[528] | 1 | #include <fstream> |
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| 2 | |
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[219] | 3 | #include "onetcdf4.hpp" |
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[2529] | 4 | #include "onetcdf4_plugin.hpp" |
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[352] | 5 | #include "group_template.hpp" |
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[382] | 6 | #include "mpi.hpp" |
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[379] | 7 | #include "netcdf.hpp" |
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[498] | 8 | #include "netCdfInterface.hpp" |
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| 9 | #include "netCdfException.hpp" |
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[1158] | 10 | #include "timer.hpp" |
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[219] | 11 | |
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[335] | 12 | namespace xios |
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[219] | 13 | { |
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| 14 | /// ////////////////////// Définitions ////////////////////// /// |
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| 15 | |
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[686] | 16 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, |
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[878] | 17 | bool useCFConvention, |
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[1639] | 18 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[686] | 19 | : path() |
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| 20 | , wmpi(false) |
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| 21 | , useClassicFormat(useClassicFormat) |
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[878] | 22 | , useCFConvention(useCFConvention) |
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[219] | 23 | { |
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[878] | 24 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
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[219] | 25 | } |
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[498] | 26 | |
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[219] | 27 | //--------------------------------------------------------------- |
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[286] | 28 | |
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[219] | 29 | CONetCDF4::~CONetCDF4(void) |
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| 30 | { |
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| 31 | } |
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| 32 | |
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| 33 | ///-------------------------------------------------------------- |
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| 34 | |
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[878] | 35 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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[1639] | 36 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[219] | 37 | { |
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[517] | 38 | this->useClassicFormat = useClassicFormat; |
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[878] | 39 | this->useCFConvention = useCFConvention; |
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[517] | 40 | |
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| 41 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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[605] | 42 | |
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| 43 | // Don't use parallel mode if there is only one process |
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| 44 | if (comm) |
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| 45 | { |
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| 46 | int commSize = 0; |
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[1639] | 47 | MPI_Comm_size(*comm, &commSize); |
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[605] | 48 | if (commSize <= 1) |
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| 49 | comm = NULL; |
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| 50 | } |
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| 51 | wmpi = comm && !multifile; |
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| 52 | |
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| 53 | if (wmpi) |
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[517] | 54 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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| 55 | |
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[528] | 56 | // If the file does not exist, we always create it |
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| 57 | if (!append || !std::ifstream(filename.c_str())) |
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[219] | 58 | { |
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[1158] | 59 | CTimer::get("Files : create").resume(); |
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[605] | 60 | if (wmpi) |
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[1639] | 61 | CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 62 | else |
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| 63 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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[1158] | 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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[1158] | 71 | CTimer::get("Files : open").resume(); |
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[605] | 72 | if (wmpi) |
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[1639] | 73 | CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 74 | else |
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| 75 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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[1158] | 76 | CTimer::get("Files : open").suspend(); |
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[528] | 77 | this->appendMode = true; |
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[219] | 78 | } |
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[517] | 79 | |
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| 80 | // If the classic NetCDF format is used, we enable the "no-fill mode" globally. |
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| 81 | // This is done per variable for the NetCDF4 format. |
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| 82 | if (useClassicFormat) |
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[606] | 83 | CNetCdfInterface::setFill(this->ncidp, false); |
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[802] | 84 | |
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| 85 | this->timeCounterName = timeCounterName; |
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[219] | 86 | } |
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[498] | 87 | |
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[286] | 88 | void CONetCDF4::close() |
