Details Ticket 4794


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Serial Number 4794
Subject r.thin
Area grass6
Queue grass
Requestors devaux@ensam.inra.fr
Owner none
Status resolved
Last User Contact Tue Aug 15 01:29:47 2006 (2 yr ago)
Current Priority 30
Final Priority 70
Due No date assigned
Last Action Tue Aug 15 01:29:47 2006 (2 yr ago)
Created Wed Jul 5 17:25:00 2006 (2 yr ago)

Transaction History Ticket 4794


Wed, Jul 5 2006 17:25:00    Request created by guest  
Subject: r.thin

Hi, I'm using r.thin command, and it seems that it changes Nodata value cells
of the original raster (surrounding cells obtained after the gereference
operation of à scanned map) to the value 1. Hence, I get an error message when
I try to use r.to.vect command because of these surrounding cells that have
the value 1 instead of Nodata and that constitute an area instead of a simple
line.

Does soemone already had this problem, how can it be avoid, is it possible to
change nodata value to 0 for example (Nodata is not allowed in the value to
recode with reclass command)?

Thanks 
Wed, Jul 5 2006 20:17:29    Mail sent by msieczka  
Hi

> Hi, I'm using r.thin command, and it seems that it changes Nodata value
> cells of the original raster (surrounding cells obtained after the
> gereference operation of à scanned map) to the value 1

Could you put screenshots that explain your problem (and the input and
problematic output data if possible) somewhere? What was your r.thin syntax
exactly?

What Grass version? Platform?

> Does soemone already had this problem,

I haven't, I think.

> is it possible to change nodata value to 0 for example

r.null?

Maciek
Thu, Jul 6 2006 00:08:45    Mail sent by mneteler  
Hi,

r.thin works (in GRASS 6.1-CVS). Quick test:

GRASS 6.1.cvs (spearfish60): > g.region -dp
projection: 1 (UTM)
zone:       13
datum:      nad27
ellipsoid:  clark66
north:      4928010
south:      4913700
west:       589980
east:       609000
nsres:      30
ewres:      30
rows:       477
cols:       634

r.thin fields out=fields_skeleton
File fields -- 477 rows X 634 columns
Bounding box:  l = 3, r = 635, t = 2, b = 468
   Pass number 1
        Deleted 5632  pixels
   Pass number 2
...
   Pass number 81
        Deleted 0  pixels
Thinning completed successfully.
Output file 477 rows X 634 columns
Window 477 rows X 634 columns

d.mon x0
d.rast fields_skeleton
# -> looks ok, no data are present

r.univar fields_skeleton
 100%
total null and non-null cells: 302418
total null cells: 299926  <-- no data are there !

Of the non-null cells:
----------------------
n: 2492
minimum: 1
maximum: 63
range: 62
mean: 44.7364
standard deviation: 21.6878
variance: 470.363
variation coefficient: 48.4792 %
sum: 111483

I suspect that the original map doesn't have NULL where
you think they should be. You can verify it with d.what.rast.

I  don't see a problem in r.thin (note that we fixed it in
April):
2006-04-04 17:07  markus
        * main.c: increased to 200 iterations default
2006-04-04 17:06  markus
        * thin_lines.c: fixed max iterations
2006-04-04 16:48  markus
        * local_proto.h, main.c, thin_lines.c: added iterations parameter.
        Added exit error message if failure. Fixed wording. Increased
        default iterations

Markus
Thu, Jul 6 2006 00:09:00    User changed to devaux@ensam.inra.fr by mneteler  
Thu, Jul 6 2006 00:09:24    Comments added by mneteler  
I have (hopefully) fixed the requestor's email address.

Markus
Fri, Jul 7 2006 12:01:19    Comments added by guest  
Sorry to answer so late,
I'm using Grass 6.O.1
I retry the r.thin command today on a subset of the original map and it worked
properly, so I retried on the original file and everything was fine....
I'm a little bit disturb because I used exactly the same commands when it
didn't work. At each path, the r.thin command deleted the same among of
pixels, and this number never decreased (around 13680)... It seems that at
each end of path, it filed the nodata pixel by 1, so at the next path, it has
to manage again this pixels... The previous result contained value Nodata, 1
and O instead of 1 and Nodata when it work properly like today.

