void DeepCopy(BigMatrix *pInMat, BigMatrix *pOutMat, SEXP rowInds, SEXP colInds)
{
in_BMAccessorType inMat( *pInMat );
out_BMAccessorType outMat( *pOutMat );
double *pRows = NUMERIC_DATA(rowInds);
double *pCols = NUMERIC_DATA(colInds);
index_type nRows = GET_LENGTH(rowInds);
index_type nCols = GET_LENGTH(colInds);
if (nRows != pOutMat->nrow())
Rf_error("length of row indices does not equal # of rows in new matrix");
if (nCols != pOutMat->ncol())
Rf_error("length of col indices does not equal # of cols in new matrix");
index_type i = 0;
index_type j = 0;
in_CType *pInColumn;
out_CType *pOutColumn;
for (i = 0; i < nCols; ++i) {
pInColumn = inMat[static_cast<index_type>(pCols[i])-1];
pOutColumn = outMat[i];
for (j = 0; j < nRows; ++j) {
pOutColumn[j] = static_cast<out_CType>(
pInColumn[static_cast<index_type>(pRows[j])-1]);
}
}
return;
}
/**
Returns the pixels in the actual image which fall insdie
the contour.
* @param:
* contour - vector of points which form a contour
* src - source Mat from which the pixels need to be extracted.
* dst - the output matrix in which the contour pixels are saved. */
void getContourPixels(std::vector <cv::Point> contour,
cv::Mat &src, cv::Mat &dst) {
cv::Rect R = cv::boundingRect(contour);
cv::Mat outMat(cv::Size(R.width, R.height), src.type());
outMat = src(cv::Range(R.y, R.y + R.height),
cv::Range(R.x, R.x + R.width));
outMat.copyTo(dst);
}
bool TextureIO::saveTexture(const string &imgPath, const Texture &texture, bool flip)
{
Mat outMat(texture.getHeight(), texture.getWidth(), CV_8UC4);
texture.bind();
glGetTexImage( GL_TEXTURE_2D, 0, GL_BGRA, GL_UNSIGNED_BYTE, outMat.data );
if(flip){cv::flip(outMat, outMat, 0);}
return imwrite(imgPath, outMat);
}
void SkyDetect::createPicBuffer( unsigned int*& imgBuffer )
{
// create ARGB 4x8bits picture
cv::Mat alpha(cv::Size( mWidth, mHeight), CV_8UC1);
cv::Mat outMat(cv::Size( mWidth, mHeight),CV_8UC4);
cv::Mat in[] = { alpha, mImageIn };
int from_to[] = { 0,3, 1,0, 2,1, 3,2 };
cv::mixChannels( in, 2, &outMat, 1, from_to, 4 );
//qDebug() << "type2: " << outMat.type();
//cv::imshow( "Input Image2", outMat );
imgBuffer = new UINT[mSize];
memcpy((void*) imgBuffer, outMat.data, mSize*sizeof(UINT) );
}
cv::Mat cropRect(const cv::Mat & image, const C2dImagePointPx & top1, const C2dImagePointPx & top2, const C2dImagePointPx & bottom2, const C2dImagePointPx & bottom1, const int nOutputRows, const int nOutputCols)
{
cv::Mat outMat(nOutputRows, nOutputCols, CV_8UC3);
for(int r=0; r<nOutputRows; r++) {
C2dImagePointPx rowStart = (bottom1 + (bottom2-bottom1)*(r/(double)nOutputRows)).eval();
C2dImagePointPx rowEnd = (top1 + (top2-top1)*(r/(double)nOutputRows)).eval();
for(int c=0; c<nOutputCols; c++) {
C2dImagePointPx rowPos = (rowStart + (rowEnd-rowStart)*(c/(double)nOutputCols)).eval();
outMat.at<cv::Vec3b>(r, c) = getSubPx_C3(image, rowPos);
}
}
return outMat;
}
SEXP CombineSubMapsTransSimple(BigMatrix *oneVox_allSubs, SEXP allVoxs_allSubs, index_type seed, double *pVoxs, index_type nvoxs, index_type nsubs) {
//using namespace Rcpp;
BMAccessorType outMat( *oneVox_allSubs );
