1 | #include "inetcdf4.hpp" |
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2 | #include "netCdfInterface.hpp" |
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3 | #include "netCdf_cf_constant.hpp" |
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4 | |
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5 | #include <boost/algorithm/string.hpp> |
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6 | |
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7 | namespace xios |
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8 | { |
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9 | CINetCDF4::CINetCDF4(const StdString& filename, const ep_lib::MPI_Comm* comm /*= NULL*/, bool multifile /*= true*/, const StdString& timeCounterName /*= "time_counter"*/) |
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10 | { |
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11 | // Don't use parallel mode if there is only one process |
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12 | if (comm) |
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13 | { |
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14 | int commSize = 0; |
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15 | ep_lib::MPI_Comm_size(*comm, &commSize); |
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16 | if (commSize <= 1) |
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17 | comm = NULL; |
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18 | } |
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19 | mpi = comm && !multifile; |
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20 | ep_lib::MPI_Info info_null; |
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21 | |
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22 | // The file format will be detected automatically by NetCDF, it is safe to always set NC_MPIIO |
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23 | // even if Parallel NetCDF ends up being used. |
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24 | if (mpi) |
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25 | CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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26 | //CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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27 | else |
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28 | CNetCdfInterface::open(filename, NC_NOWRITE, this->ncidp); |
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29 | |
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30 | this->timeCounterName = timeCounterName; |
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31 | if (!CNetCdfInterface::isDimExisted(this->ncidp, this->timeCounterName)) this->timeCounterName=this->getUnlimitedDimensionName() ; |
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32 | |
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33 | } |
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34 | |
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35 | CINetCDF4::~CINetCDF4(void) |
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36 | { /* Nothing to do */ } |
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37 | |
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38 | //--------------------------------------------------------------- |
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39 | |
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40 | void CINetCDF4::close(void) |
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41 | { |
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42 | CNetCdfInterface::close(this->ncidp); |
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43 | } |
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44 | |
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45 | //--------------------------------------------------------------- |
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46 | |
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47 | int CINetCDF4::getGroup(const CVarPath* const path) |
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48 | { |
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49 | int retvalue = this->ncidp; |
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50 | if (path == NULL) return retvalue; |
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51 | CVarPath::const_iterator it = path->begin(), end = path->end(); |
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52 | |
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53 | for (; it != end; it++) |
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54 | { |
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55 | const StdString& groupid = *it; |
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56 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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57 | } |
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58 | |
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59 | return retvalue; |
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60 | } |
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61 | |
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62 | int CINetCDF4::getVariable(const StdString& varname, |
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63 | const CVarPath* const path) |
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64 | { |
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65 | int varid = 0; |
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66 | int grpid = this->getGroup(path); |
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67 | if (this->hasVariable(varname, path)) |
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68 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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69 | return varid; |
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70 | } |
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71 | |
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72 | int CINetCDF4::getDimension(const StdString& dimname, |
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73 | const CVarPath* const path) |
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74 | { |
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75 | int dimid = 0; |
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76 | int grpid = this->getGroup(path); |
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77 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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78 | return dimid; |
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79 | } |
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80 | |
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81 | std::pair<nc_type, StdSize> CINetCDF4::getAttribute(const StdString& attname, |
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82 | const StdString* const var, |
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83 | const CVarPath* const path) |
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84 | { |
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85 | std::pair<nc_type, StdSize> retvalue; |
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86 | int grpid = this->getGroup(path); |
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87 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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88 | CNetCdfInterface::inqAtt(grpid, varid, attname, retvalue.first, retvalue.second); |
