1 | /*! |
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2 | \file netCdfInterface.cpp |
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3 | \author Ha NGUYEN |
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4 | \date 08 Oct 2014 |
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5 | \since 03 Oct 2014 |
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6 | |
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7 | \brief Wrapper of netcdf functions. |
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8 | */ |
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9 | |
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10 | #include "netCdfInterface.hpp" |
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11 | #include "netCdfException.hpp" |
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12 | // mpi_std.hpp |
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13 | |
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14 | namespace xios |
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15 | { |
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16 | /*! |
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17 | This function creates a new netcdf file and return its id |
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18 | \param [in] fileName Name of the file |
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19 | \param [in] cMode create mode |
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20 | \param [in/out] ncId id of the created file |
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21 | \return Status code |
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22 | */ |
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23 | int CNetCdfInterface::create(const StdString& fileName, int cMode, int& ncId) |
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24 | { |
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25 | int status = nc_create(fileName.c_str(), cMode, &ncId); |
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26 | if (NC_NOERR != status) |
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27 | { |
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28 | StdString errormsg(nc_strerror(status)); |
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29 | StdStringStream sstr; |
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30 | sstr << "Error when calling function: nc_create(fileName.c_str(), cMode, &ncId) " << std::endl |
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31 | << errormsg << std::endl |
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32 | << "Unable to create file, given its name: " << fileName |
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33 | << "and its creation mode " << creationMode2String(cMode) << std::endl; |
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34 | StdString e = sstr.str(); |
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35 | throw CNetCdfException(e); |
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36 | } |
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37 | |
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38 | return status; |
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39 | } |
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40 | |
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41 | /*! |
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42 | This function creates a new netcdf file on parallel file system |
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43 | \param [in] fileName Name of the file |
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44 | \param [in] cMode create mode |
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45 | \param [in] comm MPI communicator |
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46 | \param [in] info MPI information |
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47 | \param [in/out] ncId id of the created file |
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48 | \return Status code |
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49 | */ |
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50 | int CNetCdfInterface::createPar(const StdString& fileName, int cMode, MPI_Comm comm, MPI_Info info, int& ncId) |
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51 | { |
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52 | int status = xios::nc_create_par(fileName.c_str(), cMode, comm, info, &ncId); |
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53 | if (NC_NOERR != status) |
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54 | { |
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55 | StdString errormsg(nc_strerror(status)); |
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56 | StdStringStream sstr; |
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57 | sstr << "Error when calling function: nc_create_par(fileName.c_str(), cMode, comm, info, &ncId) " << std::endl |
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58 | << errormsg << std::endl |
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59 | << "Unable to create file on parallel file system, given its name: " << std::endl |
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60 | << "and its creation mode " << creationMode2String(cMode) << std::endl; |
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61 | StdString e = sstr.str(); |
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62 | throw CNetCdfException(e); |
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63 | } |
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64 | |
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65 | return status; |
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66 | } |
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67 | |
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68 | /*! |
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69 | This function opens a netcdf file, given its name and open mode, return its id |
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70 | \param [in] fileName Name of the file |
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71 | \param [in] oMode open mode |
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72 | \param [in/out] ncId id of the opening file |
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73 | \return Status code |
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74 | */ |
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75 | int CNetCdfInterface::open(const StdString& fileName, int oMode, int& ncId) |
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76 | { |
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77 | int status = nc_open(fileName.c_str(), oMode, &ncId); |
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78 | if (NC_NOERR != status) |
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79 | { |
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80 | StdString errormsg(nc_strerror(status)); |
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81 | StdStringStream sstr; |
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82 | sstr << "Error when calling function: nc_open(fileName.c_str(), oMode, &ncId) "<< std::endl |
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83 | << errormsg << std::endl |
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84 | << "Unable to open file, given its name: " << fileName |
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85 | << "and its open mode " << openMode2String(oMode) << std::endl; |
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86 | StdString e = sstr.str(); |
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87 | throw CNetCdfException(e); |
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88 | } |
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89 | |
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90 | return status; |
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91 | } |
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92 | |
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93 | |
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94 | /*! |
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95 | This function opens a new netcdf file on parallel file system |
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96 | \param [in] fileName Name of the file |
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97 | \param [in] oMode open mode |
