Re: passing arguments, contouring

Hi Jeremy,

Sorry for the delayed response. I was in a workshop then on vacation.

On Jun 14, 2013, at 4:48 PM, Jeremy Winick wrote:

>
>
> Mary,
> Thank you for the information. There are many ways of "skinning the cat"
> and as I work more with NCL and get out of the Matlab think, I will feel
> more comfortable. The use of str_get_field seems a way to get the one
> field (column) of a 24 column long (60000 line) data file that isn't
> numeric, but then using it many more times to get other fields then
> string to float seems inefficient. The readAsciiTable gets everything
> except the one string field (which happens to be a month-day
> abbreviation (such as Feb12)). Could I use the str_get_field to extract
> the one column, then use readAsciiTable for the rest? Does a file need
> to be closed or rewound in an NCL script to do this?

You should be able to do this, and you don't need to close or rewind
the file. NCL doesn't have a concept (yet) of doing this with ASCII files.

>
> I will try the contour plot with the one-dim temperature field and the
> sfYArray and sFXarray to the lat and lon variables. Do these still need
> the units "degrees_north" and "degrees_east" ?

Yes, they do. It may still work, but you will get warnings if you don't do this.

> The first attempt this
> way didn't work, I get:
> (0) Error: scalar_field: If the input data is 1-dimensional, you must
> set sfXArray and sfYArray to 1-dimensional arrays of the same length.
> warning:create: Bad HLU id passed to create, ignoring it
>
> As far as I can tell, I have set the sfYArray and sfXArray, but I don't
> understand the warning about bad HLU id passed. The script seems to be
> hanging after this error message, and I hit control-C to kill it.

The error appears to be coming from the fact that you are contouring 1D data.
When you do this, NCL is assuming that your lat/lon arrays are also 1D of
the same length. The error is indicating that your lat/lon arrays are either
not 1D, or they are not the same length.

