io: ported delimited reader. made it generic, added support for different cultures, and fixed regex bug

src/Numerics/LinearAlgebra/Double/IO/DelimitedReader.cs

@@ -0,0 +1,196 @@
+// <copyright file="DelimitedReader.cs" company="Math.NET">
+// Math.NET Numerics, part of the Math.NET Project
+// http://numerics.mathdotnet.com
+// http://github.com/mathnet/mathnet-numerics
+// http://mathnetnumerics.codeplex.com
+// Copyright (c) 2009-2010 Math.NET
+// Permission is hereby granted, free of charge, to any person
+// obtaining a copy of this software and associated documentation
+// files (the "Software"), to deal in the Software without
+// restriction, including without limitation the rights to use,
+// copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the
+// Software is furnished to do so, subject to the following
+// conditions:
+// The above copyright notice and this permission notice shall be
+// included in all copies or substantial portions of the Software.
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+// OTHER DEALINGS IN THE SOFTWARE.
+// </copyright>
+
+namespace MathNet.Numerics.LinearAlgebra.Double.IO
+{
+    using System;
+    using System.Collections.Generic;
+    using System.Globalization;
+    using System.IO;
+    using System.Reflection;
+    using System.Text.RegularExpressions;
+
+    /// <summary>
+    /// Creates a <see cref="Matrix"/> from a delimited text file. If the user does not
+    /// specify a delimiter, then any whitespace is used.
+    /// </summary>
+    /// <typeparam name="TMatrix">The type of the matrix to return.</typeparam>
+    public class DelimitedReader<TMatrix> : MatrixReader<TMatrix>
+        where TMatrix : Matrix
+    {
+        /// <summary>
+        /// Constructor to create matrix instance.
+        /// </summary>
+        private static readonly ConstructorInfo Constructor = typeof(TMatrix).GetConstructor(new[] { typeof(int), typeof(int) });
+
+        /// <summary>
+        /// Whitespace regular expression.
+        /// </summary>
+        private static readonly Regex WhiteSpace = new Regex(@"[\s]+");
+
+        /// <summary>
+        /// The delimiter to use.
+        /// </summary>
+        private readonly Regex _delimiter;
+
+        /// <summary>
+        /// The <see cref="CultureInfo"/> to use.
+        /// </summary>
+        private CultureInfo _cultureInfo = CultureInfo.CurrentCulture;
+
+        /// <summary>
+        /// Initializes a new instance of the <see cref="DelimitedReader{TMatrix}"/> class using
+        /// any whitespace as the delimiter.
+        /// </summary>
+        public DelimitedReader()
+        {
+            _delimiter = WhiteSpace;
+        }
+
+        /// <summary>
+        /// Initializes a new instance of the <see cref="DelimitedReader{TMatrix}"/> class.
+        /// </summary>
+        /// <param name="delimiter">The delimiter to use.</param>
+        public DelimitedReader(char delimiter)
+        {
+            _delimiter = new Regex("[" + new string(delimiter, 1) + "]+");
+        }
+
+        /// <summary>
+        /// Initializes a new instance of the <see cref="DelimitedReader{TMatrix}"/> class. 
+        /// </summary>
+        /// <param name="delimiter">
+        /// The delimiter to use.
+        /// </param>
+        /// <exception cref="ArgumentNullException">
+        /// If <paramref name="delimiter"/> is <see langword="null"/>.
