Re: [ferret_users] Error when subsetting NetCDF file

Hi Ansley,

Thanks so much, that has solved the problem! I now have a follow up question:

I imported these subsampled netCDF files into MATLAB, and they mysteriously changed size from 2160x586x1x60 to 2174x586x1x60. I then performed some calculations resulting in new fields called OMEGAAR and OMEGAAR2100 (also 2174x586x1x60) and used nccreate and ncwrite to append them to my original netcdf file. So now I have two sets of variables in the same .nc file which have two different x axes, with the two new variables being ever-so-slightly too long in the x-direction. Also, the new variables don't appear to be georeferenced (see out put of "grid" below). So, my question is, how can I force these two new variables to use the X grids of the original variables and save them as a new file where everything is consistent? If it involves arbitrarily trimming them by 14 in the x-direction that should be fine because the resolution is quite high and I will only be using the resulting figures for qualitative purposes.

Thanks for your help,

Nancy

yes? show data

currently SET data sets:

1> ./BSOSE20132017wOmega.nc

name title I J K L

TEMP Temperature 1:2160 1:586 1:1 1:60

S Salinity 1:2160 1:586 1:1 1:60

TCARBN DIC 1:2160 1:586 1:1 1:60

ALKALI TAlk 1:2160 1:586 1:1 1:60

PHT pHT 1:2160 1:586 1:1 1:60

PCO2 pCO2 1:2160 1:586 ... 1:60

NITRATE Nitrate 1:2160 1:586 1:1 1:60

OMEGAAR 1:2174 1:586 1:1 1:60

OMEGAAR2100

1:2174 1:586 1:1 1:60

yes? show grid S[d=1]

GRID GGB1

name axis # pts start end subset

XC LONGITUDE 2160mi 0.083E(0.083333) 0.083W(359.92) full

YC LATITUDE 586 i 77.983S 30.017S full

Z52_52 DEPTH (m) 1 r- -2.1 -2.1 full

TIME TIME 60 r 30-JAN-2013 20:48 31-DEC-2017 10:24 full

yes? show grid OMEGAAR[d=1]

GRID GGB3

name axis # pts start end subset

XCN6_2167 X 2174 r 1 2174 full

YC LATITUDE 586 i 77.983S 30.017S full

Z52_52 DEPTH (m) 1 r- -2.1 -2.1 full

TIME TIME 60 r 30-JAN-2013 20:48 31-DEC-2017 10:24 full

Nancy L. Williams

NRC Postdoctoral Fellow

NOAA Pacific Marine Environmental Laboratory

nancy.williams@xxxxxxxx

On Wed, Nov 28, 2018 at 2:54 PM Ansley C. Manke <ansley.b.manke@xxxxxxxx> wrote:

Hi ,

Nancy and I looked at this and it turns out that the file uses an INT64 data type to store the time coordinates. That's very slightly non-standard, as INT64 is a type not listed in the CF standard. We will be able to add it to the types that PyFerret (and Ferret) recognizes. That will be in a future PyFerret release.

Meanwhile, we can redefine the time axis within the PyFerret session, so PyFerret will write it out ok, and without changing any of the time information. DEFINE AXIS/LIKE= gets the time origin and units from the original axis and t[gt=time] will use the same coordinates. It just makes it a Ferret-defined axis rather than an axis from the file.

yes? define axis/t/like=time time = t[gt=time]
Replacing definition of axis TIME            *** NOTE: grid GON1 used by data set bsose_i001_2013to2017_monthly_Salt            *** NOTE: Redefinition may alter apparent contents of data set ...

There may be more lines of ***NOTE as the definition of the axis "time" from the file is being changed for all of the grids in the file. Again this is happening just in the session, making new definition of what PyFerret is going to use for the time axis of the variable.

-Ansley

On 11/28/2018 9:47 AM, Nancy Williams - NOAA Affiliate wrote:

Hello All,

I am trying to subset a large NetCDF file to sample only monthly surface salinity values for 2013-2017 using the following code but am getting a NetCDF error. Please let me know if you have any suggestions.

Thanks,

Nancy Williams

williams% pyferret

NOAA/PMEL TMAP

PyFerret v7.42 (optimized)

Darwin 14.5.0 - 08/01/18

27-Nov-18 15:35

yes? set memory/size=1000

yes? use bsose_i001_2013to2017_monthly_Salt.nc

     *** NOTE: Internal err: unknown data type

     *** NOTE: Axis coordinates are decreasing-ordered. Reversing ordering for axis Z

yes? show data

     currently SET data sets:

  1> ./bsose_i001_2013to2017_monthly_Salt.nc  (default)

name     title     I     J     K     L

ITER     model timestep number   ...     ...     ...     1:60

DEPTH   ocean depth   1:2160   1:586     ...     ...

RA     cell area   1:2160   1:586     ...     ...

DRF   cell z size   ...     ...     1:52   ...

HFACC   vertical fraction of open cell   1:2160   1:586     1:52   ...

SALT     Salinity     1:2160   1:586     1:52   1:60

yes? let S=SALT[k=52]

yes? show var

Created by DEFINE VARIABLE:

>>> Definitions that replace any file variable of same name:

     S = SALT[K=52]

yes? save/clobber/file="BSOSE20132017.nc" S

LISTing to file BSOSE20132017.nc

NetCDF: Not a valid data type or _FillValue type mismatch (OPeNDAP/netCDF Error code -45)

Failed creating coord variable TIME

yes?

--

Nancy L. Williams
NRC Postdoctoral Fellow
NOAA Pacific Marine Environmental Laboratory
nancy.williams@xxxxxxxx