TransformationDescription Class Reference

Generic description of a coordinate transformation. More...

#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>

Collaboration diagram for TransformationDescription:

Classes
struct	TransformationStatistics
	Summary statistics before/after applying the transformation. For deviations before/after transformation, the percentiles 100, 99, 95, 90, 75, 50, 25 are returned. More...

Public Types
typedef TransformationModel::DataPoint	DataPoint
	Coordinate pair. More...
typedef TransformationModel::DataPoints	DataPoints
	Vector of coordinate pairs. More...

Public Member Functions
	TransformationDescription ()
	Default constructor. More...
	TransformationDescription (const DataPoints &data)
	Constructor from data. More...
	~TransformationDescription ()
	Destructor. More...
	TransformationDescription (const TransformationDescription &rhs)
	Copy constructor. More...
TransformationDescription &	operator= (const TransformationDescription &rhs)
	Assignment operator. More...
void	fitModel (const String &model_type, const Param &params=Param())
	Fits a model to the data. More...
double	apply (double value) const
	Applies the transformation to value. More...
const String &	getModelType () const
	Gets the type of the fitted model. More...
void	setDataPoints (const DataPoints &data)
	Sets the data points. More...
void	setDataPoints (const std::vector< std::pair< double, double > > &data)
	Sets the data points (backwards-compatible overload) More...
const DataPoints &	getDataPoints () const
	Returns the data points. More...
const Param &	getModelParameters () const
	Non-mutable access to the model parameters. More...
void	invert ()
	Computes an (approximate) inverse of the transformation. More...
void	getDeviations (std::vector< double > &diffs, bool do_apply=false, bool do_sort=true) const
	Get the deviations between the data pairs. More...
TransformationStatistics	getStatistics () const
	Get summary statistics (ranges and errors before/after) More...
void	printSummary (std::ostream &os=std::cout) const
	Print summary statistics for the transformation. More...

Static Public Member Functions
static void	getModelTypes (StringList &result)
	Gets the possible types of models. More...

Protected Attributes
DataPoints	data_
	Data points. More...
String	model_type_
	Type of model. More...
TransformationModel *	model_
	Pointer to model. More...

Detailed Description

Generic description of a coordinate transformation.

This description primarily stores data points (coordinate pairs) from which a transformation model can be estimated. Applying the transformation to a coordinate (via apply) then means evaluating the model at that coordinate.

The following models are available:

• none (TransformationModel): (identity)
• identity: Same as none, but intended for reference files (used to indicate that no other model should be fit, because the identity is already optimal).
• linear (TransformationModelLinear):
• interpolated (TransformationModelInterpolated): Interpolation between pairs, extrapolation using first and last pair. Supports different interpolation types.
• b-spline (TransformationModelBSpline): Non-linear smoothing spline, with different options for extrapolation.
• lowess (TransformationModelLowess): Non-linear smoothing via local regression, with different options for extrapolation.

Remarks

TransformationDescription stores data points, TransformationModel stores parameters. That way, data can be modeled using different models/parameters, and models can still keep a representation of the data in the format they need (if at all).

Member Typedef Documentation

DataPoint

typedef TransformationModel::DataPoint DataPoint

Coordinate pair.

DataPoints

typedef TransformationModel::DataPoints DataPoints

Vector of coordinate pairs.

Constructor & Destructor Documentation

TransformationDescription() [1/3]

TransformationDescription

(

)

Default constructor.

TransformationDescription() [2/3]

TransformationDescription ( const DataPoints &  data )

explicit

Constructor from data.

~TransformationDescription()

~TransformationDescription

(

)

Destructor.

TransformationDescription() [3/3]

TransformationDescription

(

const TransformationDescription &

rhs

)

Copy constructor.

Member Function Documentation

apply()

double apply

(

double

value

)

const

Applies the transformation to value.

Returns the result of evaluating the fitted model at value. Returns value unchanged if no model was fitted.

fitModel()

void fitModel	(	const String &	model_type,
		const Param &	params = Param()
	)

Fits a model to the data.

Referenced by TOPPOpenSwathBase::performCalibration().

getDataPoints()

const DataPoints& getDataPoints

(

)

const

Returns the data points.

getDeviations()

void getDeviations	(	std::vector< double > &	diffs,
		bool	do_apply = false,
		bool	do_sort = true
	)		const

Get the deviations between the data pairs.

Parameters

diffs	Output
do_apply	Get deviations after applying the model?
do_sort	Sort diffs before returning?

getModelParameters()

const Param& getModelParameters

(

)

const

Non-mutable access to the model parameters.

getModelType()

const String& getModelType

(

)

const

Gets the type of the fitted model.

getModelTypes()

static void getModelTypes ( StringList &  result )

static

Gets the possible types of models.

getStatistics()

TransformationStatistics getStatistics

(

)

const

Get summary statistics (ranges and errors before/after)

invert()

void invert

(

)

Computes an (approximate) inverse of the transformation.

Referenced by ChromatogramExtractor::extractChromatograms().

operator=()

TransformationDescription& operator=

(

const TransformationDescription &

rhs

)

Assignment operator.

printSummary()

void printSummary

(

std::ostream &

os = std::cout

)

const

Print summary statistics for the transformation.

setDataPoints() [1/2]

void setDataPoints

(

const DataPoints &

data

)

Sets the data points.

Removes the model that was previously fitted to the data (if any).

setDataPoints() [2/2]

void setDataPoints

(

const std::vector< std::pair< double, double > > &

data

)

Sets the data points (backwards-compatible overload)

Removes the model that was previously fitted to the data (if any).

Member Data Documentation

data_

DataPoints data_

protected

Data points.

model_

TransformationModel* model_

protected

Pointer to model.

model_type_

String model_type_

protected

Type of model.