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89 | return retvalue; |
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90 | } |
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91 | |
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92 | int CINetCDF4::getUnlimitedDimension(const CVarPath* const path) |
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93 | { |
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94 | int dimid = 0; |
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95 | int grpid = this->getGroup(path); |
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96 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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97 | return dimid; |
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98 | } |
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99 | |
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100 | StdString CINetCDF4::getUnlimitedDimensionName(const CVarPath* const path) |
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101 | { |
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102 | int grpid = this->getGroup(path); |
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103 | int dimid = this->getUnlimitedDimension(path); |
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104 | |
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105 | StdString dimname; |
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106 | if (dimid != -1) |
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107 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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108 | return dimname; |
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109 | } |
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110 | |
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111 | //--------------------------------------------------------------- |
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112 | |
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113 | StdSize CINetCDF4::getNbVertex(const StdString& name, |
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114 | const CVarPath* const path) |
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115 | { |
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116 | |
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117 | if (this->isRectilinear(name, path) || |
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118 | this->isCurvilinear(name, path)) |
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119 | { |
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120 | if (this->is3Dim(name, path)) return 8; |
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121 | else return 4; |
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122 | } |
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123 | if (this->isUnstructured(name, path)) |
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124 | { |
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125 | StdString bound = this->getBoundsId |
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126 | (this->getCoordinatesIdList(name, path).back(), path); |
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127 | StdString dim = this->getDimensionsList(&bound, path).back(); |
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128 | return this->getDimensions(&bound, path)[dim]; |
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129 | } |
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130 | return size_t(-1); |
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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 | std::list<StdString> CINetCDF4::getGroups(const CVarPath* const path) |
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136 | { |
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137 | int nbgroup = 0, *groupid = NULL; |
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138 | int grpid = this->getGroup(path); |
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139 | std::list<StdString> retvalue; |
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140 | |
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141 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, NULL); |
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142 | groupid = new int[nbgroup](); |
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143 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, groupid); |
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144 | |
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145 | for (int i = 0; i < nbgroup; i++) |
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146 | { |
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147 | StdString fullGrpName; |
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148 | CNetCdfInterface::inqGrpFullName(groupid[i], fullGrpName); |
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149 | retvalue.push_back(fullGrpName); |
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150 | } |
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151 | |
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152 | delete [] groupid; |
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153 | return retvalue; |
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154 | } |
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155 | |
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156 | std::list<StdString> CINetCDF4::getVariables(const CVarPath* const path) |
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157 | { |
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158 | int nbvar = 0, *varid = NULL; |
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159 | int grpid = this->getGroup(path); |
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160 | std::list<StdString> retvalue; |
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161 | |
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162 | CNetCdfInterface::inqVarIds(grpid, nbvar, NULL); |
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163 | varid = new int[nbvar](); |
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164 | CNetCdfInterface::inqVarIds(grpid, nbvar, varid); |
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165 | |
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166 | for (int i = 0; i < nbvar; i++) |
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167 | { |
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168 | StdString varName; |
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169 | CNetCdfInterface::inqVarName(grpid, varid[i], varName); |
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170 | retvalue.push_back(varName); |
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171 | } |
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172 | |
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173 | delete [] varid; |
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174 | return retvalue; |
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175 | } |
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176 | |
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177 | StdSize CINetCDF4::getNbOfTimestep(const CVarPath* const path) |
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178 | { |
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179 | return this->getDimensions(NULL, path)[this->getUnlimitedDimensionName(path)]; |
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180 | } |
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181 | |
