mirror of
https://github.com/Unidata/netcdf-c.git
synced 2024-12-27 08:49:16 +08:00
8b9253fef2
re: https://github.com/Unidata/netcdf-c/issues/541 re: https://github.com/Unidata/netcdf-c/issues/1208 re: https://github.com/Unidata/netcdf-c/issues/2078 re: https://github.com/Unidata/netcdf-c/issues/2041 re: https://github.com/Unidata/netcdf-c/issues/2143 For a long time, there have been known problems with the management of complex types containing VLENs. This also involves the string type because it is stored as a VLEN of chars. This PR (mostly) fixes this problem. But note that it adds new functions to netcdf.h (see below) and this may require bumping the .so number. These new functions can be removed, if desired, in favor of functions in netcdf_aux.h, but netcdf.h seems the better place for them because they are intended as alternatives to the nc_free_vlen and nc_free_string functions already in netcdf.h. The term complex type refers to any type that directly or transitively references a VLEN type. So an array of VLENS, a compound with a VLEN field, and so on. In order to properly handle instances of these complex types, it is necessary to have function that can recursively walk instances of such types to perform various actions on them. The term "deep" is also used to mean recursive. At the moment, the two operations needed by the netcdf library are: * free'ing an instance of the complex type * copying an instance of the complex type. The current library does only shallow free and shallow copy of complex types. This means that only the top level is properly free'd or copied, but deep internal blocks in the instance are not touched. Note that the term "vector" will be used to mean a contiguous (in memory) sequence of instances of some type. Given an array with, say, dimensions 2 X 3 X 4, this will be stored in memory as a vector of length 2*3*4=24 instances. The use cases are primarily these. ## nc_get_vars Suppose one is reading a vector of instances using nc_get_vars (or nc_get_vara or nc_get_var, etc.). These functions will return the vector in the top-level memory provided. All interior blocks (form nested VLEN or strings) will have been dynamically allocated. After using this vector of instances, it is necessary to free (aka reclaim) the dynamically allocated memory, otherwise a memory leak occurs. So, the recursive reclaim function is used to walk the returned instance vector and do a deep reclaim of the data. Currently functions are defined in netcdf.h that are supposed to handle this: nc_free_vlen(), nc_free_vlens(), and nc_free_string(). Unfortunately, these functions only do a shallow free, so deeply nested instances are not properly handled by them. Note that internally, the provided data is immediately written so there is no need to copy it. But the caller may need to reclaim the data it passed into the function. ## nc_put_att Suppose one is writing a vector of instances as the data of an attribute using, say, nc_put_att. Internally, the incoming attribute data must be copied and stored so that changes/reclamation of the input data will not affect the attribute. Again, the code inside the netcdf library does only shallow copying rather than deep copy. As a result, one sees effects such as described in Github Issue https://github.com/Unidata/netcdf-c/issues/2143. Also, after defining the attribute, it may be necessary for the user to free the data that was provided as input to nc_put_att(). ## nc_get_att Suppose one is reading a vector of instances as the data of an attribute using, say, nc_get_att. Internally, the existing attribute data must be copied and returned to the caller, and the caller is responsible for reclaiming the returned data. Again, the code inside the netcdf library does only shallow copying rather than deep copy. So this can lead to memory leaks and errors because the deep data is shared between the library and the user. # Solution The solution is to build properly recursive reclaim and copy functions and use those as needed. These recursive functions are defined in libdispatch/dinstance.c and their signatures are defined in include/netcdf.h. For back compatibility, corresponding "ncaux_XXX" functions are defined in include/netcdf_aux.h. ```` int nc_reclaim_data(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_reclaim_data_all(int ncid, nc_type xtypeid, void* memory, size_t count); int nc_copy_data(int ncid, nc_type xtypeid, const void* memory, size_t count, void* copy); int nc_copy_data_all(int ncid, nc_type xtypeid, const void* memory, size_t count, void** copyp); ```` There are two variants. The first two, nc_reclaim_data() and nc_copy_data(), assume the top-level vector is managed by the caller. For reclaim, this is so the user can use, for example, a statically allocated vector. For copy, it assumes the user provides the space into which the copy is stored. The second two, nc_reclaim_data_all() and nc_copy_data_all(), allows the functions to manage the top-level. So for nc_reclaim_data_all, the top level is assumed to be dynamically allocated and will be free'd by nc_reclaim_data_all(). The nc_copy_data_all() function will allocate the top level and return a pointer to it to the user. The user can later pass that pointer to nc_reclaim_data_all() to reclaim the instance(s). # Internal Changes The netcdf-c library internals are changed to use the proper reclaim and copy functions. It turns out that the places where these functions are needed is quite pervasive in the netcdf-c library code. Using these functions also allows some simplification of the code since the stdata and vldata fields of NC_ATT_INFO are no longer needed. Currently this is commented out using the SEPDATA \#define macro. When any bugs are largely fixed, all this code will be removed. # Known Bugs 1. There is still one known failure that has not been solved. All the failures revolve around some variant of this .cdl file. The proximate cause of failure is the use of a VLEN FillValue. ```` netcdf x { types: float(*) row_of_floats ; dimensions: m = 5 ; variables: row_of_floats ragged_array(m) ; row_of_floats ragged_array:_FillValue = {-999} ; data: ragged_array = {10, 11, 12, 13, 14}, {20, 21, 22, 23}, {30, 31, 32}, {40, 41}, _ ; } ```` When a solution is found, I will either add it to this PR or post a new PR. # Related Changes * Mark nc_free_vlen(s) as deprecated in favor of ncaux_reclaim_data. * Remove the --enable-unfixed-memory-leaks option. * Remove the NC_VLENS_NOTEST code that suppresses some vlen tests. * Document this change in docs/internal.md * Disable the tst_vlen_data test in ncdump/tst_nccopy4.sh. * Mark types as fixed size or not (transitively) to optimize the reclaim and copy functions. # Misc. Changes * Make Doxygen process libdispatch/daux.c * Make sure the NC_ATT_INFO_T.container field is set.
