libpappsomspp
Library for mass spectrometry
pappso::MzCalibrationModel1 Class Reference

#include <mzcalibrationmodel1.h>

Inheritance diagram for pappso::MzCalibrationModel1:
pappso::MzCalibrationInterface pappso::MzCalibrationModel1Cached

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 More...
 
virtual quint32 getTofIndexFromMz (double mz) override
 get raw TOF index of a given m/z More...
 
- Public Member Functions inherited from pappso::MzCalibrationInterface
 MzCalibrationInterface (double digitizerTimebase, double digitizerDelay)
 
virtual ~MzCalibrationInterface ()
 
MzCalibrationInterfaceoperator= (const MzCalibrationInterface &other)
 
bool operator== (const MzCalibrationInterface &other) const
 
double getTofFromTofIndex (quint32 tof_index) const
 get time of flight from raw index More...
 
double getTofFromTofIndex (double tof_index) const
 get time of flight from double index More...
 
virtual double getMzFromTofIndex (quint32 tof_index)=0
 get m/z from time of flight raw index More...
 
virtual quint32 getTofIndexFromMz (double mz)=0
 get raw TOF index of a given m/z More...
 

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. More...
 

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 37 of file mzcalibrationmodel1.cpp.

50 : MzCalibrationInterface(digitizerTimebase, digitizerDelay)
51{
52
53 double temperature_correction =
54 dC1 * (T1_ref - T1_frame) + dC2 * (T2_ref - T2_frame);
55 temperature_correction = (double)1.0 + (temperature_correction / 1.0e6);
56
57 // temperature compensation
58 C1 = C1 * temperature_correction;
59 C2 = C2 / temperature_correction;
60
61
62 m_mzCalibrationArr.clear();
63
64 m_digitizerDelay = digitizerDelay;
65 m_digitizerTimebase = digitizerTimebase;
66
67 m_mzCalibrationArr.push_back(C0);
68 m_mzCalibrationArr.push_back(std::sqrt(std::pow(10, 12) / C1));
69 m_mzCalibrationArr.push_back(C2);
70 m_mzCalibrationArr.push_back(C3);
71 m_mzCalibrationArr.push_back(C4);
72}
MzCalibrationInterface(double digitizerTimebase, double digitizerDelay)
std::vector< double > m_mzCalibrationArr
MZ calibration parameters.

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

◆ ~MzCalibrationModel1()

MzCalibrationModel1::~MzCalibrationModel1 ( )
virtual

Destructor

Definition at line 74 of file mzcalibrationmodel1.cpp.

75{
76}

Member Function Documentation

◆ getMzFromTofIndex()

double MzCalibrationModel1::getMzFromTofIndex ( quint32  tof_index)
overridevirtual

get m/z from time of flight raw index

Parameters
tof_indextime of flight
Returns
m/z value

Implements pappso::MzCalibrationInterface.

Reimplemented in pappso::MzCalibrationModel1Cached.

Definition at line 79 of file mzcalibrationmodel1.cpp.

