gmane.comp.gis.gmt.user

No SI/US keyword in GMT configuration file

yacob sen — 2012-05-26T08:50:58

Hi ALL,

I have just installed GMT4.5.8 in my ubuntu 12.04 OS.  I run the following command after the a successful installation.  

awk '{print NR,$1*1e5/3600.}'  eop.x |   minmax -I0.1 > temp_minmax1

But I am keep getting the error 
GMT Fatal Error: No SI/US keyword in GMT configuration file (COLOR_BACKGROUND= black

I am using English (UK) keyboard  but that does not matter I think. I checked also 
/opt/gmt4/GMT4.5.8/share/conf/gmtdefaults_US 
does contain :

#-------- Color System Parameters -----------
COLOR_BACKGROUND        = black

)


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full resolution data error

MOFFAT, L.C. (MR. — 2012-05-25T14:41:32

Hi All,

I have just installed GMT4.5.8 under Ubuntu 12.04. Now the problem is when I try to run any script containing "pscoast" command I get the following error:
[16:00]mmaoletsekae:~$ okavangogrd.sh
pscoast: full resolution shoreline data base not installed
pscoast: full resolution political boundary data base not installed
pscoast: full resolution river data base not installed
pscoast: No databases available - aborts

This is despite the fact that I have the files required by "pscoast" in the folder "/home/lucky/GMT4.5.8/share/coast", i.e binned_border_*.cdf,  binned_GSHHS_*.cdf & binned_river_*.cdf (with * representing c,f,h,i,l). I installed GMT using Ubuntu's repositories.

Here is some info about my platform:

hostname = lucky-HP-Pavilion-g6-Notebook-PC
uname -m = i686
uname -r = 3.2.0-24-generic-pae
uname -s = Linux
uname -v = #37-Ubuntu SMP Wed Apr 25 10:47:59 UTC 2012

And the following is some of the first few lines from "config.log" file:

$ ./configure --prefix=/home/lucky/GMT4.5.8 --bindir=/home/lucky/GMT4.5.8/bin --libdir=/home/lucky/GMT4.5.8/lib --includedir=/home/lucky/GMT4.5.8/include --enable-netcdf=/home/lucky/netcdf-3.6.3 --enable-eps --enable-shared --mandir=/home/lucky/GMT4.5.8/man --docdir=/home/lucky/GMT4.5.8/share/doc/gmt --datadir=/home/lucky/GMT4.5.8/share --enable-update=ftp.soest.hawaii.edu

Any help will be appreciated.

Regards,

Lucky.

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psxy(GMT_psxy): Warning: not a valid number and may not be decoded properly.

yacob sen — 2012-05-24T20:10:55

Dear ALL,
I have got the following error message after I have installed recently GMT5 beta version on my ubuntu 12.04. I have no old GMT versions installed in my Linux box.
psxy(GMT_psxy): Warning: 3/0/0/0 not a valid number and may not be decoded properly.
The error comes when any of the GMT commands contain  "-W1/200/20/100" style from the pre GMT5 versions. 
I just wanted to install GMT5.0 beta version only but continue to use all those gmt commands that worked for pre- GMT5 versions.
I hope there is a simple solution to it. I had had  a similar problem when I tired to install GMT5 using subversion.

Kind regardsYacob 

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-W$ with a variable

Gery . — 2012-05-24T11:26:58

Hello,

I have this doubt, how could I pass a variable? this is my problem:

Based on a loop, I determined a series of names, this is, it reads several filenames and puts them into a variable, so when I echo that variable I get (inside the loop):
$ echo $name
basement (first loop)
bsr (2nd one)
fault (etc...)
lowereocene
lowermiocene
middleeocene
middlemiocene
seafloor
unknown
uppereocene
uppermiocenepliocene

based on that, every time the I call a psxy line command and try to plot another defined variable based on that name, this is for instance:

seafloor=1.5p/black

so, the problem is I get the error about the -W flag, I used for instance -W$`echo $name` but it gives me for example: psxy: Pen name $seafloor not recognized!

