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h5read.cc
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/*
*
* Copyright (C) 2012 Tom Mullins
* Copyright (C) 2015 Tom Mullins, Thorsten Liebig, Anton Starikov, Stefan Großhauser
* Copyright (C) 2008-2013 Andrew Collette
*
* This file is part of hdf5oct.
*
* hdf5oct is free software: you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* hdf5oct is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with hdf5oct. If not, see <http://www.gnu.org/licenses/>.
*
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
// integrated into the GNU Octave build
#include "oct.h"
#include "lo-ieee.h"
#else
// as a package
#include <octave/oct.h>
#include <octave/lo-ieee.h>
#endif
#include <cstdlib>
#include <cerrno>
#include <iostream>
#include <algorithm>
#include <string>
#include "gripes.h"
#include "file-stat.h"
using namespace std;
#if ((H5_VERS_MAJOR > 1) || (H5_VERS_MINOR >= 8))
// define this in case there is no configure script at work. This
// should not be necessary any more when integrated into core.
#define HAVE_HDF5_18 1
#endif
#if defined (HAVE_HDF5) && defined (HAVE_HDF5_18)
#include <hdf5.h>
#include "h5read.h"
#include "ls-hdf5.h"
bool
any_int_leq_zero (const Matrix& mat)
{
for (int i = 0; i < mat.length (); i++)
{
if (mat(i) < 0.5)
return true;
}
return false;
}
// if ALLOW_ZEROS, then Infs will be converted to 0s (used for COUNT)
// else, 0s will produce an error message (used for others)
int
check_vec (const octave_value& val, Matrix& mat/*out*/,
const char *name, bool allow_zeros)
{
mat = val.matrix_value ();
if (error_state)
return 0;
if (! mat.is_vector ())
{
error ("%s must be a vector", name);
return 0;
}
double mind, maxd;
if (allow_zeros)
{
for (int i = 0; i < mat.nelem (); i++)
{
if (mat(i) == octave_Inf)
mat(i) = 0;
}
if (! mat.all_integers (mind, maxd) || mat.any_element_is_negative ())
{
error ("%s can only contain non-negative integers", name);
return 0;
}
}
else if (! mat.all_integers (mind, maxd) || any_int_leq_zero (mat))
{
error ("%s can only contain positive integers", name);
return 0;
}
return 1;
}
#endif
DEFUN_DLD (h5read, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} {@var{data} =} h5read (@var{filename}, @var{dsetname})\n\
@deftypefnx {Loadable Function} {@var{data} =} h5read (@var{filename}, @var{dsetname}, @var{start}, @var{count})\n\
@deftypefnx {Loadable Function} {@var{data} =} h5read (@var{filename}, @var{dsetname}, @var{start}, @var{count}, @var{stride})\n\
@deftypefnx {Loadable Function} {@var{data} =} h5read (@var{filename}, @var{dsetname}, @var{start}, @var{count}, @var{stride}, @var{block})\n\
Read a hyperslab of data from an HDF5 file specified by its @var{filename}. \n\
The datatype will be coerced to double.\n\
For example:\n\
\n\
@example\n\
@group\n\
data = h5read (\"mydata.h5\", \"/grid/time\");\n\
@end group\n\
@end example\n\
\n\
The variable @var{dsetname} is the name of the dataset in the HDF5\n\
file to read. It has to be specified by its absolute path (or relative\n\
to the root group / ).\n\
\n\
The other four arguments are 1xn or nx1 matrices, where n is the number of dimensions\n\
in the dataset. If all are omitted, the entire dataset will be read.\n\
\n\
@var{start} is a 1-based starting offset\n\
@var{count} is the number of blocks to read. If 0 or Inf\n\
is specified in any dimension, as many blocks as possible \n\
are read in that dimension (this is not valid for @code{h5write}).\n\
@var{stride} is the offset between the start of each block. \n\
