bool SelectionVOI::isPointInside( const float xPos, const float yPos, const float zPos ) const
{
DatasetManager *pDM( DatasetManager::getInstance() );
unsigned int xVoxelCoord( static_cast< unsigned int >( ( xPos / pDM->getVoxelX() ) ) );
unsigned int yVoxelCoord( static_cast< unsigned int >( ( yPos / pDM->getVoxelY() ) ) );
unsigned int zVoxelCoord( static_cast< unsigned int >( ( zPos / pDM->getVoxelZ() ) ) );
unsigned int dataCoord( zVoxelCoord * m_nbCols * m_nbRows + yVoxelCoord * m_nbCols + xVoxelCoord );
return m_includedVoxels.at( dataCoord );
}
bool SelectionVOI::isPointInside( const float xPos, const float yPos, const float zPos ) const
{
// According to the nifti standard, a voxel index is mapped to the coordinate of the
// center of that voxel in real space.
// Therefore, points considered in a voxel (x, y, z) range from
// (x - 0.5dx, y - 0.5dy, z - 0.5dz) to (x + 0.5dx, y + 0.5dy, z + 0.5dz).
// That is why we need to shift the coordinates before computing the coordinate.
DatasetManager *pDM( DatasetManager::getInstance() );
unsigned int xVoxelCoord( static_cast< unsigned int >( ( xPos / pDM->getVoxelX() ) + 0.5 ) );
unsigned int yVoxelCoord( static_cast< unsigned int >( ( yPos / pDM->getVoxelY() ) + 0.5 ) );
unsigned int zVoxelCoord( static_cast< unsigned int >( ( zPos / pDM->getVoxelZ() ) + 0.5 ) );
unsigned int dataCoord( zVoxelCoord * m_nbCols * m_nbRows + yVoxelCoord * m_nbCols + xVoxelCoord );
return m_includedVoxels.at( dataCoord );
}
SelectionVOI::SelectionVOI( /*DatasetHelper *pDH, */Anatomy *pSourceAnatomy, const float threshold, const ThresholdingOperationType opType )
: SelectionObject( Vector(0.0, 0.0, 0.0), Vector(0.0, 0.0, 0.0) ),
m_voiSize( 0 )
{
m_nbRows = pSourceAnatomy->getRows();
m_nbCols = pSourceAnatomy->getColumns();
m_nbFrames = pSourceAnatomy->getFrames();
vector< float > * const pAnatDataset = pSourceAnatomy->getFloatDataset();
m_includedVoxels.assign( pAnatDataset->size(), false );
if( opType == THRESHOLD_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::equal_to< float >(), threshold ) );
}
else if( opType == THRESHOLD_GREATER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater< float >(), threshold ) );
}
else if( opType == THRESHOLD_GREATER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater_equal< float >(), threshold ) );
}
else if( opType == THRESHOLD_SMALLER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less< float >(), threshold ) );
}
else if( opType == THRESHOLD_SMALLER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less_equal< float >(), threshold ) );
}
//m_isosurface = new CIsoSurface( m_datasetHelper, pSourceAnatomy );
m_pIsoSurface = new CBoolIsoSurface( m_includedVoxels );
//m_isosurface->setThreshold( threshold );
//m_isosurface->GenerateWithThreshold();
m_pIsoSurface->GenerateSurface();
wxString mystring(wxT("[VOI] - ") + pSourceAnatomy->getName());
m_name = mystring;
m_objectType = VOI_TYPE;
//m_sourceAnatomy = i_anatomy;*/
// TODO selection HERE was going to compute the value of the
// m_center and m_size params.
