Linear Resampling of raw data with alignment. More...

#include <OpenMS/PROCESSING/RESAMPLING/LinearResamplerAlign.h>

Inheritance diagram for LinearResamplerAlign:

Collaboration diagram for LinearResamplerAlign:

Public Member Functions
	LinearResamplerAlign ()

template<class PeakContainerT >
void	raster (PeakContainerT &container)
	Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram).

template<typename PeakContainerT >
void	raster_align (PeakContainerT &container, double start_pos, double end_pos)
	Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram) with fixed coordinates. The container will be resampled at equally spaced points between the supplied start and end positions. The resampling frequency can be controlled by the "spacing" parameter.

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >
void	raster (ConstPeakTypeIterator raw_it, ConstPeakTypeIterator raw_end, PeakTypeIterator resampled_begin, PeakTypeIterator resampled_end)
	Resample points (e.g. Peak1D) from an input range onto a prepopulated output range with given m/z, modifying the output intensities.

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >
void	raster (ConstPeakTypeIterator mz_raw_it, ConstPeakTypeIterator mz_raw_end, ConstPeakTypeIterator int_raw_it, ConstPeakTypeIterator int_raw_end, ConstPeakTypeIterator mz_resample_it, ConstPeakTypeIterator mz_resample_end, PeakTypeIterator int_resample_it, PeakTypeIterator int_resample_end)
	Resample points (with m/z and intensity in separate containers, but of same length) from an input range onto a prepopulated output m/z & intensity range (each in separate containers, but of same length).

template<typename PeakTypeIterator >
void	raster_interpolate (PeakTypeIterator raw_it, PeakTypeIterator raw_end, PeakTypeIterator resampled_start, PeakTypeIterator resampled_end)
	Applies the resampling algorithm using a linear interpolation.

void	rasterExperiment (PeakMap &exp)
	Applies the resampling algorithm to all spectra of an MSExperiment.

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.

void	setParameters (const Param &param)
	Sets the parameters.

const Param &	getParameters () const
	Non-mutable access to the parameters.

const Param &	getDefaults () const
	Non-mutable access to the default parameters.

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.

virtual	~ProgressLogger ()
	Destructor.

	ProgressLogger (const ProgressLogger &other)
	Copy constructor.

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!

LogType	getLogType () const
	Returns the type of progress log being used.

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.

void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.

void	setProgress (SignedSize value) const
	Sets the current progress.

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method.

template<typename PeakType >
void	populate_raster_ (std::vector< PeakType > &resampled_peak_container, double start_pos, double end_pos, int number_resampled_points)
	Generate raster for resampled peak container.

template<typename PeakTypeIterator >
void	verifySpacing_ (PeakTypeIterator it, PeakTypeIterator end, auto access)
	helper function to warn the user when the resampling rate is too high

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.

Protected Attributes
double	spacing_
	Spacing of the resampled data.

bool	ppm_
	Whether spacing_ is interpreted in ppm (true) or Th (false)

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!

std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

bool	check_defaults_
	If this member is set to false no checking if parameters in done;.

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

Linear Resampling of raw data with alignment.

This class can be used to generate uniform data from non-uniform raw data (e.g. ESI-TOF or MALDI-TOF experiments). Therefore the intensity at every position x in the input raw data is spread to the two adjacent resampling points. This method preserves the area of the input signal and also the centroid position of a peak.

This class also allows to fix the points at which resampling will occur. This is useful if the resampling points are known in advance, e.g. if one needs to resample a chromatogram at the positions of another chromatogram. Therefore it is recommended for quantitation as well as for ProteinIdentification experiments.

Warning: If the configured spacing is smaller than the minimal distance between two adjacent input data points, intensity redistribution may produce spurious peaks. This can occur when the sampling rate is finer than the detector's dead time.

Constructor & Destructor Documentation

◆ LinearResamplerAlign()

LinearResamplerAlign ( )

inline

Member Function Documentation

◆ populate_raster_()

template<typename PeakType >

void populate_raster_	(	std::vector< PeakType > &	resampled_peak_container,
		double	start_pos,
		double	end_pos,
		int	number_resampled_points
	)

inlineprotected

Generate raster for resampled peak container.

References Peak2D::setIntensity().

◆ raster() [1/3]

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >

void raster	(	ConstPeakTypeIterator	mz_raw_it,
		ConstPeakTypeIterator	mz_raw_end,
		ConstPeakTypeIterator	int_raw_it,
		ConstPeakTypeIterator	int_raw_end,
		ConstPeakTypeIterator	mz_resample_it,
		ConstPeakTypeIterator	mz_resample_end,
		PeakTypeIterator	int_resample_it,
		PeakTypeIterator	int_resample_end
	)

inline

Resample points (with m/z and intensity in separate containers, but of same length) from an input range onto a prepopulated output m/z & intensity range (each in separate containers, but of same length).

This will use the raster provided by the output container, i.e. with alignment, to resample the data provided in the input container. The intensities will be added to the intensities in the output container (which in most cases will be zero).

The intensities will be distributed between the two closest resampling points, thus conserving the sum of intensity over the whole container.

Note that all intensity in the input data container that is in peaks outside the range of the output container will simply be added to the first or last data point.

