Support numerical arrays

MatFileHandler.Tests/MatFileReaderHdfTests.cs

@@ -50,6 +50,66 @@ namespace MatFileHandler.Tests
             Assert.That(arrayUnicodeWide.String, Is.EqualTo("🍆"));
         }
 
+        /// <summary>
+        /// Test reading a two-dimensional double array.
+        /// </summary>
+        [Test]
+        public void TestMatrix()
+        {
+            var matFile = ReadHdfTestFile("matrix");
+            var matrix = matFile["matrix"].Value as IArrayOf<double>;
+            Assert.That(matrix.Dimensions, Is.EqualTo(new[] { 3, 2 }));
+            Assert.That(matrix.ConvertToDoubleArray(), Is.EqualTo(new[] { 1.0, 3.0, 5.0, 2.0, 4.0, 6.0 }));
+            Assert.That(matrix[0, 0], Is.EqualTo(1.0));
+            Assert.That(matrix[0, 1], Is.EqualTo(2.0));
+            Assert.That(matrix[1, 0], Is.EqualTo(3.0));
+            Assert.That(matrix[1, 1], Is.EqualTo(4.0));
+            Assert.That(matrix[2, 0], Is.EqualTo(5.0));
+            Assert.That(matrix[2, 1], Is.EqualTo(6.0));
+        }
+
+        /// <summary>
+        /// Test reading lower and upper limits of integer data types.
+        /// </summary>
+        [Test]
+        public void TestLimits()
+        {
+            var matFile = ReadHdfTestFile("limits");
+            IArray array;
+            array = matFile["int8_"].Value;
+            CheckLimits(array as IArrayOf<sbyte>, CommonData.Int8Limits);
+            Assert.That(array.ConvertToDoubleArray(), Is.EqualTo(new[] { -128.0, 127.0 }));
+
+            array = matFile["uint8_"].Value;
+            CheckLimits(array as IArrayOf<byte>, CommonData.UInt8Limits);
+
+            array = matFile["int16_"].Value;
+            CheckLimits(array as IArrayOf<short>, CommonData.Int16Limits);
+
+            array = matFile["uint16_"].Value;
+            CheckLimits(array as IArrayOf<ushort>, CommonData.UInt16Limits);
+
+            array = matFile["int32_"].Value;
+            CheckLimits(array as IArrayOf<int>, CommonData.Int32Limits);
+
+            array = matFile["uint32_"].Value;
+            CheckLimits(array as IArrayOf<uint>, CommonData.UInt32Limits);
+
+            array = matFile["int64_"].Value;
+            CheckLimits(array as IArrayOf<long>, CommonData.Int64Limits);
+
+            array = matFile["uint64_"].Value;
+            CheckLimits(array as IArrayOf<ulong>, CommonData.UInt64Limits);
+        }
+
+        private static void CheckLimits<T>(IArrayOf<T> array, T[] limits)
+            where T : struct
+        {
+            Assert.That(array, Is.Not.Null);
+            Assert.That(array.Dimensions, Is.EqualTo(new[] { 1, 2 }));
+            Assert.That(array.Data, Is.EqualTo(limits));
+        }
+
         private static AbstractTestDataFactory<IMatFile> GetTests(string factoryName) =>
             new MatTestDataFactory(Path.Combine(TestDirectory, factoryName));
 

MatFileHandler/HdfFileReader.cs

@@ -8,26 +8,151 @@ using HDF.PInvoke;
 