if (nvoxs != oneVox_allSubs->ncol())
::Rf_error("nvoxs must equal oneVox_allSubs->ncol");
if (nsubs != oneVox_allSubs->nrow())
::Rf_error("nsubs must equal oneVox_allSubs->nrow");
// loop through each subject's map
index_type s = 0;
index_type v = 0;
index_type vv = 0;
LDOUBLE x = 0;
LDOUBLE delta = 0;
LDOUBLE mean = 0;
LDOUBLE M2 = 0;
LDOUBLE stdev = 0;
// CType *inCol;
CType *outCol;
LDOUBLE scaled_x;
BigMatrix *allVoxs_oneSub;
SEXP Rp;
SEXP tmp;
//RObject RallVoxs_oneSub;
for (s=0; s < nsubs; ++s) {
PROTECT(tmp = VECTOR_ELT(allVoxs_allSubs, s));
//RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
PROTECT(Rp = GET_SLOT(tmp, install("address")));
//tmp = allVoxs_allSubs[s];
//RObject RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
allVoxs_oneSub = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(Rp));
UNPROTECT(2);
BMAccessorType inMat( *allVoxs_oneSub );
for (v=0; v < nvoxs; ++v) {
vv = static_cast<index_type>(pVoxs[v]-1);
outMat[v][s] = static_cast<CType>(inMat[vv][seed]);
}
}
return R_NilValue;
}
static boost::numeric::ublas::matrix<double> transformAsMatrix(const tf::Transform& bt)
{
boost::numeric::ublas::matrix<double> outMat(4,4);
// double * mat = outMat.Store();
double mv[12];
bt.getBasis().getOpenGLSubMatrix(mv);
btVector3 origin = bt.getOrigin();
outMat(0,0)= mv[0];
outMat(0,1) = mv[4];
outMat(0,2) = mv[8];
outMat(1,0) = mv[1];
outMat(1,1) = mv[5];
outMat(1,2) = mv[9];
outMat(2,0) = mv[2];
outMat(2,1) = mv[6];
outMat(2,2) = mv[10];
outMat(3,0) = outMat(3,1) = outMat(3,2) = 0;
outMat(0,3) = origin.x();
outMat(1,3) = origin.y();
outMat(2,3) = origin.z();
outMat(3,3) = 1;
return outMat;
};
int main(int argc, char ** argv){
NcError error(NcError::verbose_nonfatal);
try{
std::string inFile;
std::string outFile;
std::string varName;
std::string inList;
// bool calcStdDev;
BeginCommandLine()
CommandLineString(inFile, "in", "");
CommandLineString(inList, "inlist","");
CommandLineString(varName, "var", "");
CommandLineString(outFile, "out", "");
// CommandLineBool(calcStdDev, "std");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
if ((inFile != "") && (inList != "")){
_EXCEPTIONT("Can only open one file (--in) or list (--inlist).");
}
//file list vector
std::vector<std::string> vecFiles;
if (inFile != ""){
vecFiles.push_back(inFile);
}
if (inList != ""){
GetInputFileList(inList,vecFiles);
}
//open up first file
NcFile readin(vecFiles[0].c_str());
if (!readin.is_valid()){
_EXCEPTION1("Unable to open file %s for reading",\
vecFiles[0].c_str());
}
int tLen,latLen,lonLen;
NcDim * time = readin.get_dim("time");
tLen = time->size();
NcVar * timeVar = readin.get_var("time");
NcDim * lat = readin.get_dim("lat");
latLen = lat->size();
NcVar * latVar = readin.get_var("lat");
NcDim * lon = readin.get_dim("lon");
lonLen = lon->size();
NcVar * lonVar = readin.get_var("lon");
//read input variable
NcVar * inVar = readin.get_var(varName.c_str());
//Create output matrix
DataMatrix<double> outMat(latLen,lonLen);
densCalc(inVar,outMat);
//Option for calculating the yearly standard deviation
