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netcdf-c/ncdump/tst_special_atts.c
Dennis Heimbigner f376c23329 Make utilities support NC_COMPACT 
re: https://github.com/Unidata/netcdf-c/issues/1642

Modify ncdump, nccopy, and ncgen to support the NC_COMPACT storage option.
Added test cases and added description to the man pages for the utilities.

1. ncdump: For compact storage variable, print special attribute __Storage_ as
````
    <var>: _Storage = "compact";
````

2. ncgen: parse and implement
````
    <var>: _Storage = "compact";
````
in a .cdl file

3. nccopy: Extend the chunk specification (-c flag) to support
   compact using the forms
````
nccopy ... -c <var>:compact
and
nccopy ... -c <var>:contiguous
````

Misc. other changes
1. cleanup the copy_chunking function in ncdump/nccopy.c
2020-02-29 12:06:21 -07:00

217 lines
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/* This is part of the netCDF package. Copyright 2018 University
Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
conditions of use. See www.unidata.ucar.edu for more info.
Create a test netCDF-4 file with compression, chunking, endianness
settings to test ncdump "-s" option for displaying special
attributes.
$Id: tst_special_atts.c,v 1.12 2009/01/28 18:19:49 russ Exp $
*/
#include <nc_tests.h>
#include "err_macros.h"
#include <netcdf.h>
#define FILE_NAME "tst_special_atts.nc"
#define DIM1_NAME "dim1"
#define DIM1_LEN 10
#define DIM2_NAME "dim2"
#define DIM2_LEN 20
#define DIM3_NAME "dim3"
#define DIM3_LEN 30
#define VAR1_NAME "var1"
#define VAR1_RANK 1
#define VAR2_NAME "var2"
#define VAR2_RANK 2
#define VAR3_NAME "var3"
#define VAR3_RANK 3
#define VAR4_NAME "var4"
#define VAR4_RANK 3
#define VAR5_NAME "var5"
#define VAR5_RANK VAR1_RANK
#define VAR6_NAME "var6"
#define VAR6_RANK 1
#define VAR7_NAME "var7"
#define CHUNK1 (DIM1_LEN/2 + 1)
#define CHUNK2 (DIM2_LEN/3 + 1)
#define CHUNK3 (DIM3_LEN/4 + 1)
#define DEFLATE_LEVEL 2
#define COMPRESS 1
#define TYPE6_NAME "obs_t"
int
main(int argc, char **argv)
{
int ncid;
int i, j, k, m;
int dimids[VAR3_RANK];
int var1id, var2id, var3id, var4id, var5id, var6id, var7id;
size_t chunksizes[] = {CHUNK1, CHUNK2, CHUNK3};
int data1[DIM1_LEN];
int data1_in[DIM1_LEN];
int data2[DIM1_LEN][DIM2_LEN];
int data2_in[DIM1_LEN][DIM2_LEN];
int data3[DIM1_LEN][DIM2_LEN][DIM3_LEN];
int data3_in[DIM1_LEN][DIM2_LEN][DIM3_LEN];
printf("\n*** Testing '-s' option for special attributes.\n");
printf("*** creating special attributes test file %s...", FILE_NAME);
if (nc_create(FILE_NAME, NC_CLOBBER | NC_NETCDF4, &ncid)) ERR;
/* Declare dimensions and variables */
if (nc_def_dim(ncid, DIM1_NAME, DIM1_LEN, &dimids[0])) ERR;
if (nc_def_dim(ncid, DIM2_NAME, DIM2_LEN, &dimids[1])) ERR;
