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ncdumpchunks.c
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ncdumpchunks.c
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#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <netcdf.h>
#include <hdf5.h>
#include <H5DSpublic.h>
#if 0
#define FILE_NAME "tst_vars.nc"
#define VAR "v1"
#define RANK 3
static const size_t dimlens[RANK] = {4,4,2};
static const size_t chunksize[RANK] = {2,2,2};
static const size_t chunkcount[RANK] = {2,2,1};
static const size_t CHUNKPROD = 8;
#endif
typedef struct Odometer {
size_t rank; /*rank */
size_t stop[NC_MAX_VAR_DIMS];
size_t max[NC_MAX_VAR_DIMS]; /* max size of ith index */
size_t index[NC_MAX_VAR_DIMS]; /* current value of the odometer*/
} Odometer;
#define floordiv(x,y) ((x) / (y))
#define ceildiv(x,y) (((x) % (y)) == 0 ? ((x) / (y)) : (((x) / (y)) + 1))
Odometer* odom_new(size_t rank, const size_t* stop, const size_t* max);
void odom_free(Odometer* odom);
int odom_more(Odometer* odom);
int odom_next(Odometer* odom);
size_t* odom_indices(Odometer* odom);
size_t odom_offset(Odometer* odom);
void setoffset(Odometer* odom, size_t* chunksizes, hsize_t* offset);
static void
usage(int err)
{
if(err != 0) {
fprintf(stderr,"Error: (%d) %s\n",err,nc_strerror(err));
}
fprintf(stderr,"usage: ncdumpchunks <file> <var>\n");
fflush(stderr);
exit(1);
}
int
main(int argc, char** argv)
{
int i,r,stat = NC_NOERR;
hid_t fileid, grpid, datasetid;
hid_t dxpl_id = H5P_DEFAULT; /*data transfer property list */
int* chunkdata = NULL; /*[CHUNKPROD];*/
unsigned int filter_mask = 0;
const char* file_name = NULL;
const char* var_name = NULL;
int ncid, varid, dimids[NC_MAX_VAR_DIMS];
int rank, vtype, storage;
size_t dimlens[NC_MAX_VAR_DIMS];
size_t chunklens[NC_MAX_VAR_DIMS];
size_t chunkcounts[NC_MAX_VAR_DIMS];
size_t chunkprod;
Odometer* odom = NULL;
hsize_t offset[NC_MAX_VAR_DIMS];
if(argc < 3)
usage(0);
file_name = argv[1];
var_name = argv[2];
/* Get the info about the var */
if((stat=nc_open(file_name,0,&ncid))) usage(stat);
if((stat=nc_inq_varid(ncid,var_name,&varid))) usage(stat);
if((stat=nc_inq_var(ncid,varid,NULL,&vtype,&rank,dimids,NULL))) usage(stat);
if(rank == 0) usage(NC_EDIMSIZE);
if((stat=nc_inq_var_chunking(ncid,varid,&storage,chunklens))) usage(stat);
if(storage != NC_CHUNKED) usage(NC_EBADCHUNK);
chunkprod = 1;
for(i=0;i<rank;i++) {
if((stat=nc_inq_dimlen(ncid,dimids[i],&dimlens[i]))) usage(stat);
chunkcounts[i] = ceildiv(dimlens[i],chunklens[i]);
chunkprod *= chunklens[i];
}
if((stat=nc_close(ncid))) usage(stat);
if ((fileid = H5Fopen(file_name, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) usage(NC_EHDFERR);
if ((grpid = H5Gopen(fileid, "/", H5P_DEFAULT)) < 0) usage(NC_EHDFERR);
if ((datasetid = H5Dopen1(grpid, var_name)) < 0) usage(NC_EHDFERR);
if((odom = odom_new(rank,chunkcounts,dimlens))==NULL) usage(NC_ENOMEM);
if((chunkdata = calloc(sizeof(int),chunkprod))==NULL) usage(NC_ENOMEM);
while(odom_more(odom)) {
setoffset(odom,chunklens,offset);
#ifdef DEBUG
fprintf(stderr,"(");
for(i=0;i<rank;i++)
fprintf(stderr,"%s%lu",(i > 0 ? "," : ""),(unsigned long)offset[i]);
fprintf(stderr,")\n");
fflush(stderr);
#endif
memset(chunkdata,0,sizeof(int)*chunkprod);
#if 1
if(H5Dread_chunk(datasetid, dxpl_id, offset, &filter_mask, chunkdata) < 0) abort();
for(r=0;r<rank;r++)
printf("[%lu/%lu]",(unsigned long)odom->index[r],(unsigned long)offset[r]);
printf(" =");
for(r=0;r<chunkprod;r++)
printf(" %02d", chunkdata[r]);
printf("\n");
fflush(stdout);
#endif
odom_next(odom);
}
/* Close up. */
if (H5Dclose(datasetid) < 0) abort();
if (H5Gclose(grpid) < 0) abort();
if (H5Fclose(fileid) < 0) abort();
/* Cleanup */
free(chunkdata);
odom_free(odom);
return 0;
}
Odometer*
odom_new(size_t rank, const size_t* stop, const size_t* max)
{
int i;
Odometer* odom = NULL;
if((odom = calloc(1,sizeof(Odometer))) == NULL)
return NULL;
odom->rank = rank;
for(i=0;i<rank;i++) {
odom->stop[i] = stop[i];
odom->max[i] = max[i];
odom->index[i] = 0;
}
return odom;
}
void
odom_free(Odometer* odom)
{
if(odom) free(odom);
}
int
odom_more(Odometer* odom)
{
return (odom->index[0] < odom->stop[0]);
}
int
odom_next(Odometer* odom)
{
size_t i;
for(i=odom->rank-1;i>=0;i--) {
odom->index[i]++;
if(odom->index[i] < odom->stop[i]) break;
if(i == 0) return 0; /* leave the 0th entry if it overflows */
odom->index[i] = 0; /* reset this position */
}
return 1;
}
/* Get the value of the odometer */
size_t*
odom_indices(Odometer* odom)
{
return odom->index;
}
size_t
odom_offset(Odometer* odom)
{
size_t offset;
int i;
offset = 0;
for(i=0;i<odom->rank;i++) {
offset *= odom->max[i];
offset += odom->index[i];
}
return offset;
}
void
setoffset(Odometer* odom, size_t* chunksizes, hsize_t* offset)
{
int i;
for(i=0;i<odom->rank;i++)
offset[i] = odom->index[i] * chunksizes[i];
}