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 important part: 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) ;
Can anyone point me in the right direction to get around this?
The problem ended up being with ncks. Converting the file with ncks resulting in repeated dimensions (e.g. ACCPA(phony_dim_0, phony_dim_0) ;)
Using nccopy instead, the converted netCDF file did not produce repeated dimensions (ACCPA(phony_dim_0, phony_dim_1) ;)