find lat/long point in a hdf5

Question

I have an HDF5 files, global coverage of temperature. The file was converted from netcdf. The conversion process set longitude from 0 to 360 and additionally flipped the map upside down, so north is now south. I have used HDFView and I can display the file but there is no way to interact with the map so locate a specific lat/long combination. The file doesn't display properly in arcmap even after setting the correct projection. Is there anyway I can display the data and click on a location and extract lat/long or draw a point in a specific lat/long?

score 0 · Answer 1 · answered Feb 11 '15 at 15:06

Short answer: No, that's not possible.

Long answer: Unlike NetCDF, HDF5 is a general purpose file format. It allows you to store n-dimensional numerical arrays (called datasets), grouped into folders (hence the name "hierarchical"). Nothing more. There is no semantics. To HDF5, your data is not a "map", it's just an array. Therefore, HDFView does not "know" about latitudes and longitudes. That information was lost in the NetCDF => HDF5 conversion process. Actually, the lat/lon arrays are probably still in the file but they no longer have any inherent meaning. NetCDF, on the other hand, imposes a common data model including coordinate systems. That's why the various visualization tools let you interact with your data in a more sophisticated way.

What tool did you use to convert your NetCDF-file to HDF5? You can use HDF5 to store meteorological data (I do that, it works well). But then you have to write your own tools for georeferencing and visualization. Check out the h5py project if you're into Python.

I used just a fortran90 script. Yes lat and long are one of the data in the h5 files — Herman Toothrot, Feb 16 '15 at 11:48

score 0 · Answer 2 · answered Feb 11 '15 at 16:55

As @heron13 has said, HDF5 is a file format.

What version of NetCDF was your file? As version 4 uses an enhanced version of HDF5 as the storage layer.

Does your NetCDF file follow (have) the CF conventions or COARDS conventions? If so I would look at the program you used to convert it to HDF5, as HDF5 can support the same conventions. For example.

Once you confirm that the conventions are in the HDF5 file, arcmap is meant to support them too (sorry I do not have access to arcmap to confirm).

Here's a look at a NetCDF file with the CF conventions:

$ ncdump tos_O1_2001-2002.nc | less
  netcdf tos_O1_2001-2002 {
  dimensions:
    lon = 180 ;
    lat = 170 ;
    time = UNLIMITED ; // (24 currently)
    bnds = 2 ;
  variables:
    double lon(lon) ;
            lon:standard_name = "longitude" ;
            lon:long_name = "longitude" ;
            lon:units = "degrees_east" ;
            lon:axis = "X" ;
            lon:bounds = "lon_bnds" ;
            lon:original_units = "degrees_east" ;
  ...

While here is a view of the same file only using h5dump:

$ h5dump tos_O1_2001-2002.nc | less
HDF5 "tos_O1_2001-2002.nc" {
GROUP "/" {
 ATTRIBUTE "Conventions" {
  DATATYPE  H5T_STRING {
     STRSIZE 6;
     STRPAD H5T_STR_NULLTERM;
     CSET H5T_CSET_ASCII;
     CTYPE H5T_C_S1;
  }
  DATASPACE  SCALAR
  DATA {
  (0): "CF-1.0"
  }
}
...

One other question, is there any reason why you are not using the NetCDF file in arcmap?

find lat/long point in a hdf5

2 Answers2