1 | #include <fstream> |
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2 | |
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3 | #include "onetcdf4.hpp" |
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4 | #include "group_template.hpp" |
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5 | #include "mpi.hpp" |
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6 | #include "netcdf.hpp" |
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7 | #include "netCdfInterface.hpp" |
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8 | #include "netCdfException.hpp" |
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9 | |
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10 | namespace xios |
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11 | { |
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12 | /// ////////////////////// Définitions ////////////////////// /// |
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13 | |
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14 | CONetCDF4::CONetCDF4 |
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15 | (const StdString & filename, bool append, bool useClassicFormat, const MPI_Comm * comm, bool multifile) |
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16 | : path() |
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17 | , useClassicFormat(useClassicFormat) |
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18 | , recordOffset(0) |
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19 | { |
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20 | this->wmpi = (comm != NULL) && !multifile; |
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21 | this->initialize(filename, append, useClassicFormat, comm,multifile); |
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22 | } |
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23 | |
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24 | //--------------------------------------------------------------- |
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25 | |
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26 | |
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27 | CONetCDF4::~CONetCDF4(void) |
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28 | { |
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29 | // CheckError(nc_close(this->ncidp)); |
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30 | } |
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31 | |
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32 | ///-------------------------------------------------------------- |
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33 | |
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34 | void CONetCDF4::initialize |
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35 | (const StdString & filename, bool append, bool useClassicFormat, const MPI_Comm * comm, bool multifile) |
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36 | { |
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37 | this->useClassicFormat = useClassicFormat; |
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38 | |
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39 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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40 | if (!multifile) |
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41 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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42 | |
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43 | // If the file does not exist, we always create it |
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44 | if (!append || !std::ifstream(filename.c_str())) |
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45 | { |
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46 | if (comm != NULL) |
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47 | { |
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48 | if (!multifile) CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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49 | else CNetCdfInterface::create(filename, mode, this->ncidp); |
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50 | } |
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51 | else CNetCdfInterface::create(filename, mode, this->ncidp); |
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52 | |
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53 | this->appendMode = false; |
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54 | this->recordOffset = 0; |
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55 | } |
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56 | else |
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57 | { |
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58 | mode |= NC_WRITE; |
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59 | if (comm != NULL) |
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60 | { |
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61 | if (!multifile) CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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62 | else CNetCdfInterface::open(filename, mode, this->ncidp); |
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63 | } |
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64 | else CNetCdfInterface::open(filename, mode, this->ncidp); |
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65 | |
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66 | this->appendMode = true; |
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67 | // Find out how many temporal records have been written already to the file we are opening |
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68 | int ncUnlimitedDimId; |
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69 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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70 | if (ncUnlimitedDimId != -1) |
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71 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, this->recordOffset); |
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72 | else |
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73 | this->recordOffset = 0; |
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74 | } |
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75 | |
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76 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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77 | // This is done per variable for the NetCDF4 format. |
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78 | if (useClassicFormat) |
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79 | CNetCdfInterface::setFill(this->ncidp, false); |
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80 | } |
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81 | |
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82 | void CONetCDF4::close() |
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83 | { |
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84 | (CNetCdfInterface::close(this->ncidp)); |
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85 | } |
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86 | |
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87 | //--------------------------------------------------------------- |
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88 | |
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89 | void CONetCDF4::definition_start(void) |
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90 | { |
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91 | (CNetCdfInterface::reDef(this->ncidp)); |
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92 | } |
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93 | |
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94 | //--------------------------------------------------------------- |
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95 | |
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96 | void CONetCDF4::definition_end(void) |
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97 | { |
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98 | (CNetCdfInterface::endDef(this->ncidp)); |
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99 | } |
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100 | |
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101 | //--------------------------------------------------------------- |
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102 | |
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103 | // Don't need it anymore? |
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104 | // void CONetCDF4::CheckError(int status) |
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105 | // { |
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106 | // if (status != NC_NOERR) |
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107 | // { |
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108 | // StdString errormsg (nc_strerror(status)); // fuite mémoire ici ? |
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109 | // ERROR("CONetCDF4::CheckError(int status)", |
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110 | // << "[ status = " << status << " ] " << errormsg); |
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111 | // } |
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112 | // } |
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113 | |
