1 | /** \file |
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2 | This header file contains the definitions of structs used to hold |
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3 | netCDF file metadata in memory. |
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4 | |
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5 | Copyright 2005-2011 University Corporation for Atmospheric |
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6 | Research/Unidata. |
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7 | */ |
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8 | |
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9 | #ifndef _NC4INTERNAL_ |
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10 | #define _NC4INTERNAL_ |
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11 | |
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12 | #include <config.h> |
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13 | #include <stdio.h> |
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14 | #include <stdlib.h> |
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15 | #include <ctype.h> |
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16 | #include <stdarg.h> |
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17 | #include <string.h> |
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18 | #include <hdf5.h> |
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19 | #include <ncdimscale.h> |
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20 | #include <nc_logging.h> |
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21 | |
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22 | #ifdef USE_PARALLEL |
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23 | #include <netcdf_par.h> |
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24 | #else |
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25 | #define MPI_Info int |
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26 | #define MPI_Comm int |
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27 | #include <netcdf.h> |
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28 | #endif /* USE_PARALLEL */ |
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29 | #include <netcdf_f.h> |
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30 | |
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31 | #ifdef USE_HDF4 |
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32 | #include <mfhdf.h> |
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33 | #endif |
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34 | |
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35 | #define FILE_ID_MASK (0xffff0000) |
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36 | #define GRP_ID_MASK (0x0000ffff) |
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37 | #define ID_SHIFT (16) |
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38 | |
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39 | typedef enum {GET, PUT} NC_PG_T; |
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40 | typedef enum {VAR, DIM, ATT} NC_OBJ_T; |
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41 | |
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42 | #define NC_MAX_HDF5_NAME (NC_MAX_NAME + 10) |
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43 | #define NC_V2_ERR (-1) |
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44 | |
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45 | /* The name of the root group. */ |
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46 | #define NC_GROUP_NAME "/" |
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47 | |
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48 | #define MEGABYTE 1048576 |
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49 | |
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50 | /* |
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51 | * limits of the external representation |
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52 | */ |
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53 | #define X_SCHAR_MIN (-128) |
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54 | #define X_SCHAR_MAX 127 |
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55 | #define X_UCHAR_MAX 255U |
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56 | #define X_SHORT_MIN (-32768) |
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57 | #define X_SHRT_MIN X_SHORT_MIN /* alias compatible with limits.h */ |
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58 | #define X_SHORT_MAX 32767 |
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59 | #define X_SHRT_MAX X_SHORT_MAX /* alias compatible with limits.h */ |
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60 | #define X_USHORT_MAX 65535U |
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61 | #define X_USHRT_MAX X_USHORT_MAX /* alias compatible with limits.h */ |
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62 | #define X_INT_MIN (-2147483647-1) |
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63 | #define X_INT_MAX 2147483647 |
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64 | #define X_LONG_MIN X_INT_MIN |
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65 | #define X_LONG_MAX X_INT_MAX |
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66 | #define X_UINT_MAX 4294967295U |
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67 | #ifdef WIN32 /* Windows, of course, has to be a *little* different. */ |
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68 | #define X_FLOAT_MAX 3.402823466e+38f |
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69 | #else |
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70 | #define X_FLOAT_MAX 3.40282347e+38f |
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71 | #endif /* WIN32 */ |
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72 | #define X_FLOAT_MIN (-X_FLOAT_MAX) |
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73 | #define X_DOUBLE_MAX 1.7976931348623157e+308 |
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74 | #define X_DOUBLE_MIN (-X_DOUBLE_MAX) |
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75 | |
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76 | /* These have to do with creating chuncked datasets in HDF5. */ |
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77 | #define NC_HDF5_UNLIMITED_DIMSIZE (0) |
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78 | #define NC_HDF5_CHUNKSIZE_FACTOR (10) |
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79 | #define NC_HDF5_MIN_CHUNK_SIZE (2) |
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80 | |
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81 | #define NC_EMPTY_SCALE "NC_EMPTY_SCALE" |
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82 | |
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83 | /* This is an attribute I had to add to handle multidimensional |
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84 | * coordinate variables. */ |
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85 | #define COORDINATES "_Netcdf4Coordinates" |
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86 | #define COORDINATES_LEN (NC_MAX_NAME * 5) |
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87 | |
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88 | /* This is used when the user defines a non-coordinate variable with |
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89 | * same name as a dimension. */ |
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90 | #define NON_COORD_PREPEND "_nc4_non_coord_" |
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91 | |
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92 | /* An attribute in the HDF5 root group of this name means that the |