Defaults to a vector of ones.\n\
@var{block} is the size of each block to read. Defaults to a vector of ones.\n\
\n\
Datasets having a compound type consisting of two double values will\n\
be interpreted as complex valued.\n\
\n\
Generally this function tries to use the Octave datatype of\n\
the appropriate size for the given HDF5 type.\n\
\n\
@seealso{h5write}\n\
@end deftypefn")
{
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature ("h5read", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (nargin < 2 || nargin == 3 || nargin > 6 || nargout > 1)
{
print_usage ();
return octave_value_list ();
}
if (! (args(0).is_string () && args (1).is_string ()))
{
print_usage ();
return octave_value_list ();
}
string filename = args(0).string_value ();
string dsetname = args(1).string_value ();
if (error_state)
return octave_value_list ();
//open the hdf5 file
H5File file (filename.c_str (), false, false);
if (error_state)
return octave_value_list ();
if (nargin < 4)
{
octave_value retval = file.read_dset_complete (dsetname.c_str ());
return retval;
}
else
{
Matrix start, count, stride, block;
int err = 0;
err = err || ! check_vec (args(2), start, "START", false);
start -= 1;
err = err || ! check_vec (args(3), count, "COUNT", true);
if (nargin < 5)
stride = Matrix ();
else
err = err || ! check_vec (args(4), stride, "STRIDE", false);
if (nargin < 6)
block = Matrix ();
else
err = err || ! check_vec (args(5), block, "BLOCK", false);
if (err)
return octave_value_list ();
return file.read_dset_hyperslab (dsetname.c_str (),
start, count, stride, block, nargin-2);
}
#endif
}
DEFUN_DLD (h5readatt, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} {@var{data} =} h5readatt (@var{filename}, @var{objectname}, @var{attname})\n\
\n\
Reads one attribute of an object from an HDF5 file, specified by the\n\
@var{filename} and the @var{objectname}.\n\
The third argument @var{attname} is the name of the attribute which \n\
is to read.\n\
\n\
@seealso{h5writeatt}\n\
@end deftypefn")
{
octave_value retval;
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature ("h5readatt", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (nargin != 3)
{
print_usage ();
return retval;
}
if (! (args(0).is_string () && args(1).is_string () && args(2).is_string ()))
{
print_usage ();
return retval;
}
string filename = args(0).string_value ();
string objname = args(1).string_value ();
string attname = args(2).string_value ();
if (error_state)
return octave_value_list ();
//open the hdf5 file
H5File file (filename.c_str (), false, false);
if (error_state)
return octave_value_list ();
retval = file.read_att (objname.c_str (), attname.c_str ());
return retval;
#endif
}
DEFUN_DLD (h5write, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} h5write (@var{filename}, @var{dsetname}, @var{data})\n\
@deftypefnx {Loadable Function} h5write (@var{filename}, @var{dsetname}, @var{data}, @var{start}, @var{count})\n\
@deftypefnx {Loadable Function} h5write (@var{filename}, @var{dsetname}, @var{data}, @var{start}, @var{count}, @var{stride})\n\
@deftypefnx {Loadable Function} h5write (@var{filename}, @var{dsetname}, @var{data}, @var{start}, @var{count}, @var{stride}, @var{block})\n\
\n\
Write a matrix @var{data} to the specified location @var{dsetname} in \n\
a HDF5 file specified by @var{filename}.\n\
\n\
In the simplest form of this function, if the file @var{filename} does\n \
not exist, it will be created and if the dataset @var{dsetname} already\n\
