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Commit 94e19258 authored by Sebastian Eichelbaum's avatar Sebastian Eichelbaum
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[MERGE]

parents ee2144bc 758df595
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Showing with 1038 additions and 67 deletions
src/dataHandler/WDataHandlerEnums.h
View file @ 94e19258
......@@ -28,7 +28,7 @@
#include <stdint.h>
/**
* Dataset types and number values taken from the nifti1.h, at this point it's unknown if it makes sense
* Data types and number values taken from the nifti1.h, at this point it's unknown if it makes sense
* to keep the bit coding, but it doesn't hurt either
* \ingroup dataHandler
*/
......@@ -173,6 +173,17 @@ enum qformOrientation
Inferior_to_Superior
};
/**
* Data set types. Not complete! Only those used for distinctions so far.
* \ingroup dataHandler
*/
enum DataSetType
{
W_DATASET_NONE = 0,
W_DATASET_SINGLE = 1,
W_DATASET_SPHERICALHARMONICS = 2
};
/**
* \defgroup dataHandler Data Handler
*
......
src/dataHandler/WDataSetSphericalHarmonics.cpp
View file @ 94e19258
......@@ -41,7 +41,7 @@ WDataSetSphericalHarmonics::WDataSetSphericalHarmonics( boost::shared_ptr< WValu
m_valueSet = boost::shared_dynamic_cast< WValueSet<double> >( newValueSet );
WAssert( newValueSet, "No value set given." );
WAssert( newGrid, "No grid given." );
WAssert( m_valueSet, "No WValueSet<double given." );
WAssert( m_valueSet, "No WValueSet<double> given." );
}
WDataSetSphericalHarmonics::WDataSetSphericalHarmonics()
......
src/dataHandler/io/WReaderNIfTI.cpp
View file @ 94e19258
......@@ -83,7 +83,7 @@ wmath::WMatrix< double > WReaderNIfTI::convertMatrix( const mat44& in )
return out;
}
boost::shared_ptr< WDataSet > WReaderNIfTI::load()
boost::shared_ptr< WDataSet > WReaderNIfTI::load( DataSetType dataSetType )
{
nifti_image* header = nifti_image_read( m_fname.c_str(), 0 );
......@@ -186,7 +186,7 @@ boost::shared_ptr< WDataSet > WReaderNIfTI::load()
// }
// else
if ( !description.compare( "WDataSetSphericalHarmonics" ) )
if ( description.compare( "WDataSetSphericalHarmonics" ) == 0 || dataSetType == W_DATASET_SPHERICALHARMONICS )
{
wlog::debug( "WReaderNIfTI" ) << "Load as spherical harmonics" << std::endl;
newDataSet = boost::shared_ptr< WDataSet >( new WDataSetSphericalHarmonics( newValueSet, newGrid ) );
......
src/dataHandler/io/WReaderNIfTI.h
View file @ 94e19258
......@@ -58,9 +58,11 @@ public:
/**
* Loads the dataset.
*
* \param dataSetType This parameter can be used to tell the function in advance how it should interprete the data.
*
* \return the dataset loaded.
*/
virtual boost::shared_ptr< WDataSet > load();
virtual boost::shared_ptr< WDataSet > load( DataSetType dataSetType = W_DATASET_NONE );
protected:
private:
......
src/graphicsEngine/WPickHandler.cpp
View file @ 94e19258
......@@ -162,6 +162,19 @@ std::string extractSuitableName( osgUtil::LineSegmentIntersector::Intersections:
return ""; // This line will not be reached.
