Hi Gerry,
Your problem stems from the fact that although the file claims to be CF-1.0 compliant, it is not quite. The dimensions are named "lat" and "lon" but the intended coordinate variables are named "latitude" and "longitude". The CF convention is that a variable is a (1D) coordinate variable only if it has the same name as the dimension. Doing a printVarSummary on the data variable you get this:
Variable: model4Ssh
Type: float
Total Size: 41445756 bytes
10361439 values
Number of Dimensions: 3
Dimensions and sizes: [time | 99] x [lat | 261] x [lon | 401]
Coordinates:
time: [734776.5.. 0]
Number Of Attributes: 5
_FillValue : 999900
units : m
__FillValue : -9999
long_name : sea-surface height
positive : up
Notice the dimensions are named but no coordinates are associated with lat and lon. The fix is simply to add these two lines after you read in model4SSh
model4Ssh&lat = model4Lat
model4Ssh&lon = model4Lon
-dave
On Oct 7, 2011, at 1:59 PM, Gerald Creager wrote:
> Adam, I'm back....
>
> We're working on a project with all sorts of purported NetCDF files I'm
> getting to sort through. Just as an idea, the one I'm on now uses Matlab
> datenum for its time variable format; that's a solved problem.
>
> It does have 1d lat/lon data as evidenced by the data from ncl_filedump
> shown below:
> [gerry@wagoneer Step3]$ ncl_filedump MITGOM_STEP-3_FCAST-2.nc
> Copyright (C) 1995-2011 - All Rights Reserved
> University Corporation for Atmospheric Research
> NCAR Command Language Version 6.0.0
> The use of this software is governed by a License Agreement.
> See http://www.ncl.ucar.edu/ for more details.
>
> Variable: f
> Type: file
> filename: MITGOM_STEP-3_FCAST-2
> path: MITGOM_STEP-3_FCAST-2.nc
> file global attributes:
> title : MITgcm GoM three-month forecast for GOMEX-PPP STEP-3:2011
> Model : MITgcm
> Filename :
> /net/wave3/ganeshgopal/WAVE5_DATA/GOM_4DVAR_2011_RUNS/run_23jul2011/res_nc/MITGOM_STEP-3_FCAST-2.nc
> Model_Resolution : 1/10 degree
> Hgrid : Arakawa-C Grid
> Stdgrid : Interpolated to standard grid : [262E-282E, 18N-31N] :
> 0.05 deg resolution : ( IM=401, JM=201 )
> Vgrid : Z - level (40 levels)
> Stdlevel : Interpolated to standard level: 22 levels ( 0, -20,
> -40, -60, -80, -100, -150, -200, -250, -300, -400, -500, -600, -700,
> -800, -900, -1000, -1500, -2000, -2500, -3000, -3500 m )
> Institution : Scripps Institution of Oceanography
> Conventions : CF-1.0
> Contact : Bruce Cornuelle (bdc@ucsd.edu), Ganesh Gopal
> (ggopalak@ucsd.edu)
> dimensions:
> lon = 401
> lat = 261
> zlev = 22
> time = 99 // unlimited
> variables:
> float longitude ( lon )
> units : degrees_east
> long_name : longitude at cell-center
>
> float latitude ( lat )
> units : degrees_north
> long_name : latitude at cell-center
>
> float zlev ( zlev )
> units : m
> long_name : depth at cell-center
> negative : down
>
> float time ( time )
> units : matlab datenum
> long_name : date
>
> float sea_floor_depth_below_sea_level ( lat, lon )
> units : m
> __FillValue : -9999
> long_name : depth
> positive : down
>
> float sea_surface_height_above_sea_level ( time, lat, lon )
> units : m
> __FillValue : -9999
> long_name : sea-surface height
> positive : up
>
> float eastward_sea_water_velocity_at_bottom ( time, lat, lon )
> units : m s-1
> __FillValue : -9999
> long_name : bottom u
>
> float northward_sea_water_velocity_at_bottom ( time, lat, lon )
> units : m s-1
> __FillValue : -9999
> long_name : bottom v
>
> float temp_at_bottom ( time, lat, lon )
> units : deg C
> __FillValue : -9999
> long_name : bottom temp
>
> float salinity_at_bottom ( time, lat, lon )
> units : psu
> __FillValue : -9999
> long_name : bottom salinity
>
> float eastward_sea_water_velocity ( time, zlev, lat, lon )
> units : m s-1
> __FillValue : -9999
> long_name : eastward component of velocity
>
> float northward_sea_water_velocity ( time, zlev, lat, lon )
> units : m s-1
> __FillValue : -9999
> long_name : northward component of velocity
>
> float sea_water_potential_temperature ( time, zlev, lat, lon )
> units : deg C
> __FillValue : -9999
> long_name : potential temperature
>
> float sea_water_salinity ( time, zlev, lat, lon )
> units : psu
> __FillValue : -9999
> long_name : salinity
>
>
> I'm getting a lat/lon error similar to what I was seeing over the last
> couple of days with the last "compliant" file data:
> (0) check_for_y_lat_coord: Warning: Data either does not contain a valid
> latitude coordinate array or d
> oesn't contain one at all.