exists, it will be overwritten.\n\
\n\
If more than three arguments are specified, an error will be raised if\n\
the file @var{filename} or the dataset @var{dsetname} do not exist\n\
(use @code{h5create} in order to create an file or an empty dataset).\n \
If the dataset exists, the data will be written into the specified \n\
hyperslab. This way it is possible to append data to existing datasets,\n\
provided their maximum size is sufficiently large.\n\
\n\
@var{start} is a 1-based starting offset\n\
@var{count} is the number of blocks to read. In view of @code{h5read}, note that 0 or Inf\n\
are not valid elements here.\n\
@var{stride} is the offset between the start of each block. \n\
Defaults to a vector of ones.\n\
@var{block} is the size of each block to read. Defaults to a vector of ones.\n\
\n\
Complex valued data will lead to datasets having a compound type consisting\n\
of two double values.\n\
\n\
Generally this function tries to use the HDF5 datatype of\n\
the appropriate size for the given Octave type.\n\
\n\
@seealso{h5read}\n\
@end deftypefn")
{
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature ("h5write", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (! (nargin == 3 || nargin == 5 || nargin == 6 || nargin == 7) || nargout != 0)
{
print_usage ();
return octave_value_list ();
}
if (! (args(0).is_string () && args(1).is_string ()))
{
print_usage ();
return octave_value_list ();
}
string filename = args(0).string_value ();
string location = args(1).string_value ();
if (error_state)
return octave_value_list ();
if (nargin == 3)
{
//open the hdf5 file, create it if it does not exist
H5File file (filename.c_str (), true, true);
if (error_state)
return octave_value_list ();
file.write_dset (location.c_str (),
args(2));
}
else
{
//open the hdf5 file, complain if it does not exist
H5File file (filename.c_str (), false, true);
if (error_state)
return octave_value_list ();
Matrix start, count, stride, block;
int err = 0;
err = err || ! check_vec (args(3), start, "START", false);
start -= 1;
// A count value 0 is not allowed when writing data.
err = err || ! check_vec (args(4), count, "COUNT", false);
if (nargin <= 5)
stride = Matrix ();
else
err = err || ! check_vec (args(5), stride, "STRIDE", false);
if (nargin <= 6)
block = Matrix ();
else
err = err || ! check_vec (args(6), block, "BLOCK", false);
if (err)
return octave_value_list ();
file.write_dset_hyperslab (location.c_str (),
args(2),
start, count, stride, block, nargin-3);
}
return octave_value_list ();
#endif
}
DEFUN_DLD (h5writeatt, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} h5writeatt (@var{filename}, @var{objectname}, @var{attname}, @var{attvalue})\n\
\n\
Write an attribute with name @var{attname} and value @var{attvalue} to\n\
the object named @var{objectname} in the HDF5 file specified by @var{filename}.\n\
\n\
@seealso{h5readatt}\n\
@end deftypefn")
{
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature ("h5writeatt", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (nargin != 4 || nargout != 0)
{
print_usage ();
return octave_value_list ();
}
if (! (args(0).is_string () && args(1).is_string () && args(2).is_string ()))
{
print_usage ();
return octave_value_list ();
}
string filename = args(0).string_value ();
string location = args(1).string_value ();
string attname = args(2).string_value ();
if (error_state)
return octave_value_list ();
//open the hdf5 file
H5File file (filename.c_str (), false, true);
if (error_state)
return octave_value_list ();
