[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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[2579] | 11 | #include "file.hpp" |
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[219] | 12 | |
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[335] | 13 | namespace xios |
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[219] | 14 | { |
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| 15 | /// ////////////////////// Définitions ////////////////////// /// |
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| 16 | |
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[686] | 17 | CONetCDF4::CONetCDF4(const StdString& filename, bool append, bool useClassicFormat, |
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[878] | 18 | bool useCFConvention, |
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[1639] | 19 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[686] | 20 | : path() |
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| 21 | , wmpi(false) |
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| 22 | , useClassicFormat(useClassicFormat) |
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[878] | 23 | , useCFConvention(useCFConvention) |
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[219] | 24 | { |
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[878] | 25 | this->initialize(filename, append, useClassicFormat, useCFConvention, comm, multifile, timeCounterName); |
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[219] | 26 | } |
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[498] | 27 | |
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[219] | 28 | //--------------------------------------------------------------- |
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[286] | 29 | |
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[219] | 30 | CONetCDF4::~CONetCDF4(void) |
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| 31 | { |
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| 32 | } |
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| 33 | |
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| 34 | ///-------------------------------------------------------------- |
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| 35 | |
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[878] | 36 | void CONetCDF4::initialize(const StdString& filename, bool append, bool useClassicFormat, bool useCFConvention, |
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[1639] | 37 | const MPI_Comm* comm, bool multifile, const StdString& timeCounterName) |
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[219] | 38 | { |
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[517] | 39 | this->useClassicFormat = useClassicFormat; |
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[878] | 40 | this->useCFConvention = useCFConvention; |
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[517] | 41 | |
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| 42 | int mode = useClassicFormat ? 0 : NC_NETCDF4; |
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[605] | 43 | |
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| 44 | // Don't use parallel mode if there is only one process |
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| 45 | if (comm) |
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| 46 | { |
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| 47 | int commSize = 0; |
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[1639] | 48 | MPI_Comm_size(*comm, &commSize); |
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[605] | 49 | if (commSize <= 1) |
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| 50 | comm = NULL; |
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| 51 | } |
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| 52 | wmpi = comm && !multifile; |
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| 53 | |
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| 54 | if (wmpi) |
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[517] | 55 | mode |= useClassicFormat ? NC_PNETCDF : NC_MPIIO; |
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| 56 | |
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[528] | 57 | // If the file does not exist, we always create it |
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| 58 | if (!append || !std::ifstream(filename.c_str())) |
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[219] | 59 | { |
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[1158] | 60 | CTimer::get("Files : create").resume(); |
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[605] | 61 | if (wmpi) |
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[1639] | 62 | CNetCdfInterface::createPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 63 | else |
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| 64 | CNetCdfInterface::create(filename, mode, this->ncidp); |
