Hi,
I am trying to read a 2 dimensional array of an unknown size from an h5file.
The first dimension size is also read from the h5 file, the second dimension
size is known and equal to 3. So I wrote the following code:
In header I declare:
struct h5_output_type {
unsigned long dimension;
float **centres;
float * radius;
};
In function I have:
H5::H5File h5file = H5::H5File();
h5file.openFile("h5filename.h5", H5F_ACC_RDWR );
H5::DataSet dataset_centre = group.openDataSet( "centre");
H5::DataSet dataset_radius = group.openDataSet( "radius");
H5::DataSpace dataspace = dataset_centre.getSpace();
int rank = dataspace.getSimpleExtentNdims();
hsize_t dims_out[2];
int ndims = dataspace.getSimpleExtentDims( dims_out, NULL);
H5::DataSpace memspace( rank, dims_out );
struct h5_output_type *h5_data = (struct h5_output_type*) malloc(
sizeof(*h5_data) );
h5_data->dimension = (unsigned long)(dims_out[0]);
h5_data->centres = (float **) malloc( sizeof(float *) * (unsigned
long)(dims_out[0]) );
for (int i=0; i<(unsigned long)(dims_out[0]) ;i++){
h5_data->centres[i] = (float *) malloc (3 * sizeof(float));
}
h5_data->radius = (float*) malloc( sizeof(float) * (unsigned
long)(dims_out[0]) );
dataset_centre.read(h5_data->centres,H5::PredType::NATIVE_FLOAT,memspace,
dataspace);
dataset_radius.read(h5_data->radius,H5::PredType::NATIVE_FLOAT,memspace_r,
dataspace_r);
then when I try to access any of h5_data->centres[i][j] data I get
"Segmentation fault" wheras h5_data->radius[i] works fine. Is the problem
lies in the buffer the H5::DataSet::read( H5std_string & strg ,...) first
input which should be a buffer? Is so then how can I correct this error
with the double pointer? I tried:
dataset_centre.read(&h5_data->centres,H5::PredType::NATIVE_FLOAT,memspace,
dataspace);
with no luck.
also in the struct can I initialize the float * radius to 0 when I didn't
declare its dimension?
Thank you in advance,
Sahar
···
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Hi Sahar,
Hi,
I am trying to read a 2 dimensional array of an unknown size from an h5file.
The first dimension size is also read from the h5 file, the second dimension
size is known and equal to 3. So I wrote the following code:
In header I declare:
struct h5_output_type {
unsigned long dimension;
float **centres;
float * radius;
};
In function I have:
H5::H5File h5file = H5::H5File();
h5file.openFile("h5filename.h5", H5F_ACC_RDWR );
H5::DataSet dataset_centre = group.openDataSet( "centre");
H5::DataSet dataset_radius = group.openDataSet( "radius");
H5::DataSpace dataspace = dataset_centre.getSpace();
int rank = dataspace.getSimpleExtentNdims();
hsize_t dims_out[2];
int ndims = dataspace.getSimpleExtentDims( dims_out, NULL);
H5::DataSpace memspace( rank, dims_out );
struct h5_output_type *h5_data = (struct h5_output_type*) malloc(
sizeof(*h5_data) );
h5_data->dimension = (unsigned long)(dims_out[0]);
h5_data->centres = (float **) malloc( sizeof(float *) * (unsigned
long)(dims_out[0]) );
for (int i=0; i<(unsigned long)(dims_out[0]) ;i++){
h5_data->centres[i] = (float *) malloc (3 * sizeof(float));
}
h5_data->radius = (float*) malloc( sizeof(float) * (unsigned
long)(dims_out[0]) );
dataset_centre.read(h5_data->centres,H5::PredType::NATIVE_FLOAT,memspace,
dataspace);
dataset_radius.read(h5_data->radius,H5::PredType::NATIVE_FLOAT,memspace_r,
dataspace_r);
then when I try to access any of h5_data->centres[i][j] data I get
"Segmentation fault" wheras h5_data->radius[i] works fine. Is the problem
lies in the buffer the H5::DataSet::read( H5std_string & strg ,...) first
input which should be a buffer? Is so then how can I correct this error
with the double pointer? I tried:
dataset_centre.read(&h5_data->centres,H5::PredType::NATIVE_FLOAT,memspace,
dataspace);
with no luck.
also in the struct can I initialize the float * radius to 0 when I didn't
declare its dimension?
You are allocating multiple, non-contiguous, arrays for the rows in the 'centres' field. Either, you have to write each row individually, or you have to allocate a single buffer to pass to the HDF5 library.
Quincey
···
On Mar 17, 2011, at 4:04 PM, sghanavati wrote:
Thank you in advance,
Sahar
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