2017-12-05 03:21:14 +08:00
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/**
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* @file
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2018-12-07 05:29:57 +08:00
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* Copyright 2018 University Corporation for Atmospheric
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2017-12-05 03:21:14 +08:00
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* Research/Unidata. See COPYRIGHT file for more info.
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*
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* This file has the var and att copy functions.
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*
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* @author Dennis Heimbigner
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2010-06-03 21:24:43 +08:00
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*/
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This PR adds EXPERIMENTAL support for accessing data in the
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
2020-06-29 08:02:47 +08:00
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#include "config.h"
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2010-08-05 10:44:59 +08:00
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#include "ncdispatch.h"
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2015-08-16 06:26:35 +08:00
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#include "nc_logging.h"
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2021-03-07 05:09:37 +08:00
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#include "nclist.h"
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2010-06-03 21:24:43 +08:00
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#ifdef USE_NETCDF4
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2021-03-07 05:09:37 +08:00
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static int searchgroup(int ncid1, int tid1, int grp, int* tid2);
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static int searchgrouptree(int ncid1, int tid1, int grp, int* tid2);
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2017-12-05 04:11:54 +08:00
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/**
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* @internal Compare two netcdf types for equality. Must have the
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2018-12-07 05:29:57 +08:00
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* ncids as well, to find user-defined types.
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2017-12-05 04:11:54 +08:00
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*
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* @param ncid1 File ID.
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* @param typeid1 Type ID.
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* @param ncid2 File ID.
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* @param typeid2 Type ID.
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* @param equalp Pointer that gets 1 of the types are equal, 0
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* otherwise.
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*
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* @return ::NC_NOERR No error.
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* @author Ed Hartnett
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*/
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2010-06-03 21:24:43 +08:00
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static int
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2021-03-07 05:09:37 +08:00
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NC_compare_nc_types(int ncid1, int typeid1, int ncid2, int typeid2, int *equalp)
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2010-06-03 21:24:43 +08:00
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{
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int ret = NC_NOERR;
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2010-10-09 02:54:53 +08:00
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/* If you don't care about the answer, neither do I! */
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2015-07-11 05:10:32 +08:00
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if(equalp == NULL)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2010-06-03 21:24:43 +08:00
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/* Assume the types are not equal. If we find any inequality, then
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exit with NC_NOERR and we're done. */
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*equalp = 0;
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/* Atomic types are so easy! */
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2015-07-11 05:10:32 +08:00
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if (typeid1 <= NC_MAX_ATOMIC_TYPE)
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2010-10-09 02:54:53 +08:00
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{
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2015-07-11 05:10:32 +08:00
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if (typeid2 != typeid1)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2010-06-03 21:24:43 +08:00
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*equalp = 1;
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}
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2015-07-11 05:10:32 +08:00
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else
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2010-10-09 02:54:53 +08:00
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{
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2010-06-03 21:24:43 +08:00
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int i, ret, equal1;
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char name1[NC_MAX_NAME];
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char name2[NC_MAX_NAME];
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size_t size1, size2;
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nc_type base1, base2;
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size_t nelems1, nelems2;
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int class1, class2;
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void* value1 = NULL;
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void* value2 = NULL;
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size_t offset1, offset2;
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nc_type ftype1, ftype2;
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int ndims1, ndims2;
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int dimsizes1[NC_MAX_VAR_DIMS];
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int dimsizes2[NC_MAX_VAR_DIMS];
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2010-10-09 02:54:53 +08:00
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/* Find out about the two types. */
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if ((ret = nc_inq_user_type(ncid1, typeid1, name1, &size1,
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&base1, &nelems1, &class1)))
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2015-07-11 05:10:32 +08:00
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return ret;
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2010-10-09 02:54:53 +08:00
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if ((ret = nc_inq_user_type(ncid2, typeid2, name2, &size2,
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&base2, &nelems2, &class2)))
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2015-07-11 05:10:32 +08:00
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return ret;
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2010-06-03 21:24:43 +08:00
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/* Check the obvious. */
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if(size1 != size2 || class1 != class2 || strcmp(name1,name2))
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return NC_NOERR;
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/* Check user-defined types in detail. */
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2015-07-11 05:10:32 +08:00
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switch(class1)
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2010-10-09 02:54:53 +08:00
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{
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2010-06-03 21:24:43 +08:00
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case NC_VLEN:
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2010-10-09 02:54:53 +08:00
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if((ret = NC_compare_nc_types(ncid1, base1, ncid2,
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base1, &equal1)))
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return ret;
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2015-07-11 05:10:32 +08:00
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if(!equal1)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2010-06-03 21:24:43 +08:00
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break;
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case NC_OPAQUE:
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/* Already checked size above. */
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break;
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case NC_ENUM:
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if(base1 != base2 || nelems1 != nelems2) return NC_NOERR;
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2010-10-09 02:54:53 +08:00
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if (!(value1 = malloc(size1)))
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return NC_ENOMEM;
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2015-07-11 05:10:32 +08:00
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if (!(value2 = malloc(size2))) {
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free(value1);
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return NC_ENOMEM;
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}
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2010-10-09 02:54:53 +08:00
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2015-07-11 05:10:32 +08:00
