returnValue Matrix::printToFile( const char* const filename,
const char* const name,
PrintScheme printScheme
) const
{
FILE* file = 0;
MatFile* matFile = 0;
switch ( printScheme )
{
case PS_MATLAB_BINARY:
matFile = new MatFile;
matFile->open( filename );
matFile->write( *this,name );
matFile->close( );
delete matFile;
return SUCCESSFUL_RETURN;
default:
file = fopen( filename,"w+" );
if ( file == 0 )
return ACADOERROR( RET_FILE_CAN_NOT_BE_OPENED );
printToFile( file, name,printScheme );
fclose( file );
return SUCCESSFUL_RETURN;
}
}
virtual void end(Voxel& voxel,MatFile& mat_writer)
{
mat_writer.add_matrix("free_water_quantity",&voxel.qa_scaling,1,1);
mat_writer.add_matrix("jdet",&*jdet.begin(),1,jdet.size());
double trans_to_mni[16];
std::fill(trans_to_mni,trans_to_mni+16,0.0);
trans_to_mni[0] = scale[0];
trans_to_mni[5] = scale[1];
trans_to_mni[10] = scale[2];
trans_to_mni[3] = bounding_box_lower[0]-scale[0];
trans_to_mni[7] = bounding_box_lower[1]-scale[1];
trans_to_mni[11] = bounding_box_lower[2]-scale[2];
mat_writer.add_matrix("mni",&*trans_to_mni,4,3);
mat_writer.add_matrix("R2",&R2,1,1);
}
returnValue GenericMatrix< T >::print( std::ostream& _stream,
const std::string& _name,
PrintScheme _printScheme
) const
{
MatFile< T >* matFile;
switch ( _printScheme )
{
case PS_MATLAB_BINARY:
matFile = new MatFile<T>();
matFile->write(_stream, *this, _name.c_str());
delete matFile;
return SUCCESSFUL_RETURN;
default:
char* startString = 0;
char* endString = 0;
uint width = 0;
uint precision = 0;
char* colSeparator = 0;
char* rowSeparator = 0;
returnValue ret = getGlobalStringDefinitions(_printScheme, &startString,
&endString, width, precision, &colSeparator, &rowSeparator);
if (ret != SUCCESSFUL_RETURN)
return ret;
returnValue status = print(_stream, _name, startString, endString, width,
precision, colSeparator, rowSeparator);
if ( startString != 0 ) delete[] startString;
if ( endString != 0 ) delete[] endString;
if ( colSeparator != 0 ) delete[] colSeparator;
if ( rowSeparator != 0 ) delete[] rowSeparator;
return status;
}
}
virtual void end(Voxel& voxel,MatFile& mat_writer)
{
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::ostringstream out;
out << index;
std::string num = out.str();
std::string index_str = "dir";
index_str += num;
set_title(index_str.c_str());
mat_writer.add_matrix(index_str.c_str(),&*dir[index].begin(),1,dir[index].size());
}
}
virtual void end(Voxel& voxel,MatFile& mat_writer)
{
if (voxel.need_odf)
{
set_title("output odfs");
for (unsigned int index = 0;index < voxel.template_odfs.size();++index)
{
std::ostringstream out;
out << "odf" << index;
mat_writer.add_matrix(out.str().c_str(),&*voxel.template_odfs[index].begin(),
voxel.ti.half_vertices_count,
voxel.template_odfs[index].size()/(voxel.ti.half_vertices_count));
}
}
}
virtual void end(Voxel& voxel,MatFile& mat_writer)
{
if (!voxel.need_odf)
return;
{
set_title("output odfs");
for (unsigned int index = 0;index < odf_data.size();++index)
{
if (!voxel.odf_deconvolusion)
std::for_each(odf_data[index].begin(),odf_data[index].end(),boost::lambda::_1 /= voxel.qa_scaling);
std::ostringstream out;
out << "odf" << index;
mat_writer.add_matrix(out.str().c_str(),&*odf_data[index].begin(),
voxel.ti.half_vertices_count,
odf_data[index].size()/(voxel.ti.half_vertices_count));
}
odf_data.clear();
}
}
virtual void end(Voxel& voxel,MatFile& mat_writer)
{
set_title("output gfa");
mat_writer.add_matrix("gfa",&*gfa.begin(),1,gfa.size());
if(!voxel.odf_deconvolusion)
{
voxel.qa_scaling = *std::max_element(iso.begin(),iso.end());
// scaled to 1mm cubic
if(voxel.vs[0] != 0.0 &&
voxel.vs[1] != 0.0 &&
voxel.vs[2] != 0.0)
{
voxel.qa_scaling /= voxel.vs[0];
voxel.qa_scaling /= voxel.vs[1];
voxel.qa_scaling /= voxel.vs[2];
}
mat_writer.add_matrix("qa_scaling",&voxel.qa_scaling,1,1);
std::for_each(iso.begin(),iso.end(),boost::lambda::_1 /= voxel.qa_scaling);
mat_writer.add_matrix("iso",&*iso.begin(),1,iso.size());
if (voxel.qa_scaling != 0.0)
for (unsigned int i = 0;i < voxel.max_fiber_number;++i)
std::for_each(fa[i].begin(),fa[i].end(),boost::lambda::_1 /= voxel.qa_scaling);
// cellularity
int max_fa_index = std::max_element(fa[0].begin(),fa[0].end())-fa[0].begin();
float ratio = iso[max_fa_index]/fa[0][max_fa_index];
for(unsigned int index = 0;index < iso.size();++index)
iso[index] -= fa[0][index]*ratio;
mat_writer.add_matrix("cell",&*iso.begin(),1,iso.size());
}
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::ostringstream out;
out << index;
std::string num = out.str();
std::string fa_str = "fa";
fa_str += num;
set_title(fa_str.c_str());
mat_writer.add_matrix(fa_str.c_str(),&*fa[index].begin(),1,fa[index].size());
}
// output normalized qa
{
float max_qa = 0.0;
for (unsigned int i = 0;i < voxel.max_fiber_number;++i)
max_qa = std::max<float>(*std::max_element(fa[i].begin(),fa[i].end()),max_qa);
if(max_qa != 0.0)
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
std::for_each(fa[index].begin(),fa[index].end(),boost::lambda::_1 /= max_qa);
std::ostringstream out;
out << index;
std::string num = out.str();
std::string fa_str = "nqa";
fa_str += num;
set_title(fa_str.c_str());
mat_writer.add_matrix(fa_str.c_str(),&*fa[index].begin(),1,fa[index].size());
}
}
}
