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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( 15 ),
m_nbSeed ( 10.0f ),
m_nbMeshPt ( 0 ),
m_puncture( 0.2f ),
m_vinvout( 0.2f ),
m_minFiberLength( 60 ),
m_maxFiberLength( 200 ),
m_alpha( 1.0f ),
m_isHARDI( false ),
m_countGMstep( 0 ),
m_stop( false ),
m_pExcludeInfo( NULL ),
m_pSeedMapInfo( NULL ),
m_pGMInfo( NULL )
{
}
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;
}
///////////////////////////////////////////////////////////////////////////
// Generate seeds and tracks
///////////////////////////////////////////////////////////////////////////
void RTTFibers::seed()
{
m_fibersRTT.clear();
m_colorsRTT.clear();
float xVoxel = DatasetManager::getInstance()->getVoxelX();
float yVoxel = DatasetManager::getInstance()->getVoxelY();
float zVoxel = DatasetManager::getInstance()->getVoxelZ();
Vector minCorner, maxCorner, middle;
SelectionTree::SelectionObjectVector selObjs = SceneManager::getInstance()->getSelectionTree().getAllObjects();
//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 ]->getSelectionType() != BOX_TYPE )
{
continue;
}
minCorner.x = selObjs[b]->getCenter().x - selObjs[b]->getSize().x * xVoxel / 2.0f;
minCorner.y = selObjs[b]->getCenter().y - selObjs[b]->getSize().y * yVoxel / 2.0f;
minCorner.z = selObjs[b]->getCenter().z - selObjs[b]->getSize().z * zVoxel / 2.0f;
maxCorner.x = selObjs[b]->getCenter().x + selObjs[b]->getSize().x * xVoxel / 2.0f;
maxCorner.y = selObjs[b]->getCenter().y + selObjs[b]->getSize().y * yVoxel / 2.0f;
maxCorner.z = selObjs[b]->getCenter().z + selObjs[b]->getSize().z * zVoxel / 2.0f;
float xstep = selObjs[b]->getSize().x * xVoxel / float( m_nbSeed - 1.0f );
float ystep = selObjs[b]->getSize().y * yVoxel / float( m_nbSeed - 1.0f );
float zstep = selObjs[b]->getSize().z * 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<Vector> pointsF; // Points to be rendered Forward
vector<Vector> colorF; //Color (local directions)Forward
vector<Vector> pointsB; // Points to be rendered Backward
vector<Vector> colorB; //Color (local directions) Backward
m_stop = false;
if(m_isHARDI)
{
//Track both sides
performHARDIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performHARDIRTT( Vector(x,y,z), -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()) * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size()) * getStep() < getMaxFiberLength() && !m_stop)
{
m_fibersRTT.push_back( pointsF );
m_colorsRTT.push_back( colorF );
m_fibersRTT.push_back( pointsB );
m_colorsRTT.push_back( colorB );
}
}
}
}
}
}
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<Vector> pointsF; // Points to be rendered Forward
vector<Vector> colorF; //Color (local directions)Forward
vector<Vector> pointsB; // Points to be rendered Backward
vector<Vector> colorB; //Color (local directions) Backward
m_stop = false;
if(m_isHARDI)
{
//Track both sides
performHARDIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performHARDIRTT( Vector(x,y,z), -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()) * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size()) * getStep() < getMaxFiberLength() && !m_stop)
{
m_fibersRTT.push_back( pointsF );
m_colorsRTT.push_back( colorF );
