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; |
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447 | |
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448 | return res; |
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449 | } |
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450 | |
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451 | /* This function is called by read_dataset when a dimension scale |
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452 | * dataset is encountered. It reads in the dimension data (creating a |
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453 | * new NC_DIM_INFO_T object), and also checks to see if this is a |
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454 | * dimension without a variable - that is, a coordinate dimension |
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455 | * which does not have any coordinate data. */ |
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456 | static int |
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457 | read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, char *obj_name, |
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458 | hsize_t scale_size, hsize_t max_scale_size, |
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459 | int *dim_without_var) |
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460 | { |
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461 | /*char *start_of_len;*/ |
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462 | char dimscale_name_att[NC_MAX_NAME + 1] = ""; |
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463 | hid_t attid = 0; |
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464 | int max_len; |
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465 | int retval; |
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466 | |
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467 | /* Add a dimension for this scale. */ |
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468 | if ((retval = nc4_dim_list_add(&grp->dim))) |
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469 | return retval; |
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470 | |
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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 | |
---|