file.write_att (location.c_str (), attname.c_str (),
args(3));
return octave_value_list ();
#endif
}
DEFUN_DLD (h5create, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} h5create (@var{filename}, @var{dsetname}, @var{size}, @var{key}, @var{val},...)\n\
\n\
Create a dataset with name @var{dsetname} and size @var{size} \n\
in the HDF5 file specified by @var{filename}.\n\
\n\
The vector @var{size} may contain one or several Inf (or \n\
equivalently: zero) values.\n\
This will lead to unlimited maximum extent of the dataset in the\n\
respective dimensions and 0 initial extent.\n\
Note that any dataset with at least one unlimited dimension must be chunked and\n\
it is generally recommended for large datasets.\n\
\n\
The list of @var{key}, @var{val} arguments allows to specify\n\
certain properties of the dataset. Allowed settings are:\n\
\n\
@table @asis\n\
@item @option{Datatype}\n\
one of the strings @samp{double} @samp{single} @samp{uint64} @samp{uint32} @samp{uint16} @samp{uint8} @samp{int64} @samp{int32} @samp{int16} @samp{int8} \n\
\n\
@item @option{ChunkSize}\n\
The value may be either a vector specifying the chunk size,\n\
or an empty vector [], which means no chunking (this is the default),\n\
or the string @samp{auto} which makes the library choose automatically \n\
an appropriate chunk size, as best as it can. Note that the @samp{auto}\n\
setting is not @sc{matlab} compatible.\n\
@end table\n\
\n\
@seealso{h5write}\n\
@end deftypefn")
{
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature("h5create", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (! (nargin == 3 || nargin == 5 || nargin == 7) || nargout != 0)
{
print_usage ();
return octave_value_list ();
}
if (! (args(0).is_string () && args(1).is_string ()))
{
print_usage ();
return octave_value_list ();
}
if ((nargin == 5 && ! args(3).is_string ())
|| (nargin == 7 && ! args(5).is_string ()))
{
print_usage ();
return octave_value_list ();
}
string filename = args(0).string_value ();
string location = args(1).string_value ();
if (error_state)
return octave_value_list ();
Matrix size;
if (! check_vec (args(2), size, "SIZE", true))
return octave_value_list ();
// loop over the key-value pairs and see what is given
string datatype = "double";
Matrix chunksize;
for (int i = 3; i+1 < nargin; i+=2)
{
if (args(i).string_value () == "Datatype")
{
datatype = args(i+1).string_value ();
if (error_state)
{
error ("Datatype argument must be a string");
return octave_value_list ();
}
}
else if (args(i).string_value () == "ChunkSize")
{
if (args(i+1).is_string ())
{
if(args(i+1).string_value () != "auto")
{
error ("ChunkSize argument must be either a vector, or the string 'auto'.");
return octave_value_list ();
}
chunksize = args(2).matrix_value ();
chunksize(0) = 0;
}
else if (! check_vec (args(i+1), chunksize, "ChunkSize", false))
return octave_value_list ();
}
else
{
error ("unknown parameter name %s", args(i).string_value ().c_str ());
return octave_value_list ();
}
}
//open the hdf5 file
H5File file (filename.c_str (), true, true);
if (error_state)
return octave_value_list ();
file.create_dset (location.c_str (), size, datatype.c_str (), chunksize);
return octave_value_list ();
#endif
}
DEFUN_DLD (h5delete, args, nargout,
"-*- texinfo -*-\n\
@deftypefn {Loadable Function} h5delete (@var{filename}, @var{objname})\n\
@deftypefnx {Loadable Function} h5delete (@var{filename}, @var{objname}, @var{attname})\n\
\n\
In the first form, delete a dataset or group with name @var{objname}\n\
