[409] | 1 | /** \file |
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| 2 | The netCDF-4 file functions. |
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| 3 | |
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| 4 | This file is part of netcdf-4, a netCDF-like interface for HDF5, or |
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| 5 | a HDF5 backend for netCDF, depending on your point of view. |
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| 6 | |
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| 7 | Copyright 2003, University Corporation for Atmospheric Research. See |
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| 8 | COPYRIGHT file for copying and redistribution conditions. |
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| 9 | */ |
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| 10 | |
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| 11 | #include "nc4internal.h" |
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| 12 | #include "nc.h" |
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| 13 | #include <H5DSpublic.h> |
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| 14 | #include "nc4dispatch.h" |
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| 15 | #include "ncdispatch.h" |
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| 16 | |
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| 17 | #ifdef USE_HDF4 |
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| 18 | #include <mfhdf.h> |
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| 19 | #endif |
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| 20 | |
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| 21 | #ifdef USE_PNETCDF |
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| 22 | #include <pnetcdf.h> |
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| 23 | #endif |
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| 24 | |
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| 25 | /* This is to track opened HDF5 objects to make sure they are |
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| 26 | * closed. */ |
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| 27 | #ifdef EXTRA_TESTS |
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| 28 | extern int num_plists; |
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| 29 | extern int num_spaces; |
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| 30 | #endif /* EXTRA_TESTS */ |
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| 31 | |
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| 32 | #define MIN_DEFLATE_LEVEL 0 |
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| 33 | #define MAX_DEFLATE_LEVEL 9 |
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| 34 | |
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| 35 | /* These are the special attributes added by the HDF5 dimension scale |
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| 36 | * API. They will be ignored by netCDF-4. */ |
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| 37 | #define REFERENCE_LIST "REFERENCE_LIST" |
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| 38 | #define CLASS "CLASS" |
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| 39 | #define DIMENSION_LIST "DIMENSION_LIST" |
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| 40 | #define NAME "NAME" |
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| 41 | |
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| 42 | /* Forward */ |
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| 43 | static int NC4_enddef(int ncid); |
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| 44 | static int nc4_rec_read_types(NC_GRP_INFO_T *grp); |
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| 45 | static int nc4_rec_read_vars(NC_GRP_INFO_T *grp); |
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| 46 | |
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| 47 | #ifdef IGNORE |
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| 48 | /* This extern points to the pointer that holds the list of open |
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| 49 | * netCDF files. */ |
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| 50 | extern NC_FILE_INFO_T *nc_file; |
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| 51 | #endif |
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| 52 | |
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| 53 | /* These are the default chunk cache sizes for HDF5 files created or |
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| 54 | * opened with netCDF-4. */ |
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| 55 | size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; |
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| 56 | size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; |
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| 57 | float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; |
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| 58 | |
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| 59 | /* This is set by nc_set_default_format in libsrc/nc.c. */ |
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| 60 | extern int default_create_format; |
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| 61 | |
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| 62 | /* To turn off HDF5 error messages, I have to catch an early |
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| 63 | invocation of a netcdf function. */ |
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| 64 | static int virgin = 1; |
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| 65 | |
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| 66 | /* For performance, fill this array only the first time, and keep it |
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| 67 | * in global memory for each further use. */ |
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| 68 | #define NUM_TYPES 12 |
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| 69 | static hid_t native_type_constant[NUM_TYPES]; |
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| 70 | |
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| 71 | static char nc_type_name[NUM_TYPES][NC_MAX_NAME + 1] = {"char", "byte", "short", "int", "float", |
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| 72 | "double", "ubyte", "ushort", "uint", |
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| 73 | "int64", "uint64", "string"}; |
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| 74 | int nc4_free_global_hdf_string_typeid(); |
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| 75 | |
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| 76 | /* Set chunk cache size. Only affects files opened/created *after* it |
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| 77 | * is called. */ |
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| 78 | int |
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| 79 | nc_set_chunk_cache(size_t size, size_t nelems, float preemption) |
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| 80 | { |
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| 81 | if (preemption < 0 || preemption > 1) |
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| 82 | return NC_EINVAL; |
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| 83 | nc4_chunk_cache_size = size; |
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| 84 | nc4_chunk_cache_nelems = nelems; |
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| 85 | nc4_chunk_cache_preemption = preemption; |
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| 86 | return NC_NOERR; |
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| 87 | } |
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| 88 | |
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| 89 | /* Get chunk cache size. Only affects files opened/created *after* it |
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| 90 | * is called. */ |
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| 91 | int |
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| 92 | nc_get_chunk_cache(size_t *sizep, size_t *nelemsp, float *preemptionp) |
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| 93 | { |
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| 94 | if (sizep) |
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| 95 | *sizep = nc4_chunk_cache_size; |
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| 96 | |
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| 97 | if (nelemsp) |
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| 98 | *nelemsp = nc4_chunk_cache_nelems; |
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| 99 | |
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| 100 | if (preemptionp) |
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| 101 | *preemptionp = nc4_chunk_cache_preemption; |
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| 102 | return NC_NOERR; |
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| 103 | } |
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| 104 | |
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| 105 | /* Required for fortran to avoid size_t issues. */ |
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| 106 | int |
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| 107 | nc_set_chunk_cache_ints(int size, int nelems, int preemption) |
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| 108 | { |
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| 109 | if (size <= 0 || nelems <= 0 || preemption < 0 || preemption > 100) |
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| 110 | return NC_EINVAL; |
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| 111 | nc4_chunk_cache_size = size; |
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| 112 | nc4_chunk_cache_nelems = nelems; |
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| 113 | nc4_chunk_cache_preemption = (float)preemption / 100; |
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| 114 | return NC_NOERR; |
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| 115 | } |
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| 116 | |
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| 117 | int |
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| 118 | nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp) |
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| 119 | { |
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| 120 | if (sizep) |
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| 121 | *sizep = (int)nc4_chunk_cache_size; |
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| 122 | if (nelemsp) |
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| 123 | *nelemsp = (int)nc4_chunk_cache_nelems; |
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| 124 | if (preemptionp) |
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| 125 | *preemptionp = (int)(nc4_chunk_cache_preemption * 100); |
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| 126 | |
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| 127 | return NC_NOERR; |
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| 128 | } |
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| 129 | |
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| 130 | /* This will return the length of a netcdf data type in bytes. */ |
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| 131 | int |
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| 132 | nc4typelen(nc_type type) |
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| 133 | { |
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| 134 | switch(type){ |
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| 135 | case NC_BYTE: |
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| 136 | case NC_CHAR: |
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| 137 | case NC_UBYTE: |
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| 138 | return 1; |
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| 139 | case NC_USHORT: |
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| 140 | case NC_SHORT: |
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| 141 | return 2; |
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| 142 | case NC_FLOAT: |
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| 143 | case NC_INT: |
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| 144 | case NC_UINT: |
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| 145 | return 4; |
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| 146 | case NC_DOUBLE: |
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| 147 | case NC_INT64: |
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| 148 | case NC_UINT64: |
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| 149 | return 8; |
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| 150 | } |
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| 151 | return -1; |
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| 152 | } |
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| 153 | |
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| 154 | /* Given a filename, check to see if it is a HDF5 file. */ |
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| 155 | #define MAGIC_NUMBER_LEN 4 |
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| 156 | #define NC_HDF5_FILE 1 |
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| 157 | #define NC_HDF4_FILE 2 |
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| 158 | static int |
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| 159 | nc_check_for_hdf(const char *path, int use_parallel, MPI_Comm comm, MPI_Info info, |
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| 160 | int *hdf_file) |
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| 161 | { |
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| 162 | char blob[MAGIC_NUMBER_LEN]; |
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| 163 | |
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| 164 | assert(hdf_file && path); |
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| 165 | LOG((3, "nc_check_for_hdf: path %s", path)); |
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| 166 | |
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| 167 | /* Get the 4-byte blob from the beginning of the file. Don't use posix |
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| 168 | * for parallel, use the MPI functions instead. */ |
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| 169 | #ifdef USE_PARALLEL |
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| 170 | if (use_parallel) |
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| 171 | { |
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| 172 | MPI_File fh; |
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| 173 | MPI_Status status; |
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| 174 | int retval; |
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| 175 | if ((retval = MPI_File_open(comm, (char *)path, MPI_MODE_RDONLY, |
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| 176 | info, &fh)) != MPI_SUCCESS) |
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| 177 | return NC_EPARINIT; |
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| 178 | if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR, |
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| 179 | &status)) != MPI_SUCCESS) |
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| 180 | return NC_EPARINIT; |
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| 181 | if ((retval = MPI_File_close(&fh)) != MPI_SUCCESS) |
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| 182 | return NC_EPARINIT; |
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| 183 | } |
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| 184 | else |
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| 185 | #endif /* USE_PARALLEL */ |
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| 186 | { |
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| 187 | FILE *fp; |
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| 188 | if (!(fp = fopen(path, "r")) || |
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| 189 | fread(blob, MAGIC_NUMBER_LEN, 1, fp) != 1) |
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| 190 | return errno; |
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| 191 | fclose(fp); |
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| 192 | } |
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| 193 | |
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| 194 | /* Ignore the first byte for HDF5. */ |
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| 195 | if (blob[1] == 'H' && blob[2] == 'D' && blob[3] == 'F') |
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| 196 | *hdf_file = NC_HDF5_FILE; |
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| 197 | else if (!strncmp(blob, "\016\003\023\001", MAGIC_NUMBER_LEN)) |
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| 198 | *hdf_file = NC_HDF4_FILE; |
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| 199 | else |
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| 200 | *hdf_file = 0; |
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| 201 | |
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| 202 | return NC_NOERR; |
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| 203 | } |
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| 204 | |
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| 205 | /* Create a HDF5/netcdf-4 file. In this case, ncid has already been |
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| 206 | * selected in ncfunc.c. */ |
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| 207 | static int |
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| 208 | nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info, |
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| 209 | NC_FILE_INFO_T *nc) |
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| 210 | { |
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| 211 | hid_t fcpl_id, fapl_id; |
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| 212 | unsigned flags; |
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| 213 | FILE *fp; |
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| 214 | int retval = NC_NOERR; |
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| 215 | int persist = 0; /* Should diskless try to persist its data into file?*/ |
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| 216 | |
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| 217 | if(cmode & NC_DISKLESS) |
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| 218 | flags = H5F_ACC_TRUNC; |
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| 219 | else if(cmode & NC_NOCLOBBER) |
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| 220 | flags = H5F_ACC_EXCL; |
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| 221 | else |
