[219] | 1 | #include "inetcdf4.hpp" |
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[599] | 2 | #include "netCdfInterface.hpp" |
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[782] | 3 | #include "netCdf_cf_constant.hpp" |
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[219] | 4 | |
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| 5 | #include <boost/algorithm/string.hpp> |
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| 6 | |
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[335] | 7 | namespace xios |
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[219] | 8 | { |
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[802] | 9 | CINetCDF4::CINetCDF4(const StdString& filename, const MPI_Comm* comm /*= NULL*/, bool multifile /*= true*/, const StdString& timeCounterName /*= "time_counter"*/) |
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[599] | 10 | { |
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[736] | 11 | // Don't use parallel mode if there is only one process |
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| 12 | if (comm) |
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[599] | 13 | { |
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[736] | 14 | int commSize = 0; |
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| 15 | MPI_Comm_size(*comm, &commSize); |
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| 16 | if (commSize <= 1) |
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| 17 | comm = NULL; |
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[599] | 18 | } |
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[736] | 19 | mpi = comm && !multifile; |
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| 20 | |
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| 21 | // The file format will be detected automatically by NetCDF, it is safe to always set NC_MPIIO |
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| 22 | // even if Parallel NetCDF ends up being used. |
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| 23 | if (mpi) |
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| 24 | CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *comm, MPI_INFO_NULL, this->ncidp); |
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| 25 | else |
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| 26 | CNetCdfInterface::open(filename, NC_NOWRITE, this->ncidp); |
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[802] | 27 | |
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| 28 | this->timeCounterName = timeCounterName; |
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[811] | 29 | if (!CNetCdfInterface::isDimExisted(this->ncidp, this->timeCounterName)) this->timeCounterName=this->getUnlimitedDimensionName() ; |
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[825] | 30 | |
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[599] | 31 | } |
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[219] | 32 | |
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[599] | 33 | CINetCDF4::~CINetCDF4(void) |
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| 34 | { /* Nothing to do */ } |
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[219] | 35 | |
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[599] | 36 | //--------------------------------------------------------------- |
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[219] | 37 | |
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[599] | 38 | void CINetCDF4::close(void) |
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| 39 | { |
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[686] | 40 | CNetCdfInterface::close(this->ncidp); |
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[599] | 41 | } |
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[219] | 42 | |
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[599] | 43 | //--------------------------------------------------------------- |
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[219] | 44 | |
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[599] | 45 | int CINetCDF4::getGroup(const CVarPath* const path) |
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| 46 | { |
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| 47 | int retvalue = this->ncidp; |
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| 48 | if (path == NULL) return retvalue; |
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| 49 | CVarPath::const_iterator it = path->begin(), end = path->end(); |
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[219] | 50 | |
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[599] | 51 | for (; it != end; it++) |
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| 52 | { |
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| 53 | const StdString& groupid = *it; |
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[686] | 54 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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[599] | 55 | } |
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[219] | 56 | |
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[599] | 57 | return retvalue; |
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| 58 | } |
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[219] | 59 | |
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[599] | 60 | int CINetCDF4::getVariable(const StdString& varname, |
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| 61 | const CVarPath* const path) |
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| 62 | { |
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| 63 | int varid = 0; |
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| 64 | int grpid = this->getGroup(path); |
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[825] | 65 | if (this->hasVariable(varname, path)) |
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| 66 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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[599] | 67 | return varid; |
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| 68 | } |
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[219] | 69 | |
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[599] | 70 | int CINetCDF4::getDimension(const StdString& dimname, |
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| 71 | const CVarPath* const path) |
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| 72 | { |
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| 73 | int dimid = 0; |
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| 74 | int grpid = this->getGroup(path); |
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[686] | 75 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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[599] | 76 | return dimid; |