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182 | std::set<StdString> CINetCDF4::getBoundVariables(const CVarPath* const path) |
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183 | { |
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184 | std::set<StdString> retvalue; |
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185 | std::list<StdString> variables = this->getVariables(path); |
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186 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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187 | for (; it != end; it++) |
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188 | { |
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189 | const StdString& var = *it; |
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190 | if (this->hasBounds(var, path)) |
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191 | retvalue.insert(retvalue.end(), this->getBoundsId(var, path)); |
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192 | } |
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193 | return retvalue; |
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194 | } |
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195 | |
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196 | std::set<StdString> CINetCDF4::getCoordVariables(const CVarPath* const path) |
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197 | { |
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198 | std::set<StdString> retvalue; |
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199 | std::list<StdString> variables = this->getVariables(path); |
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200 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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201 | for (; it != end; it++) |
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202 | { |
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203 | const StdString& var = *it; |
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204 | std::list<StdString> coords = this->getCoordinatesIdList(var, path); |
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205 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
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206 | for (; it != end; it++) |
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207 | { |
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208 | const StdString& coord = *it; |
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209 | if (this->hasVariable(coord, path)) |
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210 | retvalue.insert(retvalue.end(), coord); |
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211 | } |
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212 | } |
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213 | return retvalue; |
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214 | } |
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215 | |
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216 | std::list<StdString> CINetCDF4::getDimensionsList(const StdString* const var, const CVarPath* const path) |
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217 | { |
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218 | int nbdim = 0, *dimid = NULL; |
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219 | int grpid = this->getGroup(path); |
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220 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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221 | std::list<StdString> retvalue; |
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222 | |
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223 | if (var != NULL) |
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224 | { |
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225 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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226 | dimid = new int[nbdim](); |
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227 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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228 | } |
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229 | else |
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230 | { |
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231 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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232 | dimid = new int[nbdim](); |
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233 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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234 | } |
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235 | |
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236 | for (int i = 0; i < nbdim; i++) |
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237 | { |
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238 | std::string dimname; |
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239 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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240 | retvalue.push_back(dimname); |
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241 | } |
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242 | delete [] dimid; |
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243 | |
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244 | return retvalue; |
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245 | } |
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246 | |
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247 | std::map<StdString, StdSize> CINetCDF4::getDimensions(const StdString* const var, const CVarPath* const path) |
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248 | { |
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249 | int nbdim = 0, *dimid = NULL; |
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250 | int grpid = this->getGroup(path); |
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251 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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252 | std::map<StdString, StdSize> retvalue; |
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253 | |
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254 | if (var != NULL) |
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255 | { |
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256 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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257 | dimid = new int[nbdim](); |
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258 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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259 | } |
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260 | else |
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261 | { |
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262 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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263 | dimid = new int[nbdim](); |
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264 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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265 | } |
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266 | |
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267 | for (int i = 0; i < nbdim; i++) |
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268 | { |
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269 | std::string dimname; |