if (nc_def_dim(ncid, DIM3_NAME, DIM3_LEN, &dimids[2])) ERR;
if (nc_def_var(ncid, VAR1_NAME, NC_INT, VAR1_RANK, dimids, &var1id)) ERR;
if (nc_def_var(ncid, VAR2_NAME, NC_INT, VAR2_RANK, dimids, &var2id)) ERR;
if (nc_def_var(ncid, VAR3_NAME, NC_INT, VAR3_RANK, dimids, &var3id)) ERR;
if (nc_def_var(ncid, VAR4_NAME, NC_INT, VAR4_RANK, dimids, &var4id)) ERR;
{
typedef struct obs_t {
char day;
short elev;
int count;
float relhum;
double time;
unsigned char category;
unsigned short id;
unsigned int particularity;
long long attention_span;
} obs_t ;
nc_type typeid;
/* Create a compound type. */
if (nc_def_compound(ncid, sizeof(obs_t), TYPE6_NAME, &typeid)) ERR;
if (nc_insert_compound(ncid, typeid, "day",
NC_COMPOUND_OFFSET(struct obs_t, day), NC_BYTE)) ERR;
if (nc_insert_compound(ncid, typeid, "elev",
NC_COMPOUND_OFFSET(struct obs_t, elev), NC_SHORT)) ERR;
if (nc_insert_compound(ncid, typeid, "count",
NC_COMPOUND_OFFSET(struct obs_t, count), NC_INT)) ERR;
if (nc_insert_compound(ncid, typeid, "relhum",
NC_COMPOUND_OFFSET(struct obs_t, relhum),
NC_FLOAT)) ERR;
if (nc_insert_compound(ncid, typeid, "time",
NC_COMPOUND_OFFSET(struct obs_t, time),
NC_DOUBLE)) ERR;
if (nc_insert_compound(ncid, typeid, "category",
NC_COMPOUND_OFFSET(struct obs_t, category),
NC_UBYTE)) ERR;
if (nc_insert_compound(ncid, typeid, "id",
NC_COMPOUND_OFFSET(struct obs_t, id),
NC_USHORT)) ERR;
if (nc_insert_compound(ncid, typeid, "particularity",
NC_COMPOUND_OFFSET(struct obs_t, particularity),
NC_UINT)) ERR;
if (nc_insert_compound(ncid, typeid, "attention_span",
NC_COMPOUND_OFFSET(struct obs_t, attention_span),
NC_INT64)) ERR;
/* create a variable of that compound type */
if (nc_def_var(ncid, VAR5_NAME, typeid, VAR5_RANK, dimids, &var5id))
ERR;
}
if (nc_def_var(ncid, VAR6_NAME, NC_INT, VAR6_RANK, dimids, &var6id)) ERR;
if (nc_def_var(ncid, VAR7_NAME, NC_INT, 0, NULL, &var7id)) ERR;
/* Specify contiguous storage and endianness explicitly for var1. */
if (nc_def_var_chunking(ncid, var1id, NC_CONTIGUOUS, NULL)) ERR;
if (nc_def_var_endian(ncid, var1id, NC_ENDIAN_LITTLE)) ERR;
/* Specify chunking for var2, note only uses CHUNK1 and CHUNK2.
Also, specify using a checksum for this variable. */
if (nc_def_var_chunking(ncid, var2id, NC_CHUNKED, chunksizes)) ERR;
if (nc_def_var_fletcher32(ncid, var2id, NC_FLETCHER32)) ERR;
if (nc_def_var_endian(ncid, var2id, NC_ENDIAN_BIG)) ERR;
/* Use compression but no shuffle for var3, also set to big endian */
if (nc_def_var_deflate(ncid, var3id, NC_NOSHUFFLE, COMPRESS, DEFLATE_LEVEL)) ERR;
if (nc_def_var_chunking(ncid, var3id, NC_CHUNKED, chunksizes)) ERR;
if (nc_def_var_endian(ncid, var3id, NC_ENDIAN_LITTLE)) ERR;
/* Use compression, chunking, shuffle filter, and no-fill for var4 */