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| 77 | } |
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[219] | 78 | |
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[599] | 79 | std::pair<nc_type, StdSize> CINetCDF4::getAttribute(const StdString& attname, |
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| 80 | const StdString* const var, |
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| 81 | const CVarPath* const path) |
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| 82 | { |
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| 83 | std::pair<nc_type, StdSize> retvalue; |
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| 84 | int grpid = this->getGroup(path); |
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| 85 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[686] | 86 | CNetCdfInterface::inqAtt(grpid, varid, attname, retvalue.first, retvalue.second); |
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[599] | 87 | return retvalue; |
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| 88 | } |
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[219] | 89 | |
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[599] | 90 | int CINetCDF4::getUnlimitedDimension(const CVarPath* const path) |
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| 91 | { |
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| 92 | int dimid = 0; |
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| 93 | int grpid = this->getGroup(path); |
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[686] | 94 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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[599] | 95 | return dimid; |
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| 96 | } |
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[219] | 97 | |
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[599] | 98 | StdString CINetCDF4::getUnlimitedDimensionName(const CVarPath* const path) |
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| 99 | { |
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| 100 | int grpid = this->getGroup(path); |
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| 101 | int dimid = this->getUnlimitedDimension(path); |
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[219] | 102 | |
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[686] | 103 | StdString dimname; |
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| 104 | if (dimid != -1) |
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| 105 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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[599] | 106 | return dimname; |
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| 107 | } |
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[219] | 108 | |
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[599] | 109 | //--------------------------------------------------------------- |
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[686] | 110 | |
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[599] | 111 | StdSize CINetCDF4::getNbVertex(const StdString& name, |
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| 112 | const CVarPath* const path) |
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| 113 | { |
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[219] | 114 | |
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[599] | 115 | if (this->isRectilinear(name, path) || |
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| 116 | this->isCurvilinear(name, path)) |
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| 117 | { |
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| 118 | if (this->is3Dim(name, path)) return 8; |
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| 119 | else return 4; |
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| 120 | } |
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| 121 | if (this->isUnstructured(name, path)) |
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| 122 | { |
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| 123 | StdString bound = this->getBoundsId |
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| 124 | (this->getCoordinatesIdList(name, path).back(), path); |
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| 125 | StdString dim = this->getDimensionsList(&bound, path).back(); |
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[686] | 126 | return this->getDimensions(&bound, path)[dim]; |
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[599] | 127 | } |
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| 128 | return size_t(-1); |
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| 129 | } |
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[219] | 130 | |
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[599] | 131 | //--------------------------------------------------------------- |
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[219] | 132 | |
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[599] | 133 | std::list<StdString> CINetCDF4::getGroups(const CVarPath* const path) |
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| 134 | { |
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| 135 | int nbgroup = 0, *groupid = NULL; |
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| 136 | int grpid = this->getGroup(path); |
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| 137 | std::list<StdString> retvalue; |
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[219] | 138 | |
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[686] | 139 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, NULL); |
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[599] | 140 | groupid = new int[nbgroup](); |
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[686] | 141 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, groupid); |
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[219] | 142 | |
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[599] | 143 | for (int i = 0; i < nbgroup; i++) |
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| 144 | { |
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[686] | 145 | StdString fullGrpName; |
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| 146 | CNetCdfInterface::inqGrpFullName(groupid[i], fullGrpName); |
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| 147 | retvalue.push_back(fullGrpName); |
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[599] | 148 | } |
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[219] | 149 | |
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[599] | 150 | delete [] groupid; |
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| 151 | return retvalue; |
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| 152 | } |
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[219] | 153 | |
