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RTTFibers.cpp
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RTTFibers.cpp
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/*
* The RTTFibers class implementation.
*
*/
#include "RTTFibers.h"
#include "DatasetManager.h"
#include "RTTrackingHelper.h"
#include "RTFMRIHelper.h"
#include "../Logger.h"
#include "../gfx/ShaderHelper.h"
#include "../gfx/TheScene.h"
#include "../gui/SceneManager.h"
#include "../gui/SelectionTree.h"
#include "../misc/lic/FgeOffscreen.h"
#include "../gui/MainFrame.h"
#include "../misc/IsoSurface/CIsoSurface.h"
#include "../misc/IsoSurface/TriangleMesh.h"
#include <algorithm>
using std::sort;
#include <vector>
using std::vector;
#include "../main.h"
//////////////////////////////////////////
//Constructor
//////////////////////////////////////////
RTTFibers::RTTFibers()
: m_trackActionStep(std::numeric_limits<unsigned int>::max()),
m_timerStep( 0 ),
m_FAThreshold( 0.20f ),
m_angleThreshold( 35.0f ),
m_step( 1.0f ),
m_GMstep( 5 ),
m_nbSeed ( 10.0f ),
m_nbMeshPt ( 0 ),
m_puncture( 0.2f ),
m_vinvout( 0.6f ),
m_minFiberLength( 60 ),
m_maxFiberLength( 200 ),
m_alpha( 1.0f ),
m_currentSeedBoxID( 0 ),
m_isHARDI( false ),
m_countGMstep( 0 ),
m_stop( false ),
m_and( true ),
m_pExcludeInfo( NULL ),
m_pIncludeInfo( NULL ),
m_pSeedMapInfo( NULL ),
m_pGMInfo( NULL ),
m_render( true ),
m_steppedOnceInsideChildBox( false ),
m_steppedOnceIntoAND( false ),
m_prune(true)
{
m_bufferObjectsRTT = new GLuint[2];
}
void RTTFibers::setSeedMapInfo(Anatomy *info)
{
m_pSeedMap.clear();
m_pSeedMapInfo = info;
if( m_pSeedMapInfo != NULL )
{
int cols = DatasetManager::getInstance()->getColumns();
int rows = DatasetManager::getInstance()->getRows();
int frames = DatasetManager::getInstance()->getFrames();
for( int f = 0; f < frames; ++f )
{
for( int r = 0; r < rows; ++r )
{
for( int c = 0; c < cols; ++c )
{
if ( m_pSeedMapInfo->at(f * rows * cols + r * cols + c) > 0.0f)
{
m_pSeedMap.push_back( Vector(c, r, f) );
}
}
}
}
}
}
///////////////////////////////////////////////////////////////////////////
// Generate random seeds
///////////////////////////////////////////////////////////////////////////
Vector RTTFibers::generateRandomSeed( const Vector &min, const Vector &max )
{
float randomX = ( (float) rand() ) / (float) RAND_MAX;
float rangeX = max.x - min.x;
float seedX = ( randomX * rangeX ) + min.x;
float randomY = ( (float) rand() ) / (float) RAND_MAX;
float rangeY = max.y - min.y;
float seedY = ( randomY * rangeY ) + min.y;
float randomZ = ( (float) rand() ) / (float) RAND_MAX;
float rangeZ = max.z - min.z;
float seedZ = ( randomZ * rangeZ ) + min.z;
return Vector( seedX, seedY, seedZ );
}
///////////////////////////////////////////////////////////////////////////
// Returns the nb of vertices for shell seeding
///////////////////////////////////////////////////////////////////////////
float RTTFibers::getShellSeedNb()
{
float pts = m_nbSeed*m_nbSeed*m_nbSeed;
if( m_pShellInfo != NULL )
{
CIsoSurface* pSurf = (CIsoSurface*) m_pShellInfo;
std::vector< Vector > positions = pSurf->m_tMesh->getVerts();
pts = positions.size();
}
return pts;
}
void RTTFibers::insert(std::vector<Vector> pointsF, std::vector<Vector> pointsB, std::vector<Vector> colorF, std::vector<Vector> colorB)
{
if( (pointsF.size() + pointsB.size()) * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size()) * getStep() < getMaxFiberLength() )
{
m_fibersRTT.push_back( pointsF );
m_colorsRTT.push_back( colorF );
m_fibersRTT.push_back( pointsB );
m_colorsRTT.push_back( colorB );