927 lines
26 KiB
C
927 lines
26 KiB
C
/*
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Copyright (c) 1998-2018 University Corporation for Atmospheric Research/Unidata
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See COPYRIGHT for license information.
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*/
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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#include "config.h"
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#include <stdlib.h>
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#include <string.h>
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#include <assert.h>
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#include "config.h"
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#include "netcdf.h"
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#include "netcdf_aux.h"
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#include "ncoffsets.h"
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#include "nclog.h"
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#include "ncrc.h"
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#include "netcdf_filter.h"
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struct NCAUX_FIELD {
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char* name;
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nc_type fieldtype;
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size_t ndims;
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int dimsizes[NC_MAX_VAR_DIMS];
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size_t size;
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size_t offset;
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size_t alignment;
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};
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struct NCAUX_CMPD {
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int ncid;
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int mode;
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char* name;
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size_t nfields;
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struct NCAUX_FIELD* fields;
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size_t size;
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size_t offset; /* cumulative as fields are added */
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size_t alignment;
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};
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static int computefieldinfo(struct NCAUX_CMPD* cmpd);
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static int filterspec_cvt(const char* txt, size_t* nparamsp, unsigned int* params);
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/**************************************************/
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/*
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This code is a variant of the H5detect.c code from HDF5.
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Author: D. Heimbigner 10/7/2008
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*/
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EXTERNL int
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ncaux_begin_compound(int ncid, const char *name, int alignmode, void** tagp)
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{
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#ifdef USE_NETCDF4
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int status = NC_NOERR;
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struct NCAUX_CMPD* cmpd = NULL;
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if(tagp) *tagp = NULL;
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cmpd = (struct NCAUX_CMPD*)calloc(1,sizeof(struct NCAUX_CMPD));
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if(cmpd == NULL) {status = NC_ENOMEM; goto fail;}
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cmpd->ncid = ncid;
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cmpd->mode = alignmode;
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cmpd->nfields = 0;
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cmpd->name = strdup(name);
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if(cmpd->name == NULL) {status = NC_ENOMEM; goto fail;}
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if(tagp) {
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*tagp = (void*)cmpd;
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} else { /* Error, free cmpd to avoid memory leak. */
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free(cmpd);
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}
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return status;
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fail:
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ncaux_abort_compound((void*)cmpd);
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return status;
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#else
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return NC_ENOTBUILT;
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#endif
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}
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EXTERNL int
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ncaux_abort_compound(void* tag)
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{
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#ifdef USE_NETCDF4
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int i;
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struct NCAUX_CMPD* cmpd = (struct NCAUX_CMPD*)tag;
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if(cmpd == NULL) goto done;
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if(cmpd->name) free(cmpd->name);
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for(i=0;i<cmpd->nfields;i++) {
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struct NCAUX_FIELD* field = &cmpd->fields[i];
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if(field->name) free(field->name);
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}
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if(cmpd->fields) free(cmpd->fields);
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free(cmpd);
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done:
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return NC_NOERR;
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#else
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return NC_ENOTBUILT;
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#endif
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}
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EXTERNL int
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ncaux_add_field(void* tag, const char *name, nc_type field_type,
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int ndims, const int* dimsizes)
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{
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#ifdef USE_NETCDF4
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int i;
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int status = NC_NOERR;
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struct NCAUX_CMPD* cmpd = (struct NCAUX_CMPD*)tag;
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struct NCAUX_FIELD* newfields = NULL;
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struct NCAUX_FIELD* field = NULL;
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if(cmpd == NULL) goto done;
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if(ndims < 0) {status = NC_EINVAL; goto done;}
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for(i=0;i<ndims;i++) {
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if(dimsizes[i] <= 0) {status = NC_EINVAL; goto done;}
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}
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if(cmpd->fields == NULL) {
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newfields = (struct NCAUX_FIELD*)calloc(1,sizeof(struct NCAUX_FIELD));
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} else {
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newfields = (struct NCAUX_FIELD*)realloc(cmpd->fields,cmpd->nfields+1*sizeof(struct NCAUX_FIELD));
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}
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if(cmpd->fields == NULL) {status = NC_ENOMEM; goto done;}
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cmpd->fields = newfields;
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field = &cmpd->fields[cmpd->nfields+1];
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field->name = strdup(name);
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field->fieldtype = field_type;
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if(field->name == NULL) {status = NC_ENOMEM; goto done;}
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field->ndims = (size_t)ndims;