> (0) A valid latitude coordinate array should have a 'units' attribute
> equal to one of the following val
> ues:
> (0) 'degrees_north' 'degrees-north' 'degree_north' 'degrees north'
> 'degrees_N' 'Degrees_north' 'deg
> ree_N' 'degreeN' 'degreesN' 'deg north'
> (0) check_for_lon_coord: Warning: Data either does not contain a valid
> longitude coordinate array or do
> esn't contain one at all.
> (0) A valid longitude coordinate array should have a 'units' attribute
> equal to one of the following va
> lues:
> (0) 'degrees_east' 'degrees-east' 'degree_east' 'degrees east'
> 'degrees_E' 'Degrees_east' 'degree_E
> ' 'degreeE' 'degreesE' 'deg east'
>
>
> I'm currently uploading MITGOM_STEP-3_FCAST-2.nc to the FTP site for
> perusal, if y'all have time. I'm also uploading Step23-Model4.ncl.
>
> Both are going into 'incoming'.
>
> Thanks for all your support. I suspect this is another minor gotcha but
> I'm lost.
>
> gerry
>
> On 10/06/2011 11:28 AM, Adam Phillips wrote:
>> Hi Gerry,
>> When you have 2D latitudes/longitudes, you need to assign the 2D lat/lon
>> arrays as lat2d/lon2d attributes of your data array.
>>
>> I tried this with the data file you sent in:
>>
>> ncl 0> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>> ncl 1> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>> ncl 2> a = addfile("fcast_201009.nc","r")
>> ncl 3> t = a->t(:,0,:,:)
>> ncl 4> t@lat2d = a->alat
>> ncl 5> t@lon2d = a->alon
>> ncl 6> wks = gsn_open_wks("x11","test")
>> ncl 7> plot = gsn_csm_contour_map(wks,t(0,:,:),False)
>>
>> and it worked. Let us know if you continue to have a problem plotting
>> the data.. Adam
>>
>> On 10/06/2011 09:10 AM, Gerald Creager wrote:
>>> I just tried but passive mode was refused (I've had this problem
>>> recently here, too!). Donna or I will get a subset of one of the model
>>> files uploaded, as well as the script shortly.
>>>
>>> Thanks, Gerry
>>>
>>>
>>> On 10/06/2011 10:01 AM, Dennis Shea wrote:
>>>> GC .. Send 2 or 3 sample files and a minimalistic script that isolates
>>>> the issues you are having.
>>>>
>>>> ftp ftp.cgd.ucar.edu
>>>> anonymous
>>>> Use your email address for the password
>>>> cd incoming
>>>> put ...
>>>> put ...
>>>> :
>>>> quit
>>>>
>>>> Send email to ncl-talk with the following information:
>>>>
>>>> The names of the files after you have successfully completed the transfer.
>>>> We cannot look at the ftp/incoming directory for security reasons.
>>>> The type of system you are on (uname -a).
>>>>
>>>> THX
>>>> On 10/6/11 8:33 AM, Gerald Creager wrote:
>>>>> I checked last night. We'*ARE* running v6.0.0:
>>>>> [root@scoopdata gomexstep3]# ncl
>>>>> Copyright (C) 1995-2011 - All Rights Reserved
>>>>> University Corporation for Atmospheric Research
>>>>> NCAR Command Language Version 6.0.0
>>>>> The use of this software is governed by a License Agreement.
>>>>> See http://www.ncl.ucar.edu/ for more details.