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for(i = 0; i < nelems1; i++)
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2010-10-09 02:54:53 +08:00
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{
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if ((ret = nc_inq_enum_member(ncid1, typeid1, i, name1,
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value1)) ||
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(ret = nc_inq_enum_member(ncid2, typeid2, i, name2,
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value2)) ||
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strcmp(name1, name2) || memcmp(value1, value2, size1))
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{
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2015-07-11 05:10:32 +08:00
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free(value1);
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2010-10-09 02:54:53 +08:00
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free(value2);
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return ret;
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}
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2010-06-03 21:24:43 +08:00
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}
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2015-07-11 05:10:32 +08:00
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free(value1);
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2010-10-09 02:54:53 +08:00
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free(value2);
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2010-06-03 21:24:43 +08:00
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break;
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case NC_COMPOUND:
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2015-07-11 05:10:32 +08:00
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if(nelems1 != nelems2)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2010-06-03 21:24:43 +08:00
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/* Compare each field. Each must be equal! */
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2015-07-11 05:10:32 +08:00
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for(i = 0; i < nelems1; i++)
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2010-10-09 02:54:53 +08:00
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{
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2010-06-03 21:24:43 +08:00
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int j;
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2015-07-11 05:10:32 +08:00
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if ((ret = nc_inq_compound_field(ncid1, typeid1, i, name1, &offset1,
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2010-10-09 02:54:53 +08:00
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&ftype1, &ndims1, dimsizes1)))
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return ret;
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if ((ret = nc_inq_compound_field(ncid2, typeid2, i, name2, &offset2,
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&ftype2, &ndims2, dimsizes2)))
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return ret;
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2015-07-11 05:10:32 +08:00
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if(ndims1 != ndims2)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2015-07-11 05:10:32 +08:00
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for(j = 0; j < ndims1;j++)
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if(dimsizes1[j] != dimsizes2[j])
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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/* Compare user-defined field types. */
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if((ret = NC_compare_nc_types(ncid1, ftype1, ncid2, ftype2,
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&equal1)))
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return ret;
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2015-07-11 05:10:32 +08:00
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if(!equal1)
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2010-10-09 02:54:53 +08:00
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return NC_NOERR;
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2010-06-03 21:24:43 +08:00
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}
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break;
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default:
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return NC_EINVAL;
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}
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*equalp = 1;
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}
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return ret;
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}
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2017-12-05 04:11:54 +08:00
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/**
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2021-03-07 05:09:37 +08:00
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* @internal Recursively hunt for a netCDF type id, tid2, that is "equal" to tid1.
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* Question is: what search order do we use? Ncgen uses root group tree in pre-order.
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* But NC4_inq_typeid uses these rules:
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* 1. ncid2
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* 2. parents of ncid2 (up the tree to root)
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* 3. root group tree in pre-order.
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* We will leave ncgen for another day and use the nc_inq_typeid rule.
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*
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* Return matching typeid or 0 if not found.
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2017-12-05 04:11:54 +08:00
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*
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* @param ncid1 File ID.
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* @param tid1 Type ID.
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* @param ncid2 File ID.
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* @param tid2 Pointer that gets type ID of equal type.
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*
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* @return ::NC_NOERR No error.
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2021-03-07 05:09:37 +08:00
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* @author Ed Hartnett, Dennis Heimbigner
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2017-12-05 04:11:54 +08:00
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*/
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2010-06-03 21:24:43 +08:00
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static int
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NC_rec_find_nc_type(int ncid1, nc_type tid1, int ncid2, nc_type* tid2)
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{
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2021-03-07 05:09:37 +08:00
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int ret = NC_NOERR;
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int parent;
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if((ret = searchgroup(ncid1,tid1,ncid2,tid2)))
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goto done;
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if(*tid2 != 0)
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goto done; /* found */
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/* Look in the parents of ncid2 upto the root */
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switch (ret = nc_inq_grp_parent(ncid2,&parent)) {
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case NC_NOERR:
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/* Recurse up using parent grp */
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ret = NC_rec_find_nc_type(ncid1, tid1, parent, tid2);
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break;
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case NC_ENOGRP:
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/* do the breadth-first pre-order search of the whole tree */
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/* ncid2 should be root group */
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ret = searchgrouptree(ncid1,tid1,ncid2,tid2);
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break;
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default: break;
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2010-06-03 21:24:43 +08:00
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}
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2015-07-11 05:10:32 +08:00
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2021-03-07 05:09:37 +08:00
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done:
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return ret;
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2010-06-03 21:24:43 +08:00
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}
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2017-12-05 04:11:54 +08:00
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/**
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* @internal Given a type in one file, find its equal (if any) in
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2018-12-07 05:29:57 +08:00
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* another file. It sounds so simple, but it's a real pain!
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2017-12-05 04:11:54 +08:00
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*
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* @param ncid1 File ID.
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* @param xtype1 Type ID.
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* @param ncid2 File ID.
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* @param xtype2 Pointer that gets type ID of equal type.
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*
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* @return ::NC_NOERR No error.
