Re: problem loading hdf5 file

[Paul Kienzle]

On May 5, 2004, at 4:30 AM, David Bateman wrote:

> According to W.J. Atsma <address@hidden> (on 05/04/04):
> > Why not export all the data in a single struct if the file is not an
> > octave-created one, replacing the file-like structure "/" with ".". 
> > Then you
> > can look at the complete structure in octave and reinterpret them as 
> > you
> > like.
>
> HDF5 doesn't have the concept of a structure. The implementation of a
> structure that octave expects in files to import is as an HDF5 GROUP.
> The problem is the example given uses an HDF5 DATASET with a compound
> datatype used to contain the structure. This is much harder to 
> interpret
> if you don't know the form of the structure a-priori as you have to
> construct an HDF5  compound type internally to hold the structure 
> before
> you can import the values. It is also more limiting as all members of
> the structure must have the same size.

The matlab function hdfinfo seems to load in a complete
description of the dataset using a tree of structures, with
structure arrays for the repeating parts.  It doesn't read
in the actual data which is good because the datasets can
be very large and the user may only want to read in a part
of one.   The function hdfread takes one of the nodes of
the structure tree and reads it in.  With the appropriate
options, it can read only part of the dataset.  A similar
interface could be set up for writing to an HDF file.

Matlab also provides a direct mapping of the hdf C APIs.
It's my belief that higher level languages should hide
the details whenever they can, so I wouldn't bother with
this except if I needed it for compatibility.

Paul Kienzle
address@hidden

PS,  I didn't see a simple way to examine the tree
structure returned by hdfinfo from the matlab
command line, so I wrote my own.   Something similar
should work for octave, but with deblank(argn(1,:))
instead of inputname(1).

%SHOWSTRUCT display structure tree
%   showstruct(S[,n]) displays the contents of structure S as
%   well as any substructures.  The first bit of the data is displayed
%   for each field.  If n is supplied, only print the first n levels.

function showstruct(s,maxlevel,indent,name)
  if nargin<2, maxlevel=inf; end
  if nargin<3, indent=0; end
  if nargin<4, name=inputname(1); end
  fields=fieldnames(s);
  n = prod(size(s));
  if n==1
    fprintf(1,'%s--- %s ---\n',blanks(indent),name);
    for i=1:length(fields)
      fprintf(1,'%s%s: \t', blanks(indent), fields{i});
      showfield(s.(fields{i}),maxlevel-1,indent+2,[name,'.',fields{i}]);
    end
  else
    for j=1:n
      fprintf(1,'%s--- %s(%d) ---\n',blanks(indent),name,j);
      for i=1:length(fields)
        fprintf(1,'%s%s: \t', blanks(indent), fields{i});
        
showfield(s(j).(fields{i}),maxlevel-1,indent+2,[name,'.',fields{i}]);
      end
    end
  end

function showfield(f,maxlevel,indent,name)
  fprintf(1,'%s ',class(f));
  showdims(size(f));
  if isstruct(f)
    fprintf(1,'\n');
    if maxlevel>0, showstruct(f,maxlevel,indent,name); end
  elseif isstr(f)
    fprintf(' ''%.30s''\n',f(1,:));
  elseif isreal(f)
    if isempty(f)
      t='';
    elseif prod(size(f))<8
      t=sprintf('%g, ',double(f(1:end-1)));
      t=[t,sprintf('%g',double(f(end)))];
    else
      t=sprintf('%g, ',double(f(1:4)));
      t=[t,'...'];
    end
    fprintf(1,' [%s]\n',t);
  else
    fprintf(1,'\n');
  end

function showdims(d)
  fprintf(1,'%d',d(1));
  fprintf(1,'x%d',d(2:end));



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