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93 | * file must follow strict netCDF classic format rules. */ |
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94 | #define NC3_STRICT_ATT_NAME "_nc3_strict" |
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95 | |
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96 | /* If this attribute is present on a dimscale variable, use the value |
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97 | * as the netCDF dimid. */ |
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98 | #define NC_DIMID_ATT_NAME "_Netcdf4Dimid" |
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99 | |
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100 | /* This is a struct to handle the dim metadata. */ |
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101 | typedef struct NC_DIM_INFO |
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102 | { |
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103 | char *name; |
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104 | size_t len; |
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105 | int dimid; |
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106 | int unlimited; |
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107 | int extended; |
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108 | struct NC_DIM_INFO *next; |
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109 | struct NC_DIM_INFO *prev; |
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110 | hid_t hdf_dimscaleid; |
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111 | char *old_name; /* only used to rename dim */ |
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112 | int dirty; |
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113 | unsigned char coord_var_in_grp; |
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114 | struct NC_VAR_INFO *coord_var; /* The coord var, if it exists. */ |
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115 | int too_long; /* True if len it too big to fit in local size_t. */ |
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116 | } NC_DIM_INFO_T; |
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117 | |
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118 | typedef struct NC_ATT_INFO |
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119 | { |
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120 | int len; |
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121 | char *name; |
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122 | struct NC_ATT_INFO *next; |
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123 | struct NC_ATT_INFO *prev; |
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124 | int dirty; |
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125 | int created; |
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126 | nc_type xtype; |
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127 | hid_t native_typeid; |
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128 | int attnum; |
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129 | void *data; |
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130 | nc_vlen_t *vldata; /* only used for vlen */ |
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131 | char **stdata; /* only for string type. */ |
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132 | int class; |
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133 | } NC_ATT_INFO_T; |
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134 | |
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135 | /* This is a struct to handle the var metadata. */ |
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136 | typedef struct NC_VAR_INFO |
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137 | { |
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138 | char *name; |
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139 | char *hdf5_name; /* used if different from name */ |
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140 | int ndims; |
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141 | int *dimids; |
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142 | NC_DIM_INFO_T **dim; |
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143 | int varid; |
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144 | int natts; |
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145 | struct NC_VAR_INFO *next; |
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146 | struct NC_VAR_INFO *prev; |
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147 | int dirty; |
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148 | int created; |
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149 | int written_to; |
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150 | int *dimscale_attached; |
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151 | struct NC_TYPE_INFO *type_info; |
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152 | nc_type xtype; |
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153 | hid_t hdf_datasetid; |
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154 | NC_ATT_INFO_T *att; |
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155 | int no_fill; |
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156 | void *fill_value; |
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157 | size_t *chunksizes; |
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158 | int contiguous; |
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159 | int parallel_access; |
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160 | int dimscale; |
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161 | HDF5_OBJID_T *dimscale_hdf5_objids; |
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162 | int deflate; |
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163 | int deflate_level; |
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164 | int shuffle; |
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165 | int fletcher32; |
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166 | int options_mask; |
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167 | int pixels_per_block; |
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168 | size_t chunk_cache_size, chunk_cache_nelems; |
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169 | float chunk_cache_preemption; |
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170 | /* Stuff below is for hdf4 files. */ |
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171 | int sdsid; |
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172 | int hdf4_data_type; |
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173 | /* Stuff below for diskless data files. */ |
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174 | void *diskless_data; |
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175 | } NC_VAR_INFO_T; |
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176 | |
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177 | typedef struct NC_FIELD_INFO |
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178 | { |
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179 | struct NC_FIELD_INFO *next; |
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180 | struct NC_FIELD_INFO *prev; |
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181 | nc_type nctype; |
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182 | hid_t hdf_typeid; |
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183 | hid_t native_typeid; |
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184 | size_t offset; |
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185 | char *name; |
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186 | int fieldid; |
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187 | int ndims; |
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188 | int *dim_size; |