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| 222 | flags = H5F_ACC_TRUNC; |
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| 223 | |
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| 224 | LOG((3, "nc4_create_file: path %s mode 0x%x", path, cmode)); |
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| 225 | assert(nc && path); |
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| 226 | |
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| 227 | |
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| 228 | /* If this file already exists, and NC_NOCLOBBER is specified, |
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| 229 | return an error. */ |
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| 230 | if (cmode & NC_DISKLESS) { |
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| 231 | if(cmode & NC_WRITE) |
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| 232 | persist = 1; |
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| 233 | } else if ((cmode & NC_NOCLOBBER) && (fp = fopen(path, "r"))) { |
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| 234 | fclose(fp); |
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| 235 | return NC_EEXIST; |
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| 236 | } |
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| 237 | |
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| 238 | /* Add necessary structs to hold netcdf-4 file data. */ |
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| 239 | if ((retval = nc4_nc4f_list_add(nc, path, (NC_WRITE | cmode)))) |
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| 240 | BAIL(retval); |
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| 241 | assert(nc->nc4_info && nc->nc4_info->root_grp); |
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| 242 | |
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| 243 | /* Need this access plist to control how HDF5 handles open onjects |
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| 244 | * on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to |
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| 245 | * fail if there are any open objects in the file. */ |
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| 246 | if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) |
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| 247 | BAIL(NC_EHDFERR); |
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| 248 | #ifdef EXTRA_TESTS |
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| 249 | num_plists++; |
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| 250 | #endif |
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| 251 | #ifdef EXTRA_TESTS |
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| 252 | if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) |
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| 253 | BAIL(NC_EHDFERR); |
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| 254 | #else |
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| 255 | if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) |
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| 256 | BAIL(NC_EHDFERR); |
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| 257 | #endif /* EXTRA_TESTS */ |
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| 258 | |
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| 259 | #ifdef USE_PARALLEL |
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| 260 | /* If this is a parallel file create, set up the file creation |
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| 261 | property list. */ |
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| 262 | if ((cmode & NC_MPIIO) || (cmode & NC_MPIPOSIX)) |
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| 263 | { |
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| 264 | nc->nc4_info->parallel++; |
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| 265 | if (cmode & NC_MPIIO) /* MPI/IO */ |
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| 266 | { |
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| 267 | LOG((4, "creating parallel file with MPI/IO")); |
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| 268 | if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) |
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| 269 | BAIL(NC_EPARINIT); |
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| 270 | } |
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| 271 | else /* MPI/POSIX */ |
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| 272 | { |
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| 273 | LOG((4, "creating parallel file with MPI/posix")); |
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| 274 | if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) |
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| 275 | BAIL(NC_EPARINIT); |
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| 276 | } |
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| 277 | } |
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| 278 | #else /* only set cache for non-parallel... */ |
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| 279 | if(cmode & NC_DISKLESS) { |
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| 280 | if (H5Pset_fapl_core(fapl_id, 4096, persist)) |
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| 281 | BAIL(NC_EDISKLESS); |
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| 282 | } |
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| 283 | if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size, |
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| 284 | nc4_chunk_cache_preemption) < 0) |
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| 285 | BAIL(NC_EHDFERR); |
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| 286 | LOG((4, "nc4_create_file: set HDF raw chunk cache to size %d nelems %d preemption %f", |
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| 287 | nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption)); |
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| 288 | #endif /* USE_PARALLEL */ |
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| 289 | |
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| 290 | if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_18, H5F_LIBVER_18) < 0) |
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| 291 | BAIL(NC_EHDFERR); |
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| 292 | |
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| 293 | /* Create the property list. */ |
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| 294 | if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) |
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| 295 | BAIL(NC_EHDFERR); |
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| 296 | #ifdef EXTRA_TESTS |
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| 297 | num_plists++; |
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| 298 | #endif |
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| 299 | |
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| 300 | /* Set latest_format in access propertly list and |
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| 301 | * H5P_CRT_ORDER_TRACKED in the creation property list. This turns |
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| 302 | * on HDF5 creation ordering. */ |
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| 303 | if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED | |
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| 304 | H5P_CRT_ORDER_INDEXED)) < 0) |
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| 305 | BAIL(NC_EHDFERR); |
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| 306 | if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED | |
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| 307 | H5P_CRT_ORDER_INDEXED)) < 0) |
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| 308 | BAIL(NC_EHDFERR); |
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| 309 | |
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| 310 | /* Create the file. */ |
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| 311 | if ((nc->nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0) |
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| 312 | BAIL(NC_EFILEMETA); |
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| 313 | |
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| 314 | /* Open the root group. */ |
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| 315 | if ((nc->nc4_info->root_grp->hdf_grpid = H5Gopen2(nc->nc4_info->hdfid, "/", |
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| 316 | H5P_DEFAULT)) < 0) |
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| 317 | BAIL(NC_EFILEMETA); |
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| 318 | |
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| 319 | /* Release the property lists. */ |
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| 320 | if (H5Pclose(fapl_id) < 0 || |
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| 321 | H5Pclose(fcpl_id) < 0) |
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| 322 | BAIL(NC_EHDFERR); |
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| 323 | #ifdef EXTRA_TESTS |
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| 324 | num_plists--; |
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| 325 | num_plists--; |
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| 326 | #endif |
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| 327 | |
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| 328 | /* Define mode gets turned on automatically on create. */ |
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| 329 | nc->nc4_info->flags |= NC_INDEF; |
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| 330 | |
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| 331 | return NC_NOERR; |
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| 332 | |
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| 333 | exit: |
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| 334 | if (nc->nc4_info->hdfid > 0) H5Fclose(nc->nc4_info->hdfid); |
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| 335 | return retval; |
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| 336 | } |
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| 337 | |
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| 338 | /** \ingroup netcdf4 |
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| 339 | Create a netCDF-4/HDF5 file. |
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| 340 | |
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| 341 | \param path The file name of the new file. |
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| 342 | \param cmode The creation mode flag. |
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| 343 | \param initialsz Ignored by this function. |
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| 344 | \param basepe Ignored by this function. |
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| 345 | \param chunksizehintp Ignored by this function. |
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| 346 | \param use_parallel 0 for sequential, non-zero for parallel I/O. |
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| 347 | \param mpidata pointer to struct holdind data for parallel I/O |
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| 348 | layer. Ignored if NULL. |
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| 349 | \param dispatch Pointer to the dispatch table for this file. |
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| 350 | \param ncpp Pointer to start of linked list of open files. |
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| 351 | \return NC_INVAL Invalid input (check cmode). |
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| 352 | */ |
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| 353 | int |
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| 354 | NC4_create(const char* path, int cmode, size_t initialsz, int basepe, |
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| 355 | size_t *chunksizehintp, int use_parallel, void *mpidata, |
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| 356 | NC_Dispatch *dispatch, NC **ncpp) |
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| 357 | { |
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| 358 | NC_FILE_INFO_T *nc_file = NULL; |
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| 359 | #ifdef USE_PARALLEL |
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| 360 | MPI_Comm comm = 0; |
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| 361 | MPI_Info info = 0; |
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| 362 | #else |
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| 363 | int comm = 0, info = 0; |
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| 364 | #endif /* USE_PARALLEL */ |
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| 365 | int res; |
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| 366 | |
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| 367 | assert(ncpp && path); |
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| 368 | |
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| 369 | LOG((1, "nc4_create_file: path %s cmode 0x%x comm %d info %d", |
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| 370 | path, cmode, comm, info)); |
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| 371 | |
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| 372 | #ifdef USE_PARALLEL |
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| 373 | if (mpidata) |
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| 374 | { |
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| 375 | comm = ((NC_MPI_INFO *)mpidata)->comm; |
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| 376 | info = ((NC_MPI_INFO *)mpidata)->info; |
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| 377 | } |
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| 378 | #endif /* USE_PARALLEL */ |
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| 379 | |
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| 380 | /* If this is our first file, turn off HDF5 error messages. */ |
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| 381 | if (virgin) |
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| 382 | { |
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| 383 | if (H5Eset_auto(NULL, NULL) < 0) |
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| 384 | LOG((0, "Couldn't turn off HDF5 error messages!")); |
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| 385 | LOG((1, "HDF5 error messages have been turned off.")); |
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| 386 | virgin = 0; |
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| 387 | } |
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| 388 | |
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| 389 | /* Check the cmode for validity. */ |
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| 390 | if (cmode & ~(NC_NOCLOBBER | NC_64BIT_OFFSET |
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| 391 | | NC_NETCDF4 | NC_CLASSIC_MODEL |
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| 392 | | NC_SHARE | NC_MPIIO | NC_MPIPOSIX | NC_LOCK | NC_PNETCDF |
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| 393 | | NC_DISKLESS |
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| 394 | | NC_WRITE /* to support diskless persistence */ |
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| 395 | ) |
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| 396 | || (cmode & NC_MPIIO && cmode & NC_MPIPOSIX) |
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| 397 | || (cmode & NC_64BIT_OFFSET && cmode & NC_NETCDF4) |
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| 398 | || (cmode & (NC_MPIIO | NC_MPIPOSIX) && cmode & NC_DISKLESS) |
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| 399 | ) |
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| 400 | return NC_EINVAL; |
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| 401 | |
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| 402 | /* Allocate the storage for this file info struct, and fill it with |
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| 403 | zeros. This add the file metadata to the front of the global |
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| 404 | nc_file list. */ |
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| 405 | if ((res = nc4_file_list_add(&nc_file, dispatch))) |
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| 406 | return res; |
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| 407 | |
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| 408 | /* Apply default create format. */ |
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| 409 | if (default_create_format == NC_FORMAT_64BIT) |
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| 410 | cmode |= NC_64BIT_OFFSET; |
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| 411 | else if (default_create_format == NC_FORMAT_NETCDF4) |
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| 412 | cmode |= NC_NETCDF4; |
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| 413 | else if (default_create_format == NC_FORMAT_NETCDF4_CLASSIC) |
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| 414 | { |
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| 415 | cmode |= NC_NETCDF4; |
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| 416 | cmode |= NC_CLASSIC_MODEL; |
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| 417 | } |
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| 418 | LOG((2, "cmode after applying default format: 0x%x", cmode)); |
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| 419 | |
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| 420 | /* Check to see if we want a netcdf3 or netcdf4 file. Open it, and |
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| 421 | call the appropriate nc*_create. */ |
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| 422 | if (cmode & NC_NETCDF4) |
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| 423 | { |
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| 424 | nc_file->int_ncid = nc_file->ext_ncid; |
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| 425 | res = nc4_create_file(path, cmode, comm, info, nc_file); |
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| 426 | } |
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| 427 | #ifdef USE_PNETCDF |
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| 428 | else if (cmode & NC_PNETCDF) |
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| 429 | { |
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| 430 | nc_file->pnetcdf_file++; |
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| 431 | res = ncmpi_create(comm, path, cmode, info, &(nc_file->int_ncid)); |