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memcpy(field->dimsizes,dimsizes,sizeof(int)*field->ndims);
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cmpd->nfields++;
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done:
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if(newfields)
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free(newfields);
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return status;
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#else
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return NC_ENOTBUILT;
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#endif
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}
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EXTERNL int
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ncaux_end_compound(void* tag, nc_type* idp)
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{
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#ifdef USE_NETCDF4
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int i;
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int status = NC_NOERR;
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struct NCAUX_CMPD* cmpd = (struct NCAUX_CMPD*)tag;
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if(cmpd == NULL) {status = NC_EINVAL; goto done;}
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/* Compute field and compound info */
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status = computefieldinfo(cmpd);
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if(status != NC_NOERR) goto done;
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status = nc_def_compound(cmpd->ncid, cmpd->size, cmpd->name, idp);
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if(status != NC_NOERR) goto done;
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for(i=0;i<cmpd->nfields;i++) {
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struct NCAUX_FIELD* field = &cmpd->fields[i];
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if(field->ndims > 0) {
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status = nc_insert_compound(cmpd->ncid, *idp, field->name,
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field->offset, field->fieldtype);
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} else {
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status = nc_insert_array_compound(cmpd->ncid, *idp, field->name,
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field->offset, field->fieldtype,
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(int)field->ndims,field->dimsizes);
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}
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if(status != NC_NOERR) goto done;
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}
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done:
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return status;
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#else
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return NC_ENOTBUILT;
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#endif
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}
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/**************************************************/
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/**
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@param ncclass - type class for which alignment is requested; excludes ENUM|COMPOUND
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*/
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int
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ncaux_class_alignment(int ncclass, size_t* alignp)
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{
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int stat = NC_NOERR;
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size_t align = 0;
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if(ncclass <= NC_MAX_ATOMIC_TYPE || ncclass == NC_VLEN || ncclass == NC_OPAQUE) {
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stat = NC_class_alignment(ncclass,&align);
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} else {
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nclog(NCLOGERR,"ncaux_class_alignment: class %d; alignment cannot be determermined",ncclass);
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}
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if(alignp) *alignp = align;
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if(align == 0) stat = NC_EINVAL;
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return stat;
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}
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#ifdef USE_NETCDF4
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/* Find first primitive field of a possibly nested sequence of compounds */
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static nc_type
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findfirstfield(int ncid, nc_type xtype)
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{
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int status = NC_NOERR;
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nc_type fieldtype = xtype;
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if(xtype <= NC_MAX_ATOMIC_TYPE) goto done;
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status = nc_inq_compound_fieldtype(ncid, xtype, 0, &fieldtype);
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if(status != NC_NOERR) goto done;
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fieldtype = findfirstfield(ncid,fieldtype);
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done:
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return (status == NC_NOERR?fieldtype:NC_NAT);
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}
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static size_t
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getpadding(size_t offset, size_t alignment)
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{
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size_t rem = (alignment==0?0:(offset % alignment));
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size_t pad = (rem==0?0:(alignment - rem));
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return pad;
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}
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static size_t
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dimproduct(size_t ndims, int* dimsizes)
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{
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int i;
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size_t product = 1;
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for(i=0;i<ndims;i++) product *= (size_t)dimsizes[i];
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return product;
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}
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static int
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computefieldinfo(struct NCAUX_CMPD* cmpd)
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{
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int i;
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int status = NC_NOERR;
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size_t offset = 0;
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size_t totaldimsize;
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/* Assign the sizes for the fields */
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for(i=0;i<cmpd->nfields;i++) {
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struct NCAUX_FIELD* field = &cmpd->fields[i];
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status = nc_inq_type(cmpd->ncid,field->fieldtype,NULL,&field->size);
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if(status != NC_NOERR) goto done;
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totaldimsize = dimproduct(field->ndims,field->dimsizes);
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field->size *= totaldimsize;
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}
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for(offset=0,i=0;i<cmpd->nfields;i++) {
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struct NCAUX_FIELD* field = &cmpd->fields[i];
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int alignment = 0;
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nc_type firsttype = findfirstfield(cmpd->ncid,field->fieldtype);
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/* only support 'c' alignment for now*/
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switch (field->fieldtype) {
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case NC_OPAQUE:
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field->alignment = 1;
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break;
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case NC_ENUM:
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status = ncaux_type_alignment(firsttype,cmpd->ncid,&field->alignment);
