pappso::MzCalibrationModel1 Class Reference

#include <mzcalibrationmodel1.h>

Inheritance diagram for pappso::MzCalibrationModel1:

Public Member Functions
	MzCalibrationModel1 (double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)
virtual	~MzCalibrationModel1 ()
virtual double	getMzFromTofIndex (quint32 tof_index) override
	get m/z from time of flight raw index
virtual quint32	getTofIndexFromMz (double mz) override
	get raw TOF index of a given m/z
Public Member Functions inherited from pappso::MzCalibrationInterface
	MzCalibrationInterface (double digitizerTimebase, double digitizerDelay)
virtual	~MzCalibrationInterface ()
MzCalibrationInterface &	operator= (const MzCalibrationInterface &other)
bool	operator== (const MzCalibrationInterface &other) const
double	getTofFromTofIndex (quint32 tof_index) const
	get time of flight from raw index
double	getTofFromTofIndex (double tof_index) const
	get time of flight from double index

Additional Inherited Members
Protected Attributes inherited from pappso::MzCalibrationInterface
double	m_digitizerTimebase = 0
double	m_digitizerDelay = 0
std::vector< double >	m_mzCalibrationArr
	MZ calibration parameters.

Detailed Description

Todo

write docs

Definition at line 40 of file mzcalibrationmodel1.h.

Constructor & Destructor Documentation

MzCalibrationModel1()

MzCalibrationModel1::MzCalibrationModel1	(	double	T1_frame,
		double	T2_frame,
		double	digitizerTimebase,
		double	digitizerDelay,
		double	C0,
		double	C1,
		double	C2,
		double	C3,
		double	C4,
		double	T1_ref,
		double	T2_ref,
		double	dC1,
		double	dC2 )

Default constructor

Definition at line 38 of file mzcalibrationmodel1.cpp.

  : MzCalibrationInterface(digitizerTimebase, digitizerDelay)
{
 
  double temperature_correction =
    dC1 * (T1_ref - T1_frame) + dC2 * (T2_ref - T2_frame);
  temperature_correction = (double)1.0 + (temperature_correction / 1.0e6);
 
  // temperature compensation
  C1 = C1 * temperature_correction;
  C2 = C2 / temperature_correction;
 
 
  m_mzCalibrationArr.clear();
 
  m_digitizerDelay    = digitizerDelay;
  m_digitizerTimebase = digitizerTimebase;
 
  m_mzCalibrationArr.push_back(C0);
  m_mzCalibrationArr.push_back(std::sqrt(std::pow(10, 12) / C1));
  m_mzCalibrationArr.push_back(C2);
  m_mzCalibrationArr.push_back(C3);
  m_mzCalibrationArr.push_back(C4);
}

References pappso::MzCalibrationInterface::MzCalibrationInterface(), pappso::MzCalibrationInterface::m_digitizerDelay, pappso::MzCalibrationInterface::m_digitizerTimebase, and pappso::MzCalibrationInterface::m_mzCalibrationArr.

Referenced by pappso::MzCalibrationModel1Cached::MzCalibrationModel1Cached().

~MzCalibrationModel1()

MzCalibrationModel1::~MzCalibrationModel1 ( )

virtual

Destructor

Definition at line 75 of file mzcalibrationmodel1.cpp.

{
}

Member Function Documentation

getMzFromTofIndex()

double MzCalibrationModel1::getMzFromTofIndex ( quint32 tof_index )

overridevirtual

get m/z from time of flight raw index

Parameters

tof_index

time of flight

Returns

m/z value

Implements pappso::MzCalibrationInterface.

Reimplemented in pappso::MzCalibrationModel1Cached.

Definition at line 80 of file mzcalibrationmodel1.cpp.

{
  double tof = ((double)tof_index * m_digitizerTimebase) + m_digitizerDelay;
  // http://www.alglib.net/equations/polynomial.php
  // http://www.alglib.net/translator/man/manual.cpp.html#sub_polynomialsolve
  // https://math.stackexchange.com/questions/1291208/number-of-roots-of-a-polynomial-of-non-integer-degree
  // https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=2ahUKEwiWhLOFxqrkAhVLxYUKHVqqDFcQFjABegQIAxAB&url=https%3A%2F%2Fkluge.in-chemnitz.de%2Fopensource%2Fspline%2Fexample_alglib.cpp&usg=AOvVaw0guGejJGPmkOVg48_GJYR8
  // https://stackoverflow.com/questions/26091323/how-to-plot-a-function-curve-in-r
  /*
   * beware to put the function on a single line in R:
> eq <- function(m){ 1 + (sqrt((10^12)/670) * sqrt(m)) + (207.775676931964 * m)
+ (59.2526676368822 * (m^1.5)) }
> eq <- function(m){ 313.577620892277 + (sqrt((10^12)/157424.07710945) *
sqrt(m)) + (0.000338743021989553 * m)
+ (0 * (m^1.5)) }
> plot(eq(1:1000), type='l')
 