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[0][a][b] = outMat[a][b];
}
}
}
*/
//If multiple files, add these values to the output
if (vecFiles.size()>1){
DataMatrix<double> addMat(latLen,lonLen);
std::cout<<"There are "<<vecFiles.size()<<" files."<<std::endl;
for (int v=1; v<vecFiles.size(); v++){
NcFile addread(vecFiles[v].c_str());
NcVar * inVar = addread.get_var(varName.c_str());
densCalc(inVar,addMat);
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]+=addMat[a][b];
}
}
/* if (calcStdDev){
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
storeMat[v][a][b] = addMat[a][b];
}
}
}*/
addread.close();
}
//Divide output by number of files
double div = 1./((double) vecFiles.size());
for (int a=0; a<latLen; a++){
for (int b=0; b<lonLen; b++){
outMat[a][b]*=div;
}
}
}
NcFile readout(outFile.c_str(),NcFile::Replace, NULL,0,NcFile::Offset64Bits);
NcDim * outLat = readout.add_dim("lat", latLen);
NcDim * outLon = readout.add_dim("lon", lonLen);
NcVar * outLatVar = readout.add_var("lat",ncDouble,outLat);
NcVar * outLonVar = readout.add_var("lon",ncDouble,outLon);
std::cout<<"Copying dimension attributes."<<std::endl;
copy_dim_var(latVar,outLatVar);
copy_dim_var(lonVar,outLonVar);
std::cout<<"Creating density variable."<<std::endl;
NcVar * densVar = readout.add_var("dens",ncDouble,outLat,outLon);
densVar->set_cur(0,0);
densVar->put((&outMat[0][0]),latLen,lonLen);
/* if (calcStdDev){
NcVar * stdDevVar = readout.add_var("stddev", ncDouble,outLat,outLon);
DataMatrix<double> stdDevMat(latLen,lonLen);
yearlyStdDev(storeMat,vecFiles.size(),latLen,lonLen,stdDevMat);
stdDevVar->set_cur(0,0);
stdDevVar->put(&(stdDevMat[0][0]),latLen,lonLen);
std::cout<<" created sd variable"<<std::endl;
}
*/
readout.close();
readin.close();
}
catch (Exception &e){
std::cout<<e.ToString()<<std::endl;
}
}
SEXP CombineSubMaps(BigMatrix *oneVox_allSubs, SEXP allVoxs_allSubs, index_type seed, double *pVoxs, index_type nvoxs, index_type nsubs) {
//using namespace Rcpp;
BMAccessorType outMat( *oneVox_allSubs );
if (nsubs != oneVox_allSubs->ncol())
Rf_error("nsubs must equal oneVox_allSubs->ncol");
if (nvoxs != oneVox_allSubs->nrow())
Rf_error("nsubs must equal oneVox_allSubs->nrow");
// loop through each subject's map
index_type s = 0;
index_type v = 0;
index_type vv = 0;
LDOUBLE x = 0;
LDOUBLE delta = 0;
LDOUBLE mean = 0;
LDOUBLE M2 = 0;
LDOUBLE stdev = 0;
// CType *inCol;
CType *outCol;
LDOUBLE scaled_x;
BigMatrix *allVoxs_oneSub;
SEXP Rp;
SEXP tmp;
//RObject RallVoxs_oneSub;
for (s=0; s < nsubs; ++s) {
PROTECT(tmp = VECTOR_ELT(allVoxs_allSubs, s));
//RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
PROTECT(Rp = GET_SLOT(tmp, install("address")));
//tmp = allVoxs_allSubs[s];
//RObject RallVoxs_oneSub(tmp);
//Rp = RallVoxs_oneSub.slot("address");
allVoxs_oneSub = reinterpret_cast<BigMatrix*>(R_ExternalPtrAddr(Rp));
UNPROTECT(2);
BMAccessorType inMat( *allVoxs_oneSub );
// inCol = inMat[seed];
delta = mean = M2 = stdev = 0;
for (v=0; v < nvoxs; ++v) {
// todo: add checking for NaN...but shouldn't really have any!
// maybe can also pass the exact list of voxs to loop through!