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[1158] | 65 | CTimer::get("Files : create").suspend(); |
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| 66 | |
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[528] | 67 | this->appendMode = false; |
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[219] | 68 | } |
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| 69 | else |
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| 70 | { |
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[528] | 71 | mode |= NC_WRITE; |
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[1158] | 72 | CTimer::get("Files : open").resume(); |
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[605] | 73 | if (wmpi) |
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[1639] | 74 | CNetCdfInterface::openPar(filename, mode, *comm, MPI_INFO_NULL, this->ncidp); |
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[605] | 75 | else |
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| 76 | CNetCdfInterface::open(filename, mode, this->ncidp); |
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[1158] | 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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[1158] | 91 | CTimer::get("Files : close").resume(); |
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[686] | 92 | CNetCdfInterface::close(this->ncidp); |
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[1158] | 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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[1158] | 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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[1158] | 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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[2481] | 312 | const std::vector<StdString>& dim, bool defineChunking) |
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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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[2479] | 318 | |
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[2481] | 319 | StdSize size; |
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| 320 | |
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[2479] | 321 | int grpid = this->getCurrentGroup(); |
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| 322 | |
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| 323 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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| 324 | |
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| 325 | for (int idx = 0; it != end; it++, ++idx) |
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| 326 | { |
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| 327 | const StdString& dimid = *it; |
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| 328 | dimids.push_back(this->getDimension(dimid)); |
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[2481] | 329 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 330 | if (size == NC_UNLIMITED) size = 1; |
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| 331 | dimsizes.push_back(size); |
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[2479] | 332 | } |
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| 333 | |
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| 334 | CNetCdfInterface::defVar(grpid, name, type, dimids.size(), &dimids[0], varid); |
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[2481] | 335 | |
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| 336 | if (defineChunking) { |
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| 337 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
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| 338 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
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| 339 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
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| 340 | } |
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| 341 | |
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[878] | 342 | |
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[2479] | 343 | return varid; |
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| 344 | } |
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| 345 | |
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| 346 | //--------------------------------------------------------------- |
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| 347 | |
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| 348 | int CONetCDF4::addChunk(CField* field, nc_type type, |
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| 349 | const std::vector<StdString>& dim, int compressionLevel) |
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| 350 | { |
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| 351 | const StdString& name = field->getFieldOutputName(); |
