[528] | 1 | #include <fstream> |
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| 2 | |
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[219] | 3 | #include "onetcdf4.hpp" |
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[352] | 4 | #include "group_template.hpp" |
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[379] | 5 | #include "netcdf.hpp" |
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[498] | 6 | #include "netCdfInterface.hpp" |
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| 7 | #include "netCdfException.hpp" |
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[1205] | 8 | #include "timer.hpp" |
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[219] | 9 | |
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[335] | 10 | namespace xios |
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[219] | 11 | { |
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| 12 | /// ////////////////////// Définitions ////////////////////// /// |
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| 13 | |
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[1328] | 14 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, |
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| 15 | bool useCFConvention, |
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| 16 | const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[686] | 17 | : path() |
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| 18 | , wmpi(false) |
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| 19 | , useClassicFormat(useClassicFormat) |
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[878] | 20 | , useCFConvention(useCFConvention) |
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[219] | 21 | { |
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[878] | 22 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
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[219] | 23 | } |
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[498] | 24 | |
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[219] | 25 | //--------------------------------------------------------------- |
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[286] | 26 | |
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[219] | 27 | CONetCDF4::~CONetCDF4(void) |
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| 28 | { |
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| 29 | } |
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| 30 | |
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| 31 | ///-------------------------------------------------------------- |
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| 32 | |
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[878] | 33 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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[1328] | 34 | const ep_lib::MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[219] | 35 | { |
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[517] | 36 | this->useClassicFormat = useClassicFormat; |
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[878] | 37 | this->useCFConvention = useCFConvention; |
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[517] | 38 | |
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| 39 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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[605] | 40 | |
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| 41 | // Don't use parallel mode if there is only one process |
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| 42 | if (comm) |
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| 43 | { |
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| 44 | int commSize = 0; |
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[1328] | 45 | ep_lib::MPI_Comm_size(*comm, &commSize); |
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[605] | 46 | if (commSize <= 1) |
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| 47 | comm = NULL; |
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| 48 | } |
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| 49 | wmpi = comm && !multifile; |
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[1328] | 50 | ep_lib::MPI_Info info_null; |
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[605] | 51 | |
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| 52 | if (wmpi) |
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[517] | 53 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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| 54 | |
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[528] | 55 | // If the file does not exist, we always create it |
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| 56 | if (!append || !std::ifstream(filename.c_str())) |
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[219] | 57 | { |
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[1205] | 58 | CTimer::get("Files : create").resume(); |
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[605] | 59 | if (wmpi) |
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[1356] | 60 | CNetCdfInterface::createPar(filename, mode, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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[1355] | 61 | //CNetCdfInterface::createPar(filename, mode, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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[605] | 62 | else |
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| 63 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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[1205] | 64 | CTimer::get("Files : create").suspend(); |
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| 65 | |
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[528] | 66 | this->appendMode = false; |
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[219] | 67 | } |
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| 68 | else |
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| 69 | { |
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[528] | 70 | mode |= NC_WRITE; |
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[1205] | 71 | CTimer::get("Files : open").resume(); |
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[605] | 72 | if (wmpi) |
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[1356] | 73 | CNetCdfInterface::openPar(filename, mode, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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[1355] | 74 | //CNetCdfInterface::openPar(filename, mode, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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[605] | 75 | else |
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| 76 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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[1205] | 77 | CTimer::get("Files : open").suspend(); |
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[528] | 78 | this->appendMode = true; |
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[219] | 79 | } |
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[517] | 80 | |
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| 81 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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| 82 | // This is done per variable for the NetCDF4 format. |
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| 83 | if (useClassicFormat) |
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[606] | 84 | CNetCdfInterface::setFill(this->ncidp, false); |
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[802] | 85 | |
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| 86 | this->timeCounterName = timeCounterName; |
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[219] | 87 | } |
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[498] | 88 | |
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[286] | 89 | void CONetCDF4::close() |
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| 90 | { |
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[1205] | 91 | CTimer::get("Files : close").resume(); |
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[686] | 92 | CNetCdfInterface::close(this->ncidp); |
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[1205] | 93 | CTimer::get("Files : close").suspend(); |
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[286] | 94 | } |
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[498] | 95 | |
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[219] | 96 | //--------------------------------------------------------------- |
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[498] | 97 | |
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[219] | 98 | void CONetCDF4::definition_start(void) |
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[498] | 99 | { |
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[686] | 100 | CNetCdfInterface::reDef(this->ncidp); |
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[219] | 101 | } |
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[498] | 102 | |
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[219] | 103 | //--------------------------------------------------------------- |
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[498] | 104 | |
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[219] | 105 | void CONetCDF4::definition_end(void) |