in the HDF5 file specified by @var{filename}.\n\
\n\
In the second form, delete an attribute with name @var{attname} associated\n\
to a dataset or group with name @var{objname}\n\
in the HDF5 file specified by @var{filename}.\n\
\n\
Note that this function is not @sc{matlab} compliant.\n\
\n\
@seealso{h5create}\n\
@end deftypefn")
{
#if ! (defined (HAVE_HDF5) && defined (HAVE_HDF5_18))
gripe_disabled_feature("h5delete", "HDF5 IO");
return octave_value_list ();
#else
int nargin = args.length ();
if (! (nargin == 2 || nargin == 3) || nargout != 0)
{
print_usage ();
return octave_value_list ();
}
if (! (args(0).is_string () && args(1).is_string ()))
{
print_usage ();
return octave_value_list ();
}
if (nargin == 3 && ! args(2).is_string ())
{
print_usage ();
return octave_value_list ();
}
string filename = args(0).string_value ();
string location = args(1).string_value ();
if (error_state)
return octave_value_list ();
//open the hdf5 file
H5File file (filename.c_str (), true, true);
if (error_state)
return octave_value_list ();
if (nargin == 2)
file.delete_link (location.c_str ());
else if (nargin == 3)
{
string attname = args(2).string_value ();
if(!error_state)
file.delete_att (location.c_str (), attname.c_str ());
}
return octave_value_list ();
#endif
}
#if defined (HAVE_HDF5) && defined (HAVE_HDF5_18)
H5File::H5File (const char *filename, const bool create_if_nonexisting,
const bool write_access)
{
H5E_auto_t oef;
void *olderr;
H5Eget_auto (H5E_DEFAULT,&oef,&olderr);
//suppress hdf5 error output
H5Eset_auto (H5E_DEFAULT,0,0);
file_stat fs (filename);
if (! fs.exists () && create_if_nonexisting)
file = H5Fcreate (filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
else if (! fs.exists () && ! create_if_nonexisting)
error ("The file %s does not exist: %s", filename, strerror (errno));
else
{
// test if the existing file is in HDF5 format
if (! H5Fis_hdf5 (filename))
error ("The file is not in the HDF5 format, %s: %s", filename, strerror (errno));
else
{
file = H5Fopen (filename,
write_access ? H5F_ACC_RDWR : H5F_ACC_RDONLY,
H5P_DEFAULT);
if (file < 0)
error ("Opening the file failed, %s: %s", filename, strerror (errno));
}
}
// restore old setting
H5Eset_auto (H5E_DEFAULT,oef,olderr);
}
H5File::~H5File ()
{
if (H5Iis_valid (memspace_id))
H5Sclose (memspace_id);
if (H5Iis_valid (dspace_id))
H5Sclose (dspace_id);
if (H5Iis_valid (dset_id))
H5Dclose (dset_id);
if (H5Iis_valid (att_id))
H5Aclose (att_id);
if (H5Iis_valid (obj_id))
H5Oclose (obj_id);
if (H5Iis_valid (type_id))
H5Tclose (type_id);
if (H5Iis_valid (mem_type_id))
H5Tclose (mem_type_id);
if (H5Iis_valid (file))
H5Fclose (file);
if (h5_dims != NULL)
{
free (h5_dims);
h5_dims = NULL;
}
if (h5_maxdims != NULL)
{
free (h5_maxdims);
h5_maxdims = NULL;
}
}
// T will be Matrix or dim_vector
template <typename T>
hsize_t*
H5File::alloc_hsize (const T& dim, const int mode, const bool reverse)
{
int rank = dim.length ();
hsize_t *hsize = (hsize_t*)malloc (rank * sizeof (hsize_t));
for (int i = 0; i < rank; i++)
{
int j = reverse ? rank-i-1 : i;
if (mode == ALLOC_HSIZE_INFZERO_TO_UNLIMITED && (dim(i) == octave_Inf || dim(i) == 0))
hsize[j] = H5S_UNLIMITED;
else if (mode == ALLOC_HSIZE_INF_TO_ZERO && dim(i) == octave_Inf)
hsize[j] = 0;
else
hsize[j] = dim(i);
}
return hsize;
}
int
H5File::open_dset (const char *dsetname)
{
dset_id = H5Dopen (file, dsetname, H5P_DEFAULT);
if (dset_id < 0)
{
error ("Error opening dataset %s", dsetname);
return -1;
}
dspace_id = H5Dget_space (dset_id);
if (dspace_id < 0)
