| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Static Public Member Functions | Protected Attributes | List of all members
TransformationDescription Class Reference
Analysis » MapAlignment

Generic description of a coordinate transformation. More...

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

## 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.