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189 | } NC_FIELD_INFO_T; |
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190 | |
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191 | typedef struct NC_ENUM_MEMBER_INFO |
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192 | { |
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193 | struct NC_ENUM_MEMBER_INFO *next; |
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194 | struct NC_ENUM_MEMBER_INFO *prev; |
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195 | char *name; |
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196 | void *value; |
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197 | } NC_ENUM_MEMBER_INFO_T; |
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198 | |
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199 | typedef struct NC_TYPE_INFO |
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200 | { |
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201 | struct NC_TYPE_INFO *next; |
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202 | struct NC_TYPE_INFO *prev; |
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203 | nc_type nc_typeid; |
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204 | hid_t hdf_typeid; |
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205 | hid_t native_typeid; |
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206 | size_t size; |
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207 | int committed; /* What the pig is, but the hen isn't, at breakfast. */ |
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208 | char *name; |
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209 | int class; /* NC_VLEN, NC_COMPOUND, NC_OPAQUE, or NC_ENUM */ |
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210 | int num_enum_members; |
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211 | NC_ENUM_MEMBER_INFO_T *enum_member; |
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212 | NC_FIELD_INFO_T *field; /* Used for compound types. */ |
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213 | int num_fields; |
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214 | nc_type base_nc_type; /* for VLEN and ENUM only */ |
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215 | hid_t base_hdf_typeid; /* for VLEN only */ |
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216 | int close_hdf_typeid; /* True when hdf_typeid must be H5Tclosed. */ |
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217 | int endianness; |
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218 | } NC_TYPE_INFO_T; |
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219 | |
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220 | /* This holds information for one group. Groups reproduce with |
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221 | * parthenogenesis. */ |
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222 | typedef struct NC_GRP_INFO |
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223 | { |
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224 | int nc_grpid; |
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225 | struct NC_GRP_INFO *parent; |
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226 | struct NC_GRP_INFO *children; |
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227 | struct NC_GRP_INFO *next; /* points to siblings */ |
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228 | struct NC_GRP_INFO *prev; /* points to siblings */ |
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229 | NC_VAR_INFO_T *var; |
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230 | NC_DIM_INFO_T *dim; |
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231 | NC_ATT_INFO_T *att; |
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232 | int nvars; |
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233 | int ndims; |
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234 | int natts; |
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235 | struct NC_FILE_INFO *file; |
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236 | char *name; |
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237 | hid_t hdf_grpid; |
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238 | NC_TYPE_INFO_T *type; |
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239 | } NC_GRP_INFO_T; |
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240 | |
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241 | /* These constants apply to the cmode parameter in the |
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242 | * HDF5_FILE_INFO_T defined below. */ |
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243 | #define NC_CREAT 2 /* in create phase, cleared by ncendef */ |
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244 | #define NC_INDEF 8 /* in define mode, cleared by ncendef */ |
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245 | #define NC_NSYNC 0x10 /* synchronise numrecs on change */ |
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246 | #define NC_HSYNC 0x20 /* synchronise whole header on change */ |
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247 | #define NC_NDIRTY 0x40 /* numrecs has changed */ |
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248 | #define NC_HDIRTY 0x80 /* header info has changed */ |
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249 | |
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250 | /* This is the metadata we need to keep track of for each |
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251 | netcdf-4/HDF5 file. */ |
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252 | typedef struct |
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253 | { |
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254 | hid_t hdfid; |
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255 | int flags; |
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256 | int cmode; |
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257 | int nvars; |
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258 | int ndims; |
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259 | int natts; |
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260 | int parallel; /* true if file is open for parallel access */ |
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261 | int redef; |
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262 | char *path; |
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263 | int fill_mode; |
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264 | int no_write; /* true if nc_open has mode NC_NOWRITE. */ |
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265 | NC_GRP_INFO_T *root_grp; |
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266 | short next_nc_grpid; |
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267 | NC_TYPE_INFO_T *type; |
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268 | int next_typeid; |
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269 | int next_dimid; |
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270 | int ignore_creationorder; |
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271 | int hdf4; |
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272 | int sdid; |
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273 | } NC_HDF5_FILE_INFO_T; |
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274 | |
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275 | /* In the nc_file array there will be one entry for each open file.*/ |
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276 | |
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277 | /* There's an external ncid (ext_ncid) and an internal ncid |
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278 | * (int_ncid). The ext_ncid is the ncid returned to the user. If |