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| 106 | { |
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[686] | 107 | CNetCdfInterface::endDef(this->ncidp); |
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[219] | 108 | } |
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| 109 | |
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| 110 | //--------------------------------------------------------------- |
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[498] | 111 | |
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[219] | 112 | int CONetCDF4::getCurrentGroup(void) |
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| 113 | { |
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[686] | 114 | return this->getGroup(this->getCurrentPath()); |
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[219] | 115 | } |
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[498] | 116 | |
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[219] | 117 | //--------------------------------------------------------------- |
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[498] | 118 | |
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[686] | 119 | int CONetCDF4::getGroup(const CONetCDF4Path& path) |
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[219] | 120 | { |
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| 121 | int retvalue = this->ncidp; |
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[498] | 122 | |
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[686] | 123 | CONetCDF4Path::const_iterator it = path.begin(), end = path.end(); |
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[219] | 124 | |
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[686] | 125 | for (; it != end; it++) |
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[219] | 126 | { |
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[686] | 127 | const StdString& groupid = *it; |
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| 128 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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[219] | 129 | } |
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[686] | 130 | return retvalue; |
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[219] | 131 | } |
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[498] | 132 | |
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[219] | 133 | //--------------------------------------------------------------- |
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[498] | 134 | |
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[686] | 135 | int CONetCDF4::getVariable(const StdString& varname) |
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[219] | 136 | { |
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| 137 | int varid = 0; |
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| 138 | int grpid = this->getCurrentGroup(); |
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[686] | 139 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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| 140 | return varid; |
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[219] | 141 | } |
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[498] | 142 | |
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[219] | 143 | //--------------------------------------------------------------- |
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[498] | 144 | |
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[686] | 145 | int CONetCDF4::getDimension(const StdString& dimname) |
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[219] | 146 | { |
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| 147 | int dimid = 0; |
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| 148 | int grpid = this->getCurrentGroup(); |
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[686] | 149 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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| 150 | return dimid; |
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[219] | 151 | } |
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[498] | 152 | |
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[219] | 153 | //--------------------------------------------------------------- |
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[498] | 154 | |
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[219] | 155 | int CONetCDF4::getUnlimitedDimension(void) |
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| 156 | { |
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| 157 | int dimid = 0; |
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| 158 | int grpid = this->getCurrentGroup(); |
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[686] | 159 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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| 160 | return dimid; |
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[219] | 161 | } |
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[498] | 162 | |
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[266] | 163 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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| 164 | { |
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| 165 | int grpid = this->getGroup(path); |
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| 166 | int dimid = this->getUnlimitedDimension(); |
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[498] | 167 | |
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| 168 | StdString dimname; |
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[686] | 169 | if (dimid != -1) |
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| 170 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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| 171 | return dimname; |
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[266] | 172 | } |
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[498] | 173 | |
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[219] | 174 | //--------------------------------------------------------------- |
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[498] | 175 | |
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[686] | 176 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString& varname) |
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[219] | 177 | { |
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| 178 | StdSize size = 0; |
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| 179 | std::vector<StdSize> retvalue; |
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| 180 | int grpid = this->getCurrentGroup(); |
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| 181 | int varid = this->getVariable(varname); |
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| 182 | int nbdim = 0, *dimid = NULL; |
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| 183 | |
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[686] | 184 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[219] | 185 | dimid = new int[nbdim](); |
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[686] | 186 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[219] | 187 | |
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| 188 | for (int i = 0; i < nbdim; i++) |
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| 189 | { |
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[686] | 190 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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[219] | 191 | if (size == NC_UNLIMITED) |
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| 192 | size = UNLIMITED_DIM; |
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| 193 | retvalue.push_back(size); |
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| 194 | } |
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[401] | 195 | delete [] dimid; |
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[686] | 196 | return retvalue; |
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[219] | 197 | } |
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| 198 | |
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[686] | 199 | std::vector<std::string> CONetCDF4::getDimensionsIdList(const std::string* _varname) |
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[266] | 200 | { |
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[498] | 201 | int nDimNull = 0; |
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[266] | 202 | int nbdim = 0, *dimid = NULL; |
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| 203 | int grpid = this->getCurrentGroup(); |
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| 204 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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| 205 | std::vector<std::string> retvalue; |
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[498] | 206 | |
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[266] | 207 | if (_varname != NULL) |
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| 208 | { |
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[686] | 209 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[266] | 210 | dimid = new int[nbdim](); |
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[686] | 211 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[266] | 212 | } |
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| 213 | else |
