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 "../../../pappsoexception.h"
33 
34 
35 using namespace pappso;
36 
38  double T2_frame,
39  double digitizerTimebase,
40  double digitizerDelay,
41  double C0,
42  double C1,
43  double C2,
44  double C3,
45  double C4,
46  double T1_ref,
47  double T2_ref,
48  double dC1,
49  double dC2)
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 }
73 
75 {
76 }
77 
78 double
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) *
92 sqrt(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(
159 real_1d_array a,
160 ae_int_t n,
161 complex_1d_array& x,
162 polynomialsolverreport& rep,
163 const 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 }
209 
210 quint32
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 }
237 
239  double T1_frame,
240  double T2_frame,
241  double digitizerTimebase,
242  double digitizerDelay,
243  double C0,
244  double C1,
245  double C2,
246  double C3,
247  double C4,
248  double T1_ref,
249  double T2_ref,
250  double dC1,
251  double dC2)
252  : MzCalibrationModel1(T1_frame,
253  T2_frame,
254  digitizerTimebase,
255  digitizerDelay,
256  C0,
257  C1,
258  C2,
259  C3,
260  C4,
261  T1_ref,
262  T2_ref,
263  dC1,
264  dC2)
265 {
266 }
267 
269 {
270 }
271 
272 
273 double
275 {
276  if(m_max > tof_index)
277  {
278  if(m_arrMasses[tof_index] == 0)
279  {
280  m_arrMasses[tof_index] =
282  }
283  return m_arrMasses[tof_index];
284  }
285  else
286  {
287  return MzCalibrationModel1::getMzFromTofIndex(tof_index);
288  }
289 }
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
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 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