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[599] | 154 | std::list<StdString> CINetCDF4::getVariables(const CVarPath* const path) |
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| 155 | { |
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| 156 | int nbvar = 0, *varid = NULL; |
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| 157 | int grpid = this->getGroup(path); |
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| 158 | std::list<StdString> retvalue; |
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[219] | 159 | |
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[686] | 160 | CNetCdfInterface::inqVarIds(grpid, nbvar, NULL); |
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[599] | 161 | varid = new int[nbvar](); |
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[686] | 162 | CNetCdfInterface::inqVarIds(grpid, nbvar, varid); |
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[219] | 163 | |
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[599] | 164 | for (int i = 0; i < nbvar; i++) |
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| 165 | { |
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[686] | 166 | StdString varName; |
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| 167 | CNetCdfInterface::inqVarName(grpid, varid[i], varName); |
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| 168 | retvalue.push_back(varName); |
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[599] | 169 | } |
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| 170 | |
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| 171 | delete [] varid; |
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| 172 | return retvalue; |
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| 173 | } |
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| 174 | |
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| 175 | StdSize CINetCDF4::getNbOfTimestep(const CVarPath* const path) |
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| 176 | { |
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[686] | 177 | return this->getDimensions(NULL, path)[this->getUnlimitedDimensionName(path)]; |
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[599] | 178 | } |
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| 179 | |
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| 180 | std::set<StdString> CINetCDF4::getBoundVariables(const CVarPath* const path) |
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| 181 | { |
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| 182 | std::set<StdString> retvalue; |
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| 183 | std::list<StdString> variables = this->getVariables(path); |
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| 184 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 185 | for (; it != end; it++) |
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| 186 | { |
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| 187 | const StdString& var = *it; |
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| 188 | if (this->hasBounds(var, path)) |
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| 189 | retvalue.insert(retvalue.end(), this->getBoundsId(var, path)); |
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| 190 | } |
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| 191 | return retvalue; |
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| 192 | } |
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| 193 | |
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| 194 | std::set<StdString> CINetCDF4::getCoordVariables(const CVarPath* const path) |
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| 195 | { |
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| 196 | std::set<StdString> retvalue; |
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| 197 | std::list<StdString> variables = this->getVariables(path); |
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| 198 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 199 | for (; it != end; it++) |
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| 200 | { |
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| 201 | const StdString& var = *it; |
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| 202 | std::list<StdString> coords = this->getCoordinatesIdList(var, path); |
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| 203 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
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| 204 | for (; it != end; it++) |
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[219] | 205 | { |
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[599] | 206 | const StdString& coord = *it; |
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| 207 | if (this->hasVariable(coord, path)) |
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| 208 | retvalue.insert(retvalue.end(), coord); |
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[219] | 209 | } |
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[599] | 210 | } |
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| 211 | return retvalue; |
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| 212 | } |
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[219] | 213 | |
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[599] | 214 | std::list<StdString> CINetCDF4::getDimensionsList(const StdString* const var, const CVarPath* const path) |
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| 215 | { |
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| 216 | int nbdim = 0, *dimid = NULL; |
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| 217 | int grpid = this->getGroup(path); |
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| 218 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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| 219 | std::list<StdString> retvalue; |
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[219] | 220 | |
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[599] | 221 | if (var != NULL) |
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| 222 | { |
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[686] | 223 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[599] | 224 | dimid = new int[nbdim](); |
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[686] | 225 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[599] | 226 | } |
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| 227 | else |
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| 228 | { |
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[686] | 229 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[599] | 230 | dimid = new int[nbdim](); |
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[686] | 231 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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[599] | 232 | } |