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| 432 | } |
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| 433 | #endif /* USE_PNETCDF */ |
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| 434 | else |
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| 435 | { |
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| 436 | return NC_EINVAL; |
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| 437 | } |
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| 438 | |
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| 439 | /* Delete this file list entry if there was a failure. */ |
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| 440 | if (res) |
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| 441 | { |
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| 442 | if (nc_file) |
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| 443 | nc4_file_list_del(nc_file); |
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| 444 | } |
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| 445 | else |
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| 446 | *ncpp = (NC *)nc_file; |
---|
| 447 | |
---|
| 448 | return res; |
---|
| 449 | } |
---|
| 450 | |
---|
| 451 | /* This function is called by read_dataset when a dimension scale |
---|
| 452 | * dataset is encountered. It reads in the dimension data (creating a |
---|
| 453 | * new NC_DIM_INFO_T object), and also checks to see if this is a |
---|
| 454 | * dimension without a variable - that is, a coordinate dimension |
---|
| 455 | * which does not have any coordinate data. */ |
---|
| 456 | static int |
---|
| 457 | read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, char *obj_name, |
---|
| 458 | hsize_t scale_size, hsize_t max_scale_size, |
---|
| 459 | int *dim_without_var) |
---|
| 460 | { |
---|
| 461 | /*char *start_of_len;*/ |
---|
| 462 | char dimscale_name_att[NC_MAX_NAME + 1] = ""; |
---|
| 463 | hid_t attid = 0; |
---|
| 464 | int max_len; |
---|
| 465 | int retval; |
---|
| 466 | |
---|
| 467 | /* Add a dimension for this scale. */ |
---|
| 468 | if ((retval = nc4_dim_list_add(&grp->dim))) |
---|
| 469 | return retval; |
---|
| 470 | |
---|
| 471 | /* Assign dimid and increment number of dimensions. */ |
---|
| 472 | grp->dim->dimid = grp->file->nc4_info->next_dimid++; |
---|
| 473 | grp->ndims++; |
---|
| 474 | |
---|
| 475 | /* Does this dataset have a hidden attribute that tells us its |
---|
| 476 | * dimid? If so, read it. */ |
---|
| 477 | H5E_BEGIN_TRY { |
---|
| 478 | if ((attid = H5Aopen_by_name(datasetid, ".", NC_DIMID_ATT_NAME, |
---|
| 479 | H5P_DEFAULT, H5P_DEFAULT)) > 0) |
---|
| 480 | { |
---|
| 481 | if (H5Aread(attid, H5T_NATIVE_INT, &grp->dim->dimid) < 0) |
---|
| 482 | return NC_EHDFERR; |
---|
| 483 | if (H5Aclose(attid) < 0) |
---|
| 484 | return NC_EHDFERR; |
---|
| 485 | } |
---|
| 486 | } H5E_END_TRY; |
---|
| 487 | |
---|
| 488 | max_len = strlen(obj_name) > NC_MAX_NAME ? NC_MAX_NAME : strlen(obj_name); |
---|
| 489 | if (!(grp->dim->name = malloc((max_len + 1) * sizeof(char)))) |
---|
| 490 | return NC_ENOMEM; |
---|
| 491 | strncpy(grp->dim->name, obj_name, max_len + 1); |
---|
| 492 | if (SIZEOF_SIZE_T < 8 && scale_size > NC_MAX_UINT) |
---|
| 493 | { |
---|
| 494 | grp->dim->len = NC_MAX_UINT; |
---|
| 495 | grp->dim->too_long = 1; |
---|
| 496 | } |
---|
| 497 | else |
---|
| 498 | grp->dim->len = scale_size; |
---|
| 499 | grp->dim->hdf_dimscaleid = datasetid; |
---|
| 500 | |
---|
| 501 | /* If the dimscale has an unlimited dimension, then this dimension |
---|
| 502 | * is unlimited. */ |
---|
| 503 | if (max_scale_size == H5S_UNLIMITED) |
---|
| 504 | grp->dim->unlimited++; |
---|
| 505 | |
---|
| 506 | /* If the scale name is set to DIM_WITHOUT_VARIABLE, then this is a |
---|
| 507 | * dimension, but not a variable. (If get_scale_name returns an |
---|
| 508 | * error, just move on, there's no NAME.) */ |
---|
| 509 | if (H5DSget_scale_name(datasetid, dimscale_name_att, NC_MAX_NAME) >= 0) |
---|
| 510 | { |
---|
| 511 | if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE, |
---|
| 512 | strlen(DIM_WITHOUT_VARIABLE))) |
---|
| 513 | { |
---|
| 514 | if (grp->dim->unlimited) |
---|
| 515 | { |
---|
| 516 | size_t len = 0, *lenp = &len; |
---|
| 517 | if ((retval = nc4_find_dim_len(grp, grp->dim->dimid, &lenp))) |
---|
| 518 | return retval; |
---|
| 519 | grp->dim->len = *lenp; |
---|
| 520 | } |
---|
| 521 | (*dim_without_var)++; |
---|
| 522 | } |
---|
| 523 | } |
---|
| 524 | |
---|
| 525 | return NC_NOERR; |
---|
| 526 | } |
---|
| 527 | |
---|
| 528 | /* This function reads the hacked in coordinates attribute I use for |
---|
| 529 | * multi-dimensional coordinates. */ |
---|
| 530 | static int |
---|
| 531 | read_coord_dimids(NC_VAR_INFO_T *var) |
---|
| 532 | { |
---|
| 533 | hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1; |
---|
| 534 | hssize_t coord_array_size; |
---|
| 535 | int ret = 0; |
---|
| 536 | |
---|
| 537 | /* There is a hidden attribute telling us the ids of the |
---|
| 538 | * dimensions that apply to this multi-dimensional coordinate |
---|
| 539 | * variable. Read it. */ |
---|
| 540 | if ((coord_attid = H5Aopen_name(var->hdf_datasetid, COORDINATES)) < 0) ret++; |
---|
| 541 | if (!ret && (coord_att_typeid = H5Aget_type(coord_attid)) < 0) ret++; |
---|
| 542 | if (!ret && H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0) ret++; |
---|
| 543 | LOG((4, "dimscale %s is multidimensional and has coords", var->name)); |
---|
| 544 | |
---|
| 545 | /* How many dimensions are there? */ |
---|
| 546 | if ((spaceid = H5Aget_space(coord_attid)) < 0) ret++; |
---|
| 547 | #ifdef EXTRA_TESTS |
---|
| 548 | num_spaces++; |
---|
| 549 | #endif |
---|
| 550 | if ((coord_array_size = H5Sget_simple_extent_npoints(spaceid)) < 0) ret++; |
---|
| 551 | |
---|
| 552 | /* Malloc space to the array of pointers to dims. */ |
---|
| 553 | |
---|
| 554 | |
---|
| 555 | /* Set my HDF5 IDs free! */ |
---|
| 556 | if (spaceid >= 0 && H5Sclose(spaceid) < 0) ret++; |
---|
| 557 | #ifdef EXTRA_TESTS |
---|
| 558 | num_spaces--; |
---|
| 559 | #endif |
---|
| 560 | if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0) ret++; |
---|
| 561 | if (coord_attid >= 0 && H5Aclose(coord_attid) < 0) ret++; |
---|
| 562 | return ret ? NC_EATTMETA : NC_NOERR; |
---|
| 563 | } |
---|
| 564 | |
---|
| 565 | /* This function is called when reading a file's metadata for each |
---|
| 566 | * dimension scale attached to a variable.*/ |
---|
| 567 | static herr_t |
---|
| 568 | dimscale_visitor(hid_t did, unsigned dim, hid_t dsid, |
---|
| 569 | void *dimscale_hdf5_objids) |
---|
| 570 | { |
---|
| 571 | H5G_stat_t statbuf; |
---|
| 572 | |
---|
| 573 | /* Get more info on the dimscale object.*/ |
---|
| 574 | if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0) |
---|
| 575 | return -1; |
---|
| 576 | |
---|
| 577 | /* Pass this information back to caller. */ |
---|
| 578 | /* (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno = statbuf.fileno; |
---|
| 579 | (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno = statbuf.objno;*/ |
---|
| 580 | (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0]; |
---|
| 581 | (*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1]; |
---|
| 582 | (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0]; |
---|
| 583 | (*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1]; |
---|
| 584 | return 0; |
---|
| 585 | } |
---|
| 586 | |
---|
| 587 | /* Given an HDF5 type, set a pointer to netcdf type. */ |
---|
| 588 | static int |
---|
| 589 | get_netcdf_type(NC_HDF5_FILE_INFO_T *h5, hid_t native_typeid, |
---|
| 590 | nc_type *xtype) |
---|
| 591 | { |
---|
| 592 | NC_TYPE_INFO_T *type; |
---|
| 593 | hid_t class; |
---|
| 594 | htri_t is_str, equal = 0; |
---|
| 595 | |
---|
| 596 | assert(h5 && xtype); |
---|
| 597 | |
---|
| 598 | if ((class = H5Tget_class(native_typeid)) < 0) |
---|
| 599 | return NC_EHDFERR; |
---|
| 600 | |
---|
| 601 | /* H5Tequal doesn't work with H5T_C_S1 for some reason. But |
---|
| 602 | * H5Tget_class will return H5T_STRING if this is a string. */ |
---|
| 603 | if (class == H5T_STRING) |
---|
| 604 | { |
---|
| 605 | if ((is_str = H5Tis_variable_str(native_typeid)) < 0) |
---|
| 606 | return NC_EHDFERR; |
---|
| 607 | if (is_str) |
---|
| 608 | *xtype = NC_STRING; |
---|
| 609 | else |
---|
| 610 | *xtype = NC_CHAR; |
---|
| 611 | return NC_NOERR; |
---|
| 612 | } |
---|
| 613 | else if (class == H5T_INTEGER || class == H5T_FLOAT) |
---|
| 614 | { |
---|
| 615 | /* For integers and floats, we don't have to worry about |
---|
| 616 | * endianness if we compare native types. */ |
---|
| 617 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0) |
---|
| 618 | return NC_EHDFERR; |
---|
| 619 | if (equal) |
---|
| 620 | { |
---|
| 621 | *xtype = NC_BYTE; |
---|
| 622 | return NC_NOERR; |
---|
| 623 | } |
---|
| 624 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0) |
---|
| 625 | return NC_EHDFERR; |
---|
| 626 | if (equal) |
---|
| 627 | { |
---|
| 628 | *xtype = NC_SHORT; |
---|
| 629 | return NC_NOERR; |
---|
| 630 | } |
---|
| 631 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0) |
---|
| 632 | return NC_EHDFERR; |
---|
| 633 | if (equal) |
---|
| 634 | { |
---|
| 635 | *xtype = NC_INT; |
---|
| 636 | return NC_NOERR; |
---|
| 637 | } |
---|
| 638 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0) |
---|
| 639 | return NC_EHDFERR; |
---|
| 640 | if (equal) |
---|
| 641 | { |
---|
| 642 | *xtype = NC_FLOAT; |
---|
| 643 | return NC_NOERR; |
---|
| 644 | } |
---|
| 645 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0) |
---|
| 646 | return NC_EHDFERR; |
---|
| 647 | if (equal) |
---|
| 648 | { |
---|
| 649 | *xtype = NC_DOUBLE; |
---|
| 650 | return NC_NOERR; |
---|
| 651 | } |
---|
| 652 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0) |
---|
| 653 | return NC_EHDFERR; |
---|
| 654 | if (equal) |
---|
| 655 | { |
---|
| 656 | *xtype = NC_UBYTE; |
---|
| 657 | return NC_NOERR; |
---|
| 658 | } |
---|
| 659 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0) |
---|
| 660 | return NC_EHDFERR; |
---|
| 661 | if (equal) |
---|
| 662 | { |
---|
| 663 | *xtype = NC_USHORT; |
---|
| 664 | return NC_NOERR; |
---|
| 665 | } |
---|
| 666 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0) |
---|
| 667 | return NC_EHDFERR; |
---|
| 668 | if (equal) |
---|
| 669 | { |
---|
| 670 | *xtype = NC_UINT; |
---|
| 671 | return NC_NOERR; |
---|
| 672 | } |
---|
| 673 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0) |
---|
| 674 | return NC_EHDFERR; |
---|
| 675 | if (equal) |
---|
| 676 | { |
---|
| 677 | *xtype = NC_INT64; |
---|
| 678 | return NC_NOERR; |
---|
| 679 | } |
---|
| 680 | if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0) |
---|
| 681 | return NC_EHDFERR; |
---|
| 682 | if (equal) |
---|
| 683 | { |
---|
| 684 | *xtype = NC_UINT64; |
---|
| 685 | return NC_NOERR; |
---|
| 686 | } |
---|
| 687 | } |
---|
| 688 | |
---|
| 689 | /* Maybe we already know about this type. */ |
---|
| 690 | if (!equal) |
---|
| 691 | if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid))) |
---|
| 692 | { |
---|
| 693 | *xtype = type->nc_typeid; |
---|
| 694 | return NC_NOERR; |
---|
| 695 | } |
---|
| 696 | |
---|
| 697 | *xtype = NC_NAT; |
---|
| 698 | return NC_EBADTYPID; |
---|
| 699 | } |
---|
| 700 | |
---|
| 701 | /* Given an HDF5 type, set a pointer to netcdf type_info struct, |
---|
| 702 | * either an existing one (for user-defined types) or a newly created |
---|
| 703 | * one. */ |
---|
| 704 | static int |
---|
| 705 | get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid, |
---|
| 706 | nc_type *xtype, NC_TYPE_INFO_T **type_info) |
---|
| 707 | { |
---|
| 708 | NC_TYPE_INFO_T *type; |
---|
| 709 | htri_t is_str, equal = 0; |
---|
| 710 | hid_t class, native_typeid, hdf_typeid; |
---|
| 711 | #if 0 |
---|
| 712 | nc_type my_nc_type = 0; |
---|
| 713 | #endif |
---|
| 714 | H5T_order_t order; |
---|
| 715 | int endianness; |
---|
| 716 | nc_type nc_type_constant[NUM_TYPES] = {NC_CHAR, NC_BYTE, NC_SHORT, NC_INT, NC_FLOAT, |
---|
| 717 | NC_DOUBLE, NC_UBYTE, NC_USHORT, NC_UINT, |
---|
| 718 | NC_INT64, NC_UINT64, NC_STRING}; |
---|
| 719 | int type_size[NUM_TYPES] = {sizeof(char), sizeof(char), sizeof(short), |
---|
| 720 | sizeof(int), sizeof(float), sizeof(double), |
---|
| 721 | sizeof(unsigned char), sizeof(unsigned short), |
---|
| 722 | sizeof(unsigned int), sizeof(long long), |
---|
| 723 | sizeof(unsigned long long), 0}; |
---|
| 724 | int t; |
---|
| 725 | |
---|
| 726 | assert(h5 && xtype && type_info); |
---|
| 727 | |
---|
| 728 | /* Because these N5T_NATIVE_* constants are actually function calls |
---|
| 729 | * (!) in H5Tpublic.h, I can't initialize this array in the usual |
---|
| 730 | * way, because at least some C compilers (like Irix) complain |
---|
| 731 | * about calling functions when defining constants. So I have to do |
---|
| 732 | * it like this. Note that there's no native types for char or |
---|
| 733 | * string. Those are handled later. */ |
---|
| 734 | if (!native_type_constant[1]) |
---|
| 735 | { |
---|
| 736 | native_type_constant[1] = H5T_NATIVE_SCHAR; |
---|
| 737 | native_type_constant[2] = H5T_NATIVE_SHORT; |
---|
| 738 | native_type_constant[3] = H5T_NATIVE_INT; |
---|
| 739 | native_type_constant[4] = H5T_NATIVE_FLOAT; |
---|
| 740 | native_type_constant[5] = H5T_NATIVE_DOUBLE; |
---|
| 741 | native_type_constant[6] = H5T_NATIVE_UCHAR; |
---|
| 742 | native_type_constant[7] = H5T_NATIVE_USHORT; |
---|
| 743 | native_type_constant[8] = H5T_NATIVE_UINT; |
---|
| 744 | native_type_constant[9] = H5T_NATIVE_LLONG; |
---|
| 745 | native_type_constant[10] = H5T_NATIVE_ULLONG; |
---|
| 746 | } |
---|
| 747 | |
---|
| 748 | /* Get the HDF5 typeid - we'll need it later. */ |
---|
| 749 | if ((hdf_typeid = H5Dget_type(datasetid)) < 0) |
---|
| 750 | return NC_EHDFERR; |
---|
| 751 | |
---|
| 752 | /* Get the native typeid. Will be equivalent to hdf_typeid when |
---|
| 753 | * creating but not necessarily when reading, a variable. */ |
---|
| 754 | if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0) |
---|
| 755 | return NC_EHDFERR; |
---|
| 756 | |
---|
| 757 | /* Is this type an integer, string, compound, or what? */ |
---|
| 758 | if ((class = H5Tget_class(native_typeid)) < 0) |
---|
| 759 | return NC_EHDFERR; |
---|
| 760 | |
---|
| 761 | /* Is this an atomic type? */ |
---|
| 762 | if (class == H5T_STRING || class == H5T_INTEGER || class == H5T_FLOAT) |
---|
| 763 | { |
---|
| 764 | /* Allocate a phony NC_TYPE_INFO_T struct to hold type info. */ |
---|
| 765 | if (!(*type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) |
---|
| 766 | return NC_ENOMEM; |
---|
| 767 | (*type_info)->class = class; |
---|
| 768 | |
---|
| 769 | /* H5Tequal doesn't work with H5T_C_S1 for some reason. But |
---|
| 770 | * H5Tget_class will return H5T_STRING if this is a string. */ |
---|
| 771 | if (class == H5T_STRING) |
---|
| 772 | { |
---|
| 773 | if ((is_str = H5Tis_variable_str(native_typeid)) < 0) |
---|
| 774 | return NC_EHDFERR; |
---|
| 775 | /* Make sure fixed-len strings will work like variable-len strings */ |
---|
| 776 | if (is_str || H5Tget_size(hdf_typeid) > 1) |
---|
| 777 | t = NUM_TYPES - 1; |
---|
| 778 | else |
---|
| 779 | t = 0; |
---|
| 780 | } |
---|
| 781 | else if (class == H5T_INTEGER || class == H5T_FLOAT) |
---|
| 782 | { |
---|
| 783 | for (t = 1; t < NUM_TYPES - 1; t++) |
---|
| 784 | { |
---|
| 785 | if ((equal = H5Tequal(native_typeid, native_type_constant[t])) < 0) |
---|
| 786 | return NC_EHDFERR; |
---|
| 787 | if (equal) |
---|
| 788 | { |
---|
| 789 | #if 0 |
---|
| 790 | my_nc_type = nc_type_constant[t]; |
---|
| 791 | #endif |
---|
| 792 | break; |
---|
| 793 | } |
---|
| 794 | } |
---|
| 795 | |
---|
| 796 | /* Find out about endianness. */ |
---|
| 797 | if (class == H5T_INTEGER) |
---|
| 798 | { |
---|
| 799 | if ((order = H5Tget_order(hdf_typeid)) < 0) |
---|
| 800 | return NC_EHDFERR; |
---|
| 801 | if (order == H5T_ORDER_LE) |
---|
| 802 | endianness = NC_ENDIAN_LITTLE; |
---|
| 803 | else if (order == H5T_ORDER_BE) |
---|
| 804 | endianness = NC_ENDIAN_BIG; |
---|
| 805 | else /* don't support H5T_ORDER_VAX, H5T_ORDER_MIXED, H5T_ORDER_NONE */ |
---|
| 806 | return NC_EBADTYPE; |
---|
| 807 | /* Copy this into the type_info struct. */ |
---|
| 808 | (*type_info)->endianness = endianness; |
---|
| 809 | } |
---|
| 810 | } |
---|
| 811 | *xtype = nc_type_constant[t]; |
---|
| 812 | (*type_info)->nc_typeid = nc_type_constant[t]; |
---|
| 813 | (*type_info)->size = type_size[t]; |
---|
| 814 | if (!((*type_info)->name = malloc((strlen(nc_type_name[t]) + 1) * sizeof(char)))) |
---|
| 815 | return NC_ENOMEM; |
---|
| 816 | strcpy((*type_info)->name, nc_type_name[t]); |
---|
| 817 | (*type_info)->class = class; |
---|
| 818 | (*type_info)->hdf_typeid = hdf_typeid; |
---|
| 819 | (*type_info)->native_typeid = native_typeid; |
---|
| 820 | (*type_info)->close_hdf_typeid = 1; |
---|
| 821 | return NC_NOERR; |
---|
| 822 | } |
---|
| 823 | else |
---|
| 824 | { |
---|
| 825 | /* This is a user-defined type. */ |
---|
| 826 | if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid))) |
---|
| 827 | { |
---|
| 828 | *xtype = type->nc_typeid; |
---|
| 829 | *type_info = type; |
---|
| 830 | } |
---|
| 831 | |
---|
| 832 | /* The type entry in the array of user-defined types already has |
---|
| 833 | * an open data typeid (and native typeid), so close the ones we |
---|
| 834 | * opened above. */ |
---|
| 835 | if (H5Tclose(native_typeid) < 0) |
---|
| 836 | return NC_EHDFERR; |
---|
| 837 | if (H5Tclose(hdf_typeid) < 0) |
---|
| 838 | return NC_EHDFERR; |
---|
| 839 | |
---|
| 840 | if (type) |
---|
| 841 | return NC_NOERR; |
---|
| 842 | } |
---|
| 843 | |
---|
| 844 | *xtype = NC_NAT; |
---|
| 845 | return NC_EBADTYPID; |
---|
| 846 | } |
---|
| 847 | |
---|
| 848 | /* Read an attribute. */ |
---|
| 849 | static int |
---|
| 850 | read_hdf5_att(NC_GRP_INFO_T *grp, hid_t attid, NC_ATT_INFO_T *att) |
---|
| 851 | { |
---|
| 852 | hid_t spaceid = 0, file_typeid = 0; |
---|
| 853 | hsize_t dims[1]; /* netcdf attributes always 1-D. */ |
---|
| 854 | int retval = NC_NOERR; |
---|
| 855 | size_t type_size; |
---|
| 856 | int att_ndims; |
---|
| 857 | hssize_t att_npoints; |
---|
| 858 | H5T_class_t att_class; |
---|
| 859 | int fixed_len_string = 0; |
---|
| 860 | size_t fixed_size = 0; |
---|
| 861 | |
---|
| 862 | assert(att->name); |
---|
| 863 | LOG((5, "read_hdf5_att: att->attnum %d att->name %s " |
---|
| 864 | "att->xtype %d att->len %d", att->attnum, att->name, |
---|
| 865 | att->xtype, att->len)); |
---|
| 866 | |
---|
| 867 | /* Get type of attribute in file. */ |
---|
| 868 | if ((file_typeid = H5Aget_type(attid)) < 0) |
---|
| 869 | return NC_EATTMETA; |
---|
| 870 | if ((att->native_typeid = H5Tget_native_type(file_typeid, H5T_DIR_DEFAULT)) < 0) |
---|
| 871 | BAIL(NC_EHDFERR); |
---|
| 872 | if ((att_class = H5Tget_class(att->native_typeid)) < 0) |
---|
| 873 | BAIL(NC_EATTMETA); |
---|