+        /// </exception>
+        public DelimitedReader(string delimiter)
+        {
+            if (delimiter == null)
+            {
+                throw new ArgumentNullException("delimiter");
+            }
+
+            _delimiter = new Regex("[" + delimiter + "]+");
+        }
+
+        /// <summary>
+        /// Gets or sets the <see cref="CultureInfo"/> to use when parsing the numbers.
+        /// </summary>
+        /// <value>The culture info.</value>
+        /// <remarks>Defaults to <c>CultureInfo.CurrentCulture</c>.</remarks>
+        public CultureInfo CultureInfo
+        {
+            get
+            {
+                return _cultureInfo;
+            }
+
+            set
+            {
+                if (value != null)
+                {
+                    _cultureInfo = value;
+                }
+            }
+        }
+
+        /// <summary>
+        /// Gets or sets a value indicating whether the files has a header row.
+        /// </summary>
+        /// <value>
+        /// <c>true</c> if this instance has a header row; otherwise, <c>false</c>.
+        /// </value>
+        /// <remarks>Defaults to <see langword="false"/>.</remarks>
+        public bool HasHeaderRow
+        {
+            get;
+            set;
+        }
+
+        /// <summary>
+        /// Performs the actual reading.
+        /// </summary>
+        /// <param name="stream">The <see cref="Stream"/> to read the matrix from.</param>
+        /// <returns>
+        /// A matrix containing the data from the <see cref="Stream"/>. <see langword="null"/> is returned if the <see cref="Stream"/> is empty.
+        /// </returns>
+        protected override TMatrix DoReadMatrix(Stream stream)
+        {
+            var data = new List<string[]>();
+
+            // max is used to supports files like:
+            // 1,2
+            // 3,4,5,6
+            // 7
+            // this creates a 3x4 matrix:
+            // 1, 2, 0 ,0 
+            // 3, 4, 5, 6
+            // 7, 0, 0, 0
+            var max = -1;
+            var reader = new StreamReader(stream);
+            var line = reader.ReadLine();
+            if (HasHeaderRow)
+            {
+                line = reader.ReadLine();
+            }
+
+            while (line != null)
+            {
+                line = line.Trim();
+                if (line.Length > 0)
+                {
+                    var row = _delimiter.Split(line);
+                    max = Math.Max(max, row.Length);
+                    data.Add(row);
+                }
+
+                line = reader.ReadLine();
+            }
+
+            var ret = (TMatrix)Constructor.Invoke(new object[] { data.Count, max });
+            
+            if (data.Count != 0)
+            {
+                for (var i = 0; i < data.Count; i++)
+                {
+                    var row = data[i];
+                    for (var j = 0; j < row.Length; j++)
+                    {
+                        // strip off quotes
+                        var value = row[j].Replace("'", string.Empty).Replace("\"", string.Empty);
+                        ret[i, j] = double.Parse(value, NumberStyles.Any, _cultureInfo);
+                    }
+                }
+            }
+
+            reader.Close();
+            reader.Dispose();
+            return ret;
+        }
+    }
+}