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[219] | 233 | |
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[599] | 234 | for (int i = 0; i < nbdim; i++) |
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| 235 | { |
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[686] | 236 | std::string dimname; |
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| 237 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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[599] | 238 | retvalue.push_back(dimname); |
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| 239 | } |
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| 240 | delete [] dimid; |
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[219] | 241 | |
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[599] | 242 | return retvalue; |
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| 243 | } |
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[219] | 244 | |
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[599] | 245 | std::map<StdString, StdSize> CINetCDF4::getDimensions(const StdString* const var, const CVarPath* const path) |
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| 246 | { |
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| 247 | int nbdim = 0, *dimid = NULL; |
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| 248 | int grpid = this->getGroup(path); |
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| 249 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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| 250 | std::map<StdString, StdSize> retvalue; |
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[219] | 251 | |
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[599] | 252 | if (var != NULL) |
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| 253 | { |
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[686] | 254 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[599] | 255 | dimid = new int[nbdim](); |
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[686] | 256 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[599] | 257 | } |
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| 258 | else |
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| 259 | { |
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[686] | 260 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[599] | 261 | dimid = new int[nbdim](); |
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[686] | 262 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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[599] | 263 | } |
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[219] | 264 | |
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[599] | 265 | for (int i = 0; i < nbdim; i++) |
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| 266 | { |
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[686] | 267 | std::string dimname; |
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| 268 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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| 269 | StdSize size = 0; |
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| 270 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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[219] | 271 | |
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[599] | 272 | retvalue.insert(retvalue.end(), std::make_pair(dimname, size)); |
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| 273 | } |
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| 274 | delete [] dimid; |
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[219] | 275 | |
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[599] | 276 | return retvalue; |
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| 277 | } |
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[219] | 278 | |
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[686] | 279 | std::list<StdString> CINetCDF4::getAttributes(const StdString* const var, const CVarPath* const path) |
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[599] | 280 | { |
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| 281 | int nbatt = 0; |
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| 282 | std::list<StdString> retvalue; |
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| 283 | int grpid = this->getGroup(path); |
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| 284 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[219] | 285 | |
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[599] | 286 | if (var != NULL) |
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[686] | 287 | CNetCdfInterface::inqVarNAtts(grpid, varid, nbatt); |
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[599] | 288 | else |
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[686] | 289 | CNetCdfInterface::inqNAtts(grpid, nbatt); |
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[219] | 290 | |
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[599] | 291 | for (int i = 0; i < nbatt; i++) |
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| 292 | { |
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[686] | 293 | StdString attname; |
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| 294 | CNetCdfInterface::inqAttName(grpid, varid, i, attname); |
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[599] | 295 | retvalue.push_back(attname); |
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| 296 | } |
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| 297 | return retvalue; |
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| 298 | } |
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[219] | 299 | |
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[599] | 300 | int CINetCDF4::getAttributeId(const StdString& name, |
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| 301 | const StdString* const var, |
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| 302 | const CVarPath* const path) |
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| 303 | { |
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| 304 | int retvalue = 0; |
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| 305 | std::list<StdString> atts = this->getAttributes(var, path); |
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| 306 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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| 307 | for (; it != end; it++) |
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| 308 | { |
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| 309 | const StdString& attname = *it; |
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[782] | 310 | if (attname.compare(0, name.size(), name) == 0) |