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114 | //--------------------------------------------------------------- |
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115 | |
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116 | int CONetCDF4::getCurrentGroup(void) |
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117 | { |
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118 | return (this->getGroup(this->getCurrentPath())); |
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119 | } |
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120 | |
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121 | //--------------------------------------------------------------- |
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122 | |
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123 | int CONetCDF4::getGroup(const CONetCDF4Path & path) |
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124 | { |
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125 | int retvalue = this->ncidp; |
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126 | |
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127 | CONetCDF4Path::const_iterator |
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128 | it = path.begin(), end = path.end(); |
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129 | |
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130 | for (;it != end; it++) |
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131 | { |
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132 | const StdString & groupid = *it; |
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133 | (CNetCdfInterface::inqNcId(retvalue, groupid, retvalue)); |
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134 | } |
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135 | return (retvalue); |
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136 | } |
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137 | |
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138 | //--------------------------------------------------------------- |
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139 | |
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140 | int CONetCDF4::getVariable(const StdString & varname) |
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141 | { |
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142 | int varid = 0; |
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143 | int grpid = this->getCurrentGroup(); |
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144 | (CNetCdfInterface::inqVarId(grpid, varname, varid)); |
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145 | return (varid); |
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146 | } |
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147 | |
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148 | //--------------------------------------------------------------- |
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149 | |
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150 | int CONetCDF4::getDimension(const StdString & dimname) |
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151 | { |
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152 | int dimid = 0; |
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153 | int grpid = this->getCurrentGroup(); |
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154 | (CNetCdfInterface::inqDimId(grpid, dimname, dimid)); |
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155 | return (dimid); |
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156 | } |
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157 | |
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158 | //--------------------------------------------------------------- |
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159 | |
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160 | int CONetCDF4::getUnlimitedDimension(void) |
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161 | { |
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162 | int dimid = 0; |
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163 | int grpid = this->getCurrentGroup(); |
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164 | (CNetCdfInterface::inqUnLimDim(grpid, dimid)); |
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165 | return (dimid); |
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166 | } |
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167 | |
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168 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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169 | { |
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170 | int grpid = this->getGroup(path); |
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171 | int dimid = this->getUnlimitedDimension(); |
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172 | |
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173 | if (dimid == -1) return (std::string()); |
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174 | StdString dimname; |
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175 | (CNetCdfInterface::inqDimName(grpid, dimid, dimname)); |
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176 | |
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177 | return (dimname); |
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178 | } |
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179 | |
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180 | //--------------------------------------------------------------- |
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181 | |
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182 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString & varname) |
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183 | { |
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184 | StdSize size = 0; |
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185 | std::vector<StdSize> retvalue; |
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186 | int grpid = this->getCurrentGroup(); |
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187 | int varid = this->getVariable(varname); |
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188 | int nbdim = 0, *dimid = NULL; |
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189 | |
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190 | (CNetCdfInterface::inqVarNDims(grpid, varid, nbdim)); |
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191 | dimid = new int[nbdim](); |
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192 | (CNetCdfInterface::inqVarDimId(grpid, varid, dimid)); |
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193 | |
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194 | for (int i = 0; i < nbdim; i++) |
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195 | { |
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196 | (CNetCdfInterface::inqDimLen(grpid, dimid[i], size)); |
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197 | if (size == NC_UNLIMITED) |
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198 | size = UNLIMITED_DIM; |
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199 | retvalue.push_back(size); |
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200 | } |
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201 | delete [] dimid; |
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202 | return (retvalue); |
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203 | } |
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204 | |
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205 | std::vector<std::string> CONetCDF4::getDimensionsIdList (const std::string * _varname) |
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206 | { |
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207 | int nDimNull = 0; |
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208 | int nbdim = 0, *dimid = NULL; |
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209 | int grpid = this->getCurrentGroup(); |
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210 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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211 | std::vector<std::string> retvalue; |
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212 | |
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213 | if (_varname != NULL) |
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214 | { |
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215 | (CNetCdfInterface::inqVarNDims(grpid, varid, nbdim)); |
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216 | dimid = new int[nbdim](); |
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217 | (CNetCdfInterface::inqVarDimId(grpid, varid, dimid)); |
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218 | } |
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219 | else |
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220 | { |
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221 | (CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1)); |
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222 | dimid = new int[nbdim](); |
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223 | (CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1)); |
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224 | } |
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225 | |
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226 | for (int i = 0; i < nbdim; i++) |
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227 | { |