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98 | \param [in] comm MPI communicator |
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99 | \param [in] info MPI information |
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100 | \param [in/out] ncId id of the opened file |
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101 | \return Status code |
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102 | */ |
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103 | int CNetCdfInterface::openPar(const StdString& fileName, int oMode, MPI_Comm comm, MPI_Info info, int& ncId) |
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104 | { |
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105 | int status; |
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106 | #pragma omp critical (_netcdf) |
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107 | status = xios::nc_open_par(fileName.c_str(), oMode, comm, info, &ncId); |
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108 | if (NC_NOERR != status) |
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109 | { |
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110 | StdString errormsg(nc_strerror(status)); |
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111 | StdStringStream sstr; |
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112 | sstr << "Error when calling function nc_open_par(fileName.c_str(), oMode, comm, info, &ncId) " << std::endl |
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113 | << errormsg << std::endl |
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114 | << "Unable to open file on parallel file system, given its name: " << fileName |
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115 | << "and its open mode " << openMode2String(oMode) << std::endl; |
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116 | StdString e = sstr.str(); |
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117 | throw CNetCdfException(e); |
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118 | } |
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119 | |
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120 | return status; |
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121 | } |
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122 | |
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123 | /*! |
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124 | This function closes a netcdf file, given its id |
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125 | \param [in] ncId id of the opening netcdf file |
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126 | \return Status code |
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127 | */ |
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128 | int CNetCdfInterface::close(int ncId) |
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129 | { |
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130 | int status = NC_NOERR; |
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131 | //#pragma omp critical (_netcdf) |
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132 | #pragma omp master |
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133 | { |
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134 | status = nc_close(ncId); |
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135 | if (NC_NOERR != status) |
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136 | { |
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137 | StdString errormsg(nc_strerror(status)); |
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138 | StdStringStream sstr; |
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139 | sstr << "Error when calling function nc_close(ncId)" << std::endl |
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140 | << errormsg << std::endl |
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141 | << "Unable to close file, given its id: " << ncId << std::endl; |
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142 | StdString e = sstr.str(); |
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143 | throw CNetCdfException(e); |
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144 | } |
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145 | } |
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146 | return status; |
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147 | } |
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148 | |
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149 | /*! |
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150 | This function put a netcdf file into define mode, given its id |
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151 | \param [in] ncId id of the opening netcdf file to be put into define mode |
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152 | \return Status code |
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153 | */ |
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154 | int CNetCdfInterface::reDef(int ncId) |
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155 | { |
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156 | int status = nc_redef(ncId); |
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157 | if (NC_NOERR != status) |
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158 | { |
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159 | StdString errormsg(nc_strerror(status)); |
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160 | StdStringStream sstr; |
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161 | sstr << "Error when calling function nc_redef(ncId)" << std::endl |
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162 | << errormsg << std::endl |
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163 | << "Unable to put this file into define mode given its id: " << ncId << std::endl; |
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164 | StdString e = sstr.str(); |
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165 | throw CNetCdfException(e); |
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166 | } |
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167 | |
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168 | return status; |
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169 | } |
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170 | |
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171 | /*! |
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172 | This function ends a netcdf file define mode, given its id |
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173 | \param [in] ncId id of the opening netcdf file to be put into define mode |
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174 | \return Status code |
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175 | */ |
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176 | int CNetCdfInterface::endDef(int ncId) |
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177 | { |
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178 | int status = nc_enddef(ncId); |
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179 | if (NC_NOERR != status) |
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180 | { |
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181 | StdString errormsg(nc_strerror(status)); |
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182 | StdStringStream sstr; |
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183 | |
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184 | sstr << "Error when calling function nc_enddef(ncId)" << std::endl |
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185 | << errormsg << std::endl |
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186 | << "Unable to end define mode of this file, given its id: " << ncId << std::endl; |
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187 | StdString e = sstr.str(); |
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188 | throw CNetCdfException(e); |
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189 | } |
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190 | |
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191 | return status; |
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192 | } |
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193 | |
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194 | /*! |
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195 | This function makes a request to netcdf with ncid and group name then return ncid of the named group |
