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 "netcdf.hpp" |
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6 | #include "netCdfInterface.hpp" |
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7 | #include "netCdfException.hpp" |
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8 | |
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9 | namespace xios |
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10 | { |
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11 | /// ////////////////////// Définitions ////////////////////// /// |
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12 | |
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13 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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14 | const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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15 | : path() |
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16 | , wmpi(false) |
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17 | , useClassicFormat(useClassicFormat) |
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18 | , useCFConvention(useCFConvention) |
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19 | { |
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20 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
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21 | } |
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22 | |
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23 | //--------------------------------------------------------------- |
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24 | |
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25 | CONetCDF4::~CONetCDF4(void) |
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26 | { |
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27 | } |
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28 | |
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29 | ///-------------------------------------------------------------- |
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30 | |
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31 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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32 | const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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33 | { |
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34 | this->useClassicFormat = useClassicFormat; |
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35 | this->useCFConvention = useCFConvention; |
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36 | |
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37 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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38 | |
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39 | // Don't use parallel mode if there is only one process |
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40 | if (comm) |
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41 | { |
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42 | int commSize = 0; |
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43 | MPI_Comm_size(*comm, &commSize); |
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44 | if (commSize <= 1) |
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45 | comm = NULL; |
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46 | } |
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47 | wmpi = comm && !multifile; |
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48 | |
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49 | |
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50 | if (wmpi) |
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51 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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52 | |
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53 | // If the file does not exist, we always create it |
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54 | if (!append || !std::ifstream(filename.c_str())) |
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55 | { |
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56 | if (wmpi) |
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57 | { |
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58 | CNetCdfInterface::createPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp); |
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59 | } |
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60 | else |
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61 | { |
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62 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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63 | } |
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64 | |
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65 | |
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66 | this->appendMode = false; |
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67 | } |
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68 | else |
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69 | { |
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70 | mode |= NC_WRITE; |
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71 | if (wmpi) |
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72 | { |
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73 | CNetCdfInterface::openPar(filename, mode, static_cast<MPI_Comm>(comm->mpi_comm), MPI_INFO_NULL_STD, this->ncidp); |
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74 | } |
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75 | else |
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76 | { |
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77 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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78 | } |
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79 | |
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80 | this->appendMode = true; |
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81 | } |
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82 | |
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83 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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84 | // This is done per variable for the NetCDF4 format. |
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85 | if (useClassicFormat) |
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86 | CNetCdfInterface::setFill(this->ncidp, false); |
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87 | |
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88 | this->timeCounterName = timeCounterName; |
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89 | } |
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90 | |
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91 | void CONetCDF4::close() |
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92 | { |
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93 | CNetCdfInterface::close(this->ncidp); |
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94 | } |
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95 | |
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96 | //--------------------------------------------------------------- |
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97 | |
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98 | void CONetCDF4::definition_start(void) |
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99 | { |
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100 | CNetCdfInterface::reDef(this->ncidp); |
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101 | } |
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102 | |
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103 | //--------------------------------------------------------------- |
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104 | |
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105 | void CONetCDF4::definition_end(void) |
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106 | { |
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107 | CNetCdfInterface::endDef(this->ncidp); |
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108 | } |
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109 | |
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110 | //--------------------------------------------------------------- |
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111 | |
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112 | int CONetCDF4::getCurrentGroup(void) |
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113 | { |
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114 | return this->getGroup(this->getCurrentPath()); |
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115 | } |
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116 | |
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117 | //--------------------------------------------------------------- |
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118 | |
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119 | int CONetCDF4::getGroup(const CONetCDF4Path& path) |
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120 | { |
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121 | int retvalue = this->ncidp; |
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122 | |
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123 | CONetCDF4Path::const_iterator it = path.begin(), end = path.end(); |
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124 | |
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125 | for (; it != end; it++) |
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126 | { |
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127 | const StdString& groupid = *it; |
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128 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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129 | } |
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130 | return retvalue; |
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131 | } |
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132 | |
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133 | //--------------------------------------------------------------- |
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134 | |
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135 | int CONetCDF4::getVariable(const StdString& varname) |
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136 | { |
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137 | int varid = 0; |
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138 | int grpid = this->getCurrentGroup(); |
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139 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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140 | return varid; |
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141 | } |
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142 | |
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143 | //--------------------------------------------------------------- |
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144 | |
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145 | int CONetCDF4::getDimension(const StdString& dimname) |
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146 | { |
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147 | int dimid = 0; |
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148 | int grpid = this->getCurrentGroup(); |
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149 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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150 | return dimid; |
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151 | } |
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152 | |
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153 | //--------------------------------------------------------------- |
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154 | |
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155 | int CONetCDF4::getUnlimitedDimension(void) |
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156 | { |
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157 | int dimid = 0; |