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270 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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271 | StdSize size = 0; |
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272 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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273 | |
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274 | retvalue.insert(retvalue.end(), std::make_pair(dimname, size)); |
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275 | } |
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276 | delete [] dimid; |
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277 | |
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278 | return retvalue; |
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279 | } |
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280 | |
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281 | std::list<StdString> CINetCDF4::getAttributes(const StdString* const var, const CVarPath* const path) |
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282 | { |
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283 | int nbatt = 0; |
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284 | std::list<StdString> retvalue; |
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285 | int grpid = this->getGroup(path); |
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286 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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287 | |
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288 | if (var != NULL) |
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289 | CNetCdfInterface::inqVarNAtts(grpid, varid, nbatt); |
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290 | else |
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291 | CNetCdfInterface::inqNAtts(grpid, nbatt); |
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292 | |
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293 | for (int i = 0; i < nbatt; i++) |
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294 | { |
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295 | StdString attname; |
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296 | CNetCdfInterface::inqAttName(grpid, varid, i, attname); |
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297 | retvalue.push_back(attname); |
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298 | } |
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299 | return retvalue; |
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300 | } |
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301 | |
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302 | int CINetCDF4::getAttributeId(const StdString& name, |
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303 | const StdString* const var, |
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304 | const CVarPath* const path) |
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305 | { |
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306 | int retvalue = 0; |
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307 | std::list<StdString> atts = this->getAttributes(var, path); |
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308 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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309 | for (; it != end; it++) |
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310 | { |
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311 | const StdString& attname = *it; |
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312 | if (attname.compare(0, name.size(), name) == 0) |
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313 | return retvalue; |
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314 | retvalue++; |
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315 | } |
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316 | return -1; |
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317 | } |
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318 | |
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319 | //--------------------------------------------------------------- |
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320 | |
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321 | bool CINetCDF4::hasMissingValue(const StdString& name, |
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322 | const CVarPath* const path) |
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323 | { |
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324 | return (this->hasAttribute("missing_value", &name, path) || this->hasAttribute("_FillValue", &name, path)); |
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325 | } |
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326 | |
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327 | bool CINetCDF4::hasAttribute(const StdString& name, |
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328 | const StdString* const var , |
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329 | const CVarPath* const path) |
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330 | { |
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331 | std::list<StdString> atts = this->getAttributes(var, path); |
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332 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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333 | for (; it != end; it++) |
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334 | { |
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335 | const StdString& attname = *it; |
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336 | if (attname.compare(0, name.size(), name) == 0) return true; |
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337 | } |
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338 | return false; |
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339 | } |
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340 | |
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341 | bool CINetCDF4::hasVariable(const StdString& name, |
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342 | const CVarPath* const path) |
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343 | { |
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344 | std::list<StdString> variables = this->getVariables(path); |
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345 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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346 | for (; it != end; it++) |
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347 | { |
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348 | const StdString& varname = *it; |
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349 | if ((varname.compare(0, name.size(), name) == 0) && (0 != name.size())) return true; |
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350 | } |
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351 | return false; |
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352 | } |
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353 | |
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354 | bool CINetCDF4::hasCoordinates(const StdString& name, |
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355 | const CVarPath* const path) |
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356 | { |
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357 | return this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path); |
