Merge pull request #37 from favreau/master

Added support for sequence of volumes

brayns/Brayns.cpp

@@ -78,6 +78,7 @@ struct Brayns::Impl
 
         // Build geometry
         loadData();
+        scene->commitVolumeData();
         scene->buildEnvironment( );
         scene->buildGeometry( );
 
@@ -140,13 +141,13 @@ struct Brayns::Impl
 
         if(!volumeParameters.getFilename().empty() || !volumeParameters.getFolder().empty())
         {
+            scene->getVolumeHandler()->setTimestamp( 0.f );
             const Vector3ui& volumeDimensions = scene->getVolumeHandler()->getDimensions();
-            const Vector3f& volumeScale = volumeParameters.getScale();
+            const Vector3f& volumeElementSpacing = volumeParameters.getElementSpacing();
             Boxf& worldBounds = scene->getWorldBounds();
             worldBounds.merge( Vector3f( 0.f, 0.f, 0.f ));
-            worldBounds.merge( Vector3f( volumeDimensions ) * volumeScale );
+            worldBounds.merge( Vector3f( volumeDimensions ) * volumeElementSpacing );
         }
-        scene->commitVolumeData();
 
         if( scene->isEmpty() && !scene->getVolumeHandler() )
             scene->buildDefault();

brayns/common/scene/Scene.cpp

@@ -30,7 +30,6 @@
 #include <servus/uri.h>
 
 #include <boost/filesystem.hpp>
-#include <algorithm>
 
 namespace brayns
 {
@@ -160,6 +159,8 @@ void Scene::buildDefault( )
 {
     BRAYNS_INFO << "Building default Cornell Box scene" << std::endl;
 
+    const Vector3f WHITE = { 1.f, 1.f, 1.f };
+
     const Vector3f positions[8] =
     {
         {  0.f, 0.f, 0.f },
@@ -192,26 +193,24 @@ void Scene::buildDefault( )
         { 0.8f, 0.8f, 0.8f }
     };
 
-    const Vector3f WHITE = { 1.f, 1.f, 1.f };
-
     // Cornell box
     for( size_t material = 1; material < 6; ++material )
     {
-        _materials[material]->setColor( colors[material] );
+        _materials[material]->setColor( colors[ material ] );
         _materials[material]->setSpecularColor( WHITE );
         _materials[material]->setSpecularExponent( 10.f );
         _materials[material]->setReflectionIndex( material == 4 ? 0.8f : 0.f );
         _materials[material]->setOpacity( 1.f );
         for( size_t i = 0; i < 6; ++i )
         {
-            const Vector3f& position = positions[ indices[material][i] ];
+            const Vector3f& position = positions[ indices[ material ][ i ] ];
             _trianglesMeshes[material].getVertices().push_back( position );
             _bounds.merge( position );
-            _trianglesMeshes[material].getIndices().push_back(
-                Vector3i( 0, 1, 2 ));
-            _trianglesMeshes[material].getIndices().push_back(
-                Vector3i( 3, 4, 5 ));
         }
+        _trianglesMeshes[material].getIndices().push_back(
+            Vector3ui( 0, 1, 2 ));
+        _trianglesMeshes[material].getIndices().push_back(
+            Vector3ui( 3, 4, 5 ));
     }
 
     size_t material = 7;
@@ -514,21 +513,23 @@ AbstractSimulationHandlerPtr Scene::getSimulationHandler() const
 
 VolumeHandlerPtr Scene::getVolumeHandler()
 {
+    const std::string& volumeFile =
+        _parametersManager.getVolumeParameters().getFilename();
+    const std::string& volumeFolder =
+        _parametersManager.getVolumeParameters().getFolder();
+    if( volumeFile.empty() && volumeFolder.empty() )
+        return 0;
+
     try
     {
-        const std::string& volumeFile =
-            _parametersManager.getVolumeParameters().getFilename();
-        const std::string& volumeFolder =
-            _parametersManager.getVolumeParameters().getFolder();
-
-        if( !_volumeHandler && ( !volumeFile.empty() || !volumeFolder.empty() ))
+        if( !_volumeHandler )
         {
-            _volumeHandler.reset( new VolumeHandler( _parametersManager.getVolumeParameters() ));
+            _volumeHandler.reset( new VolumeHandler(
+                _parametersManager.getVolumeParameters(), TimestampMode::modulo ));
             if( !volumeFile.empty() )
                 _volumeHandler->attachVolumeToFile( 0.f, volumeFile );
             else
             {
-                float timestamp = 0.f;
                 strings filenames;
 
                 boost::filesystem::directory_iterator endIter;
@@ -550,6 +551,7 @@ VolumeHandlerPtr Scene::getVolumeHandler()
                     }
                 }
                 std::sort(filenames.begin(), filenames.end());
+                float timestamp = 0.f;
                 for( const auto& filename: filenames )
                 {
                     _volumeHandler->attachVolumeToFile( timestamp, filename );

brayns/common/types.h

@@ -299,6 +299,13 @@ enum CameraType
     CT_PANORAMIC
 };
 