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[599] | 311 | return retvalue; |
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| 312 | retvalue++; |
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| 313 | } |
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| 314 | return -1; |
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| 315 | } |
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[219] | 316 | |
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[599] | 317 | //--------------------------------------------------------------- |
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[219] | 318 | |
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[599] | 319 | bool CINetCDF4::hasMissingValue(const StdString& name, |
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| 320 | const CVarPath* const path) |
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| 321 | { |
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[686] | 322 | return (this->hasAttribute("missing_value", &name, path) || this->hasAttribute("_FillValue", &name, path)); |
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[599] | 323 | } |
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[219] | 324 | |
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[599] | 325 | bool CINetCDF4::hasAttribute(const StdString& name, |
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| 326 | const StdString* const var , |
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| 327 | const CVarPath* const path) |
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| 328 | { |
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| 329 | std::list<StdString> atts = this->getAttributes(var, path); |
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| 330 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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| 331 | for (; it != end; it++) |
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| 332 | { |
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| 333 | const StdString& attname = *it; |
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[782] | 334 | if (attname.compare(0, name.size(), name) == 0) return true; |
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[599] | 335 | } |
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| 336 | return false; |
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| 337 | } |
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[219] | 338 | |
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[599] | 339 | bool CINetCDF4::hasVariable(const StdString& name, |
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| 340 | const CVarPath* const path) |
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| 341 | { |
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| 342 | std::list<StdString> variables = this->getVariables(path); |
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| 343 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 344 | for (; it != end; it++) |
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| 345 | { |
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| 346 | const StdString& varname = *it; |
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[825] | 347 | if ((varname.compare(0, name.size(), name) == 0) && (0 != name.size())) return true; |
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[599] | 348 | } |
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| 349 | return false; |
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| 350 | } |
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[219] | 351 | |
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[599] | 352 | bool CINetCDF4::hasCoordinates(const StdString& name, |
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| 353 | const CVarPath* const path) |
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| 354 | { |
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[782] | 355 | return this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path); |
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[599] | 356 | } |
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[219] | 357 | |
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[599] | 358 | bool CINetCDF4::hasBounds(const StdString& name, |
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| 359 | const CVarPath* const path) |
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| 360 | { |
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[782] | 361 | return this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path); |
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[599] | 362 | } |
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[219] | 363 | |
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[599] | 364 | bool CINetCDF4::hasTemporalDim(const CVarPath* const path) |
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| 365 | { |
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[802] | 366 | std::list<StdString> dims = this->getDimensionsList(NULL, path); |
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| 367 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
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[599] | 368 | } |
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[219] | 369 | |
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[599] | 370 | //--------------------------------------------------------------- |
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[219] | 371 | |
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[686] | 372 | template <class T> |
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| 373 | std::vector<T> CINetCDF4::getAttributeValue(const StdString& name, |
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| 374 | const StdString* const var, |
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| 375 | const CVarPath* const path) |
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| 376 | { |
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| 377 | int grpid = this->getGroup(path); |
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| 378 | int varid = (var != NULL) ? this->getVariable(*var, path) : NC_GLOBAL; |
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| 379 | std::pair<nc_type , StdSize> attinfos = this->getAttribute(name, var, path); |
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| 380 | std::vector<T> retvalue(attinfos.second); |
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| 381 | nc_type type = CNetCdfInterface::getNcType<T>(); |
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| 382 | if (attinfos.first != type) |
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| 383 | ERROR("CINetCDF4::getAttributeValue<T>(name, var, path)", |
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| 384 | << "[ name : " << name |