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358 | } |
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359 | |
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360 | bool CINetCDF4::hasBounds(const StdString& name, |
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361 | const CVarPath* const path) |
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362 | { |
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363 | return this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path); |
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364 | } |
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365 | |
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366 | bool CINetCDF4::hasTemporalDim(const CVarPath* const path) |
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367 | { |
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368 | std::list<StdString> dims = this->getDimensionsList(NULL, path); |
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369 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
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370 | } |
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371 | |
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372 | //--------------------------------------------------------------- |
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373 | |
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374 | template <class T> |
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375 | std::vector<T> CINetCDF4::getAttributeValue(const StdString& name, |
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376 | const StdString* const var, |
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377 | const CVarPath* const path) |
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378 | { |
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379 | int grpid = this->getGroup(path); |
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380 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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381 | std::pair<nc_type , StdSize> attinfos = this->getAttribute(name, var, path); |
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382 | std::vector<T> retvalue(attinfos.second); |
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383 | nc_type type = CNetCdfInterface::getNcType<T>(); |
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384 | if (attinfos.first != type) |
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385 | ERROR("CINetCDF4::getAttributeValue<T>(name, var, path)", |
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386 | << "[ name : " << name |
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387 | << ", type requested :" << attinfos.first |
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388 | << ", type stored : " << type << "]" |
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389 | << " Invalid type !"); |
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390 | CNetCdfInterface::getAttType(grpid, varid, name.c_str(), &retvalue[0]); |
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391 | return retvalue; |
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392 | } |
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393 | |
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394 | template std::vector<double> CINetCDF4::getAttributeValue(const StdString& name, |
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395 | const StdString* const var, |
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396 | const CVarPath* const path); |
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397 | template std::vector<float> CINetCDF4::getAttributeValue(const StdString& name, |
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398 | const StdString* const var, |
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399 | const CVarPath* const path); |
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400 | template std::vector<int> CINetCDF4::getAttributeValue(const StdString& name, |
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401 | const StdString* const var, |
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402 | const CVarPath* const path); |
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403 | template std::vector<char> CINetCDF4::getAttributeValue(const StdString& name, |
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404 | const StdString* const var, |
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405 | const CVarPath* const path); |
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406 | |
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407 | StdString CINetCDF4::getAttributeValue(const StdString& name, |
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408 | const StdString* const var, |
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409 | const CVarPath* const path) |
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410 | { |
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411 | std::vector<char> data = this->getAttributeValue<char>(name, var, path); |
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412 | |
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413 | return StdString(data.begin(), data.end()); |
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414 | } |
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415 | |
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416 | template <class T> |
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417 | T CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path) |
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418 | { |
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419 | if (this->hasAttribute("missing_value", &name, path)) |
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420 | return this->getAttributeValue<T>("missing_value", &name, path)[0]; |
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421 | if (this->hasAttribute("_FillValue", &name, path)) |
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422 | return this->getAttributeValue<T>("_FillValue", &name, path)[0]; |
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423 | return 0; |
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424 | } |
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425 | |
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426 | template double CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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427 | template float CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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428 | template int CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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429 | template char CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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430 | |
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431 | //--------------------------------------------------------------- |
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432 | |
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433 | std::list<StdString> CINetCDF4::getCoordinatesIdList(const StdString& name, const CVarPath* const path) |
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434 | { |
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435 | std::list<StdString> retvalue; |
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436 | StdString value = this->getCoordinatesId(name, path); |
