[498] | 1 | /*! |
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| 2 | \file netCdfInterface.cpp |
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| 3 | \author Ha NGUYEN |
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| 4 | \date 08 Oct 2014 |
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| 5 | \since 03 Oct 2014 |
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| 6 | |
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| 7 | \brief Wrapper of netcdf functions. |
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| 8 | */ |
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| 9 | |
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[525] | 10 | #include "netCdfInterface.hpp" |
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| 11 | #include "netCdfException.hpp" |
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[498] | 12 | |
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[525] | 13 | namespace xios |
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| 14 | { |
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| 15 | /*! |
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| 16 | This function creates a new netcdf file and return its id |
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| 17 | \param [in] fileName Name of the file |
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| 18 | \param [in] cMode create mode |
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| 19 | \param [in/out] ncId id of the created file |
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| 20 | \return Status code |
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| 21 | */ |
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| 22 | int CNetCdfInterface::create(const StdString& fileName, int cMode, int& ncId) |
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| 23 | { |
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| 24 | int status = nc_create((fileName.c_str()), cMode, &ncId); |
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| 25 | if (NC_NOERR != status) |
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| 26 | { |
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| 27 | StdString errormsg(nc_strerror(status)); |
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| 28 | StdStringStream sstr; |
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| 29 | sstr << "Error in calling function : nc_create((fileName.c_str()), cMode, &ncId) " << std::endl |
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| 30 | << errormsg << std::endl |
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| 31 | << "Unable to create file, given its name : " << fileName |
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| 32 | << "and its creation mode " << creationMode2String(cMode) << std::endl; |
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| 33 | StdString e = sstr.str(); |
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| 34 | throw CNetCdfException(e); |
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| 35 | } |
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[498] | 36 | |
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[525] | 37 | return status; |
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| 38 | } |
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[498] | 39 | |
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[525] | 40 | /*! |
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| 41 | This function creates a new netcdf file on parallel file system |
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| 42 | \param [in] fileName Name of the file |
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| 43 | \param [in] cMode create mode |
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| 44 | \param [in] comm MPI communicator |
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| 45 | \param [in] info MPI information |
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| 46 | \param [in/out] ncId id of the created file |
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| 47 | \return Status code |
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| 48 | */ |
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| 49 | int CNetCdfInterface::createPar(const StdString& fileName, int cMode, MPI_Comm comm, MPI_Info info, int& ncId) |
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| 50 | { |
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| 51 | int status = xios::nc_create_par((fileName.c_str()), cMode, comm, info, &ncId); |
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| 52 | if (NC_NOERR != status) |
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| 53 | { |
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| 54 | StdString errormsg(nc_strerror(status)); |
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| 55 | StdStringStream sstr; |
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| 56 | sstr << "Error in calling function : nc_create_par((fileName.c_str()), cMode, comm, info, &ncId) " << std::endl |
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| 57 | << errormsg << std::endl |
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| 58 | << "Unable to create file on parallel filesys, given its name : " << std::endl |
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| 59 | << "and its creation mode " << creationMode2String(cMode) << std::endl; |
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| 60 | StdString e = sstr.str(); |
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| 61 | throw CNetCdfException(e); |
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| 62 | } |
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[498] | 63 | |
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[525] | 64 | return status; |
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| 65 | } |
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[498] | 66 | |
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[525] | 67 | /*! |
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| 68 | This function opens a netcdf file, given its name and open mode, return its id |
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| 69 | \param [in] fileName Name of the file |
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| 70 | \param [in] oMode open mode |
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| 71 | \param [in/out] ncId id of the opening file |
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| 72 | \return Status code |
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| 73 | */ |
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| 74 | int CNetCdfInterface::open(const StdString& fileName, int oMode, int& ncId) |
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| 75 | { |
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| 76 | int status = nc_open((fileName.c_str()), oMode, &ncId); |
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| 77 | if (NC_NOERR != status) |
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| 78 | { |
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| 79 | StdString errormsg(nc_strerror(status)); |