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| 352 | int varid = 0; |
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| 353 | std::vector<StdSize> dimsizes; |
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| 354 | int dimSize = dim.size(); |
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| 355 | |
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[606] | 356 | StdSize size; |
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| 357 | StdSize totalSize; |
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[498] | 358 | |
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[2479] | 359 | // default chunk size |
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| 360 | StdSize maxSize = 1024 * 1024 * 20; // = 20 Mo (exp using large NEMO like grids) |
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| 361 | StdSize targetSize = maxSize; |
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| 362 | if (!field->chunking_blocksize_target.isEmpty()) |
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| 363 | { |
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| 364 | targetSize = field->chunking_blocksize_target.getValue()*1024*1024; |
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| 365 | } |
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| 366 | StdSize recordSize = 1; //sizeof(type); |
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| 367 | if (field->prec.isEmpty()) recordSize *= 4; |
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| 368 | else recordSize *= field->prec; |
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| 369 | |
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[219] | 370 | int grpid = this->getCurrentGroup(); |
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[498] | 371 | |
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[606] | 372 | std::vector<StdString>::const_iterator it = dim.begin(), end = dim.end(); |
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[219] | 373 | |
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[878] | 374 | for (int idx = 0; it != end; it++, ++idx) |
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[219] | 375 | { |
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[686] | 376 | const StdString& dimid = *it; |
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[606] | 377 | CNetCdfInterface::inqDimLen(grpid, this->getDimension(dimid), size); |
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| 378 | if (size == NC_UNLIMITED) size = 1; |
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[2479] | 379 | recordSize *= size; |
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[606] | 380 | dimsizes.push_back(size); |
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[219] | 381 | } |
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[2479] | 382 | double chunkingRatio = (double)recordSize / (double)targetSize; |
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[453] | 383 | |
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[2479] | 384 | varid = this->getVariable(name); |
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[498] | 385 | |
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[517] | 386 | // The classic NetCDF format does not support chunking nor fill parameters |
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| 387 | if (!useClassicFormat) |
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[453] | 388 | { |
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[2479] | 389 | // Browse field's elements (domain, axis) and NetCDF meta-data to retrieve corresponding chunking coefficients |
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| 390 | // in the file order ! |
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| 391 | CGrid* grid = field->getGrid(); |
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| 392 | std::vector<CDomain*> domains = grid->getDomains(); |
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| 393 | std::vector<CAxis*> axis = grid->getAxis(); |
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[2579] | 394 | bool singleDomain = (field->getRelFile()->nbDomains == 1); |
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[2479] | 395 | |
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| 396 | std::vector<double> userChunkingWeights; // store chunking coefficients defined by users |
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| 397 | std::vector<StdString>::const_reverse_iterator itId = dim.rbegin(); // NetCDF is fed using dim, see this::addVariable() |
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| 398 | int elementIdx(0); |
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| 399 | int outerAxis(-1), outerDomJ(-1), outerDomI(-1); |
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| 400 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itId, ++elementIdx) |
