From help-octave-request at bevo dot che dot wisc dot edu Fri Jan 24 11:52:57 2003
Subject: Re: hdf5 support for more complex structures
From: Jonathan Dursi <ljdursi at eugenia dot asci dot uchicago dot edu>
To: Przemek Klosowski <przemek at jazz dot ncnr dot nist dot gov>
Cc: help-octave <help-octave at bevo dot che dot wisc dot edu>
Date: Fri, 24 Jan 2003 11:43:18 -0600

On Thu, Jan 23, 2003 at 05:08:42PM -0500, Przemek Klosowski wrote:
> 
> I am interested in HDF5 support for octave. Could you say what is the
> issue with reading your control structures? 

I'm actually having difficulty with simpler things than hierarchies or
attributes; all my datasets are in `/', and while getting the attributes
read in would be good, too, I can live without them at first.

Doing an `h5ls' on one of my (1d) data files gives me something like this:
(there are lots of similar sorts of datasets, so I'm clipping some of them
out for clairity; there are lots of variables stored all of the form
Dataset {49, 1, 1, 32}, for instance)

% h5ls flamecurvature_arr_hdf5_chk_0000
FLASH\ build\ date       Dataset {1}
FLASH\ build\ directory  Dataset {1}
FLASH\ build\ machine    Dataset {1}
FLASH\ setup\ call       Dataset {1}
FLASH\ version           Dataset {1}
block\ size              Dataset {49, 1}
bounding\ box            Dataset {49, 1, 2}
coordinates              Dataset {49, 1}
dens                     Dataset {49, 1, 1, 32}
eint                     Dataset {49, 1, 1, 32}
file\ creation\ time     Dataset {1}
file\ format\ version    Dataset {1}
integer\ runtime\ parameters Dataset {37}
logical\ runtime\ parameters Dataset {22}
node\ type               Dataset {49}
real\ runtime\ parameters Dataset {61}
refine\ level            Dataset {49}
run\ comment             Dataset {1}
simulation\ parameters   Dataset {1}
string\ runtime\ parameters Dataset {29}
unknown\ names           Dataset {14, 1}

Trying to read these into octave gives me:

octave:1> load -hdf5 -import -force flamecurvature_arr_hdf5_chk_0000
warning: load: can't read `file format version' (unknown datatype)
warning: load: can't read `gid' (unknown datatype)
warning: load: can't read `integer runtime parameters' (unknown compound datatype)
warning: load: can't read `logical runtime parameters' (unknown compound datatype)
warning: load: can't read `node type' (unknown datatype)
warning: load: can't read `real runtime parameters' (unknown compound datatype)
warning: load: can't read `refine level' (unknown datatype)
warning: load: can't read `simulation parameters' (unknown compound datatype)
warning: load: can't read `string runtime parameters' (unknown compound datatype)
warning: load: can't read 2-dim. hdf5 string vector (null)

prot  type                       rows   cols  name
====  ====                       ====   ====  ====
 rwd  matrix                        1     37  block_size
 rwd  list                          -      -  bounding_box
 rwd  matrix                        1     37  coordinates
 rwd  list                          -      -  dens
 rwd  list                          -      -  eint
 rwd  list                          -      -  ener
 rwd  list                          -      -  enuc

So none of the compound datatypes are read in, and the same for a lot of
the string information/arrays (unknown\ names, FLASH\ build\ date, etc.)
Awkwardly, many of the multidimensional arrays like dens/eint are read
in as lists.

I'm only just now starting to look at load-save.cc, and also to try
to understand Octave's data types.  It seems like getting these things read
in should be fairly do-able; is there anything I should know before trying
to tackle it?

	- Jonathan
-- 
ljdursi at flash dot uchicago dot edu



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