1 | #include "onetcdf4.hpp" |
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2 | #include "group_template.hpp" |
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3 | #include "mpi.hpp" |
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4 | #include "netcdf.hpp" |
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5 | |
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6 | namespace xios |
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7 | { |
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8 | /// ////////////////////// Définitions ////////////////////// /// |
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9 | |
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10 | CONetCDF4::CONetCDF4 |
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11 | (const StdString & filename, bool exist, const MPI_Comm * comm, bool multifile) |
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12 | : path() |
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13 | { |
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14 | this->wmpi = (comm != NULL) && !multifile; |
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15 | this->initialize(filename, exist, comm,multifile); |
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16 | } |
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17 | |
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18 | //--------------------------------------------------------------- |
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19 | |
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20 | |
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21 | |
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22 | CONetCDF4::~CONetCDF4(void) |
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23 | { |
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24 | // CheckError(nc_close(this->ncidp)); |
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25 | } |
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26 | |
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27 | ///-------------------------------------------------------------- |
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28 | |
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29 | void CONetCDF4::initialize |
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30 | (const StdString & filename, bool exist, const MPI_Comm * comm, bool multifile) |
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31 | { |
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32 | if (!exist) |
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33 | { |
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34 | if (comm != NULL) |
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35 | { |
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36 | if (!multifile) CheckError(xios::nc_create_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp)); |
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37 | else CheckError(nc_create(filename.c_str(), NC_NETCDF4, &this->ncidp)); |
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38 | } |
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39 | else CheckError(nc_create(filename.c_str(), NC_NETCDF4, &this->ncidp)); |
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40 | } |
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41 | else |
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42 | { |
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43 | if (comm != NULL) |
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44 | { |
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45 | if (!multifile) CheckError(xios::nc_open_par(filename.c_str(), NC_NETCDF4|NC_MPIIO, *comm, MPI_INFO_NULL, &this->ncidp)); |
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46 | else CheckError(nc_open(filename.c_str(), NC_NETCDF4, &this->ncidp)); |
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47 | } |
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48 | else CheckError(nc_open(filename.c_str(), NC_NETCDF4, &this->ncidp)); |
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49 | } |
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50 | } |
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51 | |
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52 | void CONetCDF4::close() |
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53 | { |
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54 | CheckError(nc_close(this->ncidp)); |
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55 | } |
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56 | |
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57 | //--------------------------------------------------------------- |
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58 | |
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59 | void CONetCDF4::definition_start(void) |
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60 | { |
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61 | CheckError(nc_redef(this->ncidp)); |
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62 | } |
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63 | |
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64 | //--------------------------------------------------------------- |
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65 | |
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66 | void CONetCDF4::definition_end(void) |
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67 | { |
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68 | CheckError(nc_enddef(this->ncidp)); |
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69 | } |
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70 | |
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71 | //--------------------------------------------------------------- |
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72 | |
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73 | void CONetCDF4::CheckError(int status) |
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74 | { |
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75 | if (status != NC_NOERR) |
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76 | { |
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77 | StdString errormsg (nc_strerror(status)); // fuite mémoire ici ? |
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78 | ERROR("CONetCDF4::CheckError(int status)", |
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79 | << "[ status = " << status << " ] " << errormsg); |
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80 | } |
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81 | } |
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82 | |
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83 | //--------------------------------------------------------------- |
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84 | |
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85 | int CONetCDF4::getCurrentGroup(void) |
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86 | { |
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87 | return (this->getGroup(this->getCurrentPath())); |
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88 | } |
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89 | |
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90 | //--------------------------------------------------------------- |
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91 | |
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92 | int CONetCDF4::getGroup(const CONetCDF4Path & path) |
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93 | { |
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94 | int retvalue = this->ncidp; |
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95 | |
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96 | CONetCDF4Path::const_iterator |
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97 | it = path.begin(), end = path.end(); |
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98 | |
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99 | for (;it != end; it++) |
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100 | { |
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101 | const StdString & groupid = *it; |
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102 | CheckError(nc_inq_ncid(retvalue, const_cast<char*>(groupid.c_str()), &retvalue)); |
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103 | } |
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104 | return (retvalue); |
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105 | } |
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106 | |
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107 | //--------------------------------------------------------------- |
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108 | |