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437 | |
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438 | boost::split(retvalue, value, boost::is_any_of(" ")); |
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439 | |
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440 | std::list<StdString>::iterator it = retvalue.begin(), end = retvalue.end(); |
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441 | for (; it != end; it++) |
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442 | { |
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443 | StdString& coord = *it; |
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444 | coord.assign(coord.data()); |
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445 | } |
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446 | return retvalue; |
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447 | } |
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448 | |
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449 | StdString CINetCDF4::getCoordinatesId(const StdString& name, const CVarPath* const path) |
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450 | { |
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451 | StdString retvalue; |
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452 | if (this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path)) |
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453 | { |
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454 | return this->getAttributeValue(CCFKeywords::XIOS_CF_coordinates, &name, path); |
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455 | } |
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456 | else |
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457 | { |
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458 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
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459 | std::list<StdString>::const_iterator it = dims.begin(), end = dims.end(); |
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460 | for (; it != end; it++) |
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461 | { |
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462 | const StdString& value = *it; |
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463 | retvalue.append(value).push_back(' '); |
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464 | } |
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465 | retvalue.erase(retvalue.end() - 1) ; |
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466 | } |
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467 | |
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468 | return retvalue; |
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469 | } |
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470 | |
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471 | StdString CINetCDF4::getBoundsId(const StdString& name, |
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472 | const CVarPath* const path) |
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473 | { |
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474 | StdString retvalue; |
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475 | if (this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path)) |
---|
476 | retvalue = this->getAttributeValue(CCFKeywords::XIOS_CF_bounds, &name, path); |
---|
477 | return retvalue; |
---|
478 | } |
---|
479 | |
---|
480 | //--------------------------------------------------------------- |
---|
481 | |
---|
482 | bool CINetCDF4::isBound(const StdString& name, |
---|
483 | const CVarPath* const path) |
---|
484 | { |
---|
485 | std::set<StdString> bounds = this->getBoundVariables(path); |
---|
486 | return (bounds.find(name) != bounds.end()); |
---|
487 | } |
---|
488 | |
---|
489 | bool CINetCDF4::isCoordinate(const StdString& name, |
---|
490 | const CVarPath* const path) |
---|
491 | { |
---|
492 | std::set<StdString> coords = this->getCoordVariables(path); |
---|
493 | return (coords.find(name) != coords.end()); |
---|
494 | } |
---|
495 | |
---|
496 | bool CINetCDF4::isRectilinear(const StdString& name, const CVarPath* const path) |
---|
497 | { |
---|
498 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
499 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
500 | for (; it != end; it++) |
---|
501 | { |
---|
502 | const StdString& coord = *it; |
---|
503 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
504 | { |
---|
505 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
506 | if ((dimvar.size() == 1) && (dimvar.find(coord) != dimvar.end())) |
---|
507 | continue; |
---|
508 | else |
---|
509 | return false; |
---|
510 | } |
---|
511 | } |
---|
512 | return true; |
---|
513 | } |
---|
514 | |
---|
515 | bool CINetCDF4::isCurvilinear(const StdString& name, const CVarPath* const path) |
---|
516 | { |
---|
517 | if (this->isRectilinear(name, path) || !this->hasCoordinates(name, path)) |
---|
518 | return false; |
---|
519 | |
---|
520 | bool isCurVi = true; |
---|
521 | unsigned int nbLonLat = 0; |
---|
522 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
523 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
524 | for (; it != end; it++) |
---|
525 | { |
---|
526 | const StdString& coord = *it; |
---|
527 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
528 | { |
---|
529 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
530 | if (2 == dimvar.size()) ++nbLonLat; |
---|
531 | } |
---|
532 | } |
---|
533 | if (2 != nbLonLat) isCurVi = false; |
---|
534 | |
---|
535 | return isCurVi; |
---|
536 | } |
---|
537 | |
---|
538 | bool CINetCDF4::isUnstructured(const StdString& name, const CVarPath* const path) |
---|
539 | { |
---|
540 | if (this->isRectilinear(name, path) || |
---|
541 | this->isCurvilinear(name, path) || |
---|
542 | !this->hasCoordinates(name, path)) |
---|
543 | return false; |
---|
544 | else return true ; |
---|
545 | |
---|
546 | // check this part above |
---|
547 | StdString dimname = this->getDimensionsList(&name, path).back(); |
---|
548 | |
---|
549 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
550 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
551 | for (; it != end; it++) |
---|
552 | { |
---|
553 | const StdString& coord = *it; |
---|
554 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
555 | { |
---|
556 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
557 | if ((dimvar.size() == 1) && |
---|
558 | (dimvar.find(dimname) != dimvar.end())) |
---|
559 | continue; |
---|
560 | else |
---|
561 | return false; |
---|
562 | } |
---|
563 | } |
---|
564 | |
---|
565 | return true; |
---|
566 | } |
---|
567 | |
---|
568 | bool CINetCDF4::isUnknown(const StdString& name, const CVarPath* const path) |
---|
569 | { |
---|
570 | return !(this->isRectilinear(name, path) || this->isCurvilinear(name, path) || this->isUnstructured(name, path)); |
---|
571 | } |
---|
572 | |
---|
573 | bool CINetCDF4::isTemporal(const StdString& name, const CVarPath* const path) |
---|
574 | { |
---|
575 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
576 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
---|
577 | } |
---|
578 | |
---|
579 | bool CINetCDF4::is3Dim(const StdString& name, const CVarPath* const path) |
---|
580 | { |
---|
581 | int i = 0; |
---|
582 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
583 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
584 | for (; it != end; it++) |
---|
585 | { |
---|
