h5repack man page

h5repack — Copy an HDF5 file to a new file with or without compression/chunking

Synopsis

h5repack -i file1 -o file2 [-h] [-v] [-f ´filter´] [-l ´layout´] [-m number] [-e file]

Description

h5repack is a command line tool that applies HDF5 filters to a input  file file1, saving the output in a new file, file2.

´filter´ is a string with the format <list of objects> : <name of filter> = <filter parameters>.

<list of objects> is a comma separated list of object names meaning  apply compression only to those objects. If no object names are  specified, the filter is applied to all objects.

<name of filter> can be:
   GZIP, to apply the HDF5 GZIP filter (GZIP compression)
   SZIP, to apply the HDF5 SZIP filter (SZIP compression)
   SHUF, to apply the HDF5 shuffle filter
   FLET, to apply the HDF5 checksum filter
   NONE, to remove the filter

<filter parameters> contains the optional compression information:
   SHUF (no parameter)
   FLET (no parameter)
   GZIP=<deflation level> from 1-9
   SZIP=<pixels per block,coding> (pixels per block is a even number in  2-32 and coding method is 'EC' or 'NN')

´layout´ is a string with the format
   <list of objects> : <layout type>

<list of objects> is a comma separated list of object names, meaning  that layout information is supplied for those objects. If no object  names are specified, the layout is applied to all objects.

<layout type> can be:
   CHUNK, to apply chunking layout
   COMPA, to apply compact layout
   CONTI, to apply continuous layout

<layout parameters> is present for the chunk case only it is the  chunk size of each dimension: <dim_1 x dim_2 x ... dim_n>

Options

file1,file2

The input and output HDF5 files

-h

Print a help message

-f filter

Filter type

-l layout

Layout type

-v

Verbose mode. Print output (list of objects in the file, filters and  layout applied).

-e file

File with the -f and -l options (only filter and layout flags)

-d delta

Print only differences that are greater than the limit delta. delta must be a positive number. The comparison criterion is whether the  absolute value of the difference of two corresponding values is greater  than delta (e.g., |a-b| > delta, where a is a value in file1 and b is a value in file2).

-m number

Do not apply the filter to objects which size in bytes is smaller  than number. If no size is specified a minimum of 1024 bytes is assumed.

Examples

Apply GZIP compression to all objects in file1 and save the output in file2:

h5repack -i file1 -o file2 -f GZIP=1 -v

Apply SZIP compression only to object ´dset1´:

h5repack -i file1 -o file2 -f dset1:SZIP=8,NN -v

Apply a chunked layout to objects ´dset1´ and ´dset2´:

h5repack -i file1 -o file2 -l dset1,dset2:CHUNK=20x10 -v

See Also

h5dump(1), h5ls(1), h5diff(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1), h5repart(1).