// if (!ISNAN(pColumn[curj]))
// NA_REAL
vv = static_cast<index_type>(pVoxs[v]-1);
x = static_cast<LDOUBLE>(inMat[vv][seed]);
delta = x - mean;
mean = mean + delta/static_cast<LDOUBLE>(v+1);
M2 = M2 + delta*(x - mean);
}
stdev = sqrt(M2/(static_cast<LDOUBLE>(nvoxs-1)));
//printf("mean: %f; stdev: %f\n", mean, stdev);
outCol = outMat[s];
for (v=0; v < nvoxs; ++v) {
vv = static_cast<index_type>(pVoxs[v]-1);
scaled_x = (static_cast<LDOUBLE>(inMat[vv][seed])-mean)/stdev;
outCol[v] = static_cast<CType>(scaled_x);
}
}
return R_NilValue;
}
void expm_eigen(int n, double *rz, double *out)
{
Eigen::Map< Eigen::MatrixXd > inMat(rz, n, n);
Eigen::Map< Eigen::MatrixXd > outMat(out, n, n);
outMat = inMat.exp();
}
SEXP invariantSimilarityHelper(
typename itk::Image< float , ImageDimension >::Pointer image1,
typename itk::Image< float , ImageDimension >::Pointer image2,
SEXP r_thetas, SEXP r_thetas2, SEXP r_thetas3,
SEXP r_lsits, SEXP r_WM, SEXP r_scale,
SEXP r_doreflection, SEXP r_txfn )
{
unsigned int mibins = 20;
unsigned int localSearchIterations =
Rcpp::as< unsigned int >( r_lsits ) ;
std::string whichMetric = Rcpp::as< std::string >( r_WM );
std::string txfn = Rcpp::as< std::string >( r_txfn );
bool useprincaxis = true;
typedef typename itk::ImageMaskSpatialObject<ImageDimension>::ImageType
maskimagetype;
typename maskimagetype::Pointer mask = ITK_NULLPTR;
Rcpp::NumericVector thetas( r_thetas );
Rcpp::NumericVector thetas2( r_thetas2 );
Rcpp::NumericVector thetas3( r_thetas3 );
Rcpp::IntegerVector doReflection( r_doreflection );
typedef float PixelType;
typedef double RealType;
RealType bestscale = Rcpp::as< RealType >( r_scale ) ;
typedef itk::Image< PixelType , ImageDimension > ImageType;
if( image1.IsNotNull() & image2.IsNotNull() )
{
typedef typename itk::ImageMomentsCalculator<ImageType> ImageCalculatorType;
typedef itk::AffineTransform<RealType, ImageDimension> AffineType0;
typedef typename ImageCalculatorType::MatrixType MatrixType;
typedef itk::Vector<float, ImageDimension> VectorType;
VectorType ccg1;
VectorType cpm1;
MatrixType cpa1;
VectorType ccg2;
VectorType cpm2;
MatrixType cpa2;
typename ImageCalculatorType::Pointer calculator1 =
ImageCalculatorType::New();
typename ImageCalculatorType::Pointer calculator2 =
ImageCalculatorType::New();
calculator1->SetImage( image1 );
calculator2->SetImage( image2 );
typename ImageCalculatorType::VectorType fixed_center;
fixed_center.Fill(0);
typename ImageCalculatorType::VectorType moving_center;
moving_center.Fill(0);
try
{
calculator1->Compute();
fixed_center = calculator1->GetCenterOfGravity();
ccg1 = calculator1->GetCenterOfGravity();
cpm1 = calculator1->GetPrincipalMoments();
cpa1 = calculator1->GetPrincipalAxes();
try
{
calculator2->Compute();
moving_center = calculator2->GetCenterOfGravity();
ccg2 = calculator2->GetCenterOfGravity();
cpm2 = calculator2->GetPrincipalMoments();
cpa2 = calculator2->GetPrincipalAxes();
}
catch( ... )
{
fixed_center.Fill(0);
}
}
catch( ... )
{
// Rcpp::Rcerr << " zero image1 error ";
}
if ( vnl_math_abs( bestscale - 1.0 ) < 1.e-6 )
{
RealType volelt1 = 1;
RealType volelt2 = 1;
for ( unsigned int d=0; d<ImageDimension; d++)
{
volelt1 *= image1->GetSpacing()[d];
volelt2 *= image2->GetSpacing()[d];
}
bestscale =
( calculator2->GetTotalMass() * volelt2 )/
( calculator1->GetTotalMass() * volelt1 );
RealType powlev = 1.0 / static_cast<RealType>(ImageDimension);
