Re: message warning check_for_y_lat_coord

Noelia,

You are creating dimension names when you don't need to. The
"printVarSummary" of "pr" is showing you that "pr" already has dimension
names:

Type: float
Total Size: 90720 bytes
            22680 values
Number of Dimensions: 3
Dimensions and sizes: [time | 45] x [lat | 18] x [lon | 28]

That means this code should be removed:

        pr!0="time" ; assign attributes
        pr!1="lat"
        pr!2="lon"

By the way, the "!" symbol is for assigning dimension names to a variable,
and not for assigning attributes, as your comment states. The "@" symbol is
what's used to assign attributes,

Also, I don't know what "wami" looks like, but you should do a
"printVarSummary" on it to see if it already has a "time" dimension. If
so, then remove this line:

        wami!0="time"

When you use "tranpose" on an array, the metadata is retained, so you don't
need this code either:

        prT!0="lon" ; assign attributes
        prT!1="lat"
        prT!2="time"

However, I don't understand why you are transposing "pr", and then
reordering the transposed array before you call escorc. Transposing an
array is basically identical to reordering a 2D array to swap the
dimensions.

I think maybe you started trying to name the dimensions and create
attributes when you started getting error messages, but I think the real
error message was coming from "escorc" being called incorrectly.

I think the code you have above can be changed to just a few lines:

       pr =a->pr
       wami =b->WAMI(:,0,0,0)

        lat@long_name="latitude"
        lat@units="degrees_north"
        lon@long_name="longitude"
        lon@units="degrees_east"

        correl=escorc(wami,pr(lat|:,lon|:,time|:))
        correl!0="lat"
        correl!1="lon"
        correl&lon=lon
        correl&lat=lat

If you continue to have problems, I will need to see your full code and
*all* the output from running "ncl" on it. It's too hard to debug this
problem with only partial codee. Also, it *really* helps if you look at
your data, and do a lot of "printVarSummary" calls to make sure the
metadata looks good before you start trying to add your own metadata.

--Mary



On Mon, Jul 7, 2014 at 12:53 PM, Noelia otero <noeli1680@gmail.com> wrote:

