This class implements baseline filtering operations using methods from mathematical morphology. More...

#include <OpenMS/FILTERING/BASELINE/MorphologicalFilter.h>

Inheritance diagram for MorphologicalFilter:

Collaboration diagram for MorphologicalFilter:

Public Member Functions
	MorphologicalFilter ()
	Constructor. More...

	~MorphologicalFilter () override
	Destructor. More...

template<typename InputIterator , typename OutputIterator >
void	filterRange (InputIterator input_begin, InputIterator input_end, OutputIterator output_begin)
	Applies the morphological filtering operation to an iterator range. More...

void	filter (MSSpectrum &spectrum)
	Applies the morphological filtering operation to an MSSpectrum. More...

void	filterExperiment (PeakMap &exp)
	Applies the morphological filtering operation to an MSExperiment. More...

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

virtual	~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 (UInt64 bytes_processed=0) const

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

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...

Protected Member Functions
template<typename InputIterator , typename OutputIterator >
void	applyErosion_ (Int struc_size, InputIterator input, InputIterator input_end, OutputIterator output)
	Applies erosion. This implementation uses van Herk's method. Only 3 min/max comparisons are required per data point, independent of struc_size. More...

template<typename InputIterator , typename OutputIterator >
void	applyDilation_ (Int struc_size, InputIterator input, InputIterator input_end, OutputIterator output)
	Applies dilation. This implementation uses van Herk's method. Only 3 min/max comparisons are required per data point, independent of struc_size. More...

template<typename InputIterator , typename OutputIterator >
void	applyErosionSimple_ (Int struc_size, InputIterator input_begin, InputIterator input_end, OutputIterator output_begin)
	Applies erosion. Simple implementation, possibly faster if struc_size is very small, and used in some special cases. More...

template<typename InputIterator , typename OutputIterator >
void	applyDilationSimple_ (Int struc_size, InputIterator input_begin, InputIterator input_end, OutputIterator output_begin)
	Applies dilation. Simple implementation, possibly faster if struc_size is very small, and used in some special cases. More...

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

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
UInt	struct_size_in_datapoints_
	Member for struct size in data points. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

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...

Private Member Functions
	MorphologicalFilter (const MorphologicalFilter &source)
	copy constructor not implemented More...

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 String &key_prefix="")
	Writes all parameters to meta values. 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

This class implements baseline filtering operations using methods from mathematical morphology.

The fundamental operations are erosion and dilation. These are defined with respect to a structuring element. In our case, this is just a straight line and the definitions can be given as follows:

Assume that the input is \(x_0, x_1, x_2, ...\). Then the erosion of \(x\) contains the minima of a sliding window of size struc_size around \( i \), i.e.

\[ \mathrm{erosion}_i = \min\{x_{i-\mathrm{struc\_size}/2}, \ldots, x_{i+\mathrm{struc\_size}/2}\} \]

. The dilation of \(x\) contains the maxima of a sliding window of size struc_size around \( i \), i.e.

\[ \mathrm{dilation}_i = \max\{x_{i-\mathrm{struc\_size}/2}, \ldots, x_{i+\mathrm{struc\_size}/2}\} \]

.

For morphological baseline filtering the tophat method is used. The tophat transform is defined as signal minus opening, where the opening is the dilation of the erosion of the signal.

Several other morphological operations are implemented as well. See the image below and the documentation for further explanation.

Note: The class MorphologicalFilter is designed for uniformly spaced profile data.; The data must be sorted according to ascending m/z!

Parameters of this class are:

Name	Type	Default	Restrictions	Description
struc_elem_length	float	3.0		Length of the structuring element. This should be wider than the expected peak width.
struc_elem_unit	string	Thomson	Thomson, DataPoints	The unit of the 'struct_elem_length'.
method	string	tophat	identity, erosion, dilation, opening, closing, gradient, tophat, bothat, erosion_simple, dilation_simple	Method to use, the default is 'tophat'. Do not change this unless you know what you are doing. The other methods may be useful for tuning the parameters, see the class documentation of MorpthologicalFilter.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ MorphologicalFilter() [1/2]

MorphologicalFilter ( )

inline

Constructor.

◆ ~MorphologicalFilter()

~MorphologicalFilter ( )

inlineoverride

Destructor.

◆ MorphologicalFilter() [2/2]

MorphologicalFilter ( const MorphologicalFilter & source )

private

copy constructor not implemented

Member Function Documentation

◆ applyDilation_()

void applyDilation_	(	Int	struc_size,
		InputIterator	input,
		InputIterator	input_end,
		OutputIterator	output
	)

inlineprotected

Applies dilation. This implementation uses van Herk's method. Only 3 min/max comparisons are required per data point, independent of struc_size.

◆ applyDilationSimple_()

void applyDilationSimple_	(	Int	struc_size,
		InputIterator	input_begin,
		InputIterator	input_end,
		OutputIterator	output_begin
	)

inlineprotected

Applies dilation. Simple implementation, possibly faster if struc_size is very small, and used in some special cases.

◆ applyErosion_()

void applyErosion_	(	Int	struc_size,
		InputIterator	input,
		InputIterator	input_end,
		OutputIterator	output
	)

inlineprotected

Applies erosion. This implementation uses van Herk's method. Only 3 min/max comparisons are required per data point, independent of struc_size.

◆ applyErosionSimple_()

void applyErosionSimple_	(	Int	struc_size,
		InputIterator	input_begin,
		InputIterator	input_end,
		OutputIterator	output_begin
	)

inlineprotected

Applies erosion. Simple implementation, possibly faster if struc_size is very small, and used in some special cases.

◆ filter()

void filter ( MSSpectrum & spectrum )

inline

Applies the morphological filtering operation to an MSSpectrum.

If the size of the structuring element is given in 'Thomson', the number of data points for the structuring element is computed as follows:

The data points are assumed to be uniformly spaced. We compute the average spacing from the position of the first and the last peak and the total number of peaks in the input range.
The number of data points in the structuring element is computed from struc_size and the average spacing, and rounded up to an odd number.

References OpenMS::Internal::intensityIteratorWrapper(), OpenMS::Math::isOdd(), SpectrumSettings::PROFILE, and SpectrumSettings::setType().

◆ filterExperiment()

void filterExperiment ( PeakMap & exp )

inline

Applies the morphological filtering operation to an MSExperiment.

The size of the structuring element is computed for each spectrum individually, if it is given in 'Thomson'. See the filtering method for MSSpectrum for details.

References MSExperiment::size().

◆ filterRange()

void filterRange	(	InputIterator	input_begin,
		InputIterator	input_end,
		OutputIterator	output_begin
	)

inline

Applies the morphological filtering operation to an iterator range.

Input and output range must be valid, i.e. allocated before. InputIterator must be a random access iterator type.

Parameters

input_begin	the begin of the input range
input_end	the end of the input range
output_begin	the begin of the output range

Exceptions

Exception::IllegalArgument The given method is not one of the values defined in the method parameter.

Member Data Documentation

◆ struct_size_in_datapoints_

UInt struct_size_in_datapoints_

protected

Member for struct size in data points.

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MorphologicalFilter() [1/2]

◆ ~MorphologicalFilter()

◆ MorphologicalFilter() [2/2]

Member Function Documentation

◆ applyDilation_()

◆ applyDilationSimple_()

◆ applyErosion_()

◆ applyErosionSimple_()

◆ filter()

◆ filterExperiment()

◆ filterRange()

Member Data Documentation

◆ struct_size_in_datapoints_