Wed, Jul 5 2006
17:25:00
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Request created by guest
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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 |
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Wed, Jul 5 2006
20:17:29
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Mail sent by msieczka
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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
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Thu, Jul 6 2006
00:08:45
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Mail sent by mneteler
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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 |
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Thu, Jul 6 2006
00:09:00
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User changed to devaux@ensam.inra.fr by mneteler
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Thu, Jul 6 2006
00:09:24
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Comments added by mneteler
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I have (hopefully) fixed the requestor's email address.
Markus |
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Fri, Jul 7 2006
12:01:19
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Comments added by guest
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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.
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Fri, Jul 7 2006
21:24:31
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Area changed to grass6 by msieczka
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Fri, Jul 7 2006
21:30:48
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Mail sent by msieczka
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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
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Mon, Jul 10 2006
10:59:45
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Comments added by guest
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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 |
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Mon, Jul 10 2006
14:34:55
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Mail sent by msieczka
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OK. Anyway, you are sure the problem is solved now, right? So can I close the
report?
Maciek
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Mon, Jul 10 2006
16:10:47
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Mon, 10 Jul 2006 16:10:18 +0200
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Maciek Sieczka via RT <grass-bugs@intevation.de>
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Re: [bug #4794] (grass) r.thin
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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/
------------------------------------------------------------------------------
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Tue, Jul 11 2006
10:29:15
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Mail sent by msieczka
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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
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Tue, Jul 11 2006
10:46:46
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Tue, 11 Jul 2006 10:46:07 +0200
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Nicolas Devaux <devaux@ensam.inra.fr>
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Maciek Sieczka via RT <grass-bugs@intevation.de>
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Re: [bug #4794] (grass) r.thin
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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
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Tue, Jul 11 2006
18:31:06
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Mail sent by msieczka
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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
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Wed, Jul 12 2006
11:19:01
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Wed, 12 Jul 2006 11:18:32 +0200
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Re: [bug #4794] (grass) r.thin
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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/
------------------------------------------------------------------------------
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Thu, Jul 13 2006
23:09:32
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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
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Mon, Aug 7 2006
14:50:37
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Mail sent by msieczka
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Nicolas,
Are you still there? What is the status of your bug report? Shall I close it?
Maciek
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Tue, Aug 15 2006
01:29:47
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Status changed to resolved by msieczka
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Tue, Aug 15 2006
01:29:47
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Mail sent by msieczka
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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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