}
}
///////////////////////////////////////////////////////////////////////////
// Returns the nb of seeds for Map seeding
///////////////////////////////////////////////////////////////////////////
float RTTFibers::getSeedMapNb()
{
float pts = m_nbSeed*m_nbSeed*m_nbSeed;
if( m_pSeedMapInfo != NULL )
{
pts *= m_pSeedMap.size();
}
return pts;
}
void RTTFibers::clearFibersRTT()
{
m_streamlinesColors.clear();
m_streamlinesPoints.clear();
m_storedDir.clear();
if( SceneManager::getInstance()->isUsingVBO() )
{
glDeleteBuffers( 2, m_bufferObjectsRTT );
}
m_nbPtsPerLine.clear();
m_LeftRightVector.clear();
m_lines = 0;
m_linePointer.clear();
m_linePointer.push_back(0);
}
///////////////////////////////////////////////////////////////////////////
// Generate seeds and tracks
///////////////////////////////////////////////////////////////////////////
void RTTFibers::seed()
{
clearFibersRTT();
int previousLinePointer = 0;
float xVoxel = DatasetManager::getInstance()->getVoxelX();
float yVoxel = DatasetManager::getInstance()->getVoxelY();
float zVoxel = DatasetManager::getInstance()->getVoxelZ();
Vector minCorner, maxCorner, middle;
selObjs = SceneManager::getInstance()->getSelectionTree().getAllObjects();
//test to optim
float invertNbSeed = 1.0f / float( m_nbSeed - 1.0f );
//Evenly distanced seeds
if( !RTTrackingHelper::getInstance()->isShellSeeds() && !RTTrackingHelper::getInstance()->isSeedMap() && !RTTrackingHelper::getInstance()->isSeedFromfMRI())
{
for( unsigned int b = 0; b < selObjs.size(); b++ )
{
if( selObjs[ b ]->getIsNOT() || !selObjs[ b ]->getIsActive() || !SceneManager::getInstance()->getSelectionTree().isFirstLevel(selObjs[ b ]) || selObjs[b]->getSelectionType() == ELLIPSOID_TYPE) //Check for ellipsoid also?
{
continue;
}
m_currentSeedBoxID = b+1;
minCorner.x = selObjs[b]->getCenter().x - selObjs[b]->getSize().x * xVoxel * 0.5f;
minCorner.y = selObjs[b]->getCenter().y - selObjs[b]->getSize().y * yVoxel * 0.5f;
minCorner.z = selObjs[b]->getCenter().z - selObjs[b]->getSize().z * zVoxel * 0.5f;
maxCorner.x = selObjs[b]->getCenter().x + selObjs[b]->getSize().x * xVoxel * 0.5f;
maxCorner.y = selObjs[b]->getCenter().y + selObjs[b]->getSize().y * yVoxel * 0.5f;
maxCorner.z = selObjs[b]->getCenter().z + selObjs[b]->getSize().z * zVoxel * 0.5f;
float xstep = selObjs[b]->getSize().x * xVoxel * invertNbSeed;
float ystep = selObjs[b]->getSize().y * yVoxel * invertNbSeed;
float zstep = selObjs[b]->getSize().z * zVoxel * invertNbSeed;
for( float x = minCorner.x; x < maxCorner.x + xstep*0.5f; x+= xstep )
{
for( float y = minCorner.y; y < maxCorner.y + ystep*0.5f; y+= ystep )
{
for( float z = minCorner.z; z < maxCorner.z + zstep*0.5f; z+= zstep )
{
vector<float> pointsF;
vector<float> pointsB;
vector<float> colorF;
vector<float> colorB;
bool draw;
m_stop = false;
if(m_isHARDI)
{
Vector seed(x,y,z);
if(RTTrackingHelper::getInstance()->isRandomInit())
{
seed = generateRandomSeed(minCorner,maxCorner);
}
//Track both sides
performHARDIRTT( seed, 1, pointsF, colorF); //First pass
draw = m_render && m_and;
performHARDIRTT( seed, -1, pointsB, colorB); //Second pass
}
else
{
//Track both sides
performDTIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performDTIRTT( Vector(x,y,z), -1, pointsB, colorB); //Second pass
}
if( (pointsF.size() + pointsB.size())/3 * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size())/3 * getStep() < getMaxFiberLength() && (m_render || draw )&& (draw || m_and))
{
bool keepRight = false;
bool keepLeft = false;
//Insert strategically for drawArray methods.
