libpappsomspp
Library for mass spectrometry
mzcalibrationmodel1.cpp
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1/**
2 * \file pappsomspp/vendors/tims/mzcalibration/mzcalibrationmodel1.cpp
3 * \date 11/11/2020
4 * \author Olivier Langella
5 * \brief implement Bruker's model type 1 formula to compute m/z
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2020 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#include "mzcalibrationmodel1.h"
29#include <solvers.h>
30#include <cmath>
31#include <QDebug>
32#include <QObject>
33#include "../../../pappsoexception.h"
34
35
36using namespace pappso;
37
38MzCalibrationModel1::MzCalibrationModel1(double T1_frame,
39 double T2_frame,
40 double digitizerTimebase,
41 double digitizerDelay,
42 double C0,
43 double C1,
44 double C2,
45 double C3,
46 double C4,
47 double T1_ref,
48 double T2_ref,
49 double dC1,
50 double dC2)
51 : MzCalibrationInterface(digitizerTimebase, digitizerDelay)
52{
53
54 double temperature_correction =
55 dC1 * (T1_ref - T1_frame) + dC2 * (T2_ref - T2_frame);
56 temperature_correction = (double)1.0 + (temperature_correction / 1.0e6);
57
58 // temperature compensation
59 C1 = C1 * temperature_correction;
60 C2 = C2 / temperature_correction;
61
62
63 m_mzCalibrationArr.clear();
64
65 m_digitizerDelay = digitizerDelay;
66 m_digitizerTimebase = digitizerTimebase;
67
68 m_mzCalibrationArr.push_back(C0);
69 m_mzCalibrationArr.push_back(std::sqrt(std::pow(10, 12) / C1));
70 m_mzCalibrationArr.push_back(C2);
71 m_mzCalibrationArr.push_back(C3);
72 m_mzCalibrationArr.push_back(C4);
73}
74
76{
77}
78
79double
81{
82 double tof = ((double)tof_index * m_digitizerTimebase) + m_digitizerDelay;
83 // http://www.alglib.net/equations/polynomial.php
84 // http://www.alglib.net/translator/man/manual.cpp.html#sub_polynomialsolve
85 // https://math.stackexchange.com/questions/1291208/number-of-roots-of-a-polynomial-of-non-integer-degree
86 // 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
87 // https://stackoverflow.com/questions/26091323/how-to-plot-a-function-curve-in-r
88 /*
89 * beware to put the function on a single line in R:
90> eq <- function(m){ 1 + (sqrt((10^12)/670) * sqrt(m)) + (207.775676931964 * m)
91+ (59.2526676368822 * (m^1.5)) }
92> eq <- function(m){ 313.577620892277 + (sqrt((10^12)/157424.07710945) *
93sqrt(m)) + (0.000338743021989553 * m)
94+ (0 * (m^1.5)) }
95> plot(eq(1:1000), type='l')
96
97
98
99> eq2 <- function(m2){ 1 + sqrt((10^12)/670) * m2 + 207.775676931964 * (m2^2)
100+ 59.2526676368822 * (m2^3) }
101> plot(eq2(1:sqrt(1000)), type='l')
102*/
103 // How to Factor a Trinomial with Fractions as Coefficients
104
105 // formula
106 // a = c0 = 1
107 // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
108 // c = c2, c2 = 207.775676931964 * m
109 // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
110 // double mz = 0;
111
112
113 /* transformation formula given by Bruker 29/8/2019 :
114 * x = m + dm
115 *
116 * time = m_mzCalibrationArr[0]
117 * + sqrt ((10^12)/m_mzCalibrationArr[1]) * x^0.5
118 * + m_mzCalibrationArr[2] * x
119 * + m_mzCalibrationArr[3] * x^1.5
120 */
121 std::vector<double> X;
122 X.push_back((m_mzCalibrationArr[0] - (double)tof));
123 X.push_back(m_mzCalibrationArr[1]);
124 if(m_mzCalibrationArr[2] != 0)
125 {
126 X.push_back(m_mzCalibrationArr[2]);
127 }
128 if(m_mzCalibrationArr[3] != 0)
129 {
130 X.push_back(m_mzCalibrationArr[3]);
131 // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
132 }
133 else
134 {
135 // qDebug() << "m_mzCalibrationArr[3]=" << m_mzCalibrationArr[3];
136 }
137 // qDebug() << "polynom_array :";
138 /*
139 for(double arg : X)