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break;
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case NC_VLEN: /*fall thru*/
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case NC_COMPOUND:
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status = ncaux_type_alignment(firsttype,cmpd->ncid,&field->alignment);
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break;
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default:
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status = ncaux_type_alignment(field->fieldtype,cmpd->ncid,&field->alignment);
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break;
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}
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offset += getpadding(offset,alignment);
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field->offset = offset;
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offset += field->size;
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}
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cmpd->size = offset;
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cmpd->alignment = cmpd->fields[0].alignment;
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done:
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return status;
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}
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#endif /*USE_NETCDF4*/
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/**************************************************/
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/* Forward */
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#define NUMCHAR "0123456789"
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#define LPAREN '('
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#define RPAREN ')'
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#define LBRACK '['
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#define RBRACK ']'
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static int gettype(const int q0, const int q1, int* unsignedp);
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/* Look at q0 and q1) to determine type */
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static int
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gettype(const int q0, const int q1, int* isunsignedp)
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{
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int type = 0;
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int isunsigned = 0;
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char typechar;
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isunsigned = (q0 == 'u' || q0 == 'U');
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if(q1 == '\0')
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typechar = q0; /* we were given only a single char */
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else if(isunsigned)
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typechar = q1; /* we have something like Ux as the tag */
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else
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typechar = q1; /* look at last char for tag */
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switch (typechar) {
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case 'f': case 'F': case '.': type = 'f'; break; /* float */
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case 'd': case 'D': type = 'd'; break; /* double */
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case 'b': case 'B': type = 'b'; break; /* byte */
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case 's': case 'S': type = 's'; break; /* short */
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case 'l': case 'L': type = 'l'; break; /* long long */
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case '0': case '1': case '2': case '3': case '4':
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case '5': case '6': case '7': case '8': case '9': type = 'i'; break;
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case 'u': case 'U': type = 'i'; isunsigned = 1; break; /* unsigned int */
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case '\0': type = 'i'; break;
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default: break;
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}
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if(isunsignedp) *isunsignedp = isunsigned;
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return type;
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}
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#ifdef WORDS_BIGENDIAN
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/* Byte swap an 8-byte integer in place */
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static void
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byteswap8(unsigned char* mem)
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{
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unsigned char c;
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c = mem[0];
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mem[0] = mem[7];
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mem[7] = c;
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c = mem[1];
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mem[1] = mem[6];
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mem[6] = c;
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c = mem[2];
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mem[2] = mem[5];
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mem[5] = c;
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c = mem[3];
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mem[3] = mem[4];
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mem[4] = c;
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}
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/* Byte swap an 8-byte integer in place */
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static void
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byteswap4(unsigned char* mem)
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{
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unsigned char c;
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c = mem[0];
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mem[0] = mem[3];
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mem[3] = c;
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c = mem[1];
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mem[1] = mem[2];
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mem[2] = c;
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}
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#endif
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/**************************************************/
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/* Moved here from netcdf_filter.h */
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/*
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This function implements the 8-byte conversion algorithms for HDF5
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Before calling *nc_def_var_filter* (unless *NC_parsefilterspec* was used),
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the client must call this function with the decode argument set to 0.
|
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Inside the filter code, this function should be called with the decode
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argument set to 1.
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* @params mem8 is a pointer to the 8-byte value either to fix.
|
|
* @params decode is 1 if the function should apply the 8-byte decoding algorithm
|
|
else apply the encoding algorithm.
|
|
*/
|
|
|
|
void
|
|
ncaux_h5filterspec_fix8(unsigned char* mem8, int decode)
|
|
{
|
|
#ifdef WORDS_BIGENDIAN
|
|
if(decode) { /* Apply inverse of the encode case */
|
|
byteswap4(mem8); /* step 1: byte-swap each piece */
|
|
byteswap4(mem8+4);
|
|
byteswap8(mem8); /* step 2: convert to little endian format */
|
|
} else { /* encode */
|
|
byteswap8(mem8); /* step 1: convert to little endian format */
|
|
byteswap4(mem8); /* step 2: byte-swap each piece */
|
|
byteswap4(mem8+4);
|
|
}
|
|
#else /* Little endian */
|
|
/* No action is necessary */
|
|
#endif
|
|
}
|
|
|
|
/*
|
|
Parse a filter spec string into a NC_FILTER_SPEC*
|
|
Note that this differs from the usual case in that the
|
|
function is called once to get both the number of parameters
|
|
and the parameters themselves (hence the unsigned int** paramsp).
|
|
|
|
@param txt - a string containing the spec as a sequence of
|
|
constants separated by commas, where first constant
|
|
is the filter id and the rest are parameters.
|
|
@param idp - store the parsed filter id here
|
|
@param nparamsp - store the number of parameters here
|
|
@param paramsp - store the vector of parameters here; caller frees.