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| 89 | { |
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[1158] | 90 | CTimer::get("Files : close").resume(); |
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[686] | 91 | CNetCdfInterface::close(this->ncidp); |
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[1158] | 92 | CTimer::get("Files : close").suspend(); |
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[286] | 93 | } |
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[498] | 94 | |
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[219] | 95 | //--------------------------------------------------------------- |
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[498] | 96 | |
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[219] | 97 | void CONetCDF4::definition_start(void) |
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[498] | 98 | { |
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[686] | 99 | CNetCdfInterface::reDef(this->ncidp); |
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[219] | 100 | } |
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[498] | 101 | |
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[219] | 102 | //--------------------------------------------------------------- |
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[498] | 103 | |
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[219] | 104 | void CONetCDF4::definition_end(void) |
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| 105 | { |
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[686] | 106 | CNetCdfInterface::endDef(this->ncidp); |
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[219] | 107 | } |
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| 108 | |
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| 109 | //--------------------------------------------------------------- |
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[498] | 110 | |
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[219] | 111 | int CONetCDF4::getCurrentGroup(void) |
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| 112 | { |
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[686] | 113 | return this->getGroup(this->getCurrentPath()); |
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[219] | 114 | } |
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[498] | 115 | |
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[219] | 116 | //--------------------------------------------------------------- |
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[498] | 117 | |
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[686] | 118 | int CONetCDF4::getGroup(const CONetCDF4Path& path) |
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[219] | 119 | { |
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| 120 | int retvalue = this->ncidp; |
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[498] | 121 | |
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[686] | 122 | CONetCDF4Path::const_iterator it = path.begin(), end = path.end(); |
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[219] | 123 | |
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[686] | 124 | for (; it != end; it++) |
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[219] | 125 | { |
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[686] | 126 | const StdString& groupid = *it; |
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| 127 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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[219] | 128 | } |
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[686] | 129 | return retvalue; |
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[219] | 130 | } |
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[498] | 131 | |
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[219] | 132 | //--------------------------------------------------------------- |
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[498] | 133 | |
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[686] | 134 | int CONetCDF4::getVariable(const StdString& varname) |
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[219] | 135 | { |
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| 136 | int varid = 0; |
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| 137 | int grpid = this->getCurrentGroup(); |
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[686] | 138 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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| 139 | return varid; |
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[219] | 140 | } |
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[498] | 141 | |
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[219] | 142 | //--------------------------------------------------------------- |
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[498] | 143 | |
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[686] | 144 | int CONetCDF4::getDimension(const StdString& dimname) |
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[219] | 145 | { |
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| 146 | int dimid = 0; |
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| 147 | int grpid = this->getCurrentGroup(); |
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[686] | 148 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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| 149 | return dimid; |
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[219] | 150 | } |
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[498] | 151 | |
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[219] | 152 | //--------------------------------------------------------------- |
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[498] | 153 | |
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[219] | 154 | int CONetCDF4::getUnlimitedDimension(void) |
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| 155 | { |
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| 156 | int dimid = 0; |
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| 157 | int grpid = this->getCurrentGroup(); |
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[686] | 158 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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| 159 | return dimid; |
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[219] | 160 | } |
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[498] | 161 | |
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[266] | 162 | StdString CONetCDF4::getUnlimitedDimensionName(void) |
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| 163 | { |
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| 164 | int grpid = this->getGroup(path); |
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| 165 | int dimid = this->getUnlimitedDimension(); |
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[498] | 166 | |
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| 167 | StdString dimname; |
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[686] | 168 | if (dimid != -1) |