}
void WPickHandler::updatePickInfoModifierKeys( WPickInfo* pickInfo )
{
if( m_shift )
{
pickInfo->setModifierKey( WPickInfo::SHIFT );
}
if ( m_ctrl )
{
pickInfo->setModifierKey( WPickInfo::STRG );
}
}
void WPickHandler::pick( osgViewer::View* view, const osgGA::GUIEventAdapter& ea )
{
osgUtil::LineSegmentIntersector::Intersections intersections;
......@@ -171,15 +184,7 @@ void WPickHandler::pick( osgViewer::View* view, const osgGA::GUIEventAdapter& ea
WPickInfo pickInfo;
if( m_shift )
{
pickInfo.setModifierKey( WPickInfo::SHIFT );
}
if ( m_ctrl )
{
pickInfo.setModifierKey( WPickInfo::STRG );
}
updatePickInfoModifierKeys( &pickInfo );
// if we are in another viewer than the main view we just need the pixel position
if ( m_viewerName != "" && m_viewerName != "main" )
......
src/graphicsEngine/WPickHandler.h
View file @ 94e19258
......@@ -128,7 +128,14 @@ protected:
private:
boost::signals2::signal1<void, WPickInfo > m_pickSignal; //!< One can register to this signal to receive pick events.
/**
* Sets the current modifiers to the provided pickInfo
*
* \param pickInfo This pickInfo will be updated.
*/
void updatePickInfoModifierKeys( WPickInfo* pickInfo );
boost::signals2::signal1< void, WPickInfo > m_pickSignal; //!< One can register to this signal to receive pick events.
};
#endif // WPICKHANDLER_H
src/modules/fiberDisplay/WMFiberDisplay.cpp
View file @ 94e19258
......@@ -70,10 +70,13 @@ void WMFiberDisplay::connectors()
{
using boost::shared_ptr;
typedef WModuleInputData< const WDataSetFibers > FiberInputData; // just an alias
typedef WModuleOutputData< WDataSetFibers > FiberOutputData; // just an alias
m_fiberInput = shared_ptr< FiberInputData >( new FiberInputData( shared_from_this(), "fiberInput", "A loaded fiber dataset." ) );
m_fiberOutput = shared_ptr< FiberOutputData >( new FiberOutputData( shared_from_this(), "fiberOutput", "The selected fibers." ) );
addConnector( m_fiberInput );
addConnector( m_fiberOutput );
WModule::connectors(); // call WModules initialization
}
......@@ -169,13 +172,12 @@ void WMFiberDisplay::properties()
m_tubeThickness->setMin( 0 );
m_tubeThickness->setMax( 300 );
m_save = m_properties->addProperty( "Save", "Saves the selected fiber bundles.", false, m_propCondition );
m_saveFileName = m_properties->addProperty( "File name", "", WPathHelper::getAppPath() );
m_cullBoxGroup = m_properties->addPropertyGroup( "Box Culling", "Properties only related to the box culling.", m_propCondition );
m_activateCullBox = m_cullBoxGroup->addProperty( "Activate", "Activates the cull box", false, m_propCondition );
m_showCullBox = m_cullBoxGroup->addProperty( "Show cull box", "Shows/hides the cull box", false, m_propCondition );
m_insideCullBox = m_cullBoxGroup->addProperty( "Inside - outside", "Show fibers inside or outside the cull box", true, m_propCondition );
m_propUpdateOutputTrigger = m_properties->addProperty( "Update Output", "Update!", WPVBaseTypes::PV_TRIGGER_READY, m_propCondition );
}
......@@ -227,6 +229,12 @@ void WMFiberDisplay::moduleMain()
m_cullBox->hide();
}
}
if ( m_propUpdateOutputTrigger->get( true ) == WPVBaseTypes::PV_TRIGGER_TRIGGERED )
{
updateOutput();
m_propUpdateOutputTrigger->set( WPVBaseTypes::PV_TRIGGER_READY, false );
}
}
con.disconnect();
......@@ -388,12 +396,6 @@ void WMFiberDisplay::updateRenderModes()