{
error ("Error opening dataspace of dataset %s", dsetname);
return -1;
}
rank = H5Sget_simple_extent_ndims (dspace_id);
if (rank < 0)
{
error ("Error reading extent of %s", dsetname);
return -1;
}
h5_dims = (hsize_t*)malloc (rank * sizeof(hsize_t));
h5_maxdims = (hsize_t*)malloc (rank * sizeof(hsize_t));
if (! h5_dims || ! h5_maxdims)
{
error ("Error allocating memory for %s", dsetname);
return -1;
}
if (H5Sget_simple_extent_dims (dspace_id, h5_dims, h5_maxdims) < 0)
{
error ("Error determining current dimensions and maximum size of dataset %s", dsetname);
return -1;
}
return 0;
}
octave_value
H5File::read_dset_complete (const char *dsetname)
{
if (open_dset (dsetname) < 0)
return octave_value_list ();
mat_dims.resize (max (rank, 2));
// .resize(1) still leaves mat_dims with a length of 2 for some reason, so
// we need at least 2 filled
mat_dims(0) = mat_dims(1) = 1;
for (int i = 0; i < rank; i++)
//note that this is reversing the order
mat_dims(i) = h5_dims[rank-i-1];
if (H5Sselect_all (dspace_id) < 0)
{
error ("Error selecting complete dataset %s", dsetname);
return octave_value_list ();
}
octave_value retval = read_dset ();
return retval;
}
octave_value
H5File::read_dset_hyperslab (const char *dsetname,
const Matrix& start, const Matrix& count,
const Matrix& stride, const Matrix& block,
int nargin)
{
if (open_dset (dsetname) < 0)
return octave_value_list ();
if (rank == 0 && ! (start.is_empty () && count.is_empty ()
&& stride.is_empty () && block.is_empty ()))
{
error ("Cannot specify hyperslab for scalar datasets (rank 0)");
return octave_value_list ();
}
if (start.nelem () != rank)
{
error ("start must be a vector of length %d, the dataset rank", rank);
return octave_value_list ();
}
if (count.nelem () != rank)
{
error ("count must be a vector of length %d, the dataset rank", rank);
return octave_value_list ();
}
Matrix _stride = stride;
if (nargin < 3)
_stride = Matrix (dim_vector(1, rank), 1);
if (_stride.nelem () != rank)
{
error ("stride must be a vector of length %d, the dataset rank", rank);
return octave_value_list ();
}
Matrix _block = block;
if (nargin < 4)
_block = Matrix (dim_vector(1, rank), 1);
if (_block.nelem () != rank)
{
error ("block must be a vector of length %d, the dataset rank", rank);
return octave_value_list ();
}
// .resize(1) still leaves mat_dims with a length of 2 for some reason, so
// we need at least 2 filled
mat_dims.resize (max (rank, 2));
mat_dims(0) = mat_dims(1) = 1;
Matrix _count = count;
for (int i = 0; i < rank; i++)
{
if (_stride(i) < _block(i))
{
error ("In dimension %d, requested stride %d smaller than block size %d",
i+1, (int)_stride(i), (int)_block(i));
return octave_value_list ();
}
if (_count(i) == 0)
{
// a value of 0 (or Inf) means that as many blocks as possible
// shall be read in this dimension
_count(i) = (h5_dims[rank-i-1] - start(i) - _block(i)) / _stride(i) + 1;
}
mat_dims(i) = _count(i)*_block(i);
int end = start(i) + _stride(i)*(_count(i)-1) + _block(i); // exclusive
if (h5_dims[rank-i-1] < end)
{
error ("In dimension %d, dataset only has %d elements, but at least %d"
" are required for requested hyperslab", i+1, (int)h5_dims[rank-i-1],
end);
return octave_value_list ();
}
}
hsize_t *hstart = alloc_hsize (start, ALLOC_HSIZE_DEFAULT, true);
hsize_t *hstride = alloc_hsize (_stride, ALLOC_HSIZE_DEFAULT, true);
hsize_t *hcount = alloc_hsize (_count, ALLOC_HSIZE_DEFAULT, true);
hsize_t *hblock = alloc_hsize (_block, ALLOC_HSIZE_DEFAULT, true);
// TODO check these (and hmem) for NULLs
