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The MassPeakShaperConfig class provides the features required to configure the shaping of a mass peak centroid into a Gaussian or a Lorentzian fully profiled shape. More...
| Header: | #include <MassPeakShaperConfig.hpp> |
| MassPeakShaperConfig() | |
| MassPeakShaperConfig(const MassPeakShaperConfig &other) | |
| virtual | ~MassPeakShaperConfig() |
| double | binSize(bool *ok) |
| double | fwhm(bool *ok) |
| double | getBinSize() const |
| int | getBinSizeDivisor() const |
| double | getFwhm() const |
| MassPeakShapeType | getMassPeakShapeType() const |
| MassPeakWidthLogic | getMassPeakWidthLogic() const |
| double | getMzStep() const |
| int | getPointCount() const |
| double | getReferencePeakMz() const |
| double | getResolution() const |
| double | halfFwhm(bool *ok) |
| double | mzStep(bool *ok) |
| void | reset() |
| int | resolution(bool *ok) |
| bool | resolve() |
| void | setBinSize(double bin_size) |
| void | setBinSizeDivisor(int factor) |
| void | setBinSizeFixed(bool is_fixed) |
| void | setFwhm(double fwhm) |
| void | setMassPeakShapeType(MassPeakShapeType mass_peak_shape_type) |
| void | setMassPeakWidthLogic(MassPeakWidthLogic logic) |
| void | setMzStep(double mz_step) |
| void | setPointCount(int point_count) |
| void | setReferencePeakMz(double mz) |
| void | setResolution(int resolution) |
| void | setWithBins(bool with_bins) |
| QString | toString() |
| bool | withBins() const |
| void | operator=(const MassPeakShaperConfig &other) |
| double | m_binSize |
| int | m_binSizeDivisor |
| double | m_fwhm |
| bool | m_isBinSizeFixed |
| MassPeakShapeType | m_massPeakShapeType |
| MassPeakWidthLogic | m_massPeakWidthLogic |
| double | m_mzStep |
| int | m_pointCount |
| double | m_referencePeakMz |
| int | m_resolution |
| bool | m_withBins |
Shaping a peak means creating a shape around a centroid m/z value such that the m/z peak is represented like it appears in a mass spectrum displayed in "profile" mode.
The model used to craft the "profiled" mass peak can be of two types:
The starting parameters are the (m/z,intensity) values of the peak centroid and the full width at half maximum (FWHM) value that will govern the width of the shape at 50% height of the peak. The width of the peak will be an inverse representation of the resolving power of the instrument: the instrument with the greatest resolving power will yield mass peaks with the smallest width. Conversely, a very old instrument will produce mass spectra where the peaks will be broad.
There are thus two possiblities for configuring the peak shape:
Constructs a MassPeakShaperConfig instance.
Constructs a MassPeakShaperConfig instance as a copy of other.
[virtual noexcept] MassPeakShaperConfig::~MassPeakShaperConfig()Destructs this MassPeakShaperConfig instance.
Computes the bin size.
If there is no requirement for bins (m_withBins is false), returns 0 and set ok to true.
In order to compute the bin size we need that at least the FWHM (m_fwhm) or the resolving power (m_resolution) be set. If none of these values are set, this function returns 0 and sets ok to false.
If the bin size was fixed (m_isBinSizeFixed is true), then the bin size (m_binSize) must be set. If that is not the case, the function returns 0 and sets ok to false.
If the FWHM value (m_fwhm) is set, then it is used right away. Otherwise, the FWHM is computed starting from the resolving power (m_resolution). If that computation fails, the function returns 0 and sets ok to false.
Starting from the FWHM value (m_fwhm), the bin size calculation requires that the m_binSizeDivisor be > 1. The bin size is thus computed as the ratio FWHM / m_binSizeDivisor, and the obtained value is set to m_binSize.
Empirically, a value of 6 for m_binSizeDivisor, yields bin sizes that allow combining correctly multiple peak shapes into a mass spectrum. Essentially, that means that 6 individual m/z bins are required to combine nicely all the peaks shapes obtained for all the peak centroids in a given isotopic cluster, for example.
At this point, the function returns the bin size and sets ok to true.
See also setBinSizeDivisor().
Calculates the fwhm (full width at half maximum).
The calculation involves using the instrument's resolving power (m_resolution) member datum and the m/z value that is considered to be the reference for the calculation (m_referencePeakMz).
If any of these two values is not set, then this function returns 0 and sets ok to false.
The calculation is that simple:
m_fwhm = m_referencePeakMz / m_resolution;
Because we used the resolution to compute the FWHM and set the calculated value to the m_fwhm member datum, we keep a record of this by:
m_massPeakWidthLogic = MassPeakWidthLogic::RESOLUTION;
Returns the FWHM value as set in m_fwhm and sets ok to true.
See also setFwhm().
Returns (no computation) the bin size.
Returns the bin size computation dividing factor.
See also setBinSizeDivisor().
Gets the fwhm (full width at half maximum).
Gets the type of mass peak shape.
See also MsXpS::libXpertMass::MassPeakShapeType.
Gets the mass peak width calculation logic.
See also MsXpS::libXpertMass::MassPeakWidthLogic.
Gets the m/z step.