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228 | std::string dimname; |
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229 | (CNetCdfInterface::inqDimName(grpid, dimid[i], dimname)); |
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230 | retvalue.push_back(dimname); |
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231 | } |
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232 | delete [] dimid; |
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233 | |
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234 | return (retvalue); |
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235 | } |
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236 | |
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237 | |
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238 | //--------------------------------------------------------------- |
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239 | |
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240 | const CONetCDF4::CONetCDF4Path & CONetCDF4::getCurrentPath(void) const |
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241 | { return (this->path); } |
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242 | |
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243 | void CONetCDF4::setCurrentPath(const CONetCDF4Path & path) |
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244 | { this->path = path; } |
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245 | |
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246 | //--------------------------------------------------------------- |
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247 | |
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248 | int CONetCDF4::addGroup(const StdString & name) |
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249 | { |
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250 | int retvalue = 0; |
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251 | int grpid = this->getCurrentGroup(); |
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252 | (CNetCdfInterface::defGrp(grpid, name, retvalue)); |
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253 | return (retvalue); |
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254 | } |
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255 | |
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256 | //--------------------------------------------------------------- |
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257 | |
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258 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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259 | { |
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260 | int retvalue = 0; |
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261 | int grpid = this->getCurrentGroup(); |
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262 | if (size != UNLIMITED_DIM) |
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263 | (CNetCdfInterface::defDim(grpid, name, size, retvalue)); |
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264 | else |
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265 | (CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue)); |
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266 | return (retvalue); |
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267 | } |
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268 | |
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269 | //--------------------------------------------------------------- |
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270 | |
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271 | int CONetCDF4::addVariable(const StdString & name, nc_type type, |
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272 | const std::vector<StdString> & dim) |
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273 | { |
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274 | int varid = 0; |
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275 | std::vector<int> dimids; |
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276 | std::vector<StdSize> dimsizes ; |
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277 | StdSize size ; |
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278 | StdSize totalSize ; |
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279 | StdSize maxSize=1024*1024*256 ; // == 2GB/8 if output double |
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280 | |
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281 | int grpid = this->getCurrentGroup(); |
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282 | |
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283 | std::vector<StdString>::const_iterator |
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284 | it = dim.begin(), end = dim.end(); |
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285 | |
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286 | for (;it != end; it++) |
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287 | { |
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288 | const StdString & dimid = *it; |
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289 | dimids.push_back(this->getDimension(dimid)); |
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290 | (CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size)); |
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291 | if (size==NC_UNLIMITED) size=1 ; |
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292 | dimsizes.push_back(size) ; |
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293 | } |
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294 | |
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295 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &(dimids[0]), varid); |
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296 | |
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297 | // The classic NetCDF format does not support chunking nor fill parameters |
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298 | if (!useClassicFormat) |
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299 | { |
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300 | // set chunksize : size of one record |
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301 | // but must not be > 2GB (netcdf or HDF5 problem) |
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302 | totalSize = 1; |
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303 | for (vector<StdSize>::reverse_iterator it = dimsizes.rbegin(); it != dimsizes.rend(); ++it) |
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304 | { |
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305 | totalSize *= *it; |
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306 | if (totalSize >= maxSize) *it = 1; |
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307 | } |
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308 | |
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309 | CNetCdfInterface::defVarChunking(grpid, varid, NC_CHUNKED, &dimsizes[0]); |
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310 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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311 | } |
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312 | |
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313 | return (varid); |
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314 | } |
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315 | |
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316 | //--------------------------------------------------------------- |
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317 | |
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318 | template <> |
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319 | void CONetCDF4::addAttribute |
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320 | (const StdString & name, const StdString & value, const StdString * varname ) |
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321 | { |
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322 | int grpid = this->getCurrentGroup(); |
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323 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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324 | (CNetCdfInterface::putAtt(grpid, varid, name, NC_CHAR, value.size(), value.c_str())); |
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325 | //CheckError(nc_put_att_string(grpid, varid, name.c_str(), 1, &str)); |
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326 | } |
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327 | |
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328 | //--------------------------------------------------------------- |
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329 | |
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330 | template <> |
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331 | void CONetCDF4::addAttribute |
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332 | (const StdString & name, const double & value, const StdString * varname ) |
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333 | { |
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334 | int grpid = this->getCurrentGroup(); |
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335 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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336 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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337 | } |
