[ADD] enhanced the WLoaderFibers to read points, added endian tools in WIOTools

src/dataHandler/io/CMakeLists.txt

@@ -3,7 +3,7 @@ ADD_SUBDIRECTORY( test )
 ADD_SUBDIRECTORY( nifti )
 ADD_SUBDIRECTORY( biosig )
 
-FILE( GLOB DATAHANDLER_LOADERS_SRC "WLoader*.cpp" )
+FILE( GLOB DATAHANDLER_LOADERS_SRC "WLoader*.cpp" "*.hpp" )
 
 # Unit tests
 IF( CXXTEST_FOUND )

src/dataHandler/io/WIOTools.hpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WIOTOOLS_HPP
+#define WIOTOOLS_HPP
+
+#include <stdint.h>
+
+#include <cassert>
+
+/**
+ * Namespaces for several tools we may need while doing IO
+ */
+namespace wiotools
+{
+    /**
+     * Checks if you are on a big endian machine or not.
+     */
+    inline bool isBigEndian()
+    {
+        union {
+            uint32_t i;
+            char c[4];
+        } some = {0x01020304}; // assigning an 32 bit unsigned integer // NOLINT
+
+        return some.c[0] == 1; 
+    }
+
+
+    /**
+     * Transforms a value of type T into the opposite byte order.
+     */
+    template< class T > T switchByteOrder( const T value )
+    {
+        size_t numBytes = sizeof( T );
+        T result = value;
+        if( numBytes == 1 )
+            return result;
+        assert( numBytes % 2 == 0  && numBytes > 0 );
+        char *s  = reinterpret_cast< char* >( &result );
+        for( size_t i = 0; i < numBytes / 2; ++i ) {
+            std::swap( s[i], s[ ( numBytes - 1 ) - i ] );
+        }
+        return result;
+    }
+
+    /**
+     * Transform a whole array of elements (of type T and size of sizeof(T))
+     * into opposite byte order.
+     */
+    template< class T > void switchByteOrderOfArray( T *array, const size_t arraySize )
+    {
+        for( size_t i = 0; i < arraySize; ++i ) {
+            array[i] = switchByteOrder< T >( array[i] );
+        }
+    }
+
+}
+
+#endif  // WIOTOOLS_HPP

src/dataHandler/io/WLoaderFibers.cpp

@@ -22,6 +22,7 @@
 //
 //---------------------------------------------------------------------------
 
+#include <stdint.h>
 #include <cassert>
 #include <fstream>
 #include <string>
@@ -31,6 +32,7 @@
 #include <boost/lexical_cast.hpp>
 
 #include "WLoaderFibers.h"
+#include "WIOTools.hpp"
 #include "../WDataHandler.h"
 #include "../../common/WStringUtils.hpp"
 #include "../../math/WPosition.h"
@@ -90,8 +92,6 @@ void WLoaderFibers::readHeader() throw( WDHIOFailure, WDHException )
     {
         throw WDHIOFailure( "Reading first 4 lines of '" + m_fileName + "': " + e.what() );
     }
-    std::cout << m_fileName << std::endl;
-    std::cout << m_header << std::endl;
 
     // check if the header may be valid for the .fib format
     if( m_header.at(0) != "# vtk DataFile Version 3.0" )
@@ -126,24 +126,34 @@ void WLoaderFibers::readPoints()
     {
         throw WDHIOFailure( "Error reading POINTS declaration '" + m_fileName + "': " + e.what() );
     }
-// TODO(math): fix this since stylecheckers complains about long, and we want
-//             int64 not W_DT_INT64 so see dataHandler/WDataHandlerEnums.h:
-//             line 49: W_DT_INT64 = 1024,  /* long long (64 bits) */
-//    namespace su = string_utils;
-//    long numPoints = 0;
-//    std::vector< std::string > tokens = su::tokenize( line );
-//    if( tokens.size() < 3 || su::toLower( tokens.at( 2 ) ) != "float" )
-//    {
-//        throw WDHException( "Invalid VTK POINTS declaration: " + line );
-//    }
-//    try
-//    {
-//        numPoints = boost::lexical_cast< long >( tokens.at( 1 ) );
-//    }
-//    catch( const boost::bad_lexical_cast &e )
-//    {
-//        throw WDHException( "Invalid number of points: " + tokens.at( 1 ) );
-//    }
-//
-//    std::vector< wmath::WPosition > points( numPoints );
+    namespace su = string_utils;
+    size_t numPoints = 0;
+    std::vector< std::string > tokens = su::tokenize( line );
+    if( tokens.size() < 3 || su::toLower( tokens.at( 2 ) ) != "float" )
+    {
+        throw WDHException( "Invalid VTK POINTS declaration: " + line );
+    }
+    try
+    {
+        numPoints = boost::lexical_cast< size_t >( tokens.at( 1 ) );
+    }
+    catch( const boost::bad_lexical_cast &e )
+    {
+        throw WDHException( "Invalid number of points: " + tokens.at( 1 ) );
+    }
+
+    m_points.reserve( numPoints );
+    float *pointData = new float[ 3 * numPoints ];
+    m_ifs->read( reinterpret_cast< char* >( pointData ), 3 * sizeof( float ) * numPoints );
+
+    // all 4 bytes of each float are in wrong order we need to reorder them
+    wiotools::switchByteOrderOfArray( pointData, 3 * numPoints );
+
+    for( size_t i = 0; i < numPoints; ++i )
+    {
+        m_points.push_back( wmath::WPosition( pointData[i * 3],
+                                              pointData[i * 3 + 1],
+                                              pointData[i * 3 + 2] ) );
+    }
+    delete[] pointData;
 }