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| 169 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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| 170 | return dimname; |
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[266] | 171 | } |
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[498] | 172 | |
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[219] | 173 | //--------------------------------------------------------------- |
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[498] | 174 | |
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[686] | 175 | std::vector<StdSize> CONetCDF4::getDimensions(const StdString& varname) |
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[219] | 176 | { |
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| 177 | StdSize size = 0; |
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| 178 | std::vector<StdSize> retvalue; |
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| 179 | int grpid = this->getCurrentGroup(); |
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| 180 | int varid = this->getVariable(varname); |
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| 181 | int nbdim = 0, *dimid = NULL; |
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| 182 | |
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[686] | 183 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[219] | 184 | dimid = new int[nbdim](); |
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[686] | 185 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[219] | 186 | |
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| 187 | for (int i = 0; i < nbdim; i++) |
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| 188 | { |
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[686] | 189 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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[219] | 190 | if (size == NC_UNLIMITED) |
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| 191 | size = UNLIMITED_DIM; |
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| 192 | retvalue.push_back(size); |
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| 193 | } |
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[401] | 194 | delete [] dimid; |
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[686] | 195 | return retvalue; |
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[219] | 196 | } |
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| 197 | |
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[686] | 198 | std::vector<std::string> CONetCDF4::getDimensionsIdList(const std::string* _varname) |
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[266] | 199 | { |
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[498] | 200 | int nDimNull = 0; |
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[266] | 201 | int nbdim = 0, *dimid = NULL; |
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| 202 | int grpid = this->getCurrentGroup(); |
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| 203 | int varid = (_varname != NULL) ? this->getVariable(*_varname) : NC_GLOBAL; |
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| 204 | std::vector<std::string> retvalue; |
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[498] | 205 | |
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[266] | 206 | if (_varname != NULL) |
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| 207 | { |
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[686] | 208 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[266] | 209 | dimid = new int[nbdim](); |
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[686] | 210 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[266] | 211 | } |
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| 212 | else |
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| 213 | { |
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[686] | 214 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[266] | 215 | dimid = new int[nbdim](); |
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[686] | 216 | CNetCdfInterface::inqDimIds(grpid, nDimNull, dimid, 1); |
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[266] | 217 | } |
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[498] | 218 | |
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[266] | 219 | for (int i = 0; i < nbdim; i++) |
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| 220 | { |
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[498] | 221 | std::string dimname; |
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[686] | 222 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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[266] | 223 | retvalue.push_back(dimname); |
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| 224 | } |
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| 225 | delete [] dimid; |
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[498] | 226 | |
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[686] | 227 | return retvalue; |
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[266] | 228 | } |
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| 229 | |
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[219] | 230 | //--------------------------------------------------------------- |
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| 231 | |
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[707] | 232 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective) |
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| 233 | { |
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| 234 | int grpid = this->getCurrentGroup(); |
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| 235 | int varid = this->getVariable(name); |
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| 236 | |
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| 237 | std::vector<StdSize> start(2), count(2); |
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| 238 | start[0] = 0; |
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| 239 | // Find out how many temporal records have been written already to the file we are opening |
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| 240 | int ncUnlimitedDimId; |
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| 241 | CNetCdfInterface::inqUnLimDim(this->ncidp, ncUnlimitedDimId); |
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| 242 | CNetCdfInterface::inqDimLen(this->ncidp, ncUnlimitedDimId, count[0]); |
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| 243 | start[1] = 0; |
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| 244 | count[1] = 2; |
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| 245 | |
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| 246 | timeAxisBounds.resize(count[1], count[0]); |
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| 247 | |
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| 248 | if (this->wmpi && collective) |