I tried eval but didn't work: -W$`eval $name`

Any idea will be very grateful,

Best regards,
       
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GMT5 in ubuntu 12.04

yacob sen — 2012-05-24T09:39:33

Hi ALL,
I have just installed GMT5 beta version on Ubuntu 12.04. When ever I run a GMT command I get the following warnings.  It seems to me that is not related to GMT issue rather an Ubuntu issue. Any idea why ?
Warning: Cannot convert string "-*-Helvetica-Medium-R-Normal--*-140-*-*-P-*-ISO8859-1" to type FontStructWarning: Cannot convert string "-*-Helvetica-Medium-R-Normal--*-120-*-*-P-*-ISO8859-1" to type FontStructWarning: Cannot convert string "-*-Helvetica-Medium-R-Normal--*-100-*-*-P-*-ISO8859-1" to type FontStructWarning: Cannot convert string "-*-Helvetica-Bold-R-Normal--*-120-*-*-P-*-ISO8859-1" to type FontStruct

Any comments please ?

Yacob

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need help using xyz2grd to convert .bil (ned) to grd

Vusi Tora — 2012-05-23T23:56:52

Hi all, I need help to convert a bil file downloaded from USGS NED

Here is my command and error message I obtained:

xyz2grd NED_74828757.bil -R-91/-88.5/34/38 -I0.5c -Gtest.grd -F -V -ZTLhw
-N-9999
xyz2grd: nx = 18000  ny = 28800
xyz2grd: Working on file NED_74828757\NED_74828757.bil
xyz2grd: Found 109573074 records, but 518400000 was expected (aborting)!

I don't know what exactly I'm doing wrong.
Thanks in advance

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COARDS/CF-1.0 problem

Frédéric Bouchette — 2012-05-23T17:38:43

Hi all,

Florian + Remko + Joaquim : thank you for these detailed answers. This
list is definitely very active.

Now, I am not sure to agree 100% with all your explanations.

Florian said:
"GMT claims to be COARDS compliant which is probably true although the
documentation says actual_range == valid_range,"

And then Remko wrote:
"CF-1.0 does NOT require valid_range, valid_min, or valid_max. It's
totally optional. In fact, valid_range is generally not very
informative, the data type often tells you already what the
valid_range is,....
I have also not encountered ANY program that actually requires
valid_range, and they shouldn't."

Well. I don't understand the last sentence: valid_range is in the norm
CF-1.0 / 1.6. Why shouldn't we use it ? It can be usefull.

We use valid_range to set the scale of color palettes in the WPS/WFS.
It is convenient.
An alternative method would be to use actual_range and _FillValue set to NANf.
Two examples:
_FillValue set to Nanf -> actual_range IS NOT affected.
_FillValue set to -999 -> actual_rang IS affected ( -999,max_value ) Hmmm...

So the equivalence actual_range / valid_range is speculative and
depends upon another attribute.

Additionally, this means that GMT asks NetCDF users to use a parameter
that IS NOT in the CF-1.0 CF-1.6 convention. Indeed, if you search the
term "actual_range" in :

http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.0/cf-conventions.html
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html

Nothing ----> Actual_range is out of Conventions CF 1.0 / 1.6.

Of course, GMT can use attributes NOT relative to convention (really :-).

But the question is:
is it logical to introduce in GMT a non-normative parametre
(usual_range) and to NOT introduce in GMT a normative parametre that
can do the same job ?

At this point, we can adapt our strategy and introduce actual_range in
the list of attributes to be catched by the WPS/WFS, with the relevant
_FillValue. This is the solution. Thank you again for the comments and
the help.

I well understood that you are convinced that GMT shouldn't be adapted.
But, presently, I am not so confident (see what I mentioned above).

Notice that i well understood the sentence of Remko: "One can also not
simply replace actual_range by valid_range, because the former is in
unpacked units, the later in packed units.". But, to my opinion, this
is a distinct questioning. Perhaps I am wrong. I am definitely not as
easy with all these concepts as you are.

Best regards,
Frederic.










2012/5/23, Joaquim Luis <jluis< at >ualg.pt>:

COARDS/CF-1.0 problem ?

Frédéric Bouchette — 2012-05-23T09:34:04

Hi all,

This concerns both GMT 4.5.6 and 5.0.0b.

We combine GMT with a WFS/WPS server. This requires to define a common langage.
GMT is COARDS/CF-1.0 compliant and that's OK to tackle this. However,
when I write a GMT script that creates a GRD file (netcdf
COARDS/CF-1.0), a ncdump of the GRD file gives what follows below
(after my text).