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[517] | 401 | { |
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[2479] | 402 | bool isAxis(false); |
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| 403 | for ( auto ax : axis ) |
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| 404 | { |
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| 405 | StdString axisDim; |
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| 406 | // Rebuild axis name from axis before comparing |
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| 407 | if (ax->dim_name.isEmpty()) axisDim = ax->getAxisOutputName(); |
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| 408 | else axisDim=ax->dim_name.getValue(); |
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| 409 | if (axisDim == *itId) |
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| 410 | { |
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| 411 | if (!ax->chunking_weight.isEmpty()) userChunkingWeights.push_back( ax->chunking_weight.getValue() ); |
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| 412 | else userChunkingWeights.push_back( 0. ); |
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| 413 | isAxis = true; |
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| 414 | outerAxis = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
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| 415 | break; |
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| 416 | } |
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| 417 | } // end scanning axis |
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| 418 | bool isDomain(false); |
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| 419 | for ( auto dom : domains ) |
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| 420 | { |
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| 421 | StdString axisDim; |
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| 422 | // Rebuild axis I name from domain before comparing |
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| 423 | if (!dom->dim_i_name.isEmpty()) axisDim = dom->dim_i_name.getValue(); |
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| 424 | else |
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| 425 | { |
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| 426 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="x"; |
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| 427 | if (dom->type==CDomain::type_attr::unstructured) axisDim="cell"; |
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| 428 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lon"; |
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| 429 | } |
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[2579] | 430 | if (!singleDomain) axisDim+="_"+dom->getDomainOutputName(); |
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[2479] | 431 | if (axisDim == *itId) |
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| 432 | { |
---|
| 433 | if (!dom->chunking_weight_i.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_i.getValue() ); |
---|
| 434 | else userChunkingWeights.push_back( 0. ); |
---|
| 435 | isDomain = true; |
---|
| 436 | outerDomI = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 437 | break; |
---|
| 438 | } |
---|
| 439 | // Rebuild axis J name from domain before comparing |
---|
| 440 | if (!dom->dim_j_name.isEmpty()) axisDim = dom->dim_j_name.getValue(); |
---|
| 441 | else { |
---|
| 442 | if (dom->type==CDomain::type_attr::curvilinear) axisDim="y"; |
---|
| 443 | if (dom->type==CDomain::type_attr::rectilinear) axisDim="lat"; |
---|
| 444 | } |
---|
[2579] | 445 | if (!singleDomain) axisDim+="_"+dom->getDomainOutputName(); |
---|
[2479] | 446 | if (axisDim == *itId) |
---|
| 447 | { |
---|
| 448 | if (!dom->chunking_weight_j.isEmpty()) userChunkingWeights.push_back( dom->chunking_weight_j.getValue() ); |
---|
| 449 | else userChunkingWeights.push_back( 0. ); |
---|
| 450 | outerDomJ = elementIdx; // Going backward in dimsizes, overwriting will keep outer |
---|
| 451 | isDomain = true; |
---|
| 452 | break; |
---|
| 453 | } |
---|
| 454 | } // end scanning domain |
---|
| 455 | // No chunking applied on scalars or time |
---|
| 456 | if ((!isAxis)&&(!isDomain)) |
---|
| 457 | { |
---|
| 458 | userChunkingWeights.push_back( 0. ); |
---|
| 459 | } |
---|
[517] | 460 | } |
---|
[2479] | 461 | |
---|
| 462 | double sumChunkingWeights(0); |
---|
| 463 | for (int i=0;i<userChunkingWeights.size();i++) sumChunkingWeights += userChunkingWeights[i]; |
---|
| 464 | if ( (!sumChunkingWeights) && (chunkingRatio > 1) ) |
---|
| 465 | { |
---|
| 466 | if (outerAxis!=-1) userChunkingWeights[outerAxis] = 1; // chunk along outer axis |
---|
| 467 | else if (outerDomJ!=-1) userChunkingWeights[outerDomJ] = 1; // if no axis ? -> along j |
---|
| 468 | else if (outerDomI!=-1) userChunkingWeights[outerDomI] = 1; // if no j -> along i |
