Name

sxhac_clustering - Hierarchical agglomerative clustering

Usage

Usage in command lines

sxhac_clustering.py stack dendoname <maskfile> --link=kind_of_linkage --dist=kind_of_distance --dissimilar

Usage in python programming

HAC_clustering(stack, dendoname, maskname, link, dist)

Example:

sxhac_clustering.py stable_ave.hdf dendo mask2d_13.hdf --link='complete' --dist='SqEuc' --dissimilar

Input

stack
the input stack of images
maskname
optional mask file to be used
dendoname
the seed name to export the dendogram
  • The parameters preceded with -- are optional and default values are given in parenthesis.

  • link
    Kind of linkage, single, complete or average (default single)
    dist

    Kind of distance, SqEuc or CCC (default SqEuc)

    dissimilar
    Change the distance value to the negative value, meaning not agglomerate the similar object but the dissimilar

    Output

    dendoname.txt
    depends on the seed name chose (seed name + .txt), text file which contains the threshold according the number of groups
    dendoname.dendo
    depends on the seed name chose (seed name + .dendo), file which contains the dendogram

    Description

    This program is a wrap from a part of python-cluster to sparx. This function use different kind of distance:

    SqEuc - squared Euclidean distance

    CCC - cross correlation coefficient

    The program returns two files. The first dendoname.txt contains the number of groups according to the cutting threshold value of the dendogram. This file is to help the user to know what number of groups is saved in the second file dendoname.dendo which contains the dendogram structure. To get the averages for a number of groups select in dendoname.txt use the function sxhac_averages.py.

    Reference

    python-cluster, Licence LGPL copyright (c) 2006 Michel Albert, http://python-cluster.sourceforge.net

    Author / Maintainer

    Julien Bert

    Keywords

    category 1
    APPLICATIONS

    Files

    applications.py

    statistics.py (python-cluster)

    See also

    sxhac_averages

    Maturity

    beta
    works for author, often works for others.

    Bugs

    None. It is perfect.

    sxhac_clustering (last edited 2013-07-01 13:12:46 by localhost)