if (nc_def_var_deflate(ncid, var4id, NC_SHUFFLE, COMPRESS, DEFLATE_LEVEL)) ERR;
if (nc_def_var_chunking(ncid, var4id, NC_CHUNKED, chunksizes)) ERR;
if (nc_def_var_endian(ncid, var4id, NC_ENDIAN_LITTLE)) ERR;
if (nc_def_var_fill(ncid, var4id, NC_NOFILL, NULL)) ERR;
/* Set endianness, chunking, checksums, shuffle, and compression for var5 */
if (nc_def_var_chunking(ncid, var5id, NC_CHUNKED, chunksizes)) ERR;
if (nc_def_var_fletcher32(ncid, var5id, NC_FLETCHER32)) ERR;
if (nc_def_var_deflate(ncid, var5id, NC_SHUFFLE, COMPRESS, DEFLATE_LEVEL)) ERR;
/* Set _Storage as compact */
if (nc_def_var_chunking(ncid, var6id, NC_COMPACT, NULL)) ERR;
if (nc_def_var_chunking(ncid, var7id, NC_COMPACT, NULL)) ERR;
if (nc_enddef(ncid)) ERR;
/* Some artificial data */
m = 0;
for(i = 0; i < DIM1_LEN; i++) {
data1[i] = m++;
for(j = 0; j < DIM2_LEN; j++) {
data2[i][j] = m++;
for(k = 0; k < DIM3_LEN; k++) {
data3[i][j][k] = m++;
}
}
}
/* Store data in each variable */
if(nc_put_var(ncid, var1id, &data1[0])) ERR;
if(nc_put_var(ncid, var2id, &data2[0][0])) ERR;
if(nc_put_var(ncid, var3id, &data3[0][0][0])) ERR;
if(nc_put_var(ncid, var4id, &data3[0][0][0])) ERR;
if(nc_put_var(ncid, var6id, &data3[0][0][0])) ERR;
if(nc_put_var(ncid, var7id, &data3[0][0][0])) ERR;
if (nc_close(ncid)) ERR;
/* Check it out. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq_varid(ncid, VAR1_NAME, &var1id)) ERR;
if (nc_inq_varid(ncid, VAR2_NAME, &var2id)) ERR;
if (nc_inq_varid(ncid, VAR3_NAME, &var3id)) ERR;
if (nc_inq_varid(ncid, VAR4_NAME, &var4id)) ERR;
/* Check chunk sizes */
{
size_t chunks_in[VAR3_RANK];
if (nc_inq_var_chunking(ncid, var2id, NULL, chunks_in)) ERR;
for(i = 0; i < VAR2_RANK; i++)
if(chunks_in[i] != chunksizes[i]) ERR;
if (nc_inq_var_chunking(ncid, var3id, NULL, chunks_in)) ERR;
for(i = 0; i < VAR3_RANK; i++)
if(chunks_in[i] != chunksizes[i]) ERR;
if (nc_inq_var_chunking(ncid, var4id, NULL, chunks_in)) ERR;
for(i = 0; i < VAR4_RANK; i++)
if(chunks_in[i] != chunksizes[i]) ERR;
}
if(nc_get_var(ncid, var1id, &data1_in[0])) ERR;
for(i = 0; i < DIM1_LEN; i++)
if(data1_in[i] != data1[i]) ERR;
if(nc_get_var(ncid, var2id, &data2_in[0][0])) ERR;
for(i = 0; i < DIM1_LEN; i++)
for(j = 0; j < DIM2_LEN; j++)
if(data2_in[i][j] != data2[i][j]) ERR;
if(nc_get_var(ncid, var3id, &data3_in[0][0][0])) ERR;
for(i = 0; i < DIM1_LEN; i++)
for(j = 0; j < DIM2_LEN; j++)
for(k = 0; k < DIM3_LEN; k++)
if(data3_in[i][j][k] != data3[i][j][k]) ERR;
if(nc_get_var(ncid, var4id, &data3_in[0][0][0])) ERR;
for(i = 0; i < DIM1_LEN; i++)
for(j = 0; j < DIM2_LEN; j++)
for(k = 0; k < DIM3_LEN; k++)
if(data3_in[i][j][k] != data3[i][j][k]) ERR;
SUMMARIZE_ERR;
FINAL_RESULTS;
}
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