586 | const StdString& coord = *it; |
---|
587 | if (this->hasVariable(coord, path)) |
---|
588 | { |
---|
589 | if (this->isTemporal(coord, path)) |
---|
590 | continue; |
---|
591 | i++; |
---|
592 | } |
---|
593 | else |
---|
594 | { |
---|
595 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
596 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
597 | continue; |
---|
598 | i++; |
---|
599 | } |
---|
600 | } |
---|
601 | return (i == 3); |
---|
602 | } |
---|
603 | |
---|
604 | bool CINetCDF4::isCellGrid(const StdString& name, const CVarPath* const path) |
---|
605 | { |
---|
606 | if (this->isCoordinate(name, path)) |
---|
607 | { |
---|
608 | return this->hasBounds(name, path); |
---|
609 | } |
---|
610 | else |
---|
611 | { |
---|
612 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
613 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
614 | for (; it != end; it++) |
---|
615 | { |
---|
616 | const StdString& coord = *it; |
---|
617 | if (this->hasVariable(coord, path)) |
---|
618 | { |
---|
619 | if (this->isTemporal(coord, path)) |
---|
620 | continue; |
---|
621 | if (this->isCellGrid(coord, path)) |
---|
622 | continue; |
---|
623 | return false; |
---|
624 | } |
---|
625 | else |
---|
626 | { |
---|
627 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
628 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
629 | continue; |
---|
630 | return false; |
---|
631 | } |
---|
632 | } |
---|
633 | } |
---|
634 | |
---|
635 | return true; |
---|
636 | } |
---|
637 | |
---|
638 | //--------------------------------------------------------------- |
---|
639 | |
---|
640 | std::list<StdString> CINetCDF4::getDataVariables(bool _is3D, bool _isRecti, |
---|
641 | bool _isCurvi, bool _isUnstr, |
---|
642 | bool _isCellData, bool _isTemporal, |
---|
643 | const CVarPath* const path) |
---|
644 | { |
---|
645 | std::list<StdString> retvalue; |
---|
646 | std::list<StdString> allvars = this->getVariables(path); |
---|
647 | std::set<StdString> allcoords = this->getCoordVariables(path); |
---|
648 | |
---|
649 | std::list<StdString>::const_iterator it = allvars.begin(), end = allvars.end(); |
---|
650 | for (; it != end; it++) |
---|
651 | { |
---|
652 | const StdString& var = *it; |
---|
653 | if (this->isCoordinate(var, path)) continue; |
---|
654 | |
---|
655 | if (!_isRecti && this->isRectilinear(var, path)) continue; |
---|
656 | if (!_isCurvi && this->isCurvilinear(var, path)) continue; |
---|
657 | if (!_isUnstr && this->isUnstructured(var, path)) continue; |
---|
658 | |
---|
659 | if (!_isTemporal && this->isTemporal(var, path)) continue; |
---|
660 | if (!_is3D && this->is3Dim(var, path)) continue; |
---|
661 | if (!_isCellData && this->isCellGrid(var, path)) continue; |
---|
662 | |
---|
663 | if (this->isUnknown(var, path)) continue; |
---|
664 | |
---|
665 | retvalue.push_back(var); |
---|
666 | } |
---|
667 | return retvalue; |
---|
668 | } |
---|
669 | |
---|
670 | //--------------------------------------------------------------- |
---|
671 | |
---|
672 | void CINetCDF4::getDataInfo(const StdString& var, const CVarPath* const path, StdSize record, |
---|
673 | std::vector<StdSize>& sstart, std::vector<StdSize>& scount, StdSize& array_size, |
---|
674 | const std::vector<StdSize>* start /*= NULL*/, const std::vector<StdSize>* count /*= NULL*/) |
---|
675 | { |
---|
676 | std::list<StdString> dimlist = this->getDimensionsList(&var, path); |
---|
677 | std::map<StdString, StdSize> dimmap = this->getDimensions(&var, path); |
---|
678 | std::list<StdString>::iterator it = dimlist.begin(); |
---|
679 | if (this->isTemporal(var, path)) |
---|
680 | { |
---|
681 | if (record != UNLIMITED_DIM) |
---|
682 | sstart.push_back(record); |
---|
683 | else |
---|
684 | sstart.push_back(0); |
---|
685 | scount.push_back(1); |
---|
686 | it++; |
---|
687 | } |
---|
688 | for (int i = 0; it != dimlist.end(); it++, i++) |
---|
689 | { |
---|
690 | if (start && count) |
---|
691 | { |
---|
692 | sstart.push_back((*start)[i]); |
---|
693 | scount.push_back((*count)[i]); |
---|
694 | array_size *= (*count)[i]; |
---|
695 | } |
---|
696 | else |
---|
697 | { |
---|
698 | sstart.push_back(0); |
---|
699 | scount.push_back(dimmap[*it]); |
---|
700 | array_size *= dimmap[*it]; |
---|
701 | } |
---|
702 | } |
---|
703 | } |
---|
704 | |
---|
705 | template <class T> |
---|
706 | void CINetCDF4::getData(CArray<T, 1>& data, const StdString& var, |
---|
707 | const CVarPath* const path, StdSize record) |
---|
708 | { |
---|
709 | std::vector<StdSize> start, count; |
---|
710 | int grpid = this->getGroup(path); |
---|
711 | int varid = this->getVariable(var, path); |
---|
712 | StdSize array_size = 1; |
---|
713 | this->getDataInfo(var, path, record, start, count, array_size); |
---|
714 | data.resize(array_size); |
---|
715 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], data.dataFirst()); |
---|
716 | } |
---|
717 | |
---|
718 | template <> |
---|
719 | void CINetCDF4::getData(CArray<int, 1>& data, const StdString& var, |
---|
720 | const CVarPath* const path, StdSize record); |
---|
721 | template <> |
---|
722 | void CINetCDF4::getData(CArray<double, 1>& data, const StdString& var, |
---|
723 | const CVarPath* const path, StdSize record); |
---|
724 | template <> |
---|
725 | void CINetCDF4::getData(CArray<float, 1>& data, const StdString& var, |
---|
726 | const CVarPath* const path, StdSize record); |
---|
727 | |
---|
728 | //--------------------------------------------------------------- |
---|
729 | |
---|
730 | StdString CINetCDF4::getLonCoordName(const StdString& varname, |
---|
731 | const CVarPath* const path) |
---|
732 | { |
---|
733 | StdString lonName; |
---|
734 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
735 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
736 | itbList = clist.begin(); iteList = clist.end(); |
---|
737 | for (itList = itbList; itList != iteList; ++itList) |
---|
738 | { |
---|
739 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
740 | { |
---|
741 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
742 | if (CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)) |
---|
743 | { |
---|
744 | lonName = *itList; |
---|
745 | return lonName; |
---|
746 | } |
---|
747 | } |
---|
748 | } |
---|
749 | return lonName; |
---|
750 | } |
---|
751 | |
---|
752 | StdString CINetCDF4::getLatCoordName(const StdString& varname, |
---|
753 | const CVarPath* const path) |
---|
754 | { |
---|
755 | StdString latName; |
---|
756 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
757 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
758 | itbList = clist.begin(); iteList = clist.end(); |
---|
759 | for (itList = itbList; itList != iteList; ++itList) |
---|
760 | { |
---|
761 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
762 | { |
---|
763 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
764 | if (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit)) |
---|
765 | { |
---|
766 | latName = *itList; |
---|
767 | return latName; |
---|
768 | } |
---|
769 | } |
---|
770 | } |
---|
771 | return latName; |
---|
772 | } |
---|
773 | |
---|
774 | StdString CINetCDF4::getVertCoordName(const StdString& varname, |
---|
775 | const CVarPath* const path) |
---|
776 | { |
---|
777 | if (!this->is3Dim(varname, path)) return ""; |
---|
778 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
779 | if (this->hasCoordinates(varname, path)) |
---|
780 | return *(++(++clist.begin())); |
---|
781 | else |
---|
782 | return *(++(++clist.rbegin())); |
---|
783 | } |
---|
784 | } // namespace xios |
---|