The m/z step value is the distance between two consecutive points in the peak shape.
Gets the count of points to be used to shape the mass peak around the m/z centroid value.
Gets the reference m/z value required for calculations.
Returns the resolution (the resolving power of the instrument).
Returns the half of the FWMH (m_fwhm) for use in the Lorentzian shape calculation.
Uses the fwhm() function to compute the FWHM value. If the FWHM calculation fails, returns 0 and ok is set to false, otherwise returns half of FWHM and ok is set to true.
See also fwhm().
Calculates the m/z step.
The m/z step value is the distance between two consecutive points in the peak shape. To compute that value, the full m/z width of the calculated shape (not only the width at half maximum, FWHM) is divided by the total number of data points that make the final shape of the m/z peak.
The first variable is FWHM_PEAK_SPAN_FACTOR * m_fwhm, and the second variable is m_pointCount. The calculation is thus:
m_mzStep = (FWHM_PEAK_SPAN_FACTOR * m_fwhm) / m_pointCount;
The first step is to compute the FWHM and then to check the value of m_pointCount (that cannot be 0). If any of these fails, the function returns 0 and set ok to false, otherwise the computed value is set to m_mzStep and returned, while ok is set to true.
See also setMzStep() and FWHM_PEAK_SPAN_FACTOR.
Resets this MassPeakShaperConfig instance to default values like at construction time.
Calculates the resolution (resolving power of the instrument).
The calculation involves using the FWHM (m_fwhm) member datum and the m/z value that is considered to be the reference for the calculation (m_referencePeakMz).
If any of these two values is not set, then this function returns 0 and sets ok to false.
The calculation is that simple:
m_resolution = m_referencePeakMz / m_fwhm;
Because we used the FWHM to compute the resolution and set the calculated value to the m_resolution member datum, we keep a record of this by:
m_massPeakWidthLogic = MassPeakWidthLogic::FWHM;
Returns the resolving power as set in m_resolution and sets ok to true.
See also setResolution().
Calculates the various parameters of the peak shape using member data.
This function first checks that all the required data are set. Then this functions computes the FWHM value required to shape the peak centroid. Once the basic data have been computed or set, the parameters of the shape are computed: c, a, gamma.
Returns true if the computation was successful, false otherwise.
Sets the bin_size.
See also binSize().
Sets the bin size computation dividing factor.
When the bin size is computed (m_isBinSizeFixed is false), that value is determined by dividing the FWHM value by this factor (m_binSizeDivisor).
Empirically, a value of 6 for m_binSizeDivisor, yields bin sizes that allow combining correctly multiple peak shapes into a mass spectrum. Essentially, that means that 6 individual m/z bins are required to combine nicely all the peaks shapes obtained for all the peak centroids in a given isotopic cluster, for example.
Sets the requirement that the bin size be set and fixed (not modifiable by computations) to is_fixed.
When is_fixed is true, the binSize() function returns the bin size without trying to compute it.
See also binSize().
Sets the fwhm (full width at half maximum).
See also fwhm().
Sets the type of mass peak shape to mass_peak_shape_type.
See also MsXpS::libXpertMass::MassPeakShapeType.
Sets the mass peak width calculation logic.
The full mass peak width at half peak maximum (FWHM) can either be set manually or be computed from a reference m/z value and the instrument's resolving power.
See also MsXpS::libXpertMass::MassPeakWidthLogic.
Sets the mz_step.
The m/z step value is the distance between two consecutive points in the peak shape.
See also mzStep().
Sets the point_count to be used to shape the mass peak around the m/z centroid value.
Typically, a value between 150 and 200 points is fine to nicely shape a m/z peak centroid.
Sets the reference m/z value required for calculations to mz.
Sets the resolution (the resolving power of the instrument).
See also resolution().
Sets the requirement to prepare m/z bins at a later computing stage to with_bins.
See also withBins() and IsotopicClusterShaper::run().
Returns a string representing this MassPeakShaperConfig instance.
No verification whatsoever is performed.
Returns the requirement to prepare m/z bins at a later computing stage.
See also setWithBins() and IsotopicClusterShaper::run().
Assigns other to this MassPeakShaperConfig instance.
This variable holds the size of the m/z bins.
Empirical division factor to apply to m_binSize to reduce the size of the bins after the bin size calculation.
Empirically, a good value is 6.
Full width at half maximum of the shaped peak.
Tells if the size of the m/z bins is fixed.
This variable holds the requested shape of the mass peak.
Describes the logic used to compute the peak shape width.
This variable holds the m/z distance (a Delta) between to consecutive data points in the shaped mass peak.
This variable holds the count of points used to shape the peak. Typically between 150 and 300.
This variable holds the m/z value to be used when computing the FWHM value starting from a mass spectrometer resolving power.
Resolving power of the instrument.
Tells if bins are requested for the computation.
There is no need in the context of the calculations performed by the MassPeakShaperConfig class to know if bins are required or not. This variable is useful when multiple peak shapes are combined into a more complex trace or mass spectrum, typically when simulating an isotopic cluster. In this case, each cluster peak centroid is shaped in sequence and then they are all merged into a single trace (no bins) or mass spectrum (binning). The width of the bins is defined using this m_withBins variable.