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| 80 | StdStringStream sstr; |
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| 81 | sstr << "Error in calling function : nc_open((fileName.c_str()), oMode, &ncId) "<< std::endl |
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| 82 | << errormsg << std::endl |
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| 83 | << "Unable to open file, given its name : " << fileName |
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| 84 | << "and its open mode " << openMode2String(oMode) << std::endl; |
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| 85 | StdString e = sstr.str(); |
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| 86 | throw CNetCdfException(e); |
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| 87 | } |
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[498] | 88 | |
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[525] | 89 | return status; |
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| 90 | } |
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[498] | 91 | |
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| 92 | |
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[525] | 93 | /*! |
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| 94 | This function opens a new netcdf file on parallel file system |
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| 95 | \param [in] fileName Name of the file |
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| 96 | \param [in] oMode open mode |
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| 97 | \param [in] comm MPI communicator |
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| 98 | \param [in] info MPI information |
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| 99 | \param [in/out] ncId id of the opened file |
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| 100 | \return Status code |
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| 101 | */ |
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| 102 | int CNetCdfInterface::openPar(const StdString& fileName, int oMode, MPI_Comm comm, MPI_Info info, int& ncId) |
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| 103 | { |
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| 104 | int status = xios::nc_open_par((fileName.c_str()), oMode, comm, info, &ncId); |
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| 105 | if (NC_NOERR != status) |
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| 106 | { |
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| 107 | StdString errormsg(nc_strerror(status)); |
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| 108 | StdStringStream sstr; |
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| 109 | sstr << "Error in calling function " << "nc_open_par((fileName.c_str()), oMode, comm, info, &ncId) " << std::endl |
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| 110 | << errormsg << std::endl |
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| 111 | << "Unable to open file on parallel filesys, given its name : " << fileName |
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| 112 | << "and its open mode " << openMode2String(oMode) << std::endl; |
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| 113 | StdString e = sstr.str(); |
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| 114 | throw CNetCdfException(e); |
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| 115 | } |
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[498] | 116 | |
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[525] | 117 | return status; |
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| 118 | } |
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[498] | 119 | |
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[525] | 120 | /*! |
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| 121 | This function closes a netcdf file, given its id |
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| 122 | \param [in] ncId id of the opening netcdf file |
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| 123 | \return Status code |
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| 124 | */ |
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| 125 | int CNetCdfInterface::close(int ncId) |
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| 126 | { |
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| 127 | int status = nc_close(ncId); |
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| 128 | if (NC_NOERR != status) |
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| 129 | { |
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| 130 | StdString errormsg(nc_strerror(status)); |
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| 131 | StdStringStream sstr; |
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| 132 | sstr << "Error in calling function " << "nc_close(ncId)" << std::endl |
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[498] | 133 | << errormsg << std::endl |
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[525] | 134 | << "Unable to close file, given its id : " << ncId << std::endl; |
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| 135 | StdString e = sstr.str(); |
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| 136 | throw CNetCdfException(e); |
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| 137 | } |
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[498] | 138 | |
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[525] | 139 | return status; |
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| 140 | } |
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[498] | 141 | |
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[525] | 142 | /*! |
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| 143 | This function put a netcdf file into define mode, given its id |
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| 144 | \param [in] ncId id of the opening netcdf file to be put into define mode |
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| 145 | \return Status code |
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| 146 | */ |
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| 147 | int CNetCdfInterface::reDef(int ncId) |
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| 148 | { |
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| 149 | int status = nc_redef(ncId); |
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| 150 | if (NC_NOERR != status) |
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| 151 | { |
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| 152 | StdString errormsg(nc_strerror(status)); |
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| 153 | StdStringStream sstr; |
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| 154 | sstr << "Error in calling function " << "nc_redef(ncId)" << std::endl |
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| 155 | << errormsg << std::endl |
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| 156 | << "Unable to put this file into define mode given its id : " << ncId << std::endl; |
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| 157 | StdString e = sstr.str(); |