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| 214 | { |
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[686] | 215 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[266] | 216 | dimid = new int[nbdim](); |
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[686] | 217 | CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1); |
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[266] | 218 | } |
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[498] | 219 | |
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[266] | 220 | for (int i = 0; i < nbdim; i++) |
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| 221 | { |
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[498] | 222 | std::string dimname; |
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[686] | 223 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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[266] | 224 | retvalue.push_back(dimname); |
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| 225 | } |
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| 226 | delete [] dimid; |
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[498] | 227 | |
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[686] | 228 | return retvalue; |
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[266] | 229 | } |
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| 230 | |
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[219] | 231 | //--------------------------------------------------------------- |
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| 232 | |
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[707] | 233 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective) |
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| 234 | { |
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| 235 | int grpid = this->getCurrentGroup(); |
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| 236 | int varid = this->getVariable(name); |
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| 237 | |
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| 238 | std::vector<StdSize> start(2), count(2); |
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| 239 | start[0] = 0; |
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| 240 | // Find out how many temporal records have been written already to the file we are opening |
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| 241 | int ncUnlimitedDimId; |
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| 242 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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| 243 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, count[0]); |
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| 244 | start[1] = 0; |
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| 245 | count[1] = 2; |
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| 246 | |
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| 247 | timeAxisBounds.resize(count[1], count[0]); |
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| 248 | |
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| 249 | if (this->wmpi && collective) |
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| 250 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 251 | if (this->wmpi && !collective) |
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| 252 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 253 | |
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| 254 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 255 | } |
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| 256 | |
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[1097] | 257 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective, size_t record) |
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| 258 | { |
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| 259 | int grpid = this->getCurrentGroup(); |
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| 260 | int varid = this->getVariable(name); |
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[707] | 261 | |
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[1097] | 262 | std::vector<StdSize> start(2), count(2); |
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| 263 | start[0] = record; |
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| 264 | count[0] = 1 ; |
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| 265 | start[1] = 0; |
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| 266 | count[1] = 2; |
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| 267 | |
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| 268 | timeAxisBounds.resize(2, 1); |
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| 269 | |
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| 270 | if (this->wmpi && collective) |
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| 271 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 272 | if (this->wmpi && !collective) |
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| 273 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 274 | |
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| 275 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 276 | } |
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| 277 | |
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| 278 | |
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| 279 | |
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[686] | 280 | const CONetCDF4::CONetCDF4Path& CONetCDF4::getCurrentPath(void) const |
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| 281 | { return this->path; } |
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[219] | 282 | |
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[686] | 283 | void CONetCDF4::setCurrentPath(const CONetCDF4Path& path) |
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[219] | 284 | { this->path = path; } |
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| 285 | |
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| 286 | //--------------------------------------------------------------- |
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| 287 | |
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[686] | 288 | int CONetCDF4::addGroup(const StdString& name) |
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[219] | 289 | { |
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| 290 | int retvalue = 0; |
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| 291 | int grpid = this->getCurrentGroup(); |
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[686] | 292 | CNetCdfInterface::defGrp(grpid, name, retvalue); |
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| 293 | return retvalue; |
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[219] | 294 | } |
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[498] | 295 | |
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[219] | 296 | //--------------------------------------------------------------- |
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[498] | 297 | |
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[219] | 298 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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| 299 | { |
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| 300 | int retvalue = 0; |
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| 301 | int grpid = this->getCurrentGroup(); |
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| 302 | if (size != UNLIMITED_DIM) |
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[686] | 303 | CNetCdfInterface::defDim(grpid, name, size, retvalue); |
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[219] | 304 | else |
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[686] | 305 | CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue); |
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| 306 | return retvalue; |
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[219] | 307 | } |
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[498] | 308 | |
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[219] | 309 | //--------------------------------------------------------------- |
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[498] | 310 | |
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[686] | 311 | int CONetCDF4::addVariable(const StdString& name, nc_type type, |
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| 312 | const std::vector<StdString>& dim) |
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[219] | 313 | { |
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[350] | 314 | int varid = 0; |
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[219] | 315 | std::vector<int> dimids; |
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[606] | 316 | std::vector<StdSize> dimsizes; |
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[857] | 317 | int dimSize = dim.size(); |
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[878] | 318 | |
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[606] | 319 | StdSize size; |
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| 320 | StdSize totalSize; |
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| 321 | StdSize maxSize = 1024 * 1024 * 256; // == 2GB/8 if output double |
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[498] | 322 | |
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[219] | 323 | int grpid = this->getCurrentGroup(); |
