| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
LinearResamplerAlign Class Reference

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

## Protected Member Functions

void | updateMembers_ () override
| 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
| ) |  |

inline protected

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_()

void updateMembers_ | ( |  | ) |

inline override protected virtual

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.