unsigned int xIdxMin( m_nbCols );
unsigned int yIdxMin( m_nbRows );
unsigned int zIdxMin( m_nbFrames );
unsigned int xIdxMax( 0 );
unsigned int yIdxMax( 0 );
unsigned int zIdxMax( 0 );
unsigned int dataIdx( 0 );
for( unsigned int zPos( 0 ); zPos < m_nbFrames; ++zPos )
{
for( unsigned int yPos( 0 ); yPos < m_nbRows; ++yPos )
{
for( unsigned int xPos( 0 ); xPos < m_nbCols; ++xPos, ++dataIdx )
{
if( m_includedVoxels[dataIdx] )
{
xIdxMin = std::min( xIdxMin, xPos );
yIdxMin = std::min( yIdxMin, yPos );
zIdxMin = std::min( zIdxMin, zPos );
xIdxMax = std::max( xIdxMax, xPos );
yIdxMax = std::max( yIdxMax, yPos );
zIdxMax = std::max( zIdxMax, zPos );
}
}
}
}
// Convert to space coordinates
DatasetManager *pDM( DatasetManager::getInstance() );
float spaceXMin( xIdxMin * pDM->getVoxelX() );
float spaceYMin( yIdxMin * pDM->getVoxelY() );
float spaceZMin( zIdxMin * pDM->getVoxelZ() );
// For the max value, since we want to grab all of the voxel,
// and the idx * the size of the voxel gives the begininng of the voxel
// in space, we adjust with the +1, then the - 0.1 * voxelSize to
// make sure not to fall in an inexisting coordinate.
float spaceXMax( ( xIdxMax + 1 ) * pDM->getVoxelX() - 0.1 * pDM->getVoxelX() );
float spaceYMax( ( yIdxMax + 1 ) * pDM->getVoxelY() - 0.1 * pDM->getVoxelY() );
float spaceZMax( ( zIdxMax + 1 ) * pDM->getVoxelZ() - 0.1 * pDM->getVoxelZ() );
//float spaceXMax( ( xIdxMax ) * pDH->m_xVoxel );
//float spaceYMax( ( yIdxMax ) * pDH->m_yVoxel );
//float spaceZMax( ( zIdxMax ) * pDH->m_zVoxel );
setCenter( ( spaceXMax + spaceXMin ) / 2.0f,
( spaceYMax + spaceYMin ) / 2.0f,
( spaceZMax + spaceZMin ) / 2.0f );
setSize( spaceXMax - spaceXMin, spaceYMax - spaceYMin, spaceZMax - spaceZMin );
m_voiSize = std::count( m_includedVoxels.begin(), m_includedVoxels.end(), true );
}
void SelectionVOI::buildSurface( Anatomy *pSourceAnatomy )
{
m_nbRows = pSourceAnatomy->getRows();
m_nbCols = pSourceAnatomy->getColumns();
m_nbFrames = pSourceAnatomy->getFrames();
vector< float > * const pAnatDataset = pSourceAnatomy->getFloatDataset();
m_includedVoxels.assign( pAnatDataset->size(), false );
if( m_thresType == THRESHOLD_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::equal_to< float >(), m_generationThreshold ) );
}
else if( m_thresType == THRESHOLD_GREATER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater< float >(), m_generationThreshold ) );
}
else if( m_thresType == THRESHOLD_GREATER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::greater_equal< float >(), m_generationThreshold ) );
}
else if( m_thresType == THRESHOLD_SMALLER )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less< float >(), m_generationThreshold ) );
}
else if( m_thresType == THRESHOLD_SMALLER_EQUAL )
{
std::transform( pAnatDataset->begin(), pAnatDataset->end(),
m_includedVoxels.begin(), bind2nd( std::less_equal< float >(), m_generationThreshold ) );
}
m_pIsoSurface = new CBoolIsoSurface( m_includedVoxels );
m_pIsoSurface->GenerateSurface();
// Compute the size and position of the bounding box of the VOI.
