Merge pull request #75 from cuda/zlib

Removed zlib dependency and fixed a sparse matrix parsing bug

src/Numerics.IO/LinearAlgebra/IO/Matlab/Adler32.cs

@@ -0,0 +1,93 @@
+// <copyright file="Adler32.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) 2013 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>
+
+/* This code is a port and simplification of 
+  adler32.c -- compute the Adler-32 checksum of a data stream
+  Copyright (C) 1995-2011 Mark Adler
+  zlib license:
+  Copyright (C) 1995-2012 Jean-loup Gailly and Mark Adler
+
+  This software is provided 'as-is', without any express or implied
+  warranty.  In no event will the authors be held liable for any damages
+  arising from the use of this software.
+
+  Permission is granted to anyone to use this software for any purpose,
+  including commercial applications, and to alter it and redistribute it
+  freely, subject to the following restrictions:
+
+  1. The origin of this software must not be misrepresented; you must not
+     claim that you wrote the original software. If you use this software
+     in a product, an acknowledgment in the product documentation would be
+     appreciated but is not required.
+  2. Altered source versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+  3. This notice may not be removed or altered from any source distribution.
+
+  Jean-loup Gailly        Mark Adler
+  jloup@gzip.org          madler@alumni.caltech.edu
+
+*/
+
+namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
+{
+    internal static class Adler32
+    {
+        /* largest prime smaller than 65536 */
+        const int Base = 65521; 
+        /* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */
+        const int Nmax = 5552;
+
+        /// <summary>
+        /// Computes the Adler-32 checksum of the given data.
+        /// </summary>
+        /// <param name="data">The data to create the checksum.</param>
+        /// <returns>The checksum</returns>
+        public static uint Compute(byte[] data)
+        {
+            uint adler = 1;
+            uint sum2 = 0;
+            var len = data.Length;
+            var offset = 0;
+            while (len > 0)
+            {
+                var tlen = len < Nmax ? len : Nmax;
+                len -= tlen;
+
+                do
+                {
+                    adler += data[offset++];
+                    sum2 += adler;
+                } while (--tlen > 0);
+
+                adler %= Base;
+                sum2 %= Base;
+            }
+            return adler | (sum2 << 16);
+        }
+    }
+}

src/Numerics.IO/LinearAlgebra/IO/Matlab/MatlabParser.cs

@@ -24,6 +24,8 @@
 // OTHER DEALINGS IN THE SOFTWARE.
 // </copyright>
 
+using System.IO.Compression;
+
 namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
 {
     using System;
@@ -34,7 +36,6 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
     using System.Text;
     using Generic;
     using Properties;
-    using zlib;
     using Complex32 = Numerics.Complex32;
 
     /// <summary>
@@ -221,11 +222,12 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
         private static byte[] DecompressBlock(byte[] compressed, ref DataType type)
         {
             byte[] data;
-            using (var decompressed = new MemoryStream())
+            using (var compressedStream = new MemoryStream(compressed, 2, compressed.Length-6))
             {
-                using (var decompressor = new ZOutputStream(decompressed))
+                using (var decompressor = new DeflateStream(compressedStream, CompressionMode.Decompress))
+                using(var decompressed = new MemoryStream())
                 {
-                    decompressor.Write(compressed, 0, compressed.Length);
+                    decompressor.CopyTo(decompressed);
                     decompressed.Position = 0;
                     var buf = new byte[4];
                     decompressed.Read(buf, 0, 4);
@@ -410,7 +412,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
             for (var i = 0; i < ir.Count; i++)
             {
                 var row = ir[i];
-                if (jc[col + 1] == i)
+                while(jc[col + 1] == i)
                 {
                     col++;
                 }
@@ -467,7 +469,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
             for (var i = 0; i < ir.Count; i++)
             {
                 var row = ir[i];
-                if (jc[col + 1] == i)
+                while (jc[col + 1] == i)
                 {
                     col++;
                 }
@@ -526,7 +528,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
             for (var i = 0; i < ir.Count; i++)
             {
                 var row = ir[i];
-                if (jc[col + 1] == i)
+                while (jc[col + 1] == i)
                 {
                     col++;
                 }
@@ -582,7 +584,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
                 for (var i = 0; i < ir.Count; i++)
                 {
                     var row = ir[i];
-                    if (jc[col + 1] == i)
+                    while (jc[col + 1] == i)
                     {
                         col++;
                     }
@@ -643,7 +645,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
             for (var i = 0; i < ir.Count; i++)
             {
                 var row = ir[i];
-                if (jc[col + 1] == i)
+                while (jc[col + 1] == i)
                 {
                     col++;
                 }
@@ -700,7 +702,7 @@ namespace MathNet.Numerics.LinearAlgebra.IO.Matlab
                 for (var i = 0; i < ir.Count; i++)
                 {
                     var row = ir[i];
-                    if (jc[col + 1] == i)
+                    while (jc[col + 1] == i)
                     {
                         col++;
                     }