}
}
void WMFiberDisplay::saveSelected()
{
boost::shared_ptr< std::vector< bool > > active = m_fiberSelector->getBitfield();
m_dataset->saveSelected( m_saveFileName->getAsString(), active );
}
void WMFiberDisplay::updateTexture()
{
osg::StateSet* rootState = m_osgNode->getOrCreateStateSet();
......@@ -450,3 +452,41 @@ void WMFiberDisplay::updateCallback()
updateRenderModes();
}
void WMFiberDisplay::updateOutput()
{
boost::shared_ptr< std::vector< bool > > active = m_fiberSelector->getBitfield();
boost::shared_ptr< std::vector< float > >vertices = boost::shared_ptr< std::vector< float > >( new std::vector< float >() );
boost::shared_ptr< std::vector< size_t > > lineStartIndexes = boost::shared_ptr< std::vector< size_t > > ( new std::vector< size_t >() );
boost::shared_ptr< std::vector< size_t > > lineLengths = boost::shared_ptr< std::vector< size_t > >( new std::vector< size_t >() );
boost::shared_ptr< std::vector< size_t > > verticesReverse = boost::shared_ptr< std::vector< size_t > >( new std::vector< size_t >() );
std::pair< wmath::WPosition, wmath::WPosition > boundingBox = m_dataset->getBoundingBox();
size_t countLines = 0;
for ( size_t l = 0; l < active->size(); ++l )
{
if ( ( *active )[l] )
{
size_t pc = m_dataset->getLineStartIndexes()->at( l ) * 3;
lineStartIndexes->push_back( vertices->size() / 3 );
lineLengths->push_back( m_dataset->getLineLengths()->at( l ) );
for ( size_t j = 0; j < m_dataset->getLineLengths()->at( l ); ++j )
{
vertices->push_back( m_dataset->getVertices()->at( pc ) );
++pc;
vertices->push_back( m_dataset->getVertices()->at( pc ) );
++pc;
vertices->push_back( m_dataset->getVertices()->at( pc ) );
++pc;
verticesReverse->push_back( countLines );
}
++countLines;
}
}
boost::shared_ptr< WDataSetFibers> newOutput =
boost::shared_ptr< WDataSetFibers>( new WDataSetFibers( vertices, lineStartIndexes, lineLengths, verticesReverse, boundingBox ) );
m_fiberOutput->updateData( newOutput );
}
src/modules/fiberDisplay/WMFiberDisplay.h
View file @ 94e19258
......@@ -39,6 +39,7 @@
#include "../../kernel/WFiberSelector.h"
#include "../../kernel/WModule.h"
#include "../../kernel/WModuleInputData.h"
#include "../../kernel/WModuleOutputData.h"
/**
* Module for drawing fibers
......@@ -148,9 +149,6 @@ private:
WPropBool m_useTubesProp; //!< Property indicating whether to use tubes for the fibers tracts.
WPropBool m_useTextureProp; //!< Property indicating whether to use tubes for the fibers tracts.
WPropDouble m_tubeThickness; //!< Property determining the thickness of tubes .
WPropBool m_save; //!< this should be a button
WPropFilename m_saveFileName; //!< the filename for saving
WBoolFlag m_noData; //!< Flag indicating whether there is data to display.
WPropGroup m_cullBoxGroup; //!< property group for box culling
......@@ -158,11 +156,22 @@ private:
WPropBool m_showCullBox; //!< Enable/Disable showing of the cull box
WPropBool m_insideCullBox; //!< if true fibers inside the cull box are shown, outside if false
/**
* This property triggers the updating of the output connector, as it would be too slow to do on every
* selection change
*/
WPropTrigger m_propUpdateOutputTrigger;
/**
* Input connector for a fiber dataset.
*/
boost::shared_ptr< WModuleInputData< const WDataSetFibers > > m_fiberInput;
/**
* Output connector for a fiber dataset.