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| 249 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 250 | if (this->wmpi && !collective) |
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| 251 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 252 | |
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| 253 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 254 | } |
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| 255 | |
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[1158] | 256 | void CONetCDF4::getTimeAxisBounds(CArray<double,2>& timeAxisBounds, const StdString& name, bool collective, size_t record) |
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| 257 | { |
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| 258 | int grpid = this->getCurrentGroup(); |
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| 259 | int varid = this->getVariable(name); |
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[707] | 260 | |
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[1158] | 261 | std::vector<StdSize> start(2), count(2); |
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| 262 | start[0] = record; |
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| 263 | count[0] = 1 ; |
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| 264 | start[1] = 0; |
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| 265 | count[1] = 2; |
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| 266 | |
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| 267 | timeAxisBounds.resize(2, 1); |
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| 268 | |
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| 269 | if (this->wmpi && collective) |
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| 270 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 271 | if (this->wmpi && !collective) |
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| 272 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 273 | |
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| 274 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], timeAxisBounds.dataFirst()); |
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| 275 | } |
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| 276 | |
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| 277 | |
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| 278 | |
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[686] | 279 | const CONetCDF4::CONetCDF4Path& CONetCDF4::getCurrentPath(void) const |
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| 280 | { return this->path; } |
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[219] | 281 | |
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[686] | 282 | void CONetCDF4::setCurrentPath(const CONetCDF4Path& path) |
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[219] | 283 | { this->path = path; } |
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| 284 | |
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| 285 | //--------------------------------------------------------------- |
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| 286 | |
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[686] | 287 | int CONetCDF4::addGroup(const StdString& name) |
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[219] | 288 | { |
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| 289 | int retvalue = 0; |
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| 290 | int grpid = this->getCurrentGroup(); |
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[686] | 291 | CNetCdfInterface::defGrp(grpid, name, retvalue); |
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| 292 | return retvalue; |
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[219] | 293 | } |
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[498] | 294 | |
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[219] | 295 | //--------------------------------------------------------------- |
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[498] | 296 | |
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[219] | 297 | int CONetCDF4::addDimension(const StdString& name, const StdSize size) |
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| 298 | { |
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| 299 | int retvalue = 0; |
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| 300 | int grpid = this->getCurrentGroup(); |
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| 301 | if (size != UNLIMITED_DIM) |
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[686] | 302 | CNetCdfInterface::defDim(grpid, name, size, retvalue); |
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[219] | 303 | else |
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[686] | 304 | CNetCdfInterface::defDim(grpid, name, NC_UNLIMITED, retvalue); |
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| 305 | return retvalue; |
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[219] | 306 | } |
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[498] | 307 | |
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[219] | 308 | //--------------------------------------------------------------- |
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[498] | 309 | |
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[686] | 310 | int CONetCDF4::addVariable(const StdString& name, nc_type type, |
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[2481] | 311 | const std::vector<StdString>& dim, bool defineChunking) |
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[219] | 312 | { |
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[350] | 313 | int varid = 0; |
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[219] | 314 | std::vector<int> dimids; |
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[606] | 315 | std::vector<StdSize> dimsizes; |
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[857] | 316 | int dimSize = dim.size(); |
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[2479] | 317 | |
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[2481] | 318 | StdSize size; |
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| 319 | |
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[2479] | 320 | int grpid = this->getCurrentGroup(); |
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| 321 | |
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| 322 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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| 323 | |
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| 324 | for (int idx = 0; it != end; it++, ++idx) |
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| 325 | { |
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| 326 | const StdString& dimid = *it; |
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| 327 | dimids.push_back(this->getDimension(dimid)); |
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[2481] | 328 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 329 | if (size == NC_UNLIMITED) size = 1; |
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| 330 | dimsizes.push_back(size); |