80{
81 double tof = ((double)tof_index * m_digitizerTimebase) + m_digitizerDelay;
82 // http://www.alglib.net/equations/polynomial.php
83 // http://www.alglib.net/translator/man/manual.cpp.html#sub_polynomialsolve
84 // https://math.stackexchange.com/questions/1291208/number-of-roots-of-a-polynomial-of-non-integer-degree
85 // 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
86 // https://stackoverflow.com/questions/26091323/how-to-plot-a-function-curve-in-r
87 /*
88 * beware to put the function on a single line in R:
89> eq <- function(m){ 1 + (sqrt((10^12)/670) * sqrt(m)) + (207.775676931964 * m)
90+ (59.2526676368822 * (m^1.5)) }
91> eq <- function(m){ 313.577620892277 + (sqrt((10^12)/157424.07710945) *
92sqrt(m)) + (0.000338743021989553 * m)
93+ (0 * (m^1.5)) }
94> plot(eq(1:1000), type='l')
95
96
97
98> eq2 <- function(m2){ 1 + sqrt((10^12)/670) * m2 + 207.775676931964 * (m2^2)
99+ 59.2526676368822 * (m2^3) }
100> plot(eq2(1:sqrt(1000)), type='l')
101*/
102 // How to Factor a Trinomial with Fractions as Coefficients
103
104 // formula
105 // a = c0 = 1
106 // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
107 // c = c2, c2 = 207.775676931964 * m
108 // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
109 // double mz = 0;
110
111
112 /* transformation formula given by Bruker 29/8/2019 :
113 * x = m + dm
114 *
115 * time = m_mzCalibrationArr[0]
116 * + sqrt ((10^12)/m_mzCalibrationArr[1]) * x^0.5
117 * + m_mzCalibrationArr[2] * x
118 * + m_mzCalibrationArr[3] * x^1.5
119 */
120 std::vector<double> X;
121 X.push_back((m_mzCalibrationArr[0] - (double)tof));
122 X.push_back(m_mzCalibrationArr[1]);
123 if(m_mzCalibrationArr[2] != 0)
124 {
125 X.push_back(m_mzCalibrationArr[2]);
126 }
127 if(m_mzCalibrationArr[3] != 0)
128 {
129 X.push_back(m_mzCalibrationArr[3]);
130 // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
131 }
132 else
133 {
134 // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
135 }
136 // qDebug() << "polynom_array :";
137 /*
138 for(double arg : X)
139 {
140 qDebug() << arg;
141 }
142 */
143 alglib::real_1d_array polynom_array;
144 try
145 {
146 polynom_array.setcontent(X.size(), &(X[0]));
147 }
148 catch(alglib::ap_error &error)
149 {
150 // PolynomialSolve: A[N]=0
152 QObject::tr("ERROR in alglib::polynom_array.setcontent :\n%1")
153 .arg(error.msg.c_str()));
154 }
155
156
157 /*
158 alglib::polynomialsolve(
159real_1d_array a,
160ae_int_t n,
161complex_1d_array& x,
162polynomialsolverreport& rep,
163const xparams _params = alglib::xdefault);
164*/
165 alglib::complex_1d_array m;
166 alglib::polynomialsolverreport rep;
167 // qDebug();
168 try
169 {
170 alglib::polynomialsolve(polynom_array, X.size() - 1, m, rep);
171 }
172 catch(alglib::ap_error &error)
173 {
174 qDebug() << " X.size() - 1 = " << X.size() - 1;
175 qDebug() << m_mzCalibrationArr[0];
176 qDebug() << m_mzCalibrationArr[1];
177 qDebug() << m_mzCalibrationArr[2];
178 qDebug() << m_mzCalibrationArr[3];
179
180 // PolynomialSolve: A[N]=0
182 QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex, "
183 "alglib::polynomialsolve :\n%1")
184 .arg(error.msg.c_str()));
185 }
186
187
188 // qDebug();
189
190 if(m.length() == 0)
191 {
192 throw pappso::PappsoException(QObject::tr(
193 "ERROR in MzCalibrationModel1::getMzFromTofIndex m.size() == 0"));
194 }
195 // qDebug();
196 if(m[0].y != 0)
197 {
199 QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex m[0].y!= "
200 "0 for tof index=%1")
201 .arg(tof_index));
202 }
203
204 // qDebug() << "m.length()=" << m.length();
205 // qDebug() << "m1=" << pow(m[0].x, 2);
206 // qDebug() << "m2=" << pow(m[1].x, 2);
207 return (pow(m[0].x, 2) - m_mzCalibrationArr[4]);
208}

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

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

◆ getTofIndexFromMz()

quint32 MzCalibrationModel1::getTofIndexFromMz ( double  mz)
overridevirtual

get raw TOF index of a given m/z

Parameters
mzthe mass to transform
Returns
integer x raw value

Implements pappso::MzCalibrationInterface.

Definition at line 211 of file mzcalibrationmodel1.cpp.

212{
213 // formula
214 // a = c0 = 1
215 // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
216 // c = c2, c2 = 207.775676931964 * m
217 // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
218 qDebug() << "mz=" << mz;
219
220 mz = mz + m_mzCalibrationArr[4]; // mz_corr
221
222 double tof = m_mzCalibrationArr[0];
223 qDebug() << "tof ( m_mzCalibrationArr[0])=" << tof;
224 // TODO cache value of std::sqrt((std::pow(10, 12) / m_mzCalibrationArr[1]))
225 tof += m_mzCalibrationArr[1] * std::sqrt(mz);
226 qDebug() << "tof=" << tof;
227 tof += m_mzCalibrationArr[2] * mz;
228 qDebug() << "tof=" << tof;
229 tof += m_mzCalibrationArr[3] * std::pow(mz, 1.5);
230 qDebug() << "tof=" << tof;
231 tof -= m_digitizerDelay;
232 qDebug() << "tof=" << tof;
233 tof = tof / m_digitizerTimebase;
234 qDebug() << "index=" << tof;
235 return (quint32)std::round(tof);
236}

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


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