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| 385 | << ", type requested :" << attinfos.first |
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| 386 | << ", type stored : " << type << "]" |
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| 387 | << " Invalid type !"); |
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| 388 | CNetCdfInterface::getAttType(grpid, varid, name.c_str(), &retvalue[0]); |
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| 389 | return retvalue; |
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[599] | 390 | } |
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[219] | 391 | |
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[686] | 392 | template std::vector<double> CINetCDF4::getAttributeValue(const StdString& name, |
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| 393 | const StdString* const var, |
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| 394 | const CVarPath* const path); |
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| 395 | template std::vector<float> CINetCDF4::getAttributeValue(const StdString& name, |
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| 396 | const StdString* const var, |
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| 397 | const CVarPath* const path); |
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| 398 | template std::vector<int> CINetCDF4::getAttributeValue(const StdString& name, |
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| 399 | const StdString* const var, |
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| 400 | const CVarPath* const path); |
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| 401 | template std::vector<char> CINetCDF4::getAttributeValue(const StdString& name, |
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| 402 | const StdString* const var, |
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| 403 | const CVarPath* const path); |
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[219] | 404 | |
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[599] | 405 | StdString CINetCDF4::getAttributeValue(const StdString& name, |
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| 406 | const StdString* const var, |
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| 407 | const CVarPath* const path) |
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| 408 | { |
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[686] | 409 | std::vector<char> data = this->getAttributeValue<char>(name, var, path); |
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[219] | 410 | |
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[686] | 411 | return StdString(data.begin(), data.end()); |
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[599] | 412 | } |
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[219] | 413 | |
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[686] | 414 | template <class T> |
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| 415 | T CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path) |
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[599] | 416 | { |
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| 417 | if (this->hasAttribute("missing_value", &name, path)) |
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[686] | 418 | return this->getAttributeValue<T>("missing_value", &name, path)[0]; |
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[599] | 419 | if (this->hasAttribute("_FillValue", &name, path)) |
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[686] | 420 | return this->getAttributeValue<T>("_FillValue", &name, path)[0]; |
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[599] | 421 | return 0; |
---|
| 422 | } |
---|
[219] | 423 | |
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[686] | 424 | template double CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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| 425 | template float CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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| 426 | template int CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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| 427 | template char CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
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[219] | 428 | |
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[599] | 429 | //--------------------------------------------------------------- |
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[219] | 430 | |
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[599] | 431 | std::list<StdString> CINetCDF4::getCoordinatesIdList(const StdString& name, const CVarPath* const path) |
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| 432 | { |
---|
| 433 | std::list<StdString> retvalue; |
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| 434 | StdString value = this->getCoordinatesId(name, path); |
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[219] | 435 | |
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[599] | 436 | boost::split(retvalue, value, boost::is_any_of(" ")); |
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[219] | 437 | |
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[599] | 438 | std::list<StdString>::iterator it = retvalue.begin(), end = retvalue.end(); |
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| 439 | for (; it != end; it++) |
---|
| 440 | { |
---|
| 441 | StdString& coord = *it; |
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| 442 | coord.assign(coord.data()); |
---|
| 443 | } |
---|
| 444 | return retvalue; |
---|
| 445 | } |
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[219] | 446 | |
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[599] | 447 | StdString CINetCDF4::getCoordinatesId(const StdString& name, const CVarPath* const path) |
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| 448 | { |
---|
| 449 | StdString retvalue; |
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[782] | 450 | if (this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path)) |
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[599] | 451 | { |
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[782] | 452 | return this->getAttributeValue(CCFKeywords::XIOS_CF_coordinates, &name, path); |
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[599] | 453 | } |
---|
| 454 | else |
---|
| 455 | { |
---|
| 456 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
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| 457 | std::list<StdString>::const_iterator it = dims.begin(), end = dims.end(); |
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| 458 | for (; it != end; it++) |
---|
[219] | 459 | { |
---|
[599] | 460 | const StdString& value = *it; |
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| 461 | retvalue.append(value).push_back(' '); |