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| 158 | throw CNetCdfException(e); |
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| 159 | } |
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[498] | 160 | |
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[525] | 161 | return status; |
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| 162 | } |
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[498] | 163 | |
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[525] | 164 | /*! |
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| 165 | This function ends a netcdf file define mode, given its id |
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| 166 | \param [in] ncId id of the opening netcdf file to be put into define mode |
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| 167 | \return Status code |
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| 168 | */ |
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| 169 | int CNetCdfInterface::endDef(int ncId) |
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| 170 | { |
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| 171 | int status = nc_enddef(ncId); |
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| 172 | if (NC_NOERR != status) |
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| 173 | { |
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| 174 | StdString errormsg(nc_strerror(status)); |
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| 175 | StdStringStream sstr; |
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[498] | 176 | |
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[525] | 177 | sstr << "Error in calling function " << "nc_enddef(ncId)" << std::endl |
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| 178 | << errormsg << std::endl |
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| 179 | << "Unable to end define mode of this file, given its id : " << ncId << std::endl; |
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| 180 | StdString e = sstr.str(); |
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| 181 | throw CNetCdfException(e); |
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| 182 | } |
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[498] | 183 | |
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[525] | 184 | return status; |
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| 185 | } |
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[498] | 186 | |
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[525] | 187 | /*! |
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| 188 | This function makes a request to netcdf with ncid and group name then return ncid of the named group |
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| 189 | \param [in] ncid Groupd id (or File Id) |
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| 190 | \param [in] grpName Name of the desired group (or file) |
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| 191 | \param [in/out] grpId Group id if the group is found |
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| 192 | \return Status code |
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| 193 | */ |
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| 194 | int CNetCdfInterface::inqNcId(int ncid, const StdString& grpName, int& grpId) |
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| 195 | { |
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| 196 | int status = nc_inq_ncid(ncid, (grpName.c_str()), &grpId); |
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| 197 | if (NC_NOERR != status) |
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| 198 | { |
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| 199 | StdString errormsg(nc_strerror(status)); |
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| 200 | StdStringStream sstr; |
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[498] | 201 | |
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[525] | 202 | sstr << "Error in calling function " << "nc_inq_ncid(ncid, (grpName.c_str()), &grpId)" << std::endl |
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| 203 | << errormsg << std::endl |
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| 204 | << "Unable to get id of a group (File), given its name : " << grpName << std::endl; |
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| 205 | StdString e = sstr.str(); |
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| 206 | throw CNetCdfException(e); |
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| 207 | } |
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[498] | 208 | |
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[525] | 209 | return status; |
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| 210 | } |
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[498] | 211 | |
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| 212 | |
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[525] | 213 | /*! |
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| 214 | This function makes a request to netcdf with ncid and variable name then return ncid of the named variable |
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| 215 | \param [in] ncid Groupd id (or File Id) |
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| 216 | \param [in] varName Name of the desired variable |
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| 217 | \param [in/out] varId Variable id if this variable is found |
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| 218 | \return Status code |
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| 219 | */ |
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| 220 | int CNetCdfInterface::inqVarId(int ncid,const StdString& varName, int& varId) |
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| 221 | { |
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| 222 | int status = nc_inq_varid(ncid, (varName.c_str()), &varId); |
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| 223 | if (NC_NOERR != status) |
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| 224 | { |
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| 225 | StdString errormsg(nc_strerror(status)); |
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| 226 | StdStringStream sstr; |
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[498] | 227 | |
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[525] | 228 | sstr << "Error in calling function : nc_inq_varid(ncid, (varName.c_str()), &varId)" << std::endl |
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| 229 | << (errormsg) << std::endl |
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| 230 | << "Unable to get id of variable with name : " << varName << std::endl; |
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| 231 | StdString e = sstr.str(); |
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| 232 | throw CNetCdfException(e); |
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| 233 | } |
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[498] | 234 | |
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[525] | 235 | return status; |