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109 | int CONetCDF4::getVariable(const StdString & varname) |
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110 | { |
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111 | int varid = 0; |
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112 | int grpid = this->getCurrentGroup(); |
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113 | CheckError(nc_inq_varid (grpid, varname.c_str(), &varid)); |
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114 | return (varid); |
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115 | } |
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116 | |
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117 | //--------------------------------------------------------------- |
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118 | |
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119 | int CONetCDF4::getDimension(const StdString & dimname) |
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120 | { |
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121 | int dimid = 0; |
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122 | int grpid = this->getCurrentGroup(); |
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123 | CheckError(nc_inq_dimid (grpid, dimname.c_str(), &dimid)); |
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124 | return (dimid); |
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125 | } |
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126 | |
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127 | //--------------------------------------------------------------- |
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128 | |
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129 | int CONetCDF4::getUnlimitedDimension(void) |
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130 | { |
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131 | int dimid = 0; |
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132 | int grpid = this->getCurrentGroup(); |
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133 | CheckError(nc_inq_unlimdim (grpid, &dimid)); |
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134 | return (dimid); |
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135 | } |
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136 | |
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137 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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138 | { |
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139 | char full_name_in[NC_MAX_NAME +1]; |
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140 | int grpid = this->getGroup(path); |
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141 | int dimid = this->getUnlimitedDimension(); |
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142 | |
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143 | if (dimid == -1) return (std::string()); |
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144 | CheckError(nc_inq_dimname(grpid, dimid, full_name_in)); |
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145 | |
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146 | StdString dimname(full_name_in); |
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147 | return (dimname); |
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148 | } |
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149 | |
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150 | //--------------------------------------------------------------- |
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151 | |
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152 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString & varname) |
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153 | { |
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154 | StdSize size = 0; |
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155 | std::vector<StdSize> retvalue; |
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156 | int grpid = this->getCurrentGroup(); |
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157 | int varid = this->getVariable(varname); |
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158 | int nbdim = 0, *dimid = NULL; |
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159 | |
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160 | CheckError(nc_inq_varndims(grpid, varid, &nbdim)); |
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161 | dimid = new int[nbdim](); |
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162 | CheckError(nc_inq_vardimid(grpid, varid, dimid)); |
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163 | |
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164 | for (int i = 0; i < nbdim; i++) |
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165 | { |
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166 | CheckError(nc_inq_dimlen (grpid, dimid[i], &size)); |
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167 | if (size == NC_UNLIMITED) |
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168 | size = UNLIMITED_DIM; |
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169 | retvalue.push_back(size); |
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170 | } |
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171 | |
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172 | return (retvalue); |
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173 | } |
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174 | |
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175 | std::vector<std::string> CONetCDF4::getDimensionsIdList (const std::string * _varname) |
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176 | { |
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177 | char full_name_in[NC_MAX_NAME +1]; |
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178 | int nbdim = 0, *dimid = NULL; |
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179 | int grpid = this->getCurrentGroup(); |
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180 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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181 | std::vector<std::string> retvalue; |
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182 | |
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183 | if (_varname != NULL) |
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184 | { |
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185 | CheckError(nc_inq_varndims(grpid, varid, &nbdim)); |
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186 | dimid = new int[nbdim](); |
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187 | CheckError(nc_inq_vardimid(grpid, varid, dimid)); |
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188 | } |
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189 | else |
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190 | { |
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191 | CheckError(nc_inq_dimids(grpid, &nbdim, NULL, 1)); |
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192 | dimid = new int[nbdim](); |
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193 | CheckError(nc_inq_dimids(grpid, NULL, dimid, 1)); |
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194 | } |
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195 | |
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196 | for (int i = 0; i < nbdim; i++) |
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197 | { |
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198 | CheckError(nc_inq_dimname(grpid, dimid[i], full_name_in)); |
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199 | std::string dimname(full_name_in); |
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200 | retvalue.push_back(dimname); |
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201 | } |
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202 | delete [] dimid; |
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203 | |
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204 | return (retvalue); |
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205 | } |
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206 | |
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207 | |
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208 | //--------------------------------------------------------------- |
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209 | |
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210 | const CONetCDF4::CONetCDF4Path & CONetCDF4::getCurrentPath(void) const |
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211 | { return (this->path); } |
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212 | |
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213 | void CONetCDF4::setCurrentPath(const CONetCDF4Path & path) |
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214 | { this->path = path; } |