>>>>>
>>>>> but the problem persisted. Not a real problem. I'm looking for SST and
>>>>> SSH at this point, so I snagged the top-level temperature and I'm good
>>>>> on this.
>>>>>
>>>>> Now, however, another problem with the same netcdf input. The snippet of
>>>>> code where I'm assigning variables for lat/lon:
>>>>>
>>>>> model2Lat=model2[:]->alat ; Degrees NORTH
>>>>> model2Lon=model2[:]->alon ; Degrees WEST (?)
>>>>>
>>>>> And, a print statement to see what the vars look like:
>>>>> print(model2Lat)
>>>>>
>>>>>
>>>>> Variable: model2Lat
>>>>> Type: float
>>>>> Total Size: 3767796 bytes
>>>>> 941949 values
>>>>> Number of Dimensions: 2
>>>>> Dimensions and sizes: [y | 2349] x [x | 401]
>>>>> Coordinates:
>>>>> Number Of Attributes: 3
>>>>> long_name : latitude
>>>>> units : deg-N
>>>>> coordinates : alon alat
>>>>> (0,0) 18
>>>>> (0,1) 18
>>>>> (0,2) 18
>>>>> (0,3) 18
>>>>> (0,4) 18
>>>>> ...
>>>>>
>>>>> print(model2Lon)
>>>>>
>>>>>
>>>>> Variable: model2Lon
>>>>> Type: float
>>>>> Total Size: 3767796 bytes
>>>>> 941949 values
>>>>> Number of Dimensions: 2
>>>>> Dimensions and sizes: [y | 2349] x [x | 401]
>>>>> Coordinates:
>>>>> Number Of Attributes: 3
>>>>> long_name : longitude
>>>>> units : deg-W
>>>>> coordinates : alon alat
>>>>> (0,0) -98
>>>>> (0,1) -97.95
>>>>> (0,2) -97.9
>>>>> (0,3) -97.85
>>>>> (0,4) -97.8
>>>>> (0,5) -97.75
>>>>> (0,6) -97.7
>>>>> ...
>>>>>
>>>>> OK, units are screwy:
>>>>> model2Lat@units = "degrees_north"
>>>>> model2Lon@units = "degrees_east"
>>>>> print(model2Lat)
>>>>>
>>>>>
>>>>> Variable: model2Lat
>>>>> Type: float
>>>>> Total Size: 3767796 bytes
>>>>> 941949 values
>>>>> Number of Dimensions: 2
>>>>> Dimensions and sizes: [y | 2349] x [x | 401]
>>>>> Coordinates:
>>>>> Number Of Attributes: 3
>>>>> long_name : latitude
>>>>> units : degrees_north
>>>>> coordinates : alon alat
>>>>> (0,0) 18
>>>>> (0,1) 18
>>>>> (0,2) 18
>>>>> (0,3) 18
>>>>> ...
>>>>> print(model2Lon)
>>>>>
>>>>>
>>>>> Variable: model2Lon
>>>>> Type: float
>>>>> Total Size: 3767796 bytes
>>>>> 941949 values
>>>>> Number of Dimensions: 2
>>>>> Dimensions and sizes: [y | 2349] x [x | 401]
>>>>> Coordinates:
>>>>> Number Of Attributes: 3
>>>>> long_name : longitude
>>>>> units : degrees_east
>>>>> coordinates : alon alat
>>>>> (0,0) -98
>>>>> (0,1) -97.95
>>>>> (0,2) -97.9
>>>>> (0,3) -97.85
>>>>> ...
>>>>>
>>>>> When I plot, I get a plot that isn't at the resolution I'm expecting,
>>>>> and I get:
>>>>> (0) check_for_y_lat_coord: Warning: Data either does not contain a valid
>>>>> latitude coordinate array or doesn't co
>>>>> ntain 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' 'd
>>>>> egreeN' 'degreesN' 'deg north'
>>>>> (0) check_for_lon_coord: Warning: Data either does not contain a valid
>>>>> longitude coordinate array or doesn't con
>>>>> tain 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' 'degree
>>>>> E' 'degreesE' 'deg east'
>>>>>
>>>>> As near as I can tell, I've reassigned units in an appropriate manner.
>>>>> I'm guessing this is is associate with gsn_csm_contour_map, but I've not
>>>>> found where I've gone wrong.