---|
| 469 | else {;} |
---|
| 470 | } |
---|
| 471 | |
---|
| 472 | int countChunkingDims(0); // number of dimensions on which chunking is operated : algo uses pow(value, 1/countChunkingDims) |
---|
| 473 | double normalizingWeight(0); // use to relativize chunking coefficients for all dimensions |
---|
| 474 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 475 | if (userChunkingWeights[i]>0.) |
---|
| 476 | { |
---|
| 477 | countChunkingDims++; |
---|
| 478 | normalizingWeight = userChunkingWeights[i]; |
---|
| 479 | } |
---|
| 480 | |
---|
| 481 | std::vector<double> chunkingRatioPerDims; // will store coefficients used to compute chunk size |
---|
| 482 | double productRatios = 1; // last_coeff = pow( shrink_ratio / (product of all ratios), 1/countChunkingDims ) |
---|
| 483 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 484 | { |
---|
| 485 | chunkingRatioPerDims.push_back( userChunkingWeights[i] / normalizingWeight ); |
---|
| 486 | if (chunkingRatioPerDims[i]) productRatios *= chunkingRatioPerDims[i]; |
---|
| 487 | } |
---|
| 488 | for (int i=0;i<userChunkingWeights.size();i++) |
---|
| 489 | { |
---|
| 490 | chunkingRatioPerDims[i] *= pow( chunkingRatio / productRatios, 1./countChunkingDims ); |
---|
| 491 | } |
---|
| 492 | |
---|
| 493 | std::vector<double>::iterator itChunkingRatios = chunkingRatioPerDims.begin(); |
---|
| 494 | //itId = dim.rbegin(); |
---|
| 495 | double correctionFromPreviousDim = 1.; |
---|
| 496 | for (vector<StdSize>::reverse_iterator itDim = dimsizes.rbegin(); itDim != dimsizes.rend(); ++itDim, ++itChunkingRatios, ++itId) |
---|
| 497 | { |
---|
| 498 | *itChunkingRatios *= correctionFromPreviousDim; |
---|
| 499 | correctionFromPreviousDim = 1; |
---|
| 500 | if (*itChunkingRatios > 1) // else target larger than size ! |
---|
| 501 | { |
---|
| 502 | StdSize dimensionSize = *itDim; |
---|
| 503 | //info(0) << *itId << " " << *itDim << " " << *itChunkingRatios << " " << (*itDim)/(*itChunkingRatios) << endl; |
---|
| 504 | *itDim = ceil( *itDim / ceil(*itChunkingRatios) ); |
---|
| 505 | correctionFromPreviousDim = *itChunkingRatios/ ((double)dimensionSize/(*itDim)); |
---|
| 506 | } |
---|
| 507 | } |
---|
[857] | 508 | int storageType = (0 == dimSize) ? NC_CONTIGUOUS : NC_CHUNKED; |
---|
| 509 | CNetCdfInterface::defVarChunking(grpid, varid, storageType, &dimsizes[0]); |
---|
[517] | 510 | CNetCdfInterface::defVarFill(grpid, varid, true, NULL); |
---|
[453] | 511 | } |
---|
[1456] | 512 | |
---|
[606] | 513 | return varid; |
---|
[219] | 514 | } |
---|
| 515 | |
---|
| 516 | //--------------------------------------------------------------- |
---|
| 517 | |
---|
[2529] | 518 | void CONetCDF4::setCompressionLevel(const StdString& varname, const StdString& compressionType, int compressionLevel, const CArray<double,1>& compressionParams) |
---|
[606] | 519 | { |
---|
[607] | 520 | if (compressionLevel < 0 || compressionLevel > 9) |
---|
| 521 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 522 | "Invalid compression level for variable \"" << varname << "\", the value should range between 0 and 9."); |
---|
[2529] | 523 | #ifndef PARALLEL_COMPRESSION |
---|
| 524 | if ( ((compressionLevel)||(compressionParams.numElements())) && wmpi) |
---|
[607] | 525 | ERROR("void CONetCDF4::setCompressionLevel(const StdString& varname, int compressionLevel)", |
---|
| 526 | "Impossible to use compression for variable \"" << varname << "\" when using parallel mode."); |
---|
[2529] | 527 | #endif |
---|
[606] | 528 | int grpid = this->getCurrentGroup(); |
---|
| 529 | int varid = this->getVariable(varname); |
---|
[2529] | 530 | if (compressionType=="None") |
---|
| 531 | { |
---|
| 532 | } |
---|
| 533 | else if (compressionType=="gzip") |
---|
| 534 | { |
---|
| 535 | CNetCdfInterface::defVarDeflate(grpid, varid, compressionLevel); |
---|
| 536 | } |
---|
| 537 | else |
---|
| 538 | { |
---|
| 539 | size_t cd_nelmts; |
---|
| 540 | unsigned int* cd_values = NULL; |
---|
| 541 | if (compressionType=="SZ") |
---|
| 542 | { |
---|
| 543 | CONetCDF4Plugin::interpretParametersSZ(compressionParams, &cd_nelmts, &cd_values); |
---|
| 544 | CNetCdfInterface::defVarFilter(grpid, varid, 32017, cd_nelmts, cd_values); |
---|
| 545 | } |
---|
[2532] | 546 | else if (compressionType=="ZFP") |
---|
| 547 | { |
---|
| 548 | CONetCDF4Plugin::interpretParametersZFP(compressionParams, &cd_nelmts, &cd_values); |
---|
| 549 | CNetCdfInterface::defVarFilter(grpid, varid, 32013, cd_nelmts, cd_values); |
---|
| 550 | } |
---|
[2529] | 551 | else |
---|
| 552 | { |
---|
| 553 | ERROR("void CONetCDF4::setCompressionLevel(...)", "compression_type = " << compressionType << " is not managed"); |
---|
| 554 | } |
---|
| 555 | if (cd_values!=NULL) delete [] cd_values; |
---|
| 556 | } |
---|
| 557 | |
---|
[606] | 558 | } |
---|
| 559 | |
---|
| 560 | //--------------------------------------------------------------- |
---|
| 561 | |
---|