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| 236 | } |
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[498] | 237 | |
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[525] | 238 | /*! |
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| 239 | This function makes a request to netcdf with a netCdf dimension name then return ncid of the named dimension |
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| 240 | \param [in] ncid Groupd id (or File Id) |
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| 241 | \param [in] dimName Name of the desired dimension |
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| 242 | \param [in/out] dimId Dimension id if this dimension is found |
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| 243 | \return Status code |
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| 244 | */ |
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| 245 | int CNetCdfInterface::inqDimId(int ncid,const StdString& dimName, int& dimId) |
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| 246 | { |
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| 247 | int status = nc_inq_dimid(ncid, (dimName.c_str()), &dimId); |
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| 248 | if (NC_NOERR != status) |
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| 249 | { |
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| 250 | StdString errormsg(nc_strerror(status)); |
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| 251 | StdStringStream sstr; |
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[498] | 252 | |
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[525] | 253 | sstr << "Error in calling function " << "nc_inq_dimid(ncid, (dimName.c_str()), &dimId)" << std::endl |
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[498] | 254 | << errormsg << std::endl |
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[525] | 255 | << "Unable to get id of dimension, given its name : " << dimName << std::endl; |
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| 256 | StdString e = sstr.str(); |
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| 257 | throw CNetCdfException(e); |
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| 258 | } |
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[498] | 259 | |
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[525] | 260 | return status; |
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| 261 | } |
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[498] | 262 | |
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[525] | 263 | /*! |
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| 264 | This function makes a request to netcdf with a netCdf dimension name then return ncid of the named dimension |
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| 265 | \param [in] ncid Groupd id (or File Id) |
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| 266 | \param [in/out] dimId Dimension id if this dimension is found |
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| 267 | \return Status code |
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| 268 | */ |
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| 269 | int CNetCdfInterface::inqUnLimDim(int ncid, int& dimId) |
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| 270 | { |
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| 271 | int status = nc_inq_unlimdim(ncid, &dimId); |
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| 272 | if (NC_NOERR != status) |
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| 273 | { |
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| 274 | StdString errormsg(nc_strerror(status)); |
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| 275 | StdStringStream sstr; |
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[498] | 276 | |
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[525] | 277 | sstr << "Error in calling function " << "nc_inq_dimid" << std::endl |
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| 278 | << errormsg << std::endl |
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| 279 | << "Unable to get id of unlimited dimension " << std::endl; |
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| 280 | StdString e = sstr.str(); |
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| 281 | throw CNetCdfException(e); |
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| 282 | } |
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[498] | 283 | |
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[525] | 284 | return status; |
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| 285 | } |
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[498] | 286 | |
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[525] | 287 | /*! |
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| 288 | This function makes a request to netcdf, returns name of a dimension, given its id |
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| 289 | \param [in] ncid Groupd id (or File Id) |
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| 290 | \param [in] dimId Id of desired dimension |
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| 291 | \param [in/out] dimName Name of desired dimension |
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| 292 | \return Status code |
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| 293 | */ |
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| 294 | int CNetCdfInterface::inqDimName(int ncid, int dimId, StdString& dimName) |
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| 295 | { |
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| 296 | char fullNameIn[NC_MAX_NAME +1]; |
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| 297 | int status = nc_inq_dimname(ncid, dimId, fullNameIn); |
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| 298 | if (NC_NOERR != status) |
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| 299 | { |
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| 300 | StdString errormsg(nc_strerror(status)); |
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| 301 | StdStringStream sstr; |
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[498] | 302 | |
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[525] | 303 | sstr << "Error in calling function " << "nc_inq_dimname(ncid, dimId, fullNameIn)" << std::endl |
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| 304 | << errormsg << std::endl |
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| 305 | << "Unable to get dimension name from its id : " << dimId << std::endl; |
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| 306 | StdString e = sstr.str(); |
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| 307 | throw CNetCdfException(e); |
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| 308 | } |
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| 309 | dimName = StdString(fullNameIn); |
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| 310 | return status; |
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| 311 | } |
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[498] | 312 | |