src/Numerics/LinearAlgebra/Double/IO/MatrixReader.cs

@@ -0,0 +1,83 @@
+// <copyright file="MatrixReader.cs" company="Math.NET">
+// Math.NET Numerics, part of the Math.NET Project
+// http://numerics.mathdotnet.com
+// http://github.com/mathnet/mathnet-numerics
+// http://mathnetnumerics.codeplex.com
+// Copyright (c) 2009-2010 Math.NET
+// Permission is hereby granted, free of charge, to any person
+// obtaining a copy of this software and associated documentation
+// files (the "Software"), to deal in the Software without
+// restriction, including without limitation the rights to use,
+// copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the
+// Software is furnished to do so, subject to the following
+// conditions:
+// The above copyright notice and this permission notice shall be
+// included in all copies or substantial portions of the Software.
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+// EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+// OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+// NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+// HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+// WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+// OTHER DEALINGS IN THE SOFTWARE.
+// </copyright>
+
+namespace MathNet.Numerics.LinearAlgebra.Double.IO
+{
+    using System;
+    using System.IO;
+    using Properties;
+
+    /// <summary>
+    /// Base class to read a single <see cref="Matrix"/> from a file or stream.
+    /// </summary>
+    /// <typeparam name="TMatrix">The type of Matrix to return.</typeparam>
+    public abstract class MatrixReader<TMatrix> where TMatrix : Matrix
+    {
+        /// <summary>
+        /// Reads a <see cref="Matrix"/> from a file.
+        /// </summary>
+        /// <param name="file">The file to read the matrix from.</param>
+        /// <returns>A <see cref="Matrix"/> containing the data from the file. <see langword="null" /> is returned if the file is empty.</returns>
+        /// <exception cref="ArgumentNullException">If <paramref name="file"/> is <see langword="null" />.</exception>
+        /// <exception cref="IOException">If the file doesn't exist.</exception>
+        /// <exception cref="FormatException">If a value is not a number or not in a valid format.</exception>
+        /// <exception cref="OverflowException">If a value represents a number less than <see cref="Double.MinValue"/> or greater than <see cref="Double.MaxValue"/>.</exception>
+        public Matrix ReadMatrix(string file)
+        {
+            if (file == null)
+            {
+                throw new ArgumentNullException("file", Resources.StringNullOrEmpty);
+            }
+
+            return ReadMatrix(File.OpenRead(file));
+        }
+
+        /// <summary>
+        /// Reads a <see cref="Matrix"/> from a <see cref="Stream"/>.
+        /// </summary>
+        /// <param name="stream">The <see cref="Stream"/> to read the matrix from.</param>
+        /// <returns>A matrix containing the data from the <see cref="Stream"/>. <see langword="null" /> is returned if the <see cref="Stream"/> is empty.</returns>
+        /// <exception cref="ArgumentNullException">If <paramref name="stream"/> is <see langword="null" />.</exception>
+        /// <exception cref="FormatException">If a value is not a number or not in a valid format.</exception>
+        /// <exception cref="OverflowException">If a value represents a number less than <see cref="Double.MinValue"/> or greater than <see cref="Double.MaxValue"/>.</exception>
+        public TMatrix ReadMatrix(Stream stream)
+        {
+            if (stream == null)
+            {
+                throw new ArgumentNullException("stream");
+            }
+
+            return DoReadMatrix(stream);
+        }
+
+        /// <summary>
+        /// Subclasses override this method to do the actual reading.
+        /// </summary>
+        /// <param name="stream">The <see cref="Stream"/> to read the matrix from.</param>
+        /// <returns>A matrix containing the data from the <see cref="Stream"/>. <see langword="null" /> is returned if the <see cref="Stream"/> is empty.</returns>
+        protected abstract TMatrix DoReadMatrix(Stream stream);
+    }
+}

src/Numerics/Numerics.csproj

@@ -107,6 +107,8 @@
     <Compile Include="LinearAlgebra\Double\Factorization\UserLU.cs" />
     <Compile Include="LinearAlgebra\Double\Factorization\UserQR.cs" />
     <Compile Include="LinearAlgebra\Double\Factorization\UserSvd.cs" />
+    <Compile Include="LinearAlgebra\Double\IO\DelimitedReader.cs" />
+    <Compile Include="LinearAlgebra\Double\IO\MatrixReader.cs" />
     <Compile Include="LinearAlgebra\Double\ISolver.cs" />
     <Compile Include="LinearAlgebra\Double\Factorization\QR.cs" />
     <Compile Include="LinearAlgebra\Double\Factorization\Svd.cs" />
@@ -264,9 +266,7 @@
       <Install>true</Install>
     </BootstrapperPackage>
   </ItemGroup>
-  <ItemGroup>
+  <ItemGroup />
-    <Folder Include="LinearAlgebra\Double\IO\" />
-  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

src/Numerics/Properties/Resources.Designer.cs

@@ -618,6 +618,15 @@ namespace MathNet.Numerics.Properties {
             }
         }
         