src/Numerics.IO/LinearAlgebra/IO/MatlabWriter.cs

@@ -4,7 +4,7 @@
 // http://github.com/mathnet/mathnet-numerics
 // http://mathnetnumerics.codeplex.com
 //
-// Copyright (c) 2009-2010 Math.NET
+// Copyright (c) 2009-2013 Math.NET
 //
 // Permission is hereby granted, free of charge, to any person
 // obtaining a copy of this software and associated documentation
@@ -29,8 +29,8 @@
 using System;
 using System.Collections.Generic;
 using System.IO;
+using System.IO.Compression;
 using System.Text;
-using zlib;
 
 namespace MathNet.Numerics.LinearAlgebra.IO
 {
@@ -285,13 +285,19 @@ namespace MathNet.Numerics.LinearAlgebra.IO
         /// <returns>The compressed data.</returns>
         private static byte[] CompressData(byte[] data)
         {
+            var adler = BitConverter.GetBytes(Adler32.Compute(data));
             using (var compressedStream = new MemoryStream())
             {
-                using (var outputStream = new ZOutputStream(compressedStream, zlibConst.Z_DEFAULT_COMPRESSION))
+                compressedStream.WriteByte(0x58);
+                compressedStream.WriteByte(0x85);
+                using (var outputStream = new DeflateStream(compressedStream, CompressionMode.Compress, true))
                 {
                     outputStream.Write(data, 0, data.Length);
                 }
-
+                compressedStream.WriteByte(adler[3]);
+                compressedStream.WriteByte(adler[2]);
+                compressedStream.WriteByte(adler[1]);
+                compressedStream.WriteByte(adler[0]);
                 return compressedStream.ToArray();
             }
         }

src/Numerics.IO/Numerics.IO.csproj

@@ -60,10 +60,6 @@
     <Reference Include="Microsoft.CSharp" />
     <Reference Include="System.Data" />
     <Reference Include="System.Xml" />
-    <Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">
-      <SpecificVersion>False</SpecificVersion>
-      <HintPath>..\..\packages\zlib.net.1.0.4.0\lib\zlib.net.dll</HintPath>
-    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="LinearAlgebra\Complex32\IO\DelimitedReader.cs" />
@@ -76,6 +72,7 @@
     <Compile Include="LinearAlgebra\IO\DelimitedWriter.cs" />
     <Compile Include="LinearAlgebra\IO\MatlabReader.cs" />
     <Compile Include="LinearAlgebra\IO\MatlabWriter.cs" />
+    <Compile Include="LinearAlgebra\IO\Matlab\Adler32.cs" />
     <Compile Include="LinearAlgebra\IO\Matlab\ArrayClass.cs" />
     <Compile Include="LinearAlgebra\IO\Matlab\ArrayFlags.cs" />
     <Compile Include="LinearAlgebra\IO\Matlab\DataType.cs" />

src/UnitTests/LinearAlgebraTests/Complex/IO/MatlabWriterTests.cs

@@ -97,16 +97,14 @@ namespace MathNet.Numerics.UnitTests.LinearAlgebraTests.Complex.IO
             }
 
             Matrix mat3 = new SparseMatrix(5, 4);
-            for (var i = 0; i < mat3.ColumnCount; i++)
+            mat3[0, 0] = new Complex(1.1, 1.1);
-            {
+            mat3[0, 2] = new Complex(2.2, 2.2);
-                mat3[i, i] = new Complex(i + .1, i + .1);
+            mat3[4, 3] = new Complex(3.3, 3.3);
-            }
 