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[525] | 313 | /*! |
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| 314 | This function makes a request to netcdf, returns length of a dimension, given its id |
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| 315 | \param [in] ncid Groupd id (or File Id) |
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| 316 | \param [in] dimId Id of desired dimension |
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| 317 | \param [in/out] dimLen Length of desired dimension |
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| 318 | \return Status code |
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| 319 | */ |
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| 320 | int CNetCdfInterface::inqDimLen(int ncid, int dimId, StdSize& dimLen) |
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| 321 | { |
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| 322 | int status = nc_inq_dimlen(ncid, dimId, &dimLen); |
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| 323 | if (NC_NOERR != status) |
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| 324 | { |
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| 325 | StdString errormsg(nc_strerror(status)); |
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| 326 | StdStringStream sstr; |
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[498] | 327 | |
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[525] | 328 | sstr << "Error in calling function " << "nc_inq_dimlen(ncid, dimId, &dimLen)" << std::endl |
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| 329 | << errormsg << std::endl |
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| 330 | << "Unable to get dimension length from its id: " << dimId << std::endl; |
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| 331 | StdString e = sstr.str(); |
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| 332 | throw CNetCdfException(e); |
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| 333 | } |
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[498] | 334 | |
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[525] | 335 | return status; |
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| 336 | } |
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[498] | 337 | |
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[525] | 338 | /*! |
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| 339 | This function makes a request to netcdf, returns number of dimensions of a variable, given its id |
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| 340 | \param [in] ncid Groupd id (or File Id) |
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| 341 | \param [in] varId Id of variable |
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| 342 | \param [in/out] ndims number of dimension of the variable |
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| 343 | \return Status code |
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| 344 | */ |
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| 345 | int CNetCdfInterface::inqVarNDims(int ncid, int varId, int& nDims) |
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| 346 | { |
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| 347 | int status = nc_inq_varndims(ncid, varId, &nDims); |
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| 348 | if (NC_NOERR != status) |
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| 349 | { |
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| 350 | StdString errormsg(nc_strerror(status)); |
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| 351 | StdStringStream sstr; |
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[498] | 352 | |
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[525] | 353 | sstr << "Error in calling function " << "nc_inq_varndims(ncid, varId, &nDims)" << std::endl |
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| 354 | << errormsg << std::endl |
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| 355 | << "Unable to get the number of dimension of variable with Id : " << varId << std::endl; |
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| 356 | StdString e = sstr.str(); |
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| 357 | throw CNetCdfException(e); |
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| 358 | } |
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[498] | 359 | |
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[525] | 360 | return status; |
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| 361 | } |
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[498] | 362 | |
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[525] | 363 | /*! |
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| 364 | This function makes a request to netcdf, returns a list of dimension ID describing the shape of the variable, given its id |
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| 365 | \param [in] ncid Groupd id (or File Id) |
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| 366 | \param [in] varId Id of variable |
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| 367 | \param [in/out] dimIds list of dimension of the variable |
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| 368 | \return Status code |
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| 369 | */ |
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| 370 | int CNetCdfInterface::inqVarDimId(int ncid, int varId, int* dimIds) |
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| 371 | { |
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| 372 | int status = nc_inq_vardimid(ncid, varId, dimIds); |
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| 373 | if (NC_NOERR != status) |
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| 374 | { |
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| 375 | StdString errormsg(nc_strerror(status)); |
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| 376 | StdStringStream sstr; |
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[498] | 377 | |
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[525] | 378 | sstr << "Error in calling function " << "nc_inq_vardimid(ncid, varId, dimIds)" << std::endl |
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| 379 | << errormsg << std::endl |
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| 380 | << "Unable to get list of dimension id of the variable with id " << varId << std::endl; |
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| 381 | StdString e = sstr.str(); |
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| 382 | throw CNetCdfException(e); |
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| 383 | } |
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[498] | 384 | |
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[525] | 385 | return status; |
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| 386 | } |
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[498] | 387 | |
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[525] | 388 | /*! |
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| 389 | This function makes a request to netcdf, to find all dimension in a group |
