bruker_read.cpp

//bruker_read.cpp

//This code is based upon the libraries released by Dr Kirk Marat from the University of Manitoba
//ftp://davinci.chem.umanitoba.ca/pub/marat/SpinWorks/source_library/

//I want to thank Dr Marat for making these libraries available.

//Pascal Fricke, August 2010
//fricke@studserv.uni-leipzig.de

#include "bruker_read.h"
#include "data_par.h"
#include <QString>
#include <QStringList>
#include <QTextStream>
#include <QDataStream>
#include <QDebug>
#include <QFile>
#include <QVector>
#include <QByteArray>
#include <iostream>

//get parameters from parfile (usually acqus) by parsing it line by line
bool bruker_read::get_par(QString parfile, data_par& p)
{
    QString instring;       // string used for reading lines of input file
    QStringList token;      // StringList for storing seperate parts of line after splitting
    QFile file(parfile);    //access to file


    if (!file.open(QIODevice::ReadOnly)) {      //access is read only
        std::cerr << "Cannot open parameter file: " << qPrintable (file.errorString()) << std::endl;
    }


    QTextStream in(&file);                      //text stream object "in"
    while (!in.atEnd()) {                       //stop loop at end of file
        instring = in.readLine();               //put read lines into QString "instring"
        if (instring.length() > 3)
        {
            token = instring.split(" ", QString::SkipEmptyParts); //splits after the " ", empty lines are skipped
            //if (token.at(0) == "##END") break;

            if (token.at(0) == "##$SFO1=")      //transmitter frequency
            {
                p.sfo1 = token.at(1).toDouble();
            }

            if (token.at(0) == "##$SFO2=")      //decoupler frequency
            {
                p.sfo2 = token.at(1).toDouble();
            }
            if (token.at(0) == "##$SFO3=")      //second decoupler frequency
            {
                p.sfo3 = token.at(1).toDouble();
            }
            if (token.at(0) == "##$SW=")      //spectral width (ppm)
            {
                p.sw = token.at(1).toDouble();
            }
            if (token.at(0) == "##$SF=")      //frequency of 0 ppm
            {
                p.sf = token.at(1).toDouble();
            }
            if (token.at(0) == "##$GB=")      //GB-factor
            {
                p.gb = token.at(1).toDouble();
            }
            if (token.at(0) == "##$LB=")      //line broadening
            {
                p.lb = token.at(1).toDouble();
            }
            if (token.at(0) == "##$TD=")      //acquired points (real+imaginary)
            {
                p.td = token.at(1).toInt();
            }
            if (token.at(0) == "##$DECIM=")      //DSP decimation factor
            {
                p.decim = token.at(1).toInt();
            }
            if (token.at(0) == "##$DSPFVS=")      //DSP firmware version
            {
                p.dspfvs = token.at(1).toInt();
            }
            if (token.at(0) == "##$GRPDLY=")      //DSP group delay
            {
                p.grpdly = token.at(1).toDouble();
            }
            if (token.at(0) == "##$SI=")      //transform size (complex)
            {
                p.si = token.at(1).toInt();
            }
            if (token.at(0) == "##$BYTORDA=")      //byte order
            {
                p.bytorda = token.at(1).toInt();
            }
            if (token.at(0) == "##$AQ_mod=")      //acquisition mode
            {
                p.aq_mod = token.at(1).toInt();
            }
            if (token.at(0) == "##$DIGMOD=")      //filter type
            {
                p.digmod = token.at(1).toInt();
            }
            if (token.at(0) == "##$NS=")      //number of scans
            {
                p.ns = token.at(1).toInt();
            }
            if (token.at(0) == "##$PULPROG=")      //pulse program
            {
                p.pulprog = token.at(1);
            }
            if (token.at(0) == "##$NUC1=")      //observed nucleus
            {
                p.nuc1 = token.at(1);
            }
            if (token.at(0) == "##$INTSRUM=")      //instrument name
            {
                p.instrum = token.at(1);
            }
            if (token.at(0) == "##$WDW=")      //window function type
            {
                p.wdw = token.at(1).toInt();
            }
            if (token.at(0) == "##$PH_mod=")      //phasing type
            {
                p.ph_mod = token.at(1).toInt();
            }
            if (token.at(0) == "##$PHC0=")      //zero order phase
            {
                p.phc0 = token.at(1).toDouble();
            }
            if (token.at(0) == "##$PHC1=")      //first order phase
            {
                p.phc1 = token.at(1).toDouble();
            }
            if (token.at(0) == "##$SSB=")      //sine bell shift
            {
                p.ssb = token.at(1).toInt();
            }
            if (token.at(0) == "##$MC2=")      //F1 detection mode
            {
                p.mc2 = token.at(1).toInt();
            }

        }




    }

    //set acquisition mode of experiment
    if (p.aq_mod == 2) p.aq_mode = p.AQ_MODE_SEQ();                     //sequential acquisition mode
    if (p.aq_mod == 1 || p.aq_mod == 3) p.aq_mode = p.AQ_MODE_SIM();    //simultaneous or DQD
    if (p.decim > 1) p.aq_mode = p.AQ_MODE_DSP();                       //simultaneous DSP
    return true;
};


//funtion for reading raw fid file input into byte array
bool bruker_read::get_fid(QString fidfile, data_par& p)
{
    QFile file(fidfile);            //access to file
    if (!file.open(QIODevice::ReadOnly)) {
        std::cerr << "Cannot open fid file: " << qPrintable (file.errorString()) << std::endl;
        return false;

    }
    QDataStream in(&file);          //binary data input stream

    p.fid.resize(p.td);             //resize fid byte array to actual td size
    p.fid.fill(0);                  //initialize (necessary?)


    //BYTORDA defines whether byte order is big oder little endian
    if (p.bytorda == 1) in.setByteOrder(QDataStream::BigEndian);    //set byte order to Big Endian
    if (p.bytorda == 0) in.setByteOrder(QDataStream::LittleEndian); //set byte order to Little Endian

    for (qint32 i=0; i<p.td; i++)       //fid file contains TD times a 4 byte integer
    {
        in >> p.fid[i];                 //load the datastream into the fid array, consisting of 32 bit signed integers (4 byte)

    }



    return true;
}

//currently function not needed, is done by endian-aware bitsToInt function
void bruker_read::rev_bytes(char* array, qint32 index)
{
    char byte0, byte1, byte2, byte3;
    byte0 = array[index];
    byte1 = array[index+1];
    byte2 = array[index+2];
    byte3 = array[index+3];

    array[index] = byte3;
    array[index+1] = byte2;
    array[index+2] = byte1;
    array[index+3] = byte0;
}