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
std::vector< double >	getGridSpacingX () const
	returns grid spacing in x direction
std::vector< double >	getGridSpacingY () const
	returns grid spacing in y direction
void	addCluster (const CellIndex &cell_index, const int &cluster_index)
	adds a cluster to this grid cell
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
void	removeAllClusters ()
	removes all clusters from this grid (and hence all cells)
std::list< int >	getClusters (const CellIndex &cell_index) const
	returns clusters in this grid cell
CellIndex	getIndex (const Point &position) const
	returns grid cell index (i,j) for the positions (x,y)
bool	isNonEmptyCell (const CellIndex &cell_index) const
	checks if there are clusters at this cell index
int	getCellCount () const
	returns number of grid cells occupied by one or more clusters

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

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

[in]	grid_spacing_x	grid spacing in x direction
[in]	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

[in]	cell_index	cell index (i,j) on the grid
[in]	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

[in]

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

[in]

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

[in]

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

[in]	cell_index	cell index (i,j) on the grid
[in]	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