Hi guys,
I am trying to read an hdf5 dataset named mask that is stored in a file that I create with a python script.
The few instructions I use in python follow:
…
mask = h5_fid.create_dataset(‘mask’, dtype=‘u1’, shape=dum.shape)
mask[:] = dum[:]
…
When I try to read this dataset with a program in C I get the following errors:
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 139713380624192:
#000: H5Dio.c line 199 in H5Dread(): can’t read data
major: Dataset
minor: Read failed
#001: H5Dio.c line 467 in H5D__read(): unable to set up type info
major: Dataset
minor: Unable to initialize object
#002: H5Dio.c line 968 in H5D__typeinfo_init(): not a datatype
major: Invalid arguments to routine
minor: Inappropriate type
The code that I am using is the following:
#include “hdf5.h”
#define FILE “mask_196_130.h5”
#define DATASETNAME “mask”
#define NX_SUB 2 /* hyperslab dimensions /
#define NY_SUB 3
#define NX 2 / output buffer dimensions */
#define NY 3
#define RANK 2
#define RANK_OUT 2
main (void)
{
hid_t file, dataset; /* handles /
hid_t datatype, dataspace;
hid_t memspace;
H5T_class_t class; / datatype class /
H5T_order_t order; / data order /
size_t size; /
* size of the data element
* stored in file
/
hsize_t dimsm[2]; / memory space dimensions /
hsize_t dims_out[2]; / dataset dimensions */
herr_t status;
int8_t data_out[NX][NY]; /* output buffer */
hsize_t count[2]; /* size of the hyperslab in the file */
hsize_t offset[2]; /* hyperslab offset in the file */
hsize_t count_out[2]; /* size of the hyperslab in memory */
hsize_t offset_out[2]; /* hyperslab offset in memory */
int i, j, k, status_n, rank;
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++) {
data_out[j][i] = 0;
}
}
/*
* Open the file and the dataset.
*/
file = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen(file, DATASETNAME);
/*
* Get datatype and dataspace handles and then query
* dataset class, order, size, rank and dimensions.
*/
datatype = H5Dget_type(dataset); /* datatype handle */
class = H5Tget_class(datatype);
if (class == H5T_INTEGER) printf("Data set has type H5T_INTEGER \n");
order = H5Tget_order(datatype);
if (order == H5T_ORDER_LE) printf("Little endian order \n");
size = H5Tget_size(datatype);
printf(" Data size is %d \n", size);
dataspace = H5Dget_space(dataset); /* dataspace handle */
rank = H5Sget_simple_extent_ndims(dataspace);
status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL);
printf("rank %d, dimensions %lu x %lu \n", rank,
(unsigned long)(dims_out[0]), (unsigned long)(dims_out[1]));
/*
* Define hyperslab in the dataset.
*/
offset[0] = 0;
offset[1] = 0;
count[0] = NX_SUB;
count[1] = NY_SUB;
status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL,
count, NULL);
/*
* Define the memory dataspace.
*/
dimsm[0] = NX;
dimsm[1] = NY;
memspace = H5Screate_simple(RANK_OUT,dimsm,NULL);
/*
* Define memory hyperslab.
*/
offset_out[0] = 0;
offset_out[1] = 0;
count_out[0] = NX_SUB;
count_out[1] = NY_SUB;
status = H5Sselect_hyperslab(memspace, H5S_SELECT_SET, offset_out, NULL,
count_out, NULL);
/*
* Read data from hyperslab in the file into the hyperslab in
* memory and display.
*/
status = H5Dread(dataset, H5T_INTEGER, memspace, dataspace,
H5P_DEFAULT, data_out);
printf("%d\n", status);
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++) printf("%d ", data_out[j][i]);
printf("\n");
}
H5Tclose(datatype);
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(memspace);
H5Fclose(file);
return 0;
}
It seems that the array data_out is properly declared, but it is apparent that the dataset is not properly read.
Is there any suggestions?
Many thanks in advance.
Giuseppe
