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Hi Jose, Just thinking that there are some data visualisation software that also allow essentially netcdf data manipulation. I like to use ferret http://ferret.wrc.noaa.gov/Ferret/ for this kind of stuff. Netcdf is the "native" format for ferret - ferret will read netcdf data with a very simple command (use ha.nc) and interpret the dimensions correctly (judging from your cdl below). You can then just extract points by referring to their lat, lon: save/file="pointdat.nc" ha[x=x0,y=y0] - you can have that also in ascii... You can also use R, though you have to jump through quite a lot of hops to read netcdf (as in matlab) - quite a big difference to ferret. But you still have to install software.... ;-) ... though I think it is worthwhile (R and ferret that is) Good luck, Cheers, Joerg -----Original Message----- From: netcdfgroup-bounces@xxxxxxxxxxxxxxxx [mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Russ Rew Sent: 19 November 2012 21:31 To: Jose Borrero Cc: netcdfgroup@xxxxxxxxxxxxxxxx Subject: Re: [netcdfgroup] Extracting time series from netCDF file Hi Jose, > 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? > > 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! I sympathize, but the approach you were suggesting is not supported by the C ncdump, though there is a netCDF-Java ncdump that comes closer to what you want: http://www.unidata.ucar.edu/software/netcdf-java/reference/manPages.html Changes to the C ncdump to support a query language on the command line are non-trivial. For those familiar with Python, I think the solution Rich Signell provided is very elegant and worth studying, because it's far more powerful than what can be accomplished with relatively primitive command-line tools. --Russ > ----- 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...) > > > > > > > > > _______________________________________________ > > > netcdfgroup mailing list > > > netcdfgroup@xxxxxxxxxxxxxxxx > > > For list information or to unsubscribe, visit: > > http://www.unidata.ucar.edu/mailing_lists/ > > > > > > -- > > Dr. Richard P. Signell (508) 457-2229 > > USGS, 384 Woods Hole Rd. > > Woods Hole, MA 02543-1598 > > > > _______________________________________________ > netcdfgroup mailing list > netcdfgroup@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/m ailing_lists/ _______________________________________________ netcdfgroup mailing list netcdfgroup@xxxxxxxxxxxxxxxx For list information or to unsubscribe, visit: http://www.unidata.ucar.edu/mailing_lists/
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