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[498] | 324 | |
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[606] | 325 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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[219] | 326 | |
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[878] | 327 | for (int idx = 0; it != end; it++, ++idx) |
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[219] | 328 | { |
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[686] | 329 | const StdString& dimid = *it; |
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[219] | 330 | dimids.push_back(this->getDimension(dimid)); |
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[606] | 331 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 332 | if (size == NC_UNLIMITED) size = 1; |
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| 333 | dimsizes.push_back(size); |
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[219] | 334 | } |
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[453] | 335 | |
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[606] | 336 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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[498] | 337 | |
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[517] | 338 | // The classic NetCDF format does not support chunking nor fill parameters |
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| 339 | if (!useClassicFormat) |
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[453] | 340 | { |
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[517] | 341 | // set chunksize : size of one record |
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| 342 | // but must not be > 2GB (netcdf or HDF5 problem) |
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| 343 | totalSize = 1; |
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| 344 | for (vector<StdSize>::reverse_iterator it = dimsizes.rbegin(); it != dimsizes.rend(); ++it) |
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| 345 | { |
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| 346 | totalSize *= *it; |
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| 347 | if (totalSize >= maxSize) *it = 1; |
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| 348 | } |
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[857] | 349 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
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| 350 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
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[517] | 351 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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[453] | 352 | } |
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| 353 | |
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[606] | 354 | return varid; |
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[219] | 355 | } |
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| 356 | |
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| 357 | //--------------------------------------------------------------- |
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| 358 | |
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[606] | 359 | void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel) |
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| 360 | { |
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[607] | 361 | if (compressionLevel < 0 || compressionLevel > 9) |
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| 362 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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| 363 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
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| 364 | if (compressionLevel && wmpi) |
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| 365 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
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| 366 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
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| 367 | |
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[606] | 368 | int grpid = this->getCurrentGroup(); |
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| 369 | int varid = this->getVariable(varname); |
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| 370 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
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| 371 | } |
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| 372 | |
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| 373 | //--------------------------------------------------------------- |
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| 374 | |
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[219] | 375 | template <> |
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[686] | 376 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
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[219] | 377 | { |
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| 378 | int grpid = this->getCurrentGroup(); |
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| 379 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 380 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
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[219] | 381 | } |
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[498] | 382 | |
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[219] | 383 | //--------------------------------------------------------------- |
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[498] | 384 | |
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[219] | 385 | template <> |
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[686] | 386 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
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[219] | 387 | { |
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| 388 | int grpid = this->getCurrentGroup(); |
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| 389 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 390 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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[219] | 391 | } |
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[391] | 392 | |
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[686] | 393 | template <> |
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| 394 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
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[391] | 395 | { |
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| 396 | int grpid = this->getCurrentGroup(); |
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| 397 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 398 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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[498] | 399 | } |
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[219] | 400 | //--------------------------------------------------------------- |
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[498] | 401 | |
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[219] | 402 | template <> |
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[686] | 403 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
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[219] | 404 | { |
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| 405 | int grpid = this->getCurrentGroup(); |
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| 406 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 407 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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[219] | 408 | } |
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[391] | 409 | |
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[686] | 410 | template <> |
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| 411 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
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[391] | 412 | { |
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| 413 | int grpid = this->getCurrentGroup(); |
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| 414 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 415 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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[498] | 416 | } |
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| 417 | |
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[219] | 418 | //--------------------------------------------------------------- |
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[498] | 419 | |
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[219] | 420 | template <> |
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[686] | 421 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
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[219] | 422 | { |
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| 423 | int grpid = this->getCurrentGroup(); |
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| 424 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 425 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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[219] | 426 | } |
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| 427 | |
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[686] | 428 | template <> |