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158 | int grpid = this->getCurrentGroup(); |
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159 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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160 | return dimid; |
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161 | } |
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162 | |
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163 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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164 | { |
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165 | int grpid = this->getGroup(path); |
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166 | int dimid = this->getUnlimitedDimension(); |
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167 | |
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168 | StdString dimname; |
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169 | if (dimid != -1) |
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170 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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171 | return dimname; |
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172 | } |
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173 | |
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174 | //--------------------------------------------------------------- |
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175 | |
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176 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString& varname) |
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177 | { |
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178 | StdSize size = 0; |
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179 | std::vector<StdSize> retvalue; |
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180 | int grpid = this->getCurrentGroup(); |
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181 | int varid = this->getVariable(varname); |
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182 | int nbdim = 0, *dimid = NULL; |
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183 | |
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184 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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185 | dimid = new int[nbdim](); |
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186 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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187 | |
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188 | for (int i = 0; i < nbdim; i++) |
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189 | { |
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190 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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191 | if (size == NC_UNLIMITED) |
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192 | size = UNLIMITED_DIM; |
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193 | retvalue.push_back(size); |
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194 | } |
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195 | delete [] dimid; |
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196 | return retvalue; |
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197 | } |
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198 | |
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199 | std::vector<std::string> CONetCDF4::getDimensionsIdList(const std::string* _varname) |
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200 | { |
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201 | int nDimNull = 0; |
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202 | int nbdim = 0, *dimid = NULL; |
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203 | int grpid = this->getCurrentGroup(); |
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204 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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205 | std::vector<std::string> retvalue; |
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206 | |
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207 | if (_varname != NULL) |
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208 | { |
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209 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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210 | dimid = new int[nbdim](); |
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211 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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212 | } |
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213 | else |
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214 | { |
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215 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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216 | dimid = new int[nbdim](); |
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217 | CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1); |
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218 | } |
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219 | |
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220 | for (int i = 0; i < nbdim; i++) |
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221 | { |
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222 | std::string dimname; |
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223 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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224 | retvalue.push_back(dimname); |
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225 | } |
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226 | delete [] dimid; |
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227 | |
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228 | return retvalue; |
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229 | } |
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230 | |
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231 | //--------------------------------------------------------------- |
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232 | |
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233 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective) |
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234 | { |
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235 | int grpid = this->getCurrentGroup(); |
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236 | int varid = this->getVariable(name); |
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237 | |
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238 | std::vector<StdSize> start(2), count(2); |
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239 | start[0] = 0; |
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240 | // Find out how many temporal records have been written already to the file we are opening |
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241 | int ncUnlimitedDimId; |
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242 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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243 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, count[0]); |
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244 | start[1] = 0; |
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245 | count[1] = 2; |
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246 | |
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247 | timeAxisBounds.resize(count[1], count[0]); |
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248 | |
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249 | if (this->wmpi && collective) |
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250 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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251 | if (this->wmpi && !collective) |
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252 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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253 | |
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254 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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255 | } |
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256 | |
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257 | //--------------------------------------------------------------- |
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258 | |
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259 | const CONetCDF4::CONetCDF4Path& CONetCDF4::getCurrentPath(void) const |
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260 | { return this->path; } |
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261 | |
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262 | void CONetCDF4::setCurrentPath(const CONetCDF4Path& path) |
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263 | { this->path = path; } |
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264 | |
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265 | //--------------------------------------------------------------- |
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266 | |
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267 | int CONetCDF4::addGroup(const StdString& name) |
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268 | { |
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269 | int retvalue = 0; |
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270 | int grpid = this->getCurrentGroup(); |
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271 | CNetCdfInterface::defGrp(grpid, name, retvalue); |
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272 | return retvalue; |
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273 | } |
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274 | |
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275 | //--------------------------------------------------------------- |
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276 | |
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277 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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278 | { |
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279 | int retvalue = 0; |
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280 | int grpid = this->getCurrentGroup(); |
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281 | if (size != UNLIMITED_DIM) |
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282 | CNetCdfInterface::defDim(grpid, name, size, retvalue); |
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283 | else |
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284 | CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue); |
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285 | return retvalue; |
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286 | } |
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287 | |
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288 | //--------------------------------------------------------------- |
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289 | |
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290 | int CONetCDF4::addVariable(const StdString& name, nc_type type, |
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291 | const std::vector<StdString>& dim) |
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292 | { |
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293 | int varid = 0; |
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294 | std::vector<int> dimids; |
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295 | std::vector<StdSize> dimsizes; |
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296 | int dimSize = dim.size(); |
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297 | |
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298 | StdSize size; |
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299 | StdSize totalSize; |
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300 | StdSize maxSize = 1024 * 1024 * 256; // == 2GB/8 if output double |
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301 | |
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302 | int grpid = this->getCurrentGroup(); |
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303 | |
