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


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


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

<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>


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

-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.


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

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