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* @author Ed Hartnett
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*/
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2010-06-03 21:24:43 +08:00
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static int
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NC_find_equal_type(int ncid1, nc_type xtype1, int ncid2, nc_type *xtype2)
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{
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int ret = NC_NOERR;
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2010-10-09 02:54:53 +08:00
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2010-06-03 21:24:43 +08:00
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/* Check input */
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2015-07-11 05:10:32 +08:00
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if(xtype1 <= NC_NAT)
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2010-10-09 02:54:53 +08:00
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return NC_EINVAL;
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2010-06-03 21:24:43 +08:00
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/* Handle atomic types. */
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2015-07-11 05:10:32 +08:00
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if (xtype1 <= NC_MAX_ATOMIC_TYPE)
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2010-10-09 02:54:53 +08:00
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{
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2015-07-11 05:10:32 +08:00
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if(xtype2)
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2010-10-09 02:54:53 +08:00
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*xtype2 = xtype1;
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2010-06-03 21:24:43 +08:00
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return NC_NOERR;
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}
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/* Recursively search group ncid2 and its children
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to find a type that is equal (using compare_type)
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to xtype1. */
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ret = NC_rec_find_nc_type(ncid1, xtype1 , ncid2, xtype2);
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return ret;
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}
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#endif /* USE_NETCDF4 */
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2017-12-05 03:21:14 +08:00
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/**
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* This will copy a variable that is an array of primitive type and
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* its attributes from one file to another, assuming dimensions in the
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* output file are already defined and have same dimension IDs and
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* length. However it doesn't work for copying netCDF-4 variables of
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* type string or a user-defined type.
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*
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* This function works even if the files are different formats,
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* (for example, one netcdf classic, the other netcdf-4).
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*
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* If you're copying into a classic-model file, from a netcdf-4 file,
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* you must be copying a variable of one of the six classic-model
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* types, and similarly for the attributes.
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*
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* For large netCDF-3 files, this can be a very inefficient way to
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* copy data from one file to another, because adding a new variable
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* to the target file may require more space in the header and thus
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* result in moving data for other variables in the target file. This
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|
|
* is not a problem for netCDF-4 files, which support efficient
|
|
|
|
* addition of variables without moving data for other variables.
|
|
|
|
*
|
|
|
|
* @param ncid_in File ID to copy from.
|
|
|
|
