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Re: [netcdfgroup] Extracting time series from netCDF file


On 11/19/2012 1:10 PM, Jose Borrero wrote:


Just curious, why can't it be done in the manner that I thought it could be 
done?

Why do I have to go install a whole other software to do what should be pretty 
simple?


Hi Jose,
Switching outlooks from a half-empty glass to a half-full glass turns your lament of "have to go install a whole other software to do what should be pretty simple" into "have numerous free and well-supported software packages to do both simple and complex tasks": http://www.unidata.ucar.edu/software/netcdf/software.html
ncdump is a rudimentary (but very useful) tool, used mostly for diagnostic purposes. NCO together with standard Unix utilities would probably achieve what you are after here. Ferret, I know, can produce the output you are after -- not an advertisement, just mentioning an option I know well. The list of options to choose from is long, but this community can guide you to a quick (free) solution. 

    - Steve




I need to do work, not install software...

I might as well just do it my own made up wonky way that works...

seem like every bag of worms just contains another bag of worms...

frustrating!

----- Original Message -----
From: "Signell, Richard" <rsignell@xxxxxxxx>
Date: Monday, November 19, 2012 3:36 pm
Subject: Re: [netcdfgroup] Extracting time series from netCDF file
To: Jose Borrero <jborrero@xxxxxxx>
Cc: netcdfgroup@xxxxxxxxxxxxxxxx


Jose,
If you were used to using Matlab but no longer have it, you might try
Python, which you can use in a similar fashion. This example shows how
to extract and plot a time series of wave heights from a remote
OPeNDAP dataset, but would work the same with a local NetCDF file:
http://nbviewer.ipython.org/4113653/

This code uses the NetCDF4-Python module, which reads NetCDF and
OPeNDAP datasets using the same syntax.  It can be a pain to install,
but I didn't have to build it because I have the Enthought Python
Distribution, which includes NetCDF4-Python with OPeNDAP support.  (I
think the full version of the EPD is free for folks with .edu
addressses, and of course there are many other options for free
scientific distributions as well).

Good luck,
-Rich


On Mon, Nov 19, 2012 at 12:59 PM, Jose Borrero <jborrero@xxxxxxx>
wrote:>

Hi All,

I have a program that produces netCDF files of water levels over

a geographic region fro different times.

the header looks like this:

===============================================
         lon = 720 ;
         lat = 330 ;
         grid_lon = 720 ;
         grid_lat = 330 ;
         rows = 3 ;
         clms = 3 ;
         time = UNLIMITED ; // (226 currently)
variables:
         double lon(lon) ;
                 lon:long_name = "longitude" ;
                 lon:units = "degrees_east" ;
                 lon:point_spacing = "even" ;
         double lat(lat) ;
                 lat:long_name = "latitude" ;
                 lat:units = "degrees_north" ;
                 lat:point_spacing = "uneven" ;
         double grid_lon(grid_lon) ;
                 grid_lon:long_name = "longitude" ;
                 grid_lon:units = "degrees_east" ;
                 grid_lon:point_spacing = "even" ;
         double grid_lat(grid_lat) ;
                 grid_lat:long_name = "latitude" ;
                 grid_lat:units = "degrees_north" ;
                 grid_lat:point_spacing = "uneven" ;
         double O2Geo(clms, rows) ;
                 O2Geo:long_name = "rotation matrix" ;
         float max_amp(grid_lat, grid_lon) ;
                 max_amp:long_name = "Maximum Wave Amplitude" ;
                 max_amp:units = "centimeters" ;
                 max_amp:_FillValue = -1.e+34f ;
                 max_amp:missing_value = -1.e+34f ;
         double time(time) ;
                 time:long_name = "time" ;
                 time:units = "seconds" ;
                 time:calendar = "gregorian" ;
         float ha(time, lat, lon) ;
                 ha:long_name = "Wave Amplitude" ;
                 ha:units = "centimeters" ;
                 ha:missing_value = -1.e+34f ;
                 ha:_FillValue = -1.e+34f ;
===============================================

i would like to extract a time series of data at a specific

location.>

I have been looking at the ncdump command and thinking there

would be a way do it at the command line, i.e. something like:

ncdump -v ha(lat,lon, time[1=>t]) datafile.nc > timeseries.cdl

(I realize the syntax is totally wrong, i am just trying to

express how I would specify a lat/lon and ask for the data over the
entire time)

then using ncgen to make a new binary netCDF that can be read by

GMT's nc2xy and output a simple 2 column time series.

but I don't  think I can specify things that way with ncdump.

I then looked in to using the ncBrowse software.  I have managed

to use that to specify a time series of data at a point, and even
write that data out to a CDL file.  However, the file generated by
ncBrowse (pasted below in an edited form) cannot be read by nc2xy
and has characters that are not compatible with ncgen

nc2xy tells me: nc2xy: NetCDF: Unknown file format [ha.cdl]

and ncgen tells me:

ncgen: ha.cdl line 7: syntax error, unexpected '=', expecting ','

or ')'

===================================================
netcdf ha.cdl {
dimensions:
      time = UNLIMITED ; // (226 currently)
      lat = 1 ;
      lon = 1 ;
variables:
    double time(time=226);
      time:long_name = "time";
      time:units = "seconds";
      time:calendar = "gregorian";
    double lat(lat=330);
      lat:long_name = "latitude";
      lat:units = "degrees_north";
      lat:point_spacing = "uneven";
    double lon(lon=720);
      lon:long_name = "longitude";
      lon:units = "degrees_east";
      lon:point_spacing = "even";
    float ha(time=226, lat=330, lon=720);
      ha:long_name = "Wave Amplitude";
      ha:units = "centimeters";
      ha:missing_value = -1.0E34f; // float
      ha:_FillValue = -1.0E34f; // float
data:

  time = 0.0, <ALL THE TIMES>, 14400.0 ;

  lat = 24.00833 ;

  lon = 60.00833 ;

  ha = 1.0723767, <ALL THE ha VALUES>1.6242466 ;

}
===================================================

so then, I go in to the ha.cdl file and edit the header in a text

editor to remove the =226, =330 and =720 bits and change the line:

    float ha(time=226, lat=330, lon=720);

to

    float ha(time);

I then run run:

ncgen -b -o ha.nc ha.cdl

and make a file ha.nc which then can be accessed by nc2xy through

the command:

nc2xy ha.nc -Ftime/ha > ha.txt

to create the file ha.txt which looks like:

===========================
0.000   17.423
64.000  61.289
128.000 36.575
<...SNIP...>
14336.000       -2.210
14400.000       -2.147
===========================

and is exactly what i want! Two columns, time and ha at that

particular lat/lon So I know it is possible...

So, if you are still with me, how can i do this more simply,

through the command line preferably, or even a small script that goes:

ncdump (args)
ncgen (args)
nc2xy (args)

would be fine, but I just need to know the right arguments to

make it all talk to each other.

if you can help me,  MANY, MANY, THANKS!!!!

-jose

(p.s. i used to do this with MATLAB, but I recently had my

computer with MATLAB die, and i can't get it up and running again,
so i am trying to do this an alternative way...)


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--
Dr. Richard P. Signell   (508) 457-2229
USGS, 384 Woods Hole Rd.
Woods Hole, MA 02543-1598


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