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338 | |
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339 | template <> |
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340 | void CONetCDF4::addAttribute |
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341 | (const StdString & name, const CArray<double,1>& value, const StdString * varname ) |
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342 | { |
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343 | int grpid = this->getCurrentGroup(); |
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344 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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345 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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346 | } |
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347 | //--------------------------------------------------------------- |
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348 | |
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349 | template <> |
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350 | void CONetCDF4::addAttribute |
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351 | (const StdString & name, const float & value, const StdString * varname ) |
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352 | { |
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353 | int grpid = this->getCurrentGroup(); |
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354 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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355 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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356 | } |
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357 | |
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358 | template <> |
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359 | void CONetCDF4::addAttribute |
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360 | (const StdString & name, const CArray<float,1>& value, const StdString * varname ) |
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361 | { |
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362 | int grpid = this->getCurrentGroup(); |
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363 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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364 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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365 | } |
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366 | |
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367 | //--------------------------------------------------------------- |
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368 | |
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369 | template <> |
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370 | void CONetCDF4::addAttribute |
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371 | (const StdString & name, const int & value, const StdString * varname ) |
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372 | { |
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373 | int grpid = this->getCurrentGroup(); |
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374 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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375 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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376 | } |
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377 | |
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378 | template <> |
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379 | void CONetCDF4::addAttribute |
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380 | (const StdString & name, const CArray<int,1>& value, const StdString * varname ) |
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381 | { |
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382 | int grpid = this->getCurrentGroup(); |
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383 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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384 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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385 | } |
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386 | |
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387 | template <> |
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388 | void CONetCDF4::addAttribute |
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389 | (const StdString & name, const short int & value, const StdString * varname ) |
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390 | { |
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391 | int grpid = this->getCurrentGroup(); |
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392 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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393 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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394 | } |
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395 | |
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396 | template <> |
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397 | void CONetCDF4::addAttribute |
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398 | (const StdString & name, const CArray<short int,1>& value, const StdString * varname ) |
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399 | { |
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400 | int grpid = this->getCurrentGroup(); |
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401 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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402 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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403 | } |
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404 | |
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405 | |
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406 | |
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407 | template <> |
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408 | void CONetCDF4::addAttribute |
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409 | (const StdString & name, const long int & value, const StdString * varname ) |
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410 | { |
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411 | int grpid = this->getCurrentGroup(); |
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412 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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413 | (CNetCdfInterface::putAttType(grpid, varid, name, 1, &value)); |
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414 | } |
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415 | |
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416 | template <> |
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417 | void CONetCDF4::addAttribute |
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418 | (const StdString & name, const CArray<long int,1>& value, const StdString * varname ) |
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419 | { |
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420 | int grpid = this->getCurrentGroup(); |
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421 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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422 | (CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst())); |
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423 | } |
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424 | |
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425 | |
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426 | |
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427 | //--------------------------------------------------------------- |
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428 | |
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429 | void CONetCDF4::getWriteDataInfos(const StdString & name, StdSize record, StdSize & array_size, |
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430 | std::vector<StdSize> & sstart, |
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431 | std::vector<StdSize> & scount, |
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432 | const std::vector<StdSize> * start, |
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433 | const std::vector<StdSize> * count) |
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434 | { |
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435 | std::vector<std::size_t> sizes = this->getDimensions(name); |
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436 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
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437 | std::vector<std::size_t>::const_iterator |
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438 | it = sizes.begin(), end = sizes.end(); |
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439 | int i = 0; |
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440 | |
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441 | if (iddims.begin()->compare(this->getUnlimitedDimensionName()) == 0) |
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442 | { |
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443 | sstart.push_back(record + recordOffset); |
