Re: [netcdfgroup] Convert from HDF5 to netCDF4 while renaming dimensions

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: Re: [netcdfgroup] Convert from HDF5 to netCDF4 while renaming dimensions
• From: Lucas Sterzinger <lsterzinger@xxxxxxxxxxx>
• Date: Thu, 9 Jul 2020 13:10:05 -0700

I think I have it figured out after a couple very quick replies (thank
you!).

The problem was ncks compacting phony_dim_0 and phony_dim_1 into a single
phony_dim_0, causing repeated dimensions in my variables. Using nccopy
instead  of ncks to convert to netcdf, I was able to maintain the
phony_dim_0 and phony_dim_1 dimensions through the conversion, and can
rename them with ncrename.

Thanks to all the replied,
Lucas

On Thu, Jul 9, 2020 at 12:52 PM Lucas Sterzinger <lsterzinger@xxxxxxxxxxx>
wrote:

> Hello,
>
> I have a set of HDF5 files that have the following header:
>
> netcdf control-A-2017-05-12-090000-g1 {
> dimensions:
>         phony_dim_0 = 16 ;
>         phony_dim_1 = 16 ;
>         phony_dim_2 = 200 ;
>         phony_dim_3 = 2 ;
>         phony_dim_4 = 1 ;
>         phony_dim_5 = 4 ;
> variables:
>         ...
>
> Since it's HDF5, the dimensions are created as phony_dim_x. In this case,
> phony_dim_0 and phony_dim_1 are the y and x coordinates, respectively. I
> would like to rename the dimensions appropriately. Since renaming
> dimensions in HDF5 is not possible (since they don't technically exist), I
> need to convert to netcdf first. to do so I use ncks in.h5 out.nc.
>
> However, the header info of the converted file is:
>
> netcdf control-A-2017-05-12-090500-g1 {
> dimensions:
>         phony_dim_0 = 16 ;
>         phony_dim_1 = 200 ;
>         phony_dim_2 = 2 ;
>         phony_dim_3 = 1 ;
>         phony_dim_4 = 4 ;
> variables:
>         ...
>
> Here's the part that's giving me issue: the two phony_dim_[0,1]
> dimensions have been combined to a single dimension, phony_dim_0. I
> assume this is because they have the same value, and so the netcdf
> conversion assumes they're the same.
>
> A variable that was listed in the hdf5 file as ACCPA(phony_dim_0,
> phony_dim_1) ; is now ACCPA(phony_dim_0, phony_dim_0) ;, with two
> identical dimensions.
>
> Thus, I am not able to rename the dimensions individually. If I do ncrename
> -d phony_dim_0,y out.nc, I get ACCPA(y, y) ;
>
> Is there a way to get around this?
>
> Thanks!
>
> Lucas
>
> --
> Lucas Sterzinger
> PhD Student
> UC Davis Cloud Physics Research Group
> Hoagland Hall 230
> lsterzinger@xxxxxxxxxxx
> https://lucassterzinger.com
>


-- 
Lucas Sterzinger
PhD Student
UC Davis Cloud Physics Research Group
Hoagland Hall 230
lsterzinger@xxxxxxxxxxx
https://lucassterzinger.com

• References:
  • [netcdfgroup] Convert from HDF5 to netCDF4 while renaming dimensions
    • From: Lucas Sterzinger