I can't explain why it works today....

Thanks for the answer and sorry for the disturbance, I appologise, but I have
to say that I try to fixe it by myself during three days before writting this
mail.

 
Fri, Jul 7 2006 21:24:31    Area changed to grass6 by msieczka  
Fri, Jul 7 2006 21:30:48    Mail sent by msieczka  
No problem, thanks for getting back to us with a reply!

So you are saying is that r.thin once put zeros, instead of nulls, in the
output, but then on your other attempt with *exactly* same input and command
syntax you couldn't reproduce that? (Sorry for this dumb question, but I want
to make sure whether I understand you fully - we are both no English speakers
:D).

Maciek
Mon, Jul 10 2006 10:59:45    Comments added by guest  
I'll try to explain it better:
I georeference a raster, consequently, the original file turn a little bit,
and has some nodata values on its hedges...
I use r.thin function to vectorized fields boundaries. When it didn't work,
the operation erase the same among of pixels at each path and the number never
decrease at it should be in normal process. After 30 path, the process stop
even if the number of deleted pixels still huge (around 13000) and when I
checked pixels values of resulting raster under Qgis, or using r.report, I
have 1 and 0 pixels value but not any nodata value. Fields boundaries pixels
hold the value 1, background pixels hold the value 0 (instead of nodata in
normal process) and all the pixels of the hedges that held Nodata at the
beginning have now the value 1.
It seems that hedge pixels were filled with value 1 at the end of each path,
hence, at each path, the same among of pixels has to be deleted at each
path... I  think I change nothing (or perhaps à region stuff) during all
tries, I restarted several time my PC or Grass, so I can't really explain what
happened.

I hope these explanations could help.

Thanks

Nicolas
Mon, Jul 10 2006 14:34:55    Mail sent by msieczka  
OK. Anyway, you are sure the problem is solved now, right? So can I close the
report?

Maciek
Mon, Jul 10 2006 16:10:47    Mail sent by devaux@ensam.inra.fr  
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To Maciek Sieczka via RT <grass-bugs@intevation.de>
Subject Re: [bug #4794] (grass) r.thin
References <20060710123455.97C8F1005B8@lists.intevation.de>
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Maciek Sieczka via RT a écrit :
> OK. Anyway, you are sure the problem is solved now, right? So can I close the
> report?
>
> Maciek
>
>
> -------------------------------------------- Managed by Request Tracker
>
>
>   
I thought it was the case, and just to be sure I retry the command, and 
it is obviously not working. It works with one of my raster maps (the 
one I use the day it worked) but not on any other...

Here are some screen shots :
 
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > 
g.region rast=test_digit_rast2 -p
projection: 99 (Lambert Conformal Conic)
zone:       0
datum:      ntf
ellipsoid:  clark80
north:      1796728.83901369
south:      1792333.83901369
west:       662147.38021708
east:       666794.38021708
nsres:      1
ewres:      1
rows:       4395
cols:       4647

GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > 
r.report test_digit_rast2 units=c
r.stats:  100%
+-----------------------------------------------------------------------------+
|                         RASTER MAP CATEGORY 
REPORT                          |
|LOCATION: zone_de_travail                            Mon Jul 10 
15:04:45 2006|
|-----------------------------------------------------------------------------|
|          north: 1796728.83901369    east: 
666794.38021708                   |
|REGION    south: 1792333.83901369    west: 
662147.38021708                   |
|          res:                  1    res:                
1                   |
|-----------------------------------------------------------------------------|
|MASK:none                                                                  
|
|-----------------------------------------------------------------------------|
|MAP: (untitled) (test_digit_rast2 in 
clape)                                  |
|-----------------------------------------------------------------------------|
|                       Category Information                         
|    cell|
|#|description                                                       |   
count|
|-----------------------------------------------------------------------------|
|1|test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 
6361357|
|*|no data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
.|14062208|
|-----------------------------------------------------------------------------|
|TOTAL                                                               
|20423565|
+-----------------------------------------------------------------------------+
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > r.thin 
in=test_digit_rast2 out=thin_test_digit3
File test_digit_rast2 -- 4395 rows X 4647 columns
Bounding box:  l = 1157, r = 4364, t = 277, b = 3013
   Path number 1
        Deleted 11922  pixels
   Path number 2
        Deleted 11911  pixels
   Path number 3
        Deleted 11903  pixels
   Path number 4
        Deleted 11895  pixels
   Path number 5
        Deleted 11887  pixels
   Path number 6
        Deleted 11879  pixels
   Path number 7
        Deleted 11871  pixels
   Path number 8
        Deleted 11863  pixels
   Path number 9
        Deleted 11855  pixels
   Path number 10
        Deleted 11846  pixels
   Path number 11
        Deleted 11837  pixels
   Path number 12
        Deleted 11829  pixels
   Path number 13
        Deleted 11821  pixels
   Path number 14
        Deleted 11813  pixels
   Path number 15
        Deleted 11805  pixels
   Path number 16
        Deleted 11797  pixels
   Path number 17
        Deleted 11789  pixels
   Path number 18
        Deleted 11781  pixels
   Path number 19
        Deleted 11771  pixels
   Path number 20
        Deleted 11763  pixels
   Path number 21
        Deleted 11755  pixels
   Path number 22
        Deleted 11747  pixels
   Path number 23
        Deleted 11737  pixels
   Path number 24
        Deleted 11728  pixels
   Path number 25
        Deleted 11720  pixels
   Path number 26
        Deleted 11712  pixels
   Path number 27
        Deleted 11703  pixels
   Path number 28
        Deleted 11694  pixels
   Path number 29
        Deleted 11686  pixels
   Path number 30
        Deleted 11678  pixels
thinning completed successfully.
Output file 4395 rows X 4647 columns
Window 4395 rows X 4647 columns
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > 
r.report thin_test_digit3 units=c
r.stats:  100%
+-----------------------------------------------------------------------------+
|                         RASTER MAP CATEGORY 
REPORT                          |
|LOCATION: zone_de_travail                            Mon Jul 10 
15:53:35 2006|
|-----------------------------------------------------------------------------|
|          north: 1796728.83901369    east: 
666794.38021708                   |
|REGION    south: 1792333.83901369    west: 
662147.38021708                   |
|          res:                  1    res:                
1                   |
|-----------------------------------------------------------------------------|
|MASK:none                                                                  
|
|-----------------------------------------------------------------------------|
|MAP: (untitled) (thin_test_digit3 in 
clape)                                  |
|-----------------------------------------------------------------------------|
|                       Category Information                         
|    cell|
|#|description                                                       |   
count|
|-----------------------------------------------------------------------------|
|1| . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 
6007359|
|*|no data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
.|14416206|
|-----------------------------------------------------------------------------|
|TOTAL                                                               
|20423565|
+-----------------------------------------------------------------------------+
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > 
r.report rcl_parc units=c
r.stats:  100%
+-----------------------------------------------------------------------------+
|                         RASTER MAP CATEGORY 
REPORT                          |
|LOCATION: zone_de_travail                            Mon Jul 10 
15:04:10 2006|
|-----------------------------------------------------------------------------|
|          north: 1796728.83901369    east: 
666794.38021708                   |
|REGION    south: 1792333.83901369    west: 
662147.38021708                   |
|          res:                  1    res:                
1                   |
|-----------------------------------------------------------------------------|
|MASK:none                                                                  
|
|-----------------------------------------------------------------------------|
|MAP: (untitled) (rcl_parc in 
clape)                                          |
|-----------------------------------------------------------------------------|
|                       Category Information                         
|    cell|
|#|description                                                       |   
count|
|-----------------------------------------------------------------------------|
|0| . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .| 
5177024|
|1| . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .|  
105762|
|*|no data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
.|15140779|
|-----------------------------------------------------------------------------|
|TOTAL                                                               
|20423565|
+-----------------------------------------------------------------------------+
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > r.thin 
in=rcl_parc out=thin_rcl_parc_tot3 File rcl_parc -- 4395 rows X 4647 columns
Bounding box:  l = 865, r = 3241, t = 1377, b = 3815
   Path number 1
        Deleted 62050  pixels
   Path number 2
        Deleted 14208  pixels
   Path number 3
        Deleted 1129  pixels
   Path number 4
       Deleted 137  pixels
   Path number 5
        Deleted 69  pixels
   Path number 6
        Deleted 56  pixels
   Path number 7
        Deleted 46  pixels
   Path number 8
        Deleted 31  pixels
   Path number 9
        Deleted 18  pixels
   Path number 10
        Deleted 4  pixels
   Path number 11
        Deleted 0  pixels
thinning completed successfully.
Output file 4395 rows X 4647 columns
Window 4395 rows X 4647 columns

GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape > 
r.report thin_rcl_parc_tot3 units=c
r.stats:  100%
+-----------------------------------------------------------------------------+
|                         RASTER MAP CATEGORY 
REPORT                          |
|LOCATION: zone_de_travail                            Mon Jul 10 
16:01:50 2006|
|-----------------------------------------------------------------------------|
|          north: 1796728.83901369    east: 
666794.38021708                   |
|REGION    south: 1792333.83901369    west: 
662147.38021708                   |
|          res:                  1    res:                
1                   |
|-----------------------------------------------------------------------------|
|MASK:none                                                                  
|
|-----------------------------------------------------------------------------|
|MAP: (untitled) (thin_rcl_parc_tot3 in 
clape)                                |
|-----------------------------------------------------------------------------|
|                       Category Information                         
|    cell|
|#|description                                                       |   
count|
|-----------------------------------------------------------------------------|
|1| . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .|   
28014|
|*|no data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
.|20395551|
|-----------------------------------------------------------------------------|
|TOTAL                                                               
|20423565|
+-----------------------------------------------------------------------------+
GRASS 6.0.1 (zone_de_travail):~/Grassdata/zone_de_travail/clape >

If you have any idea or test to do in order to fix this problem...

Thanks




-- 
------------------------------------------------------------------------------
Nicolas DEVAUX
Maître de Conférence AgroM
Laboratoire d'étude des Interactions entre Sol, Agrosystème et Hydrosystème
UMR LISAH AgroM-INRA-IRD
Bat. 24
place Viala
34060 Montpellier cedex 1
tél : +33 0(4) 99 61 25 22
fax: +33 0(4) 67 63 26 14
email: devaux@ensam.inra.fr
http://sol.ensam.inra.fr/lisah/
------------------------------------------------------------------------------
Tue, Jul 11 2006 10:29:15    Mail sent by msieczka  
Nicolas,

I can see your are using Grass 6.01. It is an old version and doesn't include
fixes and enhacements committed to r.thin few weeks ago:

http://grass.itc.it/pipermail/grass-commit/2006-April/021429.html
http://grass.itc.it/pipermail/grass-commit/2006-April/021430.html
http://grass.itc.it/pipermail/grass-commit/2006-April/021431.html

Please try Gras 6.1 CVS (soon to be relesed as stable, I recommend it) an let
us now how it works.

http://grass.itc.it/download/index.php

You still haven't answered what system you are using - if you did, I could
*maybe* recommend an optimal way of installing 6.1.

