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 <syriusz@man.poznan.pl>:
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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Kind regards,
Vlad Danilov
