MatlabFileReader.cs

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.IO;
using Ionic.Zlib;

namespace MatlabFileIO
{
    public class MatfileReader
    {
        private BinaryReader readStream;
        public Dictionary<String, Variable> Variables { get; private set; }

        public MatfileReader(string fileName)
        {
            //create stream from filename
            FileStream fileStream = new FileStream(fileName, FileMode.Open, FileAccess.Read);
            this.readStream = new BinaryReader(fileStream);

            byte[] headerBytes = readStream.ReadBytes(128);
			//Parse header (will throw if fail)
            new Header(headerBytes);

            ReadVariables();
        }

        private void ReadVariables()
        {
            Variables = new Dictionary<string, Variable>();
            while(readStream.BaseStream.Position < readStream.BaseStream.Length)
            {
                Variable v = new Variable();

                Tag t = MatfileHelper.ReadTag(readStream);
                if(t.dataType == null)
                    throw new Exception("Not an array, don't know what to do with this stuff");
                else if (t.dataType.Equals(typeof(Array))) //We use Array to indicate MiMatrix
                {
                    ReadMatrix(ref v, t.length, readStream);
                } else if (t.dataType.Equals(typeof(ZlibStream)))
                {
                    byte[] compressed = readStream.ReadBytes((int)t.length);
                    byte[] decompressed = ZlibStream.UncompressBuffer(compressed);
                    MemoryStream m = new MemoryStream(decompressed);
                    BinaryReader br = new BinaryReader(m);
                    Tag ct = MatfileHelper.ReadTag(br);
                    ReadMatrix(ref v, ct.length, br);
                }
                else
                    throw new Exception("Not an array, don't know what to do with this stuff");
                
                Variables.Add(v.name, v);
            }
        }

        private static void ReadMatrix(ref Variable vi, UInt32 length, BinaryReader matrixStream)
        {
            Tag t;
            long offset = matrixStream.BaseStream.Position;

            //Array flags
            //Will always be too large to be in small data format, so not checking t.data
            t = MatfileHelper.ReadTag(matrixStream);
            UInt32 flagsClass = matrixStream.ReadUInt32();
            byte flags = (byte)(flagsClass >> 8) ;
            if ((flags & 0x80) == 0x80)
                throw new IOException("Complex numbers not supported");
            vi.dataType = MatfileHelper.parseArrayType((byte)flagsClass);
            matrixStream.ReadUInt32();//unused flags

            //Dimensions - There are always 2 dimensions, so this
            //tag will never be of small data format, i.e. not checking for t.data
            t = MatfileHelper.ReadTag(matrixStream);
            int[] arrayDimensions = new int[t.length / MatfileHelper.MatlabBytesPerType(t.dataType)];
            int elements = 1;
            for (int i = 0; i < arrayDimensions.Length; i++)
            {
                int dimension = (int)matrixStream.ReadUInt32();
                arrayDimensions[arrayDimensions.Length - i - 1] = dimension;
                elements *= dimension;
            }
            //Don't keep single dimensions
            arrayDimensions = arrayDimensions.Where(x => x > 1).ToArray();
            //If by doing this, we end up without dimensions, it means we had a 1x...x1 array. 
            //We need at least 1 dimension to instantiate the final array, so...
            if (arrayDimensions.Length == 0)
                arrayDimensions = new int[1] { 1 };

            //Array name
            t = MatfileHelper.ReadTag(matrixStream);
            if (t.data != null)
            {
                sbyte[] varname = t.data as sbyte[];
                vi.name = Encoding.UTF8.GetString(Array.ConvertAll(varname, x => (byte)x));
            } else {
                byte[] varname = matrixStream.ReadBytes((int)t.length);
                vi.name = Encoding.UTF8.GetString(varname);
                MatfileHelper.AdvanceTo8ByteBoundary(matrixStream);
            }
            
            
            //Read and reshape data
            t = MatfileHelper.ReadTag(matrixStream);
            if (t.length / MatfileHelper.MatlabBytesPerType(t.dataType) != elements)
                throw new IOException("Read dimensions didn't correspond to header dimensions");
                    
            Array readBytes;
            if (t.data == null)
                readBytes = MatfileHelper.CastToMatlabType(vi.dataType, matrixStream.ReadBytes((int)t.length));
            else
                readBytes = (Array)t.data;

            Array reshapedData = Array.CreateInstance(vi.dataType, arrayDimensions);
            if (t.dataType != vi.dataType) //This happens when matlab choses to store the data in a smaller datatype when the values permit it
            {
                Array linearData = Array.CreateInstance(vi.dataType, readBytes.Length);
                Array.Copy(readBytes, linearData, readBytes.Length);
                Buffer.BlockCopy(linearData, 0, reshapedData, 0, linearData.Length * MatfileHelper.MatlabBytesPerType(vi.dataType));
                vi.dataType = t.dataType;
            }
            else //Readbytes is already in the correct type
                Buffer.BlockCopy(readBytes, 0, reshapedData, 0, readBytes.Length * MatfileHelper.MatlabBytesPerType(vi.dataType));

            if(reshapedData.Length == 1)
                vi.data = reshapedData.GetValue(0);
            else
                vi.data = reshapedData;

            //Move on in case the data didn't end on a 64 byte boundary
            matrixStream.BaseStream.Seek(offset + length, SeekOrigin.Begin);
        }

        public void Close()
        {
            readStream.Close();
        }
    }
}