[GRASS-user] [GRASS-dev] What is the meaning of output from i.cluster

Mon Mar 25 21:20:54 PDT 2013

Thanks for the explanation Nikos.

But see below.

Michael
____________________
C. Michael Barton
Director, Center for Social Dynamics & Complexity 
Professor of Anthropology, School of Human Evolution & Social Change
Arizona State University

voice: 	480-965-6262 (SHESC), 480-727-9746 (CSDC)
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www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu

On Mar 25, 2013, at 5:34 PM, Nikos Alexandris <nik at nikosalexandris.net>
 wrote:

> Hello Michael,
> 
> Michael Barton wrote:
>> i.cluster produces a text output file that looks like this (for the landsat
>> 2000 images from the nc_spm_08 demo data set).
> 
>> #produced by i.cluster
>> #Class 1
>> 247
>> 69.1174 50.3603 41.3482 18.9514 17.4534 117.049 14.2105
>> 10.5837
>> 12.6608 22.8737
>> 17.1663 29.6708 45.1628
>> 7.36345 9.28993 16.6389 47.4367
>> 9.14573 9.22619 16.9756 47.1115 70.631
>> 7.75037 6.67348 10.1294 13.043 14.9941 17.5505
>> 7.63372 6.74497 12.0565 27.4981 43.3025 12.0629 30.7522
>> #Class 2
>> 2059
>> 70.0257 53.2035 46.205 61.085 61.5935 121.271 35.6688
>> 9.28262
>> 7.5725 9.99696
>> 11.3514 11.8868 22.0678
>> -6.02017 -0.713125 -9.81723 54.7357
>> -1.33501 2.43359 2.91134 15.8135 40.1529
>> 4.98865 4.49973 6.3419 -2.73927 -1.77851 11.3745
>> 5.31077 6.34246 10.6505 -4.60692 19.1398 3.18893 19.0243
>> 
>> [more for the other classes]
>> 
>> So what does this mean? There is no clear explanation of this in the manual,
>> and there are no variable names in the output.
>> 
>> I am guessing that
>> line 1 is possibly the number of pixels in the class

If so, the report should be:

Number of pixels in class: #####

> 
> I think you are right.
> 
>> line 2 is the cluster mean within each original raster input file (landsat
>> maps bands in this case)

And here, there should be a headings line and explanation something like this:

              map 1     map 2      map 3    map 4
Mean values: ######### ######### ######### #########

> 
> Yes.
> 
> *Note,* however, as previously well-explained by Moritz Lennert 
> (http://lists.osgeo.org/pipermail/grass-user/2012-October/066046.html):
> 
> --%<---
> i.cluster does not cluster all pixels, but only a sample (see parameter 
> 'sample'). The result of that clustering is not that all pixels are assigned 
> to a given cluster, but only that you have signatures that are 
> "representative" of a given cluster. If you run i.cluster on the same data 
> asking for the same number of classes, but with different sample sizes, you 
> will probably get slightly different signatures for each cluster at each run.

This needs to be in the manual rather than lost in a email

> --->%--
> 
>> The remaining lines are some kind of matrix. If a correlation matrix, I
>> don't understand why the diagonal is not 1--or at least the biggest number
>> for the relevant input maps.
>> Any explanation?
> 
> It is a variance(=the diagonal)-covariance matrix(=the off diagonal elements) 
> as described in the manual and mentioned else-where in past threads in the 
> list.

So the diagonal values = the variance in the values for that band in a cluster
The off diagonal values are the covariance between the band values for a cluster

Right? This is not in the manual but should be. IMHO, it should also be in the report output something like this.

Variance (diagonal) and covariance scores (off-diagonal)

        map 1     map 2      map 3    map 4
map 1 ######### 
map 1 ######### ######### 
map 1 ######### ######### ######### 
map 1 ######### ######### ######### #########

> 
> As previously noted by Hamish Bowman, let's have a look at 
> (http://lists.osgeo.org/pipermail/grass-user/2008-June/045108.html): 

I'm not sure what the following means. Sorry. If it is necessary to delve into the source code to find out what is being reported in the report, the report needs to be changed so that is not necessary. 

It would also be useful to know how much each map contributes to each cluster.

> 
> --%<---
> I_fopen_signature_file_new() found in lib/imagery/sigfile.c
> --->%--
> 
> but I can't find/understand if it helps.
> 
> What about looking at
> 
> a) /geo/osgeo/src/grass_trunk/lib/python/ctypes/OBJ.x86_64-unknown-linux-
> gnu/imagery.py
> 
> or
> 
> b) /geo/osgeo/src/grass_trunk/lib/python/ctypes/OBJ.x86_64-unknown-linux-
> gnu/cluster.py:
> 
> --%<--- a) lines 756-781 / b) lines 579-600 --%<---
> # /geo/osgeo/src/grass_trunk/dist.x86_64-unknown-linux-
> gnu/include/grass/imagery.h: 51
> class struct_One_Sig(Structure):
>    pass
> 
> struct_One_Sig.__slots__ = [
>    'desc',
>    'npoints',
>    'mean',
>    'var',
>    'status',
>    'r',
>    'g',
>    'b',
>    'have_color',
> ]
> struct_One_Sig._fields_ = [
>    ('desc', c_char * 100),
>    ('npoints', c_int),
>    ('mean', POINTER(c_double)),
>    ('var', POINTER(POINTER(c_double))),
>    ('status', c_int),
>    ('r', c_float),
>    ('g', c_float),
>    ('b', c_float),
>    ('have_color', c_int),
> ]
> --->%--
> 
> ?
> 
> And then, of course, at
> /geo/osgeo/src/grass_trunk/dist.x86_64-unknown-linux-
> gnu/include/grass/imagery.h:
> 
> --%<---
> struct One_Sig
> {
>    char desc[100];
>    int npoints;
>    double *mean;		/* one mean for each band */
>    double **var;		/* covariance band-band   */
>    int status;		/* may be used to 'delete' a signature */
>    float r, g, b;		/* color */
>    int have_color;
> };
> -->%---
> 
> Best, Nikos