+        /// <summary>
+        ///   Looks up a localized string similar to String parameter cannot be empty or null..
+        /// </summary>
+        internal static string StringNullOrEmpty {
+            get {
+                return ResourceManager.GetString("StringNullOrEmpty", resourceCulture);
+            }
+        }
+        
         /// <summary>
         ///   Looks up a localized string similar to The moment of the distribution is undefined..
         /// </summary>

src/Numerics/Properties/Resources.resx

@@ -312,4 +312,7 @@
   <data name="WorkArrayTooSmall" xml:space="preserve">
     <value>The given work array is too small. Check work[0] for the corret size.</value>
   </data>
+  <data name="StringNullOrEmpty" xml:space="preserve">
+    <value>String parameter cannot be empty or null.</value>
+  </data>
 </root>

src/Silverlight/Silverlight.csproj

@@ -260,6 +260,12 @@
     <Compile Include="..\Numerics\LinearAlgebra\Double\Factorization\UserSvd.cs">
       <Link>LinearAlgebra\Double\Factorization\UserSvd.cs</Link>
     </Compile>
+    <Compile Include="..\Numerics\LinearAlgebra\Double\IO\DelimitedReader.cs">
+      <Link>LinearAlgebra\Double\IO\DelimitedReader.cs</Link>
+    </Compile>
+    <Compile Include="..\Numerics\LinearAlgebra\Double\IO\MatrixReader.cs">
+      <Link>LinearAlgebra\Double\IO\MatrixReader.cs</Link>
+    </Compile>
     <Compile Include="..\Numerics\LinearAlgebra\Double\ISolver.cs">
       <Link>LinearAlgebra\Double\ISolver.cs</Link>
     </Compile>
@@ -408,9 +414,7 @@
       <LastGenOutput>Version.cs</LastGenOutput>
     </None>
   </ItemGroup>
-  <ItemGroup>
+  <ItemGroup />
-    <Folder Include="LinearAlgebra\Double\IO\" />
-  </ItemGroup>
   <Import Project="$(MSBuildExtensionsPath32)\Microsoft\Silverlight\$(SilverlightVersion)\Microsoft.Silverlight.CSharp.targets" />
   <ProjectExtensions>
     <VisualStudio>