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| 429 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
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[391] | 430 | { |
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| 431 | int grpid = this->getCurrentGroup(); |
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| 432 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 433 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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[498] | 434 | } |
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| 435 | |
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[472] | 436 | template <> |
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[686] | 437 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
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[472] | 438 | { |
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| 439 | int grpid = this->getCurrentGroup(); |
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| 440 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 441 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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[472] | 442 | } |
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[219] | 443 | |
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[686] | 444 | template <> |
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| 445 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
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[472] | 446 | { |
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| 447 | int grpid = this->getCurrentGroup(); |
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| 448 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 449 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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[498] | 450 | } |
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| 451 | |
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[472] | 452 | template <> |
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[686] | 453 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
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[472] | 454 | { |
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| 455 | int grpid = this->getCurrentGroup(); |
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| 456 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 457 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
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[472] | 458 | } |
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| 459 | |
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[686] | 460 | template <> |
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| 461 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
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[472] | 462 | { |
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| 463 | int grpid = this->getCurrentGroup(); |
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| 464 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
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[686] | 465 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
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[498] | 466 | } |
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| 467 | |
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[686] | 468 | //--------------------------------------------------------------- |
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[498] | 469 | |
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[686] | 470 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
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| 471 | std::vector<StdSize>& sstart, |
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| 472 | std::vector<StdSize>& scount, |
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| 473 | const std::vector<StdSize>* start, |
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| 474 | const std::vector<StdSize>* count) |
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[498] | 475 | { |
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[266] | 476 | std::vector<std::size_t> sizes = this->getDimensions(name); |
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[857] | 477 | if (sizes.size()==0) |
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[266] | 478 | { |
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[857] | 479 | array_size=1 ; |
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| 480 | sstart.push_back(0); |
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[606] | 481 | scount.push_back(1); |
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[266] | 482 | } |
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[857] | 483 | else |
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| 484 | { |
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| 485 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
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| 486 | std::vector<std::size_t>::const_iterator |
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| 487 | it = sizes.begin(), end = sizes.end(); |
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| 488 | int i = 0; |
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[219] | 489 | |
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[857] | 490 | if (iddims.begin()->compare(timeCounterName) == 0) |
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| 491 | { |
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| 492 | sstart.push_back(record); |
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| 493 | scount.push_back(1); |
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| 494 | if ((start == NULL) && |
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| 495 | (count == NULL)) i++; |
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| 496 | it++; |
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| 497 | } |
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| 498 | |
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| 499 | for (;it != end; it++) |
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| 500 | { |
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| 501 | if ((start != NULL) && (count != NULL)) |
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| 502 | { |
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| 503 | sstart.push_back((*start)[i]); |
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| 504 | scount.push_back((*count)[i]); |
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| 505 | array_size *= (*count)[i]; |
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| 506 | i++; |
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| 507 | } |
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| 508 | else |
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| 509 | { |
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| 510 | sstart.push_back(0); |
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| 511 | scount.push_back(sizes[i]); |
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| 512 | array_size *= sizes[i]; |
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| 513 | i++; |
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| 514 | } |
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| 515 | } |
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| 516 | |
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[219] | 517 | } |
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| 518 | } |
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[498] | 519 | |
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[857] | 520 | |
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[219] | 521 | template <> |
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[686] | 522 | void CONetCDF4::writeData_(int grpid, int varid, |
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| 523 | const std::vector<StdSize>& sstart, |
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| 524 | const std::vector<StdSize>& scount, const double* data) |
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[219] | 525 | { |
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[686] | 526 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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[219] | 527 | } |
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[498] | 528 | |
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[219] | 529 | //--------------------------------------------------------------- |
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[498] | 530 | |
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[219] | 531 | template <> |
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[686] | 532 | void CONetCDF4::writeData_(int grpid, int varid, |
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| 533 | const std::vector<StdSize>& sstart, |
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[1050] | 534 | const std::vector<StdSize>& scount, char* data) |
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| 535 | { |
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| 536 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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| 537 | } |
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| 538 | |
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| 539 | template <> |
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| 540 | |