 namespace MatFileHandler
 {
-    public class HdfCharArray : ICharArray
+    internal class HdfArray : IArray
     {
-        public HdfCharArray(int[] dimensions, string data)
+        /// <summary>
+        /// Initializes a new instance of the <see cref="HdfArray"/> class.
+        /// </summary>
+        /// <param name="dimensions">Dimensions of the array.</param>
+        protected HdfArray(
+            int[] dimensions)
         {
             Dimensions = dimensions;
+        }
+
+        /// <inheritdoc />
+        public int[] Dimensions { get; }
+
+        /// <inheritdoc />
+        public int Count => Dimensions.NumberOfElements();
+
+        /// <summary>
+        /// Returns a new empty array.
+        /// </summary>
+        /// <returns>Empty array.</returns>
+        public static HdfArray Empty()
+        {
+            return new HdfArray(Array.Empty<int>());
+        }
+
+        public virtual double[] ConvertToDoubleArray()
+        {
+            return null;
+        }
+
+        public virtual Complex[] ConvertToComplexArray()
+        {
+            return null;
+        }
+
+        /// <inheritdoc />
+        public bool IsEmpty => Dimensions.Length == 0;
+    }
+
+    /// <summary>
+    /// A numerical array.
+    /// </summary>
+    /// <typeparam name="T">Element type.</typeparam>
+    internal class HdfNumericalArrayOf<T> : HdfArray, IArrayOf<T>
+      where T : struct
+    {
+        /// <summary>
+        /// Initializes a new instance of the <see cref="HdfNumericalArrayOf{T}"/> class.
+        /// </summary>
+        /// <param name="dimensions">Dimensions of the array.</param>
+        /// <param name="name">Array name.</param>
+        /// <param name="data">Array contents.</param>
+        public HdfNumericalArrayOf(int[] dimensions, T[] data)
+            : base(dimensions)
+        {
+            Data = data;
+        }
+
+        /// <inheritdoc />
+        public T[] Data { get; }
+
+        /// <inheritdoc />
+        public T this[params int[] list]
+        {
+            get => Data[Dimensions.DimFlatten(list)];
+            set => Data[Dimensions.DimFlatten(list)] = value;
+        }
+
+        /// <summary>
+        /// Tries to convert the array to an array of Double values.
+        /// </summary>
+        /// <returns>Array of values of the array, converted to Double, or null if the conversion is not possible.</returns>
+        public override double[] ConvertToDoubleArray()
+        {
+            return Data as double[] ?? Data.Select(x => Convert.ToDouble(x)).ToArray();
+        }
+
+        /// <summary>
+        /// Tries to convert the array to an array of Complex values.
+        /// </summary>
+        /// <returns>Array of values of the array, converted to Complex, or null if the conversion is not possible.</returns>
+        public override Complex[] ConvertToComplexArray()
+        {
+            if (Data is Complex[])
+            {
+                return Data as Complex[];
+            }
+            if (Data is ComplexOf<sbyte>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<sbyte>[]);
+            }
+            if (Data is ComplexOf<byte>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<byte>[]);
+            }
+            if (Data is ComplexOf<short>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<short>[]);
+            }
+            if (Data is ComplexOf<ushort>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<ushort>[]);
+            }
+            if (Data is ComplexOf<int>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<int>[]);
+            }
+            if (Data is ComplexOf<uint>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<uint>[]);
+            }
+            if (Data is ComplexOf<long>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<long>[]);
+            }
+            if (Data is ComplexOf<ulong>[])
+            {
+                return ConvertToComplex(Data as ComplexOf<ulong>[]);
+            }
+            return ConvertToDoubleArray().Select(x => new Complex(x, 0.0)).ToArray();
+        }
+
+        private static Complex[] ConvertToComplex<TS>(IEnumerable<ComplexOf<TS>> array)
+          where TS : struct
+        {
+            return array.Select(x => new Complex(Convert.ToDouble(x.Real), Convert.ToDouble(x.Imaginary))).ToArray();
+        }
+    }
+
+    internal class HdfCharArray : HdfArray, ICharArray
+    {
+        public HdfCharArray(int[] dimensions, string data)
+        : base(dimensions)
+        {
             StringData = data;
         }
 
-        public bool IsEmpty => Dimensions.Length == 0;
+        public override double[] ConvertToDoubleArray()
-
-        public int[] Dimensions { get; }
-
-        public int Count => Dimensions.NumberOfElements();
-
-        public double[] ConvertToDoubleArray()
         {
             return Data.Select(Convert.ToDouble).ToArray();
         }
 
-        public Complex[] ConvertToComplexArray()
+        public override Complex[] ConvertToComplexArray()
         {
             return ConvertToDoubleArray().Select(x => new Complex(x, 0.0)).ToArray();
         }
@@ -129,26 +254,158 @@ namespace MatFileHandler
             return dims.Select(x => (int)x).ToArray();
         }
 
+        private static ArrayType ArrayTypeFromMatlabClassName(string matlabClassName)
+        {
+            switch (matlabClassName)
+            {
+                case "char":
+                    return ArrayType.MxChar;
+                case "int8":
+                    return ArrayType.MxInt8;
+                case "uint8":
+                    return ArrayType.MxUInt8;
+                case "int16":
+                    return ArrayType.MxInt16;
+                case "uint16":
+                    return ArrayType.MxUInt16;
+                case "int32":
+                    return ArrayType.MxInt32;
+                case "uint32":
+                    return ArrayType.MxUInt32;
+                case "int64":
+                    return ArrayType.MxInt64;
+                case "uint64":
+                    return ArrayType.MxUInt64;
+                case "double":
+                    return ArrayType.MxDouble;
+            }
+            throw new NotImplementedException();
+        }
+
         private static IArray ReadDataset(long datasetId)
         {
             var dims = GetDimensionsOfDataset(datasetId);
 
             var matlabClass = GetMatlabClassOfDataset(datasetId);
+            var arrayType = ArrayTypeFromMatlabClassName(matlabClass);
 
