sxhac_clustering - Hierarchical agglomerative clustering
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)
sxhac_clustering.py stable_ave.hdf dendo mask2d_13.hdf --link='complete' --dist='SqEuc' --dissimilar
- the input stack of images
- optional mask file to be used
- the seed name to export the dendogram
The parameters preceded with -- are optional and default values are given in parenthesis.
- depends on the seed name chose (seed name + .txt), text file which contains the threshold according the number of groups
- depends on the seed name chose (seed name + .dendo), file which contains the dendogram
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.
python-cluster, Licence LGPL copyright (c) 2006 Michel Albert, http://python-cluster.sourceforge.net
Author / Maintainer
- category 1
- works for author, often works for others.
None. It is perfect.