adding r.li to GRASS

[HamishB]

Hi,

shall r.li be added to grass6 cvs? It is a modernization of the r.le
modules for "landscape indices" by Paolo Cavallini & team*.

http://www.faunalia.it/download/r_li/

* Claudio Porta and Lucio Davide Spano, students of Computer Science
University of Pisa (Italy). Commission from Faunalia Pontedera (PI)


It would be nice if it had a developer-"champion" or primary supporter
who could be in charge of commiting patches from the authors, etc.
This is well outside my field of study so I will not volunteer for the
job, nor do I have a strong opinion about the general usefulness of
these modules. (I can be the one to do the first commit to CVS though,
if desired)

The authors seem to think it is ready for CVS, a quick glance at the
code indicates that they are in the GRASS "style" and conform to
SUBMITTING guidelines.


Perhaps run indent on them first,

 $ indent -nbad -bap -bbb -nbbo -nbc -br -bli1 -bls -cbi0 -ncdb -nce \
    -ci4 -cli0 -ncs -d0 -di0 -fc1 -nfca -hnl -i4 -ip4 -l80 -lc80 -lp \
    -npcs -pi4 -nprs -npsl -sbi0 -sc -nsob -ss -ts8  main.c



?,
Hamish

[Paolo Cavallini]

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Hash: SHA1

There is still some bugfixing and minor editings to be done, but it
should be almost ready.
pc

Hamish ha scritto:

> Hi,
>
> shall r.li be added to grass6 cvs? It is a modernization of the r.le
> modules for "landscape indices" by Paolo Cavallini & team*.
>
> http://www.faunalia.it/download/r_li/
>
> * Claudio Porta and Lucio Davide Spano, students of Computer Science
> University of Pisa (Italy). Commission from Faunalia Pontedera (PI)
>
>
> It would be nice if it had a developer-"champion" or primary supporter
> who could be in charge of commiting patches from the authors, etc.
> This is well outside my field of study so I will not volunteer for the
> job, nor do I have a strong opinion about the general usefulness of
> these modules. (I can be the one to do the first commit to CVS though,
> if desired)
>
> The authors seem to think it is ready for CVS, a quick glance at the
> code indicates that they are in the GRASS "style" and conform to
> SUBMITTING guidelines.
>
>
> Perhaps run indent on them first,
>
>  $ indent -nbad -bap -bbb -nbbo -nbc -br -bli1 -bls -cbi0 -ncdb -nce \
>     -ci4 -cli0 -ncs -d0 -di0 -fc1 -nfca -hnl -i4 -ip4 -l80 -lc80 -lp \
>     -npcs -pi4 -nprs -npsl -sbi0 -sc -nsob -ss -ts8  main.c
>
>
>
> ?,
> Hamish
>

- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[Michael Barton]

I agree with putting them into the cvs. I don't know much about C program
committing guides. But the functionality of r.li would be very welcome by
people using GRASS for ecological analysis.

Michael
__________________________________________
Michael Barton, Professor of Anthropology
School of Human Evolution & Social Change
Center for Social Dynamics and Complexity
Arizona State University

phone: [phone]
fax: [phone]
www: http://www.public.asu.edu/~cmbarton

> From: Hamish <[hidden email]>
> Date: Thu, 2 Nov 2006 18:01:01 +1300
> To: <[hidden email]>
> Cc: Paolo Cavallini <[hidden email]>
> Subject: [GRASS-PSC] adding r.li to GRASS
>
> Hi,
>
> shall r.li be added to grass6 cvs? It is a modernization of the r.le
> modules for "landscape indices" by Paolo Cavallini & team*.
>
> http://www.faunalia.it/download/r_li/
>
> * Claudio Porta and Lucio Davide Spano, students of Computer Science
> University of Pisa (Italy). Commission from Faunalia Pontedera (PI)
>
>
> It would be nice if it had a developer-"champion" or primary supporter
> who could be in charge of commiting patches from the authors, etc.
> This is well outside my field of study so I will not volunteer for the
> job, nor do I have a strong opinion about the general usefulness of
> these modules. (I can be the one to do the first commit to CVS though,
> if desired)
>
> The authors seem to think it is ready for CVS, a quick glance at the
> code indicates that they are in the GRASS "style" and conform to
> SUBMITTING guidelines.
>
>
> Perhaps run indent on them first,
>
>  $ indent -nbad -bap -bbb -nbbo -nbc -br -bli1 -bls -cbi0 -ncdb -nce \
>     -ci4 -cli0 -ncs -d0 -di0 -fc1 -nfca -hnl -i4 -ip4 -l80 -lc80 -lp \
>     -npcs -pi4 -nprs -npsl -sbi0 -sc -nsob -ss -ts8  main.c
>
>
>
> ?,
> Hamish
>
> _______________________________________________
> grass-psc mailing list
> [hidden email]
> http://grass.itc.it/mailman/listinfo/grass-psc