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[2479] | 331 | } |
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| 332 | |
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| 333 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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[2481] | 334 | |
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| 335 | if (defineChunking) { |
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| 336 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
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| 337 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
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| 338 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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| 339 | } |
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| 340 | |
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[878] | 341 | |
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[2479] | 342 | return varid; |
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| 343 | } |
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| 344 | |
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| 345 | //--------------------------------------------------------------- |
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| 346 | |
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| 347 | int CONetCDF4::addChunk(CField* field, nc_type type, |
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| 348 | const std::vector<StdString>& dim, int compressionLevel) |
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| 349 | { |
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| 350 | const StdString& name = field->getFieldOutputName(); |
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| 351 | int varid = 0; |
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| 352 | std::vector<StdSize> dimsizes; |
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| 353 | int dimSize = dim.size(); |
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| 354 | |
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[606] | 355 | StdSize size; |
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| 356 | StdSize totalSize; |
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[498] | 357 | |
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[2479] | 358 | // default chunk size |
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| 359 | StdSize maxSize = 1024 * 1024 * 20; // = 20 Mo (exp using large NEMO like grids) |
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| 360 | StdSize targetSize = maxSize; |
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| 361 | if (!field->chunking_blocksize_target.isEmpty()) |
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| 362 | { |
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| 363 | targetSize = field->chunking_blocksize_target.getValue()*1024*1024; |
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| 364 | } |
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| 365 | StdSize recordSize = 1; //sizeof(type); |
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| 366 | if (field->prec.isEmpty()) recordSize *= 4; |
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| 367 | else recordSize *= field->prec; |
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| 368 | |
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[219] | 369 | int grpid = this->getCurrentGroup(); |
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[498] | 370 | |
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[606] | 371 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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[219] | 372 | |
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[878] | 373 | for (int idx = 0; it != end; it++, ++idx) |
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[219] | 374 | { |
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[686] | 375 | const StdString& dimid = *it; |
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[606] | 376 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 377 | if (size == NC_UNLIMITED) size = 1; |
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[2479] | 378 | recordSize *= size; |
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[606] | 379 | dimsizes.push_back(size); |
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[219] | 380 | } |
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[2479] | 381 | double chunkingRatio = (double)recordSize / (double)targetSize; |
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[453] | 382 | |
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[2479] | 383 | varid = this->getVariable(name); |
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[498] | 384 | |
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[517] | 385 | // The classic NetCDF format does not support chunking nor fill parameters |
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| 386 | if (!useClassicFormat) |
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[453] | 387 | { |
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[2479] | 388 | // Browse field's elements (domain, axis) and NetCDF meta-data to retrieve corresponding chunking coefficients |
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| 389 | // in the file order ! |
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| 390 | CGrid* grid = field->getGrid(); |
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| 391 | std::vector<CDomain*> domains = grid->getDomains(); |
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| 392 | std::vector<CAxis*> axis = grid->getAxis(); |
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| 393 | |
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| 394 | std::vector<double> userChunkingWeights; // store chunking coefficients defined by users |
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| 395 | std::vector<StdString>::const_reverse_iterator itId = dim.rbegin(); // NetCDF is fed using dim, see this::addVariable() |
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| 396 | int elementIdx(0); |
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| 397 | int outerAxis(-1), outerDomJ(-1), outerDomI(-1); |
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| 398 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itId, ++elementIdx) |
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[517] | 399 | { |
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[2479] | 400 | bool isAxis(false); |
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| 401 | for ( auto ax : axis ) |
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| 402 | { |
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| 403 | StdString axisDim; |
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| 404 | // Rebuild axis name from axis before comparing |
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| 405 | if (ax->dim_name.isEmpty()) axisDim = ax->getAxisOutputName(); |
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| 406 | else axisDim=ax->dim_name.getValue(); |