* @param varid_in Variable ID to copy.
|
|
|
|
* @param ncid_out File ID to copy to.
|
|
|
|
*
|
|
|
|
* @return ::NC_NOERR No error.
|
|
|
|
* @author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
2012-12-14 02:00:03 +08:00
|
|
|
*/
|
2010-06-03 21:24:43 +08:00
|
|
|
int
|
|
|
|
nc_copy_var(int ncid_in, int varid_in, int ncid_out)
|
|
|
|
{
|
|
|
|
char name[NC_MAX_NAME + 1];
|
|
|
|
char att_name[NC_MAX_NAME + 1];
|
|
|
|
nc_type xtype;
|
2013-01-24 05:46:22 +08:00
|
|
|
int ndims, dimids_in[NC_MAX_VAR_DIMS], dimids_out[NC_MAX_VAR_DIMS], natts, real_ndims;
|
2010-06-03 21:24:43 +08:00
|
|
|
int varid_out;
|
|
|
|
int a, d;
|
|
|
|
void *data = NULL;
|
|
|
|
size_t *count = NULL, *start = NULL;
|
|
|
|
size_t reclen = 1;
|
|
|
|
size_t *dimlen = NULL;
|
|
|
|
int retval = NC_NOERR;
|
|
|
|
size_t type_size;
|
|
|
|
int src_format, dest_format;
|
|
|
|
char type_name[NC_MAX_NAME+1];
|
2013-01-24 05:46:22 +08:00
|
|
|
char dimname_in[NC_MAX_NAME + 1];
|
|
|
|
int i;
|
2010-06-03 21:24:43 +08:00
|
|
|
|
|
|
|
/* Learn about this var. */
|
2015-07-11 05:10:32 +08:00
|
|
|
if ((retval = nc_inq_var(ncid_in, varid_in, name, &xtype,
|
2013-01-24 05:46:22 +08:00
|
|
|
&ndims, dimids_in, &natts)))
|
2010-06-03 21:24:43 +08:00
|
|
|
return retval;
|
2015-07-11 05:10:32 +08:00
|
|
|
/* find corresponding dimids in the output file */
|
2013-01-24 05:46:22 +08:00
|
|
|
for(i = 0; i < ndims; i++) {
|
|
|
|
dimids_out[i] = dimids_in[i];
|
|
|
|
if ((retval = nc_inq_dimname(ncid_in, dimids_in[i], dimname_in)))
|
|
|
|
return retval;
|
|
|
|
if ((retval = nc_inq_dimid(ncid_out, dimname_in, &dimids_out[i])))
|
|
|
|
return retval;
|
|
|
|
}
|
2010-06-03 21:24:43 +08:00
|
|
|
|
2015-07-11 05:10:32 +08:00
|
|
|
LOG((2, "nc_copy_var: ncid_in 0x%x varid_in %d ncid_out 0x%x",
|
2010-06-03 21:24:43 +08:00
|
|
|
ncid_in, varid_in, ncid_out));
|
|
|
|
|
|
|
|
/* Make sure we are not trying to write into a netcdf-3 file
|
|
|
|
* anything that won't fit in netcdf-3. */
|
|
|
|
if ((retval = nc_inq_format(ncid_in, &src_format)))
|
|
|
|
return retval;
|
|
|
|
if ((retval = nc_inq_format(ncid_out, &dest_format)))
|
|
|
|
return retval;
|
2015-08-16 06:26:35 +08:00
|
|
|
if ((dest_format == NC_FORMAT_CLASSIC
|
|
|
|
|| dest_format == NC_FORMAT_64BIT_DATA
|
|
|
|
|| dest_format == NC_FORMAT_64BIT_OFFSET) &&
|
2010-06-03 21:24:43 +08:00
|
|
|
src_format == NC_FORMAT_NETCDF4 && xtype > NC_DOUBLE)
|
|
|
|
return NC_ENOTNC4;
|
|
|
|
|
|
|
|
/* Later on, we will need to know the size of this type. */
|
|
|
|
if ((retval = nc_inq_type(ncid_in, xtype, type_name, &type_size)))
|
|
|
|
return retval;
|
|
|
|
LOG((3, "type %s has size %d", type_name, type_size));
|
|
|
|
|
|
|
|
/* Switch back to define mode, and create the output var. */
|
|
|
|
retval = nc_redef(ncid_out);
|
|
|
|
if (retval && retval != NC_EINDEFINE)
|
|
|
|
BAIL(retval);
|
|
|
|
if ((retval = nc_def_var(ncid_out, name, xtype,
|
2013-01-24 05:46:22 +08:00
|
|
|
ndims, dimids_out, &varid_out)))
|
2010-06-03 21:24:43 +08:00
|
|
|
BAIL(retval);
|
|
|
|
|
|
|
|
/* Copy the attributes. */
|
|
|
|
for (a=0; a<natts; a++)
|
|
|
|
{
|
|
|
|
if ((retval = nc_inq_attname(ncid_in, varid_in, a, att_name)))
|
|
|
|
BAIL(retval);
|
2015-07-11 05:10:32 +08:00
|
|
|
if ((retval = nc_copy_att(ncid_in, varid_in, att_name,
|
2010-06-03 21:24:43 +08:00
|
|
|
ncid_out, varid_out)))
|
|
|
|
BAIL(retval);
|
|
|
|
}
|
|
|
|
|
|
|
|
/* End define mode, to write metadata and create file. */
|
|
|
|
nc_enddef(ncid_out);
|
|
|
|
nc_sync(ncid_out);
|
|
|
|
|
|
|
|
/* Allocate memory for our start and count arrays. If ndims = 0
|
|
|
|
this is a scalar, which I will treat as a 1-D array with one
|
|
|
|
element. */
|
|
|
|
real_ndims = ndims ? ndims : 1;
|
2014-02-14 22:07:14 +08:00
|
|
|
if (!(start = malloc((size_t)real_ndims * sizeof(size_t))))
|
2010-06-03 21:24:43 +08:00
|
|
|
BAIL(NC_ENOMEM);
|
2014-02-14 22:07:14 +08:00
|
|
|
if (!(count = malloc((size_t)real_ndims * sizeof(size_t))))
|
2010-06-03 21:24:43 +08:00
|
|
|
BAIL(NC_ENOMEM);
|
|
|
|
|
|
|
|
/* The start array will be all zeros, except the first element,
|
|
|
|
which will be the record number. Count will be the dimension
|
|
|
|
size, except for the first element, which will be one, because
|
|
|
|
we will copy one record at a time. For this we need the var
|
|
|
|
shape. */
|
2014-02-14 22:07:14 +08:00
|
|
|
if (!(dimlen = malloc((size_t)real_ndims * sizeof(size_t))))
|
2010-06-03 21:24:43 +08:00
|
|
|
BAIL(NC_ENOMEM);
|
|
|
|
|
2013-08-06 04:36:33 +08:00
|
|
|
/* Set to 0, to correct for an unlikely dereference
|
|
|
|
error reported by clang/llvm. */
|
|
|
|
dimlen[0] = 0;
|
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
/* Find out how much data. */
|
|
|
|
for (d=0; d<ndims; d++)
|
|
|
|
{
|
2013-01-24 05:46:22 +08:00
|
|
|
