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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/bruker2DFile.h>
#include <BALL/SYSTEM/binaryFileAdaptor.h>
using namespace std;
namespace BALL
{
Bruker2DFile::Bruker2DFile()
: File()
{
//????
}
Bruker2DFile::Bruker2DFile(const String& name, OpenMode open_mode)
: File(name + FileSystem::PATH_SEPARATOR + "2rr", open_mode),
parsf1_(name + FileSystem::PATH_SEPARATOR + "proc2s"),
parsf2_(name + FileSystem::PATH_SEPARATOR + "procs")
{
parsf1_.read();
parsf2_.read();
miny_ = (int)parsf1_.getIntValue("YMIN_p");
maxy_ = (int)parsf1_.getIntValue("YMAX_p");
minx_ = (int)parsf2_.getIntValue("YMIN_p");
maxx_ = (int)parsf2_.getIntValue("YMAX_p");
read();
}
Bruker2DFile::~Bruker2DFile()
{
}
void Bruker2DFile::read(const String& name)
{
parsf1_.open(name + FileSystem::PATH_SEPARATOR + "proc2s");
parsf2_.open(name + FileSystem::PATH_SEPARATOR + "procs");
parsf1_.read();
parsf2_.read();
parsf1_.close();
parsf2_.close();
miny_ = (int)parsf1_.getIntValue("YMIN_p");
maxy_ = (int)parsf1_.getIntValue("YMAX_p");
minx_ = (int)parsf2_.getIntValue("YMIN_p");
maxx_ = (int)parsf2_.getIntValue("YMAX_p");
close();
open(name + FileSystem::PATH_SEPARATOR + "2rr");
read();
}
void Bruker2DFile::read()
{
// first we will have to find out whether we are using big or little
// endian on this machine.
unsigned int endTest = 1;
BinaryFileAdaptor<BALL_INT32> adapt_int32_t_;
adapt_int32_t_.setSwapEndian((*(char*)&endTest == 1) != (parsf1_.getDoubleValue("BYTORDP") == 1.0));
int SIF1_ = (int) parsf1_.getIntValue( "SI" ); // Y - spacing
int SIF2_ = (int) parsf2_.getIntValue( "SI" ); // X - spacing
int XDIMF1_ = (int) parsf1_.getIntValue( "XDIM" );
int XDIMF2_ = (int) parsf2_.getIntValue( "XDIM" );
#ifdef BALL_DEBUG
Log.info() << "SIF1: " << SIF1_ << "--" << parsf1_.getIntValue("SI") << parsf1_.getDoubleValue("SI")
<< " SIF2: " << SIF2_ << "--" << parsf2_.getIntValue( "SI") << parsf2_.getDoubleValue( "SI")
<< " XDIMF1: " << XDIMF1_<<"--"<< parsf1_.getIntValue( "XDIM" ) << parsf1_.getDoubleValue( "XDIM" )
<< " XDIMF2: " << XDIMF2_<<"--"<< parsf2_.getIntValue( "XDIM" ) << parsf2_.getDoubleValue( "XDIM" ) << std::endl;
#endif
// prepare the regularData
//spectrum_.setXSize(SIF2_);
//spectrum_.setYSize(SIF1_);
//spectrum_.resize(SIF2_, SIF1_);
double a = parsf2_.getDoubleValue( "OFFSET" );
double b = parsf2_.getDoubleValue( "OFFSET" ) - (parsf2_.getDoubleValue( "SW_p" ) / parsf2_.getDoubleValue( "SF" ));
#ifdef BALL_DEBUG
Log.info() << "parsf2: Offset: " << a << " b: " << b << " SW_P: " <<parsf2_.getDoubleValue( "SW_p" ) << " SF: " << parsf2_.getDoubleValue( "SF" ) << std::endl;
#endif
double lower_x = (a<b) ? a : b;
double upper_x = (a>b) ? a : b;
a = parsf1_.getDoubleValue( "OFFSET" );
b = parsf1_.getDoubleValue( "OFFSET" ) - (parsf1_.getDoubleValue( "SW_p" ) / parsf1_.getDoubleValue( "SF" ));
#ifdef BALL_DEBUG
Log.info() <<"parsf1: Offset: " << a << " SW_P: " << parsf1_.getDoubleValue( "SW_p" ) << " SF: " << parsf1_.getDoubleValue("SF") << std::endl;
#endif
double lower_y = (a<b) ? a : b;
double upper_y = (a>b) ? a : b;
//spectrum_.setLowerBound(parsf1_.getIntValue( "YMIN_p" ));
//spectrum_.setUpperBound(parsf1_.getIntValue( "YMAX_p" ));
spectrum_ = RegularData2D(RegularData2D::IndexType(SIF2_, SIF1_),
Vector2(lower_x, lower_y),
Vector2(upper_x, upper_y) - Vector2(lower_x, lower_y));
// Back to the beginning of the file.