if(pointsF.size() != 0)
{
m_nbPtsPerLine.push_back(pointsF.size()/3);
m_linePointer.push_back(previousLinePointer + pointsF.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsF.begin(), pointsF.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorF.begin(), colorF.end());
keepRight = true;
}
if(pointsB.size() != 0)
{
m_nbPtsPerLine.push_back(pointsB.size()/3);
m_linePointer.push_back(previousLinePointer + pointsB.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsB.begin(), pointsB.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorB.begin(), colorB.end());
keepLeft = true;
}
if(keepLeft && keepRight)
{
m_LeftRightVector.push_back(true);
m_LeftRightVector.push_back(true);
}
else if(keepLeft || keepRight)
{
m_LeftRightVector.push_back(false);
}
if(RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
insertPointsForTractoDriven(pointsF, pointsB);
}
m_steppedOnceInsideChildBox = false;
m_steppedOnceIntoAND = false;
}
}
}
}
}
}
//Seed from anatomy
else if ( RTTrackingHelper::getInstance()->isSeedMap())
{
for( unsigned int s = 0; s < m_pSeedMap.size(); s++ )
{
Vector val = m_pSeedMap[s];
minCorner.x = val.x * xVoxel;
minCorner.y = val.y * yVoxel;
minCorner.z = val.z * zVoxel;
maxCorner.x = val.x * xVoxel + xVoxel;
maxCorner.y = val.y * yVoxel + yVoxel;
maxCorner.z = val.z * zVoxel + zVoxel;
float xstep = xVoxel / float( m_nbSeed - 1.0f );
float ystep = yVoxel / float( m_nbSeed - 1.0f );
float zstep = zVoxel / float( m_nbSeed - 1.0f );
for( float x = minCorner.x; x < maxCorner.x + xstep/2.0f; x+= xstep )
{
for( float y = minCorner.y; y < maxCorner.y + ystep/2.0f; y+= ystep )
{
for( float z = minCorner.z; z < maxCorner.z + zstep/2.0f; z+= zstep )
{
vector<float> pointsF;
vector<float> pointsB;
vector<float> colorF;
vector<float> colorB;
bool draw;
m_stop = false;
if(m_isHARDI)
{
Vector seed(x,y,z);
if(RTTrackingHelper::getInstance()->isRandomInit())
{
seed = generateRandomSeed(minCorner,maxCorner);
}
//Track both sides
performHARDIRTT( seed, 1, pointsF, colorF); //First pass
draw = m_render && m_and;
performHARDIRTT( seed, -1, pointsB, colorB); //Second pass
}
else
{
//Track both sides
performDTIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performDTIRTT( Vector(x,y,z), -1, pointsB, colorB); //Second pass
}
if( (pointsF.size() + pointsB.size())/3 * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size())/3 * getStep() < getMaxFiberLength() && (m_render || draw )&& (draw || m_and))
{
bool keepRight = false;
bool keepLeft = false;
//Insert strategically for drawArray methods.
if(pointsF.size() != 0)
{
m_nbPtsPerLine.push_back(pointsF.size()/3);
m_linePointer.push_back(previousLinePointer + pointsF.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsF.begin(), pointsF.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorF.begin(), colorF.end());
keepRight = true;
}
if(pointsB.size() != 0)
{
m_nbPtsPerLine.push_back(pointsB.size()/3);
m_linePointer.push_back(previousLinePointer + pointsB.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsB.begin(), pointsB.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorB.begin(), colorB.end());
keepLeft = true;
}
if(keepLeft && keepRight)
{
m_LeftRightVector.push_back(true);
m_LeftRightVector.push_back(true);
}
else if(keepLeft || keepRight)
{
m_LeftRightVector.push_back(false);
}
if(RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
insertPointsForTractoDriven(pointsF, pointsB);
}
m_steppedOnceInsideChildBox = false;
m_steppedOnceIntoAND = false;
}
}
}
}
}
}
//fMRI seeding
else if(RTTrackingHelper::getInstance()->isSeedFromfMRI())
{
RTTrackingHelper::getInstance()->m_pSliderAxisSeedNb->SetValue( m_nbSeed );
RTTrackingHelper::getInstance()->m_pTxtAxisSeedNbBox->SetValue(wxString::Format( wxT( "%.1f"), m_nbSeed) );