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| 390 | \param [in] ncid Groupd id (or File Id) |
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| 391 | \param [in/out] nDims number of list of dimension |
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| 392 | \param [in/out] dimIds list of dimension in a group or any of its parent |
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| 393 | \param [in] includeParents number of parents |
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| 394 | \return Status code |
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| 395 | */ |
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| 396 | int CNetCdfInterface::inqDimIds(int ncid, int& nDims, int* dimIds, int includeParents) |
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| 397 | { |
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| 398 | int status = nc_inq_dimids(ncid, &nDims, dimIds, includeParents); |
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| 399 | if (NC_NOERR != status) |
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| 400 | { |
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| 401 | StdString errormsg(nc_strerror(status)); |
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| 402 | StdStringStream sstr; |
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[498] | 403 | |
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[525] | 404 | sstr << "Error in calling function " << "nc_inq_dimids(ncid, &nDims, dimIds, includeParents)" << std::endl; |
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| 405 | sstr << errormsg << std::endl; |
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| 406 | sstr << "Unable to retrieve number of dimension in the group with id : " << ncid << std::endl; |
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| 407 | sstr << "With number of Parents " << includeParents << std::endl; |
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| 408 | StdString e = sstr.str(); |
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| 409 | throw CNetCdfException(e); |
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| 410 | } |
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[498] | 411 | |
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[525] | 412 | return status; |
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| 413 | } |
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[498] | 414 | |
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[525] | 415 | /*! |
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| 416 | This function makes a request to netcdf with a id of a prent groupd and then return id of the created group, given its name |
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| 417 | \param [in] parentNcid Id of parent groupd(or File Id) |
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| 418 | \param [in] grpName Name of the desired group |
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| 419 | \param [in/out] grpId Group id if this group is created sucessfully |
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| 420 | \return Status code |
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| 421 | */ |
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| 422 | int CNetCdfInterface::defGrp(int parentNcid, const StdString& grpName, int& grpId) |
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| 423 | { |
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| 424 | int status = nc_def_grp(parentNcid, (grpName.c_str()), &grpId); |
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| 425 | if (NC_NOERR != status) |
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| 426 | { |
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| 427 | StdString errormsg(nc_strerror(status)); |
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| 428 | StdStringStream sstr; |
---|
[498] | 429 | |
---|
[525] | 430 | sstr << "Error in calling function " << "nc_def_grp(parentNcid, (grpName.c_str()), &grpId)" << std::endl; |
---|
| 431 | sstr << errormsg << std::endl; |
---|
| 432 | sstr << "Unable to create group Id, given its name : " << grpName << std::endl; |
---|
| 433 | StdString e = sstr.str(); |
---|
| 434 | throw CNetCdfException(e); |
---|
| 435 | } |
---|
[498] | 436 | |
---|
[525] | 437 | return status; |
---|
| 438 | } |
---|
[498] | 439 | |
---|
[525] | 440 | /*! |
---|
| 441 | This function makes a request to netcdf, add a new dimension to an open netcdf in define mode |
---|
| 442 | \param [in] ncid Id of groupd(or File Id) |
---|
| 443 | \param [in] dimName Name of the desired dimension |
---|
| 444 | \param [in/out] grpId Group id if this group is created sucessfully |
---|
| 445 | \return Status code |
---|
| 446 | */ |
---|
| 447 | int CNetCdfInterface::defDim(int ncid, const StdString& dimName, StdSize dimLen, int& dimId) |
---|
| 448 | { |
---|
| 449 | int status = nc_def_dim(ncid, (dimName.c_str()), dimLen, &dimId); |
---|
| 450 | if (NC_NOERR != status) |
---|
| 451 | { |
---|
| 452 | StdString errormsg(nc_strerror(status)); |
---|
| 453 | StdStringStream sstr; |
---|
[498] | 454 | |
---|
[525] | 455 | sstr << "Error in calling function " << "nc_def_dim(ncid, (dimName.c_str()), dimLen, &dimId)" << std::endl; |
---|
| 456 | sstr << errormsg << std::endl; |
---|
| 457 | sstr << "Unable to create dimension with name : " << dimName |
---|
| 458 | << " and with length " << dimLen << std::endl; |
---|
| 459 | StdString e = sstr.str(); |
---|
| 460 | throw CNetCdfException(e); |
---|
| 461 | } |
---|
[498] | 462 | |
---|
[525] | 463 | return status; |
---|
| 464 | } |
---|
[498] | 465 | |
---|
[525] | 466 | /*! |
---|
| 467 | This function makes a request to netcdf with its id, to add a new variable to an open netCdf in define mode, |
---|
| 468 | return a variable id, given its name, type, the number of dimensions and list of dimension id |
---|
| 469 | \param [in] ncid Id of groupd(or File Id) |
---|
| 470 | \param [in] varName Name of the desired dimension |
---|
| 471 | \param [in] xtypes One of the set of predefined netCDF data types |
---|
| 472 | \param [in] nDims Number of dimension for the variable |
---|
| 473 | \param [in] dimIds List of ndims dimension ids corresponding to the variable dimensions |
---|
| 474 | \param [in/out] varId Variable id if it is added sucessfully |
---|
| 475 | \return Status code |
---|
| 476 | */ |
---|
| 477 | int CNetCdfInterface::defVar(int ncid,const StdString& varName, nc_type xtype, |
---|
| 478 | int nDims, const int dimIds[], int& varId) |
---|
| 479 | { |
---|
| 480 | int status = nc_def_var(ncid, (varName.c_str()), xtype, nDims, dimIds, &varId); |
---|
| 481 | if (NC_NOERR != status) |
---|
| 482 | { |
---|
| 483 | StdString errormsg(nc_strerror(status)); |
---|
| 484 | StdStringStream sstr; |
---|
[498] | 485 | |
---|
[525] | 486 | sstr << "Error in calling function " << " nc_def_var(ncid, (varName.c_str()), xtype, nDims, dimIds, &varId)" << std::endl; |
---|
| 487 | sstr << errormsg << std::endl; |
---|
| 488 | sstr << "Unable to add a new variable with name : " << varName |
---|
| 489 | << " with type " << xtype |
---|