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196 | \param [in] ncid Groupd id (or File Id) |
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197 | \param [in] grpName Name of the desired group (or file) |
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198 | \param [in/out] grpId Group id if the group is found |
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199 | \return Status code |
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200 | */ |
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201 | int CNetCdfInterface::inqNcId(int ncid, const StdString& grpName, int& grpId) |
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202 | { |
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203 | int status = nc_inq_ncid(ncid, grpName.c_str(), &grpId); |
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204 | if (NC_NOERR != status) |
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205 | { |
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206 | StdString errormsg(nc_strerror(status)); |
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207 | StdStringStream sstr; |
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208 | |
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209 | sstr << "Error when calling function nc_inq_ncid(ncid, grpName.c_str(), &grpId)" << std::endl |
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210 | << errormsg << std::endl |
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211 | << "Unable to get id of a group (File), given its name: " << grpName << std::endl; |
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212 | StdString e = sstr.str(); |
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213 | throw CNetCdfException(e); |
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214 | } |
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215 | |
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216 | return status; |
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217 | } |
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218 | |
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219 | |
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220 | /*! |
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221 | This function makes a request to netcdf with ncid and variable name then return ncid of the named variable |
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222 | \param [in] ncid Groupd id (or File Id) |
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223 | \param [in] varName Name of the desired variable |
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224 | \param [in/out] varId Variable id if this variable is found |
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225 | \return Status code |
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226 | */ |
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227 | int CNetCdfInterface::inqVarId(int ncid, const StdString& varName, int& varId) |
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228 | { |
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229 | int status = nc_inq_varid(ncid, varName.c_str(), &varId); |
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230 | if (NC_NOERR != status) |
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231 | { |
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232 | StdString errormsg(nc_strerror(status)); |
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233 | StdStringStream sstr; |
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234 | |
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235 | sstr << "Error when calling function: nc_inq_varid(ncid, varName.c_str(), &varId)" << std::endl |
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236 | << (errormsg) << std::endl |
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237 | << "Unable to get id of variable with name: " << varName << std::endl; |
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238 | StdString e = sstr.str(); |
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239 | throw CNetCdfException(e); |
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240 | } |
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241 | |
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242 | return status; |
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243 | } |
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244 | |
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245 | /*! |
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246 | This function makes a request to netcdf with a netCdf dimension name then return ncid of the named dimension |
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247 | \param [in] ncid Groupd id (or File Id) |
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248 | \param [in] dimName Name of the desired dimension |
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249 | \param [in/out] dimId Dimension id if this dimension is found |
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250 | \return Status code |
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251 | */ |
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252 | int CNetCdfInterface::inqDimId(int ncid, const StdString& dimName, int& dimId) |
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253 | { |
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254 | int status = nc_inq_dimid(ncid, dimName.c_str(), &dimId); |
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255 | if (NC_NOERR != status) |
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256 | { |
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257 | StdString errormsg(nc_strerror(status)); |
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258 | StdStringStream sstr; |
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259 | |
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260 | sstr << "Error when calling function nc_inq_dimid(ncid, dimName.c_str(), &dimId)" << std::endl |
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261 | << errormsg << std::endl |
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262 | << "Unable to get id of dimension, given its name: " << dimName << std::endl; |
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263 | StdString e = sstr.str(); |
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264 | throw CNetCdfException(e); |
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265 | } |
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266 | |
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267 | return status; |
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268 | } |
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269 | |
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270 | /*! |
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271 | This function queries the name of a variable given its id. |
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272 | \param [in] ncid Groupd id (or File Id) |
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273 | \param [in] varId Id of desired variable |
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274 | \param [out] varName name of desired variable |
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275 | \return Status code |
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276 | */ |
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277 | int CNetCdfInterface::inqVarName(int ncid, int varId, StdString& varName) |
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278 | { |
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279 | char varNameBuff[NC_MAX_NAME + 1]; |
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280 | int status = nc_inq_varname(ncid, varId, varNameBuff); |
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281 | if (NC_NOERR != status) |
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282 | { |
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283 | StdString errormsg(nc_strerror(status)); |
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284 | StdStringStream sstr; |
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285 | |
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286 | sstr << "Error when calling function nc_inq_varname(ncid, varId, varNameBuff)" << std::endl |
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287 | << errormsg << std::endl |
