libpappsomspp
Library for mass spectrometry
timsframebase.h
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1 /**
2  * \file pappsomspp/vendors/tims/timsframebase.h
3  * \date 16/12/2019
4  * \author Olivier Langella
5  * \brief handle a single Bruker's TimsTof frame without binary data
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2019 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 #pragma once
29 
30 #include <memory>
31 #include <vector>
32 #include <QtGlobal>
33 #include "../../massspectrum/massspectrum.h"
35 
36 namespace pappso
37 {
38 
39 class TimsFrameBase;
40 typedef std::shared_ptr<TimsFrameBase> TimsFrameBaseSPtr;
41 typedef std::shared_ptr<const TimsFrameBase> TimsFrameBaseCstSPtr;
42 
43 
44 /**
45  * @todo write docs
46  */
48 {
49  public:
50  /** @brief constructor for binary independant tims frame
51  * @param timsId tims frame identifier in the database
52  * @param scanNum the total number of scans contained in this frame
53  */
54  TimsFrameBase(std::size_t timsId, quint32 scanNum);
55  /**
56  * Copy constructor
57  *
58  * @param other TODO
59  */
61 
62  /**
63  * Destructor
64  */
65  virtual ~TimsFrameBase();
66 
67  /** @brief tells if 2 tims frame has the same calibration data
68  * Usefull to know if raw data can be handled between frames
69  */
70  virtual bool hasSameCalibrationData(const TimsFrameBase &other) const;
71 
72  /** @brief get the number of peaks in this spectrum
73  * need the binary file
74  * @param scanNum scan number in the frame in the order it lies in binary
75  * file, from 0 to N-1
76  */
77  virtual std::size_t getNbrPeaks(std::size_t scanNum) const;
78 
79  /** @brief get the number of scans contained in this frame
80  * each scan represents an ion mobility slice
81  */
82 
83  virtual std::size_t getTotalNumberOfScans() const;
84 
85 
86  /** @brief get the maximum raw mass index contained in this frame
87  */
88  virtual quint32 getMaximumRawMassIndex() const;
89 
90  /** @brief get Mass spectrum with peaks for this scan number
91  * need the binary file
92  * @param scanNum scan number in the frame in the order it lies in binary
93  * file, from 0 to N-1
94  */
95  virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const;
96 
97  /** @brief cumulate spectrum given a scan number range
98  * need the binary file
99  * @param scanNumBegin scan number in the frame in the order it lies in binary
100  * file, from 0 to N-1
101  * @param scanNumEnd scan number in the frame in the order it lies in binary
102  * file, from 0 to N-1
103  */
104  virtual Trace cumulateScanToTrace(std::size_t scanNumBegin,
105  std::size_t scanNumEnd) const;
106 
107 
108  /** @brief cumulate scan list into a trace into a raw spectrum map
109  * @param rawSpectrum simple map of integers to cumulate raw counts
110  * @param scanNumBegin scan number in the frame in the order it lies in binary
111  * file, from 0 to N-1
112  * @param scanNumEnd scan number in the frame in the order it lies in binary
113  * file, from 0 to N-1
114  */
115  virtual void cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
116  std::size_t scanNumBegin,
117  std::size_t scanNumEnd) const;
118 
119  /** @brief check that this scan number exists
120  * @param scanNum scan number in the frame in the order it lies in binary
121  * file, from 0 to N-1
122  */
123  bool checkScanNum(std::size_t scanNum) const;
124 
125 
126  void setAccumulationTime(double accumulation_time_ms);
127  void setMzCalibration(double T1_frame,
128  double T2_frame,
129  double digitizerTimebase,
130  double digitizerDelay,
131  double C0,
132  double C1,
133  double C2,
134  double C3,
135  double C4,
136  double T1_ref,
137  double T2_ref,
138  double dC1,
139  double dC2);
140  void setTimsCalibration(int tims_model_type,
141  double C0,
142  double C1,
143  double C2,
144  double C3,
145  double C4,
146  double C5,
147  double C6,
148  double C7,
149  double C8,
150  double C9);
151  void setTime(double time);
152  void setMsMsType(quint8 type);
153  unsigned int getMsLevel() const;
154  double getTime() const;
155 
156  std::size_t getId() const;
157 
158  /** @brief get drift time of a scan number in milliseconds
159  * @param scanNum scan number in the frame in the order it lies in binary
160  * file, from 0 to N-1
161  * @return time in milliseconds of mobility delay (drift time)
162  * */
163  double getDriftTime(std::size_t scanNum) const;
164 
165  /** @brief get 1/K0 value of a given scan (mobility value)
166  * @param scanNum scan number in the frame in the order it lies in binary
167  * file, from 0 to N-1
168  * */
169  double getOneOverK0Transformation(std::size_t scanNum) const;
170 
171 
172  /** @brief get the scan number from a given 1/Ko mobility value
173  * @param one_over_k0 the mobility value to tranform
174  * @return integer the scan number in the frame in the order it lies in binary
175  * file, from 0 to N-1
176  */
177  std::size_t getScanNumFromOneOverK0(double one_over_k0) const;
178 
179  /** @brief get voltage for a given scan number
180  * @param scanNum scan number in the frame in the order it lies in binary
181  * file, from 0 to N-1
182  * @return double volt measure
183  * */
184  double getVoltageTransformation(std::size_t scanNum) const;
185 
186 
187  /** @brief transform accumulation of raw scans into a real mass spectrum
188  */
190  std::map<quint32, quint32> &accumulated_scans) const;