this->reopen( );
int matNumF2 = (int) (SIF2_ / XDIMF2_); // Number of matrices in x - direction
int matNumF1 = (int) (SIF1_ / XDIMF1_); // Number of matrices in y - direction
for (int actMat=0; actMat < matNumF2 * matNumF1; actMat++ )
{ // Walk through all submatrices
for (int f1 = 0; f1 < XDIMF1_; f1++ )
{ // for each matrix: look at every row
for (int f2 = 0; f2 < XDIMF2_; f2++ )
{ // look at every column
if (!this->good())
{
break;
}
(*this) >> adapt_int32_t_;
// We need to know the number of the matrix we are looking at
// right now.
int actMatF2 = (actMat % matNumF2); // x - coordinate of submatrix
int actMatF1 = (actMat / matNumF2); // y - coordinate of submatrix
spectrum_[ f2 + XDIMF2_ * actMatF2 + ( ( f1 + XDIMF1_ * actMatF1 ) * SIF2_ ) ]
= (float) adapt_int32_t_.getData();
}
}
}
#ifdef BALL_DEBUG
Log.info() << "end of read" << std::endl;
#endif
}
/** Returns the shift corresponding to a position in the bitmap.
*/
std::pair<double, double> Bruker2DFile::getShift(Position x, Position y)
{
std::pair<double, double> res;
res.first = soffsetf2_ - (double) x / spointnumf2_ * (double)swidthf2_ / bfreqf2_;
res.second = soffsetf1_ - (double) y / spointnumf1_ * (double)swidthf1_ / bfreqf1_;
return res;
}
/** Returns the coordinates of a point in the original data next to the given coordinates.
*/
std::pair<Position, Position> Bruker2DFile::getPosition(double x, double y)
{
pair<Position, Position> res;
res.first = (Position) (((double)(soffsetf2_ - x)) * spointnumf2_ * bfreqf2_ / swidthf2_);
res.second = (Position) (((double)(soffsetf1_ - y)) * spointnumf1_ * bfreqf1_ / swidthf1_);
return res;
}
/** Returns a list of peaks found in the spectrum.
Peaks at the edge are ignored.
*/
std::list<std::pair<int, int> > Bruker2DFile::getPeakList() const
{
std::list<std::pair<int, int> > retlist;
Size xdim = (Size)parsf2_.getIntValue("SI");
Size ydim = (Size)parsf1_.getIntValue("SI");
for (Position y = 1; y < ydim - 1; y++) // ignore edges -> y=1..ydim-1
{
for (Position x = 1; x < xdim - 1; x++)
{
double numdum = spectrum_[x + xdim * y];
if ((numdum > spectrum_[x-1 + (xdim*(y-1))]) && // upper left
(numdum > spectrum_[x + (xdim*(y-1))]) && // upper middle
(numdum > spectrum_[x+1 + (xdim*(y-1))]) && // upper right
(numdum > spectrum_[x-1 + (xdim*y)]) && // left
(numdum > spectrum_[x+1 + (xdim*y)]) && // right
(numdum > spectrum_[x-1 + (xdim*(y+1))]) && // lower left
(numdum > spectrum_[x + (xdim*(y+1))]) && // lower middle
(numdum > spectrum_[x+1 + (xdim*(y+1))]) ) // lower right
{
retlist.push_back(std::pair<int, int>(x, y));
}
}
}
return retlist;
}
void Bruker2DFile::setShiftRange(double offsetf1, double offsetf2, double swidthf1, double swidthf2,
double bfreqf1, double bfreqf2, double spointnumf1, double spointnumf2)
{
soffsetf1_ = offsetf1;
soffsetf2_ = offsetf2;
swidthf1_ = swidthf1;
swidthf2_ = swidthf2;
bfreqf1_ = bfreqf1;
bfreqf2_ = bfreqf2;
spointnumf1_ = (Size) spointnumf1;
spointnumf2_ = (Size) spointnumf2;
// ?????
/*
spectrum_.setXSize(spointnumf2_);
spectrum_.setYSize(spointnumf1_);
double dum1 = getShift(0,0).first;
double dum2 = getShift(spointnumf2_,0).first;
spectrum_.setXLower((dum1<dum2) ? dum1 : dum2);
spectrum_.setXUpper((dum1>dum2) ? dum1 : dum2);
dum1 = getShift(0,0).second;
dum2 = getShift(0, spointnumf1_).second;
spectrum_.setYLower((dum1<dum2) ? dum1 : dum2);
spectrum_.setYUpper((dum1>dum2) ? dum1 : dum2);
*/
}
}
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