bestscale = vcl_pow( bestscale , powlev );
}
unsigned int eigind1 = 1;
unsigned int eigind2 = 1;
if( ImageDimension == 3 )
{
eigind1 = 2;
}
typedef vnl_vector<RealType> EVectorType;
typedef vnl_matrix<RealType> EMatrixType;
EVectorType evec1_2ndary = cpa1.GetVnlMatrix().get_row( eigind2 );
EVectorType evec1_primary = cpa1.GetVnlMatrix().get_row( eigind1 );
EVectorType evec2_2ndary = cpa2.GetVnlMatrix().get_row( eigind2 );
EVectorType evec2_primary = cpa2.GetVnlMatrix().get_row( eigind1 );
/** Solve Wahba's problem http://en.wikipedia.org/wiki/Wahba%27s_problem */
EMatrixType B = outer_product( evec2_primary, evec1_primary );
if( ImageDimension == 3 )
{
B = outer_product( evec2_2ndary, evec1_2ndary )
+ outer_product( evec2_primary, evec1_primary );
}
vnl_svd<RealType> wahba( B );
vnl_matrix<RealType> A_solution = wahba.V() * wahba.U().transpose();
A_solution = vnl_inverse( A_solution );
RealType det = vnl_determinant( A_solution );
if( ( det < 0 ) )
{
vnl_matrix<RealType> id( A_solution );
id.set_identity();
for( unsigned int i = 0; i < ImageDimension; i++ )
{
if( A_solution( i, i ) < 0 )
{
id( i, i ) = -1.0;
}
}
A_solution = A_solution * id.transpose();
}
if ( doReflection[0] == 1 || doReflection[0] == 3 )
{
vnl_matrix<RealType> id( A_solution );
id.set_identity();
id = id - 2.0 * outer_product( evec2_primary , evec2_primary );
A_solution = A_solution * id;
}
if ( doReflection[0] > 1 )
{
vnl_matrix<RealType> id( A_solution );
id.set_identity();
id = id - 2.0 * outer_product( evec1_primary , evec1_primary );
A_solution = A_solution * id;
}
typename AffineType::Pointer affine1 = AffineType::New();
typename AffineType::OffsetType trans = affine1->GetOffset();
itk::Point<RealType, ImageDimension> trans2;
for( unsigned int i = 0; i < ImageDimension; i++ )
{
trans[i] = moving_center[i] - fixed_center[i];
trans2[i] = fixed_center[i] * ( 1 );
}
affine1->SetIdentity();
affine1->SetOffset( trans );
if( useprincaxis )
{
affine1->SetMatrix( A_solution );
}
affine1->SetCenter( trans2 );
if( ImageDimension > 3 )
{
return EXIT_SUCCESS;
}
vnl_vector<RealType> evec_tert;
if( ImageDimension == 3 )
{ // try to rotate around tertiary and secondary axis
evec_tert = vnl_cross_3d( evec1_primary, evec1_2ndary );
}
if( ImageDimension == 2 )
{ // try to rotate around tertiary and secondary axis
evec_tert = evec1_2ndary;
evec1_2ndary = evec1_primary;
}
itk::Vector<RealType, ImageDimension> axis1;
itk::Vector<RealType, ImageDimension> axis2;
itk::Vector<RealType, ImageDimension> axis3;
for( unsigned int d = 0; d < ImageDimension; d++ )
{
axis1[d] = evec_tert[d];
axis2[d] = evec1_2ndary[d];
axis3[d] = evec1_primary[d];
}
typename AffineType::Pointer simmer = AffineType::New();
simmer->SetIdentity();
simmer->SetCenter( trans2 );
simmer->SetOffset( trans );
typename AffineType0::Pointer affinesearch = AffineType0::New();
affinesearch->SetIdentity();
affinesearch->SetCenter( trans2 );
typedef itk::MultiStartOptimizerv4 OptimizerType;
typename OptimizerType::MetricValuesListType metricvalues;
typename OptimizerType::Pointer mstartOptimizer = OptimizerType::New();
typedef itk::CorrelationImageToImageMetricv4
<ImageType, ImageType, ImageType> GCMetricType;
typedef itk::MattesMutualInformationImageToImageMetricv4
<ImageType, ImageType, ImageType> MetricType;
typename MetricType::ParametersType newparams( affine1->GetParameters() );