| 490 | << " and number of dimension " << nDims << std::endl; |
---|
| 491 | StdString e = sstr.str(); |
---|
| 492 | throw CNetCdfException(e); |
---|
| 493 | } |
---|
[498] | 494 | |
---|
[525] | 495 | return status; |
---|
| 496 | } |
---|
[498] | 497 | |
---|
[525] | 498 | /*! |
---|
| 499 | This function makes a request to netcdf with a ncid, to set the chunking size of a variable, |
---|
| 500 | given variable id and type of storage |
---|
| 501 | \param [in] ncid Id groupd(or File Id) |
---|
| 502 | \param [in] varId Id of the variable |
---|
| 503 | \param [in] storage Type of storage (It can be : NC_CONTIGUOUS, NC_CHUNKED) |
---|
| 504 | \param [in/out] chunkSize array list of chunk sizes |
---|
| 505 | \return Status code |
---|
| 506 | */ |
---|
| 507 | int CNetCdfInterface::defVarChunking(int ncid, int varId, int storage, StdSize chunkSize[]) |
---|
| 508 | { |
---|
| 509 | int status = nc_def_var_chunking(ncid, varId, storage, chunkSize); |
---|
| 510 | if (NC_NOERR != status) |
---|
[517] | 511 | { |
---|
[525] | 512 | StdString errormsg(nc_strerror(status)); |
---|
| 513 | StdStringStream sstr; |
---|
[517] | 514 | |
---|
[525] | 515 | sstr << "Error in calling function " << "nc_def_var_chunking(ncid, varId, storage, chunkSize)" << std::endl; |
---|
| 516 | sstr << errormsg << std::endl; |
---|
| 517 | sstr << "Unable to set chunk size of the variable with id : " << varId |
---|
| 518 | << " and storage type " << storage << std::endl; |
---|
| 519 | StdString e = sstr.str(); |
---|
| 520 | throw CNetCdfException(e); |
---|
[517] | 521 | } |
---|
| 522 | |
---|
[525] | 523 | return status; |
---|
| 524 | } |
---|
[498] | 525 | |
---|
[525] | 526 | /*! |
---|
[606] | 527 | This function sets the compression level to the specified variable |
---|
| 528 | \param [in] ncid Groud id (or file id) |
---|
| 529 | \param [in] varId Id of the variable |
---|
| 530 | \param [in] compressionLevel The compression level from 0 to 9 (0 disables the compression, 9 is the higher compression) |
---|
| 531 | \return Status code |
---|
| 532 | */ |
---|
| 533 | int CNetCdfInterface::defVarDeflate(int ncid, int varId, int compressionLevel) |
---|
| 534 | { |
---|
| 535 | int status = nc_def_var_deflate(ncid, varId, false, (compressionLevel > 0), compressionLevel); |
---|
| 536 | if (NC_NOERR != status) |
---|
| 537 | { |
---|
| 538 | StdString errormsg(nc_strerror(status)); |
---|
| 539 | StdStringStream sstr; |
---|
| 540 | |
---|
| 541 | sstr << "Error in calling function " << "nc_def_var_deflate(ncid, varId, false, (compressionLevel > 0), compressionLevel)" << std::endl; |
---|
| 542 | sstr << errormsg << std::endl; |
---|
| 543 | sstr << "Unable to set the compression level of the variable with id: " << varId |
---|
| 544 | << " and compression level: " << compressionLevel << std::endl; |
---|
| 545 | StdString e = sstr.str(); |
---|
| 546 | throw CNetCdfException(e); |
---|
| 547 | } |
---|
| 548 | |
---|
| 549 | return status; |
---|
| 550 | } |
---|
| 551 | |
---|
| 552 | /*! |
---|
[525] | 553 | Set or unset the fill mode for a NetCDF file specified by its file id. |
---|
| 554 | \param [in] ncid File id |
---|
| 555 | \param [in] fill Define whether the fill mode should be enabled or not |
---|
| 556 | \return Status code |
---|
| 557 | */ |
---|
| 558 | int CNetCdfInterface::setFill(int ncid, bool fill) |
---|
| 559 | { |
---|
| 560 | int old_fill_mode; |
---|
| 561 | int status = nc_set_fill(ncid, fill ? NC_FILL : NC_NOFILL, &old_fill_mode); |
---|
| 562 | if (NC_NOERR != status) |
---|
| 563 | { |
---|
| 564 | StdString errormsg(nc_strerror(status)); |
---|
| 565 | StdStringStream sstr; |
---|
[498] | 566 | |
---|
[525] | 567 | sstr << "Error when calling function nc_set_fill(ncid, fill ? NC_FILL : NC_NOFILL, &old_fill_mode)" << std::endl; |
---|
| 568 | sstr << errormsg << std::endl; |
---|
| 569 | sstr << "Unable to set the fill mode to : " << (fill ? "NC_FILL" : "NC_NOFILL") << std::endl; |
---|
| 570 | StdString e = sstr.str(); |
---|
| 571 | throw CNetCdfException(e); |
---|
| 572 | } |
---|
[498] | 573 | |
---|
[525] | 574 | return status; |
---|
| 575 | } |
---|
[498] | 576 | |
---|
[525] | 577 | /*! |
---|
| 578 | This function makes a request to netcdf with a ncid, to set the fill parameters for a variable, |
---|
| 579 | given variable id and type of fill |
---|
| 580 | \param [in] ncid Id groupd(or File Id) |
---|
| 581 | \param [in] varId Id of the variable |
---|
| 582 | \param [in] noFill turn on/off nofill mode on a variable |
---|
| 583 | \param [in/out] fillValue |
---|
| 584 | \return Status code |
---|
| 585 | */ |
---|
| 586 | int CNetCdfInterface::defVarFill(int ncid, int varId, int noFill, void* fillValue) |
---|
| 587 | { |
---|
| 588 | int status = nc_def_var_fill(ncid, varId, noFill, fillValue); |
---|
| 589 | if (NC_NOERR != status) |
---|
| 590 | { |
---|
| 591 | StdString errormsg(nc_strerror(status)); |
---|
| 592 | StdStringStream sstr; |
---|
[498] | 593 | |
---|
[525] | 594 | sstr << "Error in calling function " << "nc_def_var_fill(ncid, varId, noFill, fillValue)" << std::endl; |
---|
| 595 | sstr << errormsg << std::endl; |
---|
| 596 | sstr << "Unable to set fill parameters of the variable with id : " << varId |
---|
| 597 | << " and fill option " << noFill << std::endl; |
---|
| 598 | StdString e = sstr.str(); |
---|
| 599 | throw CNetCdfException(e); |
---|
| 600 | } |
---|
[498] | 601 | |
---|
[525] | 602 | return status; |
---|
| 603 | } |
---|
[498] | 604 | |
---|
[525] | 605 | /*! |
---|
| 606 | This function makes a request to netcdf with a ncid, to change the way read/write operations are performed |
---|
| 607 | collectively or independently on the variable. |
---|
| 608 | \param [in] ncid Id groupd(or File Id) |
---|
| 609 | \param [in] varId Id of the variable |
---|
| 610 | \param [in] noFill turn on/off nofill mode on a variable |
---|
| 611 | \param [in/out] fillValue |
---|
| 612 | \return Status code |
---|
| 613 | */ |
---|
| 614 | int CNetCdfInterface::varParAccess(int ncid, int varId, int access) |
---|
| 615 | { |
---|
| 616 | int status = nc_var_par_access(ncid, varId, access); |
---|
| 617 | if (NC_NOERR != status) |
---|
| 618 | { |
---|
| 619 | StdString errormsg(nc_strerror(status)); |
---|
| 620 | StdStringStream sstr; |
---|
[498] | 621 | |
---|
[525] | 622 | sstr << "Error in calling function " << "nc_var_par_access(ncid, varId, access)" << std::endl; |
---|
| 623 | sstr << errormsg << std::endl; |
---|
| 624 | sstr << "Unable to change read/write option of the variable with id : " << varId << std::endl; |
---|
| 625 | StdString e = sstr.str(); |
---|
| 626 | throw CNetCdfException(e); |
---|
| 627 | } |
---|
[498] | 628 | |
---|
[525] | 629 | return status; |
---|
| 630 | } |
---|
[498] | 631 | |
---|
[525] | 632 | /*! |
---|
| 633 | This function makes a synchronisation of the disk copy of a netCDF dataset. |
---|
| 634 | \param [in] ncid Id groupd(or File Id) |
---|
| 635 | \return Status code |
---|
| 636 | */ |
---|
| 637 | int CNetCdfInterface::sync(int ncid) |
---|
| 638 | { |
---|
| 639 | int status = nc_sync(ncid); |
---|
| 640 | if (NC_NOERR != status) |
---|
[498] | 641 | { |
---|