RTTrackingHelper::getInstance()->m_pTxtTotalSeedNbBox->SetValue(wxString::Format( wxT( "%.1f"), m_nbSeed*m_nbSeed*m_nbSeed*m_pSeedFromfMRI.size()) );
for( size_t k = 0; k < m_pSeedFromfMRI.size(); k++)
{
float xstep = xVoxel / float( m_nbSeed - 1.0f );
float ystep = yVoxel / float( m_nbSeed - 1.0f );
float zstep = zVoxel / float( m_nbSeed - 1.0f );
float xx = m_pSeedFromfMRI[k].first.x * DatasetManager::getInstance()->getVoxelX();
float yy = m_pSeedFromfMRI[k].first.y * DatasetManager::getInstance()->getVoxelY();
float zz = m_pSeedFromfMRI[k].first.z * DatasetManager::getInstance()->getVoxelZ();
for( float x = xx - xVoxel; x < xx + xVoxel + xstep/2.0f; x+= xstep )
{
for( float y = yy - yVoxel; y < yy + yVoxel + ystep/2.0f; y+= ystep )
{
for( float z = zz - zVoxel; z < zz + zVoxel + zstep/2.0f; z+= zstep )
{
vector<float> pointsF;
vector<float> pointsB;
vector<float> colorF;
vector<float> colorB;
bool draw;
m_stop = false;
if(m_isHARDI)
{
Vector seed(x,y,z);
if(RTTrackingHelper::getInstance()->isRandomInit())
{
seed = generateRandomSeed(minCorner,maxCorner);
}
//Track both sides
performHARDIRTT( seed, 1, pointsF, colorF); //First pass
draw = m_render && m_and;
performHARDIRTT( seed, -1, pointsB, colorB); //Second pass
}
else
{
//Track both sides
performDTIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performDTIRTT( Vector(x,y,z), -1, pointsB, colorB); //Second pass
}
if( (pointsF.size() + pointsB.size())/3 * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size())/3 * getStep() < getMaxFiberLength() && (m_render || draw ) && (draw || m_and))
{
bool keepRight = false;
bool keepLeft = false;
//Insert strategically for drawArray methods.
if(pointsF.size() != 0)
{
m_nbPtsPerLine.push_back(pointsF.size()/3);
m_linePointer.push_back(previousLinePointer + pointsF.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsF.begin(), pointsF.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorF.begin(), colorF.end());
keepRight = true;
}
if(pointsB.size() != 0)
{
m_nbPtsPerLine.push_back(pointsB.size()/3);
m_linePointer.push_back(previousLinePointer + pointsB.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsB.begin(), pointsB.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorB.begin(), colorB.end());
keepLeft = true;
}
if(keepLeft && keepRight)
{
m_LeftRightVector.push_back(true);
m_LeftRightVector.push_back(true);
}
else if(keepLeft || keepRight)
{
m_LeftRightVector.push_back(false);
}
if(RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
insertPointsForTractoDriven(pointsF, pointsB);
}
m_steppedOnceInsideChildBox = false;
m_steppedOnceIntoAND = false;
}
}
}
}
}
}
//Mesh ShellSeeding
else
{
if ( m_pShellInfo->getType() == ISO_SURFACE )
{
CIsoSurface* pSurf = (CIsoSurface*) m_pShellInfo;
std::vector< Vector > positions = pSurf->m_tMesh->getVerts();
m_nbMeshPt = positions.size();
for ( size_t k = 0; k < positions.size(); ++k )
{
vector<float> pointsF;
vector<float> pointsB;
vector<float> colorF;
vector<float> colorB;
bool draw;
m_stop = false;
if(m_isHARDI)
{
//Track both sides
performHARDIRTT( Vector(positions[k].x,positions[k].y,positions[k].z), 1, pointsF, colorF); //First pass
draw = m_render && m_and;
performHARDIRTT( Vector(positions[k].x,positions[k].y,positions[k].z), -1, pointsB, colorB); //Second pass
}
else
{
//Track both sides
performDTIRTT( Vector(positions[k].x,positions[k].y,positions[k].z), 1, pointsF, colorF); //First pass
performDTIRTT( Vector(positions[k].x,positions[k].y,positions[k].z), -1, pointsB, colorB); //Second pass
}
if( (pointsF.size() + pointsB.size())/3 * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size())/3 * getStep() < getMaxFiberLength() && (m_render || draw) && (draw || m_and))
{
bool keepRight = false;
bool keepLeft = false;
//Insert strategically for drawArray methods.