m_fibersRTT.push_back( pointsB );
m_colorsRTT.push_back( colorB );
}
}
}
}
}
}
//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<Vector> pointsF; // Points to be rendered Forward
vector<Vector> colorF; //Color (local directions)Forward
vector<Vector> pointsB; // Points to be rendered Backward
vector<Vector> colorB; //Color (local directions) Backward
if(m_isHARDI)
{
//Track both sides
performHARDIRTT( Vector(x,y,z), 1, pointsF, colorF); //First pass
performHARDIRTT( Vector(x,y,z), -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()) * 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 );
}
}
}
}
}
}
//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<Vector> pointsF; // Points to be rendered Forward
vector<Vector> colorF; //Color (local directions)Forward
vector<Vector> pointsB; // Points to be rendered Backward
vector<Vector> colorB; //Color (local directions) Backward
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
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()) * getStep() > getMinFiberLength() && (pointsF.size() + pointsB.size()) * getStep() < getMaxFiberLength() && !m_stop)
{
m_fibersRTT.push_back( pointsF );
m_colorsRTT.push_back( colorF );
m_fibersRTT.push_back( pointsB );
m_colorsRTT.push_back( colorB );
}
}
}
}
renderRTTFibers(false);
RTTrackingHelper::getInstance()->setRTTDirty( false );
}
///////////////////////////////////////////////////////////////////////////
//Rendering stage
///////////////////////////////////////////////////////////////////////////
void RTTFibers::renderRTTFibers(bool isPlaying)
{
if(!isPlaying)
m_trackActionStep = std::numeric_limits<unsigned int>::max();
if( m_fibersRTT.size() > 0 )
{
glPushAttrib( GL_ALL_ATTRIB_BITS );
if(m_alpha != 1.0f)
{
glEnable( GL_BLEND );
glBlendFunc( GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA );
glDepthMask( GL_FALSE );
}
//for fmri
std::vector<Vector> positions;
for( unsigned int j = 0; j < m_fibersRTT.size() - 1; j+=2 )
{
//POINTS
if( SceneManager::getInstance()->isPointMode() )
{
//Forward
if( m_fibersRTT[j].size() > 0 )
{
for( unsigned int i = 0; i < std::min((unsigned int)m_fibersRTT[j].size(), m_trackActionStep); i++ )
{
glColor4f( std::abs(m_colorsRTT[j][i].x), std::abs(m_colorsRTT[j][i].y), std::abs(m_colorsRTT[j][i].z), m_alpha );
glBegin( GL_POINTS );
glVertex3f( m_fibersRTT[j][i].x, m_fibersRTT[j][i].y, m_fibersRTT[j][i].z );
glEnd();
}
}
//Backward
if(m_fibersRTT[j+1].size() > 0)
{
for( unsigned int i = 0; i < std::min((unsigned int)m_fibersRTT[j+1].size(), m_trackActionStep); i++ )
{
glColor4f( std::abs(m_colorsRTT[j+1][i].x), std::abs(m_colorsRTT[j+1][i].y), std::abs(m_colorsRTT[j+1][i].z), m_alpha );
glBegin( GL_POINTS );
glVertex3f( m_fibersRTT[j+1][i].x, m_fibersRTT[j+1][i].y, m_fibersRTT[j+1][i].z );
glEnd();
}
}
}
//LINES
else
{
//Forward
if( m_fibersRTT[j].size() > 2)
{
for( unsigned int i = 0; i < std::min((unsigned int)m_fibersRTT[j].size() - 1,m_trackActionStep); i++ )
{
if(i > m_fibersRTT[j].size() - 5 && RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
glPointSize(10.0f);
glColor3f( 1.0f,0.0f,0.0f );
glBegin( GL_POINTS );
glVertex3f( m_fibersRTT[j][i].x, m_fibersRTT[j][i].y, m_fibersRTT[j][i].z );
glEnd();