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| 541 | void CONetCDF4::writeData_(int grpid, int varid, |
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| 542 | const std::vector<StdSize>& sstart, |
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[686] | 543 | const std::vector<StdSize>& scount, const int* data) |
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[219] | 544 | { |
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[1328] | 545 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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[219] | 546 | } |
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| 547 | //--------------------------------------------------------------- |
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[498] | 548 | |
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[219] | 549 | template <> |
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[686] | 550 | void CONetCDF4::writeData_(int grpid, int varid, |
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| 551 | const std::vector<StdSize>& sstart, |
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| 552 | const std::vector<StdSize>& scount, const float* data) |
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[219] | 553 | { |
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[1328] | 554 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
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[219] | 555 | } |
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| 556 | |
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| 557 | //--------------------------------------------------------------- |
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| 558 | |
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[686] | 559 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
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[219] | 560 | { |
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| 561 | int grpid = this->getCurrentGroup(); |
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| 562 | int varid = this->getVariable(name); |
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| 563 | StdSize array_size = 1; |
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| 564 | std::vector<StdSize> sstart, scount; |
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| 565 | |
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| 566 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
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[1205] | 567 | |
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[369] | 568 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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[1205] | 569 | |
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[219] | 570 | } |
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| 571 | |
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[686] | 572 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
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[413] | 573 | bool collective, StdSize record, bool isRoot) |
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| 574 | { |
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| 575 | int grpid = this->getCurrentGroup(); |
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| 576 | int varid = this->getVariable(name); |
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[498] | 577 | |
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[686] | 578 | map<int,size_t>::iterator it=timeAxis.find(varid); |
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| 579 | if (it == timeAxis.end()) timeAxis[varid] = record; |
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[498] | 580 | else |
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[413] | 581 | { |
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[686] | 582 | if (it->second >= record) return; |
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| 583 | else it->second =record; |
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[413] | 584 | } |
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[498] | 585 | |
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[413] | 586 | StdSize array_size = 1; |
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| 587 | std::vector<StdSize> sstart, scount; |
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[498] | 588 | |
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[413] | 589 | if (this->wmpi && collective) |
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[686] | 590 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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[413] | 591 | if (this->wmpi && !collective) |
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[686] | 592 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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[498] | 593 | |
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[413] | 594 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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[1205] | 595 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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| 596 | } |
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| 597 | |
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| 598 | void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name, |
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| 599 | bool collective, StdSize record, bool isRoot) |
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| 600 | { |
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| 601 | int grpid = this->getCurrentGroup(); |
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| 602 | int varid = this->getVariable(name); |
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| 603 | |
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| 604 | map<int,size_t>::iterator it=timeAxis.find(varid); |
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| 605 | if (it == timeAxis.end()) timeAxis[varid] = record; |
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| 606 | else |
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[686] | 607 | { |
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[1205] | 608 | if (it->second >= record) return; |
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| 609 | else it->second =record; |
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[686] | 610 | } |
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[1205] | 611 | |
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| 612 | StdSize array_size = 1; |
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| 613 | std::vector<StdSize> sstart, scount; |
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| 614 | |
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| 615 | if (this->wmpi && collective) |
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| 616 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 617 | if (this->wmpi && !collective) |
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| 618 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 619 | |
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| 620 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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[413] | 621 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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| 622 | } |
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| 623 | |
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[1205] | 624 | |
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[219] | 625 | //--------------------------------------------------------------- |
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[498] | 626 | |
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[686] | 627 | bool CONetCDF4::varExist(const StdString& varname) |
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[219] | 628 | { |
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| 629 | int grpid = this->getCurrentGroup(); |
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[686] | 630 | return CNetCdfInterface::isVarExisted(grpid, varname); |
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[219] | 631 | } |
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| 632 | |
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[878] | 633 | bool CONetCDF4::dimExist(const StdString& dimname) |
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| 634 | { |
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| 635 | int grpid = this->getCurrentGroup(); |
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| 636 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
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| 637 | } |
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| 638 | |
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[286] | 639 | void CONetCDF4::sync(void) |
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| 640 | { |
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[686] | 641 | CNetCdfInterface::sync(this->ncidp); |
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[498] | 642 | } |
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[219] | 643 | ///-------------------------------------------------------------- |
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[337] | 644 | } // namespace xios |
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