[Markus Neteler-3]

Hi,

so far I have "guided" the r.li people and also verified their last version
which was sent offlist to me. I indicated a couple of points, more or less
along the lines of Hamish's comments.
We basically have to enforce the rules in SUBMITTING *before* code
reaches the CVS. But it's not much which has to be done, lot's of small
issues (done in an afternoon probably).

Concerning functionality, I didn't do tests. In general, each command
in GRASS should come with test cases to feed Soeren's test suite.

Markus

Michael Barton wrote on 11/02/2006 06:33 PM:

> I agree with putting them into the cvs. I don't know much about C program
> committing guides. But the functionality of r.li would be very welcome by
> people using GRASS for ecological analysis.
>
> Michael
> __________________________________________
> Michael Barton, Professor of Anthropology
> School of Human Evolution & Social Change
> Center for Social Dynamics and Complexity
> Arizona State University
>
> phone: [phone]
> fax: [phone]
> www: http://www.public.asu.edu/~cmbarton
>  

[Paolo Cavallini]

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Hash: SHA1

Will do our best to fix these issues.
All the best.
pc

Markus Neteler ha scritto:

> Hi,
>
> so far I have "guided" the r.li people and also verified their last version
> which was sent offlist to me. I indicated a couple of points, more or less
> along the lines of Hamish's comments.
> We basically have to enforce the rules in SUBMITTING *before* code
> reaches the CVS. But it's not much which has to be done, lot's of small
> issues (done in an afternoon probably).
>
> Concerning functionality, I didn't do tests. In general, each command
> in GRASS should come with test cases to feed Soeren's test suite.
>
> Markus
>
> Michael Barton wrote on 11/02/2006 06:33 PM:
>> I agree with putting them into the cvs. I don't know much about C program
>> committing guides. But the functionality of r.li would be very welcome by
>> people using GRASS for ecological analysis.
>>
>> Michael
>> __________________________________________
>> Michael Barton, Professor of Anthropology

- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[HamishB]

Scott Mitchell wrote:

>
> I'd be very happy to see r.li added.  I think there is general  
> utility to this - I get asked about the state of "LE" modules in  
> GRASS fairly regularly - there are lots of landscape ecology grad  
> students around here, and William Baker's programs are generally if  
> only vaguely familiar to them -- even before being exposed to me here
> at Carleton, many of the grad students coming into our labs have  
> heard of GRASS because of the old r.le.  I also know of groups at my  
> former workplace that still do most of their work in grass5 due to a  
> combination of continuing reliance on the old sites capabilities, and
> wanting to use r.le - the sites stuff is pretty much possible in  
> grass6 now so it's just r.le holding them back.

Due to recent fixes, the r.le modules should be fully functional in
GRASS 6.2.0 and 6.3-cvs.


> Between Paolo's group's work and William Baker looking at this again,
> it's great to see so much renewed activity.
>
> I can take some responsibility for commits, if that's what it takes.
> I'll try out the current version today on my own system.

That's great.


Hamish

[HamishB]

[re SUBMITTING rules, not r.li in particular]

Markus Neteler wrote:
> We basically have to enforce the rules in SUBMITTING *before* code
> reaches the CVS.
..
> In general, each command in GRASS should come with test cases to feed
> Soeren's test suite.


and full documentation (including examples)...


I don't mind not allowing new things into CVS without all three of these
requirements satisfied, as the probability that they will be done later
is very low + shifts burden on to the core developers.


