A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation. More...

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

Inheritance diagram for PoseClusteringAffineSuperimposer:

Public Member Functions
	PoseClusteringAffineSuperimposer ()
	Default ctor. More...

	~PoseClusteringAffineSuperimposer () override
	Destructor. More...

void	run (const ConsensusMap &map_model, const ConsensusMap &map_scene, TransformationDescription &transformation) override
	Estimates the transformation and fills the given mapping function. (Has a precondition!) More...

virtual void	run (const std::vector< Peak2D > &map_model, const std::vector< Peak2D > &map_scene, TransformationDescription &transformation)
	Perform alignment on vector of 1D peaks. More...

Public Member Functions inherited from BaseSuperimposer
	BaseSuperimposer ()
	Constructor. More...

	~BaseSuperimposer () override
	Destructor. 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...

Static Public Member Functions
static BaseSuperimposer *	create ()
	Returns an instance of this class. More...

static const String	getProductName ()
	Returns the name of this module. More...

Static Public Member Functions inherited from BaseSuperimposer
static void	registerChildren ()
	Register all derived classes here. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. 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...

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_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

A superimposer that uses a voting scheme, also known as pose clustering, to find a good affine transformation.

This algorithm works on two consensus maps. It computes an affine transformation that maps the elements of second map as near as possible to the elements in the first map.

The voting scheme hashes affine transformations between pairs of features in map one and pairs of features in map two. Each such pair of pairs defines a (potential) "pose" of the second map relative to the first. Then it finds a cluster in the parameter space of these poses. The affine transformation is then computed from this cluster of potential poses, hence the name pose clustering.

See also: PoseClusteringShiftSuperimposer

Parameters of this class are:

Name	Type	Default	Restrictions	Description
mz_pair_max_distance	float	0.5	min: 0.0	Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.
rt_pair_distance_fraction	float	0.1	min: 0.0 max: 1.0	Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).
num_used_points	int	2000	min: -1	Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.
scaling_bucket_size	float	0.005	min: 0.0	The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.
shift_bucket_size	float	3.0	min: 0.0	The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.
max_shift	float	1000.0	min: 0.0	Maximal shift which is considered during histogramming (in seconds). This applies for both directions.
max_scaling	float	2.0	min: 1.0	Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.
dump_buckets	string			[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.
dump_pairs	string			[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ PoseClusteringAffineSuperimposer()

PoseClusteringAffineSuperimposer ( )

Default ctor.

◆ ~PoseClusteringAffineSuperimposer()

~PoseClusteringAffineSuperimposer ( )

inlineoverride

Destructor.

Member Function Documentation

◆ create()

static BaseSuperimposer* create ( )

inlinestatic

Returns an instance of this class.

◆ getProductName()

static const String getProductName ( )

inlinestatic

Returns the name of this module.

◆ run() [1/2]

void run	(	const ConsensusMap &	map_model,
		const ConsensusMap &	map_scene,
		TransformationDescription &	transformation
	)

overridevirtual

Estimates the transformation and fills the given mapping function. (Has a precondition!)

Note: Exactly two input maps must be given.

Precondition: For performance reasons, we trust that (the equivalent of:)

maps[0].updateRanges(); maps[1].updateRanges();

has been done before calling this. You have been warned!

Parameters

map_model	The model map (first input map)
map_scene	The scene map (second input map)
transformation	The output affine transformation (linear model transforming the scene map onto the model map)

Exceptions

IllegalArgument is thrown if the input maps are invalid.

Implements BaseSuperimposer.

◆ run() [2/2]

virtual void run	(	const std::vector< Peak2D > &	map_model,
		const std::vector< Peak2D > &	map_scene,
		TransformationDescription &	transformation
	)

virtual

Perform alignment on vector of 1D peaks.

Public Member Functions

Static Public Member Functions

Additional Inherited Members