 
 
> eq2 <- function(m2){ 1 + sqrt((10^12)/670) * m2 + 207.775676931964 * (m2^2)
+ 59.2526676368822 * (m2^3) }
> plot(eq2(1:sqrt(1000)), type='l')
*/
  // How to Factor a Trinomial with Fractions as Coefficients
 
  // formula
  // a = c0 = 1
  // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
  // c = c2, c2 = 207.775676931964  * m
  // d = c3, c3 = 59.2526676368822  * m^1.5  (3/2)
  // double mz = 0;
 
 
  /* transformation formula given by Bruker 29/8/2019 :
   * x = m + dm
   *
   * time = m_mzCalibrationArr[0]
   * + sqrt ((10^12)/m_mzCalibrationArr[1]) * x^0.5
   * + m_mzCalibrationArr[2] * x
   * + m_mzCalibrationArr[3] * x^1.5
   */
 
 
  std::vector<double> X;
  X.push_back((m_mzCalibrationArr[0] - (double)tof));
  X.push_back(m_mzCalibrationArr[1]);
  if(m_mzCalibrationArr[2] != 0)
    {
      X.push_back(m_mzCalibrationArr[2]);
    }
  if(m_mzCalibrationArr[3] != 0)
    {
      X.push_back(m_mzCalibrationArr[3]);
      // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
    }
  else
    {
      // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
    }
 
  InHousePolynomialSolverResult res = inHousePolynomialSolve(X);
 
  if(res.type == CardanoResultCase::notvalid)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in %1 %2 %3"
                    "inHousePolynomialSolve :\nresult is not valid")
          .arg(__FILE__)
          .arg(__FUNCTION__)
          .arg(__LINE__));
    }
  return (pow(res.x1, 2) - m_mzCalibrationArr[4]);
}

References inHousePolynomialSolve(), pappso::MzCalibrationInterface::m_digitizerDelay, pappso::MzCalibrationInterface::m_digitizerTimebase, pappso::MzCalibrationInterface::m_mzCalibrationArr, and notvalid.

Referenced by pappso::MzCalibrationModel1Cached::getMzFromTofIndex().

getTofIndexFromMz()

quint32 MzCalibrationModel1::getTofIndexFromMz ( double mz )

overridevirtual

get raw TOF index of a given m/z

Parameters

mz	the mass to transform

Returns

integer x raw value

Implements pappso::MzCalibrationInterface.

Definition at line 155 of file mzcalibrationmodel1.cpp.

{
  // formula
  // a = c0 = 1
  // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
  // c = c2, c2 = 207.775676931964  * m
  // d = c3, c3 = 59.2526676368822  * m^1.5  (3/2)
  qDebug() << "mz=" << mz;
 
  mz = mz + m_mzCalibrationArr[4]; // mz_corr
 
  double tof = m_mzCalibrationArr[0];
  qDebug() << "tof ( m_mzCalibrationArr[0])=" << tof;
  // TODO cache value of  std::sqrt((std::pow(10, 12) / m_mzCalibrationArr[1]))
  tof += m_mzCalibrationArr[1] * std::sqrt(mz);
  qDebug() << "tof=" << tof;
  tof += m_mzCalibrationArr[2] * mz;
  qDebug() << "tof=" << tof;
  tof += m_mzCalibrationArr[3] * std::pow(mz, 1.5);
  qDebug() << "tof=" << tof;
  tof -= m_digitizerDelay;
  qDebug() << "tof=" << tof;
  tof = tof / m_digitizerTimebase;
  qDebug() << "index=" << tof;
  return (quint32)std::round(tof);
}

References pappso::MzCalibrationInterface::m_digitizerDelay, pappso::MzCalibrationInterface::m_digitizerTimebase, and pappso::MzCalibrationInterface::m_mzCalibrationArr.

---

The documentation for this class was generated from the following files:

• pappsomspp/core/vendors/tims/mzcalibration/mzcalibrationmodel1.h
• pappsomspp/core/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp