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netcdf-c/libnczarr/zcvt.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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/*********************************************************************
* Copyright 2018, UCAR/Unidata
* See netcdf/COPYRIGHT file for copying and redistribution conditions.
*********************************************************************/
#include "zincludes.h"
#include <math.h>
#ifdef _MSC_VER
#include <crtdbg.h>
#endif
#include "isnan.h"
/*
Code taken directly from libdap4/d4cvt.c
*/
/* Intermediate results */
struct ZCVT {
signed long long int64v;
unsigned long long uint64v;
double float64v;
};
/* Forward */
static int typeid2jtype(nc_type typeid);
/* Convert an NCJ_STRING to a memory equivalent value of specified dsttype */
int
NCZ_convert1(NCjson* jsrc, nc_type dsttype, unsigned char* memory)
{
int stat = NC_NOERR;
nc_type srctype;
struct ZCVT zcvt;
int outofrange = 0;
/* Convert the incoming jsrc string to a restricted set of values */
switch (NCJsort(jsrc)) {
case NCJ_INT: /* convert to (u)int64 */
if(NCJstring(jsrc)[0] == '-') {
if(sscanf(NCJstring(jsrc),"%lld",&zcvt.int64v) != 1)
{stat = NC_EINVAL; goto done;}
srctype = NC_INT64;
} else {
if(sscanf(NCJstring(jsrc),"%llu",&zcvt.uint64v) != 1)
{stat = NC_EINVAL; goto done;}
srctype = NC_UINT64;
}
break;
case NCJ_STRING:
case NCJ_DOUBLE:
/* Capture nan and infinity values */
if(strcasecmp(NCJstring(jsrc),"nan")==0)
zcvt.float64v = NAN;
else if(strcasecmp(NCJstring(jsrc),"-nan")==0)
zcvt.float64v = - NAN;
else if(strcasecmp(NCJstring(jsrc),"infinity")==0)
zcvt.float64v = INFINITY;
else if(strcasecmp(NCJstring(jsrc),"-infinity")==0)
zcvt.float64v = (- INFINITY);
else {
if(sscanf(NCJstring(jsrc),"%lg",&zcvt.float64v) != 1)
{stat = NC_EINVAL; goto done;}
}
srctype = NC_DOUBLE;
break;
case NCJ_BOOLEAN:
srctype = NC_UINT64;
if(strcasecmp(NCJstring(jsrc),"false")==0)
zcvt.uint64v = 0;
else
zcvt.uint64v = 1;
break;
default: stat = NC_EINTERNAL; goto done;
}
/* Now, do the down conversion */
switch (dsttype) {
case NC_BYTE: {
signed char* p = (signed char*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < NC_MIN_BYTE || zcvt.int64v > NC_MAX_BYTE) outofrange = 1;
*p = (signed char)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_BYTE) outofrange = 1;
*p = (signed char)zcvt.uint64v;
break;
}
} break;
case NC_UBYTE: {
unsigned char* p = (unsigned char*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < 0 || zcvt.int64v > NC_MAX_BYTE) outofrange = 1;
*p = (unsigned char)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_UBYTE) outofrange = 1;
*p = (unsigned char)zcvt.uint64v;
break;
}
} break;
case NC_SHORT: {
signed short* p = (signed short*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < NC_MIN_SHORT || zcvt.int64v > NC_MAX_SHORT) outofrange = 1;
*p = (signed short)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_SHORT) outofrange = 1;
*p = (signed short)zcvt.uint64v;
break;
}
} break;
case NC_USHORT: {
unsigned short* p = (unsigned short*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < 0 || zcvt.int64v > NC_MAX_USHORT) outofrange = 1;
*p = (unsigned short)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_USHORT) outofrange = 1;
*p = (unsigned short)zcvt.uint64v;
break;
}
} break;
case NC_INT: {
signed int* p = (signed int*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < NC_MIN_INT || zcvt.int64v > NC_MAX_INT) outofrange = 1;
*p = (signed int)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_INT) outofrange = 1;
*p = (signed int)zcvt.uint64v;
break;
}
} break;
case NC_UINT: {
unsigned int* p = (unsigned int*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
if(zcvt.int64v < 0 || zcvt.int64v > NC_MAX_UINT) outofrange = 1;
*p = (unsigned int)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_UINT) outofrange = 1;
*p = (unsigned int)zcvt.uint64v;
break;
}
} break;
case NC_INT64: {
signed long long* p = (signed long long*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (long long)zcvt.float64v; /* Convert to int64 */
/* fall thru */
case NC_INT64:
*p = (signed long long)zcvt.int64v;
break;
case NC_UINT64:
if(zcvt.uint64v > NC_MAX_INT64) outofrange = 1;
*p = (signed long long)zcvt.uint64v;
break;
}
} break;
case NC_UINT64: {
unsigned long long* p = (unsigned long long*)memory;
switch (srctype) {
case NC_DOUBLE:
zcvt.int64v = (signed long long)zcvt.float64v;
/* fall thru */
case NC_INT64:
if(zcvt.int64v < 0) outofrange = 1;