--Mary

>
> Here is the code, with portions that set up the grid from natgrid
> commented out.
>
> ; first test ncl script to read in ascii SABER data, say
> Monx-Mony_year_strat_v2.0_v35_g30-84N_ex_prf_dp1.data
> ; then create ncl variables for temperatures at various pressure levels,
> associated lat and lon
> ; suggestion in this script modify so not using natgrip, but use
> sfYArray set to original lat points and sfXArray set to orig lon pts.
> ; then try contour plot on polar stereographic map
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
> ; the contour map routines such as gsn_csm_contour_map_polar seem to
> want data to be 2-D and have 1-D lat and long coordinate
> ; arrays attached, and longitude coord array must have valid "units"
> attribute of something like "degrees_east" (similarly for lat)
> ; lat array same length as leftmost dimension of the 2-D array and
> longitude array must be same as the rightmost dim of data (2-d array).
> ; thus raw satellite data does not do this- it needs to be gridded
> ; 9 June 2013 works for hand-wired separating out first day. Next choose
> day or days by input parameter. Choose level by input parameter?
> : There is an ncl function day_of_year(year:integer, month:integer,
> day:integer)
> begin
> diri="/mnt/data/saber1/ascii/v2.0/"
> system("cd diri")
> system("pwd")
> ncol=13
> data =
> readAsciiTable("Feb01-Mar01_2013_strat_v2.0_v35_g30-84N_exc_prf_dp1.dat",ncol,"float",27)
> printVarSummary(data)
> latd = data(:,5)
> printVarSummary(latd)
> ; print(lat)
> lond = data(:,6)
> doy = data(:,2)
> t50mb = data(:,9)
> t20mb = data(:,10)
> t10mb = data(:,11)
> t5mb = data(:,12)
> ; test for essentially the first day, 1-477 profiles
> t1 = t50mb(0:476)
> lat1 = latd(0:476)
> lon1 = lond(0:476)
> do n=0,476
> if(lon1(n).lt.0.0) then
> lon1(n) = 360.0 + lon1(n)
> end if
> end do
> ; create lat-lon grid
> ; latp= fspan(30, 85, 12)
> ; printVarSummary(latp)
> ; lonp= fspan(0,360,37)
> ; use natgrid to grid original satellite data
> ; tgrid=natgrid(lat1,lon1,t1,latp, lonp)
> ; write_matrix(tgrid,"12f7.2", False)
> ; print(latp)
> ; print(lonp)
> ; printVarSummary(tgrid)
> ; printVarSummary(latp)
> ; printVarSummary(lonp)
> ; tgrid!0 = "lat"
> ; tgrid!1 = "lon"
> ; tgrid@units='Degrees K"
> lat1@units = "degrees_north"
> lon1@units = "degrees_east"
>
> ; tgrid&lat = latp
> ; tgrid&lon = lonp
> sfXArray = lon1
> sfYArray = lat1
> printVarSummary(t1)
> printVarSummary(lon1)
> printVarSummary(lat1)
> wks = gsn_open_wks("x11", "polar")
> res = True
> res@gsnAddCyclic = False
> res@gsnPolar = "NH"
> res@mpMinLatF = 30
> res@cnFillOn = True
>
> gsn_define_colormap(wks,"gui_default")
> plot = gsn_csm_contour_map_polar(wks,t1,res)
> wks = gsn_open_wks("ps", "polar")
> res = True
> res@gsnAddCyclic = False
> res@gsnPolar = "NH"
> res@mpMinLatF = 30
> res@cnFillOn = True
>
> gsn_define_colormap(wks,"gui_default")
> plot = gsn_csm_contour_map_polar(wks,t1,res)
> wks = gsn_open_wks("png", "polar")
> ; note in above wks open "polar" is file name for output , this case
> would be polar.png
> ; make name specific to case so each new plot has distinct name
> res = True
> res@gsnAddCyclic = False
> res@gsnPolar = "NH"
> res@mpMinLatF = 30
> res@cnFillOn = True
> gsn_define_colormap(wks,"gui_default")
> plot = gsn_csm_contour_map_polar(wks,t1,res)
> end
>
>
> Being a FORTRAN first user, it takes some getting used to variables
> indices starting at zero. There are inconsistencies, because then when
> you have functions like the get field the fields start at 1 not zero.
> Why not be consistent? (I guess no language is).
>
> Jeremy
>
> “What is wanted is not the will to believe,
> but the wish to find out, which is its exact opposite”
> ... Bertrand Russell
>
> On 06/14/2013 09:32 AM, Mary Haley wrote:
>> On Jun 11, 2013, at 2:32 PM, Jeremy Winick wrote:
>>
>>> I am trying to learn ncl as a long time matlab user who is retired and
>>> cannot afford new licenses.
>>> My first problem I am attempting is plotting contours of satellite
>>> retrieved data on map projections.
>>> I have gotten this to work to some extent, but want to automate the
>>> process and don't see how to do it efficiently. The data comes from limb
>>> retrievals of satellite passes, 15 orbits per day. At least one day is
>>> needed to get the longitudinal coverage, and sometimes two or three days
>>> will help fill in more points.
>>>
>>> To contour temperature at some altitude or pressure level, using
>>> gsn_csm_contour_map_polar I am currently using natgrid to put the
>>> temperature data at each lat, lon point on a uniform grid. Then after
>>> setting, units, named dimensions and coordinate variables I can get the
>>> plot. With one day of data these contours often have some "non-smooth"
>>> features. Is there a way to get smoother contours or better griding.
>>> Note that these temperature points are measured at different times and
>>> maybe getting a grid should not just use nearest neighbor type methods
>>> but is there a way to weight points by how far apart in time?
>> Have you tried contouring the data directly, rather than putting it on a grid?
>>
>> http://www.ncl.ucar.edu/Applications/contour1d.shtml
>>
>> It would help if you could show us some sample images.
>>
>>> Now, to the problem of automating. All the examples I see on the web
>>> pages surely don't fit my type of need. The data opened in the script
>>> uses a specific name. My data is data that has already been analyzed and
>>> it in large ascii files - column format. Although all columns are not
>>> numeric, readAsciiTable seems to work although the column of the data
>>> that are not numeric (say dates in Feb12 type format) are not usable. I
>>> want to tell the script what the file to open (changing from run to run
>>> or incorporated in an csh-shell or bourne shell script, and also pass
>>> which days, and which column (temperature at one of a few levels).
>>> Setting enumerable environment variables seems like an awkward solution.
>>> Passing these as command line arguments would be very nice (like in
>>> matlab), but I haven't seen that this is possible. My work around now
>>> would be to open a fixed name file that I read in the script and change
>>> it each run to change these important parameters. I think I must be
>>> missing something that is basic, since my problem doesn't seem to be
>>> unusual.
>> It would help if we could see a sample file and script that you've written so far.
>> As Jonathan Vigh pointed out, there are different methods for reading ascii
>> files, but it just depends on what your file looks like. If you have a mix of data
>> and numbers, then I usually find the str_get_field and str_get_cols functions
>> to be the best way of reading in columnar data. I use str_get_field if the data
>> is separated by some delimiter, like a comma. I use str_get_cols if the data
>> are in perfectly lined up columns, which can be specified by column numbers.
>>
>> If you can provide your file and script, then you can use our ftp site:
>>
>> http://www.ncl.ucar.edu/report_bug.shtml#HowToFTP
>>
>>> One other complaint is that the web page support when viewed on Firefox
>>> 20.0 does not print correctly. Only the first page (and not even all of
>>> it) prints. I know these pages are designed for online work, but having
>>> ten or more open at a time and going back to just one or two, it would
>>> be easier to have those two printed out.
>> Can you give an example of which page is not printing out properly? One issue might be
>> that you need to click on the page you want to print, to make sure you are printing the
>> text you want, and not the header information.
>>
>> --Mary
>>
>>> Jeremy
>>>
>>>
>>> --
>>> “What is wanted is not the will to believe,
>>> but the wish to find out, which is its exact opposite”
>>> ... Bertrand Russell
>>>
>>> _______________________________________________
>>> ncl-talk mailing list
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>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
>
>
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Received on Mon Jun 24 08:50:38 2013