>>>>>
>>>>> Thanks,
>>>>> gerry
>>>>>
>>>>> On 10/05/2011 06:18 PM, Gerry Creager wrote:
>>>>>> I'll give it a try in a little while (parental duties right now!)
>>>>>>
>>>>>> gc
>>>>>>
>>>>>> Adam Phillips wrote:
>>>>>>> Hi Gerry,
>>>>>>> The newest version of ncl (v6.0.0) allows array sizes larger than 2GB.
>>>>>>> Previous versions do not. I am guessing you are using a pre-6.0.0
>>>>>>> version and your aggregated T array is (potentially) larger than 2GB..
>>>>>>>
>>>>>>> If I'm off on my guess let us know.. Adam
>>>>>>>
>>>>>>> On 10/05/2011 04:50 PM, Gerald Creager wrote:
>>>>>>>> Thanks, Gentlemen. I didn't realize that (but I should have)...
>>>>>>>>
>>>>>>>> OK, so I tried this:
>>>>>>>> model2Sst=model2[:]->t ; potential temperature with
>>>>>>>> coordinates : time, zz, y, x
>>>>>>>> fatal:Aggregating variable t from file list variable model2 as
>>>>>>>> specified
>>>>>>>> would exceed maximum NCL variable size
>>>>>>>>
>>>>>>>> gerry
>>>>>>>>
>>>>>>>> On 10/05/2011 04:45 PM, David Brown wrote:
>>>>>>>>> Hi Gerry,
>>>>>>>>> When you use 'addfiles' rather than 'addfile', you get a file list
>>>>>>>>> variable rather than a file variable. It requires a different syntax.
>>>>>>>>> Try
>>>>>>>>> model2Sst=model2[:]->t
>>>>>>>>> and
>>>>>>>>> Time = model2[:]->time
>>>>>>>>>
>>>>>>>>> You can say 'model2[0]' in order to "reference a file".
>>>>>>>>> -dave
>>>>>>>>>
>>>>>>>>> On Oct 5, 2011, at 3:09 PM, Gerald Creager wrote:
>>>>>>>>>
>>>>>>>>>> I'm trying to assign values to a variable from a netcdf file
>>>>>>>>>> (ncl_filedump output for the file is attached). A sample snippet
>>>>>>>>>> of code is attached. Note the error... And, note that line 6
>>>>>>>>>> does, in fact load the data into 'model2'.
>>>>>>>>>>
>>>>>>>>>> ncl 30> model2Sst=model2->t
>>>>>>>>>> fatal:(model2) does not reference a filencl 0> load
>>>>>>>>>> "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>>>>>>>>> ncl 1> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>>>>>>>>>> ncl 2> load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
>>>>>>>>>> ncl 3> load
>>>>>>>>>> "$NCARG_ROOT/lib/ncarg/nclscripts/contrib/calendar_decode2.ncl"
>>>>>>>>>> ncl 4>
>>>>>>>>>> ncl 5> fnameModel2=systemfunc ("ls fcast_20100*.nc") ; files
>>>>>>>>>> location
>>>>>>>>>> ncl 6> model2=addfiles(fnameModel2, "r")
>>>>>>>>>> ncl 7> type="x11"
>>>>>>>>>> ncl 8> Time=model2->time
>>>>>>>>>> fatal:(model2) does not reference a file
>>>>>>>>>> fatal:Execute: Error occurred at or near line 8
>>>>>>>>>>
>>>>>>>>>> fatal:Execute: Error occurred at or near line 30
>>>>>>>>>>
>>>>>>>>>> Thanks, Gerry
>>>>>>>>>> -
>>>>>>>>>> Gerry Creager -- gerry.creager@tamu.edu
>>>>>>>>>> Texas Mesonet -- AATLT, Texas A&M University
>>>>>>>>>> Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
>>>>>>>>>> Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX
>>>>>>>>>> 77843
>>>>>>>>>> <nclfiledump-model2.txt>_______________________________________________
>>>>>>>>>>
>>>>>>>>>> ncl-talk mailing list
>>>>>>>>>> List instructions, subscriber options, unsubscribe:
>>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>>>>>>
>>>>>>
>>>>>
>>>
>>
>
> --
> Gerry Creager -- gerry.creager@tamu.edu
> Texas Mesonet -- AATLT, Texas A&M University
> Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
> Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX 77843
> _______________________________________________
> ncl-talk mailing list
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Received on Fri Oct 7 15:48:03 2011
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