if(pointsF.size() != 0)
{
m_nbPtsPerLine.push_back(pointsF.size()/3);
m_linePointer.push_back(previousLinePointer + pointsF.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsF.begin(), pointsF.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorF.begin(), colorF.end());
keepRight = true;
}
if(pointsB.size() != 0)
{
m_nbPtsPerLine.push_back(pointsB.size()/3);
m_linePointer.push_back(previousLinePointer + pointsB.size()/3);
previousLinePointer = m_linePointer[m_lines+1];
m_lines++;
m_streamlinesPoints.insert(m_streamlinesPoints.end(), pointsB.begin(), pointsB.end());
m_streamlinesColors.insert(m_streamlinesColors.end(), colorB.begin(), colorB.end());
keepLeft = true;
}
if(keepLeft && keepRight)
{
m_LeftRightVector.push_back(true);
m_LeftRightVector.push_back(true);
}
else if(keepLeft || keepRight)
{
m_LeftRightVector.push_back(false);
}
if(RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
insertPointsForTractoDriven(pointsF, pointsB);
}
m_steppedOnceInsideChildBox = false;
m_steppedOnceIntoAND = false;
}
}
}
}
renderRTTFibers(true, false, false);
RTTrackingHelper::getInstance()->setRTTDirty( false );
}
///////////////////////////////////////////////////////////////////////////
//Rendering stage
///////////////////////////////////////////////////////////////////////////
void RTTFibers::renderRTTFibers(bool bindBuffers, bool isAnimate, bool changeAlpha)
{
if(m_streamlinesPoints.size() != 0)
{
if(changeAlpha)
{
for(unsigned int i = 3; i < m_streamlinesColors.size(); i+=4)
{
m_streamlinesColors[i] = m_alpha;
}
}
bool isOK = true;
//TODO: Redo animate.
if(bindBuffers)
{
glGenBuffers( 2, m_bufferObjectsRTT );
RTTrackingHelper::getInstance()->setBufferID(m_bufferObjectsRTT[0]);
glBindBuffer( GL_ARRAY_BUFFER, m_bufferObjectsRTT[0] );
glBufferData( GL_ARRAY_BUFFER, sizeof( GLfloat ) * m_streamlinesPoints.size(), &m_streamlinesPoints[0], GL_STATIC_DRAW );
isOK = !Logger::getInstance()->printIfGLError( wxT( "initialize vbo points" ) );
if(isOK)
{
glBindBuffer( GL_ARRAY_BUFFER, m_bufferObjectsRTT[1] );
glBufferData( GL_ARRAY_BUFFER, sizeof( GLfloat ) * m_streamlinesColors.size(), &m_streamlinesColors[0], GL_STATIC_DRAW );
isOK = !Logger::getInstance()->printIfGLError( wxT( "initialize vbo colors" ) );
}
}
glEnableClientState( GL_VERTEX_ARRAY );
glEnableClientState( GL_COLOR_ARRAY );
glEnableClientState( GL_NORMAL_ARRAY );
if( !isOK )
{
glVertexPointer( 3, GL_FLOAT, 0, &m_streamlinesPoints[0] );
glColorPointer( 4, GL_FLOAT, 0, &m_streamlinesColors[0] ); // Local colors.
