ClusteringGrid Class Reference

data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering More...

#include <OpenMS/ML/CLUSTERING/ClusteringGrid.h>

Collaboration diagram for ClusteringGrid:

Public Types
typedef std::pair< int, int >	CellIndex
typedef DPosition< 2 >	Point

Public Member Functions
	ClusteringGrid (const std::vector< double > &grid_spacing_x, const std::vector< double > &grid_spacing_y)
	constructor taking two vectors More...
std::vector< double >	getGridSpacingX () const
	returns grid spacing in x direction More...
std::vector< double >	getGridSpacingY () const
	returns grid spacing in y direction More...
void	addCluster (const CellIndex &cell_index, const int &cluster_index)
	adds a cluster to this grid cell More...
void	removeCluster (const CellIndex &cell_index, const int &cluster_index)
	removes a cluster from this grid cell and removes the cell if no other cluster left More...
void	removeAllClusters ()
	removes all clusters from this grid (and hence all cells) More...
std::list< int >	getClusters (const CellIndex &cell_index) const
	returns clusters in this grid cell More...
CellIndex	getIndex (const Point &position) const
	returns grid cell index (i,j) for the positions (x,y) More...
bool	isNonEmptyCell (const CellIndex &cell_index) const
	checks if there are clusters at this cell index More...
int	getCellCount () const
	returns number of grid cells occupied by one or more clusters More...

Private Attributes
const std::vector< double >	grid_spacing_x_
	spacing of the grid in x and y direction More...
const std::vector< double >	grid_spacing_y_
std::pair< double, double >	range_x_
	[min, max] of the grid in x and y direction More...
std::pair< double, double >	range_y_
std::map< CellIndex, std::list< int > >	cells_
	grid cell index mapped to a list of clusters in it More...

Detailed Description

data structure to store 2D data to be clustered e.g. (m/z, retention time) coordinates from multiplex filtering

See also

LocalClustering

Member Typedef Documentation

CellIndex

typedef std::pair<int,int> CellIndex

coordinates of a grid cell

Point

typedef DPosition<2> Point

coordinates in x-y-plane

Constructor & Destructor Documentation

ClusteringGrid()

ClusteringGrid	(	const std::vector< double > &	grid_spacing_x,
		const std::vector< double > &	grid_spacing_y
	)

constructor taking two vectors

Parameters

grid_spacing_x	grid spacing in x direction
grid_spacing_y	grid spacing in y direction

Note

Vectors are assumed to be sorted.

Member Function Documentation

addCluster()

void addCluster	(	const CellIndex &	cell_index,
		const int &	cluster_index
	)

adds a cluster to this grid cell

Parameters

cell_index	cell index (i,j) on the grid
cluster_index	index of the cluster in the cluster list

Referenced by GridBasedClustering< Metric >::cluster(), GridBasedClustering< Metric >::extendClustersY(), and GridBasedClustering< Metric >::init_().

getCellCount()

int getCellCount

(

)

const

returns number of grid cells occupied by one or more clusters

Returns

number of non-empty cells

getClusters()

std::list<int> getClusters

(

const CellIndex &

cell_index

)

const

returns clusters in this grid cell

Parameters

cell_index

cell index (i,j) on the grid

Returns

list of cluster indices (from the list of clusters) which are centred in this cell

Referenced by GridBasedClustering< Metric >::extendClustersY(), and GridBasedClustering< Metric >::findNearestNeighbour_().

getGridSpacingX()

std::vector<double> getGridSpacingX

(

)

const

returns grid spacing in x direction

Referenced by GridBasedClustering< Metric >::extendClustersY().

getGridSpacingY()

std::vector<double> getGridSpacingY

(

)

const

returns grid spacing in y direction

Referenced by GridBasedClustering< Metric >::extendClustersY().

getIndex()

CellIndex getIndex

(

const Point &

position

)

const

returns grid cell index (i,j) for the positions (x,y)

Parameters

position

coordinates (x,y) on the grid

Returns

cell index (i,j) of the cell in which (x,y) lies

Referenced by GridBasedClustering< Metric >::cluster(), GridBasedClustering< Metric >::extendClustersY(), GridBasedClustering< Metric >::findNearestNeighbour_(), and GridBasedClustering< Metric >::init_().

isNonEmptyCell()

bool isNonEmptyCell

(

const CellIndex &

cell_index

)

const

checks if there are clusters at this cell index

Parameters

cell_index

cell index (i,j) on the grid

Returns

true if there are clusters in this cell

Exceptions

Exception::IllegalArgument	if the coordinates (x,y) lie outside the grid.
Exception::InvalidValue	if one of the two indices is negative.

Referenced by GridBasedClustering< Metric >::extendClustersY(), and GridBasedClustering< Metric >::findNearestNeighbour_().

removeAllClusters()

void removeAllClusters

(

)

removes all clusters from this grid (and hence all cells)

removeCluster()

void removeCluster	(	const CellIndex &	cell_index,
		const int &	cluster_index
	)

removes a cluster from this grid cell and removes the cell if no other cluster left

Parameters

cell_index	cell index (i,j) on the grid
cluster_index	index of the cluster in the cluster list

Referenced by GridBasedClustering< Metric >::cluster(), GridBasedClustering< Metric >::extendClustersY(), and GridBasedClustering< Metric >::init_().

Member Data Documentation

cells_

std::map<CellIndex, std::list<int> > cells_

private

grid cell index mapped to a list of clusters in it

grid_spacing_x_

const std::vector<double> grid_spacing_x_

private

spacing of the grid in x and y direction

grid_spacing_y_

const std::vector<double> grid_spacing_y_

private

range_x_

std::pair<double,double> range_x_

private

[min, max] of the grid in x and y direction

range_y_

std::pair<double,double> range_y_

private