*p = (unsigned long long)zcvt.int64v;
break;
case NC_UINT64:
*p = (unsigned long long)zcvt.uint64v;
break;
}
} break;
case NC_FLOAT: {
float* p = (float*)memory;
switch (srctype) {
case NC_DOUBLE:
*p = (float)zcvt.float64v;
break;
case NC_INT64:
*p = (float)zcvt.int64v;
break;
case NC_UINT64:
*p = (float)zcvt.uint64v;
break;
}
} break;
case NC_DOUBLE: {
double* p = (double*)memory;
switch (srctype) {
case NC_DOUBLE:
*p = (double)zcvt.float64v;
break;
case NC_INT64:
*p = (double)zcvt.int64v;
break;
case NC_UINT64:
*p = (double)zcvt.uint64v;
break;
}
} break;
default: stat = NC_EINTERNAL; goto done;
}
done:
if(stat == NC_NOERR && outofrange) stat = NC_ERANGE;
return stat;
}
/* Convert a memory value to a JSON string value */
int
NCZ_stringconvert1(nc_type srctype, size_t len, char* src, NCjson* jvalue)
{
int stat = NC_NOERR;
struct ZCVT zcvt;
nc_type dsttype = NC_NAT;
char s[1024];
assert(srctype >= NC_NAT && srctype != NC_CHAR && srctype < NC_STRING);
/* Convert to a restricted set of values */
switch (srctype) {
case NC_BYTE: {
zcvt.int64v = (signed long long)(*((signed char*)src));
dsttype = NC_INT64;
} break;
case NC_UBYTE: {
zcvt.uint64v = (unsigned long long)(*((unsigned char*)src));
dsttype = NC_UINT64;
} break;
case NC_SHORT: {
zcvt.int64v = (signed long long)(*((signed short*)src));
dsttype = NC_INT64;
} break;
case NC_USHORT: {
zcvt.uint64v = (unsigned long long)(*((unsigned short*)src));
dsttype = NC_UINT64;
} break;
case NC_INT: {
zcvt.int64v = (signed long long)(*((signed int*)src));
dsttype = NC_INT64;
} break;
case NC_UINT: {
zcvt.uint64v = (unsigned long long)(*((unsigned int*)src));
dsttype = NC_UINT64;
} break;
case NC_INT64: {
zcvt.int64v = (signed long long)(*((signed long long*)src));
dsttype = NC_INT64;
} break;
case NC_UINT64: {
zcvt.uint64v = (unsigned long long)(*((unsigned long long*)src));
dsttype = NC_UINT64;
} break;
case NC_FLOAT: {
zcvt.float64v = (double)(*((float*)src));
dsttype = NC_DOUBLE;
} break;
case NC_DOUBLE: {
dsttype = NC_DOUBLE;
zcvt.float64v= (double)(*((double*)src));
} break;
default: stat = NC_EINTERNAL; goto done;
}
/* Convert from restricted set of values to standardized string form*/
switch (dsttype) {
case NC_INT64: {
snprintf(s,sizeof(s),"%lld",zcvt.int64v);
} break;
case NC_UINT64: {
snprintf(s,sizeof(s),"%llu",zcvt.uint64v);
} break;
case NC_DOUBLE: {
#ifdef _WIN32
switch (_fpclass(zcvt.float64v)) {
case _FPCLASS_SNAN: case _FPCLASS_QNAN:
strcpy(s,"Nan"); break;
case _FPCLASS_NINF:
strcpy(s,"-Infinity"); break;
case _FPCLASS_PINF:
strcpy(s,"Infinity"); break;
default:
snprintf(s,sizeof(s),"%lg",zcvt.float64v); /* handles NAN? */
break;
}
#else
if(isnan(zcvt.float64v))
strcpy(s,"NaN");
else if(isinf(zcvt.float64v) && zcvt.float64v < 0)
strcpy(s,"-Infinity");
else if(isinf(zcvt.float64v) && zcvt.float64v > 0)
strcpy(s,"Infinity");
else {
snprintf(s,sizeof(s),"%lg",zcvt.float64v); /* handles NAN? */
}
#endif
} break;
default: stat = NC_EINTERNAL; goto done;
}
NCJsetstring(jvalue,strdup(s));
done:
return stat;
}
int
NCZ_stringconvert(nc_type typeid, size_t len, void* data0, NCjson** jdatap)
{
int stat = NC_NOERR;
int i;
char* src = data0; /* so we can do arithmetic on it */
size_t typelen;
char* str = NULL;
NCjson* jvalue = NULL;
NCjson* jdata = NULL;
int jtype = NCJ_UNDEF;
jtype = typeid2jtype(typeid);
if((stat = NC4_inq_atomic_type(typeid, NULL, &typelen)))
goto done;
/* Handle char type specially */
if(typeid == NC_CHAR) {
/* Create a string valued json object */
if((stat = NCJnewstringn(NCJ_STRING,len,src,&jdata)))
goto done;
} else if(len == 1) { /* create singleton */
if((stat = NCJnew(jtype,&jdata))) goto done;
if((stat = NCZ_stringconvert1(typeid, len, src, jdata))) goto done;
} else { /* len > 1 create array of values */
if((stat = NCJnew(NCJ_ARRAY,&jdata))) goto done;
for(i=0;i<len;i++) {
if((stat = NCJnew(jtype,&jvalue))) goto done;
if((stat = NCZ_stringconvert1(typeid, len, src, jvalue))) goto done;
NCJappend(jdata,jvalue);
jvalue = NULL;
src += typelen;
}
}
if(jdatap) {*jdatap = jdata; jdata = NULL;}
done:
nullfree(str);
NCJreclaim(jvalue);
NCJreclaim(jdata);
return stat;
}
static int
typeid2jtype(nc_type typeid)
{
switch (typeid) {
case NC_BYTE: case NC_SHORT: case NC_INT: case NC_INT64:
case NC_UBYTE: case NC_USHORT: case NC_UINT: case NC_UINT64:
return NCJ_INT;
case NC_FLOAT:
case NC_DOUBLE:
return NCJ_DOUBLE;
case NC_CHAR:
return NCJ_STRING;
default: break;
}
return NCJ_UNDEF;
}
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