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL otherwise
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_h5filterspec_parse(const char* txt, unsigned int* idp, size_t* nparamsp, unsigned int** paramsp)
|
|
{
|
|
int i,stat = NC_NOERR;
|
|
char* p;
|
|
char* sdata0 = NULL; /* what to free */
|
|
char* sdata = NULL; /* sdata0 with leading prefix skipped */
|
|
size_t nparams; /* no. of comma delimited params */
|
|
size_t nactual; /* actual number of unsigned int's */
|
|
const char* sid = NULL;
|
|
unsigned int filterid = 0;
|
|
unsigned int* params = NULL;
|
|
size_t len;
|
|
|
|
if(txt == NULL)
|
|
{stat = NC_EINVAL; goto done;}
|
|
len = strlen(txt);
|
|
if(len == 0)
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if((sdata0 = (char*)calloc(1,len+1+1))==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
memcpy(sdata0,txt,len);
|
|
sdata = sdata0;
|
|
|
|
/* Count number of parameters + id and delimit */
|
|
p=sdata;
|
|
for(nparams=0;;nparams++) {
|
|
char* q = strchr(p,',');
|
|
if(q == NULL) break;
|
|
*q++ = '\0';
|
|
p = q;
|
|
}
|
|
nparams++; /* for final piece */
|
|
|
|
if(nparams == 0)
|
|
{stat = NC_EINVAL; goto done;} /* no id and no parameters */
|
|
|
|
p = sdata;
|
|
|
|
/* Extract the filter id */
|
|
sid = p;
|
|
if((sscanf(sid,"%u",&filterid)) != 1) {stat = NC_EINVAL; goto done;}
|
|
nparams--;
|
|
|
|
/* skip past the filter id */
|
|
p = p + strlen(p) + 1;
|
|
|
|
/* Allocate the max needed space (assume all params are 64 bit) */
|
|
if((params = (unsigned int*)calloc(sizeof(unsigned int),(nparams)*2))==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
|
|
/* walk and capture */
|
|
for(nactual=0,i=0;i<nparams;i++) { /* step thru param strings */
|
|
size_t count = 0;
|
|
len = strlen(p);
|
|
/* skip leading white space */
|
|
while(strchr(" ",*p) != NULL) {p++; len--;}
|
|
if((stat = filterspec_cvt(p,&count,params+nactual))) goto done;
|
|
nactual += count;
|
|
p = p + strlen(p) + 1; /* move to next param string */
|
|
}
|
|
/* Now return results */
|
|
if(idp) *idp = filterid;
|
|
if(nparamsp) *nparamsp = nactual;
|
|
if(paramsp) {*paramsp = params; params = NULL;}
|
|
done:
|
|
nullfree(params);
|
|
nullfree(sdata0);
|
|
return stat;
|
|
}
|
|
|
|
/*
|
|
Parse a filter parameter string into a sequence of unsigned ints.
|
|
|
|
@param txt - a string containing the parameter string.
|
|
@param nuiparamsp - store the number of unsigned ints here
|
|
@param uiparamsp - store the vector of unsigned ints here; caller frees.
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL otherwise
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_h5filterspec_parse_parameter(const char* txt, size_t* nuiparamsp, unsigned int* uiparams)
|
|
{
|
|
int stat = NC_NOERR;
|
|
char* p;
|
|
char* sdata0 = NULL; /* what to free */
|
|
char* sdata = NULL; /* sdata0 with leading prefix skipped */
|
|
size_t nuiparams = 0;
|
|
size_t len;
|
|
|
|
if(txt == NULL)
|
|
{stat = NC_EINVAL; goto done;}
|
|
len = strlen(txt);
|
|
if(len == 0)
|
|
{stat = NC_EINVAL; goto done;}
|
|
|
|
if((sdata0 = (char*)calloc(1,len+1+1))==NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
memcpy(sdata0,txt,len);
|
|
sdata = sdata0;
|
|
|
|
p = sdata;
|
|
|
|
nuiparams = 0;
|
|
len = strlen(p);
|
|
/* skip leading white space */
|
|
while(strchr(" ",*p) != NULL) {p++; len--;}
|
|
if((stat = filterspec_cvt(p,&nuiparams,uiparams))) goto done;
|
|
/* Now return results */
|
|
if(nuiparamsp) *nuiparamsp = nuiparams;
|
|
done:
|
|
nullfree(sdata0);
|
|
return stat;
|
|
}
|
|
|
|
/*
|
|
Parse a string containing multiple '|' separated filter specs.
|
|
Use a vector of NC_Filterspec structs to return results.
|
|
@param txt0 - a string containing the list of filter specs.
