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netcdf-c/nc_test4/tst_interops.c
Dennis Heimbigner 11fe00ea05 Add filter support to NCZarr 
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00

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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.
Test that HDF5 and NetCDF-4 can read and write the same file.
$Id: tst_interops.c,v 1.24 2010/06/01 15:34:52 ed Exp $
*/
#include <config.h>
#include <nc_tests.h>
#include "err_macros.h"
#include <hdf5.h>
#include <H5DSpublic.h>
#define FILE_NAME "tst_interops.h5"
#define DIMSCALE_NAME "dimscale"
#define VAR1_NAME "var1"
#define NDIMS 1
#define DIM1_LEN 3
#define NAME_ATTRIBUTE "dimscale_name_attribute"
#define DIMSCALE_LABEL "dimscale_label"
#define LAT_LEN 3
#define LON_LEN 2
#define DIMS_2 2
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME "pres"
#define TEMP_NAME "temp"
#define ATT_NAME "song"
#define NEW_FLOAT 1.0
void
printRes(const char *msg, int ires)
{
printf("%s: %d\n", msg, ires);
if (ires < 0)
{
printf("bad ires: %d\n", ires);
#ifdef DEBUG
H5Eprint2(ires, stdout);
#endif
exit(1);
}
}
static char song[] = "Oh, better far to live and die\n\
Under the brave black flag I fly,\n\
Than play a sanctimonious part,\n\
With a pirate head and a pirate heart.\n\
Away to the cheating world go you,\n\
Where pirates all are well-to-do;\n\
But I.ll be true to the song I sing,\n\
And live and die a Pirate King.\n\
For I am a Pirate King!\n\
And it is, it is a glorious thing\n\
To be a Pirate King!\n";
int
main(int argc, char **argv)
{
printf("\n*** Testing HDF5/NetCDF-4 interoperability...\n");
printf("*** Creating a HDF5 file with one var with two dimension scales...");
{
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS_2];
hid_t fapl_id = H5P_DEFAULT, fcpl_id = H5P_DEFAULT;
/* Set latest_format in access propertly list and
* H5P_CRT_ORDER_TRACKED in the creation property list. This turns
* on HDF5 creation ordering. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that HDF5 file can be read by netCDF-4, and adding an att...");
{
int ncid;
char name_in[NC_MAX_NAME + 1];
int natts_in, ndims_in, nvars_in, varid_in, dimids_in[5], unlimdimid_in;
size_t len_in;
nc_type xtype_in;
size_t index[2];
float new_float = NEW_FLOAT;
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
/* Check it out. Can't count on creation order until HDF5 1.8.0,
* so the following code doesn't depend on it. */
if (nc_inq(ncid, &ndims_in, &nvars_in, &natts_in, &unlimdimid_in)) ERR;
if (ndims_in != 2 || nvars_in != 3 || natts_in != 0 || unlimdimid_in != -1) ERR;
if (nc_inq_varid(ncid, PRES_NAME, &varid_in)) ERR;
if (nc_inq_var(ncid, varid_in, name_in, &xtype_in, &ndims_in, dimids_in, &natts_in)) ERR;
if (strcmp(name_in, PRES_NAME) || xtype_in != NC_FLOAT || ndims_in != 2 ||
natts_in != 0) ERR;
if (nc_inq_dim(ncid, dimids_in[0], name_in, &len_in)) ERR;
if (len_in != LAT_LEN || strcmp(name_in, LAT_NAME)) ERR;
if (nc_inq_dim(ncid, dimids_in[1], name_in, &len_in)) ERR;
if (len_in != LON_LEN || strcmp(name_in, LON_NAME)) ERR;
/* Change some data. */
index[0] = index[1] = 0;
if (nc_put_var1_float(ncid, varid_in, index, &new_float)) ERR;
/* Just for swank, add an attribute. Now we're talking
* interoperabity, dude! */
if (nc_put_att_text(ncid, NC_GLOBAL, ATT_NAME, strlen(song)+1,
song)) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, two dimscales, one att file can still be read by HDF5...");
{
hid_t fileid, spaceid, datasetid, attid, typeid, grpid;
char song_in[1024];
float pres_in[LAT_LEN][LON_LEN];
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen1(fileid, "/")) < 0) ERR;
/* Check it out. */
if ((datasetid = H5Dopen1(grpid, PRES_NAME)) < 0) ERR;
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Dread(datasetid, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, pres_in) < 0) ERR;
if (pres_in[0][0] != NEW_FLOAT) ERR;