+enum class TimestampMode
+{
+    unchanged,
+    modulo,
+    bounded
+};
+
 }
 
 #endif // TYPES_H

brayns/common/volume/VolumeHandler.cpp

@@ -28,66 +28,170 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 
+namespace
+{
+const int NO_DESCRIPTOR = -1;
+}
+
 namespace brayns
 {
 
 VolumeHandler::VolumeHandler(
-    const VolumeParameters& volumeParameters )
-    : _dimensions( volumeParameters.getDimensions() )
+    VolumeParameters& volumeParameters,
+    const TimestampMode timestampMode )
+    : _volumeParameters( &volumeParameters )
+    , _timestamp( std::numeric_limits<float>::max( ))
+    , _timestampRange( std::numeric_limits<float>::max(), std::numeric_limits<float>::min( ))
+    , _timestampMode( timestampMode )
 {
 }
 
 VolumeHandler::~VolumeHandler()
 {
-    for( auto memoryMapPtr: _memoryMapPtrs )
-        if( memoryMapPtr.second )
-            ::munmap( (void *)memoryMapPtr.second, _size );
-
-    for( auto cacheFileDescriptor: _cacheFileDescriptors )
-        if( cacheFileDescriptor.second != -1 )
-            ::close( cacheFileDescriptor.second );
+    _volumeDescriptors.clear();
 }
 
 void VolumeHandler::attachVolumeToFile( const float timestamp, const std::string& volumeFile )
 {
-    BRAYNS_INFO << "Attaching " << volumeFile << " to timestamp " << timestamp << std::endl;
-    _cacheFileDescriptors[ timestamp ] = open( volumeFile.c_str(), O_RDONLY );
-    if( _cacheFileDescriptors[ timestamp ] == -1 )
-        BRAYNS_THROW( std::runtime_error( "Failed to attach " + volumeFile ));
+    // Add volume descriptor for specified timestamp
+    _volumeDescriptors[ timestamp ].reset( new VolumeDescriptor(
+        volumeFile,
+        _volumeParameters->getDimensions(),
+        _volumeParameters->getElementSpacing(),
+        _volumeParameters->getOffset()));
 
-    struct stat sb;
-    if( ::fstat( _cacheFileDescriptors[ timestamp ], &sb ) == -1 )
-        BRAYNS_THROW( std::runtime_error( "Failed to attach " + volumeFile ));
+    // Update timestamp range
+    for( const auto& volumeDescriptor: _volumeDescriptors )
+    {
+        _timestampRange.x() = std::min( _timestampRange.x(), volumeDescriptor.first );
+        _timestampRange.y() = std::max( _timestampRange.y(), volumeDescriptor.first );
+    }
+    BRAYNS_INFO << "Attached " << volumeFile << " to timestamp "
+                << timestamp << " " << _timestampRange << std::endl;
+}
 
-    _memoryMapPtrs[ timestamp ] = ::mmap(
-        0, sb.st_size, PROT_READ, MAP_PRIVATE, _cacheFileDescriptors[ timestamp ], 0 );
-    if( _memoryMapPtrs[ timestamp ] == MAP_FAILED )
+void VolumeHandler::setTimestamp( const float timestamp )
+{
+    const float ts = _getBoundedTimestamp( timestamp );
+    if( ts != _timestamp &&
+        _volumeDescriptors.find( ts ) != _volumeDescriptors.end( ))
     {
-        _memoryMapPtrs[ timestamp ] = 0;
-        ::close( _cacheFileDescriptors[ timestamp ] );
-        BRAYNS_THROW( std::runtime_error( "Failed to attach " + volumeFile ));
+        if( _volumeDescriptors.find( _timestamp ) != _volumeDescriptors.end( ))
+            _volumeDescriptors[ _timestamp ]->unmap();
+        _timestamp = ts;
+        _volumeDescriptors[ _timestamp ]->map();
     }
+}
 
-    _size = sb.st_size;
+void* VolumeHandler::getData() const
+{
+    return _volumeDescriptors.at( _timestamp )->getMemoryMapPtr();
+}
 