|
|
@param formatp - store any leading format integer here
|
|
@param nspecsp - # of parsed specs
|
|
@param specsp - pointer to hold vector of parsed specs. Caller frees
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL if bad parameters or parse failed
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_h5filterspec_parselist(const char* txt0, int* formatp, size_t* nspecsp, NC_H5_Filterspec*** vectorp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
int format = 0;
|
|
size_t len = 0;
|
|
size_t nspecs = 0;
|
|
NC_H5_Filterspec** vector = NULL;
|
|
char* spec = NULL; /* without prefix */
|
|
char* p = NULL;
|
|
char* q = NULL;
|
|
|
|
if(txt0 == NULL) return NC_EINVAL;
|
|
/* Duplicate txt0 so we can modify it */
|
|
len = strlen(txt0);
|
|
if((spec = calloc(1,len+1+1)) == NULL) {stat = NC_ENOMEM; goto done;}
|
|
memcpy(spec,txt0,len); /* Note double ending nul */
|
|
|
|
/* See if there is a prefix '[format]' tag */
|
|
if(spec[0] == LBRACK) {
|
|
p = spec + 1;
|
|
q = strchr(p,RBRACK);
|
|
if(q == NULL) {stat = NC_EINVAL; goto done;}
|
|
*q++ = '\0'; /* delimit tag */
|
|
if(sscanf(p,"%d",&format) != 1) {stat = NC_EINVAL; goto done;}
|
|
spec = q; /* skip tag wrt later processing */
|
|
}
|
|
|
|
/* pass 1: count number of specs */
|
|
p = spec;
|
|
nspecs = 0;
|
|
while(*p) {
|
|
q = strchr(p,'|');
|
|
if(q == NULL) q = p + strlen(p); /* fake it */
|
|
nspecs++;
|
|
p = q + 1;
|
|
}
|
|
if(nspecs > 0) {
|
|
int count = 0;
|
|
if((vector = (NC_H5_Filterspec**)calloc(sizeof(NC_H5_Filterspec*),nspecs)) == NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
/* pass 2: parse */
|
|
p = spec;
|
|
for(count=0;count<nspecs;count++) {
|
|
NC_H5_Filterspec* spec = (NC_H5_Filterspec*)calloc(1,sizeof(NC_H5_Filterspec));
|
|
if(spec == NULL) {stat = NC_ENOMEM; goto done;}
|
|
vector[count] = spec;
|
|
q = strchr(p,'|');
|
|
if(q == NULL) q = p + strlen(p); /* fake it */
|
|
*q = '\0';
|
|
if((stat=ncaux_h5filterspec_parse(p,&spec->filterid,&spec->nparams,&spec->params))) goto done;
|
|
p = q+1; /* ok because of double nul */
|
|
}
|
|
}
|
|
if(formatp) *formatp = format;
|
|
if(nspecsp) *nspecsp = nspecs;
|
|
if(vectorp) {*vectorp = vector; vector = NULL;}
|
|
done:
|
|
nullfree(spec);
|
|
if(vector) {
|
|
int i;
|
|
for(i=0;i<nspecs;i++)
|
|
ncaux_h5filterspec_free(vector[i]);
|
|
nullfree(vector);
|
|
}
|
|
return stat;
|
|
}
|
|
|
|
/*
|
|
Parse a string containing multiple '|' separated filter specs.
|
|
Use a vector of NC_Filterspec structs to return results.
|
|
@param txt0 - a string containing the list of filter specs.
|
|
@param formatp - store any leading format integer here
|
|
@param nspecsp - # of parsed specs
|
|
@param specsp - pointer to hold vector of parsed specs. Caller frees
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL if bad parameters or parse failed
|
|
*/
|
|
|
|
EXTERNL void
|
|
ncaux_h5filterspec_free(NC_H5_Filterspec* f)
|
|
{
|
|
if(f) nullfree(f->params);
|
|
nullfree(f);
|
|
}
|
|
|
|
|
|
/*
|
|
Convert a parameter string to one or two unsigned ints/
|
|
@param txt - (in) string constant
|
|
@param nparamsp - (out) # of unsigned ints produced
|
|
@param params - (out) produced unsigned ints
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL if bad parameters or parse failed
|
|
*/
|
|
|
|
static int
|
|
filterspec_cvt(const char* txt, size_t* nparamsp, unsigned int* params)
|
|
{
|
|
int stat = NC_NOERR;
|
|
size_t nparams = 0; /*actual count*/
|
|
unsigned long long val64u;
|
|
unsigned int val32u;
|
|
double vald;
|
|