[219] | 562 | template <> |
---|
[686] | 563 | void CONetCDF4::addAttribute(const StdString& name, const StdString& value, const StdString* varname) |
---|
[219] | 564 | { |
---|
| 565 | int grpid = this->getCurrentGroup(); |
---|
| 566 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 567 | CNetCdfInterface::putAttType(grpid, varid, name, value.size(), value.c_str()); |
---|
[219] | 568 | } |
---|
[498] | 569 | |
---|
[219] | 570 | //--------------------------------------------------------------- |
---|
[498] | 571 | |
---|
[219] | 572 | template <> |
---|
[686] | 573 | void CONetCDF4::addAttribute(const StdString& name, const double& value, const StdString* varname) |
---|
[219] | 574 | { |
---|
| 575 | int grpid = this->getCurrentGroup(); |
---|
| 576 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 577 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 578 | } |
---|
[391] | 579 | |
---|
[686] | 580 | template <> |
---|
| 581 | void CONetCDF4::addAttribute(const StdString& name, const CArray<double,1>& value, const StdString* varname) |
---|
[391] | 582 | { |
---|
| 583 | int grpid = this->getCurrentGroup(); |
---|
| 584 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 585 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 586 | } |
---|
[219] | 587 | //--------------------------------------------------------------- |
---|
[498] | 588 | |
---|
[219] | 589 | template <> |
---|
[686] | 590 | void CONetCDF4::addAttribute(const StdString& name, const float& value, const StdString* varname) |
---|
[219] | 591 | { |
---|
| 592 | int grpid = this->getCurrentGroup(); |
---|
| 593 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 594 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 595 | } |
---|
[391] | 596 | |
---|
[686] | 597 | template <> |
---|
| 598 | void CONetCDF4::addAttribute(const StdString& name, const CArray<float,1>& value, const StdString* varname) |
---|
[391] | 599 | { |
---|
| 600 | int grpid = this->getCurrentGroup(); |
---|
| 601 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 602 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 603 | } |
---|
| 604 | |
---|
[219] | 605 | //--------------------------------------------------------------- |
---|
[498] | 606 | |
---|
[219] | 607 | template <> |
---|
[686] | 608 | void CONetCDF4::addAttribute(const StdString& name, const int& value, const StdString* varname) |
---|
[219] | 609 | { |
---|
| 610 | int grpid = this->getCurrentGroup(); |
---|
| 611 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 612 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[219] | 613 | } |
---|
| 614 | |
---|
[686] | 615 | template <> |
---|
| 616 | void CONetCDF4::addAttribute(const StdString& name, const CArray<int,1>& value, const StdString* varname) |
---|
[391] | 617 | { |
---|
| 618 | int grpid = this->getCurrentGroup(); |
---|
| 619 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 620 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 621 | } |
---|
| 622 | |
---|
[472] | 623 | template <> |
---|
[686] | 624 | void CONetCDF4::addAttribute(const StdString& name, const short int& value, const StdString* varname) |
---|
[472] | 625 | { |
---|
| 626 | int grpid = this->getCurrentGroup(); |
---|
| 627 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 628 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 629 | } |
---|
[219] | 630 | |
---|
[686] | 631 | template <> |
---|
| 632 | void CONetCDF4::addAttribute(const StdString& name, const CArray<short int,1>& value, const StdString* varname) |
---|
[472] | 633 | { |
---|
| 634 | int grpid = this->getCurrentGroup(); |
---|
| 635 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 636 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 637 | } |
---|
| 638 | |
---|
[472] | 639 | template <> |
---|
[686] | 640 | void CONetCDF4::addAttribute(const StdString& name, const long int& value, const StdString* varname) |
---|
[472] | 641 | { |
---|
| 642 | int grpid = this->getCurrentGroup(); |
---|
| 643 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 644 | CNetCdfInterface::putAttType(grpid, varid, name, 1, &value); |
---|
[472] | 645 | } |
---|
| 646 | |
---|
[686] | 647 | template <> |
---|
| 648 | void CONetCDF4::addAttribute(const StdString& name, const CArray<long int,1>& value, const StdString* varname) |
---|
[472] | 649 | { |
---|
| 650 | int grpid = this->getCurrentGroup(); |
---|
| 651 | int varid = (varname == NULL) ? NC_GLOBAL : this->getVariable(*varname); |
---|
[686] | 652 | CNetCdfInterface::putAttType(grpid, varid, name, value.numElements(), value.dataFirst()); |
---|
[498] | 653 | } |
---|
| 654 | |
---|
[686] | 655 | //--------------------------------------------------------------- |
---|
[498] | 656 | |
---|
[686] | 657 | void CONetCDF4::getWriteDataInfos(const StdString& name, StdSize record, StdSize& array_size, |
---|
| 658 | std::vector<StdSize>& sstart, |
---|