-    BRAYNS_INFO << "Volume size      : " << _size << " bytes ["
-                <<  _size / 1048576 << " MB]" << std::endl;
-    BRAYNS_INFO << "Volume dimensions: " << _dimensions << std::endl;
-    BRAYNS_INFO << "Successfully attached to " << volumeFile << std::endl;
+float VolumeHandler::getEpsilon(
+    const Vector3f& elementSpacing,
+    const uint16_t samplesPerRay )
+{
+    const Vector3f diag = _volumeDescriptors.at( _timestamp )->getDimensions( ) * elementSpacing;
+    return diag.find_max() / float( samplesPerRay );
+}
+
+const Vector3ui VolumeHandler::getDimensions() const
+{
+    return _volumeDescriptors.at( _timestamp )->getDimensions();
+}
+
+const Vector3f VolumeHandler::getElementSpacing() const
+{
+    return _volumeDescriptors.at( _timestamp )->getElementSpacing();
 }
 
-void* VolumeHandler::getData( const float timestamp )
+const Vector3f VolumeHandler::getOffset() const
 {
-    size_t ts = timestamp;
-    ts = ts % _memoryMapPtrs.size();
-    BRAYNS_INFO << "Assigning volume for timestamp " << ts << std::endl;
-    return _memoryMapPtrs[ ts ];
+    return _volumeDescriptors.at( _timestamp )->getOffset();
 }
 
-float VolumeHandler::getEpsilon( const Vector3f& scale, const uint16_t samplesPerRay )
+uint64_t VolumeHandler::getSize() const
 {
-    Vector3f diag = Vector3f(_dimensions) * scale;
-    return std::max(diag.x(), std::max( diag.y(), diag.z())) / float( samplesPerRay );
+    return _volumeDescriptors.at( _timestamp )->getSize();
+}
+
+float VolumeHandler::_getBoundedTimestamp( const float timestamp ) const
+{
+    float result;
+    switch( _timestampMode )
+    {
+    case TimestampMode::modulo:
+        result = size_t( timestamp + _timestampRange.x( )) % _volumeDescriptors.size();
+        break;
+    case TimestampMode::bounded:
+        result = std::max( std::min( timestamp, _timestampRange.y( )), _timestampRange.x( ));
+    case TimestampMode::unchanged:
+    default:
+        result = timestamp;
+    }
+    return result;
+}
+
+VolumeHandler::VolumeDescriptor::VolumeDescriptor(
+    const std::string& filename,
+    const Vector3ui& dimensions,
+    const Vector3f& elementSpacing,
+    const Vector3f& offset )
+    : _filename( filename )
+    , _memoryMapPtr( 0 )
+    , _cacheFileDescriptor( NO_DESCRIPTOR )
+    , _dimensions( dimensions )
+    , _elementSpacing( elementSpacing )
+    , _offset( offset )
+{
+}
+
+VolumeHandler::VolumeDescriptor::~VolumeDescriptor()
+{
+    unmap();
+}
+
+void VolumeHandler::VolumeDescriptor::map()
+{
+    _cacheFileDescriptor = open( _filename.c_str(), O_RDONLY );
+    if( _cacheFileDescriptor == NO_DESCRIPTOR )
+    {
+        BRAYNS_ERROR << "Failed to attach " << _filename << std::endl;
+        return;
+    }
+
+    struct stat sb;
+    if( ::fstat( _cacheFileDescriptor, &sb ) == NO_DESCRIPTOR )
+    {
+        BRAYNS_ERROR << "Failed to attach " << _filename << std::endl;
+        return;
+    }
+
+    _size = sb.st_size;
+    _memoryMapPtr = ::mmap( 0, _size, PROT_READ, MAP_PRIVATE, _cacheFileDescriptor, 0 );
+    if( _memoryMapPtr == MAP_FAILED )
+    {
+        _memoryMapPtr = 0;
+        ::close( _cacheFileDescriptor );
+        _cacheFileDescriptor = NO_DESCRIPTOR;
+        BRAYNS_ERROR << "Failed to attach " << _filename << std::endl;
+        return;
+    }
+}
+
+void VolumeHandler::VolumeDescriptor::unmap()
+{
+    if( _memoryMapPtr )
+    {
+        ::munmap( (void*)_memoryMapPtr, _size );
+        _memoryMapPtr = 0;
+    }
+    if( _cacheFileDescriptor != NO_DESCRIPTOR )
+    {
+        ::close( _cacheFileDescriptor );
+        _cacheFileDescriptor = NO_DESCRIPTOR;
+    }
 }
 
 }