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

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

Inheritance diagram for MorphologicalFilter:

Public Member Functions
	MorphologicalFilter ()
	Constructor.
virtual	~MorphologicalFilter ()
	Destructor.
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.
template<typename PeakType >
void	filter (MSSpectrum< PeakType > &spectrum)
	Applies the morphological filtering operation to an MSSpectrum.
template<typename PeakType >
void	filterExperiment (MSExperiment< PeakType > &exp)
	Applies the morphological filtering operation to an MSExperiment.
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.
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.
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.
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.
Protected Attributes
UInt	struct_size_in_datapoints_
	Member for struct size in data points.
Private Member Functions
	MorphologicalFilter (const MorphologicalFilter &source)
	copy constructor not implemented

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		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 ( ) [inline]

Constructor.

References StringList::create().

virtual ~MorphologicalFilter ( ) [inline, virtual]

Destructor.

MorphologicalFilter ( const MorphologicalFilter & source ) [private]

copy constructor not implemented

Member Function Documentation

void applyDilation_	(	Int	struc_size,
		InputIterator	input,
		InputIterator	input_end,
		OutputIterator	output
	)			`[inline, protected]`

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

void applyDilationSimple_	(	Int	struc_size,
		InputIterator	input_begin,
		InputIterator	input_end,
		OutputIterator	output_begin
	)			`[inline, protected]`

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

void applyErosion_	(	Int	struc_size,
		InputIterator	input,
		InputIterator	input_end,
		OutputIterator	output
	)			`[inline, protected]`

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

void applyErosionSimple_	(	Int	struc_size,
		InputIterator	input_begin,
		InputIterator	input_end,
		OutputIterator	output_begin
	)			`[inline, protected]`

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

void filter ( MSSpectrum< PeakType > & 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::RAWDATA, and SpectrumSettings::setType().

void filterExperiment ( MSExperiment< PeakType > & 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.

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 paramter.

Member Data Documentation

UInt struct_size_in_datapoints_ [protected]

Member for struct size in data points.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1

MorphologicalFilter Class Reference [SignalProcessing]

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

MorphologicalFilter Class Reference
[SignalProcessing]