tar.close()

Loading raw images

mx.image.imdecode lets us load the images. imdecode provides a similar interface to OpenCV.

Note: You will still need OpenCV(not the CV2 Python library) installed to use mx.image.imdecode.

img = mx.image.imdecode(open(os.path.join('data','test_images','ILSVRC2012_val_00000001.JPEG'), 'rb').read())
plt.imshow(img.asnumpy()); plt.show()

Image Transformations

# resize to w x h
tmp = mx.image.imresize(img, 100, 70)
plt.imshow(tmp.asnumpy()); plt.show()

# crop a random w x h region from image
tmp, coord = mx.image.random_crop(img, (150, 200))
print(coord)
plt.imshow(tmp.asnumpy()); plt.show()

Loading Data using Image Iterators

Before we see how to read data using the two built-in Image iterators, lets get a sample Caltech 101 dataset that contains 101 classes of objects and converts them into record io format. Download and unzip

fname = mx.test_utils.download(url='http://www.vision.caltech.edu/Image_Datasets/Caltech101/101_ObjectCategories.tar.gz', dirname='data', overwrite=False)
tar = tarfile.open(fname)
tar.extractall(path=os.path.join('.','data'))
tar.close()

Let’s take a look at the data. As you can see, under the root folder (./data/101_ObjectCategories) every category has a subfolder(./data/101_ObjectCategories/yin_yang).

Now let’s convert them into record io format using the im2rec.py utility script. First, we need to make a list that contains all the image files and their categories:

im2rec_path = mx.test_utils.get_im2rec_path()
data_path = os.path.join('data','101_ObjectCategories')
prefix_path = os.path.join('data','caltech')

with open(os.devnull, 'wb') as devnull:
    subprocess.check_call(['python', im2rec_path, '--list', '--recursive', '--test-ratio=0.2', prefix_path, data_path],
                          stdout=devnull)

The resulting list file (./data/caltech_train.lst) is in the format index\t(one or more label)\tpath. In this case, there is only one label for each image but you can modify the list to add in more for multi-label training.

Then we can use this list to create our record io file:

with open(os.devnull, 'wb') as devnull:
    subprocess.check_call(['python', im2rec_path, '--num-thread=4', '--pass-through', '--test-ratio=0.2', prefix_path, data_path],
                          stdout=devnull)

The record io files are now saved at here (./data)

Using ImageRecordIter

ImageRecordIter can be used for loading image data saved in record io format. To use ImageRecordIter, simply create an instance by loading your record file:

data_iter = mx.io.ImageRecordIter(
    path_imgrec=os.path.join('.','data','caltech.rec'),
    data_shape=(3, 227, 227), # output data shape. An 227x227 region will be cropped from the original image.
    batch_size=4, # number of samples per batch
    resize=256 # resize the shorter edge to 256 before cropping
    # ... you can add more augmentation options as defined in ImageRecordIter.
    )
data_iter.reset()
batch = data_iter.next()
data = batch.data[0]
for i in range(4):
    plt.subplot(1,4,i+1)
    plt.imshow(data[i].asnumpy().astype(np.uint8).transpose((1,2,0)))
plt.show()

Using ImageIter

ImageIter is a flexible interface that supports loading of images in both RecordIO and Raw format.

data_iter = mx.image.ImageIter(batch_size=4, data_shape=(3, 227, 227),
                              path_imgrec=os.path.join('.','data','caltech.rec'),
                              path_imgidx=os.path.join('.','data','caltech.idx') )
data_iter.reset()
batch = data_iter.next()
data = batch.data[0]
for i in range(4):
    plt.subplot(1,4,i+1)
    plt.imshow(data[i].asnumpy().astype(np.uint8).transpose((1,2,0)))
plt.show()
data.ipynb

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