| 874 | if (att_class == H5T_STRING && !H5Tis_variable_str(att->native_typeid)) |
---|
| 875 | { |
---|
| 876 | fixed_len_string++; |
---|
| 877 | if (!(fixed_size = H5Tget_size(att->native_typeid))) |
---|
| 878 | BAIL(NC_EATTMETA); |
---|
| 879 | } |
---|
| 880 | if ((retval = get_netcdf_type(grp->file->nc4_info, att->native_typeid, &(att->xtype)))) |
---|
| 881 | BAIL(retval); |
---|
| 882 | |
---|
| 883 | |
---|
| 884 | /* Get len. */ |
---|
| 885 | if ((spaceid = H5Aget_space(attid)) < 0) |
---|
| 886 | BAIL(NC_EATTMETA); |
---|
| 887 | #ifdef EXTRA_TESTS |
---|
| 888 | num_spaces++; |
---|
| 889 | #endif |
---|
| 890 | if ((att_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) |
---|
| 891 | BAIL(NC_EATTMETA); |
---|
| 892 | if ((att_npoints = H5Sget_simple_extent_npoints(spaceid)) < 0) |
---|
| 893 | BAIL(NC_EATTMETA); |
---|
| 894 | |
---|
| 895 | /* If both att_ndims and att_npoints are zero, then this is a |
---|
| 896 | * zero length att. */ |
---|
| 897 | if (att_ndims == 0 && att_npoints == 0) |
---|
| 898 | { |
---|
| 899 | dims[0] = 0; |
---|
| 900 | } |
---|
| 901 | else if (att->xtype == NC_STRING) { |
---|
| 902 | dims[0] = att_npoints; |
---|
| 903 | } |
---|
| 904 | else if (att->xtype == NC_CHAR) |
---|
| 905 | { |
---|
| 906 | /* NC_CHAR attributes are written as a scalar in HDF5, of type |
---|
| 907 | * H5T_C_S1, of variable length. */ |
---|
| 908 | if (att_ndims == 0) |
---|
| 909 | { |
---|
| 910 | if (!(dims[0] = H5Tget_size(file_typeid))) |
---|
| 911 | BAIL(NC_EATTMETA); |
---|
| 912 | } |
---|
| 913 | else |
---|
| 914 | { |
---|
| 915 | /* This is really a string type! */ |
---|
| 916 | att->xtype = NC_STRING; |
---|
| 917 | dims[0] = att_npoints; |
---|
| 918 | } |
---|
| 919 | } |
---|
| 920 | else |
---|
| 921 | { |
---|
| 922 | /* All netcdf attributes are scalar or 1-D only. */ |
---|
| 923 | if (att_ndims > 1) |
---|
| 924 | BAIL(NC_EATTMETA); |
---|
| 925 | |
---|
| 926 | /* Read the size of this attribute. */ |
---|
| 927 | if (H5Sget_simple_extent_dims(spaceid, dims, NULL) < 0) |
---|
| 928 | BAIL(NC_EATTMETA); |
---|
| 929 | } |
---|
| 930 | |
---|
| 931 | /* Tell the user what the length if this attribute is. */ |
---|
| 932 | att->len = dims[0]; |
---|
| 933 | |
---|
| 934 | /* Allocate some memory if the len is not zero, and read the |
---|
| 935 | attribute. */ |
---|
| 936 | if (dims[0]) |
---|
| 937 | { |
---|
| 938 | if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, att->xtype, 0, |
---|
| 939 | &type_size))) |
---|
| 940 | return retval; |
---|
| 941 | if (att_class == H5T_VLEN) |
---|
| 942 | { |
---|
| 943 | if (!(att->vldata = malloc((unsigned int)(att->len * sizeof(hvl_t))))) |
---|
| 944 | BAIL(NC_ENOMEM); |
---|
| 945 | if (H5Aread(attid, att->native_typeid, att->vldata) < 0) |
---|
| 946 | BAIL(NC_EATTMETA); |
---|
| 947 | } |
---|
| 948 | else if (att->xtype == NC_STRING) |
---|
| 949 | { |
---|
| 950 | if (!(att->stdata = calloc(att->len, sizeof(char *)))) |
---|
| 951 | BAIL(NC_ENOMEM); |
---|
| 952 | /* For a fixed length HDF5 string, the read requires |
---|
| 953 | * contiguous memory. Meanwhile, the netCDF API requires that |
---|
| 954 | * nc_free_string be called on string arrays, which would not |
---|
| 955 | * work if one contiguous memory block were used. So here I |
---|
| 956 | * convert the contiguous block of strings into an array of |
---|
| 957 | * malloced strings (each string with its own malloc). Then I |
---|
| 958 | * copy the data and free the contiguous memory. This |
---|
| 959 | * involves copying the data, which is bad, but this only |
---|
| 960 | * occurs for fixed length string attributes, and presumably |
---|
| 961 | * these are small. (And netCDF-4 does not create them - it |
---|
| 962 | * always uses variable length strings. */ |
---|
| 963 | if (fixed_len_string) |
---|
| 964 | { |
---|
| 965 | int i; |
---|
| 966 | char *contig_buf, *cur; |
---|
| 967 | |
---|
| 968 | /* Alloc space for the contiguous memory read. */ |
---|
| 969 | if (!(contig_buf = malloc(att->len * fixed_size * sizeof(char)))) |
---|
| 970 | BAIL(NC_ENOMEM); |
---|
| 971 | |
---|
| 972 | /* Read the fixed-len strings as one big block. */ |
---|
| 973 | if (H5Aread(attid, att->native_typeid, contig_buf) < 0) |
---|
| 974 | BAIL(NC_EATTMETA); |
---|
| 975 | |
---|
| 976 | /* Copy strings, one at a time, into their new home. Alloc |
---|
| 977 | space for each string. The user will later free this |
---|
| 978 | space with nc_free_string. */ |
---|
| 979 | cur = contig_buf; |
---|
| 980 | for (i = 0; i < att->len; i++) |
---|
| 981 | { |
---|
| 982 | if (!(att->stdata[i] = malloc(fixed_size))) |
---|
| 983 | BAIL(NC_ENOMEM); |
---|
| 984 | strncpy(att->stdata[i], cur, fixed_size); |
---|
| 985 | cur += fixed_size; |
---|
| 986 | } |
---|
| 987 | |
---|
| 988 | /* Free contiguous memory buffer. */ |
---|
| 989 | free(contig_buf); |
---|
| 990 | } |
---|
| 991 | else |
---|
| 992 | { |
---|
| 993 | /* Read variable-length string atts. */ |
---|
| 994 | if (H5Aread(attid, att->native_typeid, att->stdata) < 0) |
---|
| 995 | BAIL(NC_EATTMETA); |
---|
| 996 | } |
---|
| 997 | } |
---|
| 998 | else |
---|
| 999 | { |
---|
| 1000 | if (!(att->data = malloc((unsigned int)(att->len * type_size)))) |
---|
| 1001 | BAIL(NC_ENOMEM); |
---|
| 1002 | if (H5Aread(attid, att->native_typeid, att->data) < 0) |
---|
| 1003 | BAIL(NC_EATTMETA); |
---|
| 1004 | } |
---|
| 1005 | } |
---|
| 1006 | |
---|
| 1007 | if (H5Tclose(file_typeid) < 0) |
---|
| 1008 | BAIL(NC_EHDFERR); |
---|
| 1009 | if (H5Sclose(spaceid) < 0) |
---|
| 1010 | return NC_EHDFERR; |
---|
| 1011 | #ifdef EXTRA_TESTS |
---|
| 1012 | num_spaces--; |
---|
| 1013 | #endif |
---|
| 1014 | |
---|
| 1015 | return NC_NOERR; |
---|
| 1016 | |
---|
| 1017 | exit: |
---|
| 1018 | if (H5Tclose(file_typeid) < 0) |
---|
| 1019 | BAIL2(NC_EHDFERR); |
---|
| 1020 | if (spaceid > 0 && H5Sclose(spaceid) < 0) |
---|
| 1021 | BAIL2(NC_EHDFERR); |
---|
| 1022 | #ifdef EXTRA_TESTS |
---|
| 1023 | num_spaces--; |
---|
| 1024 | #endif |
---|
| 1025 | return retval; |
---|
| 1026 | } |
---|
| 1027 | |
---|
| 1028 | /* Read information about a user defined type from the HDF5 file, and |
---|
| 1029 | * stash it in the group's list of types. Return the netcdf typeid |
---|
| 1030 | * through a pointer, if caller desires it. */ |
---|
| 1031 | static int |
---|
| 1032 | read_type(NC_GRP_INFO_T *grp, char *type_name) |
---|
| 1033 | { |
---|
| 1034 | NC_TYPE_INFO_T *type; |
---|
| 1035 | H5T_class_t class; |
---|
| 1036 | hid_t hdf_typeid, native_typeid = 0; |
---|
| 1037 | int nmembers; |
---|
| 1038 | hid_t member_hdf_typeid, base_hdf_typeid = 0; |
---|
| 1039 | char *member_name = NULL; |
---|
| 1040 | size_t type_size = 0, member_offset; |
---|
| 1041 | unsigned int m; |
---|
| 1042 | nc_type ud_type_type = NC_NAT, base_nc_type = NC_NAT, member_xtype; |
---|
| 1043 | htri_t ret; |
---|
| 1044 | int retval = NC_NOERR; |
---|
| 1045 | void *value; |
---|
| 1046 | int i; |
---|
| 1047 | |
---|
| 1048 | assert(grp && type_name); |
---|
| 1049 | |
---|
| 1050 | if (strlen(type_name) > NC_MAX_NAME) |
---|
| 1051 | return NC_EBADNAME; |
---|
| 1052 | |
---|
| 1053 | LOG((4, "read_type: type_name %s grp->name %s", type_name, grp->name)); |
---|
| 1054 | |
---|
| 1055 | if ((hdf_typeid = H5Topen2(grp->hdf_grpid, type_name, H5P_DEFAULT)) < 0) |
---|
| 1056 | return NC_EHDFERR; |
---|
| 1057 | |
---|
| 1058 | /* What is the native type for this platform? */ |
---|
| 1059 | if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0) |
---|
| 1060 | return NC_EHDFERR; |
---|
| 1061 | |
---|
| 1062 | /* What is the size of this type on this platform. */ |
---|
| 1063 | if (!(type_size = H5Tget_size(native_typeid))) |
---|
| 1064 | return NC_EHDFERR; |
---|
| 1065 | LOG((5, "type_size %d", type_size)); |
---|
| 1066 | |
---|
| 1067 | /* What is the class of this type, compound, vlen, etc. */ |
---|
| 1068 | if ((class = H5Tget_class(hdf_typeid)) < 0) |
---|
| 1069 | return NC_EHDFERR; |
---|
| 1070 | switch (class) |
---|
| 1071 | { |
---|
| 1072 | case H5T_STRING: |
---|
| 1073 | ud_type_type = NC_STRING; |
---|
| 1074 | break; |
---|
| 1075 | case H5T_COMPOUND: |
---|
| 1076 | ud_type_type = NC_COMPOUND; |
---|
| 1077 | break; |
---|
| 1078 | case H5T_VLEN: |
---|
| 1079 | /* For conveninence we allow user to pass vlens of strings |
---|
| 1080 | * with null terminated strings. This means strings are |
---|
| 1081 | * treated slightly differently by the API, although they are |
---|
| 1082 | * really just VLENs of characters. */ |
---|
| 1083 | if ((ret = H5Tis_variable_str(hdf_typeid)) < 0) |
---|
| 1084 | return NC_EHDFERR; |
---|
| 1085 | if (ret) |
---|
| 1086 | ud_type_type = NC_STRING; |
---|
| 1087 | else |
---|
| 1088 | { |
---|
| 1089 | ud_type_type = NC_VLEN; |
---|
| 1090 | |
---|
| 1091 | /* Find the base type of this vlen (i.e. what is this a |
---|
| 1092 | * vlen of?) */ |
---|
| 1093 | if (!(base_hdf_typeid = H5Tget_super(native_typeid))) |
---|
| 1094 | return NC_EHDFERR; |
---|
| 1095 | |
---|
| 1096 | /* What size is this type? */ |
---|
| 1097 | if (!(type_size = H5Tget_size(base_hdf_typeid))) |
---|
| 1098 | return NC_EHDFERR; |
---|
| 1099 | |
---|
| 1100 | /* What is the netcdf corresponding type. */ |
---|
| 1101 | if ((retval = get_netcdf_type(grp->file->nc4_info, base_hdf_typeid, |
---|
| 1102 | &base_nc_type))) |
---|
| 1103 | return retval; |
---|
| 1104 | LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d", |
---|
| 1105 | base_hdf_typeid, type_size, base_nc_type)); |
---|
| 1106 | } |
---|
| 1107 | break; |
---|
| 1108 | case H5T_OPAQUE: |
---|
| 1109 | ud_type_type = NC_OPAQUE; |
---|
| 1110 | /* What size is this type? */ |
---|
| 1111 | if (!(type_size = H5Tget_size(hdf_typeid))) |
---|
| 1112 | return NC_EHDFERR; |
---|
| 1113 | LOG((5, "type_size %d", type_size)); |
---|
| 1114 | break; |
---|
| 1115 | case H5T_ENUM: |
---|
| 1116 | ud_type_type = NC_ENUM; |
---|
| 1117 | |
---|
| 1118 | /* Find the base type of this enum (i.e. what is this a |
---|
| 1119 | * enum of?) */ |
---|
| 1120 | if (!(base_hdf_typeid = H5Tget_super(hdf_typeid))) |
---|
| 1121 | return NC_EHDFERR; |
---|
| 1122 | /* What size is this type? */ |
---|
| 1123 | if (!(type_size = H5Tget_size(base_hdf_typeid))) |
---|
| 1124 | return NC_EHDFERR; |
---|
| 1125 | /* What is the netcdf corresponding type. */ |
---|
| 1126 | if ((retval = get_netcdf_type(grp->file->nc4_info, base_hdf_typeid, |
---|
| 1127 | &base_nc_type))) |
---|
| 1128 | return retval; |
---|
| 1129 | LOG((5, "base_hdf_typeid 0x%x type_size %d base_nc_type %d", |
---|
| 1130 | base_hdf_typeid, type_size, base_nc_type)); |
---|
| 1131 | break; |
---|
| 1132 | default: |
---|
| 1133 | LOG((0, "unknown class")); |
---|
| 1134 | return NC_EBADCLASS; |
---|
| 1135 | } |
---|
| 1136 | |
---|
| 1137 | /* Add to the list for this new type, and get a local pointer to it. */ |
---|
| 1138 | if ((retval = nc4_type_list_add(&grp->type, &type))) |
---|
| 1139 | return retval; |
---|
| 1140 | assert(type); |
---|
| 1141 | |
---|
| 1142 | /* Remember info about this type. */ |
---|
| 1143 | type->nc_typeid = grp->file->nc4_info->next_typeid++; |
---|
| 1144 | type->size = type_size; |
---|
| 1145 | if (!(type->name = malloc((strlen(type_name) + 1) * sizeof(char)))) |
---|
| 1146 | return NC_ENOMEM; |
---|
| 1147 | strcpy(type->name, type_name); |
---|
| 1148 | type->class = ud_type_type; |
---|
| 1149 | type->base_nc_type = base_nc_type; |
---|
| 1150 | type->committed++; |
---|
| 1151 | type->hdf_typeid = hdf_typeid; |
---|
| 1152 | type->native_typeid = native_typeid; |
---|
| 1153 | |
---|
| 1154 | /* Read info about each member of this compound type. */ |
---|
| 1155 | if (ud_type_type == NC_COMPOUND) |
---|
| 1156 | { |
---|
| 1157 | if ((nmembers = H5Tget_nmembers(hdf_typeid)) < 0) |
---|
| 1158 | return NC_EHDFERR; |
---|
| 1159 | LOG((5, "compound type has %d members", nmembers)); |
---|
| 1160 | for (m = 0; m < nmembers; m++) |
---|
| 1161 | { |
---|
| 1162 | H5T_class_t mem_class; |
---|
| 1163 | hid_t member_native_typeid; |
---|
| 1164 | int ndims = 0, dim_size[NC_MAX_VAR_DIMS]; |
---|
| 1165 | hsize_t dims[NC_MAX_VAR_DIMS]; |
---|
| 1166 | int d; |
---|
| 1167 | |
---|
| 1168 | /* Get the typeid and native typeid of this member of the |
---|
| 1169 | * compound type. */ |
---|
| 1170 | if ((member_hdf_typeid = H5Tget_member_type(type->native_typeid, m)) < 0) |
---|
| 1171 | return NC_EHDFERR; |
---|
| 1172 | if ((member_native_typeid = H5Tget_native_type(member_hdf_typeid, H5T_DIR_DEFAULT)) < 0) |
---|
| 1173 | return NC_EHDFERR; |
---|
| 1174 | |
---|
| 1175 | /* Get the name of the member.*/ |
---|
| 1176 | member_name = H5Tget_member_name(type->native_typeid, m); |
---|
| 1177 | if (!member_name || strlen(member_name) > NC_MAX_NAME) |
---|
| 1178 | return NC_EBADNAME; |
---|
| 1179 | |
---|
| 1180 | /* Offset in bytes on *this* platform. */ |
---|
| 1181 | member_offset = H5Tget_member_offset(type->native_typeid, m); |
---|
| 1182 | |
---|
| 1183 | /* Get dimensional data if this member is an array of something. */ |
---|
| 1184 | if ((mem_class = H5Tget_class(member_hdf_typeid)) < 0) |
---|
| 1185 | return NC_EHDFERR; |
---|
| 1186 | if (mem_class == H5T_ARRAY) |
---|
| 1187 | { |
---|
| 1188 | if ((ndims = H5Tget_array_ndims(member_hdf_typeid)) < 0) |
---|
| 1189 | return NC_EHDFERR; |
---|
| 1190 | if (H5Tget_array_dims(member_hdf_typeid, dims, NULL) != ndims) |
---|
| 1191 | return NC_EHDFERR; |
---|
| 1192 | for (d = 0; d < ndims; d++) |
---|
| 1193 | dim_size[d] = dims[d]; |
---|
| 1194 | /* What is the netCDF typeid of this member? */ |
---|
| 1195 | if ((retval = get_netcdf_type(grp->file->nc4_info, H5Tget_super(member_hdf_typeid), |
---|
| 1196 | &member_xtype))) |
---|
| 1197 | return retval; |
---|
| 1198 | } |
---|
| 1199 | else |
---|
| 1200 | { |
---|
| 1201 | /* What is the netCDF typeid of this member? */ |
---|
| 1202 | if ((retval = get_netcdf_type(grp->file->nc4_info, member_native_typeid, |
---|
| 1203 | &member_xtype))) |
---|
| 1204 | return retval; |
---|
| 1205 | } |
---|
| 1206 | |
---|
| 1207 | /* Add this member to our list of fields in this compound type. */ |
---|
| 1208 | if (ndims) |
---|
| 1209 | { |
---|
| 1210 | if ((retval = nc4_field_list_add(&type->field, type->num_fields++, member_name, |
---|
| 1211 | member_offset, H5Tget_super(member_hdf_typeid), |
---|
| 1212 | H5Tget_super(member_native_typeid), |
---|
| 1213 | member_xtype, ndims, dim_size))) |
---|
| 1214 | return retval; |
---|
| 1215 | } |
---|
| 1216 | else |
---|
| 1217 | { |
---|
| 1218 | if ((retval = nc4_field_list_add(&type->field, type->num_fields++, member_name, |
---|
| 1219 | member_offset, member_hdf_typeid, member_native_typeid, |
---|
| 1220 | member_xtype, 0, NULL))) |
---|
| 1221 | return retval; |
---|
| 1222 | } |
---|
| 1223 | |
---|
| 1224 | /* HDF5 allocated this for us. */ |
---|
| 1225 | free(member_name); |
---|
| 1226 | } |
---|
| 1227 | } |
---|
| 1228 | else if (ud_type_type == NC_VLEN) |
---|
| 1229 | { |
---|
| 1230 | type->base_hdf_typeid = base_hdf_typeid; |
---|
| 1231 | } |
---|
| 1232 | else if (ud_type_type == NC_ENUM) |
---|
| 1233 | { |
---|
| 1234 | /* Remember the base HDF5 type for this enum. */ |
---|
| 1235 | type->base_hdf_typeid = base_hdf_typeid; |
---|
| 1236 | |
---|
| 1237 | /* Find out how many member are in the enum. */ |
---|
| 1238 | if ((type->num_enum_members = H5Tget_nmembers(hdf_typeid)) < 0) |
---|
| 1239 | return NC_EHDFERR; |
---|
| 1240 | |
---|
| 1241 | /* Allocate space for one value. */ |
---|
| 1242 | if (!(value = calloc(1, type_size))) |
---|
| 1243 | return NC_ENOMEM; |
---|
| 1244 | |
---|
| 1245 | /* Read each name and value defined in the enum. */ |
---|
| 1246 | for (i = 0; i < type->num_enum_members; i++) |
---|
| 1247 | { |
---|
| 1248 | /* Get the name and value from HDF5. */ |
---|
| 1249 | if (!(member_name = H5Tget_member_name(hdf_typeid, i))) |
---|
| 1250 | return NC_EHDFERR; |
---|
| 1251 | if (!member_name || strlen(member_name) > NC_MAX_NAME) |
---|
| 1252 | return NC_EBADNAME; |
---|
| 1253 | if (H5Tget_member_value(hdf_typeid, i, value) < 0) |
---|
| 1254 | return NC_EHDFERR; |
---|
| 1255 | |
---|
| 1256 | /* Insert new field into this type's list of fields. */ |
---|
| 1257 | if ((retval = nc4_enum_member_add(&type->enum_member, type->size, |
---|
| 1258 | member_name, value))) |
---|
| 1259 | return retval; |
---|
| 1260 | free(member_name); |
---|
| 1261 | } |
---|
| 1262 | |
---|
| 1263 | /* Free the tempory memory for one value, and the member name |
---|
| 1264 | * (which HDF5 allocated for us). */ |
---|
| 1265 | free(value); |
---|
| 1266 | } |
---|
| 1267 | |
---|
| 1268 | return retval; |
---|
| 1269 | } |
---|
| 1270 | |
---|
| 1271 | /* This function is called by read_dataset, (which is called by |
---|
| 1272 | * nc4_rec_read_metadata) when a netCDF variable is found in the |
---|
| 1273 | * file. This function reads in all the metadata about the var, |
---|
| 1274 | * including the attributes. */ |
---|
| 1275 | static int |
---|
| 1276 | read_var(NC_GRP_INFO_T *grp, hid_t datasetid, char *obj_name, |
---|
| 1277 | size_t ndims, int is_scale, int num_scales, hid_t access_pid) |
---|
| 1278 | { |
---|
| 1279 | NC_VAR_INFO_T *var; |
---|
| 1280 | int natts, a, d; |
---|
| 1281 | |
---|
| 1282 | NC_ATT_INFO_T *att; |
---|
| 1283 | hid_t attid = 0; |
---|
| 1284 | char att_name[NC_MAX_HDF5_NAME + 1]; |
---|
| 1285 | |
---|
| 1286 | #define CD_NELEMS_ZLIB 1 |
---|
| 1287 | #define CD_NELEMS_SZIP 4 |
---|
| 1288 | H5Z_filter_t filter; |
---|
| 1289 | int num_filters; |
---|
| 1290 | unsigned int cd_values[CD_NELEMS_SZIP]; |
---|
| 1291 | size_t cd_nelems = CD_NELEMS_SZIP; |
---|
| 1292 | hid_t propid = 0; |
---|
| 1293 | H5D_fill_value_t fill_status; |
---|
| 1294 | H5D_layout_t layout; |
---|
| 1295 | hsize_t chunksize[NC_MAX_VAR_DIMS]; |
---|
| 1296 | int retval = NC_NOERR; |
---|
| 1297 | double rdcc_w0; |
---|
| 1298 | int f; |
---|
| 1299 | |
---|
| 1300 | assert(obj_name && grp); |
---|
| 1301 | LOG((4, "read_var: obj_name %s", obj_name)); |
---|
| 1302 | |
---|
| 1303 | /* Add a variable to the end of the group's var list. */ |
---|
| 1304 | if ((retval = nc4_var_list_add(&grp->var, &var))) |
---|
| 1305 | return retval; |
---|
| 1306 | |
---|
| 1307 | /* Fill in what we already know. */ |
---|
| 1308 | var->hdf_datasetid = datasetid; |
---|
| 1309 | var->varid = grp->nvars++; |
---|
| 1310 | var->created++; |
---|
| 1311 | var->ndims = ndims; |
---|
| 1312 | |
---|
| 1313 | /* We need some room to store information about dimensions for this |
---|
| 1314 | * var. */ |
---|
| 1315 | if (var->ndims) |
---|
| 1316 | { |
---|
| 1317 | if (!(var->dim = calloc(var->ndims, sizeof(NC_DIM_INFO_T *)))) |
---|
| 1318 | return NC_ENOMEM; |
---|
| 1319 | if (!(var->dimids = calloc(var->ndims, sizeof(int)))) |
---|
| 1320 | return NC_ENOMEM; |
---|
| 1321 | } |
---|
| 1322 | |
---|
| 1323 | /* Learn about current chunk cache settings. */ |
---|
| 1324 | if ((H5Pget_chunk_cache(access_pid, &(var->chunk_cache_nelems), |
---|
| 1325 | &(var->chunk_cache_size), &rdcc_w0)) < 0) |