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304 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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305 | |
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306 | for (int idx = 0; it != end; it++, ++idx) |
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307 | { |
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308 | const StdString& dimid = *it; |
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309 | dimids.push_back(this->getDimension(dimid)); |
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310 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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311 | if (size == NC_UNLIMITED) size = 1; |
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312 | dimsizes.push_back(size); |
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313 | } |
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314 | |
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315 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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316 | |
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317 | // The classic NetCDF format does not support chunking nor fill parameters |
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318 | if (!useClassicFormat) |
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319 | { |
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320 | // set chunksize : size of one record |
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321 | // but must not be > 2GB (netcdf or HDF5 problem) |
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322 | totalSize = 1; |
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323 | for (vector<StdSize>::reverse_iterator it = dimsizes.rbegin(); it != dimsizes.rend(); ++it) |
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324 | { |
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325 | totalSize *= *it; |
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326 | if (totalSize >= maxSize) *it = 1; |
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327 | } |
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328 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
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329 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
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330 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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331 | } |
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332 | |
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333 | return varid; |
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334 | } |
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335 | |
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336 | //--------------------------------------------------------------- |
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337 | |
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338 | void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel) |
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339 | { |
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340 | if (compressionLevel < 0 || compressionLevel > 9) |
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341 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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342 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
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343 | if (compressionLevel && wmpi) |
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344 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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345 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
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346 | |
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347 | int grpid = this->getCurrentGroup(); |
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348 | int varid = this->getVariable(varname); |
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349 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
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350 | } |
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351 | |
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352 | //--------------------------------------------------------------- |
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353 | |
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354 | template <> |
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355 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
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356 | { |
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357 | int grpid = this->getCurrentGroup(); |
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358 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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359 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
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360 | } |
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361 | |
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362 | //--------------------------------------------------------------- |
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363 | |
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364 | template <> |
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365 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
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366 | { |
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367 | int grpid = this->getCurrentGroup(); |
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368 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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369 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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370 | } |
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371 | |
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372 | template <> |
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373 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
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374 | { |
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375 | int grpid = this->getCurrentGroup(); |
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376 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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377 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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378 | } |
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379 | //--------------------------------------------------------------- |
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380 | |
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381 | template <> |
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382 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
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383 | { |
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384 | int grpid = this->getCurrentGroup(); |
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385 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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386 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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387 | } |
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388 | |
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389 | template <> |
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390 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
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391 | { |
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392 | int grpid = this->getCurrentGroup(); |
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393 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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394 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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395 | } |
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396 | |
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397 | //--------------------------------------------------------------- |
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398 | |
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399 | template <> |
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400 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
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401 | { |
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402 | int grpid = this->getCurrentGroup(); |
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403 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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404 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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405 | } |
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406 | |
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407 | template <> |
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408 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
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409 | { |
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410 | int grpid = this->getCurrentGroup(); |
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411 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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412 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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413 | } |
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414 | |
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415 | template <> |
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416 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
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417 | { |
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418 | int grpid = this->getCurrentGroup(); |
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419 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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420 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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421 | } |
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422 | |
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423 | template <> |
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424 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
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425 | { |
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426 | int grpid = this->getCurrentGroup(); |
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427 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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428 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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429 | } |
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430 | |
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431 | template <> |
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432 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
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433 | { |
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434 | int grpid = this->getCurrentGroup(); |
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435 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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436 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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437 | } |
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438 | |
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439 | template <> |
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440 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
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441 | { |
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442 | int grpid = this->getCurrentGroup(); |
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443 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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444 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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445 | } |