Parameters

[in]	mz_raw_it	Start of the input container to be resampled (containing the m/z data)
[in]	mz_raw_end	End of the input container to be resampled (containing the m/z data)
[in]	int_raw_it	Start of the input container to be resampled (containing the intensity data)
[in]	int_raw_end	End of the input container to be resampled (containing the intensity data)
[in]	mz_resample_it	Iterator pointing to start of the output spectrum range (m/z which need to be populated)
[in]	mz_resample_end	Iterator pointing to end of the output spectrum range (m/z which need to be populated)
[in,out]	int_resample_it	Iterator pointing to start of the output spectrum range (intensities)
[in,out]	int_resample_end	Iterator pointing to end of the output spectrum range (intensities)

References OPENMS_PRECONDITION.

◆ raster() [2/3]

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >

void raster	(	ConstPeakTypeIterator	raw_it,
		ConstPeakTypeIterator	raw_end,
		PeakTypeIterator	resampled_begin,
		PeakTypeIterator	resampled_end
	)

inline

Resample points (e.g. Peak1D) from an input range onto a prepopulated output range with given m/z, modifying the output intensities.

This will use the raster provided by the output container, i.e. with alignment, to resample the data provided in the input container. The intensities will be added to the intensities in the output container (which in most cases will be zero).

The intensities will be distributed between the two closest resampling points, thus conserving the sum of intensity over the whole container.

Note that all intensity in the input data container that is in peaks outside the range of the output container will simply be added to the first or last data point.

Parameters

[in]	raw_it	Start of the input container to be resampled (containing the data)
[in]	raw_end	End of the input container to be resampled (containing the data)
[in,out]	resampled_begin	Iterator pointing to start of the output spectrum range (m/z need to be populated, intensities should be zero)
[in,out]	resampled_end	Iterator pointing to end of the output spectrum range (m/z need to be populated, intensities should be zero)

References OPENMS_PRECONDITION.

◆ raster() [3/3]

template<class PeakContainerT >

void raster ( PeakContainerT & container )

inline

Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram).

The container will be resampled at equally spaced points between the start and end of the container. The resampling frequency can be controlled by the "spacing" parameter.

Parameters

[in,out] container The container to be resampled

Referenced by MRMTransitionGroupPicker::resampleChromatogram_().

◆ raster_align()

template<typename PeakContainerT >

void raster_align	(	PeakContainerT &	container,
		double	start_pos,
		double	end_pos
	)

inline

Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram) with fixed coordinates. The container will be resampled at equally spaced points between the supplied start and end positions. The resampling frequency can be controlled by the "spacing" parameter.

This allows the user to specify the grid for alignment explicitly. This is especially useful if multiple spectra or chromatograms need to be resampled according to the same raster.

Parameters

[in,out]	container	The container to be resampled
[in]	start_pos	The start position to be used for resampling
[in]	end_pos	The end position to be used for resampling

◆ raster_interpolate()

template<typename PeakTypeIterator >

void raster_interpolate	(	PeakTypeIterator	raw_it,
		PeakTypeIterator	raw_end,
		PeakTypeIterator	resampled_start,
		PeakTypeIterator	resampled_end
	)

inline

Applies the resampling algorithm using a linear interpolation.

This will use the raster provided by the output container to resample the data provided in the input container. The intensities will be added to the intensities in the output container (which in most cases will be zero).

The intensities at the resampling point is computed by a linear interpolation between the two closest resampling points.

Parameters

[in]	raw_it	Start of the input (raw) spectrum to be resampled
[in]	raw_end	End of the input (raw) spectrum to be resampled
[in,out]	resampled_start	Iterator pointing to start of the output spectrum range (m/z need to be populated, intensities should be zero)
[in,out]	resampled_end	Iterator pointing to end of the output spectrum range (m/z need to be populated, intensities should be zero)

References OPENMS_PRECONDITION.

◆ rasterExperiment()

void rasterExperiment ( PeakMap & exp )

inline

Applies the resampling algorithm to all spectra of an MSExperiment.

Chromatograms stored in exp are not resampled.

Parameters

[in,out] exp The experiment whose spectra will be resampled in place.

References MSExperiment::size().

◆ updateMembers_()

void updateMembers_ ( )

inlineoverrideprotectedvirtual

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.

◆ verifySpacing_()

template<typename PeakTypeIterator >

void verifySpacing_	(	PeakTypeIterator	it,
		PeakTypeIterator	end,
		auto	access
	)

inlineprotected

helper function to warn the user when the resampling rate is too high

References OPENMS_LOG_WARN, and OpenMS::suppress_resampling_spacing_warning.

Member Data Documentation

◆ ppm_

bool ppm_

protected

Whether spacing_ is interpreted in ppm (true) or Th (false)

◆ spacing_

double spacing_

protected

Spacing of the resampled data.

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LinearResamplerAlign()

Member Function Documentation

◆ populate_raster_()

◆ raster() [1/3]

◆ raster() [2/3]

◆ raster() [3/3]

◆ raster_align()

◆ raster_interpolate()

◆ rasterExperiment()

◆ updateMembers_()

◆ verifySpacing_()

Member Data Documentation

◆ ppm_

◆ spacing_