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288 | << "Unable to get variable name: "<< varName << " given its id: " << varId << std::endl; |
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289 | StdString e = sstr.str(); |
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290 | throw CNetCdfException(e); |
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291 | } |
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292 | varName = varNameBuff; |
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293 | return status; |
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294 | } |
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295 | |
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296 | /*! |
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297 | This function makes a request to netcdf with a netCdf dimension name then return ncid of the named dimension |
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298 | \param [in] ncid Groupd id (or File Id) |
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299 | \param [in/out] dimId Dimension id if this dimension is found |
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300 | \return Status code |
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301 | */ |
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302 | int CNetCdfInterface::inqUnLimDim(int ncid, int& dimId) |
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303 | { |
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304 | int status = nc_inq_unlimdim(ncid, &dimId); |
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305 | if (NC_NOERR != status) |
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306 | { |
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307 | StdString errormsg(nc_strerror(status)); |
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308 | StdStringStream sstr; |
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309 | |
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310 | sstr << "Error when calling function nc_inq_dimid" << std::endl |
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311 | << errormsg << std::endl |
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312 | << "Unable to get id of unlimited dimension " << std::endl; |
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313 | StdString e = sstr.str(); |
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314 | throw CNetCdfException(e); |
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315 | } |
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316 | |
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317 | return status; |
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318 | } |
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319 | |
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320 | /*! |
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321 | This function makes a request to netcdf, returns name of a dimension, given its id |
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322 | \param [in] ncid Groupd id (or File Id) |
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323 | \param [in] dimId Id of desired dimension |
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324 | \param [out] dimName Name of desired dimension |
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325 | \return Status code |
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326 | */ |
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327 | int CNetCdfInterface::inqDimName(int ncid, int dimId, StdString& dimName) |
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328 | { |
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329 | char fullNameIn[NC_MAX_NAME + 1]; |
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330 | int status = nc_inq_dimname(ncid, dimId, fullNameIn); |
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331 | if (NC_NOERR != status) |
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332 | { |
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333 | StdString errormsg(nc_strerror(status)); |
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334 | StdStringStream sstr; |
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335 | |
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336 | sstr << "Error when calling function nc_inq_dimname(ncid, dimId, fullNameIn)" << std::endl |
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337 | << errormsg << std::endl |
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338 | << "Unable to get dimension name: " << dimName << " given its id: " << dimId << std::endl; |
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339 | StdString e = sstr.str(); |
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340 | throw CNetCdfException(e); |
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341 | } |
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342 | dimName = StdString(fullNameIn); |
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343 | return status; |
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344 | } |
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345 | |
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346 | /*! |
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347 | This function makes a request to netcdf, returns length of a dimension, given its id |
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348 | \param [in] ncid Groupd id (or File Id) |
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349 | \param [in] dimId Id of desired dimension |
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350 | \param [in/out] dimLen Length of desired dimension |
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351 | \return Status code |
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352 | */ |
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353 | int CNetCdfInterface::inqDimLen(int ncid, int dimId, StdSize& dimLen) |
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354 | { |
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355 | int status; |
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356 | #pragma omp critical (_netcdf) |
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357 | status = nc_inq_dimlen(ncid, dimId, &dimLen); |
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358 | if (NC_NOERR != status) |
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359 | { |
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360 | StdString errormsg(nc_strerror(status)); |
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361 | StdStringStream sstr; |
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362 | |
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363 | sstr << "Error when calling function nc_inq_dimlen(ncid, dimId, &dimLen)" << std::endl |
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364 | << errormsg << std::endl |
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365 | << "Unable to get dimension length given its id: " << dimId << std::endl; |
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366 | StdString e = sstr.str(); |
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367 | throw CNetCdfException(e); |
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368 | } |
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369 | |
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370 | return status; |
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371 | } |
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372 | |
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373 | /*! |
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374 | This function makes a request to netcdf, returns number of dimensions of a variable, given its id |
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375 | \param [in] ncid Groupd id (or File Id) |
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376 | \param [in] varId Id of variable |
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377 | \param [in/out] ndims number of dimension of the variable |
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378 | \return Status code |
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379 | */ |
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380 | int CNetCdfInterface::inqVarNDims(int ncid, int varId, int& nDims) |
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381 | { |
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382 | int status = nc_inq_varndims(ncid, varId, &nDims); |