Hamish

[Paolo Cavallini]

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is there anybody willing to help for test cases etc?
All the best.
pc

Hamish ha scritto:

> [re SUBMITTING rules, not r.li in particular]
>
> Markus Neteler wrote:
>> We basically have to enforce the rules in SUBMITTING *before* code
>> reaches the CVS.
> ..
>> In general, each command in GRASS should come with test cases to feed
>> Soeren's test suite.
>
>
> and full documentation (including examples)...
>
>
> I don't mind not allowing new things into CVS without all three of these
> requirements satisfied, as the probability that they will be done later
> is very low + shifts burden on to the core developers.
>
>
> Hamish

- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[Massimiliano Cannata]

I agree with all the previous mail in thread.
Just one note:
I think that references should always be included in the
description.html to help people understanding the implemented equations.

Cheers,
Massimiliano

Paolo Cavallini wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> is there anybody willing to help for test cases etc?
> All the best.
> pc
>
> Hamish ha scritto:
>  
>> [re SUBMITTING rules, not r.li in particular]
>>
>> Markus Neteler wrote:
>>    
>>> We basically have to enforce the rules in SUBMITTING *before* code
>>> reaches the CVS.
>>>      
>> ..
>>    
>>> In general, each command in GRASS should come with test cases to feed
>>> Soeren's test suite.
>>>      
>> and full documentation (including examples)...
>>
>>
>> I don't mind not allowing new things into CVS without all three of these
>> requirements satisfied, as the probability that they will be done later
>> is very low + shifts burden on to the core developers.
>>
>>
>> Hamish
>>    
> - --
> Paolo Cavallini
> email+jabber: [hidden email]
> www.faunalia.it
> Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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> =DVCT
> -----END PGP SIGNATURE-----
>
> _______________________________________________
> grass-psc mailing list
> [hidden email]
> http://grass.itc.it/mailman/listinfo/grass-psc
>
>
>  

--

Dr. Eng. Massimiliano Cannata
Responsabile Area Geomatica
Istituto Scienze della Terra
Scuola Universitaria Professionale della Svizzera Italiana
Via Trevano, c.p. 72
CH-6952 Canobbio-Lugano
Tel: [phone]
Fax [phone]

[Paolo Cavallini]

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right.
the references are the same as for r.le: for the time being, we just
replicated the same indices.
pc

Massimiliano Cannata ha scritto:
> I agree with all the previous mail in thread.
> Just one note:
> I think that references should always be included in the
> description.html to help people understanding the implemented equations.
>
> Cheers,
> Massimiliano
- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[Paolo Cavallini]

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Hi all.
Some speed testing; on the same data set:
rows:       451
cols:       652
cells:      294052
moving window 10x10
Shannon analysis is almost 3 times faster:

r.li.shannon
real    7m41.768s
user    0m43.475s
sys     1m15.213s

r.le
real    21m47.613s
user    13m56.812s
sys     2m41.030s

AFAICU, IO (disk access) time is the limiting factor.

All the best.
pc
- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[Brad Douglas]

It is very important that references be included, especially when
algorithms or methodologies are involved.

On Fri, 2006-11-03 at 09:27 +0100, Massimiliano Cannata wrote:
> I agree with all the previous mail in thread.
> Just one note:
> I think that references should always be included in the
> description.html to help people understanding the implemented equations.


--
Brad Douglas <rez touchofmadness com>                    KB8UYR/6
Address: 37.493,-121.924 / WGS84    National Map Corps #TNMC-3785

[Markus Neteler-2]

Paolo, Serena,

I have now submitted your latest version to CVS in
raster/r.li/ to simplify the further development.

A few remaining things should be done soon:
- add relevant references
- change AUTHORS as indicated by you (offlist, see below)
- fix static local r.li.daemon library "libr_li.a" to dynamic
 (see raster/simwe/simlib/ how to do that)
- fix "clean" target in r.li.daemon (ipc binary and library)

So far I didn't add r.li yet to raster/Makefile .

We should also discuss CVS write access for the future r.li
development.

Thanks again for the r.li development
and congrats!

Markus

On 11/6/06, Paolo Cavallini <[hidden email]> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Please note: the credits should be modified.
> AUTHORS
>  Claudio Porta, Lucio Davide Spano, and Serena Pallecchi students of
> Computer Science University of Pisa (Italy).
>  Commission from Faunalia Pontedera (PI) www.faunalia.it
>  This program is free software under the GPL (>=v2) Read the COPYING
> file that comes with GRASS for details.
> BUGS
>  Please send bugs reports to [hidden email],
> [hidden email], [hidden email], [hidden email]
>
> For style, feel free to modify it.
> pc

[Michael Barton]

Once this is all done, we need to decide if it should replace r.le in the
menu, and if so what are the specific modules that need to be run. Also,
does this **require** an interactive xterm like parts of r.le?