It seems that the netcdf file does not fit the actual convention CF
for the  attribute "actual_range". Indeed, the convention CF requires
"valid_range".

So my question is : is there any way in GMT to modify the name of the
attributes ?
grdedit seems to redefine the values, but not the var names, isn't it ?

If no command-line-solution exists, we can recompile GMT and changing
things accordingly to our requirement. However, is using
"actual_range" a bug, or is this planed by the dev team ?

Tusen takk,
Fred Bouchette

ncdump -h temp.grd
netcdf temp {
dimensions:
  x = 607 ;
  y = 526 ;
variables:
  double x(x) ;
      x:long_name = "x" ;
      x:actual_range = 160550., 221163. ;
  double y(y) ;
      y:long_name = "y" ;
      y:actual_range = 5365341., 5417837. ;
  float z(y, x) ;
      z:long_name = "z" ;
      z:_FillValue = NaNf ;
      z:actual_range = -9.33745384216309, 64.7867050170898 ;

// global attributes:
      :Conventions = "COARDS/CF-1.0" ;
      :title = "surface" ;
      :history = "surface -V -R160550/221163/5365341/5417837 -I100
-T0.35 ./garbage/temp2.cols -Ggarbage/temp.grd" ;
      :GMT_version = "4.5.0 [64-bit]" ;
}

mgd77list separator

Zohar Ehrlich — 2012-05-22T16:43:03

hi all,

i have a list of say 30 ocean voyages created with *x2sys_get*
i would like to use *mgd77list* to retrieve the lon,lat data so i can plot
their tracks with *psxy -m*

is there a way to get mgd77list to add a '>' after each file entry?
something similar to:

...
107.88166 -16.30028
107.88166 -16.30167
107.88138 -16.30306
107.8811 -16.30445
97.72027 7.71236
97.72252 7.71206
97.72478 7.71177
97.72704 7.71147
...



many thanks,
*Zohar L. Ehrlich*

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calculate the position (longitude, latitude) from the distance of 2 points.

Namba Takaya — 2012-05-22T06:32:25

Dear Sir
I would like to calculate the location of the point (longitude, latitude) from 2 points by a certain distance (for example 12 miles).
For example, there are two points, A(longitude=E125.25, latitude=N25.25) and B(longitude=E125.30, latitude=N25.20).I would like to calculate the location of the point, C, at the distance of 12 miles form A and B.
 Thank you in advance.
Takaya Namba       

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Clipping Mask and GRD Masked

Michael Merrell — 2012-05-15T18:17:01

 GMT Help,

Version 4.5.7

I have the following script below where I clip a GRD file using "grdmask"
and anything outside of the clipping polygon I set to "NaN". I then use
makecpt to make a color palette and set NaN to white. For some reason the
entire background/NaN is coming out red and I can not seem to figure out
why. I have attach an image of what the problem is. Note that the big
rotated rectangle is the file wideazi_outline.xy


psbasemap -R$region -J$map -G255/255/255 -Bf0.03a0.05WeSn
-Lf269.6595/27.4/27.4/20 -P -K -V > $target.ps
grdmask salt_thickness_polygon.xy -R$region -I0.0001 -NNaN/1/1 -fg
-G$Masked_Surface.grd -V

# This says if the masked_surface is NAN then disregard it and output a new
surface
grdmath $Surface.grd $Masked_Surface.grd OR =
salt_thickness_test_surface.grd -V

# Makes a color pallette and sets NAN values to white
makecpt -Cgray -I -T0/15100/50 -M --COLOR_NAN=255/255/255 -V -Z >
salt_bw.cpt

grdimage salt_thickness_test_surface.grd -J$map -R$region -E300 -P -Q -V -K
-O -Csalt_bw.cpt>> $target.ps
grdcontour salt_thickness_test_surface.grd -C2000 -J$map -A4000 -GD20km
-R$region -O -K -V >> $target.ps

psclip wideazi_outline.xy -R$region -J$map -V -O -K >> $target.ps

dash line in pslegend

Gery . — 2012-05-15T13:30:15


Hello,

This is very likely a very basic question but so far haven't found the right way to make this, I'm trying to plot a horizontal dashed line in a legend using pslegend, this is what I have:

S .2i - .025i -                2p,red,-                .5i  =)p

I know that .025i above control the size of the line, but it just appears one very small line, and I thought I will get a dashed line instead.