glNormalPointer( GL_FLOAT, 0, &m_streamlinesColors[0] );
}
else
{
glBindBuffer( GL_ARRAY_BUFFER, m_bufferObjectsRTT[0] );
glVertexPointer( 3, GL_FLOAT, 0, 0 );
glBindBuffer( GL_ARRAY_BUFFER, m_bufferObjectsRTT[1] );
glColorPointer( 4, GL_FLOAT, 0, 0 );
glBindBuffer( GL_ARRAY_BUFFER, m_bufferObjectsRTT[1] );
glNormalPointer( GL_FLOAT, 0, 0 );
}
glPushAttrib( GL_ALL_ATTRIB_BITS );
if(m_alpha != 1.0f)
{
glEnable( GL_BLEND );
glBlendFunc( GL_ONE, GL_ONE );
if(RTTrackingHelper::getInstance()->isSrcAlpha())
{
glBlendFunc( GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA );
}
glDepthMask( GL_FALSE );
}
for( int i = 0; i < m_lines; i++)
{
glDrawArrays( GL_LINE_STRIP, m_linePointer[ i ], m_nbPtsPerLine[i] );
}
glDisable( GL_BLEND );
glPopAttrib();
glDisableClientState( GL_VERTEX_ARRAY );
glDisableClientState( GL_COLOR_ARRAY );
glDisableClientState( GL_NORMAL_ARRAY );
}
}
///////////////////////////////////////////////////////////////////////////
// Trilinear interpolation for realtime tracking (tensors)
///////////////////////////////////////////////////////////////////////////
FMatrix RTTFibers::trilinearInterp( float fx, float fy, float fz )
{
using std::min;
using std::max;
int columns = DatasetManager::getInstance()->getColumns();
int rows = DatasetManager::getInstance()->getRows();
int frames = DatasetManager::getInstance()->getFrames();
const int x = (unsigned int) min( (int)std::floor(fx / DatasetManager::getInstance()->getVoxelX() ), columns-1 );
const int y = (unsigned int) min( (int)std::floor(fy / DatasetManager::getInstance()->getVoxelY() ), rows-1 );
const int z = (unsigned int) min( (int)std::floor(fz / DatasetManager::getInstance()->getVoxelZ() ), frames-1 );
const float dx = ( fx / DatasetManager::getInstance()->getVoxelX() )-x;
const float dy = ( fy / DatasetManager::getInstance()->getVoxelY() )-y;
const float dz = ( fz / DatasetManager::getInstance()->getVoxelZ() )-z;
const int nx = dx > 0.0 ? min( max(x+1,0), columns-1 ) : min( max(x,0), columns-1 );
const int ny = dy > 0.0 ? min( max(y+1,0), rows-1 ) : min( max(y,0), rows-1 );
const int nz = dz > 0.0 ? min( max(z+1,0), frames-1 ) : min( max(z,0), frames-1 );
// Compute interpolated value at (fx,fy,fz)
//Corresponding tensor number
int tensor_xyz = z * columns * rows + y * columns + x;
int tensor_nxyz = z * columns * rows + y * columns + nx;
int tensor_xnyz = z * columns * rows + ny * columns + x;
int tensor_nxnyz = z * columns * rows + ny * columns + nx;
int tensor_xynz = nz * columns * rows + y * columns + x;
int tensor_nxynz = nz * columns * rows + y * columns + nx;
int tensor_xnynz = nz * columns * rows + ny * columns + x;
int tensor_nxnynz = nz * columns * rows + ny * columns + nx;
FMatrix valx0 = (1-dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_xyz) + (dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_nxyz);
FMatrix valx1 = (1-dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_xnyz) + (dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_nxnyz);
const FMatrix valy0 = (1-dy) * valx0 + (dy) * valx1;
valx0 = (1-dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_xynz) + (dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_nxynz);
valx1 = (1-dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_xnynz) + (dx) * m_pTensorsInfo->getTensorsMatrix()->at(tensor_nxnynz);
const FMatrix valy1 = (1-dy) * valx0 + (dy) * valx1;
return (1-dz) * valy0 + (dz) * valy1;
}
/////////////////////////////////////////////////////////////////////
// Advection integration
// Returns the next direction for RTT