Michael
__________________________________________
Michael Barton, Professor of Anthropology
School of Human Evolution & Social Change
Center for Social Dynamics & Complexity
Arizona State University

phone: [phone]
fax: [phone]
www: http://www.public.asu.edu/~cmbarton

> From: Markus Neteler <[hidden email]>
> Date: Mon, 6 Nov 2006 16:00:51 +0100
> To: Paolo Cavallini <[hidden email]>
> Cc: <[hidden email]>, Serena Pallecchi <[hidden email]>
> Subject: Re: [GRASS-PSC] adding r.li to GRASS
>
> Paolo, Serena,
>
> I have now submitted your latest version to CVS in
> raster/r.li/ to simplify the further development.
>
> A few remaining things should be done soon:
> - add relevant references
> - change AUTHORS as indicated by you (offlist, see below)
> - fix static local r.li.daemon library "libr_li.a" to dynamic
>  (see raster/simwe/simlib/ how to do that)
> - fix "clean" target in r.li.daemon (ipc binary and library)
>
> So far I didn't add r.li yet to raster/Makefile .
>
> We should also discuss CVS write access for the future r.li
> development.
>
> Thanks again for the r.li development
> and congrats!
>
> Markus
>
> On 11/6/06, Paolo Cavallini <[hidden email]> wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Please note: the credits should be modified.
>> AUTHORS
>>  Claudio Porta, Lucio Davide Spano, and Serena Pallecchi students of
>> Computer Science University of Pisa (Italy).
>>  Commission from Faunalia Pontedera (PI) www.faunalia.it
>>  This program is free software under the GPL (>=v2) Read the COPYING
>> file that comes with GRASS for details.
>> BUGS
>>  Please send bugs reports to [hidden email],
>> [hidden email], [hidden email], [hidden email]
>>
>> For style, feel free to modify it.
>> pc
>
> _______________________________________________
> grass-psc mailing list
> [hidden email]
> http://grass.itc.it/mailman/listinfo/grass-psc

[Paolo Cavallini]

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Hash: SHA1



Michael Barton ha scritto:
> Once this is all done, we need to decide if it should replace r.le in the
> menu, and if so what are the specific modules that need to be run.

As for now, r.li calculates less indices than r.le, so it cannot be
considered a full replacement.

> Also,
> does this **require** an interactive xterm like parts of r.le?

It shouldn't, AFAIK.
pc
- --
Paolo Cavallini
email+jabber: [hidden email]
www.faunalia.it
Piazza Garibaldi 5 - 56025 Pontedera (PI), Italy   Tel: [phone]
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[Markus Neteler-2]

Let me suggest to move these technical questions back to the
dev list (I should have done so, too, sorry).

Markus

On 11/6/06, Michael Barton <[hidden email]> wrote:

> Once this is all done, we need to decide if it should replace r.le in the
> menu, and if so what are the specific modules that need to be run. Also,
> does this **require** an interactive xterm like parts of r.le?
>
> Michael
> __________________________________________
> Michael Barton, Professor of Anthropology
> School of Human Evolution & Social Change
> Center for Social Dynamics & Complexity
> Arizona State University
>
> phone: [phone]
> fax: [phone]
> www: http://www.public.asu.edu/~cmbarton
>
>
>
> > From: Markus Neteler <[hidden email]>
> > Date: Mon, 6 Nov 2006 16:00:51 +0100
> > To: Paolo Cavallini <[hidden email]>
> > Cc: <[hidden email]>, Serena Pallecchi <[hidden email]>
> > Subject: Re: [GRASS-PSC] adding r.li to GRASS
> >
> > Paolo, Serena,
> >
> > I have now submitted your latest version to CVS in
> > raster/r.li/ to simplify the further development.
> >
> > A few remaining things should be done soon:
> > - add relevant references
> > - change AUTHORS as indicated by you (offlist, see below)
> > - fix static local r.li.daemon library "libr_li.a" to dynamic
> >  (see raster/simwe/simlib/ how to do that)
> > - fix "clean" target in r.li.daemon (ipc binary and library)
> >
> > So far I didn't add r.li yet to raster/Makefile .
> >
> > We should also discuss CVS write access for the future r.li
> > development.
> >
> > Thanks again for the r.li development
> > and congrats!
> >
> > Markus