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215 | |
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216 | //--------------------------------------------------------------- |
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217 | |
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218 | int CONetCDF4::addGroup(const StdString & name) |
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219 | { |
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220 | int retvalue = 0; |
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221 | int grpid = this->getCurrentGroup(); |
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222 | CheckError(nc_def_grp(grpid, const_cast<char*>(name.c_str()), &retvalue)); |
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223 | return (retvalue); |
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224 | } |
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225 | |
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226 | //--------------------------------------------------------------- |
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227 | |
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228 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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229 | { |
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230 | int retvalue = 0; |
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231 | int grpid = this->getCurrentGroup(); |
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232 | if (size != UNLIMITED_DIM) |
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233 | CheckError(nc_def_dim (grpid, name.c_str(), size, &retvalue)); |
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234 | else |
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235 | CheckError(nc_def_dim (grpid, name.c_str(), NC_UNLIMITED, &retvalue)); |
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236 | return (retvalue); |
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237 | } |
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238 | |
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239 | //--------------------------------------------------------------- |
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240 | |
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241 | int CONetCDF4::addVariable(const StdString & name, nc_type type, |
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242 | const std::vector<StdString> & dim) |
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243 | { |
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244 | int varid = 0; |
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245 | std::vector<int> dimids; |
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246 | std::vector<StdSize> dimsizes ; |
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247 | StdSize size ; |
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248 | |
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249 | int grpid = this->getCurrentGroup(); |
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250 | |
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251 | std::vector<StdString>::const_iterator |
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252 | it = dim.begin(), end = dim.end(); |
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253 | |
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254 | for (;it != end; it++) |
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255 | { |
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256 | const StdString & dimid = *it; |
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257 | dimids.push_back(this->getDimension(dimid)); |
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258 | CheckError(nc_inq_dimlen (grpid, this->getDimension(dimid), &size)); |
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259 | if (size==NC_UNLIMITED) size=1 ; |
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260 | dimsizes.push_back(size) ; |
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261 | } |
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262 | |
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263 | CheckError(nc_def_var (grpid, name.c_str(), type, dimids.size(), &(dimids[0]), &varid)); |
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264 | CheckError(nc_def_var_chunking (grpid, varid, NC_CHUNKED, &(dimsizes[0]))); |
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265 | CheckError(nc_def_var_fill(grpid, varid, true, NULL)); |
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266 | return (varid); |
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267 | } |
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268 | |
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269 | //--------------------------------------------------------------- |
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270 | |
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271 | template <> |
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272 | void CONetCDF4::addAttribute |
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273 | (const StdString & name, const StdString & value, const StdString * varname ) |
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274 | { |
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275 | int grpid = this->getCurrentGroup(); |
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276 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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277 | CheckError(nc_put_att(grpid, varid, name.c_str(), NC_CHAR, value.size()+1, value.c_str())); |
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278 | //CheckError(nc_put_att_string(grpid, varid, name.c_str(), 1, &str)); |
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279 | } |
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280 | |
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281 | //--------------------------------------------------------------- |
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282 | |
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283 | template <> |
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284 | void CONetCDF4::addAttribute |
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285 | (const StdString & name, const double & value, const StdString * varname ) |
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286 | { |
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287 | int grpid = this->getCurrentGroup(); |
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288 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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289 | CheckError(nc_put_att_double(grpid, varid, name.c_str(), NC_DOUBLE,1, &value)); |
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290 | } |
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291 | |
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292 | //--------------------------------------------------------------- |
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293 | |
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294 | template <> |
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295 | void CONetCDF4::addAttribute |
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296 | (const StdString & name, const float & value, const StdString * varname ) |
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297 | { |
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298 | int grpid = this->getCurrentGroup(); |
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299 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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300 | CheckError(nc_put_att_float(grpid, varid, name.c_str(), NC_FLOAT, 1, &value)); |
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301 | } |
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302 | |
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303 | //--------------------------------------------------------------- |
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304 | |
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305 | template <> |
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306 | void CONetCDF4::addAttribute |
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307 | (const StdString & name, const int & value, const StdString * varname ) |
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308 | { |
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309 | int grpid = this->getCurrentGroup(); |
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310 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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311 | CheckError(nc_put_att_int(grpid, varid, name.c_str(), NC_INT,1, &value)); |
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312 | } |
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313 | |