*/
boost::shared_ptr< WModuleOutputData< WDataSetFibers > > m_fiberOutput;
/**
* Pointer to the fiber data set
*/
......@@ -250,9 +259,10 @@ private:
osg::ref_ptr< WROIBox > m_cullBox; //!< stores a pointer to the cull box
/**
* saves the currently selected (active field from roi manager) fibers to a file
* updates the output connector with the currently selected fiber,
* this is done on demand to avoid recomputation every time the selection changes
*/
void saveSelected();
void updateOutput();
/**
* creates and initializes the uniform parameters for the shader
......
src/modules/modules-io.toolbox
View file @ 94e19258
ADD_SUBDIRECTORY( exportGeometry )
ADD_SUBDIRECTORY( readMesh )
ADD_SUBDIRECTORY( readSphericalHarmonics )
ADD_SUBDIRECTORY( writeMesh )
ADD_SUBDIRECTORY( writeNIfTI )
ADD_SUBDIRECTORY( writeTracts )
src/modules/readMesh/WMReadMesh.cpp
View file @ 94e19258
......@@ -55,7 +55,7 @@ boost::shared_ptr< WModule > WMReadMesh::factory() const
const char** WMReadMesh::getXPMIcon() const
{
return readMesh_xpm;
return WMReadMesh_xpm;
}
const std::string WMReadMesh::getName() const
......
src/modules/readMesh/WMReadMesh.h
View file @ 94e19258
......@@ -111,8 +111,8 @@ private:
virtual boost::shared_ptr< WTriangleMesh > read();
boost::shared_ptr< WTriangleMesh > m_triMesh; //!< This triangle mesh is provided as output through the connector.
boost::shared_ptr< WModuleOutputData< WTriangleMesh > > m_output; //!< Input connector required by this module.
boost::shared_ptr< WCondition > m_propCondition; //!<A condition used to notify about changes in several properties.
boost::shared_ptr< WModuleOutputData< WTriangleMesh > > m_output; //!< Output connector provided by this module.
boost::shared_ptr< WCondition > m_propCondition; //!< A condition used to notify about changes in several properties.
WPropTrigger m_readTriggerProp; //!< This property triggers the actual reading,
WPropFilename m_meshFile; //!< The mesh will be read from this file.
};
......
src/modules/readMesh/WMReadMesh.xpm
View file @ 94e19258
/* XPM */
static const char * readMesh_xpm[] = {
static const char * WMReadMesh_xpm[] = {
"32 32 3 1",
" c None",
". c #7F6DC5",
"+ c #000000",
" ",
" .. ",
" ...... ..... ",
" .......... ...... .. ",
" ..... ............. .. ",
" .. ... ..... .. ",
" . .. ... .. ",
" . .. .... .. ",
" .. ... .. ... .. ",
" .. ... .. ... .. ",
" .. .. .. ... .. ",
" . .. . .. .. ",
" . .... .. .. ",
" .. ... .... ",
" ......................... ",
" ........ ... ....... ",
" .. ... .... ",
" .. .... .. .. ",
" . ... . .. .. ",
" .. ... . .. +.. ",
" .. ... .. .. ++. ",
" .. .. .. .. +++ ",
" . .. .. .. ++++ ",
" . .. +++++++++++++++ ",
" .. ... ++++++++++++++++",
" ..... ++++++++++++++++",
" .... .....++++++++++++++++",
" .. ........ +++++++++++++++ ",
" ........ ++++ ",
" ... +++ ",
" ++ ",
" + "};
". c #000000",
"+ c #7F6DC5",
"......... ",
".......... ",
"..++++++... +++++ ",
"..+++++++..+ ++++++ ++ ",
"..+++++ ...++++++++++++ ++ ",
".......... +++++ ++ ",
"......... +++ ++ ",
".. + ..++ ++++ ++ ",
".. ++ ...+++ ++ +++ ++ ",
".. ++ ...+++ ++ +++ ++ ",
".. ++ .. ++ ++ +++ ++ ",
".. + ... ++ + ++ ++ ",
".. + ... ++++ ++ ++ ",
" ++ +++ ++++ ",
" +++++++++++++++++++++++++ ",
" ++++++++ +++ +++++++ ",
" ++ +++ ++++ ",