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[219] | 462 | } |
---|
[599] | 463 | retvalue.erase(retvalue.end() - 1) ; |
---|
| 464 | } |
---|
[219] | 465 | |
---|
[599] | 466 | return retvalue; |
---|
| 467 | } |
---|
| 468 | |
---|
| 469 | StdString CINetCDF4::getBoundsId(const StdString& name, |
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| 470 | const CVarPath* const path) |
---|
| 471 | { |
---|
| 472 | StdString retvalue; |
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[782] | 473 | if (this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path)) |
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| 474 | retvalue = this->getAttributeValue(CCFKeywords::XIOS_CF_bounds, &name, path); |
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[599] | 475 | return retvalue; |
---|
| 476 | } |
---|
| 477 | |
---|
| 478 | //--------------------------------------------------------------- |
---|
| 479 | |
---|
| 480 | bool CINetCDF4::isBound(const StdString& name, |
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| 481 | const CVarPath* const path) |
---|
| 482 | { |
---|
| 483 | std::set<StdString> bounds = this->getBoundVariables(path); |
---|
| 484 | return (bounds.find(name) != bounds.end()); |
---|
| 485 | } |
---|
| 486 | |
---|
| 487 | bool CINetCDF4::isCoordinate(const StdString& name, |
---|
| 488 | const CVarPath* const path) |
---|
| 489 | { |
---|
| 490 | std::set<StdString> coords = this->getCoordVariables(path); |
---|
| 491 | return (coords.find(name) != coords.end()); |
---|
| 492 | } |
---|
| 493 | |
---|
| 494 | bool CINetCDF4::isRectilinear(const StdString& name, const CVarPath* const path) |
---|
| 495 | { |
---|
| 496 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 497 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 498 | for (; it != end; it++) |
---|
| 499 | { |
---|
| 500 | const StdString& coord = *it; |
---|
| 501 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
[219] | 502 | { |
---|
[599] | 503 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
| 504 | if ((dimvar.size() == 1) && (dimvar.find(coord) != dimvar.end())) |
---|
| 505 | continue; |
---|
| 506 | else |
---|
| 507 | return false; |
---|
[219] | 508 | } |
---|
[599] | 509 | } |
---|
| 510 | return true; |
---|
| 511 | } |
---|
[219] | 512 | |
---|
[599] | 513 | bool CINetCDF4::isCurvilinear(const StdString& name, const CVarPath* const path) |
---|
| 514 | { |
---|
| 515 | if (this->isRectilinear(name, path) || !this->hasCoordinates(name, path)) |
---|
| 516 | return false; |
---|
| 517 | |
---|
[782] | 518 | bool isCurVi = true; |
---|
| 519 | unsigned int nbLonLat = 0; |
---|
[599] | 520 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 521 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 522 | for (; it != end; it++) |
---|
| 523 | { |
---|
| 524 | const StdString& coord = *it; |
---|
[782] | 525 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
[219] | 526 | { |
---|
[599] | 527 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
[782] | 528 | if (2 == dimvar.size()) ++nbLonLat; |
---|
[219] | 529 | } |
---|
[599] | 530 | } |
---|
[782] | 531 | if (2 != nbLonLat) isCurVi = false; |
---|
| 532 | |
---|
| 533 | return isCurVi; |
---|
[599] | 534 | } |
---|
[219] | 535 | |
---|
[599] | 536 | bool CINetCDF4::isUnstructured(const StdString& name, const CVarPath* const path) |
---|
| 537 | { |
---|
| 538 | if (this->isRectilinear(name, path) || |
---|
| 539 | this->isCurvilinear(name, path) || |
---|
| 540 | !this->hasCoordinates(name, path)) |
---|
| 541 | return false; |
---|
[948] | 542 | else return true ; |
---|
| 543 | |
---|
| 544 | // check this part above |
---|
[599] | 545 | StdString dimname = this->getDimensionsList(&name, path).back(); |
---|
[219] | 546 | |
---|
[599] | 547 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 548 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 549 | for (; it != end; it++) |
---|
| 550 | { |
---|
| 551 | const StdString& coord = *it; |
---|
[782] | 552 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
[219] | 553 | { |
---|
[599] | 554 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
| 555 | if ((dimvar.size() == 1) && |
---|
| 556 | (dimvar.find(dimname) != dimvar.end())) |
---|
| 557 | continue; |
---|
| 558 | else |
---|
| 559 | return false; |
---|
| 560 | } |
---|
| 561 | } |
---|
[219] | 562 | |
---|
[599] | 563 | return true; |
---|
| 564 | } |
---|
[219] | 565 | |
---|
[599] | 566 | bool CINetCDF4::isUnknown(const StdString& name, const CVarPath* const path) |
---|
| 567 | { |
---|
| 568 | return !(this->isRectilinear(name, path) || this->isCurvilinear(name, path) || this->isUnstructured(name, path)); |
---|
| 569 | } |
---|
[219] | 570 | |
---|
[599] | 571 | bool CINetCDF4::isTemporal(const StdString& name, const CVarPath* const path) |
---|
| 572 | { |
---|
[802] | 573 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
| 574 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
---|
[599] | 575 | } |
---|
[219] | 576 | |
---|
[599] | 577 | bool CINetCDF4::is3Dim(const StdString& name, const CVarPath* const path) |
---|
| 578 | { |
---|
| 579 | int i = 0; |
---|
| 580 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 581 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 582 | for (; it != end; it++) |
---|
| 583 | { |
---|
| 584 | const StdString& coord = *it; |
---|
| 585 | if (this->hasVariable(coord, path)) |
---|
[219] | 586 | { |
---|
[599] | 587 | if (this->isTemporal(coord, path)) |
---|
| 588 | continue; |
---|
| 589 | i++; |
---|
[219] | 590 | } |
---|
[599] | 591 | else |
---|
[219] | 592 | { |
---|
[782] | 593 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 594 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 595 | continue; |
---|
| 596 | i++; |
---|
[219] | 597 | } |
---|
[599] | 598 | } |
---|
| 599 | return (i == 3); |
---|
| 600 | } |
---|
[219] | 601 | |
---|
[599] | 602 | bool CINetCDF4::isCellGrid(const StdString& name, const CVarPath* const path) |
---|
| 603 | { |
---|
| 604 | if (this->isCoordinate(name, path)) |
---|
| 605 | { |
---|
[686] | 606 | return this->hasBounds(name, path); |
---|
[599] | 607 | } |
---|
| 608 | else |
---|
| 609 | { |
---|
| 610 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 611 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 612 | for (; it != end; it++) |
---|
[219] | 613 | { |
---|
[599] | 614 | const StdString& coord = *it; |
---|
| 615 | if (this->hasVariable(coord, path)) |
---|
| 616 | { |
---|
| 617 | if (this->isTemporal(coord, path)) |
---|
| 618 | continue; |
---|
| 619 | if (this->isCellGrid(coord, path)) |
---|
| 620 | continue; |
---|
| 621 | return false; |
---|
| 622 | } |
---|
| 623 | else |
---|
| 624 | { |
---|
[782] | 625 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 626 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 627 | continue; |