Any hint is very welcome!!!!

Cheers,

Gery

       
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Losing Parts of Map - psclip issue?

Daniel Cole — 2012-05-12T01:53:00

The basics of my mapping script is laid out below.  Most of the maps I am
making are between 10 and 1000 acres, and contain points with z values
scattered inside one to 20 adjacent polygons.   The problem I am having is
that if the shape is much longer than it is wide (more than about a 3:1
ratio) it starts cutting off the top of the image.



I assume that it is the psclip doing that , but I don’t understand why it
would crop the map inside of the polygon.  I thought that minmax would make
it go outside of the image.  It seems to help if I adjust the –Jm8 to –Jm2
or so, but doesn’t fix every map like that.  Maybe I shouldn’t be using the
–Jm projection, but I don’t know.





OGR for Border Polygon(s) > border.gmt

REG=Minmax-m border ogr

psclip border.gmt -m –JM8 -R$REG -K > map.ps

psxy border.gmt -m -R -J -W1 -O -K >> map.ps

ps2raster map.ps -A -Tg -P -E100 map.ps




Please give me any thoughts you have.

Thanks,


Daniel

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gmtmath UPPER and LOWER with NaNs

John Robbins — 2012-05-11T17:24:44

OK - there is probably a simple solution to this problem... Background: 
I'm using GMT 4.5.7 on OSX Lion.

I have a table with NaNs found sporadically in it, including on the 
first and last lines. I'd like to use the UPPER and LOWER operators on a 
range of columns of a very large table and have it report a numerical 
value, regardless of the existence of a NaN on the first or last lines.

It seems that if a NaN is found in the first (or last) record of a 
column, UPPER and LOWER will report NaN when using -Sf (or -Sl, 
respectively). I desire a numerical report from UPPER or LOWER 
regardless of the existence of a NaN on the first or last records. How 
can it be done?

The MEAN and STD operators report a numerical value regardless of an 
existence of a NaN on the first or last lines, when using -Sf or -Sl, 
respectively.

John

example:

NaN as the response to the command: gmtmath -Sl t1.txt LOWER =
-1.442 as the response to gmtmath -Sf t1.txt LOWER =

where t1.txt is the following

     0.609
     NaN
     -1.442
     2.670
    NaN

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windows installation

Abigail Jiménez Lloret — 2012-05-11T13:44:51

Dear Sirs,

I have problems with the windows version of GMT.
I downloaded and installed it, and also the cygwin but some of the functions don't work, in particular, the examples given do not work, because they don't read some of the functions. The folder functions does not exit. Should I add a gcc compiler for the libraries before installing the windows version, or I do I have to compile them directly? In that case, which archive should I compile for the whole set of functions?
Thanks in advance,

Abigail Jiménez Lloret

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Retain attributes using 'blockmedian'

Jan Erik Arndt — 2012-05-10T14:05:56

Dear Paul, Walter and all others,

I am currently using some GMT programs to generate a bathymetric grid 
using data from several sources. One of these steps is 'blockmedian'. 
Before this step every point used in the calculation has the values 'LON 
LAT DEP WEIGHT SOURCE_ID'. I intent to create a source id grid 
afterwards. Unfortunately after 'blockmedian' the information about the 
SOURCE_ID gets lost and I have not found a way of retaining that 
information within the standard 'blockmedian' program.

So my question is:
Is it possible to retain the attributes, like 'SOURCE_ID', corresponding 
to the blockmedian value using the standard commands or would I have to 
work on the 'blockmedian' code itself to keep this information?

Many thanks in advance,
Jan

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xyz2grd values set to Nan

Vusi Tora — 2012-05-09T23:33:47

Hi all,
I am trying to convert a xyz format file to grd
here is my command and what I got :

xyz2grd file.xyz -R-91.5/-88.7/34.1/37.5 -Ddegree/degree/height1/0/=/=
-Gfile.grd -I1m/5m -V
xyz2grd: Given domain implies x_inc = 0.0166667
xyz2grd: Given domain implies y_inc = 0.0829268
xyz2grd: nx = 169  ny = 42
xyz2grd: Working on file day120diff.xyz
xyz2grd:  n_read: 137088  n_used: 0  n_filled: 0  n_empty: 7098 set to NaN
xyz2grd: Warning: No valid values in grid [file.grd]


Could anyone tell me what is wrong or how to fix the problem.

here is an example of my xyz text file.

