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

#include <OpenMS/FILTERING/TRANSFORMERS/LinearResamplerAlign.h>

Inheritance diagram for LinearResamplerAlign:

Public Member Functions
	LinearResamplerAlign ()

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

template<typename SpecT >
void	raster_align (SpecT &container, double start_pos, double end_pos)
	Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram) with fixed coordinates. More...

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >
void	raster (ConstPeakTypeIterator raw_it, ConstPeakTypeIterator raw_end, PeakTypeIterator resample_it, PeakTypeIterator resample_end)
	Applies the resampling algorithm. More...

template<typename PeakTypeIterator , typename ConstPeakTypeIterator >
void	raster (ConstPeakTypeIterator mz_raw_it, ConstPeakTypeIterator mz_raw_end, ConstPeakTypeIterator int_raw_it, ConstPeakTypeIterator, PeakTypeIterator mz_resample_it, PeakTypeIterator mz_resample_end, PeakTypeIterator int_resample_it, PeakTypeIterator)
	Applies the resampling algorithm. More...

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

Public Member Functions inherited from LinearResampler
	LinearResampler ()
	Constructor. More...

	~LinearResampler ()
	Destructor. More...

void	raster (MSSpectrum &spectrum)
	Applies the resampling algorithm to an MSSpectrum. More...

void	rasterExperiment (PeakMap &exp)
	Resamples the data in an MSExperiment. More...

Public Member Functions inherited from DefaultParamHandler
	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 &param)
	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...

Public Member Functions inherited from ProgressLogger
	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...

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

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. More...

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

Protected Attributes
bool	ppm_
	Spacing of the resampled data. More...

Protected Attributes inherited from LinearResampler
double	spacing_
	Spacing of the resampled data. More...

Protected Attributes inherited from DefaultParamHandler
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...

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 Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

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. Therefore it is recommended for quantitation as well as for ProteinIdentification experiments.

In addition to the LinearResampler, 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.

Constructor & Destructor Documentation

◆ LinearResamplerAlign()

LinearResamplerAlign ( )

inline

Member Function Documentation

◆ populate_raster_()

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(), and Peak2D::setMZ().

◆ raster() [1/3]

void raster ( SpecT & 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

container The container to be resampled

Referenced by MRMTransitionGroupPicker::resampleChromatogram_().

◆ raster() [2/3]

void raster	(	ConstPeakTypeIterator	raw_it,
		ConstPeakTypeIterator	raw_end,
		PeakTypeIterator	resample_it,
		PeakTypeIterator	resample_end
	)

inline

Applies the resampling algorithm.

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 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

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

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

inline

Applies the resampling algorithm.

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 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

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

References OPENMS_PRECONDITION.

◆ raster_align()

void raster_align	(	SpecT &	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

container	The container to be resampled
start_pos	The start position to be used for resampling
end_pos	The end position to be used for resampling

◆ raster_interpolate()

void raster_interpolate	(	PeakTypeIterator	raw_it,
		PeakTypeIterator	raw_end,
		PeakTypeIterator	resample_it,
		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

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

References OPENMS_PRECONDITION.

◆ updateMembers_()

virtual void updateMembers_ ( )

inlineprotectedvirtual

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 LinearResampler.

Member Data Documentation

◆ ppm_

bool ppm_

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()

◆ updateMembers_()

Member Data Documentation

◆ ppm_