140 {
141 qDebug() << arg;
142 }
143 */
144 alglib::real_1d_array polynom_array;
145 try
146 {
147 polynom_array.setcontent(X.size(), &(X[0]));
148 }
149 catch(alglib::ap_error &error)
150 {
151 // PolynomialSolve: A[N]=0
153 QObject::tr("ERROR in alglib::polynom_array.setcontent :\n%1")
154 .arg(error.msg.c_str()));
155 }
156
157
158 /*
159 alglib::polynomialsolve(
160real_1d_array a,
161ae_int_t n,
162complex_1d_array& x,
163polynomialsolverreport& rep,
164const xparams _params = alglib::xdefault);
165*/
166 alglib::complex_1d_array m;
167 alglib::polynomialsolverreport rep;
168
169 alglib::xparams params = alglib::xdefault;
170 // qDebug();
171 try
172 {
173 alglib::polynomialsolve(polynom_array, X.size() - 1, m, rep, params);
174 }
175 catch(alglib::ap_error &error)
176 {
177 qDebug() << " X.size() - 1 = " << X.size() - 1;
178 qDebug() << m_mzCalibrationArr[0];
179 qDebug() << m_mzCalibrationArr[1];
180 qDebug() << m_mzCalibrationArr[2];
181 qDebug() << m_mzCalibrationArr[3];
182
183 // PolynomialSolve: A[N]=0
185 QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex, "
186 "alglib::polynomialsolve :\n%1")
187 .arg(error.msg.c_str()));
188 }
189
190
191 // qDebug();
192
193 if(m.length() == 0)
194 {
195 throw pappso::PappsoException(QObject::tr(
196 "ERROR in MzCalibrationModel1::getMzFromTofIndex m.size() == 0"));
197 }
198 // qDebug();
199 if(m[0].y != 0)
200 {
202 QObject::tr("ERROR in MzCalibrationModel1::getMzFromTofIndex m[0].y!= "
203 "0 for tof index=%1")
204 .arg(tof_index));
205 }
206
207 // qDebug() << "m.length()=" << m.length();
208 // qDebug() << "m1=" << pow(m[0].x, 2);
209 // qDebug() << "m2=" << pow(m[1].x, 2);
210 return (pow(m[0].x, 2) - m_mzCalibrationArr[4]);
211}
212
213quint32
215{
216 // formula
217 // a = c0 = 1
218 // b = sqrt((10^12)/c1), c1 = 670 * m^0.5 (1/2)
219 // c = c2, c2 = 207.775676931964 * m
220 // d = c3, c3 = 59.2526676368822 * m^1.5 (3/2)
221 qDebug() << "mz=" << mz;
222
223 mz = mz + m_mzCalibrationArr[4]; // mz_corr
224
225 double tof = m_mzCalibrationArr[0];
226 qDebug() << "tof ( m_mzCalibrationArr[0])=" << tof;
227 // TODO cache value of std::sqrt((std::pow(10, 12) / m_mzCalibrationArr[1]))
228 tof += m_mzCalibrationArr[1] * std::sqrt(mz);
229 qDebug() << "tof=" << tof;
230 tof += m_mzCalibrationArr[2] * mz;
231 qDebug() << "tof=" << tof;
232 tof += m_mzCalibrationArr[3] * std::pow(mz, 1.5);
233 qDebug() << "tof=" << tof;
234 tof -= m_digitizerDelay;
235 qDebug() << "tof=" << tof;
236 tof = tof / m_digitizerTimebase;
237 qDebug() << "index=" << tof;
238 return (quint32)std::round(tof);
239}
240
242 double T1_frame,
243 double T2_frame,
244 double digitizerTimebase,
245 double digitizerDelay,
246 double C0,
247 double C1,
248 double C2,
249 double C3,
250 double C4,
251 double T1_ref,
252 double T2_ref,
253 double dC1,
254 double dC2)
255 : MzCalibrationModel1(T1_frame,
256 T2_frame,
257 digitizerTimebase,
258 digitizerDelay,
259 C0,
260 C1,
261 C2,
262 C3,
263 C4,
264 T1_ref,
265 T2_ref,
266 dC1,
267 dC2)
268{
269}
270
272{
273}
274
275
276double
278{
279 if(m_max > tof_index)
280 {
281 if(m_arrMasses[tof_index] == 0)
282 {
283 m_arrMasses[tof_index] =
285 }
286 return m_arrMasses[tof_index];
287 }
288 else
289 {
291 }
292}
std::vector< double > m_mzCalibrationArr
MZ calibration parameters.
MzCalibrationModel1Cached(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 double getMzFromTofIndex(quint32 tof_index) override
get m/z from time of flight raw index
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
implement Bruker's model type 1 formula to compute m/z
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39