if ((retval = nc_inq_dimlen(ncid_in, dimids_in[d], &dimlen[d])))
|
2010-06-03 21:24:43 +08:00
|
|
|
BAIL(retval);
|
|
|
|
LOG((4, "nc_copy_var: there are %d data", dimlen[d]));
|
|
|
|
}
|
|
|
|
|
|
|
|
/* If this is really a scalar, then set the dimlen to 1. */
|
|
|
|
if (ndims == 0)
|
|
|
|
dimlen[0] = 1;
|
|
|
|
|
|
|
|
for (d=0; d<real_ndims; d++)
|
|
|
|
{
|
|
|
|
start[d] = 0;
|
|
|
|
count[d] = d ? dimlen[d] : 1;
|
|
|
|
if (d) reclen *= dimlen[d];
|
|
|
|
}
|
|
|
|
|
|
|
|
/* If there are no records, we're done. */
|
|
|
|
if (!dimlen[0])
|
|
|
|
goto exit;
|
|
|
|
|
|
|
|
/* Allocate memory for one record. */
|
2014-08-01 06:20:50 +08:00
|
|
|
if (!(data = malloc(reclen * type_size))) {
|
|
|
|
if(count) free(count);
|
|
|
|
if(dimlen) free(dimlen);
|
|
|
|
if(start) free(start);
|
|
|
|
return NC_ENOMEM;
|
2015-07-11 05:10:32 +08:00
|
|
|
}
|
2014-08-01 06:20:50 +08:00
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
/* Copy the var data one record at a time. */
|
|
|
|
for (start[0]=0; !retval && start[0]<(size_t)dimlen[0]; start[0]++)
|
|
|
|
{
|
|
|
|
switch (xtype)
|
|
|
|
{
|
|
|
|
case NC_BYTE:
|
|
|
|
retval = nc_get_vara_schar(ncid_in, varid_in, start, count,
|
|
|
|
(signed char *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_schar(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(const signed char *)data);
|
|
|
|
break;
|
|
|
|
case NC_CHAR:
|
|
|
|
retval = nc_get_vara_text(ncid_in, varid_in, start, count,
|
|
|
|
(char *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_text(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(char *)data);
|
|
|
|
break;
|
|
|
|
case NC_SHORT:
|
|
|
|
retval = nc_get_vara_short(ncid_in, varid_in, start, count,
|
|
|
|
(short *)data);
|
|
|
|
if (!retval)
|
|
|
|
retval = nc_put_vara_short(ncid_out, varid_out, start, count,
|
|
|
|
(short *)data);
|
|
|
|
break;
|
|
|
|
case NC_INT:
|
|
|
|
retval = nc_get_vara_int(ncid_in, varid_in, start, count,
|
|
|
|
(int *)data);
|
|
|
|
if (!retval)
|
|
|
|
retval = nc_put_vara_int(ncid_out, varid_out, start, count,
|
|
|
|
(int *)data);
|
|
|
|
break;
|
|
|
|
case NC_FLOAT:
|
|
|
|
retval = nc_get_vara_float(ncid_in, varid_in, start, count,
|
|
|
|
(float *)data);
|
|
|
|
if (!retval)
|
|
|
|
retval = nc_put_vara_float(ncid_out, varid_out, start, count,
|
|
|
|
(float *)data);
|
|
|
|
break;
|
|
|
|
case NC_DOUBLE:
|
|
|
|
retval = nc_get_vara_double(ncid_in, varid_in, start, count,
|
|
|
|
(double *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_double(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(double *)data);
|
|
|
|
break;
|
|
|
|
case NC_UBYTE:
|
2010-06-23 06:41:04 +08:00
|
|
|
retval = nc_get_vara_uchar(ncid_in, varid_in, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(unsigned char *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_uchar(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(unsigned char *)data);
|
|
|
|
break;
|
|
|
|
case NC_USHORT:
|
|
|
|
retval = nc_get_vara_ushort(ncid_in, varid_in, start, count,
|
|
|
|
(unsigned short *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_ushort(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(unsigned short *)data);
|
|
|
|
break;
|
|
|
|
case NC_UINT:
|
|
|
|
retval = nc_get_vara_uint(ncid_in, varid_in, start, count,
|
|
|
|
(unsigned int *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_uint(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(unsigned int *)data);
|
|
|
|
break;
|
|
|
|
case NC_INT64:
|
|
|
|
retval = nc_get_vara_longlong(ncid_in, varid_in, start, count,
|
|
|
|
(long long *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_longlong(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(long long *)data);
|
|
|
|
break;
|
|
|
|
case NC_UINT64:
|
|
|
|
retval = nc_get_vara_ulonglong(ncid_in, varid_in, start, count,
|
|
|
|
(unsigned long long *)data);
|
|
|
|
if (!retval)
|
2015-07-11 05:10:32 +08:00
|
|
|
retval = nc_put_vara_ulonglong(ncid_out, varid_out, start, count,
|
2010-06-03 21:24:43 +08:00
|
|
|
(unsigned long long *)data);
|
|
|
|
break;
|
|
|
|
default:
|
|
|
|
retval = NC_EBADTYPE;
|
|
|
|
}
|
|
|
|
}
|
2015-07-11 05:10:32 +08:00
|
|
|
|
2010-06-03 21:24:43 +08:00
|
|
|
exit:
|
|
|
|
if (data) free(data);
|
|
|
|
if (dimlen) free(dimlen);
|
|
|
|
if (start) free(start);
|
|
|
|
if (count) free(count);
|
|
|
|
return retval;
|
|
|
|
}
|
|
|
|
|
2017-12-05 04:11:54 +08:00
|
|
|
/**
|
|
|
|
* Copy an attribute from one open file to another. This is called by
|
|
|
|
* nc_copy_att().
|
|
|
|
*
|
|
|
|
* @param ncid_in File ID to copy from.
|
|
|
|
* @param varid_in Variable ID to copy from.
|
|
|
|
* @param name Name of attribute to copy.
|
|
|
|
* @param ncid_out File ID to copy to.
|
|
|
|
* @param varid_out Variable ID to copy to.
|
|
|
|
*
|
|
|
|
* @return ::NC_NOERR No error.
