Reading MNIST Database

Question

I am currently exploring neural networks and machine learning and I implemented a basic neural network in c#. Now I wanted to test my back propagation training algorithm with the MNIST database. Although I am having serious trouble reading the files correctly.

Spoiler the code is currently very badly optimised for performance. My aim currently is to grasp the subject and get a structured view how things work before I start throwing out my data structures for faster ones.

To train the network I want to feed it a custom TrainingSet data structure:

[Serializable]
public class TrainingSet
{
    public Dictionary<List<double>, List<double>> data = new Dictionary<List<double>, List<double>>();
}

Keys will be my input data (784 pixels per entry(image) which will represent the greyscale values in range from 0 to 1). Values will be my output data (10 entries representing the digits from 0-9 with all entries on 0 except the exspected one at 1)

Now I want to read the MNIST database according to this contract. I am currentl on my 2nd try which is inspired by this blogpost: https://jamesmccaffrey.wordpress.com/2013/11/23/reading-the-mnist-data-set-with-c/ . Sadly it is still producing the same nonsense as my first try scattering the pixels in a strange pattern:

My current reading algorithm:

    public static TrainingSet GenerateTrainingSet(FileInfo imagesFile, FileInfo labelsFile)
    {
        MnistImageView imageView = new MnistImageView();
        imageView.Show();

        TrainingSet trainingSet = new TrainingSet();

        List<List<double>> labels = new List<List<double>>();
        List<List<double>> images = new List<List<double>>();

        using (BinaryReader brLabels = new BinaryReader(new FileStream(labelsFile.FullName, FileMode.Open)))
        {
            using (BinaryReader brImages = new BinaryReader(new FileStream(imagesFile.FullName, FileMode.Open)))
            {
                int magic1 = brImages.ReadBigInt32(); //Reading as BigEndian
                int numImages = brImages.ReadBigInt32();
                int numRows = brImages.ReadBigInt32();
                int numCols = brImages.ReadBigInt32();

                int magic2 = brLabels.ReadBigInt32();
                int numLabels = brLabels.ReadBigInt32();

                byte[] pixels = new byte[numRows * numCols];

                // each image
                for (int imageCounter = 0; imageCounter < numImages; imageCounter++)
                {
                    List<double> imageInput = new List<double>();
                    List<double> exspectedOutput = new List<double>();

                    for (int i = 0; i < 10; i++) //generate empty exspected output
                        exspectedOutput.Add(0);

                    //read image
                    for (int p = 0; p < pixels.Length; p++)
                    {
                        byte b = brImages.ReadByte();
                        pixels[p] = b;

                        imageInput.Add(b / 255.0f); //scale in 0 to 1 range
                    }

                    //read label
                    byte lbl = brLabels.ReadByte();
                    exspectedOutput[lbl] = 1; //modify exspected output

                    labels.Add(exspectedOutput);
                    images.Add(imageInput);

                    //Debug view showing parsed image.......................
                    Bitmap image = new Bitmap(numCols, numRows);

                    for (int y = 0; y < numRows; y++)
                    {
                        for (int x = 0; x < numCols; x++)
                        {
                            image.SetPixel(x, y, Color.FromArgb(255 - pixels[x * y], 255 - pixels[x * y], 255 - pixels[x * y])); //invert colors to have 0,0,0 be white as specified by mnist
                        }
                    }

                    imageView.SetImage(image);
                    imageView.Refresh();
                    //.......................................................
                }

                brImages.Close();
                brLabels.Close();
            }
        }

        for (int i = 0; i < images.Count; i++)
        {
            trainingSet.data.Add(images[i], labels[i]);
        }

        return trainingSet;
    }

All images produce a pattern as shown above. It's never the exact same pattern but always seems to have the pixels "pulled" down to the right corner.

Dibasic

pixels[x * y] should probably be pixels[(y * numCols) + x] – Chadwell

well that was the mistake thanks so much. What would be a good project without math stopping by and screwing you over. – Dibasic

Answer 1

That is how I did it:

public static class MnistReader
{
    private const string TrainImages = "mnist/train-images.idx3-ubyte";
    private const string TrainLabels = "mnist/train-labels.idx1-ubyte";
    private const string TestImages = "mnist/t10k-images.idx3-ubyte";
    private const string TestLabels = "mnist/t10k-labels.idx1-ubyte";

    public static IEnumerable<Image> ReadTrainingData()
    {
        foreach (var item in Read(TrainImages, TrainLabels))
        {
            yield return item;
        }
    }

    public static IEnumerable<Image> ReadTestData()
    {
        foreach (var item in Read(TestImages, TestLabels))
        {
            yield return item;
        }
    }

    private static IEnumerable<Image> Read(string imagesPath, string labelsPath)
    {
        BinaryReader labels = new BinaryReader(new FileStream(labelsPath, FileMode.Open));
        BinaryReader images = new BinaryReader(new FileStream(imagesPath, FileMode.Open));

        int magicNumber = images.ReadBigInt32();
        int numberOfImages = images.ReadBigInt32();
        int width = images.ReadBigInt32();
        int height = images.ReadBigInt32();

        int magicLabel = labels.ReadBigInt32();
        int numberOfLabels = labels.ReadBigInt32();

        for (int i = 0; i < numberOfImages; i++)
        {
            var bytes = images.ReadBytes(width * height);
            var arr = new byte[height, width];

            arr.ForEach((j,k) => arr[j, k] = bytes[j * height + k]);

            yield return new Image()
            {
                Data = arr,
                Label = labels.ReadByte()
            };
        }
    }
}

Image class:

public class Image
{
    public byte Label { get; set; }
    public byte[,] Data { get; set; }
}

Some extension methods:

public static class Extensions
{
    public static int ReadBigInt32(this BinaryReader br)
    {
        var bytes = br.ReadBytes(sizeof(Int32));
        if (BitConverter.IsLittleEndian) Array.Reverse(bytes);
        return BitConverter.ToInt32(bytes, 0);
    }

    public static void ForEach<T>(this T[,] source, Action<int, int> action)
    {
        for (int w = 0; w < source.GetLength(0); w++)
        {
            for (int h = 0; h < source.GetLength(1); h++)
            {
                action(w, h);
            }
        }
    }
}

Usage:

foreach (var image in MnistReader.ReadTrainingData())
{
    //use image here     
}

or

foreach (var image in MnistReader.ReadTestData())
{
    //use image here     
}

Remembrance

The original files here (yann.lecun.com/exdb/mnist) are .gz files. Did you modify them in any way or reading directly from them ? – Coke

@Coke I believe I unziped them – Remembrance

Whats the difference between ReadBigInt32 and the default ReadInt32? – Sparoid

@Sparoid The bytes are encoded in "high endian" so if you are on an Intel processor you'll have to reverse them; the ReadBigInt32 is checking for that and then reversing the bytes – Brucebrucellosis

@DomenicoRotolo And BinaryReader.ReadInt32/BitConverter.ToInt32 does not do this by default? – Sparoid

@Sparoid from the wiki it says: 'The order of bytes in the array must reflect the endianness of the computer system's architecture' so I guess not – Brucebrucellosis

Answer 2

Why not use a nuget package:

• MNIST.IO Just a datareader (disclaimer: my package)
• Accord.DataSets Contains classes to download and parse machine learning datasets such as MNIST, News20, Iris. This package is part of the Accord.NET Framework.

Hailstorm