typename GCMetricType::Pointer gcmetric = GCMetricType::New();
gcmetric->SetFixedImage( image1 );
gcmetric->SetVirtualDomainFromImage( image1 );
gcmetric->SetMovingImage( image2 );
gcmetric->SetMovingTransform( simmer );
gcmetric->SetParameters( newparams );
typename MetricType::Pointer mimetric = MetricType::New();
mimetric->SetNumberOfHistogramBins( mibins );
mimetric->SetFixedImage( image1 );
mimetric->SetMovingImage( image2 );
mimetric->SetMovingTransform( simmer );
mimetric->SetParameters( newparams );
if( mask.IsNotNull() )
{
typename itk::ImageMaskSpatialObject<ImageDimension>::Pointer so =
itk::ImageMaskSpatialObject<ImageDimension>::New();
so->SetImage( const_cast<maskimagetype *>( mask.GetPointer() ) );
mimetric->SetFixedImageMask( so );
gcmetric->SetFixedImageMask( so );
}
typedef itk::ConjugateGradientLineSearchOptimizerv4 LocalOptimizerType;
typename LocalOptimizerType::Pointer localoptimizer =
LocalOptimizerType::New();
RealType localoptimizerlearningrate = 0.1;
localoptimizer->SetLearningRate( localoptimizerlearningrate );
localoptimizer->SetMaximumStepSizeInPhysicalUnits(
localoptimizerlearningrate );
localoptimizer->SetNumberOfIterations( localSearchIterations );
localoptimizer->SetLowerLimit( 0 );
localoptimizer->SetUpperLimit( 2 );
localoptimizer->SetEpsilon( 0.1 );
localoptimizer->SetMaximumLineSearchIterations( 50 );
localoptimizer->SetDoEstimateLearningRateOnce( true );
localoptimizer->SetMinimumConvergenceValue( 1.e-6 );
localoptimizer->SetConvergenceWindowSize( 5 );
if( true )
{
typedef typename MetricType::FixedSampledPointSetType PointSetType;
typedef typename PointSetType::PointType PointType;
typename PointSetType::Pointer pset(PointSetType::New());
unsigned int ind=0;
unsigned int ct=0;
itk::ImageRegionIteratorWithIndex<ImageType> It(image1,
image1->GetLargestPossibleRegion() );
for( It.GoToBegin(); !It.IsAtEnd(); ++It )
{
// take every N^th point
if ( ct % 10 == 0 )
{
PointType pt;
image1->TransformIndexToPhysicalPoint( It.GetIndex(), pt);
pset->SetPoint(ind, pt);
ind++;
}
ct++;
}
mimetric->SetFixedSampledPointSet( pset );
mimetric->SetUseFixedSampledPointSet( true );
gcmetric->SetFixedSampledPointSet( pset );
gcmetric->SetUseFixedSampledPointSet( true );
}
if ( whichMetric.compare("MI") == 0 ) {
mimetric->Initialize();
typedef itk::RegistrationParameterScalesFromPhysicalShift<MetricType>
RegistrationParameterScalesFromPhysicalShiftType;
typename RegistrationParameterScalesFromPhysicalShiftType::Pointer
shiftScaleEstimator =
RegistrationParameterScalesFromPhysicalShiftType::New();
shiftScaleEstimator->SetMetric( mimetric );
shiftScaleEstimator->SetTransformForward( true );
typename RegistrationParameterScalesFromPhysicalShiftType::ScalesType
movingScales( simmer->GetNumberOfParameters() );
shiftScaleEstimator->EstimateScales( movingScales );
mstartOptimizer->SetScales( movingScales );
mstartOptimizer->SetMetric( mimetric );
localoptimizer->SetMetric( mimetric );
localoptimizer->SetScales( movingScales );
}
if ( whichMetric.compare("MI") != 0 ) {
gcmetric->Initialize();
typedef itk::RegistrationParameterScalesFromPhysicalShift<GCMetricType>
RegistrationParameterScalesFromPhysicalShiftType;
typename RegistrationParameterScalesFromPhysicalShiftType::Pointer
shiftScaleEstimator =
RegistrationParameterScalesFromPhysicalShiftType::New();
shiftScaleEstimator->SetMetric( gcmetric );
shiftScaleEstimator->SetTransformForward( true );