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383 | if (NC_NOERR != status) |
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384 | { |
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385 | StdString errormsg(nc_strerror(status)); |
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386 | StdStringStream sstr; |
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387 | |
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388 | sstr << "Error when calling function nc_inq_varndims(ncid, varId, &nDims)" << std::endl |
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389 | << errormsg << std::endl |
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390 | << "Unable to get the number of dimension of variable with Id: " << varId << std::endl; |
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391 | StdString e = sstr.str(); |
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392 | throw CNetCdfException(e); |
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393 | } |
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394 | |
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395 | return status; |
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396 | } |
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397 | |
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398 | /*! |
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399 | This function makes a request to netcdf, returns a list of dimension ID describing the shape of the variable, given its id |
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400 | \param [in] ncid Groupd id (or File Id) |
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401 | \param [in] varId Id of variable |
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402 | \param [in/out] dimIds list of dimension of the variable |
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403 | \return Status code |
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404 | */ |
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405 | int CNetCdfInterface::inqVarDimId(int ncid, int varId, int* dimIds) |
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406 | { |
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407 | int status = nc_inq_vardimid(ncid, varId, dimIds); |
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408 | if (NC_NOERR != status) |
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409 | { |
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410 | StdString errormsg(nc_strerror(status)); |
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411 | StdStringStream sstr; |
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412 | |
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413 | sstr << "Error when calling function nc_inq_vardimid(ncid, varId, dimIds)" << std::endl |
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414 | << errormsg << std::endl |
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415 | << "Unable to get list of dimension id of the variable with id " << varId << std::endl; |
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416 | StdString e = sstr.str(); |
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417 | throw CNetCdfException(e); |
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418 | } |
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419 | |
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420 | return status; |
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421 | } |
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422 | |
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423 | /*! |
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424 | This function makes a request to netcdf, to find all dimension in a group |
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425 | \param [in] ncid Groupd id (or File Id) |
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426 | \param [in/out] nDims number of list of dimension |
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427 | \param [in/out] dimIds list of dimension in a group or any of its parent |
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428 | \param [in] includeParents number of parents |
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429 | \return Status code |
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430 | */ |
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431 | int CNetCdfInterface::inqDimIds(int ncid, int& nDims, int* dimIds, int includeParents) |
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432 | { |
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433 | int status = nc_inq_dimids(ncid, &nDims, dimIds, includeParents); |
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434 | if (NC_NOERR != status) |
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435 | { |
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436 | StdString errormsg(nc_strerror(status)); |
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437 | StdStringStream sstr; |
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438 | |
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439 | sstr << "Error when calling function nc_inq_dimids(ncid, &nDims, dimIds, includeParents)" << std::endl; |
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440 | sstr << errormsg << std::endl; |
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441 | sstr << "Unable to retrieve number of dimension in the group with id: " << ncid << std::endl; |
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442 | sstr << "With number of Parents " << includeParents << std::endl; |
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443 | StdString e = sstr.str(); |
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444 | throw CNetCdfException(e); |
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445 | } |
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446 | |
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447 | return status; |
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448 | } |
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449 | |
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450 | /*! |
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451 | This function queries the full name of a group given its id. |
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452 | \param [in] ncid Groupd id (or File Id) |
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453 | \param [in/out] grpFullName the full name of the group |
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454 | \return Status code |
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455 | */ |
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456 | int CNetCdfInterface::inqGrpFullName(int ncid, StdString& grpFullName) |
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457 | { |
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458 | StdSize strlen = 0; |
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459 | std::vector<char> buff; |
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460 | int status = nc_inq_grpname_full(ncid, &strlen, NULL); |
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461 | if (NC_NOERR == status) |
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462 | { |
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463 | buff.resize(strlen + 1); |
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464 | status = nc_inq_grpname_full(ncid, NULL, &buff[0]); |
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465 | } |
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466 | |
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467 | if (NC_NOERR != status) |
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468 | { |
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469 | StdString errormsg(nc_strerror(status)); |
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470 | StdStringStream sstr; |
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471 | |
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472 | sstr << "Error when calling function nc_inq_grpname_full(ncid, &strlen, &buff[0])" << std::endl |
---|
473 | << errormsg << std::endl |
---|
474 | << "Unable to get the full group name given its id: " << ncid << std::endl; |
---|
475 | StdString e = sstr.str(); |
---|
476 | throw CNetCdfException(e); |
---|
477 | } |
---|
478 | |
---|
479 | grpFullName.assign(buff.begin(), buff.end()); |
---|
480 | |