[525] | 642 | StdString errormsg(nc_strerror(status)); |
---|
| 643 | StdStringStream sstr; |
---|
[498] | 644 | |
---|
[525] | 645 | sstr << "Error in calling function " << "nc_sync(ncid)" << std::endl; |
---|
| 646 | sstr << errormsg << std::endl; |
---|
| 647 | sstr << "Unable to make a synchronization of a netCDF file with id : " << ncid << std::endl; |
---|
| 648 | StdString e = sstr.str(); |
---|
| 649 | throw CNetCdfException(e); |
---|
[498] | 650 | } |
---|
| 651 | |
---|
[525] | 652 | return status; |
---|
| 653 | } |
---|
[498] | 654 | |
---|
[525] | 655 | /*! |
---|
| 656 | This function makes a request to netcdf with its id, to add or change a variable attribute or gloabl attribute, |
---|
| 657 | given its name, type, number of values provided for attribute |
---|
| 658 | \param [in] ncid Id of groupd(or File Id) |
---|
| 659 | \param [in] varId Id of the variable |
---|
| 660 | \param [in] attrName Name of the attribute |
---|
| 661 | \param [in] xtypes One of the set of predefined netCDF data types |
---|
| 662 | \param [in] numVal Number of values |
---|
| 663 | \param [in] op Array of values provided for attribute |
---|
| 664 | \return Status code |
---|
| 665 | */ |
---|
| 666 | int CNetCdfInterface::putAtt(int ncid, int varId, const StdString& attrName, nc_type xtype, |
---|
| 667 | StdSize numVal, const void* op) |
---|
| 668 | { |
---|
| 669 | int status = nc_put_att(ncid, varId, (attrName.c_str()), xtype, numVal, op); |
---|
| 670 | if (NC_NOERR != status) |
---|
[498] | 671 | { |
---|
[525] | 672 | StdString errormsg(nc_strerror(status)); |
---|
| 673 | StdStringStream sstr; |
---|
[498] | 674 | |
---|
[525] | 675 | sstr << "Error in calling function " << "nc_put_att(ncid, varId, (attrName.c_str()), xtype, numVal, op)" << std::endl; |
---|
| 676 | sstr << errormsg << std::endl; |
---|
| 677 | sstr << "Unable to set attribute " << attrName << " for a variable with id : " << varId |
---|
| 678 | << " with number of attribute " << numVal |
---|
| 679 | << " with type " << xtype << std::endl; |
---|
| 680 | StdString e = sstr.str(); |
---|
| 681 | throw CNetCdfException(e); |
---|
[498] | 682 | } |
---|
| 683 | |
---|
[525] | 684 | return status; |
---|
| 685 | } |
---|
[498] | 686 | |
---|
[525] | 687 | // Some specilization of putAttributeType |
---|
| 688 | template<> |
---|
| 689 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
| 690 | StdSize numVal, const double* op) |
---|
| 691 | { |
---|
| 692 | return (nc_put_att_double(ncid, varid, attrName, NC_DOUBLE, numVal, op)); |
---|
| 693 | } |
---|
[498] | 694 | |
---|
[525] | 695 | template<> |
---|
| 696 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
| 697 | StdSize numVal, const float* op) |
---|
| 698 | { |
---|
| 699 | return (nc_put_att_float(ncid, varid, attrName, NC_FLOAT, numVal, op)); |
---|
| 700 | } |
---|
[498] | 701 | |
---|
[525] | 702 | template<> |
---|
| 703 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
| 704 | StdSize numVal, const int* op) |
---|
| 705 | { |
---|
| 706 | return (nc_put_att_int(ncid, varid, attrName, NC_INT, numVal, op)); |
---|
| 707 | } |
---|
[498] | 708 | |
---|
[525] | 709 | template<> |
---|
| 710 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
| 711 | StdSize numVal, const long* op) |
---|
| 712 | { |
---|
| 713 | return (nc_put_att_long(ncid, varid, attrName, NC_LONG, numVal, op)); |
---|
| 714 | } |
---|
[498] | 715 | |
---|
[525] | 716 | template<> |
---|
| 717 | int CNetCdfInterface::ncPutAttType(int ncid, int varid, const char* attrName, |
---|
| 718 | StdSize numVal, const short* op) |
---|
| 719 | { |
---|
| 720 | return (nc_put_att_short(ncid, varid, attrName, NC_SHORT, numVal, op)); |
---|
| 721 | } |
---|
| 722 | |
---|
| 723 | |
---|
| 724 | // Some specilization of putVariableType |
---|
| 725 | template<> |
---|
| 726 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const double* op) |
---|
| 727 | { |
---|
| 728 | return (nc_put_vara_double(ncid, varid, start, count, op)); |
---|
| 729 | } |
---|
| 730 | |
---|
| 731 | template<> |
---|
| 732 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const float* op) |
---|
| 733 | { |
---|
| 734 | return (nc_put_vara_float(ncid, varid, start, count, op)); |
---|
| 735 | } |
---|
| 736 | |
---|
| 737 | template<> |
---|
| 738 | int CNetCdfInterface::ncPutVaraType(int ncid, int varid, const StdSize* start, const StdSize* count, const int* op) |
---|
| 739 | { |
---|
| 740 | return (nc_put_vara_int(ncid, varid, start, count, op)); |
---|
| 741 | } |
---|
| 742 | |
---|
| 743 | /*! |
---|
| 744 | This function verifies an existence of a variable by using its name. |
---|
| 745 | Be careful, althoug false means variable doens't exist, it could show that netCDF file doesn't either |
---|
| 746 | \param [in] ncid Id of groupd(or File Id) |
---|
| 747 | \param [in] attrName Name of the variable |
---|
| 748 | \return Existence of variable |
---|
| 749 | */ |
---|
| 750 | bool CNetCdfInterface::isVarExisted(int ncId, const StdString& varName) |
---|
| 751 | { |
---|
| 752 | int varId = 0; |
---|
| 753 | return (NC_NOERR == (nc_inq_varid(ncId, varName.c_str(), &varId))); |
---|
| 754 | } |
---|
| 755 | |
---|
| 756 | StdString CNetCdfInterface::openMode2String(int oMode) |
---|
| 757 | { |
---|
| 758 | StdString modeMes; |
---|
| 759 | switch (oMode) |
---|
[498] | 760 | { |
---|
[525] | 761 | case NC_NOWRITE: |
---|
| 762 | modeMes = StdString("NC_NOWRITE : Opening netCDF file with read-only access with buffering and caching access"); |
---|
| 763 | break; |
---|
| 764 | case NC_SHARE: |
---|
| 765 | modeMes = StdString("NC_SHARE : Several processes can read the file concurrently"); |
---|
| 766 | break; |
---|
| 767 | case NC_WRITE: |
---|
| 768 | modeMes = StdString("NC_WRITE : NetCDF file is readable and writable"); |
---|
| 769 | break; |
---|
| 770 | default: |
---|
| 771 | modeMes = StdString("In the composed opening mode"); |
---|
| 772 | break; |
---|
[578] | 773 | } |
---|
[525] | 774 | return modeMes; |
---|
| 775 | } |
---|
[498] | 776 | |
---|
[525] | 777 | StdString CNetCdfInterface::creationMode2String(int cMode) |
---|
| 778 | { |
---|
| 779 | StdString modeMes; |
---|
| 780 | switch (cMode) |
---|
[498] | 781 | { |
---|
[525] | 782 | case NC_NOCLOBBER: |
---|
| 783 | modeMes = StdString("NC_NOCLOBBER : Not overwrite an exisiting netCDF file "); |
---|
| 784 | break; |
---|
| 785 | case NC_SHARE: |
---|
| 786 | modeMes = StdString("NC_SHARE : Several processes can read from and write into the file concurrently"); |
---|
| 787 | break; |
---|
| 788 | case NC_64BIT_OFFSET: |
---|
| 789 | modeMes = StdString("NC_64BIT_OFFSET : NetCDF file is 64-bit offset"); |
---|
| 790 | break; |
---|
| 791 | case NC_NETCDF4: |
---|
| 792 | modeMes = StdString("NC_NETCDF4 : NetCDF file is HDF5/NetCDF-4"); |
---|
| 793 | break; |
---|
| 794 | case NC_CLASSIC_MODEL: |
---|
| 795 | modeMes = StdString("NC_CLASSIC_MODEL : NetCDF file is classical model"); |
---|
| 796 | break; |
---|
| 797 | default: |
---|
| 798 | modeMes = StdString("In the composed creation mode"); |
---|
| 799 | break; |
---|
[578] | 800 | } |
---|
[525] | 801 | return modeMes; |
---|
| 802 | } |
---|
[498] | 803 | |
---|
[525] | 804 | } |
---|