" ++ ++++ ++ ++ ",
" + +++ + ++ ++ ",
" ++ +++ + ++ .++ ",
" ++ +++ ++ ++ ..+ ",
" ++ ++ ++ ++ ... ",
" + ++ ++ ++ .... ",
" + ++ ............... ",
" ++ +++ ................",
" +++++ ................",
" ++++ +++++................",
" ++ ++++++++ ............... ",
" ++++++++ .... ",
" +++ ... ",
" .. ",
" . "};
src/modules/readSphericalHarmonics/CMakeLists.txt 0 → 100644
View file @ 94e19258
FILE( GLOB_RECURSE MODULES_SRC "*.cpp" "*.h" )
# Grab module name and setup target directories
GET_FILENAME_COMPONENT( MODULE_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME )
SET( MODULE_TARGET_DIR ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/modules/${MODULE_NAME} )
SET( CMAKE_LIBRARY_OUTPUT_DIRECTORY ${MODULE_TARGET_DIR} )
SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${MODULE_TARGET_DIR} )
SET( MODULE_DIRNAME ${MODULE_NAME} )
SET( MODULE_NAME "OWmodule_${MODULE_NAME}" ) # prefix all module names with "OWmodule_" to separate them from other libs
# Build module lib
ADD_LIBRARY( ${MODULE_NAME} SHARED ${MODULES_SRC} )
TARGET_LINK_LIBRARIES( ${MODULE_NAME} OWkernel )
IF(MSVC_IDE)
SET_TARGET_PROPERTIES( ${MODULE_NAME} PROPERTIES PREFIX "../")
ENDIF(MSVC_IDE)
# Copy local shaders to module target directory
IF( OW_COPY_SHADERS AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/shaders ) # copy shaders only if the user wants it
ADD_CUSTOM_TARGET( ${MODULE_NAME}_CopyShaders
COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/shaders ${MODULE_TARGET_DIR}/shaders/
COMMENT "Copy shaders of ${MODULE_NAME}"
)
ADD_DEPENDENCIES( ${MODULE_NAME} ${MODULE_NAME}_CopyShaders )
ENDIF()
# Build unit tests
IF( OW_COMPILE_TESTS )
# This ensures that the test is copied to the module directory
SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${MODULE_TARGET_DIR} )
CXXTEST_ADD_TESTS_FROM_LIST( "${MODULES_SRC}"
"OWkernel;${MODULE_NAME}"
)
# Copy fixtures if they exist
IF( EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/test/fixtures )
ADD_CUSTOM_TARGET( ${MODULE_NAME}_CopyFixtures
# as the "test" target runs in CMakes temporary build dir, the fixtures need to be placed there too.
COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/test/fixtures ${CMAKE_BINARY_DIR}/modules/${MODULE_DIRNAME}/fixtures/
COMMENT "Copy fixtures of ${MODULE_NAME}"
)
ADD_DEPENDENCIES( ${MODULE_NAME} ${MODULE_NAME}_CopyFixtures )
ENDIF( EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/test/fixtures )
ENDIF( OW_COMPILE_TESTS )
src/modules/readSphericalHarmonics/WMReadSphericalHarmonics.cpp 0 → 100644
View file @ 94e19258
//---------------------------------------------------------------------------
//
// Project: OpenWalnut ( http://www.openwalnut.org )
//
// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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/>.
//
//---------------------------------------------------------------------------
#include <string>
#include "../../dataHandler/WDataHandlerEnums.h"
#include "../../dataHandler/io/WReaderNIfTI.h"
#include "../../graphicsEngine/WGERequirement.h"
#include "../../kernel/WKernel.h"
#include "WMReadSphericalHarmonics.xpm"
#include "WMReadSphericalHarmonics.h"
// This line is needed by the module loader to actually find your module. Do not remove. Do NOT add a ";" here.