---|
481 | return status; |
---|
482 | } |
---|
483 | |
---|
484 | /*! |
---|
485 | This function queries the list of group ids given a location id. |
---|
486 | \param [in] ncid Groupd id (or File Id) |
---|
487 | \param [in/out] numgrps number of groups |
---|
488 | \param [in/out] ncids list of group ids |
---|
489 | \return Status code |
---|
490 | */ |
---|
491 | int CNetCdfInterface::inqGrpIds(int ncid, int& numgrps, int* ncids) |
---|
492 | { |
---|
493 | int status = nc_inq_grps(ncid, &numgrps, ncids); |
---|
494 | if (NC_NOERR != status) |
---|
495 | { |
---|
496 | StdString errormsg(nc_strerror(status)); |
---|
497 | StdStringStream sstr; |
---|
498 | |
---|
499 | sstr << "Error when calling function nc_inq_grps(ncid, &numgrps, ncids)" << std::endl; |
---|
500 | sstr << errormsg << std::endl; |
---|
501 | sstr << "Unable to retrieve the list of groups for location id: " << ncid << std::endl; |
---|
502 | StdString e = sstr.str(); |
---|
503 | throw CNetCdfException(e); |
---|
504 | } |
---|
505 | |
---|
506 | return status; |
---|
507 | } |
---|
508 | |
---|
509 | /*! |
---|
510 | This function queries the list of variable ids given a location id. |
---|
511 | \param [in] ncid Groupd id (or File Id) |
---|
512 | \param [in/out] nvars number of variables |
---|
513 | \param [in/out] varids list of variable ids |
---|
514 | \return Status code |
---|
515 | */ |
---|
516 | int CNetCdfInterface::inqVarIds(int ncid, int& nvars, int* varids) |
---|
517 | { |
---|
518 | int status = nc_inq_varids(ncid, &nvars, varids); |
---|
519 | if (NC_NOERR != status) |
---|
520 | { |
---|
521 | StdString errormsg(nc_strerror(status)); |
---|
522 | StdStringStream sstr; |
---|
523 | |
---|
524 | sstr << "Error when calling function nc_inq_varids(ncid, &nvars, varids)" << std::endl; |
---|
525 | sstr << errormsg << std::endl; |
---|
526 | sstr << "Unable to retrieve the list of variables for location id: " << ncid << std::endl; |
---|
527 | StdString e = sstr.str(); |
---|
528 | throw CNetCdfException(e); |
---|
529 | } |
---|
530 | |
---|
531 | return status; |
---|
532 | } |
---|
533 | |
---|
534 | /*! |
---|
535 | This function queries the type and the size of an attribute given its name and the id of the variable to which it is attached. |
---|
536 | \param [in] ncid Groupd id (or File Id) |
---|
537 | \param [in] varid the id of the variable to which the attribute is attached |
---|
538 | \param [in] name the name of the attribute |
---|
539 | \param [out] type the type of the attribute |
---|
540 | \param [out] len the size of the attribute |
---|
541 | \return Status code |
---|
542 | */ |
---|
543 | int CNetCdfInterface::inqAtt(int ncid, int varid, const StdString& name, nc_type& type, size_t& len) |
---|
544 | { |
---|
545 | int status = nc_inq_att(ncid, varid, name.c_str(), &type, &len); |
---|
546 | if (NC_NOERR != status) |
---|
547 | { |
---|
548 | StdString errormsg(nc_strerror(status)); |
---|
549 | StdStringStream sstr; |
---|
550 | |
---|
551 | sstr << "Error when calling function nc_inq_att(ncid, varid, name.c_str(), &type, &len)" << std::endl; |
---|
552 | sstr << errormsg << std::endl; |
---|
553 | sstr << "Unable to query the attribute information given its name: " << name << " and its variable id:" << varid << std::endl; |
---|
554 | StdString e = sstr.str(); |
---|
555 | throw CNetCdfException(e); |
---|
556 | } |
---|
557 | |
---|
558 | return status; |
---|
559 | } |
---|
560 | |
---|
561 | /*! |
---|
562 | This function queries the number of global attributes given a location id. |
---|
563 | \param [in] ncid Groupd id (or File Id) |
---|
564 | \param [out] ngatts the number of global attributes |
---|
565 | \return Status code |
---|
566 | */ |
---|
567 | int CNetCdfInterface::inqNAtts(int ncid, int& ngatts) |
---|
568 | { |
---|
569 | int status = nc_inq_natts(ncid, &ngatts); |
---|
570 | if (NC_NOERR != status) |
---|
571 | { |
---|
572 | StdString errormsg(nc_strerror(status)); |
---|
573 | StdStringStream sstr; |
---|
574 | |
---|
575 | sstr << "Error when calling function nc_inq_natts(ncid, &ngatts)" << std::endl; |
---|
576 | sstr << errormsg << std::endl; |
---|
577 | sstr << "Unable to query the number of global attributes given the location id:" << ncid << std::endl; |
---|
578 | StdString e = sstr.str(); |
---|
579 | throw CNetCdfException(e); |
---|
580 | } |
---|
581 | |
---|
582 | return status; |
---|
583 | } |
---|
584 | |
---|
585 | /*! |
---|
586 | This function queries the number of global attributes given a location id and a variable id. |
---|
587 | \param [in] ncid Groupd id (or File Id) |
---|
588 | \param [in] varid the id of the variable |
---|
589 | \param [out] natts the number of global attributes |
---|
590 | \return Status code |
---|
591 | */ |
---|
592 | int CNetCdfInterface::inqVarNAtts(int ncid, int varid, int& natts) |
---|
593 | { |
---|
594 | int status = nc_inq_varnatts(ncid, varid, &natts); |
---|
595 | if (NC_NOERR != status) |
---|
596 | { |
---|
597 | StdString errormsg(nc_strerror(status)); |
---|
598 | StdStringStream sstr; |
---|
599 | |
---|
600 | sstr << "Error when calling function nc_inq_varnatts(ncid, varid, &natts)" << std::endl; |
---|
601 | sstr << errormsg << std::endl; |
---|
602 | sstr << "Unable to query the number of attributes given the location id:" << ncid << " and the variable id:" << varid << std::endl; |
---|
603 | StdString e = sstr.str(); |
---|
604 | throw CNetCdfException(e); |
---|
605 | } |
---|
606 | |
---|
607 | return status; |
---|
608 | } |
---|
609 | |
---|
610 | |
---|
611 | //! Query the name of an attribute given a location id, a variable id and the attribute number |
---|
612 | int CNetCdfInterface::inqAttName(int ncid, int varid, int attnum, StdString& name) |
---|
613 | { |
---|
614 | std::vector<char> attName(NC_MAX_NAME + 1,' '); |
---|
615 | int status = nc_inq_attname(ncid, varid, attnum, &attName[0]); |
---|
616 | if (NC_NOERR != status) |
---|
617 | { |
---|
618 | StdString errormsg(nc_strerror(status)); |
---|
619 | StdStringStream sstr; |
---|
620 | |
---|
621 | sstr << "Error when calling function nc_inq_attname(ncid, varid, attnum, attName)" << std::endl; |
---|
622 | sstr << errormsg << std::endl; |
---|
623 | sstr << "Unable to query the name: " << name << " of attribute " << attnum << " given the location id:" << ncid << " and the variable id:" << varid << std::endl; |
---|
624 | StdString e = sstr.str(); |
---|
625 | throw CNetCdfException(e); |
---|
626 | } |
---|
627 | |
---|
628 | int nameSize = 0; |
---|
629 | while ((nameSize < NC_MAX_NAME) && (' ' != attName[nameSize] )) ++nameSize; |
---|
630 | name.resize(nameSize); |
---|
631 | // for (int idx = 0; idx < nameSize; ++idx) name.at(idx) = attName[idx]; |
---|
632 | std::copy(&attName[0], &attName[nameSize-1], name.begin()); |
---|
633 | |
---|
634 | return status; |
---|
635 | } |
---|
636 | |
---|
637 | /*! |
---|
638 | This function makes a request to netcdf with a id of a prent groupd and then return id of the created group, given its name |
---|
639 | \param [in] parentNcid Id of parent groupd(or File Id) |
---|
640 | \param [in] grpName Name of the desired group |
---|
641 | \param [in/out] grpId Group id if this group is created sucessfully |
---|
642 | \return Status code |
---|
643 | */ |
---|
644 | int CNetCdfInterface::defGrp(int parentNcid, const StdString& grpName, int& grpId) |
---|
645 | { |
---|
646 | int status = nc_def_grp(parentNcid, grpName.c_str(), &grpId); |
---|
647 | if (NC_NOERR != status) |
---|
648 | { |
---|
649 | StdString errormsg(nc_strerror(status)); |
---|
650 | StdStringStream sstr; |
---|
651 | |
---|
652 | sstr << "Error when calling function nc_def_grp(parentNcid, grpName.c_str(), &grpId)" << std::endl; |
---|
653 | sstr << errormsg << std::endl; |
---|
654 | sstr << "Unable to create group Id, given its name: " << grpName << std::endl; |
---|
655 | StdString e = sstr.str(); |
---|
656 | throw CNetCdfException(e); |
---|
657 | } |
---|
658 | |
---|
659 | return status; |
---|
660 | } |
---|
661 | |
---|
662 | /*! |
---|
663 | This function makes a request to netcdf, add a new dimension to an open netcdf in define mode |
---|
664 | \param [in] ncid Id of groupd(or File Id) |
---|
665 | \param [in] dimName Name of the desired dimension |
---|
666 | \param [in/out] grpId Group id if this group is created sucessfully |
---|
667 | \return Status code |
---|
668 | */ |
---|
669 | int CNetCdfInterface::defDim(int ncid, const StdString& dimName, StdSize dimLen, int& dimId) |