positions.push_back(Vector(m_fibersRTT[j][i].x,m_fibersRTT[j][i].y,m_fibersRTT[j][i].z));
}
else
{
glPointSize(1.0f);
glColor4f( std::abs(m_colorsRTT[j][i].x), std::abs(m_colorsRTT[j][i].y), std::abs(m_colorsRTT[j][i].z), m_alpha );
glBegin( GL_LINES );
glVertex3f( m_fibersRTT[j][i].x, m_fibersRTT[j][i].y, m_fibersRTT[j][i].z );
glVertex3f( m_fibersRTT[j][i+1].x, m_fibersRTT[j][i+1].y, m_fibersRTT[j][i+1].z );
glEnd();
}
}
}
//Backward
if ( m_fibersRTT[j+1].size() > 2)
{
for( unsigned int i = 0; i < std::min((unsigned int)m_fibersRTT[j+1].size() - 1, m_trackActionStep); i++ )
{
if(i > m_fibersRTT[j+1].size() - 5 && RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
glPointSize(10.0f);
glColor3f( 1.0f, 0.0f, 0.0f );
glBegin( GL_POINTS );
glVertex3f( m_fibersRTT[j+1][i].x, m_fibersRTT[j+1][i].y, m_fibersRTT[j+1][i].z );
glEnd();
positions.push_back(Vector(m_fibersRTT[j+1][i].x,m_fibersRTT[j+1][i].y,m_fibersRTT[j+1][i].z));
}
else
{
glPointSize(1.0f);
glColor4f( std::abs(m_colorsRTT[j+1][i].x), std::abs(m_colorsRTT[j+1][i].y), std::abs(m_colorsRTT[j+1][i].z), m_alpha );
glBegin( GL_LINES );
glVertex3f( m_fibersRTT[j+1][i].x, m_fibersRTT[j+1][i].y, m_fibersRTT[j+1][i].z );
glVertex3f( m_fibersRTT[j+1][i+1].x, m_fibersRTT[j+1][i+1].y, m_fibersRTT[j+1][i+1].z );
glEnd();
}
}
}
}
}
glDisable(GL_BLEND);
glPopAttrib();
if(RTTrackingHelper::getInstance()->isTractoDrivenRSN())
{
DatasetManager::getInstance()->m_pRestingStateNetwork->setSeedFromTracto(positions);
RTFMRIHelper::getInstance()->setRTFMRIDirty(true);
}
}
}
///////////////////////////////////////////////////////////////////////////
// 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 vOut(0,0,0);
float angleMin = 360.0f;
float angle = 0.0f;
float puncture = m_vinvout;
float wm = m_pMaskInfo->at(s_number);
float gm = 0;
if(m_pGMInfo != NULL)
{
gm = m_pGMInfo->at(s_number);
}
vin.normalize();
for(unsigned int i=0; i < sticks.size()/3; i++)
{
Vector v1(sticks[i*3],sticks[i*3+1], sticks[i*3+2]);
v1.normalize();
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;
}
}
Vector res = 0.5f * wm * vOut + (0.5f * wm) * ( (1.0 - puncture ) * vin + puncture * vOut);
if(gm != 0)
{
res = (1.0 - gm) * vOut + (gm) * ( (1.0 - puncture ) * vin + puncture * vOut);
}
return res;
}
/////////////////////////////////////////////////////////////////////
// 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;
e3.z = 1;
}
else
{
e2.z = 1;
e3.y = 1;
}
}
else if ( lvy > lvx && lvy > lvz )
{
e1.y = 1;
if( lvx > lvz )
{
e2.x = 1;
e3.z = 1;
}
else
{
e2.z = 1;
e3.x = 1;
}
}
else
{
e1.z = 1;
if( lvx > lvy )
{
e2.x = 1;
e3.y = 1;
}
else
{
e2.y = 1;
e3.x = 1;
}
}
}
///////////////////////////////////////////////////////////////////////////
// Performs realtime fiber tracking along direction bwdfwd (backward, forward)
///////////////////////////////////////////////////////////////////////////
void RTTFibers::performDTIRTT(Vector seed, int bwdfwd, vector<Vector>& points, vector<Vector>& color)
{
//Vars
Vector currPosition(seed); //Current PIXEL position
Vector nextPosition; //Next Pixel position
Vector e1(0,0,0); //Direction of the tensor (axis aligned)
Vector e2(0,0,0); //Direction of the tensor (axis aligned)