src/UnitTests/LinearAlgebraTests/Double/IO/DelimitedReaderTests.cs

@@ -0,0 +1,121 @@
+namespace MathNet.Numerics.UnitTests.LinearAlgebraTests.Double.IO
+{
+    using System;
+    using System.Globalization;
+    using System.IO;
+    using System.Text;
+    using LinearAlgebra.Double;
+    using LinearAlgebra.Double.IO;
+    using MbUnit.Framework;
+
+    [TestFixture]
+    public class DelimitedReaderTests
+    {
+        [Test]
+        [MultipleAsserts]
+        public void CanParseCommaDelimitedData()
+        {
+            const string data =
+                @"a,b,c
+1
+""2.2"",0.3e1
+'4',5,6
+";
+            var reader = new DelimitedReader<DenseMatrix>(',')
+                         {
+                             HasHeaderRow = true
+                         };
+            var matrix = reader.ReadMatrix(new MemoryStream(Encoding.UTF8.GetBytes(data)));
+            Assert.AreEqual(3, matrix.RowCount);
+            Assert.AreEqual(3, matrix.ColumnCount);
+            Assert.AreEqual(1.0, matrix[0, 0]);
+            Assert.AreEqual(0.0, matrix[0, 1]);
+            Assert.AreEqual(0.0, matrix[0, 2]);
+            Assert.AreEqual(2.2, matrix[1, 0]);
+            Assert.AreEqual(3.0, matrix[1, 1]);
+            Assert.AreEqual(0.0, matrix[1, 2]);
+            Assert.AreEqual(4.0, matrix[2, 0]);
+            Assert.AreEqual(5.0, matrix[2, 1]);
+            Assert.AreEqual(6.0, matrix[2, 2]);
+        }
+
+        [Test]
+        [MultipleAsserts]
+        public void CanParseTabDelimtedData()
+        {
+            var data = "1"
+                       + Environment.NewLine
+                       + "\"2.2\"\t\t0.3e1"
+                       + Environment.NewLine
+                       + "'4'\t5\t6";
+
+            var reader = new DelimitedReader<DenseMatrix>('\t');
+            var matrix = reader.ReadMatrix(new MemoryStream(Encoding.UTF8.GetBytes(data)));
+            Assert.AreEqual(3, matrix.RowCount);
+            Assert.AreEqual(3, matrix.ColumnCount);
+            Assert.AreEqual(1.0, matrix[0, 0]);
+            Assert.AreEqual(0.0, matrix[0, 1]);
+            Assert.AreEqual(0.0, matrix[0, 2]);
+            Assert.AreEqual(2.2, matrix[1, 0]);
+            Assert.AreEqual(3.0, matrix[1, 1]);
+            Assert.AreEqual(0.0, matrix[1, 2]);
+            Assert.AreEqual(4.0, matrix[2, 0]);
+            Assert.AreEqual(5.0, matrix[2, 1]);
+            Assert.AreEqual(6.0, matrix[2, 2]);
+        }
+
+        [Test]
+        [MultipleAsserts]
+        public void CanParseWhiteSpaceDelimitedData()
+        {
+            const string data =
+                @"1
+""2.2"" 0.3e1
+'4'   5      6
+";
+            var reader = new DelimitedReader<DenseMatrix>();
+            var matrix = reader.ReadMatrix(new MemoryStream(Encoding.UTF8.GetBytes(data)));
+            Assert.AreEqual(3, matrix.RowCount);
+            Assert.AreEqual(3, matrix.ColumnCount);
+            Assert.AreEqual(1.0, matrix[0, 0]);
+            Assert.AreEqual(0.0, matrix[0, 1]);
+            Assert.AreEqual(0.0, matrix[0, 2]);
+            Assert.AreEqual(2.2, matrix[1, 0]);
+            Assert.AreEqual(3.0, matrix[1, 1]);
+            Assert.AreEqual(0.0, matrix[1, 2]);
+            Assert.AreEqual(4.0, matrix[2, 0]);
+            Assert.AreEqual(5.0, matrix[2, 1]);
+            Assert.AreEqual(6.0, matrix[2, 2]);
+        }
+
+        [Test]
+        [MultipleAsserts]
+        public void CanParsePeriodDelimitedData()
+        {
+            const string data =
+                @"a.b.c
+1
+""2,2"".0,3e1
+'4,0'.5,0.6,0
+";
+            var reader = new DelimitedReader<DenseMatrix>('.')
+                         {
+                             HasHeaderRow = true, 
+                             CultureInfo = new CultureInfo("tr-TR")
+                         };
+
+            var matrix = reader.ReadMatrix(new MemoryStream(Encoding.UTF8.GetBytes(data)));
+            Assert.AreEqual(3, matrix.RowCount);
+            Assert.AreEqual(3, matrix.ColumnCount);
+            Assert.AreEqual(1.0, matrix[0, 0]);
+            Assert.AreEqual(0.0, matrix[0, 1]);
+            Assert.AreEqual(0.0, matrix[0, 2]);
+            Assert.AreEqual(2.2, matrix[1, 0]);
+            Assert.AreEqual(3.0, matrix[1, 1]);
+            Assert.AreEqual(0.0, matrix[1, 2]);
+            Assert.AreEqual(4.0, matrix[2, 0]);
+            Assert.AreEqual(5.0, matrix[2, 1]);
+            Assert.AreEqual(6.0, matrix[2, 2]);
+        }
+    }
+}

src/UnitTests/UnitTests.csproj

@@ -96,6 +96,7 @@
     <Compile Include="LinearAlgebraTests\Double\Factorization\UserSvdTests.cs" />
     <Compile Include="LinearAlgebraTests\Double\Factorization\SvdTests.cs" />
     <Compile Include="LinearAlgebraTests\Double\Factorization\QRTests.cs" />
+    <Compile Include="LinearAlgebraTests\Double\IO\DelimitedReaderTests.cs" />
     <Compile Include="LinearAlgebraTests\Double\SparseMatrixTests.cs" />
     <Compile Include="PermutationTest.cs" />
     <Compile Include="DistributionTests\CommonDistributionTests.cs" />