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| 407 | if (axisDim == *itId) |
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| 408 | { |
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| 409 | if (!ax->chunking_weight.isEmpty()) userChunkingWeights.push_back( ax->chunking_weight.getValue() ); |
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| 410 | else userChunkingWeights.push_back( 0. ); |
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| 411 | isAxis = true; |
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| 412 | outerAxis = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
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| 413 | break; |
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| 414 | } |
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| 415 | } // end scanning axis |
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| 416 | bool isDomain(false); |
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| 417 | for ( auto dom : domains ) |
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| 418 | { |
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| 419 | StdString axisDim; |
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| 420 | // Rebuild axis I name from domain before comparing |
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| 421 | if (!dom->dim_i_name.isEmpty()) axisDim = dom->dim_i_name.getValue(); |
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| 422 | else |
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| 423 | { |
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| 424 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="x"; |
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| 425 | if (dom->type==CDomain::type_attr::unstructured) axisDim="cell"; |
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| 426 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lon"; |
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| 427 | } |
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| 428 | if (axisDim == *itId) |
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| 429 | { |
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| 430 | if (!dom->chunking_weight_i.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_i.getValue() ); |
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| 431 | else userChunkingWeights.push_back( 0. ); |
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| 432 | isDomain = true; |
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| 433 | outerDomI = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 434 | break; |
---|
| 435 | } |
---|
| 436 | // Rebuild axis J name from domain before comparing |
---|
| 437 | if (!dom->dim_j_name.isEmpty()) axisDim = dom->dim_j_name.getValue(); |
---|
| 438 | else { |
---|
| 439 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="y"; |
---|
| 440 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lat"; |
---|
| 441 | } |
---|
| 442 | if (axisDim == *itId) |
---|
| 443 | { |
---|
| 444 | if (!dom->chunking_weight_j.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_j.getValue() ); |
---|
| 445 | else userChunkingWeights.push_back( 0. ); |
---|
| 446 | outerDomJ = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 447 | isDomain = true; |
---|
| 448 | break; |
---|
| 449 | } |
---|
| 450 | } // end scanning domain |
---|
| 451 | // No chunking applied on scalars or time |
---|
| 452 | if ((!isAxis)&&(!isDomain)) |
---|
| 453 | { |
---|
| 454 | userChunkingWeights.push_back( 0. ); |
---|
| 455 | } |
---|
[517] | 456 | } |
---|
[2479] | 457 | |
---|
| 458 | double sumChunkingWeights(0); |
---|
| 459 | for (int i=0;i<userChunkingWeights.size();i++) sumChunkingWeights += userChunkingWeights[i]; |
---|
| 460 | if ( (!sumChunkingWeights) && (chunkingRatio > 1) ) |
---|
| 461 | { |
---|
| 462 | if (outerAxis!=-1) userChunkingWeights[outerAxis] = 1; // chunk along outer axis |
---|
| 463 | else if (outerDomJ!=-1) userChunkingWeights[outerDomJ] = 1; // if no axis ? -> along j |
---|
| 464 | else if (outerDomI!=-1) userChunkingWeights[outerDomI] = 1; // if no j -> along i |
---|
| 465 | else {;} |
---|
| 466 | } |
---|
| 467 | |
---|
| 468 | int countChunkingDims(0); // number of dimensions on which chunking is operated : algo uses pow(value, 1/countChunkingDims) |
---|
| 469 | double normalizingWeight(0); // use to relativize chunking coefficients for all dimensions |
---|
| 470 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 471 | if (userChunkingWeights[i]>0.) |
---|
| 472 | { |
---|
| 473 | countChunkingDims++; |
---|
| 474 | normalizingWeight = userChunkingWeights[i]; |
---|
| 475 | } |
---|
| 476 | |
---|
| 477 | std::vector<double> chunkingRatioPerDims; // will store coefficients used to compute chunk size |
---|
| 478 | double productRatios = 1; // last_coeff = pow( shrink_ratio / (product of all ratios), 1/countChunkingDims ) |
---|
| 479 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 480 | { |
---|
| 481 | chunkingRatioPerDims.push_back( userChunkingWeights[i] / normalizingWeight ); |
---|
| 482 | if (chunkingRatioPerDims[i]) productRatios *= chunkingRatioPerDims[i]; |
---|
| 483 | } |
---|
| 484 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 485 | { |
---|
| 486 | chunkingRatioPerDims[i] *= pow( chunkingRatio / productRatios, 1./countChunkingDims ); |
---|
| 487 | } |
---|
| 488 | |
---|
| 489 | std::vector<double>::iterator itChunkingRatios = chunkingRatioPerDims.begin(); |
---|
| 490 | //itId = dim.rbegin(); |
---|
| 491 | double correctionFromPreviousDim = 1.; |
---|
| 492 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itChunkingRatios, ++itId) |
---|
| 493 | { |
---|
| 494 | *itChunkingRatios *= correctionFromPreviousDim; |
---|
| 495 | correctionFromPreviousDim = 1; |
---|
| 496 | if (*itChunkingRatios > 1) // else target larger than size ! |
---|
| 497 | { |
---|
| 498 | StdSize dimensionSize = *itDim; |
---|
| 499 | //info(0) << *itId << " " << *itDim << " " << *itChunkingRatios << " " << (*itDim)/(*itChunkingRatios) << endl; |
---|
| 500 | *itDim = ceil( *itDim / ceil(*itChunkingRatios) ); |
---|
| 501 | correctionFromPreviousDim = *itChunkingRatios/ ((double)dimensionSize/(*itDim)); |
---|
| 502 | } |
---|
| 503 | } |
---|
[857] | 504 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
---|
| 505 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
---|
[517] | 506 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
---|
[453] | 507 | } |
---|
[1456] | 508 | |
---|
[606] | 509 | return varid; |
---|
[219] | 510 | } |
---|
| 511 | |
---|
| 512 | //--------------------------------------------------------------- |
---|
| 513 | |
---|
[2529] | 514 | void CONetCDF4::setCompressionLevel(const StdString& varname, const StdString& compressionType, int compressionLevel, const CArray<double,1>& compressionParams) |
---|
[606] | 515 | { |
---|
[607] | 516 | if (compressionLevel < 0 || compressionLevel > 9) |
---|
| 517 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 518 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
---|
[2529] | 519 | #ifndef PARALLEL_COMPRESSION |