> Hi,
>
> Thanks, yes I know that it might be a problem with the arrays and actually
> I realized of one error in the lat dimension but afterwards the problem is
> the same:
> this is my try again:
>
> pr =a->pr
> wami =b->WAMI(:,0,0,0)
>
> printVarSummary(pr)
> pr!0="time" ; assign attributes
> pr!1="lat"
> pr!2="lon"
> wami!0="time"
> prT = transpose(pr) ; need to transpose to get the correlations
> prT!0="lon" ; assign attributes
> prT!1="lat"
> prT!2="time"
> printVarSummary(prT)
> ;copy_VarCoords(prT,correl) ; copy attributes from temp to pcp
>
> correl=escorc(wami,prT(lon|:,lat|:,time|:))
> correl!0="lon"
> lon@long_name="longitude"
> lon@units="degrees_east"
> correl&lon=lon
> correl!1="lat"
> lat@long_name="latitude"
> lat@units="degrees_north"
> correl&lat=lat
>
> the print messages are:
> printVarSummary (pr)
>
> Type: float
> Total Size: 90720 bytes
> 22680 values
> Number of Dimensions: 3
> Dimensions and sizes: [time | 45] x [lat | 18] x [lon | 28]
> Coordinates:
> time: [40800..56871]
> lat: [37.67308962904533..-9.767145559195573]
> lon: [-28.125..47.8125]
> Number Of Attributes: 9
> standard_name : precipitation_flux
> long_name : Precipitation
> units : kg m-2 s-1
> grid_type : gaussian
> _FillValue : 1e+20
> comment : at surface; includes both liquid and solid phases from all
> types of clouds (both large-scale and convective)
> original_name : PRECC+PRECL
> cell_methods : time: mean (interval: 20 mintues)
> associated_files : baseURL:
> http://cmip-pcmdi.llnl.gov/CMIP5/dataLocation gridspecFile:
> gridspec_atmos_fx_bcc-csm1-1_historical_r0i0p0.nc areacella:
> areacella_fx_bcc-csm1-1_historical_r0i0p0.nc
>
>
> I don't know where the problem is, I tried to repeat it for several times
> but I always have the same error about the coordinates... and the
> coordinates seem correct to me in the correl variable..I though that the
> problem could be in the transposition of pr, but that is neccesary, since
> the dimensions have to be changed for the correlation, ( The last dimension
> of x must be equal to the last dimension of y).
>
> I really apreciate your help.
>
> Thanks!
>
> Cheers,
>
> Noelia
>
>
>
>
>
> 2014-07-07 17:52 GMT+02:00 Mary Haley <haley@ucar.edu>:
>
> Hi,
>>
>> I think you are almost there. The confusion seems to be with how to
>> reorder the various arrays.
>>
>> First, are you sure "pr" is dimensioned time x lon x lat? I'm asking,
>> because this part seems wrong to me:
>>
>> pr!0="time" ; assign attributes
>> pr!1="lon"
>> pr!2="lat"
>>
>> Normally, it would be:
>>
>> pr!0="time" ; assign attributes
>> pr!1="lat"
>> pr!2="lon"
>>
>> But, are you sure you even need to do those assignments? When you read
>> "pr" off the file, it may already have named dimensions, and hence you
>> shouldn't have to do this yourself.
>>
>> Right after this line:
>>
>> pr =a->pr
>>
>> please add this line, and tell me what it reports:
>>
>> printVarSummary(pr)
>>
>>
>> Moving further down in your code, before you call escorc, you are
>> reordering the array to lon x lat x time, but I think you want lat x lon x
>> time:
>>
>> correl=escorc(wami,prT(lat|:,lon|:,time|:))
>>
>> Your "correl" array should now be dimensioned lat x lon, which is the
>> correct order for plotting.
>>
>> The rest of your code, then, is mostly correct. You want to be sure to
>> set up the "lat" and "lon" arrays with the correct names and units *before*
>> you assign them with the "&" operator:
>>
>> lon@long_name="longitude"
>> lon@units="degrees_east"
>> lat@long_name="latitude"
>> lat@units="degrees_north"
>> correl!0="lon"
>> correl!1="lat"
>> correl&lon=lon
>> correl&lat=lat
>>
>> --Mary
>>
>>
>> On Sat, Jul 5, 2014 at 9:25 AM, Noelia otero <noeli1680@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Thanks for your suggestions. Unfortunately I still have the same problem
>>> with the coordinates and the code is not working....I can't figure out
>>> why.
>>> I think that it might be a problem with the coordinates in the correl:
>>>
>>> a =
>>> addfile("/home/nof/pruebas/ensem_means/pr_Amon_bcc-csm1-1_historical_ensmean_t42_westA_meanJAS.nc","r")
>>> b =
>>> addfile("/home/nof/pruebas/WAMI_CEOF/WAMI_Amon_bcc-csm1-1_historical_ensmean.nc","r")
>>>
>>>
>>> pr =a->pr
>>> wami =b->WAMI(:,0,0,0)
>>> lat = a->lat
>>> lon = a->lon
>>> ;*****Transpose the dimension to get the correlations
>>> prT = transpose(pr)