191 
192  /** @brief transform accumulation of raw scans into a real mass spectrum with
193  * a simple centroid on raw integers
194  */
196  std::map<quint32, quint32> &accumulated_scans) const;
197 
198  /** @brief get the MzCalibration model to compute mz and TOF for this frame
199  */
200  virtual const MzCalibrationInterfaceSPtr &
201  getMzCalibrationInterfaceSPtr() const final;
202 
204 
205 
206  /** @brief get raw index list for one given scan
207  * index are not TOF nor m/z, just index on digitizer
208  */
209  virtual std::vector<quint32> getScanIndexList(std::size_t scanNum) const;
210 
211  /** @brief get raw intensities without transformation from one scan
212  * it needs intensity normalization
213  */
214  virtual std::vector<quint32> getScanIntensities(std::size_t scanNum) const;
215 
216  /** @brief get a mobility trace cumulating intensities inside the given mass
217  * index range
218  * @param mz_index_lower_bound raw mass index lower bound
219  * @param mz_index_upper_bound raw mass index upper bound
220  * @param method max or sum intensities
221  */
222  virtual Trace
223  getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound,
224  std::size_t mz_index_upper_bound,
225  XicExtractMethod method) const;
226 
227 
228  protected:
229  /** @brief total number of scans contained in this frame
230  */
231  quint32 m_scanNumber;
232 
233  /** @brief Tims frame database id (the SQL identifier of this frame)
234  * @warning in sqlite, there is another field called TimsId : this is not
235  * that, because it is in fact an offset in bytes in the binary file.
236  * */
237  std::size_t m_timsId;
238 
239  /** @brief accumulation time in milliseconds
240  */
241  double m_accumulationTime = 0;
242 
243  quint8 m_msMsType = 0;
244 
245  /** @brief retention time
246  */
247  double m_time = 0;
248 
249  double m_timsDvStart = 0; // C2 from TimsCalibration
250  double m_timsSlope =
251  0; // (dv_end - dv_start) / ncycles //C3 from TimsCalibration // C2 from
252  // TimsCalibration // C1 from TimsCalibration
253  double m_timsTtrans = 0; // C4 from TimsCalibration
254  double m_timsNdelay = 0; // C0 from TimsCalibration
255  double m_timsVmin = 0; // C8 from TimsCalibration
256  double m_timsVmax = 0; // C9 from TimsCalibration
257  double m_timsC6 = 0;
258  double m_timsC7 = 0;
259 
261 };
262 } // namespace pappso
double m_accumulationTime
accumulation time in milliseconds
TimsFrameBase(const TimsFrameBase &other)
double getTime() const
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate spectrum given a scan number range need the binary file
virtual std::size_t getTotalNumberOfScans() const
get the number of scans contained in this frame each scan represents an ion mobility slice
virtual Trace getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound, std::size_t mz_index_upper_bound, XicExtractMethod method) const
get a mobility trace cumulating intensities inside the given mass index range
virtual std::size_t getNbrPeaks(std::size_t scanNum) const
get the number of peaks in this spectrum need the binary file
MzCalibrationInterfaceSPtr msp_mzCalibration
virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const
get Mass spectrum with peaks for this scan number need the binary file
TimsFrameBase(std::size_t timsId, quint32 scanNum)
constructor for binary independant tims frame
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
double getDriftTime(std::size_t scanNum) const
get drift time of a scan number in milliseconds
pappso::Trace getTraceFromCumulatedScansBuiltinCentroid(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers
double m_time
retention time
void setAccumulationTime(double accumulation_time_ms)
quint32 m_scanNumber
total number of scans contained in this frame
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate scan list into a trace into a raw spectrum map
void setTime(double time)
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
pappso::Trace getTraceFromCumulatedScans(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
virtual bool hasSameCalibrationData(const TimsFrameBase &other) const
tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled betwee...
virtual quint32 getMaximumRawMassIndex() const
get the maximum raw mass index contained in this frame
unsigned int getMsLevel() const
void setTimsCalibration(int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
std::size_t getScanNumFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
void setMsMsType(quint8 type)
void setMzCalibration(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)
double getOneOverK0Transformation(std::size_t scanNum) const
get 1/K0 value of a given scan (mobility value)
bool checkScanNum(std::size_t scanNum) const
check that this scan number exists
void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration)
std::size_t getId() const
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
A simple container of DataPoint instances.
Definition: trace.h:147
handles different ways to compute m/z using calibration parameters
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
Definition: timsframebase.h:41
std::shared_ptr< TimsFrameBase > TimsFrameBaseSPtr
Definition: timsframebase.h:39
std::shared_ptr< MzCalibrationInterface > MzCalibrationInterfaceSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
XicExtractMethod
Definition: types.h:200