Maciek
Tue, Jul 11 2006 10:46:46    Mail sent by devaux@ensam.inra.fr  
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To Maciek Sieczka via RT <grass-bugs@intevation.de>
Subject Re: [bug #4794] (grass) r.thin
References <20060711082915.98CE5100160@lists.intevation.de>
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Maciek Sieczka via RT a écrit :
> Nicolas,
>
> I can see your are using Grass 6.01. It is an old version and doesn't include
> fixes and enhacements committed to r.thin few weeks ago:
>
> http://grass.itc.it/pipermail/grass-commit/2006-April/021429.html
> http://grass.itc.it/pipermail/grass-commit/2006-April/021430.html
> http://grass.itc.it/pipermail/grass-commit/2006-April/021431.html
>
> Please try Gras 6.1 CVS (soon to be relesed as stable, I recommend it) an let
> us now how it works.
>
> http://grass.itc.it/download/index.php
>
> You still haven't answered what system you are using - if you did, I could
> *maybe* recommend an optimal way of installing 6.1.
>
> Maciek
>
>
> -------------------------------------------- Managed by Request Tracker
>
>
>   

Maciek, I really appreciate the time you spend for this probelm...
I'm using Ubuntu 6.06 LTS, Dapper Drake.
As you proposed, if you could recommend me an optimal way for this 
installation I will appreciate in order to install Grass 6.1 and check 
this problem.

Thanks

Nicolas


Tue, Jul 11 2006 18:31:06    Mail sent by msieczka  
devaux@ensam.inra.fr wrote (Tue, Jul 11 2006 10:46:46):

> I'm using Ubuntu 6.06 LTS, Dapper Drake.

Good for you. Me too.

> As you proposed, if you could recommend me an optimal way for this 
> installation I will appreciate in order to install Grass 6.1 and check 
> this problem.

I'm building most of my GIS stuff from source (GEOS, HDF4, PROJ, GDAL,
POSTGIS, GRASS, GDAL-GRASS, QGIS 0.8) and package+install as debs. I'm
currently moving from Breezy to Dapper, so I might be able to give you all the
deb packages in few days, if you wish. But this might take time (I had issues
with GEOS, GDAL and QGIS 0.8 yesterday which I'm, hopefully, going to solve;
though I can't promise).

For now, nothing easier than

http://grass.itc.it/grass61/binary/linux/snapshot/

It will not conflict with your Grass 6.01 instalation. Run Grass 6.1 with
grass61 command.

All the instruction is there. In case of troubles - search the Grass user
mailing list archive. If you can't find a solution, ask the list.

Please CC me, tutey at o2.pl, when you reply - the message will reach me sooner.
Good luck, let us know how it worked if you try.

Maciek
Wed, Jul 12 2006 11:19:01    Mail sent by devaux@ensam.inra.fr  
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Date Wed, 12 Jul 2006 11:18:32 +0200
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To Maciek Sieczka via RT <grass-bugs@intevation.de>
Subject Re: [bug #4794] (grass) r.thin
References <20060711163106.2056B1006A4@lists.intevation.de>
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Maciek Sieczka via RT a écrit :
> devaux@ensam.inra.fr wrote (Tue, Jul 11 2006 10:46:46):
>
>   
>> I'm using Ubuntu 6.06 LTS, Dapper Drake.
>>     
>
> Good for you. Me too.
>
>   
>> As you proposed, if you could recommend me an optimal way for this 
>> installation I will appreciate in order to install Grass 6.1 and check 
>> this problem.
>>     
>
> I'm building most of my GIS stuff from source (GEOS, HDF4, PROJ, GDAL,
> POSTGIS, GRASS, GDAL-GRASS, QGIS 0.8) and package+install as debs. I'm
> currently moving from Breezy to Dapper, so I might be able to give you all
the
> deb packages in few days, if you wish. But this might take time (I had issues
> with GEOS, GDAL and QGIS 0.8 yesterday which I'm, hopefully, going to solve;
> though I can't promise).
>
> For now, nothing easier than
>
> http://grass.itc.it/grass61/binary/linux/snapshot/
>
> It will not conflict with your Grass 6.01 instalation. Run Grass 6.1 with
> grass61 command.
>
> All the instruction is there. In case of troubles - search the Grass user
> mailing list archive. If you can't find a solution, ask the list.
>
> Please CC me, tutey at o2.pl, when you reply - the message will reach me sooner.
>
> Good luck, let us know how it worked if you try.
>
> Maciek
>
>
> -------------------------------------------- Managed by Request Tracker
>
>
>   
Thanks for this tip. I tried to use the binary snapshot, but 
unfortunately it was for a 64bits system and I just have a 32 one. I was 
ready to build from sources, but  it seems that this operation will 
replace my actual Grass version (6.0.1). To run the new grass version 
that I could compile, the command would be Grass and not Grass61 like 
the binary version. I'm not enough comfortable with linux and compiling 
operations to act on the final run command of Grass version, and I don't 
want to erase my actual stable Grass version...