>>> prT!0="lon" ; assign attributes
>>> prT!1="lat"
>>> prT!2="time"
>>> ;copy_VarCoords(prT,correl) ; copy attributes from temp to pcp
>>>
>>> correl=escorc(wami,prT(lon|:,lat|:,time|:))
>>> correl!0="lon"
>>> lon@long_name="longitude"
>>> lon@units="degrees_east"
>>> correl&lon=lon
>>> correl!1="lat"
>>> lat@long_name="latitude"
>>> lat@units="degrees_north"
>>> correl&lat=lat
>>> ;printVarSummary(correl)
>>>
>>> When I do printVarSummary(correl) the values seem to me correct, but if
>>> I do:
>>> printVarSummary(correl&lat)
>>>
>>> ;********
>>> Variable: lat (coordinate)
>>> Type: double
>>> Total Size: 144 bytes
>>> 18 values
>>> Number of Dimensions: 1
>>> Dimensions and sizes: [lat | 18]
>>> Coordinates:
>>> Number Of Attributes: 4
>>> axis : Y
>>> units : degrees_north
>>> long_name : latitude
>>> standard_name : latitude
>>>
>>> Could it be the problem here? Any idea??
>>> Thanks again,
>>>
>>> Cheers,
>>>
>>> Noelia
>>>
>>>
>>>
>>> 2014-07-04 8:22 GMT+02:00 Mahesh Varma <mkmvarma@gmail.com>:
>>>
>>> I think left most dimension of correl should be lat. Try correl(lat |:,
>>>> lon|:) in the plotting statement.
>>>> On Jul 3, 2014 11:08 PM, "Noelia otero" <noeli1680@gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I am looking for some support to fix the next problem. I have already
>>>>> read some posts concerning this message, but so far, I did not solve this
>>>>> (I am start learning the language).
>>>>>
>>>>> after running the script, this is the message:
>>>>>
>>>>>
>>>>> Variable: correl
>>>>> Type: float
>>>>> Total Size: 2016 bytes
>>>>> 504 values
>>>>> Number of Dimensions: 2
>>>>> Dimensions and sizes: [lon | 18] x [lat | 28]
>>>>> Coordinates:
>>>>> lon: [37.67308962904533..-9.767145559195573]
>>>>> lat: [-28.125..47.8125]
>>>>> Number Of Attributes: 1
>>>>> _FillValue : 1e+20
>>>>> (0) check_for_y_lat_coord: Warning: Data either does not contain a
>>>>> valid latitude coordinate array or doesn't contain one at all.
>>>>> (0) A valid latitude coordinate array should have a 'units' attribute
>>>>> equal to one of the following values:
>>>>> (0) 'degrees_north' 'degrees-north' 'degree_north' 'degrees
>>>>> north' 'degrees_N' 'Degrees_north' 'degree_N' 'degreeN' 'degreesN' 'deg
>>>>> north'
>>>>> (0) check_for_lon_coord: Warning: Data either does not contain a
>>>>> valid longitude coordinate array or doesn't contain one at all.
>>>>> (0) A valid longitude coordinate array should have a 'units'
>>>>> attribute equal to one of the following values:
>>>>> (0) 'degrees_east' 'degrees-east' 'degree_east' 'degrees east'
>>>>> 'degrees_E' 'Degrees_east' 'degree_E' 'degreeE' 'degreesE' 'deg east'
>>>>>
>>>>> And this is the code :
>>>>>
>>>>> ;*****************************************************************************
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>>>>> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/shea_util.ncl"
>>>>>
>>>>> ;*******************************************************************************
>>>>> begin
>>>>>
>>>>> a =
>>>>> addfile("/home/nof/pruebas/ensem_means/pr_Amon_bcc-csm1-1_historical_ensmean_t42_westA_meanJAS.nc","r")
>>>>> b =
>>>>> addfile("/home/nof/pruebas/WAMI_CEOF/WAMI_Amon_bcc-csm1-1_historical_ensmean.nc","r")
>>>>>
>>>>>
>>>>> pr =a->pr
>>>>> wami =b->WAMI(:,0,0,0)
>>>>> lat = a->lat
>>>>> lon = a->lon
>>>>>
>>>>> pr!0="time" ; assign attributes
>>>>> pr!1="lon"
>>>>> pr!2="lat"
>>>>> wami!0="time"
>>>>> ;pr&lat=lat
>>>>> ;pr&lon=lon
>>>>> prT = transpose(pr)
>>>>> copy_VarCoords(pr,wami) ; copy attributes from temp to pcp
>>>>> correl=escorc(wami,prT(lon|:,lat|:,time|:))
>>>>> correl!1="lat"
>>>>> correl!0="lon"
>>>>> correl&lat=pr&lat
>>>>> correl&lon=pr&lon
>>>>> correl&lat@units = "degrees_north"
>>>>> correl&lon@units = "degrees_east"
>>>>> printVarSummary(correl)
>>>>> wks = gsn_open_wks("x11","example")
>>>>> plot = gsn_csm_contour_map_ce(wks,correl,False)
>>>>>
>>>>> end
>>>>>
>>>>> I don't understand the message very much,because looking into the
>>>>> variables and dimensions, the names seem correct to me, so I don't know
>>>>> where the problem is...what am I missing?
>>>>> Thanks a lot in advance!
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Noelia
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>
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>>
>

Received on Tue Jul 08 04:02:51 2014