| 659 | std::vector<StdSize>& scount, |
---|
| 660 | const std::vector<StdSize>* start, |
---|
| 661 | const std::vector<StdSize>* count) |
---|
[498] | 662 | { |
---|
[266] | 663 | std::vector<std::size_t> sizes = this->getDimensions(name); |
---|
[857] | 664 | if (sizes.size()==0) |
---|
[266] | 665 | { |
---|
[2264] | 666 | |
---|
| 667 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 668 | array_size*=(*count)[0] ; |
---|
| 669 | else array_size=1 ; |
---|
[266] | 670 | } |
---|
[857] | 671 | else |
---|
| 672 | { |
---|
| 673 | std::vector<std::string> iddims = this->getDimensionsIdList (&name); |
---|
| 674 | std::vector<std::size_t>::const_iterator |
---|
| 675 | it = sizes.begin(), end = sizes.end(); |
---|
| 676 | int i = 0; |
---|
[219] | 677 | |
---|
[857] | 678 | if (iddims.begin()->compare(timeCounterName) == 0) |
---|
| 679 | { |
---|
| 680 | sstart.push_back(record); |
---|
| 681 | scount.push_back(1); |
---|
[2264] | 682 | if ((start == NULL) && (count == NULL)) i++; |
---|
| 683 | it++; |
---|
| 684 | if (it==end) |
---|
| 685 | { |
---|
| 686 | if ((start != NULL) && (count != NULL) && start->size()==1 && count->size()==1) // pur scalar case |
---|
| 687 | { |
---|
| 688 | scount[0]=(*count)[0] ; |
---|
| 689 | array_size *= (*count)[0]; |
---|
| 690 | } |
---|
| 691 | } |
---|
[857] | 692 | } |
---|
[2264] | 693 | |
---|
[857] | 694 | for (;it != end; it++) |
---|
| 695 | { |
---|
| 696 | if ((start != NULL) && (count != NULL)) |
---|
| 697 | { |
---|
| 698 | sstart.push_back((*start)[i]); |
---|
| 699 | scount.push_back((*count)[i]); |
---|
| 700 | array_size *= (*count)[i]; |
---|
| 701 | i++; |
---|
| 702 | } |
---|
| 703 | else |
---|
| 704 | { |
---|
| 705 | sstart.push_back(0); |
---|
| 706 | scount.push_back(sizes[i]); |
---|
| 707 | array_size *= sizes[i]; |
---|
| 708 | i++; |
---|
| 709 | } |
---|
| 710 | } |
---|
| 711 | |
---|
[219] | 712 | } |
---|
| 713 | } |
---|
[498] | 714 | |
---|
[857] | 715 | |
---|
[219] | 716 | template <> |
---|
[686] | 717 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 718 | const std::vector<StdSize>& sstart, |
---|
| 719 | const std::vector<StdSize>& scount, const double* data) |
---|
[219] | 720 | { |
---|
[686] | 721 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 722 | } |
---|
[498] | 723 | |
---|
[219] | 724 | //--------------------------------------------------------------- |
---|
[498] | 725 | |
---|
[219] | 726 | template <> |
---|
[686] | 727 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 728 | const std::vector<StdSize>& sstart, |
---|
[1158] | 729 | const std::vector<StdSize>& scount, char* data) |
---|
| 730 | { |
---|
| 731 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 732 | } |
---|
| 733 | |
---|
| 734 | template <> |
---|
| 735 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 736 | const std::vector<StdSize>& sstart, |
---|
[2600] | 737 | const std::vector<StdSize>& scount, const short* data) |
---|
| 738 | { |
---|
| 739 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 740 | } |
---|
| 741 | |
---|
| 742 | template <> |
---|
| 743 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 744 | const std::vector<StdSize>& sstart, |
---|
[686] | 745 | const std::vector<StdSize>& scount, const int* data) |
---|
[219] | 746 | { |
---|
[686] | 747 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 748 | } |
---|
| 749 | //--------------------------------------------------------------- |
---|
[498] | 750 | |
---|
[219] | 751 | template <> |
---|
[686] | 752 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 753 | const std::vector<StdSize>& sstart, |
---|
[1957] | 754 | const std::vector<StdSize>& scount, const size_t* data) |
---|
| 755 | { |
---|
| 756 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
| 757 | } |
---|
| 758 | //--------------------------------------------------------------- |
---|
| 759 | |
---|
| 760 | template <> |
---|
| 761 | void CONetCDF4::writeData_(int grpid, int varid, |
---|
| 762 | const std::vector<StdSize>& sstart, |
---|
[686] | 763 | const std::vector<StdSize>& scount, const float* data) |
---|
[219] | 764 | { |
---|
[686] | 765 | CNetCdfInterface::putVaraType(grpid, varid, &sstart[0], &scount[0], data); |
---|
[219] | 766 | } |
---|
| 767 | |
---|
| 768 | //--------------------------------------------------------------- |
---|
| 769 | |
---|
[686] | 770 | void CONetCDF4::writeData(const CArray<int, 2>& data, const StdString& name) |
---|
[219] | 771 | { |
---|
| 772 | int grpid = this->getCurrentGroup(); |
---|
| 773 | int varid = this->getVariable(name); |
---|
[2264] | 774 | |
---|
[219] | 775 | StdSize array_size = 1; |
---|
| 776 | std::vector<StdSize> sstart, scount; |
---|
| 777 | |
---|
| 778 | this->getWriteDataInfos(name, 0, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 779 | |
---|
[369] | 780 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
[1158] | 781 | |
---|
[219] | 782 | } |
---|