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279 | * the user has opened or created a netcdf-4 file, then the |
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280 | * ext_ncid is the same as the int_ncid. If he has opened or |
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281 | * created a netcdf-3 file ext_ncid (which the user sees) is |
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282 | * different from the int_ncid, which is the ncid returned by the |
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283 | * netcdf-3 layer, which insists on inventing its own ncids, |
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284 | * regardless of what is already in use due to previously opened |
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285 | * netcdf-4 files. The ext_ncid contains the ncid for the root |
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286 | * group (i.e. group zero). */ |
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287 | |
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288 | /* Warning: fields from BEGIN COMMON to END COMMON must be same for: |
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289 | 1. NCcommon (include/ncdispatch.h) |
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290 | 2. NC (libsrc/nc.h) |
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291 | 3. NC_FILE_INFO (libsrc4/nc4internal.h) |
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292 | 4. whatever libdiskless uses |
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293 | */ |
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294 | typedef struct NC_FILE_INFO |
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295 | { |
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296 | /*BEGIN COMMON*/ |
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297 | int ext_ncid; |
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298 | int int_ncid; |
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299 | struct NC_Dispatch* dispatch; |
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300 | void* dispatchdata; |
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301 | char* path; |
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302 | int substrate; |
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303 | /*END COMMON*/ |
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304 | |
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305 | #ifdef USE_PNETCDF |
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306 | /* pnetcdf_file will be true if the file is created/opened with the |
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307 | * parallel-netcdf library. pnetcdf_access_mode keeps track of |
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308 | * whether independpent or collective mode is |
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309 | * desired. pnetcdf_ndims keeps track of how many dims each var |
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310 | * has, which I need to know to convert start, count, and stride |
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311 | * arrays from size_t to MPI_Offset. (I can't use an inq function |
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312 | * to find out the number of dims, because these are collective in |
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313 | * pnetcdf.) */ |
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314 | int pnetcdf_file; |
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315 | int pnetcdf_access_mode; |
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316 | int pnetcdf_ndims[NC_MAX_VARS]; |
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317 | #endif /* USE_PNETCDF */ |
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318 | |
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319 | /* The nc4_info pointer will remain NULL for netcdf3 files, |
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320 | * otherwise it points to information about the netcdf-4 file. */ |
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321 | NC_HDF5_FILE_INFO_T *nc4_info; |
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322 | } NC_FILE_INFO_T; |
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323 | |
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324 | /* These functions only use the netcdf API calls, so they will work on |
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325 | both new format and old format files. */ |
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326 | /*int copy_dataset(int ncid_in, int ncid_out);*/ |
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327 | |
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328 | |
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329 | /* These functions convert beteen netcdf and HDF5 types. */ |
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330 | int nc4_get_typelen_mem(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, |
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331 | int is_long, size_t *len); |
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332 | int nc4_convert_type(const void *src, void *dest, |
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333 | const nc_type src_type, const nc_type dest_type, |
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334 | const size_t len, int *range_error, |
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335 | const void *fill_value, int strict_nc3, int src_long, |
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336 | int dest_long); |
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337 | |
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338 | /* These functions do HDF5 things. */ |
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339 | int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset); |
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340 | int pg_var(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, nc_type xtype, int is_long, |
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341 | void *ip); |
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342 | int nc4_pg_var1(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *indexp, |
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343 | nc_type xtype, int is_long, void *ip); |
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344 | int nc4_put_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, |
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345 | const size_t *countp, nc_type xtype, int is_long, void *op); |
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346 | int nc4_get_vara(NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, |
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347 | const size_t *countp, nc_type xtype, int is_long, void *op); |
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348 | int nc4_pg_varm(NC_PG_T pg, NC_FILE_INFO_T *nc, int ncid, int varid, const size_t *startp, |
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349 | const size_t *countp, const ptrdiff_t *stridep, |
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350 | const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op); |
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351 | int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp); |
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352 | int nc4_rec_write_metadata(NC_GRP_INFO_T *grp); |
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353 | int nc4_rec_write_types(NC_GRP_INFO_T *grp); |
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354 | int nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5); |
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355 | int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var); |