37.4958333333 -91.4958333333 -261.411
37.4958333333 -91.4875 -268.411
37.4958333333 -91.4791666667 -272.411
37.4958333333 -91.4708333333 -285.411
37.4958333333 -91.4625 -301.411
37.4958333333 -91.4541666667 -301.411
37.4958333333 -91.4458333333 -313.411
37.4958333333 -91.4375 -311.411
37.4958333333 -91.4291666667 -311.411
37.4958333333 -91.4208333333 -313.411
37.4958333333 -91.4125 -313.411
37.4958333333 -91.4041666667 -306.411
37.4958333333 -91.3958333333 -292.411
37.4958333333 -91.3875 -293.411
37.4958333333 -91.3791666667 -313.411
37.4958333333 -91.3708333333 -321.411
37.4958333333 -91.3625 -325.411
37.4958333333 -91.3541666667 -317.411
37.4958333333 -91.3458333333 -317.411
37.4958333333 -91.3375 -318.411

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GMT Animations

Pedro da Silva Peixoto — 2012-05-09T21:17:14

Hi all,

I just need a quick tip here, and would be glad if anyone could help. I generate GMT animation (GIFs), using convert, but I am lacking a way to view the animation in a proper way (that I can stop at a frame, forward frame by frame, and stuff like that).

I use Linux (Ubuntu), and general tools like the imageviewer, gThumb and Firefox do not allow me to control the animation. I converted (using convert/avconv) the gif to other formats that could be read by video programs (such as xine), but I looses to much of its original frame to frame resolution (tried things like avi, mpeg, mp4 in with all kinds of quality flags). 

Is there any appropriate viewer for this kind of animation? Or any tips to sort this?

Thanks, 


Pedro.
 
_____________________
Pedro da Silva Peixoto
Matemática Aplicada
Instituto de Matemática e Estatística
Universidade de São Paulo - Brasil
e-mail: pedrosp< at >ime.usp.br

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missing GSHHG

Dan Kokron — 2012-05-09T16:52:17

I am getting the following conflicting warnings while configuring SVN
(rev 10070).  Any ideas what I'm doing wrong?

The systems is ...
Linux-2.6.32.54 x86_64
cmake version 2.8.8

missing graticules after ps/eps/pdf import into inkscape

rdbriggs — 2012-05-09T16:23:57

Good day everyone,

I'm trying to import a ps file into inkscape (so I can add an extra 
layer and lots of text) but the graticules disappear. The problem can be 
seen with this command :

pscoast -R-180/180/-90/-60 -Js0/-90/1:40000000 -B30g30/g10 -Dc -G200 -P 
-V > map1.ps

Once imported into inkscape the graticules disappear. They are, however, 
still visible in the import window.

Does anyone have an explanation for this and how I can fix it (I'm 
guessing it is an inkscape problem because they are visible with the gs, 
pdf viewers), can others repeat it ?

regards,

Rob Briggs

GMT Help on nearneighbor

Sutatch — 2012-05-08T21:59:59

Hello All,
      I am trying to plot data with nearneighbor, but it does not work. There 
are some spurious areas at (0, 360) or (-180, 180), depend on selecting 
REGION. 


BORDER="-Bwesn"
PROJ="-JS-90/90/5c"
REGION="-R0/360/0/90" or ="-R-180/180/0/90"
COLORSCHEME="rainbow"
TXTCOORDS="-D-0.2i/2.6i"
HDRCOORDS="-D-0.5i/10.6i"
ARROWCOORDS="-D5.0i/10.5i"
XARROWCOORDS="-D6.0i/10.9i"
STEREOCOORDS="-D4.5i/10.0i"

nearneighbor gbcd_Ag_gmt_1.dat -GTempPDFnn.grd -Lg -I3/3 -Rg -H1 -S10

It seems like search_radius  could not go through the boundary 0/360 or -
180/180.

Is there anything I could do to fix the problem?


Thank you,

Sutatch


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