if ((attid = H5Aopen_name(grpid, ATT_NAME)) < 0) ERR;
if ((typeid = H5Aget_type(attid)) < 0) ERR;
if (H5Aread(attid, typeid, song_in) < 0) ERR;
if (strcmp(song, song_in)) ERR;
/* Close up the shop. */
if (H5Tclose(typeid) < 0 ||
H5Aclose(attid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Dclose(datasetid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a HDF5 file with one var and no dimension scales...");
{
hid_t fileid, pres_spaceid, pres_datasetid;
hsize_t dims[DIMS_2];
hid_t fapl_id, fcpl_id;
int ncid, nvars_in, ndims_in, natts_in, unlimdim_in;
size_t len_in;
/* Set latest_format in access propertly list and
* H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create a variable. It will not have dimension scales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
/* Ring down the curtain. */
if (H5Dclose(pres_datasetid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Read the data with netCDF. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims_in, &nvars_in, &natts_in, &unlimdim_in)) ERR;
if (ndims_in != 2 || nvars_in != 1 || natts_in != 0 || unlimdim_in != -1) ERR;
if (nc_inq_dim(ncid, 0, NULL, &len_in)) ERR;
if (len_in != LAT_LEN) ERR;
if (nc_inq_dim(ncid, 1, NULL, &len_in)) ERR;
if (len_in != LON_LEN) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a HDF5 file with one var and no dimension scales, without creation ordering...");
{
hid_t fileid, pres_spaceid, pres_datasetid;
hsize_t dims[DIMS_2];
int ncid, nvars_in, ndims_in, natts_in, unlimdim_in;
size_t len_in;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create a variable. It will not have dimension scales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
/* Ring down the curtain. */
if (H5Dclose(pres_datasetid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Read the data with netCDF. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims_in, &nvars_in, &natts_in, &unlimdim_in)) ERR;
if (ndims_in != 2 || nvars_in != 1 || natts_in != 0 || unlimdim_in != -1) ERR;
if (nc_inq_dim(ncid, 0, NULL, &len_in)) ERR;
if (len_in != LAT_LEN) ERR;
if (nc_inq_dim(ncid, 1, NULL, &len_in)) ERR;
if (len_in != LON_LEN) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a HDF5 file with two vars and no dimension scales, without creation ordering...");
{
hid_t fileid, spaceid, pres_datasetid, temp_datasetid;
hsize_t dims[DIMS_2];
int ncid, nvars_in, ndims_in, natts_in, unlimdim_in;
size_t len_in;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the space for the datasets. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create two datasets. They will not have dimension scales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
spaceid, H5P_DEFAULT)) < 0) ERR;
if ((temp_datasetid = H5Dcreate1(fileid, TEMP_NAME, H5T_NATIVE_FLOAT,
spaceid, H5P_DEFAULT)) < 0) ERR;
/* Ring down the curtain. */
if (H5Dclose(pres_datasetid) < 0 ||
H5Dclose(temp_datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Read the data with netCDF. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims_in, &nvars_in, &natts_in, &unlimdim_in)) ERR;
if (ndims_in != 2 || nvars_in != 2 || natts_in != 0 || unlimdim_in != -1) ERR;
if (nc_inq_dim(ncid, 0, NULL, &len_in)) ERR;
if (len_in != LAT_LEN) ERR;
if (nc_inq_dim(ncid, 1, NULL, &len_in)) ERR;
if (len_in != LON_LEN) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a HDF5 file with fixed length string...");
{
#define ATT_LEN 3
#define ATT_NAME2 "genius"
#define MAX_LEN 6
hid_t fileid, spaceid, typeid, attid, fapl_id;
hid_t class;
int ncid, nvars_in, ndims_in, natts_in, unlimdim_in;
char data[ATT_LEN][MAX_LEN + 1] = {"Larry_", "Curley", "Moe111"};
char *data_in, *cur, *data_in2[ATT_LEN];
hsize_t dims[1] = {ATT_LEN};
nc_type type_in;
size_t size_in;
int i;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((typeid = H5Tcopy(H5T_C_S1)) < 0) ERR;
if (H5Tset_size(typeid, MAX_LEN + 1) < 0) ERR;
/* Write an attribute of this (string) type. */
