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OpenMS
2.5.0
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This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width. More...
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
Classes | |
struct | PeakBoundary |
structure for peak boundaries More... | |
Public Member Functions | |
PeakPickerHiRes () | |
Constructor. More... | |
~PeakPickerHiRes () override | |
Destructor. More... | |
void | pick (const MSSpectrum &input, MSSpectrum &output) const |
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. More... | |
void | pick (const MSChromatogram &input, MSChromatogram &output) const |
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram. More... | |
void | pick (const MSSpectrum &input, MSSpectrum &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true) const |
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. Peak boundaries are written to a separate structure. More... | |
void | pick (const MSChromatogram &input, MSChromatogram &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=false) const |
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram. More... | |
void | pickExperiment (const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More... | |
void | pickExperiment (const PeakMap &input, PeakMap &output, std::vector< std::vector< PeakBoundary > > &boundaries_spec, std::vector< std::vector< PeakBoundary > > &boundaries_chrom, const bool check_spectrum_type=true) const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More... | |
void | pickExperiment (OnDiscMSExperiment &input, PeakMap &output, const bool check_spectrum_type=true) const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map. More... | |
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DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Protected Member Functions | |
template<typename ContainerType > | |
void | pick_ (const ContainerType &input, ContainerType &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true) const |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
double | signal_to_noise_ |
double | spacing_difference_gap_ |
double | spacing_difference_ |
unsigned | missing_ |
std::vector< Int > | ms_levels_ |
bool | report_FWHM_ |
add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM More... | |
bool | report_FWHM_as_ppm_ |
unit of 'FWHM' float data array (can be absolute or ppm). More... | |
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Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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static int | recursion_depth_ |
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-MS, Orbitrap). In high resolution data, the signals of ions with similar mass-to-charge ratios (m/z) exhibit little or no overlapping and therefore allow for a clear separation. Furthermore, ion signals tend to show well-defined peak shapes with narrow peak width.
This peak-picking algorithm detects ion signals in profile data and reconstructs the corresponding peak shape by cubic spline interpolation. Signal detection depends on the signal-to-noise ratio which is adjustable by the user (see parameter signal_to_noise). A picked peak's m/z and intensity value is given by the maximum of the underlying peak spline.
So far, this peak picker was mainly tested on high resolution data. With appropriate preprocessing steps (e.g. noise reduction and baseline subtraction), it might be also applied to low resolution data.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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signal_to_noise | float | 0.0 | min: 0.0 | Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!) |
spacing_difference_gap | float | 4.0 | min: 0.0 | The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms. |
spacing_difference | float | 1.5 | min: 0.0 | Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms. |
missing | int | 1 | min: 0 | Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms. |
ms_levels | int list | [] | min: 1 | List of MS levels for which the peak picking is applied. If empty, auto mode is enabled, all peaks which aren't picked yet will get picked. Other scans are copied to the output without changes. |
report_FWHM | string | false | true, false | Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak. |
report_FWHM_unit | string | relative | relative, absolute | Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms). |
SignalToNoise:max_intensity | int | -1 | min: -1 | maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N. |
SignalToNoise:auto_max_stdev_factor | float | 3.0 | min: 0.0 max: 999.0 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev |
SignalToNoise:auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile |
SignalToNoise:auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method |
SignalToNoise:win_len | float | 200.0 | min: 1.0 | window length in Thomson |
SignalToNoise:bin_count | int | 30 | min: 3 | number of bins for intensity values |
SignalToNoise:min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse) |
SignalToNoise:noise_for_empty_window | float | 1.0e20 | noise value used for sparse windows | |
SignalToNoise:write_log_messages | string | true | true, false | Write out log messages in case of sparse windows or median in rightmost histogram bin |
struct OpenMS::PeakPickerHiRes::PeakBoundary |
PeakPickerHiRes | ( | ) |
Constructor.
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override |
Destructor.
void pick | ( | const MSChromatogram & | input, |
MSChromatogram & | output | ||
) | const |
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram.
input | input chromatogram in profile mode |
output | output chromatogram with picked peaks |
void pick | ( | const MSChromatogram & | input, |
MSChromatogram & | output, | ||
std::vector< PeakBoundary > & | boundaries, | ||
bool | check_spacings = false |
||
) | const |
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked peaks are written to the output chromatogram.
input | input chromatogram in profile mode |
output | output chromatogram with picked peaks |
boundaries | boundaries of the picked peaks |
void pick | ( | const MSSpectrum & | input, |
MSSpectrum & | output | ||
) | const |
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum.
input | input spectrum in profile mode |
output | output spectrum with picked peaks |
Referenced by PeakPickerIterative::pick().
void pick | ( | const MSSpectrum & | input, |
MSSpectrum & | output, | ||
std::vector< PeakBoundary > & | boundaries, | ||
bool | check_spacings = true |
||
) | const |
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are written to the output spectrum. Peak boundaries are written to a separate structure.
input | input spectrum in profile mode |
output | output spectrum with picked peaks |
boundaries | boundaries of the picked peaks |
check_spacings | check spacing constraints? (yes for spectra, no for chromatograms) |
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protected |
void pickExperiment | ( | const PeakMap & | input, |
PeakMap & | output, | ||
const bool | check_spectrum_type = true |
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) | const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.
input | input map in profile mode |
output | output map with picked peaks |
check_spectrum_type | if set, checks spectrum type and throws an exception if a centroided spectrum is passed |
void pickExperiment | ( | const PeakMap & | input, |
PeakMap & | output, | ||
std::vector< std::vector< PeakBoundary > > & | boundaries_spec, | ||
std::vector< std::vector< PeakBoundary > > & | boundaries_chrom, | ||
const bool | check_spectrum_type = true |
||
) | const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.
input | input map in profile mode |
output | output map with picked peaks |
boundaries_spec | boundaries of the picked peaks in spectra |
boundaries_chrom | boundaries of the picked peaks in chromatograms |
check_spectrum_type | if set, checks spectrum type and throws an exception if a centroided spectrum is passed |
void pickExperiment | ( | OnDiscMSExperiment & | input, |
PeakMap & | output, | ||
const bool | check_spectrum_type = true |
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) | const |
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in the map consecutively. The resulting picked peaks are written to the output map.
Currently we have to give up const-correctness but we know that everything on disc is constant
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overrideprotectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM
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unit of 'FWHM' float data array (can be absolute or ppm).
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