IMP::kmeans Namespace Reference

Interface to the GPL k-means clustering library More...

Detailed Description

Interface to the GPL k-means clustering library

This module allows clustering of multi-dimensional data points using the k-means algorithms, based on the GPL kmeans library.

Info

Author(s): Barak Raveh

Maintainer: barakr

License: GPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• See main IMP papers list.

Classes
class	KMeans

Enumerations
enum	KM_ALG_TYPE { KM_LLOYDS = 1, KM_LOCAL_SWAP = 2, KM_LOCAL_EZ_HYBRID = 3, KM_HYBRID = 4 }

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Enumeration Type Documentation

enum IMP::kmeans::KM_ALG_TYPE

Different k-means algorithm variants that are implemented in the library, see also http://www.cs.umd.edu/~mount/Projects/KMeans/

Enumerator
KM_LLOYDS	Repeatedly applies Lloyd's algorithm with randomly sampled starting points.
KM_LOCAL_SWAP	A local search heuristic, which works by performing swaps between existing centers and a set of candidate centers.
KM_LOCAL_EZ_HYBRID	A simple hybrid algorithm, which does one swap followed by some number of iterations of Lloyd's.
KM_HYBRID	A more complex hybrid of Lloyd's and Swap, which performs some number of swaps followed by some number of iterations of Lloyd's algorithm. To avoid getting trapped in local minima, an approach similar to simulated annealing is included as well.

Definition at line 35 of file kmeans/KMeans.h.

Function Documentation

std::string IMP::kmeans::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

std::string IMP::kmeans::get_example_path

(

std::string

file_name

)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

 IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",
model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.