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446 | |
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447 | //--------------------------------------------------------------- |
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448 | |
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449 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
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450 | std::vector<StdSize>& sstart, |
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451 | std::vector<StdSize>& scount, |
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452 | const std::vector<StdSize>* start, |
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453 | const std::vector<StdSize>* count) |
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454 | { |
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455 | std::vector<std::size_t> sizes = this->getDimensions(name); |
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456 | if (sizes.size()==0) |
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457 | { |
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458 | array_size=1 ; |
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459 | sstart.push_back(0); |
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460 | scount.push_back(1); |
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461 | } |
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462 | else |
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463 | { |
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464 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
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465 | std::vector<std::size_t>::const_iterator |
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466 | it = sizes.begin(), end = sizes.end(); |
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467 | int i = 0; |
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468 | |
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469 | if (iddims.begin()->compare(timeCounterName) == 0) |
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470 | { |
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471 | sstart.push_back(record); |
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472 | scount.push_back(1); |
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473 | if ((start == NULL) && |
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474 | (count == NULL)) i++; |
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475 | it++; |
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476 | } |
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477 | |
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478 | for (;it != end; it++) |
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479 | { |
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480 | if ((start != NULL) && (count != NULL)) |
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481 | { |
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482 | sstart.push_back((*start)[i]); |
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483 | scount.push_back((*count)[i]); |
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484 | array_size *= (*count)[i]; |
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485 | i++; |
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486 | } |
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487 | else |
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488 | { |
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489 | sstart.push_back(0); |
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490 | scount.push_back(sizes[i]); |
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491 | array_size *= sizes[i]; |
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492 | i++; |
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493 | } |
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494 | } |
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495 | |
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496 | } |
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497 | } |
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498 | |
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499 | |
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500 | template <> |
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501 | void CONetCDF4::writeData_(int grpid, int varid, |
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502 | const std::vector<StdSize>& sstart, |
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503 | const std::vector<StdSize>& scount, const double* data) |
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504 | { |
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505 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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506 | } |
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507 | |
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508 | //--------------------------------------------------------------- |
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509 | |
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510 | template <> |
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511 | void CONetCDF4::writeData_(int grpid, int varid, |
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512 | const std::vector<StdSize>& sstart, |
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513 | const std::vector<StdSize>& scount, const int* data) |
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514 | { |
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515 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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516 | } |
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517 | |
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518 | //--------------------------------------------------------------- |
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519 | |
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520 | template <> |
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521 | void CONetCDF4::writeData_(int grpid, int varid, |
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522 | const std::vector<StdSize>& sstart, |
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523 | const std::vector<StdSize>& scount, const float* data) |
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524 | { |
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525 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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526 | } |
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527 | |
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528 | //--------------------------------------------------------------- |
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529 | |
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530 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
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531 | { |
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532 | int grpid = this->getCurrentGroup(); |
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533 | int varid = this->getVariable(name); |
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534 | StdSize array_size = 1; |
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535 | std::vector<StdSize> sstart, scount; |
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536 | |
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537 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
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538 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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539 | } |
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540 | |
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541 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
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542 | bool collective, StdSize record, bool isRoot) |
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543 | { |
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544 | int grpid = this->getCurrentGroup(); |
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545 | int varid = this->getVariable(name); |
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546 | |
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547 | map<int,size_t>::iterator it=timeAxis.find(varid); |
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548 | if (it == timeAxis.end()) timeAxis[varid] = record; |
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549 | else |
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550 | { |
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551 | if (it->second >= record) return; |
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552 | else it->second =record; |
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553 | } |
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554 | |
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555 | StdSize array_size = 1; |
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556 | std::vector<StdSize> sstart, scount; |
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557 | |
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558 | if (this->wmpi && collective) |
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559 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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560 | if (this->wmpi && !collective) |
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561 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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562 | |
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563 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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564 | if (using_netcdf_internal) |
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565 | { |
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566 | if (!isRoot) |
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567 | { |
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568 | sstart[0] = sstart[0] + 1; |
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569 | scount[0] = 0; |
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570 | } |
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571 | } |
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572 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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573 | } |
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574 | |
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575 | //--------------------------------------------------------------- |
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576 | |
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577 | bool CONetCDF4::varExist(const StdString& varname) |
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578 | { |
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579 | int grpid = this->getCurrentGroup(); |
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580 | return CNetCdfInterface::isVarExisted(grpid, varname); |
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581 | } |
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582 | |
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583 | bool CONetCDF4::dimExist(const StdString& dimname) |
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584 | { |
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585 | int grpid = this->getCurrentGroup(); |
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586 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
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587 | } |
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588 | |
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589 | void CONetCDF4::sync(void) |
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590 | { |
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591 | CNetCdfInterface::sync(this->ncidp); |
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592 | } |
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593 | ///-------------------------------------------------------------- |
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594 | } // namespace xios |
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