---|
| 520 | if ( ((compressionLevel)||(compressionParams.numElements())) && wmpi) |
---|
[607] | 521 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 522 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
---|
[2529] | 523 | #endif |
---|
[606] | 524 | int grpid = this->getCurrentGroup(); |
---|
| 525 | int varid = this->getVariable(varname); |
---|
[2529] | 526 | if (compressionType=="None") |
---|
| 527 | { |
---|
| 528 | } |
---|
| 529 | else if (compressionType=="gzip") |
---|
| 530 | { |
---|
| 531 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
---|
| 532 | } |
---|
| 533 | else |
---|
| 534 | { |
---|
| 535 | size_t cd_nelmts; |
---|
| 536 | unsigned int* cd_values = NULL; |
---|
| 537 | if (compressionType=="SZ") |
---|
| 538 | { |
---|
| 539 | CONetCDF4Plugin::interpretParametersSZ(compressionParams, &cd_nelmts, &cd_values); |
---|
| 540 | CNetCdfInterface::defVarFilter(grpid, varid, 32017, cd_nelmts, cd_values); |
---|
| 541 | } |
---|
[2532] | 542 | else if (compressionType=="ZFP") |
---|
| 543 | { |
---|
| 544 | CONetCDF4Plugin::interpretParametersZFP(compressionParams, &cd_nelmts, &cd_values); |
---|
| 545 | CNetCdfInterface::defVarFilter(grpid, varid, 32013, cd_nelmts, cd_values); |
---|
| 546 | } |
---|
[2529] | 547 | else |
---|
| 548 | { |
---|
| 549 | ERROR("void CONetCDF4::setCompressionLevel(...)", "compression_type = " << compressionType << " is not managed"); |
---|
| 550 | } |
---|
| 551 | if (cd_values!=NULL) delete [] cd_values; |
---|
| 552 | } |
---|
| 553 | |
---|
[606] | 554 | } |
---|
| 555 | |
---|
| 556 | //--------------------------------------------------------------- |
---|
| 557 | |
---|
[219] | 558 | template <> |
---|
[686] | 559 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
---|
[219] | 560 | { |
---|
| 561 | int grpid = this->getCurrentGroup(); |
---|
| 562 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 563 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
---|
[219] | 564 | } |
---|
[498] | 565 | |
---|
[219] | 566 | //--------------------------------------------------------------- |
---|
[498] | 567 | |
---|
[219] | 568 | template <> |
---|
[686] | 569 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
---|
[219] | 570 | { |
---|
| 571 | int grpid = this->getCurrentGroup(); |
---|
| 572 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 573 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 574 | } |
---|
[391] | 575 | |
---|
[686] | 576 | template <> |
---|
| 577 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
---|
[391] | 578 | { |
---|
| 579 | int grpid = this->getCurrentGroup(); |
---|
| 580 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 581 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 582 | } |
---|
[219] | 583 | //--------------------------------------------------------------- |
---|
[498] | 584 | |
---|
[219] | 585 | template <> |
---|
[686] | 586 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
---|
[219] | 587 | { |
---|
| 588 | int grpid = this->getCurrentGroup(); |
---|
| 589 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 590 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 591 | } |
---|
[391] | 592 | |
---|
[686] | 593 | template <> |
---|
| 594 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
---|
[391] | 595 | { |
---|
| 596 | int grpid = this->getCurrentGroup(); |
---|
| 597 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 598 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 599 | } |
---|
| 600 | |
---|
[219] | 601 | //--------------------------------------------------------------- |
---|
[498] | 602 | |
---|
[219] | 603 | template <> |
---|
[686] | 604 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
---|
[219] | 605 | { |
---|
| 606 | int grpid = this->getCurrentGroup(); |
---|
| 607 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 608 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 609 | } |
---|
| 610 | |
---|
[686] | 611 | template <> |
---|
| 612 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
---|
[391] | 613 | { |
---|
| 614 | int grpid = this->getCurrentGroup(); |
---|
| 615 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 616 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 617 | } |
---|
| 618 | |
---|
[472] | 619 | template <> |
---|
[686] | 620 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
---|
[472] | 621 | { |
---|
| 622 | int grpid = this->getCurrentGroup(); |
---|
| 623 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 624 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 625 | } |
---|
[219] | 626 | |
---|
[686] | 627 | template <> |
---|
| 628 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
---|
[472] | 629 | { |
---|
| 630 | int grpid = this->getCurrentGroup(); |
---|
| 631 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 632 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 633 | } |
---|
| 634 | |
---|
[472] | 635 | template <> |
---|
[686] | 636 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
---|
[472] | 637 | { |
---|
| 638 | int grpid = this->getCurrentGroup(); |
---|
| 639 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 640 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 641 | } |
---|
| 642 | |
---|
[686] | 643 | template <> |
---|
| 644 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
---|
[472] | 645 | { |
---|
| 646 | int grpid = this->getCurrentGroup(); |
---|
| 647 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 648 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 649 | } |
---|
| 650 | |
---|
[686] | 651 | //--------------------------------------------------------------- |
---|
[498] | 652 | |
---|
[686] | 653 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
---|
| 654 | std::vector<StdSize>& sstart, |
---|
| 655 | std::vector<StdSize>& scount, |
---|
| 656 | const std::vector<StdSize>* start, |
---|
| 657 | const std::vector<StdSize>* count) |
---|
[498] | 658 | { |
---|
[266] | 659 | std::vector<std::size_t> sizes = this->getDimensions(name); |
---|
[857] | 660 | if (sizes.size()==0) |
---|
[266] | 661 | { |
---|
[2264] | 662 | |
---|
| 663 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 664 | array_size*=(*count)[0] ; |
---|
| 665 | else array_size=1 ; |
---|
[266] | 666 | } |
---|
[857] | 667 | else |
---|
| 668 | { |
---|
| 669 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
---|
| 670 | std::vector<std::size_t>::const_iterator |
---|
| 671 | it = sizes.begin(), end = sizes.end(); |
---|
| 672 | int i = 0; |
---|
[219] | 673 | |
---|
[857] | 674 | if (iddims.begin()->compare(timeCounterName) == 0) |
---|
| 675 | { |
---|
| 676 | sstart.push_back(record); |
---|
| 677 | scount.push_back(1); |
---|
[2264] | 678 | if ((start == NULL) && (count == NULL)) i++; |
---|
| 679 | it++; |
---|
| 680 | if (it==end) |
---|
| 681 | { |
---|
| 682 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 683 | { |
---|
| 684 | scount[0]=(*count)[0] ; |
---|
| 685 | array_size *= (*count)[0]; |
---|
| 686 | } |
---|
| 687 | } |
---|
[857] | 688 | } |
---|
[2264] | 689 | |
---|
[857] | 690 | for (;it != end; it++) |
