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TopHatFilter Class Reference
[Spectrum filters]

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

Inheritance diagram for TopHatFilter:

MorphFilter DefaultParamHandler ProgressLogger

List of all members.


Detailed Description

This class represents a Top Hat baseline filter.

This filter can be used by supposing that the required lineaments are brighter than the environment. The main advantage of this filter is to be able to detect an over brightness even if the environment is not uniform. Moreover it is possible to regulate the size or the width of the over brightnesses very easily. The principle is based on the subtraction of an signal $ s $ from its opening $ \gamma $. The opening consists of an erosion followed by a dilation, the size (the frameSize) of the structuring element (here a flat line) being conditioned by the width of the lineament to be detected.

Note:
This filter works only for uniform raw data!
TopHatFilter Parameters are explained on a separate page.

Public Types

typedef MorphFilter BaseClass

Public Member Functions

 TopHatFilter ()
 Constructor.
virtual ~TopHatFilter ()
 Destructor.
template<typename InputPeakIterator, typename OutputPeakContainer>
void filter (InputPeakIterator first, InputPeakIterator last, OutputPeakContainer &baseline_filtered_container)
 Applies the baseline removal algorithm to an given iterator range.
template<typename InputPeakContainer, typename OutputPeakContainer>
void filter (const InputPeakContainer &input_peak_container, OutputPeakContainer &baseline_filtered_container)
 Applies the baseline removal algorithm to to a raw data point container.
template<typename InputSpectrumIterator, typename OutputPeakType, typename OutputAllocType>
void filterExperiment (InputSpectrumIterator first, InputSpectrumIterator last, MSExperiment< OutputPeakType, OutputAllocType > &ms_exp_filtered)
 Removes the baseline in a range of MSSpectra.
template<typename InputPeakType, typename InputAllocType, typename OutputPeakType, typename OutputAllocType>
void filterExperiment (const MSExperiment< InputPeakType, InputAllocType > &ms_exp_raw, MSExperiment< OutputPeakType, OutputAllocType > &ms_exp_filtered)
 Removes the baseline in a MSExperiment.

Member Typedef Documentation

typedef MorphFilter BaseClass


Constructor & Destructor Documentation

TopHatFilter (  )  [inline]

Constructor.

virtual ~TopHatFilter (  )  [inline, virtual]

Destructor.


Member Function Documentation

void filter ( InputPeakIterator  first,
InputPeakIterator  last,
OutputPeakContainer &  baseline_filtered_container 
) [inline]

Applies the baseline removal algorithm to an given iterator range.

Removes the baseline in the given iterator intervall [first,last) and writes the resulting data to the baseline_filtered_container.

Note:
This method assumes that the InputPeakIterator (e.g. of type MSSpectrum<RawDataPoint1D >::const_iterator) points to a data point of type RawDataPoint1D or any other class derived from RawDataPoint1D.

The resulting peaks in the baseline_filtered_container (e.g. of type MSSpectrum<RawDataPoint1D >) can be of type RawDataPoint1D or any other class derived from DRawDataPoint.

void filter ( const InputPeakContainer &  input_peak_container,
OutputPeakContainer &  baseline_filtered_container 
) [inline]

Applies the baseline removal algorithm to to a raw data point container.

Removes the baseline in the the input container (e.g. of type MSSpectrum<RawDataPoint1D >) and writes the resulting data to the baseline_filtered_container.

Note:
This method assumes that the InputPeakIterator (e.g. of type MSSpectrum<RawDataPoint1D >::const_iterator) points to a data point of type RawDataPoint1D or any other class derived from RawDataPoint1D.

The resulting peaks in the baseline_filtered_container (e.g. of type MSSpectrum<RawDataPoint1D >) can be of type RawDataPoint1D or any other class derived from DRawDataPoint.

void filterExperiment ( InputSpectrumIterator  first,
InputSpectrumIterator  last,
MSExperiment< OutputPeakType, OutputAllocType > &  ms_exp_filtered 
) [inline]

Removes the baseline in a range of MSSpectra.

Filters the data successive in every scan in the intervall [first,last). The filtered data are stored in a MSExperiment.

Note:
The InputSpectrumIterator should point to a MSSpectrum. Elements of the input spectra should be of type RawDataPoint1D or any other derived class of DRawDataPoint.

You have to copy the ExperimentalSettings of the raw data by your own.

void filterExperiment ( const MSExperiment< InputPeakType, InputAllocType > &  ms_exp_raw,
MSExperiment< OutputPeakType, OutputAllocType > &  ms_exp_filtered 
) [inline]

Removes the baseline in a MSExperiment.

Filters the data every scan in the MSExperiment. The filtered data are stored in a MSExperiment.

Note:
The InputSpectrumIterator should point to a MSSpectrum. Elements of the input spectra should be of type RawDataPoint1D or any other derived class of DRawDataPoint.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1