---|
| 1326 | return NC_EHDFERR; |
---|
| 1327 | var->chunk_cache_preemption = rdcc_w0; |
---|
| 1328 | |
---|
| 1329 | /* Allocate space for the name. */ |
---|
| 1330 | if (!(var->name = malloc((strlen(obj_name) + 1) * sizeof(char)))) |
---|
| 1331 | return NC_ENOMEM; |
---|
| 1332 | |
---|
| 1333 | /* Check for a weird case: a non-coordinate (and non-scalar) |
---|
| 1334 | * variable that has the same name as a dimension. It's legal in |
---|
| 1335 | * netcdf, and requires that the HDF5 dataset name be changed. */ |
---|
| 1336 | if (var->ndims && |
---|
| 1337 | !strncmp(obj_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND))) |
---|
| 1338 | { |
---|
| 1339 | if (strlen(obj_name) > NC_MAX_NAME) |
---|
| 1340 | return NC_EMAXNAME; |
---|
| 1341 | strcpy(var->name, &obj_name[strlen(NON_COORD_PREPEND)]); |
---|
| 1342 | } |
---|
| 1343 | else |
---|
| 1344 | strcpy(var->name, obj_name); |
---|
| 1345 | |
---|
| 1346 | /* Find out what filters are applied to this HDF5 dataset, |
---|
| 1347 | * fletcher32, deflate, and/or shuffle. All other filters are |
---|
| 1348 | * ignored. */ |
---|
| 1349 | if ((propid = H5Dget_create_plist(datasetid)) < 0) |
---|
| 1350 | BAIL(NC_EHDFERR); |
---|
| 1351 | #ifdef EXTRA_TESTS |
---|
| 1352 | num_plists++; |
---|
| 1353 | #endif /* EXTRA_TESTS */ |
---|
| 1354 | |
---|
| 1355 | /* Get the chunking info for non-scalar vars. */ |
---|
| 1356 | if ((layout = H5Pget_layout(propid)) < -1) |
---|
| 1357 | BAIL(NC_EHDFERR); |
---|
| 1358 | if (layout == H5D_CHUNKED) |
---|
| 1359 | { |
---|
| 1360 | if (H5Pget_chunk(propid, NC_MAX_VAR_DIMS, chunksize) < 0) |
---|
| 1361 | BAIL(NC_EHDFERR); |
---|
| 1362 | if (!(var->chunksizes = malloc(var->ndims * sizeof(size_t)))) |
---|
| 1363 | BAIL(NC_ENOMEM); |
---|
| 1364 | for (d = 0; d < var->ndims; d++) |
---|
| 1365 | var->chunksizes[d] = chunksize[d]; |
---|
| 1366 | } |
---|
| 1367 | else if (layout == H5D_CONTIGUOUS) |
---|
| 1368 | var->contiguous++; |
---|
| 1369 | |
---|
| 1370 | /* The possible values of filter (which is just an int) can be |
---|
| 1371 | * found in H5Zpublic.h. */ |
---|
| 1372 | if ((num_filters = H5Pget_nfilters(propid)) < 0) |
---|
| 1373 | BAIL(NC_EHDFERR); |
---|
| 1374 | for (f = 0; f < num_filters; f++) |
---|
| 1375 | { |
---|
| 1376 | if ((filter = H5Pget_filter2(propid, f, NULL, &cd_nelems, |
---|
| 1377 | cd_values, 0, NULL, NULL)) < 0) |
---|
| 1378 | BAIL(NC_EHDFERR); |
---|
| 1379 | switch (filter) |
---|
| 1380 | { |
---|
| 1381 | case H5Z_FILTER_SHUFFLE: |
---|
| 1382 | var->shuffle = 1; |
---|
| 1383 | break; |
---|
| 1384 | case H5Z_FILTER_FLETCHER32: |
---|
| 1385 | var->fletcher32 = 1; |
---|
| 1386 | break; |
---|
| 1387 | case H5Z_FILTER_DEFLATE: |
---|
| 1388 | var->deflate++; |
---|
| 1389 | if (cd_nelems != CD_NELEMS_ZLIB || |
---|
| 1390 | cd_values[0] > MAX_DEFLATE_LEVEL) |
---|
| 1391 | BAIL(NC_EHDFERR); |
---|
| 1392 | var->deflate_level = cd_values[0]; |
---|
| 1393 | break; |
---|
| 1394 | case H5Z_FILTER_SZIP: |
---|
| 1395 | var->deflate++; |
---|
| 1396 | if (cd_nelems != CD_NELEMS_SZIP) |
---|
| 1397 | BAIL(NC_EHDFERR); |
---|
| 1398 | var->options_mask = cd_values[0]; |
---|
| 1399 | var->pixels_per_block = cd_values[1]; |
---|
| 1400 | break; |
---|
| 1401 | default: |
---|
| 1402 | LOG((1, "Yikes! Unknown filter type found on dataset!")); |
---|
| 1403 | break; |
---|
| 1404 | } |
---|
| 1405 | } |
---|
| 1406 | |
---|
| 1407 | /* Learn all about the type of this variable. */ |
---|
| 1408 | if ((retval = get_type_info2(grp->file->nc4_info, datasetid, |
---|
| 1409 | &var->xtype, &var->type_info))) |
---|
| 1410 | BAIL(retval); |
---|
| 1411 | |
---|
| 1412 | /* Is there a fill value associated with this dataset? */ |
---|
| 1413 | if (H5Pfill_value_defined(propid, &fill_status) < 0) |
---|
| 1414 | BAIL(NC_EHDFERR); |
---|
| 1415 | |
---|
| 1416 | /* Get the fill value, if there is one defined. */ |
---|
| 1417 | if (fill_status == H5D_FILL_VALUE_USER_DEFINED) |
---|
| 1418 | { |
---|
| 1419 | /* Allocate space to hold the fill value. */ |
---|
| 1420 | if (!var->fill_value) |
---|
| 1421 | { |
---|
| 1422 | if (var->type_info->class == NC_VLEN) |
---|
| 1423 | { |
---|
| 1424 | if (!(var->fill_value = malloc(sizeof(nc_vlen_t)))) |
---|
| 1425 | BAIL(NC_ENOMEM); |
---|
| 1426 | } |
---|
| 1427 | else if (var->type_info->size) |
---|
| 1428 | { |
---|
| 1429 | if (!(var->fill_value = malloc(var->type_info->size))) |
---|
| 1430 | BAIL(NC_ENOMEM); |
---|
| 1431 | } |
---|
| 1432 | else |
---|
| 1433 | { |
---|
| 1434 | if (!(var->fill_value = malloc(sizeof(char *)))) |
---|
| 1435 | BAIL(NC_ENOMEM); |
---|
| 1436 | } |
---|
| 1437 | } |
---|
| 1438 | |
---|
| 1439 | /* Get the fill value from the HDF5 property lust. */ |
---|
| 1440 | if (H5Pget_fill_value(propid, var->type_info->native_typeid, |
---|
| 1441 | var->fill_value) < 0) |
---|
| 1442 | BAIL(NC_EHDFERR); |
---|
| 1443 | } |
---|
| 1444 | else |
---|
| 1445 | var->no_fill = 1; |
---|
| 1446 | |
---|
| 1447 | /* If it's a scale, mark it as such. If not, allocate space to |
---|
| 1448 | * remember whether the dimscale has been attached for each |
---|
| 1449 | * dimension. */ |
---|
| 1450 | if (is_scale) |
---|
| 1451 | { |
---|
| 1452 | assert(ndims); |
---|
| 1453 | var->dimscale++; |
---|
| 1454 | if (var->ndims > 1) |
---|
| 1455 | { |
---|
| 1456 | if ((retval = read_coord_dimids(var))) |
---|
| 1457 | BAIL(retval); |
---|
| 1458 | } |
---|
| 1459 | else |
---|
| 1460 | { |
---|
| 1461 | var->dimids[0] = grp->dim->dimid; |
---|
| 1462 | var->dim[0] = grp->dim; |
---|
| 1463 | } |
---|
| 1464 | } |
---|
| 1465 | else |
---|
| 1466 | if (num_scales && ndims && |
---|
| 1467 | !(var->dimscale_attached = calloc(ndims, sizeof(int)))) |
---|
| 1468 | BAIL(NC_ENOMEM); |
---|
| 1469 | |
---|
| 1470 | /* If this is not a scale, and has scales, iterate |
---|
| 1471 | * through them. (i.e. this is a variable that is not a |
---|
| 1472 | * coordinate variable) */ |
---|
| 1473 | if (!is_scale && num_scales) |
---|
| 1474 | { |
---|
| 1475 | /* Store id information allowing us to match hdf5 |
---|
| 1476 | * dimscales to netcdf dimensions. */ |
---|
| 1477 | if (!(var->dimscale_hdf5_objids = malloc(ndims * sizeof(struct hdf5_objid)))) |
---|
| 1478 | BAIL(NC_ENOMEM); |
---|
| 1479 | for (d = 0; d < var->ndims; d++) |
---|
| 1480 | { |
---|
| 1481 | LOG((5, "read_var: about to iterate over scales for dim %d", d)); |
---|
| 1482 | if (H5DSiterate_scales(var->hdf_datasetid, d, NULL, dimscale_visitor, |
---|
| 1483 | &(var->dimscale_hdf5_objids[d])) < 0) |
---|
| 1484 | BAIL(NC_EHDFERR); |
---|
| 1485 | /* LOG((5, "read_var: collected scale info for dim %d " |
---|
| 1486 | "var %s fileno[0] %d objno[0] %d fileno[1] %d objno[1] %d", |
---|
| 1487 | d, var->name, var->dimscale_hdf5_objids[d].fileno[0], |
---|
| 1488 | var->dimscale_hdf5_objids[d].objno[0], |
---|
| 1489 | var->dimscale_hdf5_objids[d].fileno[1], |
---|
| 1490 | var->dimscale_hdf5_objids[d].objno[1]));*/ |
---|
| 1491 | var->dimscale_attached[d]++; |
---|
| 1492 | } |
---|
| 1493 | } |
---|
| 1494 | |
---|
| 1495 | /* Now read all the attributes of this variable, ignoring the |
---|
| 1496 | ones that hold HDF5 dimension scale information. */ |
---|
| 1497 | if ((natts = H5Aget_num_attrs(var->hdf_datasetid)) < 0) |
---|
| 1498 | BAIL(NC_EATTMETA); |
---|
| 1499 | for (a = 0; a < natts; a++) |
---|
| 1500 | { |
---|
| 1501 | /* Close the attribute and try to move on with our |
---|
| 1502 | * lives. Like bits through the network port, so |
---|
| 1503 | * flows the Days of Our Lives! */ |
---|
| 1504 | if (attid && H5Aclose(attid) < 0) |
---|
| 1505 | BAIL(NC_EHDFERR); |
---|
| 1506 | |
---|
| 1507 | /* Open the att and get its name. */ |
---|
| 1508 | if ((attid = H5Aopen_idx(var->hdf_datasetid, (unsigned int)a)) < 0) |
---|
| 1509 | BAIL(NC_EATTMETA); |
---|
| 1510 | if (H5Aget_name(attid, NC_MAX_HDF5_NAME, att_name) < 0) |
---|
| 1511 | BAIL(NC_EATTMETA); |
---|
| 1512 | LOG((4, "read_var: a %d att_name %s", a, att_name)); |
---|
| 1513 | |
---|
| 1514 | /* Should we ignore this attribute? */ |
---|
| 1515 | if (strcmp(att_name, REFERENCE_LIST) && |
---|
| 1516 | strcmp(att_name, CLASS) && |
---|
| 1517 | strcmp(att_name, DIMENSION_LIST) && |
---|
| 1518 | strcmp(att_name, NAME) && |
---|
| 1519 | strcmp(att_name, COORDINATES)) |
---|
| 1520 | { |
---|
| 1521 | /* Is this the hidden attribute that holds the netCDF |
---|
| 1522 | * dimension id for a coordinate variable? */ |
---|
| 1523 | if (!strcmp(att_name, NC_DIMID_ATT_NAME)) |
---|
| 1524 | { |
---|
| 1525 | |
---|
| 1526 | } |
---|
| 1527 | else |
---|
| 1528 | { |
---|
| 1529 | /* Add to the end of the list of atts for this var. */ |
---|
| 1530 | if ((retval = nc4_att_list_add(&var->att))) |
---|
| 1531 | BAIL(retval); |
---|
| 1532 | for (att = var->att; att->next; att = att->next) |
---|
| 1533 | ; |
---|
| 1534 | |
---|
| 1535 | /* Fill in the information we know. */ |
---|
| 1536 | att->attnum = var->natts++; |
---|
| 1537 | if (!(att->name = malloc((strlen(att_name) + 1) * sizeof(char)))) |
---|
| 1538 | BAIL(NC_ENOMEM); |
---|
| 1539 | strcpy(att->name, att_name); |
---|
| 1540 | |
---|
| 1541 | /* Read the rest of the info about the att, |
---|
| 1542 | * including its values. */ |
---|
| 1543 | if ((retval = read_hdf5_att(grp, attid, att))) |
---|
| 1544 | BAIL(retval); |
---|
| 1545 | |
---|
| 1546 | att->created++; |
---|
| 1547 | } /* endif not HDF5 att */ |
---|
| 1548 | } |
---|
| 1549 | } /* next attribute */ |
---|
| 1550 | |
---|
| 1551 | /* Is this a deflated variable with a chunksize greater than the |
---|
| 1552 | * current cache size? */ |
---|
| 1553 | if ((retval = nc4_adjust_var_cache(grp, var))) |
---|
| 1554 | BAIL(retval); |
---|
| 1555 | |
---|
| 1556 | exit: |
---|
| 1557 | if (propid > 0 && H5Pclose(propid) < 0) |
---|
| 1558 | BAIL2(NC_EHDFERR); |
---|
| 1559 | #ifdef EXTRA_TESTS |
---|
| 1560 | num_plists--; |
---|
| 1561 | #endif |
---|
| 1562 | if (attid > 0 && H5Aclose(attid) < 0) |
---|
| 1563 | BAIL2(NC_EHDFERR); |
---|
| 1564 | return retval; |
---|
| 1565 | } |
---|
| 1566 | |
---|
| 1567 | /* This function is called by nc4_rec_read_metadata to read all the |
---|
| 1568 | * group level attributes (the NC_GLOBAL atts for this group). */ |
---|
| 1569 | static int |
---|
| 1570 | read_grp_atts(NC_GRP_INFO_T *grp) |
---|
| 1571 | { |
---|
| 1572 | hid_t attid = 0; |
---|
| 1573 | hsize_t num_obj, i; |
---|
| 1574 | NC_ATT_INFO_T *att; |
---|
| 1575 | NC_TYPE_INFO_T *type; |
---|
| 1576 | char obj_name[NC_MAX_HDF5_NAME + 1]; |
---|
| 1577 | int max_len; |
---|
| 1578 | int retval = NC_NOERR; |
---|
| 1579 | |
---|
| 1580 | num_obj = H5Aget_num_attrs(grp->hdf_grpid); |
---|
| 1581 | for (i = 0; i < num_obj; i++) |
---|
| 1582 | { |
---|
| 1583 | if (attid > 0) |
---|
| 1584 | H5Aclose(attid); |
---|
| 1585 | if ((attid = H5Aopen_idx(grp->hdf_grpid, (unsigned int)i)) < 0) |
---|
| 1586 | BAIL(NC_EATTMETA); |
---|
| 1587 | if (H5Aget_name(attid, NC_MAX_NAME + 1, obj_name) < 0) |
---|
| 1588 | BAIL(NC_EATTMETA); |
---|
| 1589 | LOG((3, "reading attribute of _netCDF group, named %s", obj_name)); |
---|
| 1590 | |
---|
| 1591 | /* This may be an attribute telling us that strict netcdf-3 |
---|
| 1592 | * rules are in effect. If so, we will make note of the fact, |
---|
| 1593 | * but not add this attribute to the metadata. It's not a user |
---|
| 1594 | * attribute, but an internal netcdf-4 one. */ |
---|
| 1595 | if (!strcmp(obj_name, NC3_STRICT_ATT_NAME)) |
---|
| 1596 | grp->file->nc4_info->cmode |= NC_CLASSIC_MODEL; |
---|
| 1597 | else |
---|
| 1598 | { |
---|
| 1599 | /* Add an att struct at the end of the list, and then go to it. */ |
---|
| 1600 | if ((retval = nc4_att_list_add(&grp->att))) |
---|
| 1601 | BAIL(retval); |
---|
| 1602 | for (att = grp->att; att->next; att = att->next) |
---|
| 1603 | ; |
---|
| 1604 | |
---|
| 1605 | /* Add the info about this attribute. */ |
---|
| 1606 | max_len = strlen(obj_name) > NC_MAX_NAME ? NC_MAX_NAME : strlen(obj_name); |
---|
| 1607 | if (!(att->name = malloc((max_len + 1) * sizeof(char)))) |
---|
| 1608 | BAIL(NC_ENOMEM); |
---|
| 1609 | strncpy(att->name, obj_name, max_len); |
---|
| 1610 | att->name[max_len] = 0; |
---|
| 1611 | att->attnum = grp->natts++; |
---|
| 1612 | if ((retval = read_hdf5_att(grp, attid, att))) |
---|
| 1613 | BAIL(retval); |
---|
| 1614 | att->created++; |
---|
| 1615 | if ((retval = nc4_find_type(grp->file->nc4_info, att->xtype, &type))) |
---|
| 1616 | BAIL(retval); |
---|
| 1617 | if (type) |
---|
| 1618 | att->class = type->class; |
---|
| 1619 | } |
---|
| 1620 | } |
---|
| 1621 | |
---|
| 1622 | exit: |
---|
| 1623 | if (attid > 0 && H5Aclose(attid) < 0) |
---|
| 1624 | BAIL2(NC_EHDFERR); |
---|
| 1625 | return retval; |
---|
| 1626 | } |
---|
| 1627 | |
---|
| 1628 | /* This function is called when nc4_rec_read_vars encounters an HDF5 |
---|
| 1629 | * dataset when reading a file. */ |
---|
| 1630 | static int |
---|
| 1631 | read_dataset(NC_GRP_INFO_T *grp, char *obj_name) |
---|
| 1632 | { |
---|
| 1633 | hid_t datasetid = 0; |
---|
| 1634 | hid_t spaceid = 0, access_pid = 0; |
---|
| 1635 | int ndims; |
---|
| 1636 | hsize_t dims[NC_MAX_DIMS], max_dims[NC_MAX_DIMS]; |
---|
| 1637 | int is_scale = 0; |
---|
| 1638 | int dim_without_var = 0; |
---|
| 1639 | int num_scales = 0; |
---|
| 1640 | int retval = NC_NOERR; |
---|
| 1641 | |
---|
| 1642 | /* Open this dataset. */ |
---|
| 1643 | if ((datasetid = H5Dopen2(grp->hdf_grpid, obj_name, H5P_DEFAULT)) < 0) |
---|
| 1644 | BAIL(NC_EVARMETA); |
---|
| 1645 | |
---|
| 1646 | /* Get the current chunk cache settings. */ |
---|
| 1647 | if ((access_pid = H5Dget_access_plist(datasetid)) < 0) |
---|
| 1648 | BAIL(NC_EVARMETA); |
---|
| 1649 | #ifdef EXTRA_TESTS |
---|
| 1650 | num_plists++; |
---|
| 1651 | #endif |
---|
| 1652 | |
---|
| 1653 | /* Get the dimension information for this dataset. */ |
---|
| 1654 | if ((spaceid = H5Dget_space(datasetid)) < 0) |
---|
| 1655 | BAIL(NC_EHDFERR); |
---|
| 1656 | #ifdef EXTRA_TESTS |
---|
| 1657 | num_spaces++; |
---|
| 1658 | #endif |
---|
| 1659 | if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) |
---|
| 1660 | BAIL(NC_EHDFERR); |
---|
| 1661 | if (ndims > NC_MAX_DIMS) |
---|
| 1662 | BAIL(NC_EMAXDIMS); |
---|
| 1663 | if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0) |
---|
| 1664 | BAIL(NC_EHDFERR); |
---|
| 1665 | |
---|
| 1666 | /* Is this a dimscale? */ |
---|
| 1667 | if ((is_scale = H5DSis_scale(datasetid)) < 0) |
---|
| 1668 | BAIL(NC_EHDFERR); |
---|
| 1669 | if (is_scale) |
---|
| 1670 | { |
---|
| 1671 | /* Read the scale information. */ |
---|
| 1672 | if ((retval = read_scale(grp, datasetid, obj_name, dims[0], |
---|
| 1673 | max_dims[0], &dim_without_var))) |
---|
| 1674 | BAIL(retval); |
---|
| 1675 | } |
---|
| 1676 | else |
---|
| 1677 | { |
---|
| 1678 | /* Find out how many scales are attached to this |
---|
| 1679 | * dataset. H5DSget_num_scales returns an error if there are no |
---|
| 1680 | * scales, so convert a negative return value to zero. */ |
---|
| 1681 | num_scales = H5DSget_num_scales(datasetid, 0); |
---|
| 1682 | if (num_scales < 0) |
---|
| 1683 | num_scales = 0; |
---|
| 1684 | } |
---|
| 1685 | |
---|
| 1686 | /* Add a var to the linked list, and get its metadata, |
---|
| 1687 | * unless this is one of those funny dimscales that are a |
---|
| 1688 | * dimension in netCDF but not a variable. (Spooky!) */ |
---|
| 1689 | if (!dim_without_var) |
---|
| 1690 | if ((retval = read_var(grp, datasetid, obj_name, ndims, |
---|
| 1691 | is_scale, num_scales, access_pid))) |
---|
| 1692 | BAIL(retval); |
---|
| 1693 | |
---|
| 1694 | if (access_pid && H5Pclose(access_pid) < 0) |
---|
| 1695 | BAIL2(retval); |
---|
| 1696 | #ifdef EXTRA_TESTS |
---|
| 1697 | num_plists--; |
---|
| 1698 | #endif |
---|
| 1699 | if (spaceid && H5Sclose(spaceid) < 0) |
---|
| 1700 | BAIL2(retval); |
---|
| 1701 | #ifdef EXTRA_TESTS |
---|
| 1702 | num_spaces--; |
---|
| 1703 | #endif |
---|
| 1704 | return NC_NOERR; |
---|
| 1705 | |
---|
| 1706 | exit: |
---|
| 1707 | if (access_pid && H5Pclose(access_pid) < 0) |
---|
| 1708 | BAIL2(retval); |
---|
| 1709 | #ifdef EXTRA_TESTS |
---|
| 1710 | num_plists--; |
---|
| 1711 | #endif |
---|
| 1712 | if (datasetid && H5Dclose(datasetid) < 0) |
---|
| 1713 | BAIL2(retval); |
---|
| 1714 | if (spaceid && H5Sclose(spaceid) <0) |
---|
| 1715 | BAIL2(retval); |
---|
| 1716 | #ifdef EXTRA_TESTS |
---|
| 1717 | num_spaces--; |
---|
| 1718 | #endif |
---|
| 1719 | return retval; |
---|
| 1720 | } |
---|
| 1721 | |
---|
| 1722 | /* Given index, get the HDF5 name of an object and the class of the |
---|
| 1723 | * object (group, type, dataset, etc.). This function will try to use |
---|
| 1724 | * creation ordering, but if that fails it will use default |
---|
| 1725 | * (i.e. alphabetical) ordering. (This is necessary to read existing |
---|
| 1726 | * HDF5 archives without creation ordering). */ |
---|
| 1727 | /* static int */ |
---|
| 1728 | /* get_name_by_idx(NC_HDF5_FILE_INFO_T *h5, hid_t hdf_grpid, int i, */ |
---|
| 1729 | /* int *obj_class, char *obj_name) */ |
---|
| 1730 | /* { */ |
---|
| 1731 | /* H5O_info_t obj_info; */ |
---|
| 1732 | /* H5_index_t idx_field = H5_INDEX_CRT_ORDER; */ |
---|
| 1733 | /* ssize_t size; */ |
---|
| 1734 | /* herr_t res; */ |
---|
| 1735 | |
---|
| 1736 | /* /\* These HDF5 macros prevent an HDF5 error message when a */ |
---|
| 1737 | /* * non-creation-ordered HDF5 file is opened. *\/ */ |
---|
| 1738 | /* H5E_BEGIN_TRY { */ |
---|
| 1739 | /* res = H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, */ |
---|
| 1740 | /* i, &obj_info, H5P_DEFAULT); */ |
---|
| 1741 | /* } H5E_END_TRY; */ |
---|
| 1742 | |
---|
| 1743 | /* /\* Creation ordering not available, so make sure this file is */ |
---|
| 1744 | /* * opened for read-only access. This is a plain old HDF5 file being */ |
---|
| 1745 | /* * read by netCDF-4. *\/ */ |
---|
| 1746 | /* if (res < 0) */ |
---|
| 1747 | /* { */ |
---|
| 1748 | /* if (H5Oget_info_by_idx(hdf_grpid, ".", H5_INDEX_NAME, H5_ITER_INC, */ |
---|
| 1749 | /* i, &obj_info, H5P_DEFAULT) < 0) */ |
---|
| 1750 | /* return NC_EHDFERR; */ |
---|
| 1751 | /* if (!h5->no_write) */ |
---|
| 1752 | /* return NC_ECANTWRITE; */ |
---|
| 1753 | /* h5->ignore_creationorder = 1; */ |
---|
| 1754 | /* idx_field = H5_INDEX_NAME; */ |
---|
| 1755 | /* } */ |
---|
| 1756 | |
---|
| 1757 | /* *obj_class = obj_info.type; */ |
---|
| 1758 | /* if ((size = H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i, */ |
---|
| 1759 | /* NULL, 0, H5P_DEFAULT)) < 0) */ |
---|
| 1760 | /* return NC_EHDFERR; */ |
---|
| 1761 | /* if (size > NC_MAX_NAME) */ |
---|
| 1762 | /* return NC_EMAXNAME; */ |
---|
| 1763 | /* if (H5Lget_name_by_idx(hdf_grpid, ".", idx_field, H5_ITER_INC, i, */ |
---|
| 1764 | /* obj_name, size+1, H5P_DEFAULT) < 0) */ |
---|
| 1765 | /* return NC_EHDFERR; */ |
---|
| 1766 | |
---|
| 1767 | /* LOG((4, "get_name_by_idx: encountered HDF5 object obj_name %s", obj_name)); */ |
---|
| 1768 | |
---|