---|
670 | { |
---|
671 | int status = nc_def_dim(ncid, dimName.c_str(), dimLen, &dimId); |
---|
672 | if (NC_NOERR != status) |
---|
673 | { |
---|
674 | StdString errormsg(nc_strerror(status)); |
---|
675 | StdStringStream sstr; |
---|
676 | |
---|
677 | sstr << "Error when calling function nc_def_dim(ncid, dimName.c_str(), dimLen, &dimId)" << std::endl; |
---|
678 | sstr << errormsg << std::endl; |
---|
679 | sstr << "Unable to create dimension with name: " << dimName |
---|
680 | << " and with length " << dimLen << std::endl; |
---|
681 | StdString e = sstr.str(); |
---|
682 | throw CNetCdfException(e); |
---|
683 | } |
---|
684 | |
---|
685 | return status; |
---|
686 | } |
---|
687 | |
---|
688 | /*! |
---|
689 | This function makes a request to netcdf with its id, to add a new variable to an open netCdf in define mode, |
---|
690 | return a variable id, given its name, type, the number of dimensions and list of dimension id |
---|
691 | \param [in] ncid Id of groupd(or File Id) |
---|
692 | \param [in] varName Name of the desired dimension |
---|
693 | \param [in] xtypes One of the set of predefined netCDF data types |
---|
694 | \param [in] nDims Number of dimension for the variable |
---|
695 | \param [in] dimIds List of ndims dimension ids corresponding to the variable dimensions |
---|
696 | \param [in/out] varId Variable id if it is added sucessfully |
---|
697 | \return Status code |
---|
698 | */ |
---|
699 | int CNetCdfInterface::defVar(int ncid, const StdString& varName, nc_type xtype, |
---|
700 | int nDims, const int dimIds[], int& varId) |
---|
701 | { |
---|
702 | int status = nc_def_var(ncid, varName.c_str(), xtype, nDims, dimIds, &varId); |
---|
703 | if (NC_NOERR != status) |
---|
704 | { |
---|
705 | StdString errormsg(nc_strerror(status)); |
---|
706 | StdStringStream sstr; |
---|
707 | |
---|
708 | sstr << "Error when calling function nc_def_var(ncid, varName.c_str(), xtype, nDims, dimIds, &varId)" << std::endl; |
---|
709 | sstr << errormsg << std::endl; |
---|
710 | sstr << "Unable to add a new variable with name: " << varName |
---|
711 | << " with type " << xtype |
---|
712 | << " and number of dimension " << nDims << std::endl; |
---|
713 | StdString e = sstr.str(); |
---|
714 | throw CNetCdfException(e); |
---|
715 | } |
---|
716 | |
---|
717 | return status; |
---|
718 | } |
---|
719 | |
---|
720 | /*! |
---|
721 | This function makes a request to netcdf with a ncid, to set the chunking size of a variable, |
---|
722 | given variable id and type of storage |
---|
723 | \param [in] ncid Id groupd(or File Id) |
---|
724 | \param [in] varId Id of the variable |
---|
725 | \param [in] storage Type of storage (It can be: NC_CONTIGUOUS, NC_CHUNKED) |
---|
726 | \param [in/out] chunkSize array list of chunk sizes |
---|
727 | \return Status code |
---|
728 | */ |
---|
729 | int CNetCdfInterface::defVarChunking(int ncid, int varId, int storage, StdSize chunkSize[]) |
---|
730 | { |
---|
731 | int status = nc_def_var_chunking(ncid, varId, storage, chunkSize); |
---|
732 | if (NC_NOERR != status) |
---|
733 | { |
---|
734 | StdString errormsg(nc_strerror(status)); |
---|
735 | StdStringStream sstr; |
---|
736 | |
---|
737 | sstr << "Error when calling function nc_def_var_chunking(ncid, varId, storage, chunkSize)" << std::endl; |
---|
738 | sstr << errormsg << std::endl; |
---|
739 | sstr << "Unable to set chunk size of the variable with id: " << varId |
---|
740 | << " and storage type " << storage << std::endl; |
---|
741 | StdString e = sstr.str(); |
---|
742 | throw CNetCdfException(e); |
---|
743 | } |
---|
744 | |
---|
745 | return status; |
---|
746 | } |
---|
747 | |
---|
748 | /*! |
---|
749 | This function sets the compression level to the specified variable |
---|
750 | \param [in] ncid Groud id (or file id) |
---|
751 | \param [in] varId Id of the variable |
---|
752 | \param [in] compressionLevel The compression level from 0 to 9 (0 disables the compression, 9 is the higher compression) |
---|
753 | \return Status code |
---|
754 | */ |
---|
755 | int CNetCdfInterface::defVarDeflate(int ncid, int varId, int compressionLevel) |
---|
756 | { |
---|
757 | |
---|
758 | if (compressionLevel == 0) return NC_NOERR ; |
---|
759 | int status = nc_def_var_deflate(ncid, varId, false, (compressionLevel > 0), compressionLevel); |
---|
760 | if (NC_NOERR != status) |
---|
761 | { |
---|
762 | StdString errormsg(nc_strerror(status)); |
---|
763 | StdStringStream sstr; |
---|
764 | |
---|
765 | sstr << "Error when calling function nc_def_var_deflate(ncid, varId, false, (compressionLevel > 0), compressionLevel)" << std::endl; |
---|
766 | sstr << errormsg << std::endl; |
---|
767 | sstr << "Unable to set the compression level of the variable with id: " << varId |
---|
768 | << " and compression level: " << compressionLevel << std::endl; |
---|
769 | StdString e = sstr.str(); |
---|
770 | throw CNetCdfException(e); |
---|
771 | } |
---|
772 | |
---|
773 | return status; |
---|
774 | } |
---|
775 | |
---|
776 | /*! |
---|
777 | Set or unset the fill mode for a NetCDF file specified by its file id. |
---|
778 | \param [in] ncid File id |
---|
779 | \param [in] fill Define whether the fill mode should be enabled or not |
---|
780 | \return Status code |
---|
781 | */ |
---|
782 | int CNetCdfInterface::setFill(int ncid, bool fill) |
---|
783 | { |
---|
784 | int old_fill_mode; |
---|
785 | int status = nc_set_fill(ncid, fill ? NC_FILL: NC_NOFILL, &old_fill_mode); |
---|
786 | if (NC_NOERR != status) |
---|
787 | { |
---|
788 | StdString errormsg(nc_strerror(status)); |
---|
789 | StdStringStream sstr; |
---|
790 | |
---|
791 | sstr << "Error when calling function nc_set_fill(ncid, fill ? NC_FILL: NC_NOFILL, &old_fill_mode)" << std::endl; |
---|
792 | sstr << errormsg << std::endl; |
---|
793 | sstr << "Unable to set the fill mode to: " << (fill ? "NC_FILL": "NC_NOFILL") << std::endl; |
---|
794 | StdString e = sstr.str(); |
---|
795 | throw CNetCdfException(e); |
---|
796 | } |
---|
797 | |
---|
798 | return status; |
---|
799 | } |
---|
800 | |
---|
801 | /*! |
---|
802 | This function makes a request to netcdf with a ncid, to set the fill parameters for a variable, |
---|
803 | given variable id and type of fill |
---|
804 | \param [in] ncid Id groupd(or File Id) |
---|
805 | \param [in] varId Id of the variable |
---|
806 | \param [in] noFill turn on/off nofill mode on a variable |
---|
807 | \param [in/out] fillValue |
---|
808 | \return Status code |
---|
809 | */ |
---|
810 | int CNetCdfInterface::defVarFill(int ncid, int varId, int noFill, void* fillValue) |
---|
811 | { |
---|
812 | int status = nc_def_var_fill(ncid, varId, noFill, fillValue); |
---|
813 | if (NC_NOERR != status) |
---|
814 | { |
---|
815 | StdString errormsg(nc_strerror(status)); |
---|
816 | StdStringStream sstr; |
---|
817 | |
---|
818 | sstr << "Error when calling function nc_def_var_fill(ncid, varId, noFill, fillValue)" << std::endl; |
---|
819 | sstr << errormsg << std::endl; |
---|
820 | sstr << "Unable to set fill parameters of the variable with id: " << varId |
---|
821 | << " and fill option " << noFill << std::endl; |
---|
822 | StdString e = sstr.str(); |
---|
823 | throw CNetCdfException(e); |
---|
824 | } |
---|
825 | |
---|
826 | return status; |
---|
827 | } |
---|
828 | |
---|
829 | /*! |
---|
830 | This function makes a request to netcdf with a ncid, to change the way read/write operations are performed |
---|
831 | collectively or independently on the variable. |
---|
832 | \param [in] ncid Id groupd(or File Id) |
---|
833 | \param [in] varId Id of the variable |
---|
834 | \param [in] noFill turn on/off nofill mode on a variable |
---|
835 | \param [in/out] fillValue |
---|
836 | \return Status code |
---|
837 | */ |
---|
838 | int CNetCdfInterface::varParAccess(int ncid, int varId, int access) |
---|
839 | { |
---|
840 | int status = nc_var_par_access(ncid, varId, access); |
---|
841 | if (NC_NOERR != status) |
---|
842 | { |
---|
843 | StdString errormsg(nc_strerror(status)); |
---|
844 | StdStringStream sstr; |
---|
845 | |
---|
846 | sstr << "Error when calling function nc_var_par_access(ncid, varId, access)" << std::endl; |
---|
847 | sstr << errormsg << std::endl; |
---|
848 | sstr << "Unable to change read/write option of the variable with id: " << varId << std::endl; |
---|
849 | StdString e = sstr.str(); |
---|
850 | throw CNetCdfException(e); |
---|
851 | } |
---|
852 | |
---|
853 | return status; |
---|
854 | } |
---|