typename RegistrationParameterScalesFromPhysicalShiftType::ScalesType
movingScales( simmer->GetNumberOfParameters() );
shiftScaleEstimator->EstimateScales( movingScales );
mstartOptimizer->SetScales( movingScales );
mstartOptimizer->SetMetric( gcmetric );
localoptimizer->SetMetric( gcmetric );
localoptimizer->SetScales( movingScales );
}
typename OptimizerType::ParametersListType parametersList =
mstartOptimizer->GetParametersList();
affinesearch->SetIdentity();
affinesearch->SetCenter( trans2 );
affinesearch->SetOffset( trans );
for ( unsigned int i = 0; i < thetas.size(); i++ )
{
RealType ang1 = thetas[i];
RealType ang2 = 0; // FIXME should be psi
RealType ang3 = 0; // FIXME should be psi
if( ImageDimension == 3 )
{
for ( unsigned int jj = 0; jj < thetas2.size(); jj++ )
{
ang2=thetas2[jj];
for ( unsigned int kk = 0; kk < thetas3.size(); kk++ )
{
ang3=thetas3[kk];
affinesearch->SetIdentity();
affinesearch->SetCenter( trans2 );
affinesearch->SetOffset( trans );
if( useprincaxis )
{
affinesearch->SetMatrix( A_solution );
}
affinesearch->Rotate3D(axis1, ang1, 1);
affinesearch->Rotate3D(axis2, ang2, 1);
affinesearch->Rotate3D(axis3, ang3, 1);
// affinesearch->Scale( bestscale ); // BUG: annoying, cant do for rigid
simmer->SetMatrix( affinesearch->GetMatrix() );
parametersList.push_back( simmer->GetParameters() );
} // kk
}
}
if( ImageDimension == 2 )
{
affinesearch->SetIdentity();
affinesearch->SetCenter( trans2 );
affinesearch->SetOffset( trans );
if( useprincaxis )
{
affinesearch->SetMatrix( A_solution );
}
affinesearch->Rotate2D( ang1, 1);
// affinesearch->Scale( bestscale );
simmer->SetMatrix( affinesearch->GetMatrix() );
typename AffineType::ParametersType pp =
simmer->GetParameters();
parametersList.push_back( simmer->GetParameters() );
}
}
mstartOptimizer->SetParametersList( parametersList );
if( localSearchIterations > 0 )
{
mstartOptimizer->SetLocalOptimizer( localoptimizer );
}
mstartOptimizer->StartOptimization();
typename AffineType::Pointer bestaffine = AffineType::New();
bestaffine->SetCenter( trans2 );
bestaffine->SetParameters( mstartOptimizer->GetBestParameters() );
if ( txfn.length() > 3 )
{
typename AffineType::Pointer bestaffine = AffineType::New();
bestaffine->SetCenter( trans2 );
bestaffine->SetParameters( mstartOptimizer->GetBestParameters() );
typedef itk::TransformFileWriter TransformWriterType;
typename TransformWriterType::Pointer transformWriter =
TransformWriterType::New();
transformWriter->SetInput( bestaffine );
transformWriter->SetFileName( txfn.c_str() );
transformWriter->Update();
}
metricvalues = mstartOptimizer->GetMetricValuesList();
unsigned int ncols = mstartOptimizer->GetBestParameters().Size() +
1 + ImageDimension;
Rcpp::NumericMatrix outMat( metricvalues.size(), ncols );
for ( unsigned int k = 0; k < metricvalues.size(); k++ )
{
outMat( k, 0 ) = metricvalues[ k ];
typename MetricType::ParametersType resultParams =
mstartOptimizer->GetParametersList( )[ k ];
for ( unsigned int kp = 0; kp < resultParams.Size(); kp++ )
{
outMat( k, kp + 1 ) = resultParams[ kp ];
}
// set the fixed parameters
unsigned int baseind = resultParams.Size() + 1;
for ( unsigned int kp = 0; kp < ImageDimension; kp++ )
outMat( k, baseind + kp ) = bestaffine->GetFixedParameters()[ kp ];
}
return Rcpp::wrap( outMat );
}
else
{
Rcpp::NumericMatrix outMat( 1, 1 );
outMat( 0, 0 ) = 0;
return Rcpp::wrap( outMat );
}
}