unsigned int xIdxMin( m_nbCols );
unsigned int yIdxMin( m_nbRows );
unsigned int zIdxMin( m_nbFrames );
unsigned int xIdxMax( 0 );
unsigned int yIdxMax( 0 );
unsigned int zIdxMax( 0 );
unsigned int dataIdx( 0 );
for( unsigned int zPos( 0 ); zPos < m_nbFrames; ++zPos )
{
for( unsigned int yPos( 0 ); yPos < m_nbRows; ++yPos )
{
for( unsigned int xPos( 0 ); xPos < m_nbCols; ++xPos, ++dataIdx )
{
if( m_includedVoxels[dataIdx] )
{
xIdxMin = std::min( xIdxMin, xPos );
yIdxMin = std::min( yIdxMin, yPos );
zIdxMin = std::min( zIdxMin, zPos );
xIdxMax = std::max( xIdxMax, xPos );
yIdxMax = std::max( yIdxMax, yPos );
zIdxMax = std::max( zIdxMax, zPos );
}
}
}
}
// Convert to space coordinates
DatasetManager *pDM( DatasetManager::getInstance() );
float spaceXMin( xIdxMin * pDM->getVoxelX() );
float spaceYMin( yIdxMin * pDM->getVoxelY() );
float spaceZMin( zIdxMin * pDM->getVoxelZ() );
// For the max value, since we want to grab all of the voxel,
// and the idx * the size of the voxel gives the begininng of the voxel
// in space, we adjust with the +1, then the - 0.1 * voxelSize to
// make sure not to fall in an inexisting coordinate.
float spaceXMax( ( xIdxMax + 1 ) * pDM->getVoxelX() - 0.1 * pDM->getVoxelX() );
float spaceYMax( ( yIdxMax + 1 ) * pDM->getVoxelY() - 0.1 * pDM->getVoxelY() );
float spaceZMax( ( zIdxMax + 1 ) * pDM->getVoxelZ() - 0.1 * pDM->getVoxelZ() );
setCenter( ( spaceXMax + spaceXMin ) / 2.0f,
( spaceYMax + spaceYMin ) / 2.0f,
( spaceZMax + spaceZMin ) / 2.0f );
setSize( spaceXMax - spaceXMin, spaceYMax - spaceYMin, spaceZMax - spaceZMin );
m_voiSize = std::count( m_includedVoxels.begin(), m_includedVoxels.end(), true );
}
std::vector< Vector > CIsoSurfaceBase::getSurfaceVoxelPositions()
{
// TODO selection iso check this out
if ( m_threshold == 0.0 || m_threshold == 1.0 )
{
m_svPositions.clear();
return m_svPositions;
}
if ( !m_positionsCalculated )
{
DatasetManager *pDM( DatasetManager::getInstance() );
Vector v( 0, 0, 0 );
size_t nSize = pDM->getColumns() * pDM->getRows() * pDM->getFrames();
std::vector< Vector > accu( nSize, v );
std::vector< int > hits( nSize, 0 );
std::vector< Vector > vertices = m_tMesh->getVerts();
m_svPositions.clear();
for ( size_t i = 0; i < vertices.size(); ++i )
{
v = vertices[i];
int index = (int) v.x + (int) v.y * pDM->getColumns() + (int) v.z * pDM->getColumns() * pDM->getRows();
if ( !( index < 0 || index > pDM->getColumns() * pDM->getRows() * pDM->getFrames()) )
{
accu[index].x += v.x;
accu[index].y += v.y;
accu[index].z += v.z;
hits[index] += 1;
}
}
int pointsInVoxels = 0;
int voxelsHit = 1;
for ( size_t i = 0; i < nSize; ++i )
{
if ( hits[i] > 0 )
{
++voxelsHit;
pointsInVoxels += hits[i];
}
}
pointsInVoxels /= voxelsHit;
int threshold = pointsInVoxels / 2;
for ( size_t i = 0; i < nSize; ++i )
{
if ( hits[i] > threshold )
{
accu[i].x /= hits[i];
accu[i].y /= hits[i];
accu[i].z /= hits[i];
if ( (int) accu[i].x )
{
accu[i].x = wxMin( pDM->getColumns(), wxMax ( accu[i].x, 0 ) );
accu[i].y = wxMin( pDM->getRows(), wxMax ( accu[i].y, 0 ) );
accu[i].z = wxMin( pDM->getFrames(), wxMax ( accu[i].z, 0 ) );
Vector v( accu[i].x, accu[i].y, accu[i].z );
m_svPositions.push_back( v );
}
}
}
m_positionsCalculated = true;
}
return m_svPositions;
}