855 | |
---|
856 | /*! |
---|
857 | This function makes a synchronisation of the disk copy of a netCDF dataset. |
---|
858 | \param [in] ncid Id groupd(or File Id) |
---|
859 | \return Status code |
---|
860 | */ |
---|
861 | int CNetCdfInterface::sync(int ncid) |
---|
862 | { |
---|
863 | int status = nc_sync(ncid); |
---|
864 | if (NC_NOERR != status) |
---|
865 | { |
---|
866 | StdString errormsg(nc_strerror(status)); |
---|
867 | StdStringStream sstr; |
---|
868 | |
---|
869 | sstr << "Error when calling function nc_sync(ncid)" << std::endl; |
---|
870 | sstr << errormsg << std::endl; |
---|
871 | sstr << "Unable to make a synchronization of a netCDF file with id: " << ncid << std::endl; |
---|
872 | StdString e = sstr.str(); |
---|
873 | throw CNetCdfException(e); |
---|
874 | } |
---|
875 | |
---|
876 | return status; |
---|
877 | } |
---|
878 | |
---|
879 | // Some specializations of getAttributeType |
---|
880 | template<> |
---|
881 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, double* data) |
---|
882 | { |
---|
883 | return nc_get_att_double(ncid, varid, attrName, data); |
---|
884 | } |
---|
885 | |
---|
886 | template<> |
---|
887 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, float* data) |
---|
888 | { |
---|
889 | return nc_get_att_float(ncid, varid, attrName, data); |
---|
890 | } |
---|
891 | |
---|
892 | template<> |
---|
893 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, int* data) |
---|
894 | { |
---|
895 | return nc_get_att_int(ncid, varid, attrName, data); |
---|
896 | } |
---|
897 | |
---|
898 | template<> |
---|
899 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, long* data) |
---|
900 | { |
---|
901 | return nc_get_att_long(ncid, varid, attrName, data); |
---|
902 | } |
---|
903 | |
---|
904 | template<> |
---|
905 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, short* data) |
---|
906 | { |
---|
907 | return nc_get_att_short(ncid, varid, attrName, data); |
---|
908 | } |
---|
909 | |
---|
910 | template<> |
---|
911 | int CNetCdfInterface::ncGetAttType(int ncid, int varid, const char* attrName, char* data) |
---|
912 | { |
---|
913 | return nc_get_att_text(ncid, varid, attrName, data); |
---|
914 | } |
---|
915 | |
---|
916 | // Some specializations of putAttributeType |
---|
917 | template<> |
---|
918 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
919 | StdSize numVal, const double* data) |
---|
920 | { |
---|
921 | return nc_put_att_double(ncid, varid, attrName, NC_DOUBLE, numVal, data); |
---|
922 | } |
---|
923 | |
---|
924 | template<> |
---|
925 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
926 | StdSize numVal, const float* data) |
---|
927 | { |
---|
928 | return nc_put_att_float(ncid, varid, attrName, NC_FLOAT, numVal, data); |
---|
929 | } |
---|
930 | |
---|
931 | template<> |
---|
932 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
933 | StdSize numVal, const int* data) |
---|
934 | { |
---|
935 | return nc_put_att_int(ncid, varid, attrName, NC_INT, numVal, data); |
---|
936 | } |
---|
937 | |
---|
938 | template<> |
---|
939 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
940 | StdSize numVal, const long* data) |
---|
941 | { |
---|
942 | return nc_put_att_long(ncid, varid, attrName, NC_LONG, numVal, data); |
---|
943 | } |
---|
944 | |
---|
945 | template<> |
---|
946 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
947 | StdSize numVal, const short* data) |
---|
948 | { |
---|
949 | return nc_put_att_short(ncid, varid, attrName, NC_SHORT, numVal, data); |
---|
950 | } |
---|
951 | |
---|
952 | template<> |
---|
953 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
954 | StdSize numVal, const char* data) |
---|
955 | { |
---|
956 | return nc_put_att_text(ncid, varid, attrName, numVal, data); |
---|
957 | } |
---|
958 | |
---|
959 | // Some specializations of getVariableType |
---|
960 | template<> |
---|
961 | int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, double* data) |
---|
962 | { |
---|
963 | return nc_get_vara_double(ncid, varid, start, count, data); |
---|
964 | } |
---|
965 | |
---|
966 | template<> |
---|
967 | int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, float* data) |
---|
968 | { |
---|
969 | return nc_get_vara_float(ncid, varid, start, count, data); |
---|
970 | } |
---|
971 | |
---|
972 | template<> |
---|
973 | int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, int* data) |
---|
974 | { |
---|
975 | return nc_get_vara_int(ncid, varid, start, count, data); |
---|
976 | } |
---|
977 | |
---|
978 | template<> |
---|
979 | int CNetCdfInterface::ncGetVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, char* data) |
---|
980 | { |
---|
981 | return nc_get_vara_text(ncid, varid, start, count, data); |
---|
982 | } |
---|
983 | |
---|
984 | // Some specializations of putVariableType |
---|
985 | template<> |
---|
986 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const double* data) |
---|
987 | { |
---|
988 | return nc_put_vara_double(ncid, varid, start, count, data); |
---|
989 | } |
---|
990 | |
---|
991 | template<> |
---|
992 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const float* data) |
---|
993 | { |
---|
994 | return nc_put_vara_float(ncid, varid, start, count, data); |
---|
995 | } |
---|
996 | |
---|
997 | template<> |
---|
998 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const int* data) |
---|
999 | { |
---|
1000 | return nc_put_vara_int(ncid, varid, start, count, data); |
---|
1001 | } |
---|
1002 | |
---|
1003 | template<> |
---|
1004 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const char* data) |
---|
1005 | { |
---|
1006 | return nc_put_vara_text(ncid, varid, start, count, data); |
---|
1007 | } |
---|
1008 | |
---|
1009 | /*! |
---|
1010 | This function verifies an existence of a variable by using its name. |
---|
1011 | Be careful, althoug false means variable doens't exist, it could show that netCDF file doesn't either |
---|
1012 | \param [in] ncid Id of groupd(or File Id) |
---|
1013 | \param [in] attrName Name of the variable |
---|
1014 | \return Existence of variable |
---|
1015 | */ |
---|
1016 | bool CNetCdfInterface::isVarExisted(int ncId, const StdString& varName) |
---|
1017 | { |
---|
1018 | int varId = 0; |
---|
1019 | return (NC_NOERR == (nc_inq_varid(ncId, varName.c_str(), &varId))); |
---|
1020 | } |
---|
1021 | |
---|
1022 | bool CNetCdfInterface::isDimExisted(int ncId, const StdString& dimName) |
---|
1023 | { |
---|
1024 | int dimId = 0; |
---|
1025 | return (NC_NOERR == (nc_inq_dimid(ncId, dimName.c_str(), &dimId))); |
---|
1026 | } |
---|
1027 | |
---|
1028 | StdString CNetCdfInterface::openMode2String(int oMode) |
---|
1029 | { |
---|
1030 | StdString modeMes; |
---|
1031 | switch (oMode) |
---|
1032 | { |
---|
1033 | case NC_NOWRITE: |
---|
1034 | modeMes = StdString("NC_NOWRITE: Opening netCDF file with read-only access with buffering and caching access"); |
---|
1035 | break; |
---|
1036 | case NC_SHARE: |
---|
1037 | modeMes = StdString("NC_SHARE: Several processes can read the file concurrently"); |
---|
1038 | break; |
---|
1039 | case NC_WRITE: |
---|
1040 | modeMes = StdString("NC_WRITE: NetCDF file is readable and writable"); |
---|
1041 | break; |
---|
1042 | default: |
---|
1043 | modeMes = StdString("In the composed opening mode"); |
---|
1044 | break; |
---|
1045 | } |
---|
1046 | return modeMes; |
---|
1047 | } |
---|
1048 | |
---|
1049 | StdString CNetCdfInterface::creationMode2String(int cMode) |
---|
1050 | { |
---|
1051 | StdString modeMes; |
---|
1052 | switch (cMode) |
---|
1053 | { |
---|
1054 | case NC_NOCLOBBER: |
---|
1055 | modeMes = StdString("NC_NOCLOBBER: Not overwrite an exisiting netCDF file "); |
---|
1056 | break; |
---|
1057 | case NC_SHARE: |
---|
1058 | modeMes = StdString("NC_SHARE: Several processes can read from and write into the file concurrently"); |
---|
1059 | break; |
---|
1060 | case NC_64BIT_OFFSET: |
---|
1061 | modeMes = StdString("NC_64BIT_OFFSET: NetCDF file is 64-bit offset"); |
---|
1062 | break; |
---|
1063 | case NC_NETCDF4: |
---|
1064 | modeMes = StdString("NC_NETCDF4: NetCDF file is HDF5/NetCDF-4"); |
---|
1065 | break; |
---|
1066 | case NC_CLASSIC_MODEL: |
---|
1067 | modeMes = StdString("NC_CLASSIC_MODEL: NetCDF file is classical model"); |
---|
1068 | break; |
---|
1069 | default: |
---|
1070 | modeMes = StdString("In the composed creation mode"); |
---|
1071 | break; |
---|
1072 | } |
---|
1073 | return modeMes; |
---|
1074 | } |
---|
1075 | |
---|
1076 | } |
---|