float valf;
|
|
unsigned int *vector;
|
|
unsigned char mem[8];
|
|
int isunsigned = 0;
|
|
int isnegative = 0;
|
|
int type = 0;
|
|
const char* q;
|
|
const char* p = txt;
|
|
size_t len = strlen(p);
|
|
int sstat;
|
|
|
|
/* skip leading white space */
|
|
while(strchr(" ",*p) != NULL) {p++; len--;}
|
|
/* Get leading sign character, if any */
|
|
if(*p == '-') isnegative = 1;
|
|
/* Get trailing type tag characters */
|
|
switch (len) {
|
|
case 0: stat = NC_EINVAL; goto done; /* empty parameter */
|
|
case 1: case 2:
|
|
q = (p + len) - 1; /* point to last char */
|
|
type = gettype(*q,'\0',&isunsigned);
|
|
break;
|
|
default: /* > 2 => we might have a two letter tag */
|
|
q = (p + len) - 2;
|
|
type = gettype(*q,*(q+1),&isunsigned);
|
|
break;
|
|
}
|
|
/* Now parse */
|
|
switch (type) {
|
|
case 'b': case 's': case 'i':
|
|
/* special case for a positive integer;for back compatibility.*/
|
|
if(!isnegative)
|
|
sstat = sscanf(p,"%u",&val32u);
|
|
else
|
|
sstat = sscanf(p,"%d",(int*)&val32u);
|
|
if(sstat != 1) {stat = NC_EINVAL; goto done;}
|
|
switch(type) {
|
|
case 'b': val32u = (val32u & 0xFF); break;
|
|
case 's': val32u = (val32u & 0xFFFF); break;
|
|
}
|
|
params[nparams++] = val32u;
|
|
break;
|
|
case 'f':
|
|
sstat = sscanf(p,"%lf",&vald);
|
|
if(sstat != 1) {stat = NC_EINVAL; goto done;}
|
|
valf = (float)vald;
|
|
params[nparams++] = *(unsigned int*)&valf;
|
|
break;
|
|
/* The following are 8-byte values, so we must swap pieces if this
|
|
is a little endian machine */
|
|
case 'd':
|
|
sstat = sscanf(p,"%lf",&vald);
|
|
if(sstat != 1) {stat = NC_EINVAL; goto done;};
|
|
memcpy(mem,&vald,sizeof(mem));
|
|
ncaux_h5filterspec_fix8(mem,0);
|
|
vector = (unsigned int*)mem;
|
|
params[nparams++] = vector[0];
|
|
params[nparams++] = vector[1];
|
|
break;
|
|
case 'l': /* long long */
|
|
if(isunsigned)
|
|
sstat = sscanf(p,"%llu",&val64u);
|
|
else
|
|
sstat = sscanf(p,"%lld",(long long*)&val64u);
|
|
if(sstat != 1) {stat = NC_EINVAL; goto done;};
|
|
memcpy(mem,&val64u,sizeof(mem));
|
|
ncaux_h5filterspec_fix8(mem,0);
|
|
vector = (unsigned int*)&mem;
|
|
params[nparams++] = vector[0];
|
|
params[nparams++] = vector[1];
|
|
break;
|
|
default:
|
|
{stat = NC_EINVAL; goto done;};
|
|
}
|
|
*nparamsp = nparams;
|
|
|
|
done:
|
|
return stat;
|
|
}
|
|
|
|
#if 0
|
|
/*
|
|
Parse a filter spec string into a NC_H5_Filterspec*
|
|
@param txt - a string containing the spec as a sequence of
|
|
constants separated by commas.
|
|
@param specp - store the parsed filter here -- caller frees
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL otherwise
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_filter_parsespec(const char* txt, NC_H5_Filterspec** h5specp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NC_Filterspec* spec = NULL;
|
|
NC_H5_Filterspec* h5spec = NULL;
|
|
size_t len;
|
|
|
|
if(txt == NULL)
|
|
{stat = NC_EINVAL; goto done;}
|
|
len = strlen(txt);
|
|
if(len == 0) {stat = NC_EINVAL; goto done;}
|
|
|
|
/* Parse as strings */
|
|
if((stat = ncaux_filterspec_parse(txt,&spec))) goto done;
|
|
/* walk and convert */
|
|
if((stat = ncaux_filterspec_cvt(spec,&h5spec))) goto done;
|
|
/* Now return results */
|
|
if(h5specp != NULL) {*h5specp = h5spec; h5spec = NULL;}
|
|
|
|
done:
|
|
ncaux_filterspec_free(spec);
|
|
if(h5spec) nullfree(h5spec->params);
|
|
nullfree(h5spec);
|
|
return stat;
|
|
}
|
|
|
|
/*
|
|
Parse a string containing multiple '|' separated filter specs.
|
|
|
|
@param spec0 - a string containing the list of filter specs.