---|
| 691 | { |
---|
| 692 | if ((start != NULL) && (count != NULL)) |
---|
| 693 | { |
---|
| 694 | sstart.push_back((*start)[i]); |
---|
| 695 | scount.push_back((*count)[i]); |
---|
| 696 | array_size *= (*count)[i]; |
---|
| 697 | i++; |
---|
| 698 | } |
---|
| 699 | else |
---|
| 700 | { |
---|
| 701 | sstart.push_back(0); |
---|
| 702 | scount.push_back(sizes[i]); |
---|
| 703 | array_size *= sizes[i]; |
---|
| 704 | i++; |
---|
| 705 | } |
---|
| 706 | } |
---|
| 707 | |
---|
[219] | 708 | } |
---|
| 709 | } |
---|
[498] | 710 | |
---|
[857] | 711 | |
---|
[219] | 712 | template <> |
---|
[686] | 713 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 714 | const std::vector<StdSize>& sstart, |
---|
| 715 | const std::vector<StdSize>& scount, const double* data) |
---|
[219] | 716 | { |
---|
[686] | 717 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 718 | } |
---|
[498] | 719 | |
---|
[219] | 720 | //--------------------------------------------------------------- |
---|
[498] | 721 | |
---|
[219] | 722 | template <> |
---|
[686] | 723 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 724 | const std::vector<StdSize>& sstart, |
---|
[1158] | 725 | const std::vector<StdSize>& scount, char* data) |
---|
| 726 | { |
---|
| 727 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 728 | } |
---|
| 729 | |
---|
| 730 | template <> |
---|
| 731 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 732 | const std::vector<StdSize>& sstart, |
---|
[686] | 733 | const std::vector<StdSize>& scount, const int* data) |
---|
[219] | 734 | { |
---|
[686] | 735 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 736 | } |
---|
| 737 | //--------------------------------------------------------------- |
---|
[498] | 738 | |
---|
[219] | 739 | template <> |
---|
[686] | 740 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 741 | const std::vector<StdSize>& sstart, |
---|
[1957] | 742 | const std::vector<StdSize>& scount, const size_t* data) |
---|
| 743 | { |
---|
| 744 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 745 | } |
---|
| 746 | //--------------------------------------------------------------- |
---|
| 747 | |
---|
| 748 | template <> |
---|
| 749 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 750 | const std::vector<StdSize>& sstart, |
---|
[686] | 751 | const std::vector<StdSize>& scount, const float* data) |
---|
[219] | 752 | { |
---|
[686] | 753 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 754 | } |
---|
| 755 | |
---|
| 756 | //--------------------------------------------------------------- |
---|
| 757 | |
---|
[686] | 758 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
---|
[219] | 759 | { |
---|
| 760 | int grpid = this->getCurrentGroup(); |
---|
| 761 | int varid = this->getVariable(name); |
---|
[2264] | 762 | |
---|
[219] | 763 | StdSize array_size = 1; |
---|
| 764 | std::vector<StdSize> sstart, scount; |
---|
| 765 | |
---|
| 766 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 767 | |
---|
[369] | 768 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
[1158] | 769 | |
---|
[219] | 770 | } |
---|
| 771 | |
---|
[686] | 772 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
---|
[413] | 773 | bool collective, StdSize record, bool isRoot) |
---|
| 774 | { |
---|
| 775 | int grpid = this->getCurrentGroup(); |
---|
| 776 | int varid = this->getVariable(name); |
---|
[498] | 777 | |
---|
[686] | 778 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 779 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
[498] | 780 | else |
---|
[413] | 781 | { |
---|
[686] | 782 | if (it->second >= record) return; |
---|
| 783 | else it->second =record; |
---|
[413] | 784 | } |
---|
[498] | 785 | |
---|
[413] | 786 | StdSize array_size = 1; |
---|
| 787 | std::vector<StdSize> sstart, scount; |
---|
[498] | 788 | |
---|
[413] | 789 | if (this->wmpi && collective) |
---|
[686] | 790 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
[413] | 791 | if (this->wmpi && !collective) |
---|
[686] | 792 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
[498] | 793 | |
---|
[413] | 794 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 795 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 796 | } |
---|
| 797 | |
---|
| 798 | void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name, |
---|
| 799 | bool collective, StdSize record, bool isRoot) |
---|
| 800 | { |
---|
| 801 | int grpid = this->getCurrentGroup(); |
---|
| 802 | int varid = this->getVariable(name); |
---|
| 803 | |
---|
| 804 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 805 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
| 806 | else |
---|
[686] | 807 | { |
---|
[1158] | 808 | if (it->second >= record) return; |
---|
| 809 | else it->second =record; |
---|
[686] | 810 | } |
---|
[1158] | 811 | |
---|
| 812 | StdSize array_size = 1; |
---|
| 813 | std::vector<StdSize> sstart, scount; |
---|
| 814 | |
---|
| 815 | if (this->wmpi && collective) |
---|
| 816 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
| 817 | if (this->wmpi && !collective) |
---|
| 818 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
| 819 | |
---|
| 820 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[413] | 821 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 822 | } |
---|
| 823 | |
---|
[1158] | 824 | |
---|
[219] | 825 | //--------------------------------------------------------------- |
---|
[498] | 826 | |
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[686] | 827 | bool CONetCDF4::varExist(const StdString& varname) |
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[219] | 828 | { |
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| 829 | int grpid = this->getCurrentGroup(); |
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[686] | 830 | return CNetCdfInterface::isVarExisted(grpid, varname); |
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[219] | 831 | } |
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| 832 | |
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[878] | 833 | bool CONetCDF4::dimExist(const StdString& dimname) |
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| 834 | { |
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| 835 | int grpid = this->getCurrentGroup(); |
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| 836 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
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| 837 | } |
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| 838 | |
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[286] | 839 | void CONetCDF4::sync(void) |
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| 840 | { |
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[686] | 841 | CNetCdfInterface::sync(this->ncidp); |
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[498] | 842 | } |
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[219] | 843 | ///-------------------------------------------------------------- |
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[337] | 844 | } // namespace xios |
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