////////////////////////////////////////////////////////////////////
Vector RTTFibers::advecIntegrate( Vector vin, const FMatrix &tensor, Vector e1, Vector e2, Vector e3, float t_number )
{
Vector vout, vprop, ee1, ee2, ee3;
float dp1, dp2, dp3;
float cl = m_pTensorsInfo->getTensorsFA()->at(t_number);
float puncture = getPuncture();
GLfloat flippedAxes[3];
m_pTensorsInfo->isAxisFlipped(X_AXIS) ? flippedAxes[0] = -1.0f : flippedAxes[0] = 1.0f;
m_pTensorsInfo->isAxisFlipped(Y_AXIS) ? flippedAxes[1] = -1.0f : flippedAxes[1] = 1.0f;
m_pTensorsInfo->isAxisFlipped(Z_AXIS) ? flippedAxes[2] = -1.0f : flippedAxes[2] = 1.0f;
// Unit vectors of local basis (e1 > e2 > e3)
ee1.x = flippedAxes[0] * (tensor(0,0) * e1.x +
tensor(0,1) * e1.y +
tensor(0,2) * e1.z);
ee1.y = flippedAxes[1] * (tensor(1,0) * e1.x +
tensor(1,1) * e1.y +
tensor(1,2) * e1.z);
ee1.z = flippedAxes[2] * (tensor(2,0) * e1.x +
tensor(2,1) * e1.y +
tensor(2,2) * e1.z);
//e2
ee2.x = flippedAxes[0] * (tensor(0,0) * e2.x +
tensor(0,1) * e2.y +
tensor(0,2) * e2.z);
ee2.y = flippedAxes[1] * (tensor(1,0) * e2.x +
tensor(1,1) * e2.y +
tensor(1,2) * e2.z);
ee2.z = flippedAxes[2] * (tensor(2,0) * e2.x +
tensor(2,1) * e2.y +
tensor(2,2) * e2.z);
//e3
ee3.x = flippedAxes[0] * (tensor(0,0) * e3.x +
tensor(0,1) * e3.y +
tensor(0,2) * e3.z);
ee3.y = flippedAxes[1] * (tensor(1,0) * e3.x +
tensor(1,1) * e3.y +
tensor(1,2) * e3.z);
ee3.z = flippedAxes[2] * (tensor(2,0) * e3.x +
tensor(2,1) * e3.y +
tensor(2,2) * e3.z);
if( vin.Dot(ee1) < 0.0 )
{
ee1 *= -1;
}
ee1.normalize();
ee2.normalize();
ee3.normalize();
// Lets first expand vin in local basis
dp1 = vin.Dot(ee1);
dp2 = vin.Dot(ee2);
dp3 = vin.Dot(ee3);
//Sort eigen values
float eValues[] = { m_pTensorsInfo->getTensorsEV()->at(t_number)[0], m_pTensorsInfo->getTensorsEV()->at(t_number)[1], m_pTensorsInfo->getTensorsEV()->at(t_number)[2] };
sort( eValues, eValues+3 );
// Compute vout
vout = dp1 * eValues[0] * ee1 + dp2 * eValues[1] * ee2 + dp3 * eValues[2] * ee3;
// Normalization (see Lazar paper for more explanations)
vout.normalize();
ee1.normalize();
vin.normalize();
vprop = cl * ee1 + (1.0 - cl) * ( (1.0 - puncture) * vin + puncture * vout );
return vprop;
}
Vector RTTFibers::advecIntegrateHARDI( Vector vin, const std::vector<float> &sticks, float s_number, Vector pos )
{
Vector vOut(0,0,0);
Vector vMagnet(0,0,0);
float angleMin = 360.0f;
float angle = 0.0f;
float g = m_vinvout;
float wm = m_pMaskInfo->at(s_number);
float gm = 0;
float F = 0;
if(m_pGMInfo != NULL && RTTrackingHelper::getInstance()->isGMAllowed())
{
gm = m_pGMInfo->at(s_number);
}
vin.normalize();
//MAGNET
bool isMagnetOn = RTTrackingHelper::getInstance()->isMagnetOn();
if(isMagnetOn)
{
vMagnet = magneticField(vin, sticks, s_number, pos, vOut, F, g);
}
else
{
for(unsigned int i=0; i < sticks.size()/3; i++)
{
Vector v1(sticks[i*3],sticks[i*3+1], sticks[i*3+2]);
if(v1.normalizeAndReturn() != 0)
{
if( vin.Dot(v1) < 0 ) //Ensures both vectors points in the same direction
{
v1 *= -1;
}
//Angle value
float dot = vin.Dot(v1);
float acos = std::acos( dot );
angle = 180 * acos / M_PI;
//Direction most probable
if( angle < angleMin )
{
angleMin = angle;
vOut = v1;
}
}
}
}
//White Matter version of Chamberland et al. 2014 Frontiers in Neuroinformatics
//Vector res = 0.5f * wm * vOut + (0.5f * wm) * ( (1.0 - puncture ) * vin + puncture * vOut);
//Previous Chamberland et al. 2014 Frontiers in Neuroinformatics
//if(gm != 0)
//{
// res = (1.0 - gm) * vOut + (gm) * ( (1.0 - puncture ) * vin + puncture * vOut);
//}
//Weight between in and out directions. Magnet will also be weighted by distance.