---|
| 628 | return false; |
---|
| 629 | } |
---|
[219] | 630 | } |
---|
[599] | 631 | } |
---|
[219] | 632 | |
---|
[599] | 633 | return true; |
---|
| 634 | } |
---|
[219] | 635 | |
---|
[599] | 636 | //--------------------------------------------------------------- |
---|
[219] | 637 | |
---|
[599] | 638 | std::list<StdString> CINetCDF4::getDataVariables(bool _is3D, bool _isRecti, |
---|
| 639 | bool _isCurvi, bool _isUnstr, |
---|
| 640 | bool _isCellData, bool _isTemporal, |
---|
| 641 | const CVarPath* const path) |
---|
| 642 | { |
---|
| 643 | std::list<StdString> retvalue; |
---|
| 644 | std::list<StdString> allvars = this->getVariables(path); |
---|
| 645 | std::set<StdString> allcoords = this->getCoordVariables(path); |
---|
[219] | 646 | |
---|
[599] | 647 | std::list<StdString>::const_iterator it = allvars.begin(), end = allvars.end(); |
---|
| 648 | for (; it != end; it++) |
---|
| 649 | { |
---|
| 650 | const StdString& var = *it; |
---|
| 651 | if (this->isCoordinate(var, path)) continue; |
---|
[219] | 652 | |
---|
[599] | 653 | if (!_isRecti && this->isRectilinear(var, path)) continue; |
---|
| 654 | if (!_isCurvi && this->isCurvilinear(var, path)) continue; |
---|
| 655 | if (!_isUnstr && this->isUnstructured(var, path)) continue; |
---|
[219] | 656 | |
---|
[599] | 657 | if (!_isTemporal && this->isTemporal(var, path)) continue; |
---|
| 658 | if (!_is3D && this->is3Dim(var, path)) continue; |
---|
| 659 | if (!_isCellData && this->isCellGrid(var, path)) continue; |
---|
[219] | 660 | |
---|
[599] | 661 | if (this->isUnknown(var, path)) continue; |
---|
[219] | 662 | |
---|
[599] | 663 | retvalue.push_back(var); |
---|
| 664 | } |
---|
| 665 | return retvalue; |
---|
| 666 | } |
---|
[219] | 667 | |
---|
[599] | 668 | //--------------------------------------------------------------- |
---|
[219] | 669 | |
---|
[599] | 670 | void CINetCDF4::getDataInfo(const StdString& var, const CVarPath* const path, StdSize record, |
---|
| 671 | std::vector<StdSize>& sstart, std::vector<StdSize>& scount, StdSize& array_size, |
---|
| 672 | const std::vector<StdSize>* start /*= NULL*/, const std::vector<StdSize>* count /*= NULL*/) |
---|
| 673 | { |
---|
| 674 | std::list<StdString> dimlist = this->getDimensionsList(&var, path); |
---|
| 675 | std::map<StdString, StdSize> dimmap = this->getDimensions(&var, path); |
---|
| 676 | std::list<StdString>::iterator it = dimlist.begin(); |
---|
| 677 | if (this->isTemporal(var, path)) |
---|
| 678 | { |
---|
| 679 | if (record != UNLIMITED_DIM) |
---|
| 680 | sstart.push_back(record); |
---|
| 681 | else |
---|
| 682 | sstart.push_back(0); |
---|
| 683 | scount.push_back(1); |
---|
| 684 | it++; |
---|
| 685 | } |
---|
| 686 | for (int i = 0; it != dimlist.end(); it++, i++) |
---|
| 687 | { |
---|
| 688 | if (start && count) |
---|
[219] | 689 | { |
---|
[599] | 690 | sstart.push_back((*start)[i]); |
---|
| 691 | scount.push_back((*count)[i]); |
---|
| 692 | array_size *= (*count)[i]; |
---|
[219] | 693 | } |
---|
[599] | 694 | else |
---|
[219] | 695 | { |
---|
[599] | 696 | sstart.push_back(0); |
---|
| 697 | scount.push_back(dimmap[*it]); |
---|
| 698 | array_size *= dimmap[*it]; |
---|
[219] | 699 | } |
---|
[599] | 700 | } |
---|
| 701 | } |
---|
[219] | 702 | |
---|
[686] | 703 | template <class T> |
---|
| 704 | void CINetCDF4::getData(CArray<T, 1>& data, const StdString& var, |
---|
[599] | 705 | const CVarPath* const path, StdSize record) |
---|
| 706 | { |
---|
| 707 | std::vector<StdSize> start, count; |
---|
| 708 | int grpid = this->getGroup(path); |
---|
| 709 | int varid = this->getVariable(var, path); |
---|
| 710 | StdSize array_size = 1; |
---|
| 711 | this->getDataInfo(var, path, record, start, count, array_size); |
---|
| 712 | data.resize(array_size); |
---|
[686] | 713 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], data.dataFirst()); |
---|
[599] | 714 | } |
---|
[219] | 715 | |
---|
[599] | 716 | template <> |
---|
[686] | 717 | void CINetCDF4::getData(CArray<int, 1>& data, const StdString& var, |
---|
| 718 | const CVarPath* const path, StdSize record); |
---|
| 719 | template <> |
---|
[599] | 720 | void CINetCDF4::getData(CArray<double, 1>& data, const StdString& var, |
---|
[686] | 721 | const CVarPath* const path, StdSize record); |
---|
[599] | 722 | template <> |
---|
| 723 | void CINetCDF4::getData(CArray<float, 1>& data, const StdString& var, |
---|
[686] | 724 | const CVarPath* const path, StdSize record); |
---|
[219] | 725 | |
---|
[599] | 726 | //--------------------------------------------------------------- |
---|
| 727 | |
---|
| 728 | StdString CINetCDF4::getLonCoordName(const StdString& varname, |
---|
| 729 | const CVarPath* const path) |
---|
| 730 | { |
---|
[825] | 731 | StdString lonName; |
---|
[782] | 732 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 733 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 734 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 735 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 736 | { |
---|
| 737 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 738 | { |
---|
| 739 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 740 | if (CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)) |
---|
[825] | 741 | { |
---|
| 742 | lonName = *itList; |
---|
| 743 | return lonName; |
---|
| 744 | } |
---|
[782] | 745 | } |
---|
| 746 | } |
---|
[825] | 747 | return lonName; |
---|
[599] | 748 | } |
---|
| 749 | |
---|
| 750 | StdString CINetCDF4::getLatCoordName(const StdString& varname, |
---|
| 751 | const CVarPath* const path) |
---|
| 752 | { |
---|
[825] | 753 | StdString latName; |
---|
[782] | 754 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 755 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 756 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 757 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 758 | { |
---|
| 759 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 760 | { |
---|
| 761 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 762 | if (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit)) |
---|
[825] | 763 | { |
---|
| 764 | latName = *itList; |
---|
| 765 | return latName; |
---|
| 766 | } |
---|
[782] | 767 | } |
---|
| 768 | } |
---|
[825] | 769 | return latName; |
---|
[599] | 770 | } |
---|
| 771 | |
---|
| 772 | StdString CINetCDF4::getVertCoordName(const StdString& varname, |
---|
| 773 | const CVarPath* const path) |
---|
| 774 | { |
---|
| 775 | if (!this->is3Dim(varname, path)) return ""; |
---|
| 776 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
| 777 | if (this->hasCoordinates(varname, path)) |
---|
[686] | 778 | return *(++(++clist.begin())); |
---|
[599] | 779 | else |
---|
[686] | 780 | return *(++(++clist.rbegin())); |
---|
[599] | 781 | } |
---|
[335] | 782 | } // namespace xios |
---|