             Matrix mat4 = new SparseMatrix(3, 5);
-            for (var i = 0; i < mat4.RowCount; i++)
+            mat4[0, 0] = new Complex(1.1, 1.1);
-            {
+            mat4[0, 2] = new Complex(2.2, 2.2);
-                mat4[i, i] = new Complex(i + .1, i + .1);
+            mat4[2, 4] = new Complex(3.3, 3.3);
-            }
 
             var write = new[] { mat1, mat2, mat3, mat4 };
 

src/UnitTests/LinearAlgebraTests/Complex32/IO/MatlabWriterTests.cs

@@ -97,16 +97,14 @@ namespace MathNet.Numerics.UnitTests.LinearAlgebraTests.Complex32.IO
             }
 
             Matrix mat3 = new SparseMatrix(5, 4);
-            for (var i = 0; i < mat3.ColumnCount; i++)
+            mat3[0, 0] = new Complex32(1.1f, 1.1f);
-            {
+            mat3[0, 2] = new Complex32(2.2f, 2.2f);
-                mat3[i, i] = new Complex32(i + .1f, i + .1f);
+            mat3[4, 3] = new Complex32(3.3f, 3.3f);
-            }
 
             Matrix mat4 = new SparseMatrix(3, 5);
-            for (var i = 0; i < mat4.RowCount; i++)
+            mat4[0, 0] = new Complex32(1.1f, 1.1f);
-            {
+            mat4[0, 2] = new Complex32(2.2f, 2.2f);
-                mat4[i, i] = new Complex32(i + .1f, i + .1f);
+            mat4[2, 4] = new Complex32(3.3f, 3.3f);
-            }
 
             var write = new[] { mat1, mat2, mat3, mat4 };
 

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

@@ -96,16 +96,14 @@ namespace MathNet.Numerics.UnitTests.LinearAlgebraTests.Double.IO
             }
 
             Matrix mat3 = new SparseMatrix(5, 4);
-            for (var i = 0; i < mat3.ColumnCount; i++)
+            mat3[0, 0] = 1.1;
-            {
+            mat3[0, 2] = 2.2;
-                mat3[i, i] = i + .1;
+            mat3[4, 3] = 3.3;
-            }
 
             Matrix mat4 = new SparseMatrix(3, 5);
-            for (var i = 0; i < mat4.RowCount; i++)
+            mat4[0, 0] = 1.1;
-            {
+            mat4[0, 2] = 2.2;
-                mat4[i, i] = i + .1;
+            mat4[2, 4] = 3.3;
-            }
 
             var write = new[] { mat1, mat2, mat3, mat4 };
 

src/UnitTests/LinearAlgebraTests/Single/IO/MatlabWriterTests.cs

@@ -95,16 +95,14 @@ namespace MathNet.Numerics.UnitTests.LinearAlgebraTests.Single.IO
             }
 
             Matrix mat3 = new SparseMatrix(5, 4);
-            for (var i = 0; i < mat3.ColumnCount; i++)
+            mat3[0, 0] = 1.1f;
-            {
+            mat3[0, 2] = 2.2f;
-                mat3[i, i] = i + .1f;
+            mat3[4, 3] = 3.3f;
-            }
 
             Matrix mat4 = new SparseMatrix(3, 5);
-            for (var i = 0; i < mat4.RowCount; i++)
+            mat4[0, 0] = 1.1f;
-            {
+            mat4[0, 2] = 2.2f;
-                mat4[i, i] = i + .1f;
+            mat4[2, 4] = 3.3f;
-            }
 
             var write = new[] { mat1, mat2, mat3, mat4 };
 

src/UnitTests/UnitTests.csproj

@@ -62,10 +62,6 @@
     <Reference Include="Microsoft.CSharp" />
     <Reference Include="System.Data" />
     <Reference Include="System.Xml" />
-    <Reference Include="zlib.net, Version=1.0.3.0, Culture=neutral, PublicKeyToken=47d7877cb3620160">
-      <SpecificVersion>False</SpecificVersion>
-      <HintPath>..\..\packages\zlib.net.1.0.4.0\lib\zlib.net.dll</HintPath>
-    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="ArrayHelpers.cs" />