Vector e3(0,0,0); //Direction of the tensor (axis aligned)
Vector currDirection, nextDirection; //Directions re-aligned
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;
unsigned int tensorNumber;
int currVoxelx, currVoxely, currVoxelz;
float FAvalue, angle;
float FAthreshold = getFAThreshold();
float angleThreshold = getAngleThreshold();
float step = getStep();
int columns = DatasetManager::getInstance()->getColumns();
int rows = DatasetManager::getInstance()->getRows();
float xVoxel = DatasetManager::getInstance()->getVoxelX();
float yVoxel = DatasetManager::getInstance()->getVoxelY();
float zVoxel = DatasetManager::getInstance()->getVoxelZ();
FMatrix tensor;
//Get the seed voxel
currVoxelx = (int)( floor(currPosition.x / xVoxel) );
currVoxely = (int)( floor(currPosition.y / yVoxel) );
currVoxelz = (int)( floor(currPosition.z / zVoxel) );
//Corresponding tensor number
tensorNumber = currVoxelz * columns * rows + currVoxely *columns + currVoxelx;
if( tensorNumber < m_pTensorsInfo->getTensorsMatrix()->size() )
{
//Use Interpolation
if( RTTrackingHelper::getInstance()->isTensorsInterpolated() )
{
tensor = trilinearInterp( currPosition.x, currPosition.y, currPosition.z );
}
else
{
tensor = m_pTensorsInfo->getTensorsMatrix()->at(tensorNumber);
}
//Find the MAIN axis
setDiffusionAxis( tensor, e1, e2, e3 );
//Align the main direction my mult AxisAlign * tensorMatrix
currDirection.x = flippedAxes[0] * (tensor(0,0) * e1.x +
tensor(0,1) * e1.y +
tensor(0,2) * e1.z);
currDirection.y = flippedAxes[1] * (tensor(1,0) * e1.x +
tensor(1,1) * e1.y +
tensor(1,2) * e1.z);
currDirection.z = flippedAxes[2] * (tensor(2,0) * e1.x +
tensor(2,1) * e1.y +
tensor(2,2) * e1.z);
//Direction for seeding (forward or backward)
currDirection.normalize();
currDirection *= bwdfwd;
//Next position
nextPosition = currPosition + ( step * currDirection );
//Get the voxel stepped into
currVoxelx = (int)( floor(nextPosition.x / xVoxel) );
currVoxely = (int)( floor(nextPosition.y / yVoxel) );
currVoxelz = (int)( floor(nextPosition.z / zVoxel) );
//Corresponding tensor number
tensorNumber = currVoxelz * columns * rows + currVoxely * columns + currVoxelx;
if( tensorNumber < m_pTensorsInfo->getTensorsMatrix()->size() )
{
//Use interpolation
if( RTTrackingHelper::getInstance()->isTensorsInterpolated() )
{
tensor = trilinearInterp( nextPosition.x, nextPosition.y, nextPosition.z );
}
else
{
tensor = m_pTensorsInfo->getTensorsMatrix()->at(tensorNumber);
}
//Find the main diffusion axis
e1.zero();
e2.zero();
e3.zero();
setDiffusionAxis( tensor, e1, e2, e3 );
//Advection next direction
nextDirection = advecIntegrate( currDirection, tensor, e1, e2, e3, tensorNumber );
//Direction of seeding
nextDirection.normalize();
nextDirection *= bwdfwd;
if( currDirection.Dot(nextDirection) < 0 ) //Ensures the two vectors have the same directions
{
nextDirection *= -1;
}
//FA value
FAvalue = m_pTensorsInfo->getTensorsFA()->at(tensorNumber);
//Angle value
angle = 180 * std::acos( currDirection.Dot(nextDirection) ) / M_PI;
if( angle > 90 )
{
angle = 180 - angle; //Ensures that we have the smallest angle
}
///////////////////////////
//Tracking along the fiber
//////////////////////////
while( FAvalue >= FAthreshold && angle <= angleThreshold )