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356 | int nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T * var); |
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357 | |
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358 | /* The following functions manipulate the in-memory linked list of |
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359 | metadata, without using HDF calls. */ |
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360 | int nc4_find_nc_grp_h5(int ncid, NC_FILE_INFO_T **nc, NC_GRP_INFO_T **grp, |
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361 | NC_HDF5_FILE_INFO_T **h5); |
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362 | int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_HDF5_FILE_INFO_T **h5); |
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363 | int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp); |
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364 | NC_GRP_INFO_T *nc4_find_nc_grp(int ncid); |
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365 | NC_GRP_INFO_T *nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid); |
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366 | NC_FILE_INFO_T *nc4_find_nc_file(int ncid); |
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367 | int nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim, NC_GRP_INFO_T **dim_grp); |
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368 | int nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len); |
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369 | int nc4_find_type(NC_HDF5_FILE_INFO_T *h5, int typeid, NC_TYPE_INFO_T **type); |
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370 | NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, hid_t target_nc_typeid); |
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371 | NC_TYPE_INFO_T *nc4_rec_find_hdf_type(NC_GRP_INFO_T *start_grp, hid_t target_hdf_typeid); |
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372 | NC_TYPE_INFO_T *nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name); |
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373 | NC_TYPE_INFO_T *nc4_rec_find_equal_type(NC_GRP_INFO_T *start_grp, int ncid1, NC_TYPE_INFO_T *type); |
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374 | int nc4_find_nc_att(int ncid, int varid, const char *name, int attnum, |
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375 | NC_ATT_INFO_T **att); |
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376 | int nc4_find_g_var_nc(NC_FILE_INFO_T *nc, int ncid, int varid, |
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377 | NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var); |
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378 | int nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name, int attnum, |
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379 | NC_ATT_INFO_T **att); |
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380 | int nc4_get_hdf_typeid(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, |
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381 | hid_t *hdf_typeid, int endianness); |
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382 | /*int var_info_nc(NC_PG_T pg, hid_t dataset, NC_VAR_INFO_T *var_info);*/ |
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383 | |
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384 | /* These list functions add and delete vars, atts, and files. */ |
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385 | int nc4_file_list_add(NC_FILE_INFO_T**, struct NC_Dispatch*); |
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386 | void nc4_file_list_free(void); |
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387 | |
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388 | int nc4_nc4f_list_add(NC_FILE_INFO_T *nc, const char *path, int mode); |
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389 | int nc4_var_list_add(NC_VAR_INFO_T **list, NC_VAR_INFO_T **var); |
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390 | int nc4_dim_list_add(NC_DIM_INFO_T **list); |
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391 | int nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim); |
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392 | int nc4_att_list_add(NC_ATT_INFO_T **list); |
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393 | int nc4_type_list_add(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T **new_type); |
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394 | int nc4_field_list_add(NC_FIELD_INFO_T **list, int fieldid, const char *name, |
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395 | size_t offset, hid_t field_hdf_typeid, hid_t native_typeid, |
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396 | nc_type xtype, int ndims, const int *dim_sizesp); |
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397 | void nc4_file_list_del(NC_FILE_INFO_T *nc); |
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398 | int nc4_att_list_del(NC_ATT_INFO_T **list, NC_ATT_INFO_T *att); |
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399 | int nc4_grp_list_add(NC_GRP_INFO_T **list, int new_nc_grpid, NC_GRP_INFO_T *parent_grp, |
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400 | NC_FILE_INFO_T *nc, char *name, NC_GRP_INFO_T **grp); |
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401 | int nc4_rec_grp_del(NC_GRP_INFO_T **list, NC_GRP_INFO_T *grp); |
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402 | int nc4_enum_member_add(NC_ENUM_MEMBER_INFO_T **list, size_t size, |
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403 | const char *name, const void *value); |
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404 | |
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405 | int NC_check_name(const char *name); |
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406 | |
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407 | /* Check and normalize names. */ |
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408 | int nc4_check_name(const char *name, char *norm_name); |
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409 | int nc4_normalize_name(const char *name, char *norm_name); |
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410 | |
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411 | /* Check for name collisions. */ |
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412 | int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name); |
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413 | |
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414 | /* Insert and read one element into an already allocated vlen array |
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415 | * element (this is for F77). */ |
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416 | /*int nc_put_vlen_element(int ncid, int typeid, void *vlen_element, size_t len, const void *data); |
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417 | int nc_get_vlen_element(int ncid, int typeid, const void *vlen_element, size_t *len, void *data);*/ |
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418 | |
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419 | /* This is only included if --enable-logging is used for configure; it |
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420 | prints info about the metadata to stderr. */ |
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421 | #ifdef LOGGING |
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422 | int log_metadata_nc(NC_FILE_INFO_T *nc); |
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423 | #endif |
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424 | |
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425 | #endif /* _NETCDF4_ */ |
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