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314 | //--------------------------------------------------------------- |
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315 | |
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316 | void CONetCDF4::getWriteDataInfos(const StdString & name, StdSize record, StdSize & array_size, |
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317 | std::vector<StdSize> & sstart, |
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318 | std::vector<StdSize> & scount, |
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319 | const std::vector<StdSize> * start, |
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320 | const std::vector<StdSize> * count) |
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321 | { |
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322 | std::vector<std::size_t> sizes = this->getDimensions(name); |
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323 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
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324 | std::vector<std::size_t>::const_iterator |
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325 | it = sizes.begin(), end = sizes.end(); |
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326 | int i = 0; |
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327 | |
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328 | if (iddims.begin()->compare(this->getUnlimitedDimensionName()) == 0) |
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329 | { |
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330 | sstart.push_back(record); |
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331 | scount.push_back(1); |
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332 | if ((start == NULL) && |
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333 | (count == NULL)) i++; |
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334 | it++; |
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335 | } |
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336 | |
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337 | for (;it != end; it++) |
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338 | { |
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339 | if ((start != NULL) && (count != NULL)) |
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340 | { |
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341 | sstart.push_back((*start)[i]); |
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342 | scount.push_back((*count)[i]); |
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343 | array_size *= (*count)[i]; |
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344 | i++; |
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345 | } |
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346 | else |
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347 | { |
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348 | sstart.push_back(0); |
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349 | scount.push_back(sizes[i]); |
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350 | array_size *= sizes[i]; |
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351 | i++; |
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352 | } |
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353 | } |
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354 | |
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355 | } |
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356 | |
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357 | //--------------------------------------------------------------- |
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358 | |
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359 | template <> |
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360 | void CONetCDF4::writeData_(int grpid, int varid, |
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361 | const std::vector<StdSize> & sstart, |
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362 | const std::vector<StdSize> & scount, const double * data) |
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363 | { |
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364 | CheckError(nc_put_vara_double(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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365 | // sync() ; |
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366 | } |
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367 | |
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368 | //--------------------------------------------------------------- |
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369 | |
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370 | template <> |
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371 | void CONetCDF4::writeData_(int grpid, int varid, |
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372 | const std::vector<StdSize> & sstart, |
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373 | const std::vector<StdSize> & scount, const int * data) |
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374 | { |
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375 | CheckError(nc_put_vara_int(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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376 | // sync() ; |
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377 | } |
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378 | |
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379 | //--------------------------------------------------------------- |
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380 | |
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381 | template <> |
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382 | void CONetCDF4::writeData_(int grpid, int varid, |
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383 | const std::vector<StdSize> & sstart, |
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384 | const std::vector<StdSize> & scount, const float * data) |
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385 | { |
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386 | CheckError(nc_put_vara_float(grpid, varid, &(sstart[0]), &(scount[0]), data)); |
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387 | // sync() ; |
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388 | } |
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389 | |
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390 | //--------------------------------------------------------------- |
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391 | |
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392 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString & name) |
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393 | { |
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394 | int grpid = this->getCurrentGroup(); |
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395 | int varid = this->getVariable(name); |
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396 | StdSize array_size = 1; |
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397 | std::vector<StdSize> sstart, scount; |
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398 | |
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399 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
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400 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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401 | } |
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402 | |
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403 | //--------------------------------------------------------------- |
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404 | |
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405 | bool CONetCDF4::varExist(const StdString & varname) |
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406 | { |
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407 | int varid = 0; |
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408 | int grpid = this->getCurrentGroup(); |
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409 | return (nc_inq_varid (grpid, varname.c_str(), &varid) == NC_NOERR); |
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410 | } |
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411 | |
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412 | void CONetCDF4::sync(void) |
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413 | { |
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414 | CheckError(nc_sync(this->ncidp)) ; |
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415 | } |
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416 | ///-------------------------------------------------------------- |
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417 | } // namespace xios |
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