| 1769 | /* return NC_NOERR; */ |
---|
| 1770 | /* } */ |
---|
| 1771 | |
---|
| 1772 | #define USE_ITERATE_CODE |
---|
| 1773 | #ifdef USE_ITERATE_CODE |
---|
| 1774 | |
---|
| 1775 | static int |
---|
| 1776 | nc4_rec_read_types_cb(hid_t grpid, const char *name, const H5L_info_t *info, |
---|
| 1777 | void *_op_data) |
---|
| 1778 | { |
---|
| 1779 | hid_t oid=-1; |
---|
| 1780 | H5I_type_t otype=-1; |
---|
| 1781 | char oname[NC_MAX_NAME + 1]; |
---|
| 1782 | NC_GRP_INFO_T *child_grp; |
---|
| 1783 | NC_GRP_INFO_T *grp = (NC_GRP_INFO_T *) (_op_data); |
---|
| 1784 | NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info; |
---|
| 1785 | |
---|
| 1786 | /* Open this critter. */ |
---|
| 1787 | if ((oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0) |
---|
| 1788 | return H5_ITER_ERROR; |
---|
| 1789 | |
---|
| 1790 | if ((otype = H5Iget_type( oid ))<0) { |
---|
| 1791 | H5Oclose(oid); |
---|
| 1792 | return H5_ITER_ERROR; |
---|
| 1793 | } |
---|
| 1794 | H5Oclose(oid); |
---|
| 1795 | |
---|
| 1796 | strncpy(oname, name, NC_MAX_NAME); |
---|
| 1797 | |
---|
| 1798 | /* Deal with groups and types; ignore the rest. */ |
---|
| 1799 | if (otype == H5I_GROUP) |
---|
| 1800 | { |
---|
| 1801 | LOG((3, "found group %s", oname)); |
---|
| 1802 | if (nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++, |
---|
| 1803 | grp, grp->file, oname, &child_grp)) |
---|
| 1804 | return H5_ITER_ERROR; |
---|
| 1805 | |
---|
| 1806 | if (nc4_rec_read_types(child_grp)) |
---|
| 1807 | return H5_ITER_ERROR; |
---|
| 1808 | } |
---|
| 1809 | else if (otype == H5I_DATATYPE) |
---|
| 1810 | { |
---|
| 1811 | LOG((3, "found datatype %s", oname)); |
---|
| 1812 | if (read_type(grp, oname)) |
---|
| 1813 | return H5_ITER_ERROR; |
---|
| 1814 | } |
---|
| 1815 | |
---|
| 1816 | return (H5_ITER_CONT); |
---|
| 1817 | } |
---|
| 1818 | |
---|
| 1819 | static int |
---|
| 1820 | nc4_rec_read_types(NC_GRP_INFO_T *grp) |
---|
| 1821 | { |
---|
| 1822 | hsize_t idx=0; |
---|
| 1823 | int res = 0; |
---|
| 1824 | hid_t pid = 0; |
---|
| 1825 | unsigned crt_order_flags = 0; |
---|
| 1826 | NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info; |
---|
| 1827 | |
---|
| 1828 | assert(grp && grp->name); |
---|
| 1829 | LOG((3, "nc4_rec_read_types: grp->name %s", grp->name)); |
---|
| 1830 | |
---|
| 1831 | /* Open this HDF5 group and retain its grpid. It will remain open |
---|
| 1832 | * with HDF5 until this file is nc_closed. */ |
---|
| 1833 | if (!grp->hdf_grpid) |
---|
| 1834 | { |
---|
| 1835 | if (grp->parent) |
---|
| 1836 | { |
---|
| 1837 | if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid, |
---|
| 1838 | grp->name, H5P_DEFAULT)) < 0) |
---|
| 1839 | return NC_EHDFERR; |
---|
| 1840 | } |
---|
| 1841 | else |
---|
| 1842 | { |
---|
| 1843 | if ((grp->hdf_grpid = H5Gopen2(grp->file->nc4_info->hdfid, |
---|
| 1844 | "/", H5P_DEFAULT)) < 0) |
---|
| 1845 | return NC_EHDFERR; |
---|
| 1846 | } |
---|
| 1847 | } |
---|
| 1848 | assert(grp->hdf_grpid > 0); |
---|
| 1849 | |
---|
| 1850 | pid = H5Gget_create_plist(grp->hdf_grpid); |
---|
| 1851 | H5Pget_link_creation_order(pid, &crt_order_flags); |
---|
| 1852 | H5Pclose(pid); |
---|
| 1853 | |
---|
| 1854 | crt_order_flags = crt_order_flags & H5_INDEX_CRT_ORDER; |
---|
| 1855 | |
---|
| 1856 | if (crt_order_flags == H5_INDEX_CRT_ORDER) |
---|
| 1857 | { |
---|
| 1858 | res = H5Literate(grp->hdf_grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, |
---|
| 1859 | &idx, nc4_rec_read_types_cb, (void *)grp); |
---|
| 1860 | } else |
---|
| 1861 | { |
---|
| 1862 | /* Without creation ordering, file must be read-only. */ |
---|
| 1863 | if (!idx && !h5->no_write) |
---|
| 1864 | return NC_ECANTWRITE; |
---|
| 1865 | |
---|
| 1866 | res = H5Literate(grp->hdf_grpid, H5_INDEX_NAME, H5_ITER_INC, |
---|
| 1867 | &idx, nc4_rec_read_types_cb, (void *)grp); |
---|
| 1868 | } |
---|
| 1869 | if (res<0) |
---|
| 1870 | return NC_EHDFERR; |
---|
| 1871 | return NC_NOERR; /* everything worked! */ |
---|
| 1872 | } |
---|
| 1873 | |
---|
| 1874 | static int |
---|
| 1875 | nc4_rec_read_vars_cb(hid_t grpid, const char *name, const H5L_info_t *info, |
---|
| 1876 | void *_op_data) |
---|
| 1877 | { |
---|
| 1878 | hid_t oid=-1; |
---|
| 1879 | H5I_type_t otype=-1; |
---|
| 1880 | char oname[NC_MAX_NAME + 1]; |
---|
| 1881 | NC_GRP_INFO_T *child_grp; |
---|
| 1882 | NC_GRP_INFO_T *grp = (NC_GRP_INFO_T *) (_op_data); |
---|
| 1883 | #if 0 |
---|
| 1884 | NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info; |
---|
| 1885 | #endif |
---|
| 1886 | |
---|
| 1887 | memset(oname, 0, NC_MAX_NAME); |
---|
| 1888 | /* Open this critter. */ |
---|
| 1889 | if ((oid = H5Oopen(grpid, name, H5P_DEFAULT)) < 0) |
---|
| 1890 | return H5_ITER_ERROR; |
---|
| 1891 | |
---|
| 1892 | if ((otype = H5Iget_type( oid ))<0) { |
---|
| 1893 | H5Oclose(oid); |
---|
| 1894 | return H5_ITER_ERROR; |
---|
| 1895 | } |
---|
| 1896 | H5Oclose(oid); |
---|
| 1897 | |
---|
| 1898 | strncpy(oname, name, NC_MAX_NAME); |
---|
| 1899 | |
---|
| 1900 | /* Deal with datasets. */ |
---|
| 1901 | switch(otype) |
---|
| 1902 | { |
---|
| 1903 | case H5I_GROUP: |
---|
| 1904 | LOG((3, "re-encountering group %s", oname)); |
---|
| 1905 | |
---|
| 1906 | /* The NC_GROUP_INFO_T for this group already exists. Find it. */ |
---|
| 1907 | for (child_grp = grp->children; child_grp; child_grp = child_grp->next) |
---|
| 1908 | if (!strcmp(child_grp->name, oname)) |
---|
| 1909 | break; |
---|
| 1910 | if (!child_grp) |
---|
| 1911 | return H5_ITER_ERROR; |
---|
| 1912 | |
---|
| 1913 | /* Recursively read the child group's vars. */ |
---|
| 1914 | if (nc4_rec_read_vars(child_grp)) |
---|
| 1915 | return H5_ITER_ERROR; |
---|
| 1916 | break; |
---|
| 1917 | case H5I_DATASET: |
---|
| 1918 | LOG((3, "found dataset %s", oname)); |
---|
| 1919 | |
---|
| 1920 | /* Learn all about this dataset, which may be a dimscale |
---|
| 1921 | * (i.e. dimension metadata), or real data. */ |
---|
| 1922 | if (read_dataset(grp, oname)) |
---|
| 1923 | return H5_ITER_ERROR; |
---|
| 1924 | break; |
---|
| 1925 | case H5I_DATATYPE: |
---|
| 1926 | LOG((3, "already handled type %s", oname)); |
---|
| 1927 | break; |
---|
| 1928 | default: |
---|
| 1929 | LOG((0, "Unknown object class %d in nc4_rec_read_vars!", otype)); |
---|
| 1930 | } |
---|
| 1931 | return (H5_ITER_CONT); |
---|
| 1932 | } |
---|
| 1933 | |
---|
| 1934 | static int |
---|
| 1935 | nc4_rec_read_vars(NC_GRP_INFO_T *grp) |
---|
| 1936 | { |
---|
| 1937 | hsize_t idx = 0; |
---|
| 1938 | int retval = NC_NOERR; |
---|
| 1939 | int res = 0; |
---|
| 1940 | hid_t pid = 0; |
---|
| 1941 | unsigned crt_order_flags = 0; |
---|
| 1942 | NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info; |
---|
| 1943 | |
---|
| 1944 | assert(grp && grp->name && grp->hdf_grpid > 0); |
---|
| 1945 | LOG((3, "nc4_rec_read_vars: grp->name %s", grp->name)); |
---|
| 1946 | |
---|
| 1947 | pid = H5Gget_create_plist(grp->hdf_grpid); |
---|
| 1948 | H5Pget_link_creation_order(pid, &crt_order_flags); |
---|
| 1949 | H5Pclose(pid); |
---|
| 1950 | |
---|
| 1951 | crt_order_flags = crt_order_flags & H5_INDEX_CRT_ORDER; |
---|
| 1952 | |
---|
| 1953 | if (crt_order_flags == H5_INDEX_CRT_ORDER) |
---|
| 1954 | { |
---|
| 1955 | res = H5Literate(grp->hdf_grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, |
---|
| 1956 | &idx, nc4_rec_read_vars_cb, (void *)grp); |
---|
| 1957 | } else |
---|
| 1958 | { |
---|
| 1959 | /* Without creation ordering, file must be read-only. */ |
---|
| 1960 | if (!idx && !h5->no_write) |
---|
| 1961 | return NC_ECANTWRITE; |
---|
| 1962 | |
---|
| 1963 | res = H5Literate(grp->hdf_grpid, H5_INDEX_NAME, H5_ITER_INC, |
---|
| 1964 | &idx, nc4_rec_read_vars_cb, (void *)grp); |
---|
| 1965 | } |
---|
| 1966 | if (res<0) |
---|
| 1967 | return NC_EHDFERR; |
---|
| 1968 | |
---|
| 1969 | /* Scan the group for global (i.e. group-level) attributes. */ |
---|
| 1970 | if ((retval = read_grp_atts(grp))) |
---|
| 1971 | return retval; |
---|
| 1972 | |
---|
| 1973 | return NC_NOERR; /* everything worked! */ |
---|
| 1974 | } |
---|
| 1975 | |
---|
| 1976 | #else |
---|
| 1977 | |
---|
| 1978 | /** \internal |
---|
| 1979 | This struct is used to pass information back from the callback |
---|
| 1980 | function used with H5Literate. |
---|
| 1981 | */ |
---|
| 1982 | struct nc_hdf5_link_info |
---|
| 1983 | { |
---|
| 1984 | char name[NC_MAX_NAME + 1]; |
---|
| 1985 | H5I_type_t obj_type; |
---|
| 1986 | }; |
---|
| 1987 | |
---|
| 1988 | /* This is a callback function for H5Literate(). |
---|
| 1989 | |
---|
| 1990 | The parameters of this callback function have the following values or |
---|
| 1991 | meanings: |
---|
| 1992 | |
---|
| 1993 | g_id Group that serves as root of the iteration; same value as the |
---|
| 1994 | H5Lvisit group_id parameter |
---|
| 1995 | |
---|
| 1996 | name Name of link, relative to g_id, being examined at current step of |
---|
| 1997 | the iteration |
---|
| 1998 | |
---|
| 1999 | info H5L_info_t struct containing information regarding that link |
---|
| 2000 | |
---|
| 2001 | op_data User-defined pointer to data required by the application in |
---|
| 2002 | processing the link; a pass-through of the op_data pointer provided |
---|
| 2003 | with the H5Lvisit function call |
---|
| 2004 | |
---|
| 2005 | */ |
---|
| 2006 | static herr_t |
---|
| 2007 | visit_link(hid_t g_id, const char *name, const H5L_info_t *info, |
---|
| 2008 | void *op_data) |
---|
| 2009 | { |
---|
| 2010 | /* A positive return value causes the visit iterator to immediately |
---|
| 2011 | * return that positive value, indicating short-circuit |
---|
| 2012 | * success. The iterator can be restarted at the next group |
---|
| 2013 | * member. */ |
---|
| 2014 | int ret = 1; |
---|
| 2015 | hid_t id; |
---|
| 2016 | |
---|
| 2017 | /* Get the name, truncating at NC_MAX_NAME. */ |
---|
| 2018 | strncpy(((struct nc_hdf5_link_info *)op_data)->name, name, |
---|
| 2019 | NC_MAX_NAME); |
---|
| 2020 | |
---|
| 2021 | /* Open this critter. */ |
---|
| 2022 | if ((id = H5Oopen_by_addr(g_id, info->u.address)) < 0) |
---|
| 2023 | return NC_EHDFERR; |
---|
| 2024 | |
---|
| 2025 | /* Is this critter a group, type, data, attribute, or what? */ |
---|
| 2026 | if ((((struct nc_hdf5_link_info *)op_data)->obj_type = H5Iget_type(id)) < 0) |
---|
| 2027 | ret = NC_EHDFERR; |
---|
| 2028 | |
---|
| 2029 | /* Close the critter to release resouces. */ |
---|
| 2030 | if (H5Oclose(id) < 0) |
---|
| 2031 | return NC_EHDFERR; |
---|
| 2032 | |
---|
| 2033 | return ret; |
---|
| 2034 | } |
---|
| 2035 | |
---|
| 2036 | /* Iterate over one link in the group at a time, returning |
---|
| 2037 | * link_info. The creation_ordering and idx pointers keep track of |
---|
| 2038 | * whether creation ordering works and the most recently examined |
---|
| 2039 | * link. */ |
---|
| 2040 | static int |
---|
| 2041 | nc4_iterate_link(int *ordering_checked, int *creation_ordering, |
---|
| 2042 | hid_t grpid, hsize_t *idx, struct nc_hdf5_link_info *link_info) |
---|
| 2043 | { |
---|
| 2044 | int res = 0; |
---|
| 2045 | |
---|
| 2046 | if (*creation_ordering) |
---|
| 2047 | { |
---|
| 2048 | /* These HDF5 macros prevent an HDF5 error message when a |
---|
| 2049 | * non-creation-ordered HDF5 file is opened. */ |
---|
| 2050 | H5E_BEGIN_TRY { |
---|
| 2051 | res = H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, |
---|
| 2052 | idx, visit_link, (void *)link_info); |
---|
| 2053 | if (res < 0 && *ordering_checked) |
---|
| 2054 | return NC_EHDFERR; |
---|
| 2055 | } H5E_END_TRY; |
---|
| 2056 | } |
---|
| 2057 | |
---|
| 2058 | if (!*creation_ordering || res < 0) |
---|
| 2059 | { |
---|
| 2060 | if (H5Literate(grpid, H5_INDEX_NAME, H5_ITER_INC, idx, |
---|
| 2061 | visit_link, link_info) != 1) |
---|
| 2062 | return NC_EHDFERR; |
---|
| 2063 | /* If it didn't work with creation ordering, but did without, |
---|
| 2064 | * then we don't have creation ordering. */ |
---|
| 2065 | *creation_ordering = 0; |
---|
| 2066 | } |
---|
| 2067 | |
---|
| 2068 | *ordering_checked = 1; |
---|
| 2069 | return NC_NOERR; |
---|
| 2070 | } |
---|
| 2071 | |
---|
| 2072 | /* Recursively open groups and read types. */ |
---|
| 2073 | int |
---|
| 2074 | nc4_rec_read_types(NC_GRP_INFO_T *grp) |
---|
| 2075 | { |
---|
| 2076 | hsize_t num_obj, i; |
---|
| 2077 | NC_HDF5_FILE_INFO_T *h5 = grp->file->nc4_info; |
---|
| 2078 | NC_GRP_INFO_T *child_grp; |
---|
| 2079 | hsize_t idx = 0; |
---|
| 2080 | struct nc_hdf5_link_info link_info; |
---|
| 2081 | int ordering_checked = 0; |
---|
| 2082 | int creation_ordering = 1; /* Assume we have it. */ |
---|
| 2083 | int retval = NC_NOERR; |
---|
| 2084 | |
---|
| 2085 | assert(grp && grp->name); |
---|
| 2086 | LOG((3, "nc4_rec_read_types: grp->name %s", grp->name)); |
---|
| 2087 | |
---|
| 2088 | /* Open this HDF5 group and retain its grpid. It will remain open |
---|
| 2089 | * with HDF5 until this file is nc_closed. */ |
---|
| 2090 | if (!grp->hdf_grpid) |
---|
| 2091 | { |
---|
| 2092 | if (grp->parent) |
---|
| 2093 | { |
---|
| 2094 | if ((grp->hdf_grpid = H5Gopen2(grp->parent->hdf_grpid, |
---|
| 2095 | grp->name, H5P_DEFAULT)) < 0) |
---|
| 2096 | return NC_EHDFERR; |
---|
| 2097 | } |
---|
| 2098 | else |
---|
| 2099 | { |
---|
| 2100 | if ((grp->hdf_grpid = H5Gopen2(grp->file->nc4_info->hdfid, |
---|
| 2101 | "/", H5P_DEFAULT)) < 0) |
---|
| 2102 | return NC_EHDFERR; |
---|
| 2103 | } |
---|
| 2104 | } |
---|
| 2105 | assert(grp->hdf_grpid > 0); |
---|
| 2106 | |
---|
| 2107 | /* How many objects in this group? */ |
---|
| 2108 | if (H5Gget_num_objs(grp->hdf_grpid, &num_obj) < 0) |
---|
| 2109 | return NC_EVARMETA; |
---|
| 2110 | |
---|
| 2111 | /* For each object in the group... */ |
---|
| 2112 | for (i = 0; i < num_obj; i++) |
---|
| 2113 | { |
---|
| 2114 | if ((retval = nc4_iterate_link(&ordering_checked, &creation_ordering, |
---|
| 2115 | grp->hdf_grpid, &idx, &link_info))) |
---|
| 2116 | return retval; |
---|
| 2117 | |
---|
| 2118 | /* Without creation ordering, file must be read-only. */ |
---|
| 2119 | if (!i && !creation_ordering && !h5->no_write) |
---|
| 2120 | return NC_ECANTWRITE; |
---|
| 2121 | |
---|
| 2122 | /* Deal with groups and types; ignore the rest. */ |
---|
| 2123 | if (link_info.obj_type == H5I_GROUP) |
---|
| 2124 | { |
---|
| 2125 | LOG((3, "found group %s", link_info.name)); |
---|
| 2126 | if ((retval = nc4_grp_list_add(&(grp->children), h5->next_nc_grpid++, |
---|
| 2127 | grp, grp->file, link_info.name, &child_grp))) |
---|
| 2128 | return retval; |
---|
| 2129 | if ((retval = nc4_rec_read_types(child_grp))) |
---|
| 2130 | return retval; |
---|
| 2131 | } |
---|
| 2132 | else if (link_info.obj_type == H5I_DATATYPE) |
---|
| 2133 | { |
---|
| 2134 | LOG((3, "found datatype %s", link_info.name)); |
---|
| 2135 | if ((retval = read_type(grp, link_info.name))) |
---|
| 2136 | return retval; |
---|
| 2137 | } |
---|
| 2138 | } |
---|
| 2139 | |
---|
| 2140 | return NC_NOERR; /* everything worked! */ |
---|
| 2141 | } |
---|
| 2142 | |
---|
| 2143 | /* This function recursively reads all the var and attribute metadata |
---|
| 2144 | in a HDF5 group, and creates and fills in the netCDF-4 global |
---|
| 2145 | metadata structure. */ |
---|
| 2146 | int |
---|
| 2147 | nc4_rec_read_vars(NC_GRP_INFO_T *grp) |
---|
| 2148 | { |
---|
| 2149 | hsize_t num_obj, i; |
---|
| 2150 | NC_GRP_INFO_T *child_grp; |
---|
| 2151 | struct nc_hdf5_link_info link_info; |
---|
| 2152 | hsize_t idx = 0; |
---|
| 2153 | int ordering_checked = 0; |
---|
| 2154 | int creation_ordering = 1; /* Assume we have it. */ |
---|
| 2155 | int retval = NC_NOERR; |
---|
| 2156 | |
---|
| 2157 | assert(grp && grp->name && grp->hdf_grpid > 0); |
---|
| 2158 | LOG((3, "nc4_rec_read_vars: grp->name %s", grp->name)); |
---|
| 2159 | |
---|
| 2160 | /* How many objects in this group? */ |
---|
| 2161 | if (H5Gget_num_objs(grp->hdf_grpid, &num_obj) < 0) |
---|
| 2162 | return NC_EVARMETA; |
---|
| 2163 | |
---|
| 2164 | /* For each object in the group... */ |
---|
| 2165 | for (i = 0; i < num_obj; i++) |
---|
| 2166 | { |
---|
| 2167 | if ((retval = nc4_iterate_link(&ordering_checked, &creation_ordering, |
---|
| 2168 | grp->hdf_grpid, &idx, &link_info))) |
---|
| 2169 | return retval; |
---|
| 2170 | |
---|
| 2171 | /* Deal with datasets. */ |
---|
| 2172 | switch(link_info.obj_type) |
---|
| 2173 | { |
---|
| 2174 | case H5I_GROUP: |
---|
| 2175 | LOG((3, "re-encountering group %s", link_info.name)); |
---|
| 2176 | |
---|
| 2177 | /* The NC_GROUP_INFO_T for this group already exists. Find it. */ |
---|
| 2178 | for (child_grp = grp->children; child_grp; child_grp = child_grp->next) |
---|
| 2179 | if (!strcmp(child_grp->name, link_info.name)) |
---|
| 2180 | break; |
---|
| 2181 | if (!child_grp) |
---|
| 2182 | return NC_EHDFERR; |
---|
| 2183 | |
---|
| 2184 | /* Recursively read the child group's vars. */ |
---|
| 2185 | if ((retval = nc4_rec_read_vars(child_grp))) |
---|
| 2186 | return retval; |
---|
| 2187 | break; |
---|
| 2188 | case H5I_DATASET: |
---|
| 2189 | LOG((3, "found dataset %s", link_info.name)); |
---|
| 2190 | |
---|
| 2191 | /* Learn all about this dataset, which may be a dimscale |
---|
| 2192 | * (i.e. dimension metadata), or real data. */ |
---|
| 2193 | if ((retval = read_dataset(grp, link_info.name))) |
---|
| 2194 | return retval; |
---|
| 2195 | break; |
---|
| 2196 | case H5I_DATATYPE: |
---|
| 2197 | LOG((3, "already handled type %s", link_info.name)); |
---|
| 2198 | break; |
---|
| 2199 | default: |
---|
| 2200 | LOG((0, "Unknown object class %d in nc4_rec_read_vars!", |
---|
| 2201 | link_info.obj_type)); |
---|
| 2202 | } |
---|
| 2203 | } |
---|
| 2204 | |
---|
| 2205 | /* Scan the group for global (i.e. group-level) attributes. */ |
---|
| 2206 | if ((retval = read_grp_atts(grp))) |
---|
| 2207 | return retval; |
---|
| 2208 | |
---|
| 2209 | return NC_NOERR; /* everything worked! */ |
---|
| 2210 | } |
---|
| 2211 | #endif |
---|
| 2212 | |
---|
| 2213 | /* Open a netcdf-4 file. Things have already been kicked off in |
---|
| 2214 | * ncfunc.c in nc_open, but here the netCDF-4 part of opening a file |
---|
| 2215 | * is handled. */ |
---|
| 2216 | static int |
---|
| 2217 | nc4_open_file(const char *path, int mode, MPI_Comm comm, |
---|
| 2218 | MPI_Info info, NC_FILE_INFO_T *nc) |
---|
| 2219 | { |
---|
| 2220 | hid_t fapl_id = H5P_DEFAULT; |
---|
| 2221 | unsigned flags = (mode & NC_WRITE) ? |
---|
| 2222 | H5F_ACC_RDWR : H5F_ACC_RDONLY; |
---|
| 2223 | int retval; |
---|
| 2224 | |
---|
| 2225 | LOG((3, "nc4_open_file: path %s mode %d", path, mode)); |
---|
| 2226 | assert(path && nc); |
---|
| 2227 | |
---|
| 2228 | /* Stop diskless open in its tracks */ |
---|
| 2229 | if(mode & NC_DISKLESS) |
---|
| 2230 | return NC_EDISKLESS; |
---|
| 2231 | |
---|
| 2232 | /* Add necessary structs to hold netcdf-4 file data. */ |
---|
| 2233 | if ((retval = nc4_nc4f_list_add(nc, path, mode))) |
---|
| 2234 | BAIL(retval); |
---|
| 2235 | assert(nc->nc4_info && nc->nc4_info->root_grp); |
---|
| 2236 | |
---|
