Hello Rafal,
thank You for Your reply.
I found that i can use 'H5Tget_native_type' function, but i have another error.
First - the code itself:
#include "hdf5.h"
#include <stdio.h>
#include <stdlib.h>
#define H5FILE_NAME "6336_305739_1710261824_1710261836.h5"
//"SDSextendible.h5" //
#define DATASETNAME "ExtendibleArray"
#define RANK 2
#define RANKC 1
#define NX 10
#define NY 5
#define TOPIC "topic"
#define TIMESTAMPSEC "timestampsec"
#define AVGRAW "avgraw"
#define RUNNUM "runnum"
#define LSNUM "lsnum"
#define NBNUM "nbnum"
int
main (void)
{
typedef struct {
unsigned int fillnum;
unsigned int runnum;
unsigned int lsnum;
unsigned int nbnum;
unsigned int timestampsec;
unsigned int timestampmsec;
unsigned char publishnnb;
unsigned char datasourceid;
unsigned char algoid;
unsigned char channelid;
unsigned short data;
} bcm1fagghist_type;
hid_t dataSetName;
hid_t file; /* handles */
hid_t dataset;
hid_t filespace;
hid_t memspace, memtype;
hid_t cparms,file_s1_t;
hid_t var_id;
int s2_t;
hsize_t dims[200]; /* dataset and chunk dimensions*/
hsize_t chunk_dims[2];
hsize_t col_dims[1];
hsize_t count[2];
hsize_t offset[2];
size_t size;
/**********************************************/
bcm1fagghist_type *read_data;
/**********************************************/
herr_t status, status_n, status_k;
int data_out[NX][NY]; /* buffer for dataset to be read */
int chunk_out[2][5]; /* buffer for chunk to be read */
int column[10]; /* buffer for column to be read */
int rank, rank_chunk;
int i, j;
int data[144];
/*
* Open the file and the dataset.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
dataset = H5Dopen2(file, "/bcm1fagghist", H5P_DEFAULT);
/*
* Get dataset rank and dimension.
*/
filespace = H5Dget_space(dataset); /* Get filespace handle first. */
rank = H5Sget_simple_extent_ndims(filespace);
status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
read_data = (bcm1fagghist_type*) malloc(dims[0]*sizeof(bcm1fagghist_type));
printf("dataset rank %d, dimensions %lu x %lu, filespace %d\n", rank,
(unsigned long)(dims[0]), (unsigned long)(dims[1]), filespace);
/*
* Define the memory space to read dataset.
*/
//memtype = H5Tcreate(H5T_COMPOUND, sizeof (bcm1fagghist_type));
file_s1_t = H5Dget_type(dataset);
memtype = H5Tget_native_type(file_s1_t, H5T_DIR_DEFAULT);
memspace = H5Screate_simple(rank,dims,0);
/*
* Read dataset back and display.
*/
printf(" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> var_id =
H5Tinsert(memspace, fillnum, 0, H5T_STD_U32LE); - IS DONE\n");
status = H5Dread(dataset, memtype,H5S_ALL, H5S_ALL,/* memspace, filespace,
*/H5P_DEFAULT, read_data);
printf(" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> status = H5Dread(dataset,
H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, data_out); - is DONE\n");
printf("\n");
printf("Dataset: \n");
for (j = 0; j < dims[0]; j++) {
printf("%d ", read_data[j].fillnum);
printf("\n");
if (j == 10) break;
}
it's not full code but the problem part. I have an errors in the line s tatus
= H5Dread(dataset, memtype,H5S_ALL, H5S_ALL,/* memspace, filespace,
*/H5P_DEFAULT, read_data);
The errors itself:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> var_id = H5Tinsert(memspace,
fillnum, 0, H5T_STD_U32LE); - IS DONE
HDF5-DIAG: Error detected in HDF5 (1.8.19) thread 0:
#000: H5Dio.c line 223 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: H5Dio.c line 605 in H5D__read(): can't read data
major: Dataset
minor: Read failed
#002: H5Dchunk.c line 2092 in H5D__chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#003: H5Dchunk.c line 3122 in H5D__chunk_lock(): data pipeline read failed
major: Data filters
minor: Filter operation failed
#004: H5Z.c line 1345 in H5Z_pipeline(): required filter 'blosc' is not
registered
major: Data filters
minor: Read failed
#005: H5PL.c line 380 in H5PL_load(): search in paths failed
major: Plugin for dynamically loaded library
minor: Can't get value
#006: H5PL.c line 738 in H5PL__find(): can't open directory:
/usr/local/hdf5/lib/plugin
major: Plugin for dynamically loaded library
minor: Can't open directory or file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> status = H5Dread(dataset,
H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, data_out); - is DONE
I would be very glad if you could give an advise in that case.
It seams like i have a wrong path to a filter 'blosc', but i can't find where
the filters are.
After installation i passed all tests.
Kind regards,
Vlad
>Понедельник, 20 ноября 2017, 15:30 +01:00 от Rafal Lichwala
><[email protected]>:
>
>Hello Vlad,
>
>Please send me example HDF5 file and your current C code which you are
>trying to use to read that file and I will try to find a solution.
>
>Regards,
>Rafal
>
>
>W dniu 2017-11-19 o 19:46, Vlad Danilov pisze:
>>
>> Hello,
>>
>> my name is Vlad and HDF5 is new for me.
>> I want to ask an advise in one case.
>> i have a datatype and there i have smth like:
>>
>> DATATYPE H5T_COMPOUND {
>> H5T_STD_U32LE "fillnum";
>> H5T_STD_U32LE "runnum";
>> H5T_STD_U32LE "lsnum";
>> H5T_STD_U32LE "nbnum";
>> H5T_STD_U32LE "timestampsec";
>> H5T_STD_U32LE "timestampmsec";
>> H5T_STD_U8LE "publishnnb";
>> H5T_STD_U8LE "datasourceid";
>> H5T_STD_U8LE "algoid";
>> H5T_STD_U8LE "channelid";
>> H5T_ARRAY { [3564] H5T_STD_U16LE } "data";
>> }
>>
>> to read it i'm creating a structure and then read the file into it, i
>> define the structure in my code like this:
>> typedef struct {
>> unsigned int fillnum;
>> unsigned int runnum;
>> unsigned int lsnum;
>> unsigned int nbnum;
>> unsigned int timestampsec;
>> unsigned int timestampmsec;
>> unsigned char publishnnb;
>> unsigned char datasourceid;
>> unsigned char algoid;
>> unsigned char channelid;
>> unsigned short data[3564];
>> } bcm1fagghist_type;
>> but looks like for H5T_ARRAY line 'unsigned short data[3564];' is wrong.
>> could You advise me how to read it?
>> ------------------------------------------------------------------------
>>
>> Kind regards,
>> Vlad Danilov
>>
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> [email protected]
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>> Twitter: https://twitter.com/hdf5
>>
>
>
>_______________________________________________
>Hdf-forum is for HDF software users discussion.
>[email protected]
>http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>Twitter: https://twitter.com/hdf5
Kind regards,
Vlad Danilov
_______________________________________________
Hdf-forum is for HDF software users discussion.
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http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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