Vector res = (1-F)*((1.0 - g) * vin + g * vOut) + F * vMagnet;
return res;
}
Vector RTTFibers::magneticField(Vector vin, const std::vector<float> &sticks, float s_number, Vector pos, Vector& vOut, float& F, float& G)
{
Vector final = vin;
bool alreadyAffected = false;
for( unsigned int b = 0; b < selObjs.size(); b++ )
{
if( selObjs[ b ]->isMagnet() && !alreadyAffected)
{
//TEST BOX
Vector minCorner;
Vector maxCorner;
float xVoxel = DatasetManager::getInstance()->getVoxelX();
float yVoxel = DatasetManager::getInstance()->getVoxelY();
float zVoxel = DatasetManager::getInstance()->getVoxelZ();
minCorner.x = selObjs[b]->getCenter().x - selObjs[b]->getSize().x * xVoxel * 0.5f;
minCorner.y = selObjs[b]->getCenter().y - selObjs[b]->getSize().y * yVoxel * 0.5f;
minCorner.z = selObjs[b]->getCenter().z - selObjs[b]->getSize().z * zVoxel * 0.5f;
maxCorner.x = selObjs[b]->getCenter().x + selObjs[b]->getSize().x * xVoxel * 0.5f;
maxCorner.y = selObjs[b]->getCenter().y + selObjs[b]->getSize().y * yVoxel * 0.5f;
maxCorner.z = selObjs[b]->getCenter().z + selObjs[b]->getSize().z * zVoxel * 0.5f;
//Compare sticks with vector field, pick min
float angleMin = 360.0f;
float angle = 0.0f;
float angleMinOut = 360.0f;
float angleOut = 0.0f;
Vector field = selObjs[b]->getMagnetField();
//If INSIDE MAGNET
if(pos.x <= maxCorner.x && pos.x >= minCorner.x &&
pos.y <= maxCorner.y && pos.y >= minCorner.y &&
pos.z <= maxCorner.z && pos.z >= minCorner.z)
{
for(unsigned int i=0; i < sticks.size()/3; i++)
{
Vector v1(sticks[i*3],sticks[i*3+1], sticks[i*3+2]);
if(v1.normalizeAndReturn() != 0)
{
//Field direction
if( field.Dot(v1) < 0 ) //Ensures both vectors points in the same direction
{
v1 *= -1;
}
//Angle value
float dot = field.Dot(v1);
float acos = std::acos( dot );
angle = 180 * acos / M_PI;
//Direction most probable
if( angle < angleMin )
{
angleMin = angle;
vOut = v1;
}
}
}
//F = selObjs[b]->getStrength();
//G = 0;
alreadyAffected = true;
}
else
{
for(unsigned int i=0; i < sticks.size()/3; i++)
{
Vector v1(sticks[i*3],sticks[i*3+1], sticks[i*3+2]);
if(v1.normalizeAndReturn() != 0)
{
//check real direction
if( vin.Dot(v1) < 0 ) //Ensures both vectors points in the same direction
{
v1 *= -1;
}
//Angle value
float dotOut = vin.Dot(v1);
float acosOut = std::acos( dotOut );
angleOut = 180 * acosOut / M_PI;
//Direction most probable
if( angleOut < angleMinOut )
{
angleMinOut = angleOut;
vOut = v1;
}
}
}
}
}
}
return final;
}
/////////////////////////////////////////////////////////////////////
// Classify (1 or 0) the 3 eigenVecs within Axis-Aligned vecs e1 > e2 > e3
////////////////////////////////////////////////////////////////////
void RTTFibers::setDiffusionAxis( const FMatrix &tensor, Vector& e1, Vector& e2, Vector& e3 )
{
float lvx,lvy,lvz;
GLfloat flippedAxes[3];
m_pTensorsInfo->isAxisFlipped(X_AXIS) ? flippedAxes[0] = -1.0f : flippedAxes[0] = 1.0f;
m_pTensorsInfo->isAxisFlipped(Y_AXIS) ? flippedAxes[1] = -1.0f : flippedAxes[1] = 1.0f;
m_pTensorsInfo->isAxisFlipped(Z_AXIS) ? flippedAxes[2] = -1.0f : flippedAxes[2] = 1.0f;
//Find the 3 axes
lvx = flippedAxes[0] * (tensor(0,0) * tensor(0,0)
+ tensor(1,0) * tensor(1,0)
+ tensor(2,0) * tensor(2,0));
lvy = flippedAxes[1] * (tensor(0,1) * tensor(0,1)
+ tensor(1,1) * tensor(1,1)
+ tensor(2,1) * tensor(2,1));
lvz = flippedAxes[2] * (tensor(0,2) * tensor(0,2)
+ tensor(1,2) * tensor(1,2)
+ tensor(2,2) * tensor(2,2));
if ( lvx > lvy && lvx > lvz )
{
e1.x = 1;
if( lvy > lvz )
{
e2.y = 1;