| 2237 | /* Need this access plist to control how HDF5 handles open onjects |
---|
| 2238 | * on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to |
---|
| 2239 | * fail if there are any open objects in the file. */ |
---|
| 2240 | if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) |
---|
| 2241 | BAIL(NC_EHDFERR); |
---|
| 2242 | #ifdef EXTRA_TESTS |
---|
| 2243 | num_plists++; |
---|
| 2244 | #endif |
---|
| 2245 | #ifdef EXTRA_TESTS |
---|
| 2246 | if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) |
---|
| 2247 | BAIL(NC_EHDFERR); |
---|
| 2248 | #else |
---|
| 2249 | if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) |
---|
| 2250 | BAIL(NC_EHDFERR); |
---|
| 2251 | #endif |
---|
| 2252 | |
---|
| 2253 | #ifdef USE_PARALLEL |
---|
| 2254 | /* If this is a parallel file create, set up the file creation |
---|
| 2255 | property list. */ |
---|
| 2256 | if (mode & NC_MPIIO || mode & NC_MPIPOSIX) |
---|
| 2257 | { |
---|
| 2258 | nc->nc4_info->parallel++; |
---|
| 2259 | if (mode & NC_MPIIO) /* MPI/IO */ |
---|
| 2260 | { |
---|
| 2261 | LOG((4, "opening parallel file with MPI/IO")); |
---|
| 2262 | if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) |
---|
| 2263 | BAIL(NC_EPARINIT); |
---|
| 2264 | } |
---|
| 2265 | else /* MPI/POSIX */ |
---|
| 2266 | { |
---|
| 2267 | LOG((4, "opening parallel file with MPI/posix")); |
---|
| 2268 | if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) |
---|
| 2269 | BAIL(NC_EPARINIT); |
---|
| 2270 | } |
---|
| 2271 | } |
---|
| 2272 | #else /* only set cache for non-parallel. */ |
---|
| 2273 | if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size, |
---|
| 2274 | nc4_chunk_cache_preemption) < 0) |
---|
| 2275 | BAIL(NC_EHDFERR); |
---|
| 2276 | LOG((4, "nc4_open_file: set HDF raw chunk cache to size %d nelems %d preemption %f", |
---|
| 2277 | nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption)); |
---|
| 2278 | #endif /* USE_PARALLEL */ |
---|
| 2279 | |
---|
| 2280 | /* The NetCDF-3.x prototype contains an mode option NC_SHARE for |
---|
| 2281 | multiple processes accessing the dataset concurrently. As there |
---|
| 2282 | is no HDF5 equivalent, NC_SHARE is treated as NC_NOWRITE. */ |
---|
| 2283 | if ((nc->nc4_info->hdfid = H5Fopen(path, flags, fapl_id)) < 0) |
---|
| 2284 | BAIL(NC_EHDFERR); |
---|
| 2285 | |
---|
| 2286 | /* Does the mode specify that this file is read-only? */ |
---|
| 2287 | if ((mode & NC_WRITE) == 0) |
---|
| 2288 | nc->nc4_info->no_write++; |
---|
| 2289 | |
---|
| 2290 | /* Now read in all the metadata. Some types and dimscale |
---|
| 2291 | * information may be difficult to resolve here, if, for example, a |
---|
| 2292 | * dataset of user-defined type is encountered before the |
---|
| 2293 | * definition of that type. */ |
---|
| 2294 | if ((retval = nc4_rec_read_types(nc->nc4_info->root_grp))) |
---|
| 2295 | BAIL(retval); |
---|
| 2296 | if ((retval = nc4_rec_read_vars(nc->nc4_info->root_grp))) |
---|
| 2297 | BAIL(retval); |
---|
| 2298 | |
---|
| 2299 | /* Now figure out which netCDF dims are indicated by the dimscale |
---|
| 2300 | * information. */ |
---|
| 2301 | if ((retval = nc4_rec_match_dimscales(nc->nc4_info->root_grp))) |
---|
| 2302 | BAIL(retval); |
---|
| 2303 | |
---|
| 2304 | #ifdef LOGGING |
---|
| 2305 | /* This will print out the names, types, lens, etc of the vars and |
---|
| 2306 | atts in the file, if the logging level is 2 or greater. */ |
---|
| 2307 | log_metadata_nc(nc); |
---|
| 2308 | #endif |
---|
| 2309 | |
---|
| 2310 | /* Close the property list. */ |
---|
| 2311 | if (H5Pclose(fapl_id) < 0) |
---|
| 2312 | BAIL(NC_EHDFERR); |
---|
| 2313 | #ifdef EXTRA_TESTS |
---|
| 2314 | num_plists--; |
---|
| 2315 | #endif |
---|
| 2316 | |
---|
| 2317 | return NC_NOERR; |
---|
| 2318 | |
---|
| 2319 | exit: |
---|
| 2320 | if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id); |
---|
| 2321 | #ifdef EXTRA_TESTS |
---|
| 2322 | num_plists--; |
---|
| 2323 | #endif |
---|
| 2324 | if (nc->nc4_info->hdfid > 0) H5Fclose(nc->nc4_info->hdfid); |
---|
| 2325 | if (nc->nc4_info) free(nc->nc4_info); |
---|
| 2326 | return retval; |
---|
| 2327 | } |
---|
| 2328 | |
---|
| 2329 | /* Given an HDF4 type, set a pointer to netcdf type. */ |
---|
| 2330 | #ifdef USE_HDF4 |
---|
| 2331 | static int |
---|
| 2332 | get_netcdf_type_from_hdf4(NC_HDF5_FILE_INFO_T *h5, int32 hdf4_typeid, |
---|
| 2333 | nc_type *xtype, NC_TYPE_INFO_T *type_info) |
---|
| 2334 | { |
---|
| 2335 | int t; |
---|
| 2336 | assert(h5 && xtype); |
---|
| 2337 | |
---|
| 2338 | switch(hdf4_typeid) |
---|
| 2339 | { |
---|
| 2340 | case DFNT_CHAR: |
---|
| 2341 | *xtype = NC_CHAR; |
---|
| 2342 | t = 0; |
---|
| 2343 | break; |
---|
| 2344 | case DFNT_UCHAR: |
---|
| 2345 | case DFNT_UINT8: |
---|
| 2346 | *xtype = NC_UBYTE; |
---|
| 2347 | t = 6; |
---|
| 2348 | break; |
---|
| 2349 | case DFNT_INT8: |
---|
| 2350 | *xtype = NC_BYTE; |
---|
| 2351 | t = 1; |
---|
| 2352 | break; |
---|
| 2353 | case DFNT_INT16: |
---|
| 2354 | *xtype = NC_SHORT; |
---|
| 2355 | t = 2; |
---|
| 2356 | break; |
---|
| 2357 | case DFNT_UINT16: |
---|
| 2358 | *xtype = NC_USHORT; |
---|
| 2359 | t = 7; |
---|
| 2360 | break; |
---|
| 2361 | case DFNT_INT32: |
---|
| 2362 | *xtype = NC_INT; |
---|
| 2363 | t = 3; |
---|
| 2364 | break; |
---|
| 2365 | case DFNT_UINT32: |
---|
| 2366 | *xtype = NC_UINT; |
---|
| 2367 | t = 8; |
---|
| 2368 | break; |
---|
| 2369 | case DFNT_FLOAT32: |
---|
| 2370 | *xtype = NC_FLOAT; |
---|
| 2371 | t = 4; |
---|
| 2372 | break; |
---|
| 2373 | case DFNT_FLOAT64: |
---|
| 2374 | *xtype = NC_DOUBLE; |
---|
| 2375 | t = 5; |
---|
| 2376 | break; |
---|
| 2377 | default: |
---|
| 2378 | *xtype = NC_NAT; |
---|
| 2379 | return NC_EBADTYPID; |
---|
| 2380 | } |
---|
| 2381 | |
---|
| 2382 | if (type_info) |
---|
| 2383 | { |
---|
| 2384 | if (hdf4_typeid == DFNT_FLOAT32 || hdf4_typeid == DFNT_FLOAT64) |
---|
| 2385 | type_info->class = H5T_FLOAT; |
---|
| 2386 | else if (hdf4_typeid == DFNT_CHAR) |
---|
| 2387 | type_info->class = H5T_STRING; |
---|
| 2388 | else |
---|
| 2389 | type_info->class = H5T_INTEGER; |
---|
| 2390 | type_info->endianness = NC_ENDIAN_BIG; |
---|
| 2391 | type_info->nc_typeid = *xtype; |
---|
| 2392 | if (type_info->name) |
---|
| 2393 | free(type_info->name); |
---|
| 2394 | if (!(type_info->name = malloc((strlen(nc_type_name[t]) + 1) * sizeof(char)))) |
---|
| 2395 | return NC_ENOMEM; |
---|
| 2396 | strcpy(type_info->name, nc_type_name[t]); |
---|
| 2397 | } |
---|
| 2398 | |
---|
| 2399 | return NC_NOERR; |
---|
| 2400 | } |
---|
| 2401 | #endif /* USE_HDF4 */ |
---|
| 2402 | |
---|
| 2403 | /* Open a HDF4 file. Things have already been kicked off in nc_open, |
---|
| 2404 | * but here the netCDF-4 part of opening a file is handled. */ |
---|
| 2405 | static int |
---|
| 2406 | nc4_open_hdf4_file(const char *path, int mode, NC_FILE_INFO_T *nc) |
---|
| 2407 | { |
---|
| 2408 | #ifdef USE_HDF4 |
---|
| 2409 | NC_HDF5_FILE_INFO_T *h5; |
---|
| 2410 | NC_GRP_INFO_T *grp; |
---|
| 2411 | NC_ATT_INFO_T *att; |
---|
| 2412 | NC_VAR_INFO_T *var; |
---|
| 2413 | int32 num_datasets, num_gatts; |
---|
| 2414 | int32 rank; |
---|
| 2415 | int v, d, a; |
---|
| 2416 | int retval; |
---|
| 2417 | |
---|
| 2418 | LOG((3, "nc4_open_hdf4_file: path %s mode %d", path, mode)); |
---|
| 2419 | assert(path && nc); |
---|
| 2420 | |
---|
| 2421 | /* Must be read-only access to hdf4 files. */ |
---|
| 2422 | if (mode & NC_WRITE) |
---|
| 2423 | return NC_EINVAL; |
---|
| 2424 | |
---|
| 2425 | /* Add necessary structs to hold netcdf-4 file data. */ |
---|
| 2426 | if ((retval = nc4_nc4f_list_add(nc, path, mode))) |
---|
| 2427 | return retval; |
---|
| 2428 | assert(nc->nc4_info && nc->nc4_info->root_grp); |
---|
| 2429 | h5 = nc->nc4_info; |
---|
| 2430 | h5->hdf4++; |
---|
| 2431 | grp = h5->root_grp; |
---|
| 2432 | h5->no_write++; |
---|
| 2433 | |
---|
| 2434 | /* Open the file and initialize SD interface. */ |
---|
| 2435 | if ((h5->sdid = SDstart(path, DFACC_READ)) == FAIL) |
---|
| 2436 | return NC_EHDFERR; |
---|
| 2437 | |
---|
| 2438 | /* Learn how many datasets and global atts we have. */ |
---|
| 2439 | if (SDfileinfo(h5->sdid, &num_datasets, &num_gatts)) |
---|
| 2440 | return NC_EHDFERR; |
---|
| 2441 | |
---|
| 2442 | /* Read the atts. */ |
---|
| 2443 | for (a = 0; a < num_gatts; a++) |
---|
| 2444 | { |
---|
| 2445 | int32 att_data_type, att_count; |
---|
| 2446 | size_t att_type_size; |
---|
| 2447 | |
---|
| 2448 | /* Add to the end of the list of atts for this var. */ |
---|
| 2449 | if ((retval = nc4_att_list_add(&h5->root_grp->att))) |
---|
| 2450 | return retval; |
---|
| 2451 | for (att = h5->root_grp->att; att->next; att = att->next) |
---|
| 2452 | ; |
---|
| 2453 | att->attnum = grp->natts++; |
---|
| 2454 | att->created++; |
---|
| 2455 | |
---|
| 2456 | /* Learn about this attribute. */ |
---|
| 2457 | if (!(att->name = malloc(NC_MAX_HDF4_NAME * sizeof(char)))) |
---|
| 2458 | return NC_ENOMEM; |
---|
| 2459 | if (SDattrinfo(h5->sdid, a, att->name, &att_data_type, &att_count)) |
---|
| 2460 | return NC_EATTMETA; |
---|
| 2461 | if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type, |
---|
| 2462 | &att->xtype, NULL))) |
---|
| 2463 | return retval; |
---|
| 2464 | att->len = att_count; |
---|
| 2465 | |
---|
| 2466 | /* Allocate memory to hold the data. */ |
---|
| 2467 | if ((retval = nc4_get_typelen_mem(h5, att->xtype, 0, &att_type_size))) |
---|
| 2468 | return retval; |
---|
| 2469 | if (!(att->data = malloc(att_type_size * att->len))) |
---|
| 2470 | return NC_ENOMEM; |
---|
| 2471 | |
---|
| 2472 | /* Read the data. */ |
---|
| 2473 | if (SDreadattr(h5->sdid, a, att->data)) |
---|
| 2474 | return NC_EHDFERR; |
---|
| 2475 | } |
---|
| 2476 | |
---|
| 2477 | /* Read each dataset. */ |
---|
| 2478 | for (v = 0; v < num_datasets; v++) |
---|
| 2479 | { |
---|
| 2480 | int32 data_type, num_atts; |
---|
| 2481 | int32 dimsize[NC_MAX_DIMS]; |
---|
| 2482 | size_t var_type_size; |
---|
| 2483 | int a; |
---|
| 2484 | |
---|
| 2485 | /* Add a variable to the end of the group's var list. */ |
---|
| 2486 | if ((retval = nc4_var_list_add(&grp->var, &var))) |
---|
| 2487 | return retval; |
---|
| 2488 | var->varid = grp->nvars++; |
---|
| 2489 | var->created = 1; |
---|
| 2490 | var->written_to = 1; |
---|
| 2491 | |
---|
| 2492 | /* Open this dataset in HDF4 file. */ |
---|
| 2493 | if ((var->sdsid = SDselect(h5->sdid, v)) == FAIL) |
---|
| 2494 | return NC_EVARMETA; |
---|
| 2495 | |
---|
| 2496 | /* Get shape, name, type, and attribute info about this dataset. */ |
---|
| 2497 | if (!(var->name = malloc(NC_MAX_HDF4_NAME + 1))) |
---|
| 2498 | return NC_ENOMEM; |
---|
| 2499 | if (SDgetinfo(var->sdsid, var->name, &rank, dimsize, &data_type, &num_atts)) |
---|
| 2500 | return NC_EVARMETA; |
---|
| 2501 | var->ndims = rank; |
---|
| 2502 | var->hdf4_data_type = data_type; |
---|
| 2503 | |
---|
| 2504 | /* Fill special type_info struct for variable type information. */ |
---|
| 2505 | if (!(var->type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) |
---|
| 2506 | return NC_ENOMEM; |
---|
| 2507 | if ((retval = get_netcdf_type_from_hdf4(h5, data_type, &var->xtype, var->type_info))) |
---|
| 2508 | return retval; |
---|
| 2509 | if ((retval = nc4_get_typelen_mem(h5, var->xtype, 0, &var_type_size))) |
---|
| 2510 | return retval; |
---|
| 2511 | var->type_info->size = var_type_size; |
---|
| 2512 | LOG((3, "reading HDF4 dataset %s, rank %d netCDF type %d", var->name, |
---|
| 2513 | rank, var->xtype)); |
---|
| 2514 | |
---|
| 2515 | /* Get the fill value. */ |
---|
| 2516 | if (!(var->fill_value = malloc(var_type_size))) |
---|
| 2517 | return NC_ENOMEM; |
---|
| 2518 | if (SDgetfillvalue(var->sdsid, var->fill_value)) |
---|
| 2519 | { |
---|
| 2520 | /* Whoops! No fill value! */ |
---|
| 2521 | free(var->fill_value); |
---|
| 2522 | var->fill_value = NULL; |
---|
| 2523 | } |
---|
| 2524 | |
---|
| 2525 | /* Allocate storage for dimension info in this variable. */ |
---|
| 2526 | if (var->ndims) |
---|
| 2527 | { |
---|
| 2528 | if (!(var->dim = malloc(sizeof(NC_DIM_INFO_T *) * var->ndims))) |
---|
| 2529 | return NC_ENOMEM; |
---|
| 2530 | if (!(var->dimids = malloc(sizeof(int) * var->ndims))) |
---|
| 2531 | return NC_ENOMEM; |
---|
| 2532 | } |
---|
| 2533 | |
---|
| 2534 | /* Find its dimensions. */ |
---|
| 2535 | for (d = 0; d < var->ndims; d++) |
---|
| 2536 | { |
---|
| 2537 | int32 dimid, dim_len, dim_data_type, dim_num_attrs; |
---|
| 2538 | char dim_name[NC_MAX_NAME + 1]; |
---|
| 2539 | NC_DIM_INFO_T *dim; |
---|
| 2540 | |
---|
| 2541 | if ((dimid = SDgetdimid(var->sdsid, d)) == FAIL) |
---|
| 2542 | return NC_EDIMMETA; |
---|
| 2543 | if (SDdiminfo(dimid, dim_name, &dim_len, &dim_data_type, |
---|
| 2544 | &dim_num_attrs)) |
---|
| 2545 | return NC_EDIMMETA; |
---|
| 2546 | |
---|
| 2547 | /* Do we already have this dimension? HDF4 explicitly uses |
---|
| 2548 | * the name to tell. */ |
---|
| 2549 | for (dim = grp->dim; dim; dim = dim->next) |
---|
| 2550 | if (!strcmp(dim->name, dim_name)) |
---|
| 2551 | break; |
---|
| 2552 | |
---|
| 2553 | /* If we didn't find this dimension, add one. */ |
---|
| 2554 | if (!dim) |
---|
| 2555 | { |
---|
| 2556 | LOG((4, "adding dimension %s for HDF4 dataset %s", |
---|
| 2557 | dim_name, var->name)); |
---|
| 2558 | if ((retval = nc4_dim_list_add(&grp->dim))) |
---|
| 2559 | return retval; |
---|
| 2560 | grp->ndims++; |
---|
| 2561 | dim = grp->dim; |
---|
| 2562 | dim->dimid = grp->file->nc4_info->next_dimid++; |
---|
| 2563 | if (strlen(dim_name) > NC_MAX_HDF4_NAME) |
---|
| 2564 | return NC_EMAXNAME; |
---|
| 2565 | if (!(dim->name = malloc(NC_MAX_HDF4_NAME + 1))) |
---|
| 2566 | return NC_ENOMEM; |
---|
| 2567 | strcpy(dim->name, dim_name); |
---|
| 2568 | if (dim_len) |
---|
| 2569 | dim->len = dim_len; |
---|
| 2570 | else |
---|
| 2571 | dim->len = *dimsize; |
---|
| 2572 | } |
---|
| 2573 | |
---|
| 2574 | /* Tell the variable the id of this dimension. */ |
---|
| 2575 | var->dimids[d] = dim->dimid; |
---|
| 2576 | } |
---|
| 2577 | |
---|
| 2578 | /* Read the atts. */ |
---|
| 2579 | for (a = 0; a < num_atts; a++) |
---|
| 2580 | { |
---|
| 2581 | int32 att_data_type, att_count; |
---|
| 2582 | size_t att_type_size; |
---|
| 2583 | |
---|
| 2584 | /* Add to the end of the list of atts for this var. */ |
---|
| 2585 | if ((retval = nc4_att_list_add(&var->att))) |
---|
| 2586 | return retval; |
---|
| 2587 | for (att = var->att; att->next; att = att->next) |
---|
| 2588 | ; |
---|
| 2589 | att->attnum = var->natts++; |
---|
| 2590 | att->created++; |
---|
| 2591 | |
---|
| 2592 | /* Learn about this attribute. */ |
---|
| 2593 | if (!(att->name = malloc(NC_MAX_HDF4_NAME * sizeof(char)))) |
---|
| 2594 | return NC_ENOMEM; |
---|
| 2595 | if (SDattrinfo(var->sdsid, a, att->name, &att_data_type, &att_count)) |
---|
| 2596 | return NC_EATTMETA; |
---|
| 2597 | if ((retval = get_netcdf_type_from_hdf4(h5, att_data_type, |
---|
| 2598 | &att->xtype, NULL))) |
---|
| 2599 | return retval; |
---|
| 2600 | att->len = att_count; |
---|
| 2601 | |
---|
| 2602 | /* Allocate memory to hold the data. */ |
---|
| 2603 | if ((retval = nc4_get_typelen_mem(h5, att->xtype, 0, &att_type_size))) |
---|
| 2604 | return retval; |
---|
| 2605 | if (!(att->data = malloc(att_type_size * att->len))) |
---|
| 2606 | return NC_ENOMEM; |
---|
| 2607 | |
---|
| 2608 | /* Read the data. */ |
---|
| 2609 | if (SDreadattr(var->sdsid, a, att->data)) |
---|
| 2610 | return NC_EHDFERR; |
---|
| 2611 | } |
---|
| 2612 | } /* next var */ |
---|
| 2613 | |
---|
| 2614 | #ifdef LOGGING |
---|
| 2615 | /* This will print out the names, types, lens, etc of the vars and |
---|
| 2616 | atts in the file, if the logging level is 2 or greater. */ |
---|
| 2617 | log_metadata_nc(h5->root_grp->file); |
---|
| 2618 | #endif |
---|
| 2619 | return NC_NOERR; |
---|
| 2620 | #endif /* USE_HDF4 */ |
---|
| 2621 | return NC_ENOTBUILT; |
---|
| 2622 | } |
---|
| 2623 | |
---|
| 2624 | int |
---|
| 2625 | NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp, |
---|
| 2626 | int use_parallel, void *mpidata, NC_Dispatch *dispatch, NC **ncpp) |
---|
| 2627 | { |
---|
| 2628 | int hdf_file = 0; |
---|
| 2629 | NC_FILE_INFO_T *nc_file; |
---|
| 2630 | #ifdef USE_PARALLEL |
---|
| 2631 | MPI_Comm comm = 0; |
---|
| 2632 | MPI_Info info = 0; |
---|
| 2633 | #else |
---|
| 2634 | int comm = 0, info = 0; |
---|
| 2635 | #endif /* USE_PARALLEL */ |
---|
| 2636 | int res; |
---|
| 2637 | |
---|
| 2638 | assert(ncpp && path); |
---|
| 2639 | |
---|
| 2640 | LOG((1, "nc_open_file: path %s mode %d comm %d info %d", |
---|
| 2641 | path, mode, comm, info)); |
---|
| 2642 | |
---|
| 2643 | #ifdef USE_PARALLEL |
---|
| 2644 | if (mpidata) |
---|
| 2645 | { |
---|
| 2646 | NC_MPI_INFO *nmi = (NC_MPI_INFO *)mpidata; |
---|
| 2647 | comm = nmi->comm; info = nmi->info; |
---|
| 2648 | } |
---|
| 2649 | #endif /* USE_PARALLEL */ |
---|
| 2650 | |
---|
| 2651 | /* If this is our first file, turn off HDF5 error messages. */ |
---|
| 2652 | if (virgin) |
---|
| 2653 | { |
---|
| 2654 | if (H5Eset_auto(NULL, NULL) < 0) |
---|
| 2655 | LOG((0, "Couldn't turn off HDF5 error messages!")); |
---|
| 2656 | LOG((1, "HDF5 error messages turned off!")); |
---|
| 2657 | virgin = 0; |
---|
| 2658 | } |
---|
| 2659 | |
---|
| 2660 | /* Check the mode for validity. First make sure only certain bits |
---|
| 2661 | * are turned on. Also MPI I/O and MPI POSIX cannot both be |
---|
| 2662 | * selected at once. */ |
---|
| 2663 | if (mode & ~(NC_WRITE | NC_SHARE | NC_MPIIO | NC_MPIPOSIX | |
---|
| 2664 | NC_PNETCDF | NC_NOCLOBBER | NC_NETCDF4 | NC_CLASSIC_MODEL) || |
---|
| 2665 | (mode & NC_MPIIO && mode & NC_MPIPOSIX)) |
---|
| 2666 | return NC_EINVAL; |
---|
| 2667 | |
---|
| 2668 | /* Figure out if this is a hdf4 or hdf5 file. */ |
---|
| 2669 | if ((res = nc_check_for_hdf(path, use_parallel, comm, info, &hdf_file))) |
---|
| 2670 | return res; |
---|
| 2671 | |
---|
| 2672 | /* Allocate the storage for this file info struct, and fill it with |
---|
| 2673 | zeros. */ |
---|
| 2674 | if ((res = nc4_file_list_add(&nc_file,dispatch))) |
---|
| 2675 | return res; |
---|
| 2676 | |
---|
| 2677 | /* Depending on the type of file, open it. */ |
---|
| 2678 | if (hdf_file == NC_HDF5_FILE) |
---|
| 2679 | { |
---|
| 2680 | nc_file->int_ncid = nc_file->ext_ncid; |
---|
| 2681 | res = nc4_open_file(path, mode, comm, info, nc_file); |
---|
| 2682 | } |
---|
| 2683 | else if (hdf_file == NC_HDF4_FILE) |
---|
| 2684 | { |
---|
| 2685 | nc_file->int_ncid = nc_file->ext_ncid; |
---|
| 2686 | res = nc4_open_hdf4_file(path, mode, nc_file); |
---|
| 2687 | } |
---|
| 2688 | #ifdef USE_PNETCDF |
---|
| 2689 | else if (mode & NC_PNETCDF) |
---|
| 2690 | { |
---|
| 2691 | int pnetcdf_nvars, i; |
---|
| 2692 | |
---|
| 2693 | res = ncmpi_open(comm, path, mode, info, &(nc_file->int_ncid)); |
---|
| 2694 | nc_file->pnetcdf_file++; |
---|
| 2695 | |
---|
| 2696 | /* Default to independent access, like netCDF-4/HDF5 files. */ |
---|
| 2697 | if (!res) |
---|