-            if (matlabClass == "char")
+            switch (arrayType)
             {
-                return ReadCharArray(datasetId, dims);
+                case ArrayType.MxChar:
+                    return ReadCharArray(datasetId, dims);
+                case ArrayType.MxInt8:
+                    return ReadNumericalArray<sbyte>(datasetId, dims, arrayType);
+                case ArrayType.MxUInt8:
+                    return ReadNumericalArray<byte>(datasetId, dims, arrayType);
+                case ArrayType.MxInt16:
+                    return ReadNumericalArray<short>(datasetId, dims, arrayType);
+                case ArrayType.MxUInt16:
+                    return ReadNumericalArray<ushort>(datasetId, dims, arrayType);
+                case ArrayType.MxInt32:
+                    return ReadNumericalArray<int>(datasetId, dims, arrayType);
+                case ArrayType.MxUInt32:
+                    return ReadNumericalArray<uint>(datasetId, dims, arrayType);
+                case ArrayType.MxInt64:
+                    return ReadNumericalArray<long>(datasetId, dims, arrayType);
+                case ArrayType.MxUInt64:
+                    return ReadNumericalArray<ulong>(datasetId, dims, arrayType);
+                case ArrayType.MxSingle:
+                    return ReadNumericalArray<float>(datasetId, dims, arrayType);
+                case ArrayType.MxDouble:
+                    return ReadNumericalArray<double>(datasetId, dims, arrayType);
+            }
+            throw new NotImplementedException($"Unknown array type: {arrayType}.");
+        }
+
+        private static int SizeOfArrayElement(ArrayType arrayType)
+        {
+            switch (arrayType)
+            {
+                case ArrayType.MxInt8:
+                case ArrayType.MxUInt8:
+                    return 1;
+                case ArrayType.MxInt16:
+                case ArrayType.MxUInt16:
+                    return 2;
+                case ArrayType.MxInt32:
+                case ArrayType.MxUInt32:
+                case ArrayType.MxSingle:
+                    return 4;
+                case ArrayType.MxInt64:
+                case ArrayType.MxUInt64:
+                case ArrayType.MxDouble:
+                    return 8;
+            }
+
+            throw new NotImplementedException();
+        }
+
+        private static long H5tTypeFromArrayType(ArrayType arrayType)
+        {
+            switch (arrayType)
+            {
+                case ArrayType.MxInt8:
+                    return H5T.NATIVE_INT8;
+                case ArrayType.MxUInt8:
+                    return H5T.NATIVE_UINT8;
+                case ArrayType.MxInt16:
+                    return H5T.NATIVE_INT16;
+                case ArrayType.MxUInt16:
+                    return H5T.NATIVE_UINT16;
+                case ArrayType.MxInt32:
+                    return H5T.NATIVE_INT32;
+                case ArrayType.MxUInt32:
+                    return H5T.NATIVE_UINT32;
+                case ArrayType.MxInt64:
+                    return H5T.NATIVE_INT64;
+                case ArrayType.MxUInt64:
+                    return H5T.NATIVE_UINT64;
+                case ArrayType.MxSingle:
+                    return H5T.NATIVE_FLOAT;
+                case ArrayType.MxDouble:
+                    return H5T.NATIVE_DOUBLE;
             }
             throw new NotImplementedException();
         }
 
+        private static T[] ConvertDataToProperType<T>(byte[] bytes, ArrayType arrayType)
+            where T : struct
+        {
+            var length = bytes.Length;
+            var arrayElementSize = SizeOfArrayElement(arrayType);
+            var data = new T[length / arrayElementSize];
+            Buffer.BlockCopy(bytes, 0, data, 0, length);
+            return data;
+        }
+
+        private static byte[] ReadDataset(long datasetId, long elementType, int dataSize)
+        {
+            var dataBuffer = Marshal.AllocHGlobal(dataSize);
+            H5D.read(datasetId, elementType, H5S.ALL, H5S.ALL, H5P.DEFAULT, dataBuffer);
+            var data = new byte[dataSize];
+            Marshal.Copy(dataBuffer, data, 0, dataSize);
+            return data;
+        }
+
+        private static IArray ReadNumericalArray<T>(long datasetId, int[] dims, ArrayType arrayType)
+            where T : struct
+        {
+            var numberOfElements = dims.NumberOfElements();
+            var dataSize = numberOfElements * SizeOfArrayElement(arrayType);
+            var storageSize = (int)H5D.get_storage_size(datasetId);
+            if (dataSize != storageSize)
+            {
+                throw new Exception("Data size mismatch.");
+            }
+            var data = ReadDataset(datasetId, H5tTypeFromArrayType(arrayType), dataSize);
+            var convertedData = ConvertDataToProperType<T>(data, arrayType);
+            return new HdfNumericalArrayOf<T>(dims, convertedData);
+        }
+
         private static IArray ReadCharArray(long datasetId, int[] dims)
         {
             var storageSize = (int)H5D.get_storage_size(datasetId);
-            var data = new byte[storageSize];
+            var data = ReadDataset(datasetId, H5T.NATIVE_UINT16, storageSize);
-            var dataBuffer = Marshal.AllocHGlobal(storageSize);
-            H5D.read(datasetId, H5T.NATIVE_UINT16, H5S.ALL, H5S.ALL, H5P.DEFAULT, dataBuffer);
-            Marshal.Copy(dataBuffer, data, 0, storageSize);
             var str = Encoding.Unicode.GetString(data);
             return new HdfCharArray(dims, str);
         }

MatFileHandler/MatFileHdfReader.cs

@@ -1,9 +1,7 @@
-using System;
+using HDF.PInvoke;
-using System.Collections.Generic;
+using System;
 using System.IO;
 using System.Runtime.InteropServices;
-using System.Text;
-using HDF.PInvoke;
 
 namespace MatFileHandler
 {