src/dataHandler/io/WLoaderFibers.h

@@ -33,6 +33,7 @@
 
 #include "../WLoader.h"
 #include "../exceptions/WDHIOFailure.h"
+#include "../../math/WPosition.h"
 
 class WDataHandler;
 
@@ -83,6 +84,11 @@ protected:
      */
     std::vector< std::string > m_header;
 
+    /**
+     * Point vector for all fibers
+     */
+    std::vector< wmath::WPosition > m_points;
+
     /**
      * Pointer to the input file stream reader.
      */

src/dataHandler/io/test/WIOTools_test.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WIOTOOLS_TEST_H
+#define WIOTOOLS_TEST_H
+
+#include <cxxtest/TestSuite.h>
+
+#include "../WIOTools.hpp"
+
+/**
+ * Unit test helper functions in the wiotools namespace
+ */
+class WIOToolsTest : public CxxTest::TestSuite
+{
+public:
+    /**
+     * When switching byte order, the first and last bytes should be swapped
+     * and the bytes inbetween too.
+     */
+    void testByteOrderSwitching( void )
+    {
+        uint32_t x = 1;
+        TS_ASSERT_EQUALS( x, 1 );
+        x = wiotools::switchByteOrder( x );
+        TS_ASSERT_EQUALS( x, 16777216 );
+        x = wiotools::switchByteOrder( x );
+        TS_ASSERT_EQUALS( x, 1 );
+    }
+
+    /**
+     * Since templates should work on multiple types we just use double here.
+     */
+    void testByteOrderSwitchingOnFloats( void )
+    {
+        double x = 3.141592653589793238462643383279502884197169399375105820974;
+        double original = x;
+        x = wiotools::switchByteOrder( x );
+        TS_ASSERT_DIFFERS( x, original );
+        x = wiotools::switchByteOrder( x );
+        TS_ASSERT_EQUALS( x, original );
+    }
+
+    /**
+     * On single bytes we should do nothing.
+     */
+    void testByteOrderSwitchingOnSingleBytes( void )
+    {
+        char x = 1;
+        TS_ASSERT_EQUALS( wiotools::switchByteOrder( x ), x );
+    }
+
+    /**
+     * When switching the byte order of an whole array every element should be
+     * switched.
+     */
+    void testByteOrderSwitchOnArray( void )
+    {
+        uint32_t x[] = { 1, 16777216 };
+        wiotools::switchByteOrderOfArray( x, 2 );
+        TS_ASSERT_EQUALS( x[0], 16777216 );
+        TS_ASSERT_EQUALS( x[1], 1 );
+    }
+};
+
+#endif  // WIOTOOLS_TEST_H

src/dataHandler/io/test/WLoaderFibers_test.h

@@ -182,7 +182,22 @@ public:
                                  std::string( "Unexpected end of file: fixtures/Fibers/crippled_header.fib" ) );
     }
 
-
+    /**
+     * After reading the points the point vector of WLoaderFibers should be
+     * filled with valid numbers.
+     */
+    void testReadPoints( void )
+    {
+        WLoaderFibers loader( "fixtures/Fibers/valid_small_example.fib", m_dataHandler );
+        loader.readHeader();
+        loader.readPoints();
+        double delta = 0.0001;
+        TS_ASSERT_EQUALS( loader.m_points.size(), 1224 );
+        TS_ASSERT_DELTA( loader.m_points.at( 1223 )[2], 60.4135, delta );
+        TS_ASSERT_DELTA( loader.m_points.at( 0 )[0], 46.2582, delta );
+        TS_ASSERT_DELTA( loader.m_points.at( 0 )[1], 36.7184, delta );
+        TS_ASSERT_DELTA( loader.m_points.at( 0 )[2], 65.7245, delta );
+    }
 
 private:
     /**