|
|
|
|
* @author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
|
|
|
*/
|
2010-11-30 06:23:16 +08:00
|
|
|
static int
|
2015-07-11 05:10:32 +08:00
|
|
|
NC_copy_att(int ncid_in, int varid_in, const char *name,
|
2010-06-03 21:24:43 +08:00
|
|
|
int ncid_out, int varid_out)
|
|
|
|
{
|
|
|
|
nc_type xtype;
|
|
|
|
size_t len;
|
|
|
|
void *data=NULL;
|
|
|
|
int res;
|
2015-07-11 05:10:32 +08:00
|
|
|
|
|
|
|
LOG((2, "nc_copy_att: ncid_in 0x%x varid_in %d name %s",
|
2010-06-03 21:24:43 +08:00
|
|
|
ncid_in, varid_in, name));
|
2015-07-11 05:10:32 +08:00
|
|
|
|
2010-11-30 06:23:16 +08:00
|
|
|
/* Find out about the attribute to be copied. */
|
2010-06-03 21:24:43 +08:00
|
|
|
if ((res = nc_inq_att(ncid_in, varid_in, name, &xtype, &len)))
|
|
|
|
return res;
|
2015-07-11 05:10:32 +08:00
|
|
|
|
|
|
|
if (xtype < NC_STRING)
|
2010-10-09 02:54:53 +08:00
|
|
|
{
|
2010-11-30 06:23:16 +08:00
|
|
|
/* Handle non-string atomic types. */
|
2015-07-11 05:10:32 +08:00
|
|
|
if (len)
|
2014-02-14 22:07:14 +08:00
|
|
|
{
|
|
|
|
size_t size = NC_atomictypelen(xtype);
|
|
|
|
|
|
|
|
assert(size > 0);
|
|
|
|
if (!(data = malloc(len * size)))
|
2010-06-03 21:24:43 +08:00
|
|
|
return NC_ENOMEM;
|
2014-02-14 22:07:14 +08:00
|
|
|
}
|
2010-06-03 21:24:43 +08:00
|
|
|
|
|
|
|
res = nc_get_att(ncid_in, varid_in, name, data);
|
|
|
|
if (!res)
|
2015-07-11 05:10:32 +08:00
|
|
|
res = nc_put_att(ncid_out, varid_out, name, xtype,
|
2010-06-03 21:24:43 +08:00
|
|
|
len, data);
|
|
|
|
if (len)
|
|
|
|
free(data);
|
2010-10-09 02:54:53 +08:00
|
|
|
}
|
|
|
|
#ifdef USE_NETCDF4
|
2015-07-11 05:10:32 +08:00
|
|
|
else if (xtype == NC_STRING)
|
2010-10-09 02:54:53 +08:00
|
|
|
{
|
2010-06-03 21:24:43 +08:00
|
|
|
/* Copy string attributes. */
|
|
|
|
char **str_data;
|
|
|
|
if (!(str_data = malloc(sizeof(char *) * len)))
|
|
|
|
return NC_ENOMEM;
|
|
|
|
res = nc_get_att_string(ncid_in, varid_in, name, str_data);
|
|
|
|
if (!res)
|
2015-07-11 05:10:32 +08:00
|
|
|
res = nc_put_att_string(ncid_out, varid_out, name, len,
|
2010-06-03 21:24:43 +08:00
|
|
|
(const char **)str_data);
|
|
|
|
nc_free_string(len, str_data);
|
|
|
|
free(str_data);
|
2015-07-11 05:10:32 +08:00
|
|
|
}
|
|
|
|
else
|
2010-10-09 02:54:53 +08:00
|
|
|
{
|
2010-06-03 21:24:43 +08:00
|
|
|
/* Copy user-defined type attributes. */
|
|
|
|
int class;
|
|
|
|
size_t size;
|
|
|
|
void *data;
|
|
|
|
nc_type xtype_out = NC_NAT;
|
|
|
|
|
|
|
|
/* Find out if there is an equal type in the output file. */
|
|
|
|
/* Note: original code used a libsrc4 specific internal function
|
|
|
|
which we had to "duplicate" here */
|
|
|
|
if ((res = NC_find_equal_type(ncid_in, xtype, ncid_out, &xtype_out)))
|
|
|
|
return res;
|
2015-07-11 05:10:32 +08:00
|
|
|
if (xtype_out)
|
2010-10-09 02:54:53 +08:00
|
|
|
{
|
2010-06-03 21:24:43 +08:00
|
|
|
/* We found an equal type! */
|
2015-07-11 05:10:32 +08:00
|
|
|
if ((res = nc_inq_user_type(ncid_in, xtype, NULL, &size,
|
2010-06-03 21:24:43 +08:00
|
|
|
NULL, NULL, &class)))
|
|
|
|
return res;
|
2010-10-09 02:54:53 +08:00
|
|
|
if (class == NC_VLEN) /* VLENs are different... */
|
2015-07-11 05:10:32 +08:00
|
|
|
{
|
2010-06-03 21:24:43 +08:00
|
|
|
nc_vlen_t *vldata;
|
|
|
|
int i;
|
2010-10-09 02:54:53 +08:00
|
|
|
if (!(vldata = malloc(sizeof(nc_vlen_t) * len)))
|
2010-06-03 21:24:43 +08:00
|
|
|
return NC_ENOMEM;
|
2010-10-09 02:54:53 +08:00
|
|
|
if ((res = nc_get_att(ncid_in, varid_in, name, vldata)))
|
2010-06-03 21:24:43 +08:00
|
|
|
return res;
|
2015-07-11 05:10:32 +08:00
|
|
|
if ((res = nc_put_att(ncid_out, varid_out, name, xtype_out,
|
2010-06-03 21:24:43 +08:00
|
|
|
len, vldata)))
|
|
|
|
return res;
|
2015-07-11 05:10:32 +08:00
|
|
|
for (i = 0; i < len; i++)
|
|
|
|
if((res = nc_free_vlen(&vldata[i])))
|
2010-10-09 02:54:53 +08:00
|
|
|
return res;
|
2010-06-03 21:24:43 +08:00
|
|
|
free(vldata);
|
2015-07-11 05:10:32 +08:00
|
|
|
}
|
2010-10-09 02:54:53 +08:00
|
|
|
else /* not VLEN */
|
|
|
|
{
|
|
|
|
if (!(data = malloc(size * len)))
|
2010-06-03 21:24:43 +08:00
|
|
|
return NC_ENOMEM;
|
2010-10-09 02:54:53 +08:00
|
|
|
res = nc_get_att(ncid_in, varid_in, name, data);
|
|
|
|
if (!res)
|
|
|
|
res = nc_put_att(ncid_out, varid_out, name, xtype_out, len, data);
|
2010-06-03 21:24:43 +08:00
|
|
|
free(data);
|
|
|
|
}
|
|
|
|
}
|
|
|
|
}
|
|
|
|
#endif /*!USE_NETCDF4*/
|
|
|
|
return res;
|
|
|
|
}
|
|
|
|
|
2017-12-05 03:21:14 +08:00
|
|
|
/**
|
|
|
|
* Copy an attribute from one open file to another.