W_LOADABLE_MODULE( WMReadSphericalHarmonics )
WMReadSphericalHarmonics::WMReadSphericalHarmonics():
WModule()
{
}
WMReadSphericalHarmonics::~WMReadSphericalHarmonics()
{
}
boost::shared_ptr< WModule > WMReadSphericalHarmonics::factory() const
{
return boost::shared_ptr< WModule >( new WMReadSphericalHarmonics() );
}
const char** WMReadSphericalHarmonics::getXPMIcon() const
{
return WMReadSphericalHarmonics_xpm;
}
const std::string WMReadSphericalHarmonics::getName() const
{
// Specify your module name here. This name must be UNIQUE!
return "Read Spherical Harmonics";
}
const std::string WMReadSphericalHarmonics::getDescription() const
{
return "This modules loads data from vectors in NIfTI files as SphericalHarmonicsDatasets.";
}
void WMReadSphericalHarmonics::connectors()
{
m_output= boost::shared_ptr< WModuleOutputData< WDataSetSphericalHarmonics > >( new WModuleOutputData< WDataSetSphericalHarmonics >(
shared_from_this(), "Spherical Harmonics", "A loaded spherical harmonics dataset." )
);
addConnector( m_output );
WModule::connectors();
}
void WMReadSphericalHarmonics::properties()
{
m_propCondition = boost::shared_ptr< WCondition >( new WCondition() );
m_dataFile = m_properties->addProperty( "NIfTI file", "", WPathHelper::getAppPath() );
m_readTriggerProp = m_properties->addProperty( "Do read", "Press!", WPVBaseTypes::PV_TRIGGER_READY, m_propCondition );
WPropertyHelper::PC_PATHEXISTS::addTo( m_dataFile );
WModule::properties();
}
void WMReadSphericalHarmonics::requirements()
{
m_requirements.push_back( new WGERequirement() );
}
void WMReadSphericalHarmonics::moduleMain()
{
m_moduleState.add( m_propCondition );
ready();
while( !m_shutdownFlag() )
{
m_moduleState.wait();
if( m_shutdownFlag() )
{
break;
}
std::string fileName = m_dataFile->get().string();
WReaderNIfTI niiLoader( fileName );
boost::shared_ptr< WDataSet > data;
data = niiLoader.load( W_DATASET_SPHERICALHARMONICS );
if( data )
{
m_data = boost::shared_dynamic_cast< WDataSetSphericalHarmonics >( data );
if( m_data )
{
m_runtimeName->set( string_utils::tokenize( fileName, "/" ).back() );
m_output->updateData( m_data );
}
}
m_readTriggerProp->set( WPVBaseTypes::PV_TRIGGER_READY, false );
}
}
src/modules/readSphericalHarmonics/WMReadSphericalHarmonics.h 0 → 100644
View file @ 94e19258
//---------------------------------------------------------------------------
//
// Project: OpenWalnut ( http://www.openwalnut.org )
//
// Copyright 2009 OpenWalnut Community, BSV-Leipzig and CNCF-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 WMREADSPHERICALHARMONICS_H
#define WMREADSPHERICALHARMONICS_H
#include <string>
#include <osg/Geode>
#include "../../dataHandler/WDataSetSphericalHarmonics.h"
#include "../../kernel/WModule.h"
#include "../../kernel/WModuleInputData.h"
#include "../../kernel/WModuleOutputData.h"
/**
* This module loads spherical harmonics data given as vectors of coefficients from NIfTI files.
*
* \ingroup modules
*/
class WMReadSphericalHarmonics: public WModule
{
public:
/**
*
*/
WMReadSphericalHarmonics();
/**
*
*/
virtual ~WMReadSphericalHarmonics();
/**