| 2698 | res = ncmpi_begin_indep_data(nc_file->int_ncid); |
---|
| 2699 | |
---|
| 2700 | /* I need to keep track of the ndims of each var to translate |
---|
| 2701 | * start, count, and stride arrays to MPI_Offset type. */ |
---|
| 2702 | if (!res) |
---|
| 2703 | { |
---|
| 2704 | res = ncmpi_inq_nvars(nc_file->int_ncid, &pnetcdf_nvars); |
---|
| 2705 | for (i = 0; i < pnetcdf_nvars; i++) |
---|
| 2706 | res = ncmpi_inq_varndims(nc_file->int_ncid, i, |
---|
| 2707 | &(nc_file->pnetcdf_ndims[i])); |
---|
| 2708 | |
---|
| 2709 | } |
---|
| 2710 | } |
---|
| 2711 | #endif /* USE_PNETCDF */ |
---|
| 2712 | else /* netcdf */ |
---|
| 2713 | { |
---|
| 2714 | assert(0); |
---|
| 2715 | } |
---|
| 2716 | |
---|
| 2717 | /* If it succeeds, pass back the new ncid. Otherwise, remove this |
---|
| 2718 | file from the list. */ |
---|
| 2719 | if (res) |
---|
| 2720 | { |
---|
| 2721 | if(nc_file != NULL) nc4_file_list_del(nc_file); |
---|
| 2722 | } |
---|
| 2723 | else |
---|
| 2724 | { |
---|
| 2725 | *ncpp = (NC*)nc_file; |
---|
| 2726 | } |
---|
| 2727 | |
---|
| 2728 | return res; |
---|
| 2729 | } |
---|
| 2730 | |
---|
| 2731 | /* Unfortunately HDF only allows specification of fill value only when |
---|
| 2732 | a dataset is created. Whereas in netcdf, you first create the |
---|
| 2733 | variable and then (optionally) specify the fill value. To |
---|
| 2734 | accomplish this in HDF5 I have to delete the dataset, and recreate |
---|
| 2735 | it, with the fill value specified. */ |
---|
| 2736 | int |
---|
| 2737 | NC4_set_fill(int ncid, int fillmode, int *old_modep) |
---|
| 2738 | { |
---|
| 2739 | NC_FILE_INFO_T *nc; |
---|
| 2740 | |
---|
| 2741 | LOG((2, "nc_set_fill: ncid 0x%x fillmode %d", ncid, fillmode)); |
---|
| 2742 | |
---|
| 2743 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
| 2744 | return NC_EBADID; |
---|
| 2745 | |
---|
| 2746 | /* Is this a netcdf-3 file? */ |
---|
| 2747 | assert(nc->nc4_info); |
---|
| 2748 | |
---|
| 2749 | /* Trying to set fill on a read-only file? You sicken me! */ |
---|
| 2750 | if (nc->nc4_info->no_write) |
---|
| 2751 | return NC_EPERM; |
---|
| 2752 | |
---|
| 2753 | /* Did you pass me some weird fillmode? */ |
---|
| 2754 | if (fillmode != NC_FILL && fillmode != NC_NOFILL) |
---|
| 2755 | return NC_EINVAL; |
---|
| 2756 | |
---|
| 2757 | /* If the user wants to know, tell him what the old mode was. */ |
---|
| 2758 | if (old_modep) |
---|
| 2759 | *old_modep = nc->nc4_info->fill_mode; |
---|
| 2760 | |
---|
| 2761 | nc->nc4_info->fill_mode = fillmode; |
---|
| 2762 | |
---|
| 2763 | return NC_NOERR; |
---|
| 2764 | } |
---|
| 2765 | |
---|
| 2766 | /* Put the file back in redef mode. This is done automatically for |
---|
| 2767 | * netcdf-4 files, if the user forgets. */ |
---|
| 2768 | int |
---|
| 2769 | NC4_redef(int ncid) |
---|
| 2770 | { |
---|
| 2771 | NC_FILE_INFO_T *nc; |
---|
| 2772 | |
---|
| 2773 | LOG((1, "nc_redef: ncid 0x%x", ncid)); |
---|
| 2774 | |
---|
| 2775 | /* Find this file's metadata. */ |
---|
| 2776 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
| 2777 | return NC_EBADID; |
---|
| 2778 | |
---|
| 2779 | #ifdef USE_PNETCDF |
---|
| 2780 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
| 2781 | if (nc->pnetcdf_file) |
---|
| 2782 | return ncmpi_redef(nc->int_ncid); |
---|
| 2783 | #endif /* USE_PNETCDF */ |
---|
| 2784 | |
---|
| 2785 | /* Handle netcdf-3 files. */ |
---|
| 2786 | assert(nc->nc4_info); |
---|
| 2787 | |
---|
| 2788 | /* If we're already in define mode, return an error. */ |
---|
| 2789 | if (nc->nc4_info->flags & NC_INDEF) |
---|
| 2790 | return NC_EINDEFINE; |
---|
| 2791 | |
---|
| 2792 | /* If the file is read-only, return an error. */ |
---|
| 2793 | if (nc->nc4_info->no_write) |
---|
| 2794 | return NC_EPERM; |
---|
| 2795 | |
---|
| 2796 | /* Set define mode. */ |
---|
| 2797 | nc->nc4_info->flags |= NC_INDEF; |
---|
| 2798 | |
---|
| 2799 | /* For nc_abort, we need to remember if we're in define mode as a |
---|
| 2800 | redef. */ |
---|
| 2801 | nc->nc4_info->redef++; |
---|
| 2802 | |
---|
| 2803 | return NC_NOERR; |
---|
| 2804 | } |
---|
| 2805 | |
---|
| 2806 | /* For netcdf-4 files, this just calls nc_enddef, ignoring the extra |
---|
| 2807 | * parameters. */ |
---|
| 2808 | int |
---|
| 2809 | NC4__enddef(int ncid, size_t h_minfree, size_t v_align, |
---|
| 2810 | size_t v_minfree, size_t r_align) |
---|
| 2811 | { |
---|
| 2812 | if (!nc4_find_nc_file(ncid)) |
---|
| 2813 | return NC_EBADID; |
---|
| 2814 | |
---|
| 2815 | return NC4_enddef(ncid); |
---|
| 2816 | } |
---|
| 2817 | |
---|
| 2818 | /* Take the file out of define mode. This is called automatically for |
---|
| 2819 | * netcdf-4 files, if the user forgets. */ |
---|
| 2820 | static int NC4_enddef(int ncid) |
---|
| 2821 | { |
---|
| 2822 | NC_FILE_INFO_T *nc; |
---|
| 2823 | |
---|
| 2824 | LOG((1, "nc_enddef: ncid 0x%x", ncid)); |
---|
| 2825 | |
---|
| 2826 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
| 2827 | return NC_EBADID; |
---|
| 2828 | |
---|
| 2829 | #ifdef USE_PNETCDF |
---|
| 2830 | if (nc->pnetcdf_file) |
---|
| 2831 | { |
---|
| 2832 | int res; |
---|
| 2833 | res = ncmpi_enddef(nc->int_ncid); |
---|
| 2834 | if (!res) |
---|
| 2835 | { |
---|
| 2836 | if (nc->pnetcdf_access_mode == NC_INDEPENDENT) |
---|
| 2837 | res = ncmpi_begin_indep_data(nc->int_ncid); |
---|
| 2838 | } |
---|
| 2839 | return res; |
---|
| 2840 | } |
---|
| 2841 | #endif /* USE_PNETCDF */ |
---|
| 2842 | |
---|
| 2843 | /* Take care of netcdf-3 files. */ |
---|
| 2844 | assert(nc->nc4_info); |
---|
| 2845 | |
---|
| 2846 | return nc4_enddef_netcdf4_file(nc->nc4_info); |
---|
| 2847 | } |
---|
| 2848 | |
---|
| 2849 | /* This function will write all changed metadata, and (someday) reread |
---|
| 2850 | * all metadata from the file. */ |
---|
| 2851 | static int |
---|
| 2852 | sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5) |
---|
| 2853 | { |
---|
| 2854 | int retval; |
---|
| 2855 | |
---|
| 2856 | assert(h5); |
---|
| 2857 | LOG((3, "sync_netcdf4_file")); |
---|
| 2858 | |
---|
| 2859 | /* If we're in define mode, that's an error, for strict nc3 rules, |
---|
| 2860 | * otherwise, end define mode. */ |
---|
| 2861 | if (h5->flags & NC_INDEF) |
---|
| 2862 | { |
---|
| 2863 | if (h5->cmode & NC_CLASSIC_MODEL) |
---|
| 2864 | return NC_EINDEFINE; |
---|
| 2865 | |
---|
| 2866 | /* Turn define mode off. */ |
---|
| 2867 | h5->flags ^= NC_INDEF; |
---|
| 2868 | |
---|
| 2869 | /* Redef mode needs to be tracked seperately for nc_abort. */ |
---|
| 2870 | h5->redef = 0; |
---|
| 2871 | } |
---|
| 2872 | |
---|
| 2873 | #ifdef LOGGING |
---|
| 2874 | /* This will print out the names, types, lens, etc of the vars and |
---|
| 2875 | atts in the file, if the logging level is 2 or greater. */ |
---|
| 2876 | log_metadata_nc(h5->root_grp->file); |
---|
| 2877 | #endif |
---|
| 2878 | |
---|
| 2879 | /* Write any metadata that has changed. */ |
---|
| 2880 | if (!(h5->cmode & NC_NOWRITE)) |
---|
| 2881 | { |
---|
| 2882 | if ((retval = nc4_rec_write_types(h5->root_grp))) |
---|
| 2883 | return retval; |
---|
| 2884 | if ((retval = nc4_rec_write_metadata(h5->root_grp))) |
---|
| 2885 | return retval; |
---|
| 2886 | } |
---|
| 2887 | |
---|
| 2888 | H5Fflush(h5->hdfid, H5F_SCOPE_GLOBAL); |
---|
| 2889 | |
---|
| 2890 | /* Reread all the metadata. */ |
---|
| 2891 | /*if ((retval = nc4_rec_read_metadata(grp))) |
---|
| 2892 | return retval;*/ |
---|
| 2893 | |
---|
| 2894 | return retval; |
---|
| 2895 | } |
---|
| 2896 | |
---|
| 2897 | /* Flushes all buffers associated with the file, after writing all |
---|
| 2898 | changed metadata. This may only be called in data mode. */ |
---|
| 2899 | int |
---|
| 2900 | NC4_sync(int ncid) |
---|
| 2901 | { |
---|
| 2902 | NC_FILE_INFO_T *nc; |
---|
| 2903 | int retval; |
---|
| 2904 | |
---|
| 2905 | LOG((2, "nc_sync: ncid 0x%x", ncid)); |
---|
| 2906 | |
---|
| 2907 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
| 2908 | return NC_EBADID; |
---|
| 2909 | |
---|
| 2910 | #ifdef USE_PNETCDF |
---|
| 2911 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
| 2912 | if (nc->pnetcdf_file) |
---|
| 2913 | return ncmpi_sync(nc->int_ncid); |
---|
| 2914 | #endif /* USE_PNETCDF */ |
---|
| 2915 | |
---|
| 2916 | /* Take care of netcdf-3 files. */ |
---|
| 2917 | assert(nc->nc4_info); |
---|
| 2918 | |
---|
| 2919 | /* If we're in define mode, we can't sync. */ |
---|
| 2920 | if (nc->nc4_info && nc->nc4_info->flags & NC_INDEF) |
---|
| 2921 | { |
---|
| 2922 | if (nc->nc4_info->cmode & NC_CLASSIC_MODEL) |
---|
| 2923 | return NC_EINDEFINE; |
---|
| 2924 | if ((retval = nc_enddef(ncid))) |
---|
| 2925 | return retval; |
---|
| 2926 | } |
---|
| 2927 | |
---|
| 2928 | return sync_netcdf4_file(nc->nc4_info); |
---|
| 2929 | } |
---|
| 2930 | |
---|
| 2931 | /* This function will free all allocated metadata memory, and close |
---|
| 2932 | the HDF5 file. The group that is passed in must be the root group |
---|
| 2933 | of the file. */ |
---|
| 2934 | static int |
---|
| 2935 | close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5, int abort) |
---|
| 2936 | { |
---|
| 2937 | int retval; |
---|
| 2938 | |
---|
| 2939 | assert(h5 && h5->root_grp); |
---|
| 2940 | LOG((3, "close_netcdf4_file: h5->path %s abort %d", |
---|
| 2941 | h5->path, abort)); |
---|
| 2942 | |
---|
| 2943 | /* According to the docs, always end define mode on close. */ |
---|
| 2944 | if (h5->flags & NC_INDEF) |
---|
| 2945 | h5->flags ^= NC_INDEF; |
---|
| 2946 | |
---|
| 2947 | /* Sync the file, unless we're aborting, or this is a read-only |
---|
| 2948 | * file. */ |
---|
| 2949 | if (!h5->no_write && !abort) |
---|
| 2950 | if ((retval = sync_netcdf4_file(h5))) |
---|
| 2951 | return retval; |
---|
| 2952 | |
---|
| 2953 | /* Delete all the list contents for vars, dims, and atts, in each |
---|
| 2954 | * group. */ |
---|
| 2955 | if ((retval = nc4_rec_grp_del(&h5->root_grp, h5->root_grp))) |
---|
| 2956 | return retval; |
---|
| 2957 | |
---|
| 2958 | /* Close hdf file. */ |
---|
| 2959 | if (h5->hdf4) |
---|
| 2960 | { |
---|
| 2961 | #ifdef USE_HDF4 |
---|
| 2962 | if (SDend(h5->sdid)) |
---|
| 2963 | return NC_EHDFERR; |
---|
| 2964 | #endif /* USE_HDF4 */ |
---|
| 2965 | } |
---|
| 2966 | else |
---|
| 2967 | { |
---|
| 2968 | if (H5Fclose(h5->hdfid) < 0) |
---|
| 2969 | { |
---|
| 2970 | int nobjs; |
---|
| 2971 | nobjs = H5Fget_obj_count(h5->hdfid, H5F_OBJ_ALL); |
---|
| 2972 | /* Apparently we can get an error even when nobjs == 0 */ |
---|
| 2973 | if(nobjs < 0) { |
---|
| 2974 | return NC_EHDFERR; |
---|
| 2975 | } else if(nobjs > 0) { |
---|
| 2976 | #ifdef LOGGING |
---|
| 2977 | /* If the close doesn't work, probably there are still some HDF5 |
---|
| 2978 | * objects open, which means there's a bug in the library. So |
---|
| 2979 | * print out some info on to help the poor programmer figure it |
---|
| 2980 | * out. */ |
---|
| 2981 | LOG((0, "There are %d HDF5 objects open!", nobjs)); |
---|
| 2982 | #endif |
---|
| 2983 | return NC_EHDFERR; |
---|
| 2984 | } |
---|
| 2985 | } |
---|
| 2986 | /* if (H5garbage_collect() < 0) |
---|
| 2987 | return NC_EHDFERR; */ |
---|
| 2988 | } |
---|
| 2989 | |
---|
| 2990 | /* Delete the memory for the path, if it's been allocated. */ |
---|
| 2991 | if (h5->path) |
---|
| 2992 | free(h5->path); |
---|
| 2993 | |
---|
| 2994 | /* Free the nc4_info struct. */ |
---|
| 2995 | free(h5); |
---|
| 2996 | return NC_NOERR; |
---|
| 2997 | } |
---|
| 2998 | |
---|
| 2999 | /* From the netcdf-3 docs: The function nc_abort just closes the |
---|
| 3000 | netCDF dataset, if not in define mode. If the dataset is being |
---|
| 3001 | created and is still in define mode, the dataset is deleted. If |
---|
| 3002 | define mode was entered by a call to nc_redef, the netCDF dataset |
---|
| 3003 | is restored to its state before definition mode was entered and the |
---|
| 3004 | dataset is closed. */ |
---|
| 3005 | int |
---|
| 3006 | NC4_abort(int ncid) |
---|
| 3007 | { |
---|
| 3008 | NC_FILE_INFO_T *nc; |
---|
| 3009 | int delete_file = 0; |
---|
| 3010 | char path[NC_MAX_NAME + 1]; |
---|
| 3011 | int retval = NC_NOERR; |
---|
| 3012 | |
---|
| 3013 | LOG((2, "nc_abort: ncid 0x%x", ncid)); |
---|
| 3014 | |
---|
| 3015 | /* Find metadata for this file. */ |
---|
| 3016 | if (!(nc = nc4_find_nc_file(ncid))) |
---|
| 3017 | return NC_EBADID; |
---|
| 3018 | |
---|
| 3019 | #ifdef USE_PNETCDF |
---|
| 3020 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
| 3021 | if (nc->pnetcdf_file) |
---|
| 3022 | return ncmpi_abort(nc->int_ncid); |
---|
| 3023 | #endif /* USE_PNETCDF */ |
---|
| 3024 | |
---|
| 3025 | /* If this is a netcdf-3 file, let the netcdf-3 library handle it. */ |
---|
| 3026 | assert(nc->nc4_info); |
---|
| 3027 | |
---|
| 3028 | /* If we're in define mode, but not redefing the file, delete it. */ |
---|
| 3029 | if (nc->nc4_info->flags & NC_INDEF && !nc->nc4_info->redef) |
---|
| 3030 | { |
---|
| 3031 | delete_file++; |
---|
| 3032 | strcpy(path, nc->nc4_info->path); |
---|
| 3033 | /*strcpy(path, nc->path);*/ |
---|
| 3034 | } |
---|
| 3035 | |
---|
| 3036 | /* Free any resources the netcdf-4 library has for this file's |
---|
| 3037 | * metadata. */ |
---|
| 3038 | if ((retval = close_netcdf4_file(nc->nc4_info, 1))) |
---|
| 3039 | return retval; |
---|
| 3040 | |
---|
| 3041 | /* Delete the file, if we should. */ |
---|
| 3042 | if (delete_file) |
---|
| 3043 | remove(path); |
---|
| 3044 | |
---|
| 3045 | /* Delete this entry from our list of open files. */ |
---|
| 3046 | nc4_file_list_del(nc); |
---|
| 3047 | |
---|
| 3048 | return retval; |
---|
| 3049 | } |
---|
| 3050 | |
---|
| 3051 | /* Close the netcdf file, writing any changes first. */ |
---|
| 3052 | int |
---|
| 3053 | NC4_close(int ncid) |
---|
| 3054 | { |
---|
| 3055 | NC_GRP_INFO_T *grp; |
---|
| 3056 | NC_FILE_INFO_T *nc; |
---|
| 3057 | NC_HDF5_FILE_INFO_T *h5; |
---|
| 3058 | int retval; |
---|
| 3059 | |
---|
| 3060 | LOG((1, "nc_close: ncid 0x%x", ncid)); |
---|
| 3061 | |
---|
| 3062 | /* Find our metadata for this file. */ |
---|
| 3063 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
| 3064 | return retval; |
---|
| 3065 | |
---|
| 3066 | #ifdef USE_PNETCDF |
---|
| 3067 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
| 3068 | if (nc->pnetcdf_file) |
---|
| 3069 | return ncmpi_close(nc->int_ncid); |
---|
| 3070 | #endif /* USE_PNETCDF */ |
---|
| 3071 | |
---|
| 3072 | assert(h5 && nc); |
---|
| 3073 | |
---|
| 3074 | /* This must be the root group. */ |
---|
| 3075 | if (grp->parent) |
---|
| 3076 | return NC_EBADGRPID; |
---|
| 3077 | |
---|
| 3078 | /* Call the nc4 close. */ |
---|
| 3079 | if ((retval = close_netcdf4_file(grp->file->nc4_info, 0))) |
---|
| 3080 | return retval; |
---|
| 3081 | |
---|
| 3082 | /* Delete this entry from our list of open files. */ |
---|
| 3083 | if (nc->path) |
---|
| 3084 | free(nc->path); |
---|
| 3085 | nc4_file_list_del(nc); |
---|
| 3086 | |
---|
| 3087 | /* Reset the ncid numbers if there are no more files open. */ |
---|
| 3088 | if(count_NCList() == 0) |
---|
| 3089 | nc4_file_list_free(); |
---|
| 3090 | |
---|
| 3091 | return NC_NOERR; |
---|
| 3092 | } |
---|
| 3093 | |
---|
| 3094 | /* It's possible for any of these pointers to be NULL, in which case |
---|
| 3095 | don't try to figure out that value. */ |
---|
| 3096 | int |
---|
| 3097 | NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp) |
---|
| 3098 | { |
---|
| 3099 | NC_FILE_INFO_T *nc; |
---|
| 3100 | NC_HDF5_FILE_INFO_T *h5; |
---|
| 3101 | NC_GRP_INFO_T *grp; |
---|
| 3102 | NC_DIM_INFO_T *dim; |
---|
| 3103 | NC_ATT_INFO_T *att; |
---|
| 3104 | NC_VAR_INFO_T *var; |
---|
| 3105 | int retval; |
---|
| 3106 | |
---|
| 3107 | LOG((2, "nc_inq: ncid 0x%x", ncid)); |
---|
| 3108 | |
---|
| 3109 | /* Find file metadata. */ |
---|
| 3110 | if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) |
---|
| 3111 | return retval; |
---|
| 3112 | |
---|
| 3113 | #ifdef USE_PNETCDF |
---|
| 3114 | /* Take care of files created/opened with parallel-netcdf library. */ |
---|
| 3115 | if (nc->pnetcdf_file) |
---|
| 3116 | return ncmpi_inq(nc->int_ncid, ndimsp, nvarsp, nattsp, unlimdimidp); |
---|
| 3117 | #endif /* USE_PNETCDF */ |
---|
| 3118 | |
---|
| 3119 | /* Netcdf-3 files are already taken care of. */ |
---|
| 3120 | assert(h5 && grp && nc); |
---|
| 3121 | |
---|
| 3122 | /* Count the number of dims, vars, and global atts. */ |
---|
| 3123 | if (ndimsp) |
---|
| 3124 | { |
---|
| 3125 | *ndimsp = 0; |
---|
| 3126 | for (dim = grp->dim; dim; dim = dim->next) |
---|
| 3127 | (*ndimsp)++; |
---|
| 3128 | } |
---|
| 3129 | if (nvarsp) |
---|
| 3130 | { |
---|
| 3131 | *nvarsp = 0; |
---|
| 3132 | for (var = grp->var; var; var= var->next) |
---|
| 3133 | (*nvarsp)++; |
---|
| 3134 | } |
---|
| 3135 | if (nattsp) |
---|
| 3136 | { |
---|
| 3137 | *nattsp = 0; |
---|
| 3138 | for (att = grp->att; att; att = att->next) |
---|
| 3139 | (*nattsp)++; |
---|
| 3140 | } |
---|
| 3141 | |
---|
| 3142 | if (unlimdimidp) |
---|
| 3143 | { |
---|
| 3144 | /* Default, no unlimited dimension */ |
---|
| 3145 | int found = 0; |
---|
| 3146 | *unlimdimidp = -1; |
---|
| 3147 | |
---|
| 3148 | /* If there's more than one unlimited dim, which was not possible |
---|
| 3149 | with netcdf-3, then only the last unlimited one will be reported |
---|
| 3150 | back in xtendimp. */ |
---|
| 3151 | /* Note that this code is inconsistent with nc_inq_unlimid() */ |
---|
| 3152 | for (dim = grp->dim; dim; dim = dim->next) |
---|
| 3153 | if (dim->unlimited) |
---|
| 3154 | { |
---|
| 3155 | *unlimdimidp = dim->dimid; |
---|
| 3156 | break; |
---|
| 3157 | } |
---|
| 3158 | } |
---|
| 3159 | |
---|
| 3160 | return NC_NOERR; |
---|
| 3161 | } |
---|
| 3162 | |
---|
| 3163 | |
---|
| 3164 | /* This function will do the enddef stuff for a netcdf-4 file. */ |
---|
| 3165 | int |
---|
| 3166 | nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5) |
---|
| 3167 | { |
---|
| 3168 | assert(h5); |
---|
| 3169 | LOG((3, "nc4_enddef_netcdf4_file")); |
---|
| 3170 | |
---|
| 3171 | /* If we're not in define mode, return an error. */ |
---|
| 3172 | if (!(h5->flags & NC_INDEF)) |
---|
| 3173 | return NC_ENOTINDEFINE; |
---|
| 3174 | |
---|
| 3175 | /* Turn define mode off. */ |
---|
| 3176 | h5->flags ^= NC_INDEF; |
---|
| 3177 | |
---|
| 3178 | /* Redef mode needs to be tracked seperately for nc_abort. */ |
---|
| 3179 | h5->redef = 0; |
---|
| 3180 | |
---|
| 3181 | return sync_netcdf4_file(h5); |
---|
| 3182 | } |
---|
| 3183 | |
---|
| 3184 | #ifdef EXTRA_TESTS |
---|
| 3185 | int |
---|
| 3186 | nc_exit() |
---|
| 3187 | { |
---|
| 3188 | if (num_plists || num_spaces) |
---|
| 3189 | return NC_EHDFERR; |
---|
| 3190 | |
---|
| 3191 | return NC_NOERR; |
---|
| 3192 | } |
---|
| 3193 | #endif /* EXTRA_TESTS */ |
---|
| 3194 | |
---|
| 3195 | #ifdef USE_PARALLEL |
---|
| 3196 | int |
---|
| 3197 | nc_use_parallel_enabled() |
---|
| 3198 | { |
---|
| 3199 | return 0; |
---|
| 3200 | } |
---|
| 3201 | #endif /* USE_PARALLEL */ |
---|
| 3202 | |
---|
| 3203 | |
---|