|
|
|
|
*
|
|
|
|
* Special programming challenge: this function must work even if one
|
|
|
|
* of the other of the files is a netcdf version 1.0 file (i.e. not
|
|
|
|
* HDF5). So only use top level netcdf api functions.
|
|
|
|
*
|
|
|
|
* From the netcdf-3 docs: The output netCDF dataset should be in
|
|
|
|
* define mode if the attribute to be copied does not already exist
|
|
|
|
* for the target variable, or if it would cause an existing target
|
|
|
|
* attribute to grow.
|
|
|
|
*
|
|
|
|
* @param ncid_in File ID to copy from.
|
|
|
|
* @param varid_in Variable ID to copy from.
|
|
|
|
* @param name Name of attribute to copy.
|
|
|
|
* @param ncid_out File ID to copy to.
|
|
|
|
* @param varid_out Variable ID to copy to.
|
|
|
|
*
|
|
|
|
* @return ::NC_NOERR No error.
|
|
|
|
* @author Glenn Davis, Ed Hartnett, Dennis Heimbigner
|
2010-11-30 06:23:16 +08:00
|
|
|
*/
|
|
|
|
int
|
2015-07-11 05:10:32 +08:00
|
|
|
nc_copy_att(int ncid_in, int varid_in, const char *name,
|
2010-11-30 06:23:16 +08:00
|
|
|
int ncid_out, int varid_out)
|
|
|
|
{
|
2010-12-16 05:45:05 +08:00
|
|
|
int format, target_natts, target_attid;
|
2010-11-30 06:23:16 +08:00
|
|
|
char att_name[NC_MAX_NAME + 1];
|
|
|
|
int a, retval;
|
|
|
|
|
|
|
|
/* What is the destination format? */
|
|
|
|
if ((retval = nc_inq_format(ncid_out, &format)))
|
|
|
|
return retval;
|
2015-07-11 05:10:32 +08:00
|
|
|
|
2010-11-30 06:23:16 +08:00
|
|
|
/* Can't copy to same var in same file. */
|
|
|
|
if (ncid_in == ncid_out && varid_in == varid_out)
|
|
|
|
return NC_NOERR;
|
2015-07-11 05:10:32 +08:00
|
|
|
|
2010-11-30 06:23:16 +08:00
|
|
|
/* For classic model netCDF-4 files, order of attributes must be
|
|
|
|
* maintained during copies. We MUST MAINTAIN ORDER! */
|
|
|
|
if (format == NC_FORMAT_NETCDF4_CLASSIC)
|
|
|
|
{
|
|
|
|
/* Does this attribute already exist in the target file? */
|
|
|
|
retval = nc_inq_attid(ncid_out, varid_out, name, &target_attid);
|
|
|
|
if (retval == NC_ENOTATT)
|
|
|
|
{
|
|
|
|
/* Attribute does not exist. No order to be preserved. */
|
|
|
|
return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
|
|
|
|
}
|
|
|
|
else if (retval == NC_NOERR)
|
|
|
|
{
|
|
|
|
/* How many atts for this var? */
|
|
|
|
if ((retval = nc_inq_varnatts(ncid_out, varid_out, &target_natts)))
|
|
|
|
return retval;
|
|
|
|
|
|
|
|
/* If this is the last attribute in the target file, we are
|
|
|
|
* off the hook. */
|
|
|
|
if (target_attid == target_natts - 1)
|
|
|
|
return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
|
2015-07-11 05:10:32 +08:00
|
|
|
|
2010-11-30 06:23:16 +08:00
|
|
|
/* Order MUST BE MAINTAINED! Copy all existing atts in the target
|
|
|
|
* file, stopping at our target att. */
|
|
|
|
for (a = 0; a < target_natts; a++)
|
|
|
|
{
|
|
|
|
if (a == target_attid)
|
|
|
|
{
|
|
|
|
if ((retval = NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out)))
|
|
|
|
return retval;
|
2015-07-11 05:10:32 +08:00
|
|
|
}
|
2010-11-30 06:23:16 +08:00
|
|
|
else
|
|
|
|
{
|
2010-12-16 05:45:05 +08:00
|
|
|
if ((retval = nc_inq_attname(ncid_out, varid_out, a, att_name)))
|
2010-11-30 06:23:16 +08:00
|
|
|
return retval;
|
2015-07-11 05:10:32 +08:00
|
|
|
if ((retval = NC_copy_att(ncid_out, varid_out, att_name,
|
2010-11-30 06:23:16 +08:00
|
|
|
ncid_out, varid_out)))
|
|
|
|
return retval;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
}
|
|
|
|
else
|
2015-08-20 17:42:05 +08:00
|
|
|
return retval; /* Some other error occurred. */
|
2010-11-30 06:23:16 +08:00
|
|
|
}
|
|
|
|
else
|
|
|
|
return NC_copy_att(ncid_in, varid_in, name, ncid_out, varid_out);
|
|
|
|
|
|
|
|
return NC_NOERR;
|
|
|
|
}
|
2021-03-07 05:09:37 +08:00
|
|
|
|
|
|
|
#ifdef USE_NETCDF4
|
|
|
|
|
|
|
|
/* Helper function for NC_rec_find_nc_type();
|
|
|
|
search a specified group for matching type.