So, if you know a 32bits binary version I'm interested, or if you 
compile your own grass61 and that you have a 32bits system, I could wait 
until you finish your installation....
It's a little bit confused, I hope you understand my poor English.

Nicolas

------------------------------------------------------------------------------
Nicolas DEVAUX
Maître de Conférence AgroM
Laboratoire d'étude des Interactions entre Sol, Agrosystème et Hydrosystème
UMR LISAH AgroM-INRA-IRD
Bat. 24
place Viala
34060 Montpellier cedex 1
tél : +33 0(4) 99 61 25 22
fax: +33 0(4) 67 63 26 14
email: devaux@ensam.inra.fr
http://sol.ensam.inra.fr/lisah/
------------------------------------------------------------------------------
Thu, Jul 13 2006 23:09:32    Mail sent by msieczka  
devaux@ensam.inra.fr wrote (Wed, Jul 12 2006 11:19:01):

> Thanks for this tip. I tried to use the binary snapshot, but 
> unfortunately it was for a 64bits system and I just have a 32 one.

Shoot! I didn't know that was still an issue. Hopefully Markus will sort it
out, one day. Sorry for confusing you.

> I was ready to build from sources, but  it seems that this operation will 
> replace my actual Grass version (6.0.1).

No, not at all. Grass 6.0x and 6.x coexist perfectly and can share the same
database without any problems.

> To run the new grass version 
> that I could compile, the command would be Grass and not Grass61 like 
> the binary version.

That's not true. The command for 6.1 would be "grass61" and for Grass 6.01 it
would be "grass6".

> I'm not enough comfortable with linux and compiling 
> operations to act on the final run command of Grass version, and I don't 
> want to erase my actual stable Grass version...

That shouldn't happen. Try bulding from source, this doesn't hurt and will
give you more flexibility :).

> So, if you know a 32bits binary version I'm interested, or if you 
> compile your own grass61 and that you have a 32bits system, I could wait 
> until you finish your installation....

I'm done. I about an hour you receive an email from YouSendIt service with a
link for the download (about 40 MB, will be valid for 7 days; if you don't
receive the link let me know), including:

proj 4.4.9 + CVS
hdf 4.2 r1 p4
geos 2.2.3
gdal 1.3.2 + CVS
grass 6.1 CVS
gdal-grass plugin 1.3.1.2

Packaged into debs using checkinstall (also included). checkinstall replaces
"make install" command for easy installing/upgrading software. These packages
do *not* come with full dependencies, but are a lot easier to maintain than
something you install with "make install" (eg. apt/Synaptic and dpkg will be
able to handle them).

You would need to install packages in this particular order, removing your
gdal, proj, geos and gdal-grass instalations first to avoid conflicts. Install
using "sudo dpkg -i package_name.deb". Copy the included /etc/ld.so.conf to
your system and issue "sudo ldconfig" afterwards.

> It's a little bit confused, I hope you understand my poor English.

We understand each other and that's the point :).

Please test r.thin in 6.1 and report back.

Maciek
Mon, Aug 7 2006 14:50:37    Mail sent by msieczka  
Nicolas,

Are you still there? What is the status of your bug report? Shall I close it?
Maciek
Tue, Aug 15 2006 01:29:47    Status changed to resolved by msieczka  
Tue, Aug 15 2006 01:29:47    Mail sent by msieczka  
It's been about a month since no sign of life from the reporter. I'm closing
the bug. Please reopen if needed - by replying to this email simply.

Maciek
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