herr_t sel_result = H5Sselect_hyperslab (dspace_id, H5S_SELECT_SET, hstart,
hstride, hcount, hblock);
free (hstart);
free (hstride);
free (hcount);
free (hblock);
if (sel_result < 0)
return octave_value_list ();
octave_value retval = read_dset ();
return retval;
}
octave_value
H5File::read_dset ()
{
bool is_cmplx = false;
type_id = H5Dget_type (dset_id);
hid_t complex_type_id = hdf5_make_complex_type (H5T_NATIVE_DOUBLE);
// hsize_t *hmem = alloc_hsize (mat_dims, ALLOC_HSIZE_DEFAULT, false);
// hid_t memspace_id = H5Screate_simple (rank, hmem, hmem);
// free (hmem);
octave_value retval;
if (H5Tget_class (type_id) == H5T_COMPOUND &&
H5Tget_class (complex_type_id) == H5T_COMPOUND &&
hdf5_types_compatible (type_id, complex_type_id) > 0)
{
ComplexNDArray ret (mat_dims);
// macro begin
#define HDF5_READ_DATA(type) \
if (H5Sselect_valid (dspace_id) <= 0) \
{ \
error ("selected dataspace is not valid"); \
return octave_value_list (); \
} \
\
int mdc_nelem = -1; \
size_t rdcc_nelem = -1; \
size_t rdcc_nbytes = -1; \
double rdcc_w0 = -1; \
if (H5Pget_cache (H5Fget_access_plist (file), &mdc_nelem, \
&rdcc_nelem, &rdcc_nbytes, &rdcc_w0 ) < 0) \
{ \
error ("could not determine raw data chunk cache parameters."); \
return octave_value_list (); \
} \
/*cout << "cache params:" << rdcc_nelem << "," << rdcc_nbytes << endl;*/ \
herr_t read_result = H5Dread (dset_id, \
type, \
H5S_ALL, dspace_id, \
H5P_DEFAULT, ret.fortran_vec ()); \
if (read_result < 0) \
{ \
error ("error when reading dataset"); \
return octave_value_list (); \
} \
retval = octave_value (ret)
// macro end
HDF5_READ_DATA (type_id);
}
else if (H5Tget_class (type_id) == H5T_INTEGER)
{
switch (H5Tget_size (type_id)*8)
{
case 64:
if (H5Tget_sign (type_id) == H5T_SGN_NONE)
{
uint64NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
else
{
int64NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
break;
case 32:
if (H5Tget_sign (type_id) == H5T_SGN_NONE)
{
uint32NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
else
{
int32NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
break;
case 16:
if (H5Tget_sign (type_id) == H5T_SGN_NONE)
{
uint16NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
else
{
int16NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
break;
case 8:
if (H5Tget_sign (type_id) == H5T_SGN_NONE)
{
uint8NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
else
{
int8NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
break;
}
break;
default:
{
error ("unknown integer size %d", H5Tget_size (type_id));
NDArray ret (mat_dims);
HDF5_READ_DATA (type_id);
}
}
}
else
{
NDArray ret (mat_dims);
HDF5_READ_DATA (H5T_NATIVE_DOUBLE);
}
H5Tclose (complex_type_id);
return retval;
}
void
H5File::write_dset (const char *dsetname,
const octave_value ov_data)
{
int rank = ov_data.dims ().length ();
hsize_t *dims = alloc_hsize (ov_data.dims(), ALLOC_HSIZE_DEFAULT, true);
dspace_id = H5Screate_simple (rank, dims, NULL);
free (dims);
// determine the endianness of this system
H5T_order_t o = H5Tget_order (H5T_NATIVE_INT);
if (o == H5T_ORDER_ERROR)
{
error ("HDF5 lib could not determine endianness of current system");
return;
}
//check if all groups in the path dsetname exist. if not, create them
string path (dsetname);
for (int i=1; i < path.length (); i++)
{
if (path[i] == '/')
{
if (! H5Lexists (file, path.substr(0,i).c_str (), H5P_DEFAULT))
{
hid_t group_id = H5Gcreate (file, path.substr(0,i).c_str (), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose (group_id);
}
}
}