| 783 | |
---|
[686] | 784 | void CONetCDF4::writeTimeAxisData(const CArray<double, 1>& data, const StdString& name, |
---|
[413] | 785 | bool collective, StdSize record, bool isRoot) |
---|
| 786 | { |
---|
| 787 | int grpid = this->getCurrentGroup(); |
---|
| 788 | int varid = this->getVariable(name); |
---|
[498] | 789 | |
---|
[686] | 790 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 791 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
[498] | 792 | else |
---|
[413] | 793 | { |
---|
[686] | 794 | if (it->second >= record) return; |
---|
| 795 | else it->second =record; |
---|
[413] | 796 | } |
---|
[498] | 797 | |
---|
[413] | 798 | StdSize array_size = 1; |
---|
| 799 | std::vector<StdSize> sstart, scount; |
---|
[498] | 800 | |
---|
[413] | 801 | if (this->wmpi && collective) |
---|
[686] | 802 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
---|
[413] | 803 | if (this->wmpi && !collective) |
---|
[686] | 804 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
---|
[498] | 805 | |
---|
[413] | 806 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
---|
[1158] | 807 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
---|
| 808 | } |
---|
| 809 | |
---|
| 810 | void CONetCDF4::writeTimeAxisDataBounds(const CArray<double, 1>& data, const StdString& name, |
---|
| 811 | bool collective, StdSize record, bool isRoot) |
---|
| 812 | { |
---|
| 813 | int grpid = this->getCurrentGroup(); |
---|
| 814 | int varid = this->getVariable(name); |
---|
| 815 | |
---|
| 816 | map<int,size_t>::iterator it=timeAxis.find(varid); |
---|
| 817 | if (it == timeAxis.end()) timeAxis[varid] = record; |
---|
| 818 | else |
---|
[686] | 819 | { |
---|
[1158] | 820 | if (it->second >= record) return; |
---|
| 821 | else it->second =record; |
---|
[686] | 822 | } |
---|
[1158] | 823 | |
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| 824 | StdSize array_size = 1; |
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| 825 | std::vector<StdSize> sstart, scount; |
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| 826 | |
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| 827 | if (this->wmpi && collective) |
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| 828 | CNetCdfInterface::varParAccess(grpid, varid, NC_COLLECTIVE); |
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| 829 | if (this->wmpi && !collective) |
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| 830 | CNetCdfInterface::varParAccess(grpid, varid, NC_INDEPENDENT); |
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| 831 | |
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| 832 | this->getWriteDataInfos(name, record, array_size, sstart, scount, NULL, NULL); |
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[413] | 833 | this->writeData_(grpid, varid, sstart, scount, data.dataFirst()); |
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| 834 | } |
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| 835 | |
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[1158] | 836 | |
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[219] | 837 | //--------------------------------------------------------------- |
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[498] | 838 | |
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[686] | 839 | bool CONetCDF4::varExist(const StdString& varname) |
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[219] | 840 | { |
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| 841 | int grpid = this->getCurrentGroup(); |
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[686] | 842 | return CNetCdfInterface::isVarExisted(grpid, varname); |
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[219] | 843 | } |
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| 844 | |
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[878] | 845 | bool CONetCDF4::dimExist(const StdString& dimname) |
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| 846 | { |
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| 847 | int grpid = this->getCurrentGroup(); |
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| 848 | return CNetCdfInterface::isDimExisted(grpid, dimname); |
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| 849 | } |
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| 850 | |
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[286] | 851 | void CONetCDF4::sync(void) |
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| 852 | { |
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[686] | 853 | CNetCdfInterface::sync(this->ncidp); |
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[498] | 854 | } |
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[219] | 855 | ///-------------------------------------------------------------- |
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[337] | 856 | } // namespace xios |
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