|
|
@param nspecsp - # of parsed specs
|
|
@param specsp - pointer to hold vector of parsed specs. Caller frees
|
|
@return NC_NOERR if parse succeeded
|
|
@return NC_EINVAL if bad parameters or parse failed
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_filter_parselist(const char* txt0, size_t* nspecsp, NC_H5_Filterspec*** vectorp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
size_t len = 0;
|
|
size_t nspecs = 0;
|
|
NC_H5_Filterspec** vector = NULL;
|
|
char* spec0 = NULL; /* with prefix */
|
|
char* spec = NULL; /* without prefix */
|
|
char* p = NULL;
|
|
char* q = NULL;
|
|
|
|
if(txt0 == NULL) return NC_EINVAL;
|
|
/* Duplicate txt0 so we can modify it */
|
|
len = strlen(txt0);
|
|
if((spec = calloc(1,len+1+1)) == NULL) return NC_ENOMEM;
|
|
memcpy(spec,txt0,len); /* Note double ending nul */
|
|
spec0 = spec; /* Save for later free */
|
|
|
|
/* See if there is a prefix '[format]' tag; ignore it */
|
|
if(spec[0] == LBRACK) {
|
|
spec = q; /* skip tag wrt later processing */
|
|
}
|
|
/* pass 1: count number of specs */
|
|
p = spec;
|
|
nspecs = 0;
|
|
while(*p) {
|
|
q = strchr(p,'|');
|
|
if(q == NULL) q = p + strlen(p); /* fake it */
|
|
nspecs++;
|
|
p = q + 1;
|
|
}
|
|
if(nspecs > 0) {
|
|
int count = 0;
|
|
if((vector = (NC_H5_Filterspec**)malloc(sizeof(NC_H5_Filterspec*)*nspecs)) == NULL)
|
|
{stat = NC_ENOMEM; goto done;}
|
|
/* pass 2: parse */
|
|
p = spec;
|
|
for(count=0;count<nspecs;count++) {
|
|
NC_H5_Filterspec* aspec = NULL;
|
|
q = strchr(p,'|');
|
|
if(q == NULL) q = p + strlen(p); /* fake it */
|
|
*q = '\0';
|
|
if(ncaux_filter_parsespec(p,&aspec))
|
|
{stat = NC_EINVAL; goto done;}
|
|
vector[count] = aspec; aspec = NULL;
|
|
p = q+1; /* ok because of double nul */
|
|
}
|
|
}
|
|
if(nspecsp) *nspecsp = nspecs;
|
|
if(vectorp) *vectorp = (nspecs == 0 ? NULL : vector);
|
|
vector = NULL;
|
|
done:
|
|
nullfree(spec0);
|
|
if(vector != NULL) {
|
|
int k;
|
|
for(k=0;k<nspecs;k++) {
|
|
NC_H5_Filterspec* nfs = vector[k];
|
|
if(nfs->params) free(nfs->params);
|
|
nullfree(nfs);
|
|
}
|
|
free(vector);
|
|
}
|
|
return stat;
|
|
}
|
|
#endif
|
|
|
|
/**************************************************/
|
|
/* Wrappers to export selected functions from libnetcdf */
|
|
|
|
EXTERNL int
|
|
ncaux_readfile(const char* filename, size_t* sizep, void** contentp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
NCbytes* content = ncbytesnew();
|
|
stat = NC_readfile(filename,content);
|
|
if(stat == NC_NOERR && sizep)
|
|
*sizep = ncbyteslength(content);
|
|
if(stat == NC_NOERR && contentp)
|
|
*contentp = ncbytesextract(content);
|
|
ncbytesfree(content);
|
|
return stat;
|
|
}
|
|
|
|
EXTERNL int
|
|
ncaux_writefile(const char* filename, size_t size, void* content)
|
|
{
|
|
return NC_writefile(filename,size,content);
|
|
}
|
|
|
|
/**************************************************/
|
|
/**
|
|
Reclaim the output tree of data from a call
|
|
to e.g. nc_get_vara or the input to e.g. nc_put_vara.
|
|
This recursively walks the top-level instances to
|
|
reclaim any nested data such as vlen or strings or such.
|
|
|
|
This function is just a wrapper around nc_reclaim_data.
|
|
|
|
@param ncid file ncid
|
|
@param xtype type id
|
|
@param memory to reclaim
|
|
@param count number of instances of the type in memory
|
|
@return error code
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_reclaim_data(int ncid, int xtype, void* memory, size_t count)
|
|
{
|
|
/* Defer to the internal version */
|
|
return nc_reclaim_data(ncid, xtype, memory, count);
|
|
}
|
|
|
|
/*
|
|
This function is just a wrapper around nc_reclaim_data_all.
|
|
@param ncid file ncid
|
|
@param xtype type id
|
|
@param memory to reclaim
|
|
@param count number of instances of the type in memory
|
|
@return error code
|
|
*/
|
|
|
|
EXTERNL int
|
|
ncaux_reclaim_data_all(int ncid, int xtype, void* memory, size_t count)
|
|
{
|
|
/* Defer to the internal version */
|
|
return nc_reclaim_data_all(ncid, xtype, memory, count);
|
|
}
|
|
|
|
/**
|
|
@param ncid - only needed for a compound type
|
|
@param xtype - type for which alignment is requested
|
|
*/
|
|
int
|
|
ncaux_type_alignment(int xtype, int ncid, size_t* alignp)
|
|
{
|
|
/* Defer to the internal version */
|
|
return NC_type_alignment(ncid, xtype, alignp);
|
|
}
|