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444 | scount.push_back(1); |
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445 | if ((start == NULL) && |
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446 | (count == NULL)) i++; |
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447 | it++; |
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448 | } |
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449 | |
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450 | for (;it != end; it++) |
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451 | { |
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452 | if ((start != NULL) && (count != NULL)) |
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453 | { |
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454 | sstart.push_back((*start)[i]); |
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455 | scount.push_back((*count)[i]); |
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456 | array_size *= (*count)[i]; |
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457 | i++; |
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458 | } |
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459 | else |
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460 | { |
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461 | sstart.push_back(0); |
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462 | scount.push_back(sizes[i]); |
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463 | array_size *= sizes[i]; |
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464 | i++; |
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465 | } |
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466 | } |
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467 | |
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468 | } |
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469 | |
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470 | |
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471 | |
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472 | template <> |
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473 | void CONetCDF4::writeData_(int grpid, int varid, |
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474 | const std::vector<StdSize> & sstart, |
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475 | const std::vector<StdSize> & scount, const double * data) |
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476 | { |
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477 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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478 | // sync() ; |
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479 | } |
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480 | |
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481 | //--------------------------------------------------------------- |
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482 | |
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483 | template <> |
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484 | void CONetCDF4::writeData_(int grpid, int varid, |
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485 | const std::vector<StdSize> & sstart, |
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486 | const std::vector<StdSize> & scount, const int * data) |
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487 | { |
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488 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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489 | // sync() ; |
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490 | } |
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491 | |
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492 | //--------------------------------------------------------------- |
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493 | |
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494 | template <> |
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495 | void CONetCDF4::writeData_(int grpid, int varid, |
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496 | const std::vector<StdSize> & sstart, |
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497 | const std::vector<StdSize> & scount, const float * data) |
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498 | { |
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499 | (CNetCdfInterface::putVaraType(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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500 | // sync() ; |
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501 | } |
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502 | |
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503 | //--------------------------------------------------------------- |
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504 | |
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505 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString & name) |
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506 | { |
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507 | int grpid = this->getCurrentGroup(); |
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508 | int varid = this->getVariable(name); |
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509 | StdSize array_size = 1; |
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510 | std::vector<StdSize> sstart, scount; |
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511 | |
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512 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
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513 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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514 | } |
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515 | |
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516 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString & name, |
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517 | bool collective, StdSize record, bool isRoot) |
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518 | { |
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519 | int grpid = this->getCurrentGroup(); |
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520 | int varid = this->getVariable(name); |
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521 | |
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522 | map<int,size_t>::iterator it=timeAxis.find(varid) ; |
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523 | if (it==timeAxis.end()) timeAxis[varid]=record ; |
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524 | else |
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525 | { |
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526 | if (it->second >= record) return ; |
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527 | else it->second =record ; |
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528 | } |
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529 | |
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530 | StdSize array_size = 1; |
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531 | std::vector<StdSize> sstart, scount; |
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532 | |
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533 | if (this->wmpi && collective) |
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534 | (CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE)); |
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535 | if (this->wmpi && !collective) |
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536 | (CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT)); |
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537 | |
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538 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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539 | if (using_netcdf_internal) if (!isRoot) { sstart[0]=sstart[0]+1 ; scount[0]=0 ;} |
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540 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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541 | } |
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542 | |
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543 | //--------------------------------------------------------------- |
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544 | |
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545 | bool CONetCDF4::varExist(const StdString & varname) |
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546 | { |
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547 | int grpid = this->getCurrentGroup(); |
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548 | return (CNetCdfInterface::isVarExisted(grpid, varname)); |
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549 | } |
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550 | |
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551 | void CONetCDF4::sync(void) |
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552 | { |
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553 | (CNetCdfInterface::sync(this->ncidp)) ; |
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554 | } |
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555 | ///-------------------------------------------------------------- |
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556 | } // namespace xios |
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