|
|
|
|
*/
|
|
|
|
static int
|
|
|
|
searchgroup(int ncid1, int tid1, int grp, int* tid2)
|
|
|
|
{
|
|
|
|
int i,ret = NC_NOERR;
|
|
|
|
int nids;
|
|
|
|
int* ids = NULL;
|
|
|
|
|
|
|
|
/* Get all types in grp */
|
|
|
|
if(tid2)
|
|
|
|
*tid2 = 0;
|
|
|
|
if ((ret = nc_inq_typeids(grp, &nids, NULL)))
|
|
|
|
goto done;
|
|
|
|
if (nids)
|
|
|
|
{
|
|
|
|
if (!(ids = (int *)malloc((size_t)nids * sizeof(int))))
|
|
|
|
{ret = NC_ENOMEM; goto done;}
|
|
|
|
if ((ret = nc_inq_typeids(grp, &nids, ids)))
|
|
|
|
goto done;
|
|
|
|
for(i = 0; i < nids; i++)
|
|
|
|
{
|
|
|
|
int equal = 0;
|
|
|
|
if ((ret = NC_compare_nc_types(ncid1, tid1, grp, ids[i], &equal)))
|
|
|
|
goto done;
|
|
|
|
if(equal)
|
|
|
|
{
|
|
|
|
if(tid2)
|
|
|
|
*tid2 = ids[i];
|
|
|
|
goto done;
|
|
|
|
}
|
|
|
|
}
|
|
|
|
}
|
|
|
|
|
|
|
|
done:
|
|
|
|
nullfree(ids);
|
|
|
|
return ret;
|
|
|
|
}
|
|
|
|
|
|
|
|
/* Helper function for NC_rec_find_nc_type();
|
|
|
|
search a tree of groups for a matching type
|
|
|
|
using a breadth first queue
|
|
|
|
*/
|
|
|
|
static int
|
|
|
|
searchgrouptree(int ncid1, int tid1, int grp, int* tid2)
|
|
|
|
{
|
|
|
|
int i,ret = NC_NOERR;
|
|
|
|
int nids;
|
|
|
|
int* ids = NULL;
|
|
|
|
NClist* queue = nclistnew();
|
|
|
|
int gid;
|
|
|
|
uintptr_t id;
|
|
|
|
|
|
|
|
id = grp;
|
|
|
|
nclistpush(queue,(void*)id); /* prime the queue */
|
|
|
|
while(nclistlength(queue) > 0) {
|
|
|
|
id = (uintptr_t)nclistremove(queue,0);
|
|
|
|
gid = (int)id;
|
|
|
|
if((ret = searchgroup(ncid1,tid1,gid,tid2)))
|
|
|
|
goto done;
|
|
|
|
if(*tid2 != 0)
|
|
|
|
goto done; /*we found it*/
|
|
|
|
/* Get subgroups of gid and push onto front of the queue (for breadth first) */
|
|
|
|
if((ret = nc_inq_grps(gid,&nids,NULL)))
|
|
|
|
goto done;
|
|
|
|
if (!(ids = (int *)malloc((size_t)nids * sizeof(int))))
|
|
|
|
{ret = NC_ENOMEM; goto done;}
|
|
|
|
if ((ret = nc_inq_grps(gid, &nids, ids)))
|
|
|
|
goto done;
|
|
|
|
/* push onto the end of the queue */
|
|
|
|
for(i=0;i<nids;i++) {
|
|
|
|
id = ids[i];
|
|
|
|
nclistpush(queue,(void*)id);
|
|
|
|
}
|
Regularize the scoping of dimensions
This is a follow-on to pull request
````https://github.com/Unidata/netcdf-c/pull/1959````,
which fixed up type scoping.
The primary changes are to _nc\_inq\_dimid()_ and to ncdump.
The _nc\_inq\_dimid()_ function is supposed to allow the name to be
and FQN, but this apparently never got implemented. So if was modified
to support FQNs.
The ncdump program is supposed to output fully qualified dimension names
in its generated CDL file under certain conditions.
Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group
is G. For each dimension id D referenced by V, ncdump needs to determine
whether to print its name as a simple name or as a fully qualified name (FQN).
The algorithm is as follows:
1. Search up the tree of ancestor groups.
2. If one of those ancestor groups contains the dimid, then call it dimgrp.
3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true.
4. If dimgrp is defined and duplicate == false, then we do not need an fqn.
5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate.
6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid.
7. If found, then use the fqn of the first found such dimension location.
8. If not found, then fail.
Test case ncdump/test_scope.sh was modified to test the proper
operation of ncdump and _nc\_inq\_dimid()_.
Misc. Other Changes:
* Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL.
* Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
|
|
|
free(ids); ids = NULL;
|
2021-03-07 05:09:37 +08:00
|
|
|
}
|
|
|
|
/* Not found */
|
|
|
|
ret = NC_EBADTYPE;
|
|
|
|
|
|
|
|
done:
|
|
|
|
nclistfree(queue);
|
|
|
|
nullfree(ids);
|
|
|
|
return ret;
|
|
|
|
}
|
|
|
|
|
|
|
|
#endif
|