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
if ((attid = H5Acreate1(fileid, ATT_NAME2, typeid, spaceid,
H5P_DEFAULT)) < 0) ERR;
if (H5Awrite(attid, typeid, data) < 0) ERR;
/* Close HDF5 objects. */
if (H5Aclose(attid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
if (H5Tclose(typeid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
/* Open the file and read the attribute of fixed length
* strings. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((attid = H5Aopen_name(fileid, ATT_NAME2)) < 0) ERR;
if ((typeid = H5Aget_type(attid)) < 0) ERR;
/* Given this type id, how would we know this is a string
* attribute? */
if ((class = H5Tget_class(typeid)) < 0)
return NC_EHDFERR;
if (class != H5T_STRING) ERR;
/* if (!(type_size = H5Tget_size(typeid))) ERR;
if ((is_str = H5Tis_variable_str(typeid)) < 0) ERR;*/
/* How many strings are in the string array? */
if ((spaceid = H5Aget_space(attid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0) ERR;
if (!(data_in = malloc(dims[0] * sizeof(char *) * (MAX_LEN + 1)))) ERR;
/* Now read the array of strings. The HDF5 library will allocate
* space for each string. */
if (H5Aread(attid, typeid, data_in) < 0) ERR;
/* Compare the values to make sure it worked... */
for (cur = data_in, i = 0; i < ATT_LEN; i++)
{
if (strcmp(data[i], cur)) ERR;
cur += MAX_LEN + 1;
}
/* Free the memory that we allocated. */
free(data_in);
/* Close everything up. */
if (H5Aclose(attid) < 0) ERR;
if (H5Tclose(typeid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
/* Read the data with netCDF. */
if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims_in, &nvars_in, &natts_in, &unlimdim_in)) ERR;
if (ndims_in != 0 || nvars_in != 0 || natts_in != 1 || unlimdim_in != -1) ERR;
if (nc_inq_att(ncid, NC_GLOBAL, ATT_NAME2, &type_in, &size_in)) ERR;
if (type_in != NC_STRING || size_in != ATT_LEN) ERR;
if (nc_get_att_string(ncid, NC_GLOBAL, ATT_NAME2, data_in2)) ERR;
for (i = 0; i < size_in; i++)
if (strcmp(data[i], data_in2[i])) ERR;
if (nc_free_string(size_in, data_in2)) ERR;
/* Open the file with HDF5 while netcdf still has it open. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
/* Turn this off for*/
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_WEAK)) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
printf("**** testing 2D coordinate variable...");
{
#define VAR_NAME "Britany"
#define NDIMS2 2
#define TEXT_LEN 15
#define D0_NAME "time"
#define D1_NAME "tl"
int ncid, nvars_in, varids_in[1];
int time_dimids[NDIMS2], time_id;
size_t time_count[NDIMS2], time_index[NDIMS2] = {0, 0};
const char ttext[TEXT_LEN]="20051224.150000";
int nvars, ndims, ngatts, unlimdimid;
int ndims_in, natts_in, dimids_in[NDIMS2];
char var_name_in[NC_MAX_NAME + 1];
nc_type xtype_in;
/* Create a netcdf-4 file with 2D coordinate var. */
if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
if (nc_def_dim(ncid, D0_NAME, NC_UNLIMITED, &time_dimids[0])) ERR;
if (nc_def_dim(ncid, D1_NAME, TEXT_LEN, &time_dimids[1])) ERR;
if (nc_def_var(ncid, D0_NAME, NC_CHAR, NDIMS2, time_dimids, &time_id)) ERR;
/* Write one time to the coordinate variable. */
time_count[0] = 1;
time_count[1] = TEXT_LEN;
if (nc_put_vara_text(ncid, time_id, time_index, time_count, ttext)) ERR;
if (nc_close(ncid)) ERR;
/* Open the file and check. */
if (nc_open(FILE_NAME, NC_WRITE, &ncid)) ERR;
if (nc_inq(ncid, &ndims, &nvars, &ngatts, &unlimdimid)) ERR;
if (nvars != 1 || ndims != 2 || ngatts != 0 || unlimdimid != 0) ERR;
if (nc_inq_varids(ncid, &nvars_in, varids_in)) ERR;
if (nvars_in != 1 || varids_in[0] != 0) ERR;
if (nc_inq_var(ncid, 0, var_name_in, &xtype_in, &ndims_in, dimids_in, &natts_in)) ERR;
if (strcmp(var_name_in, D0_NAME) || xtype_in != NC_CHAR || ndims_in != 2 ||
dimids_in[0] != 0 || dimids_in[1] != 1 || natts_in != 0) ERR;
if (nc_close(ncid)) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
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