{
//Insert point to be rendered
points.push_back( currPosition );
color.push_back( currDirection );
//Advance
currPosition = nextPosition;
currDirection = nextDirection;
//Next position
nextPosition = currPosition + ( step * currDirection );
//Stepped voxels
currVoxelx = (int)( floor(nextPosition.x / xVoxel) );
currVoxely = (int)( floor(nextPosition.y / yVoxel) );
currVoxelz = (int)( floor(nextPosition.z / zVoxel) );
//Corresponding tensor number
tensorNumber = currVoxelz * columns * rows + currVoxely * columns + currVoxelx;
if( tensorNumber > m_pTensorsInfo->getTensorsMatrix()->size() ) //Out of anatomy
{
break;
}
//Use interpolation
if( RTTrackingHelper::getInstance()->isTensorsInterpolated() )
{
tensor = trilinearInterp( nextPosition.x, nextPosition.y, nextPosition.z );
}
else
{
tensor = m_pTensorsInfo->getTensorsMatrix()->at(tensorNumber);
}
//Find the MAIN axis
e1.zero();
e2.zero();
e3.zero();
setDiffusionAxis( tensor, e1, e2, e3 );
//Advection next direction
nextDirection = advecIntegrate( currDirection, tensor, e1, e2, e3, tensorNumber );
//Direction of seeding (backward of forward)
nextDirection.normalize();
nextDirection *= bwdfwd;
if( currDirection.Dot(nextDirection) < 0 ) //Ensures both vectors points in the same direction
{
nextDirection *= -1;
}
//FA value
FAvalue = m_pTensorsInfo->getTensorsFA()->at(tensorNumber);
//Angle value
angle = 180 * std::acos( currDirection.Dot(nextDirection) ) / M_PI;
if( angle > 90 )
{
angle = 180 - angle; //Ensures we have the minimal angle
}
}
}
}
}
///////////////////////////////////////////////////////////////////////////
// Draft a direction to start the tracking process using a probabilistic random
// [0 --- |v1| --- |v2| --- |v3|]
///////////////////////////////////////////////////////////////////////////
std::vector<float> RTTFibers::pickDirection(std::vector<float> initialPeaks, bool initWithDir)
{
std::vector<float> draftedPeak;
if(!initWithDir)
{
float norms[3];
float sum = 0.0f;
for(unsigned int i=0; i < initialPeaks.size()/3; i++)
{
Vector v1(initialPeaks[i*3],initialPeaks[i*3+1], initialPeaks[i*3+2]);
norms[i] = v1.getLength();
sum += norms[i];
}
float random = ( (float) rand() ) / (float) RAND_MAX;
float weight = ( random * sum );
if(weight < norms[0])
{
draftedPeak.push_back(initialPeaks[0]);
draftedPeak.push_back(initialPeaks[1]);
draftedPeak.push_back(initialPeaks[2]);
}
else if(weight < norms[0] + norms[1])
{
draftedPeak.push_back(initialPeaks[3]);
draftedPeak.push_back(initialPeaks[4]);
draftedPeak.push_back(initialPeaks[5]);
}
else
{
draftedPeak.push_back(initialPeaks[6]);
draftedPeak.push_back(initialPeaks[7]);
draftedPeak.push_back(initialPeaks[8]);
}
}
else
{
Vector vOut(0,0,0);
float angleMin = 360.0f;
float angle = 0.0f;
float puncture = m_vinvout;
for(unsigned int i=0; i < initialPeaks.size()/3; i++)
{
Vector v1(initialPeaks[i*3],initialPeaks[i*3+1], initialPeaks[i*3+2]);
v1.normalize();
if( m_initVec.Dot(v1) < 0 ) //Ensures both vectors points in the same direction
{
v1 *= -1;
}
//Angle value
float dot = m_initVec.Dot(v1);
float acos = std::acos( dot );
angle = 180 * acos / M_PI;
//Direction most probable
if( angle < angleMin )
{
angleMin = angle;
vOut = v1;