[ncl-talk] Read HDF5 file

[David Brown]

This is a bit confusing, because you say HDF5 in the subject, but then
you say that the data is in hdf4 format. The current version of NCL
handles HDF4 groups differently from HDF5 groups. The HDF4 module uses
group tag numbers appended to the variable names to differentiate
groups. Eventually we would like to make both modules work the same
way but that is not the case now.
You have not said whether you tried your code on a sample file. If it
worked, then you actually have HDF5 data.
Basically you should be able to treat a group just like a file, so you
should be able to get subgroups of a group the same way you get the
top level groups from the file.
 -dave



On Tue, Jun 9, 2015 at 11:35 AM, dream916 <dream916 at gmail.com> wrote:
> Hi,
>
> I was trying to read global fire emission dataset v4 in hdf4 format. I
> searched online and couldn't find any examples how to read groups within
> group. My code is as follows:
>
> ; read hdf5 fire dataset
> begin
> setfileoption("h5", "FileStructure", "Advanced")
> f = addfile("GFED4.0s_1997.hdf5","r")
> grps = getfilegroups(f,"/",0)
> print(grps)
> grps2 = getfilegroups(f,"/emissions/",0)
> print(grps2)
> lat = f->lat
> lon = f->lon
> printVarSummary(lat)
> printVarSummary(lon)
> g = f=>ancill
> gridarea = g->grid_cell_area
> printVarSummary(gridarea)
> emissions = f=>emissions
>
> in the dataset, emissions is a group which contains two subgroups (month and
> partitioning) (see below).
>
> group: emissions {
>
>
>   group: \01 {
>
>     dimensions:
>
>     phony_dim_52 = 720 ;
>
>     phony_dim_53 = 1440 ;
>
>     variables:
>
>     float C(phony_dim_52, phony_dim_53) ;
>
>     string C:long_name = "GFED4s biomass burning carbon emissions" ;
>
>     string C:units = "g C / m^2 / month" ;
>
>     float DM(phony_dim_52, phony_dim_53) ;
>
>     string DM:long_name = "GFED4s biomass burning dry matter emissions" ;
>
>     string DM:units = "kg DM / m^2 / month" ;
>
>     float small_fire_fraction(phony_dim_52, phony_dim_53) ;
>
>     string small_fire_fraction:long_name = "Fraction of total GFED4s biomass
> burning emissions originating from \"small fire burned area\"" ;
>
>     string small_fire_fraction:units = "Unitless (fraction)" ;
>
>
>     group: partitioning {
>
>       dimensions:
>
>       phony_dim_50 = 720 ;
>
>       phony_dim_51 = 1440 ;
>
>       variables:
>
>       float C_AGRI(phony_dim_50, phony_dim_51) ;
>
>       string C_AGRI:long_name = "Contribution of agricultural waste burning
> to total monthly biomass burning carbon emissions" ;
>
>       string C_AGRI:units = "Unitless" ;
>
>       float C_BORF(phony_dim_50, phony_dim_51) ;
>
>       string C_BORF:long_name = "Contribution of boreal forest fires to
> total monthly biomass burning carbon emissions" ;
>
>       string C_BORF:units = "Unitless" ;
>
>
> So my question is how to read the monthly emissions and partitioning
> associated with each month into an array.
> Thanks,
> Lei Meng
>
>
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