#ifdef HAVE_CONFIG_H #include "config.h" #endif #ifdef HAVE_LIBNETCDF #include "dmemory.h" #include "cdi.h" #include "cdi_int.h" #include "stream_cdf.h" #include "cdf.h" #include "cdf_int.h" #include "vlist.h" #include "vlist_var.h" void cdfDefVarDeflate(int ncid, int ncvarid, int deflate_level) { #if defined(HAVE_NETCDF4) int retval; /* Set chunking, shuffle, and deflate. */ int shuffle = 1; int deflate = 1; if ( deflate_level < 1 || deflate_level > 9 ) deflate_level = 1; if ( (retval = nc_def_var_deflate(ncid, ncvarid, shuffle, deflate, deflate_level)) ) { Error("nc_def_var_deflate failed, status = %d", retval); } #else static bool lwarn = true; if ( lwarn ) { lwarn = false; Warning("Deflate compression failed, NetCDF4 not available!"); } #endif } int cdfDefDatatype(int datatype, int filetype) { int xtype = NC_FLOAT; if ( datatype == CDI_DATATYPE_CPX32 || datatype == CDI_DATATYPE_CPX64 ) Error("CDI/NetCDF library does not support complex numbers!"); if ( filetype == CDI_FILETYPE_NC4 ) { if ( datatype == CDI_DATATYPE_INT8 ) xtype = NC_BYTE; else if ( datatype == CDI_DATATYPE_INT16 ) xtype = NC_SHORT; else if ( datatype == CDI_DATATYPE_INT32 ) xtype = NC_INT; #if defined (HAVE_NETCDF4) else if ( datatype == CDI_DATATYPE_UINT8 ) xtype = NC_UBYTE; else if ( datatype == CDI_DATATYPE_UINT16 ) xtype = NC_USHORT; else if ( datatype == CDI_DATATYPE_UINT32 ) xtype = NC_UINT; #else else if ( datatype == CDI_DATATYPE_UINT8 ) xtype = NC_SHORT; else if ( datatype == CDI_DATATYPE_UINT16 ) xtype = NC_INT; else if ( datatype == CDI_DATATYPE_UINT32 ) xtype = NC_INT; #endif else if ( datatype == CDI_DATATYPE_FLT64 ) xtype = NC_DOUBLE; else xtype = NC_FLOAT; } else { if ( datatype == CDI_DATATYPE_INT8 ) xtype = NC_BYTE; else if ( datatype == CDI_DATATYPE_INT16 ) xtype = NC_SHORT; else if ( datatype == CDI_DATATYPE_INT32 ) xtype = NC_INT; else if ( datatype == CDI_DATATYPE_UINT8 ) xtype = NC_SHORT; else if ( datatype == CDI_DATATYPE_UINT16 ) xtype = NC_INT; else if ( datatype == CDI_DATATYPE_UINT32 ) xtype = NC_INT; else if ( datatype == CDI_DATATYPE_FLT64 ) xtype = NC_DOUBLE; else xtype = NC_FLOAT; } return xtype; } static void cdfDefVarMissval(stream_t *streamptr, int varID, int dtype, int lcheck) { if ( streamptr->vars[varID].defmiss == false ) { int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; int ncvarid = streamptr->vars[varID].ncvarid; double missval = vlistInqVarMissval(vlistID, varID); if ( lcheck && streamptr->ncmode == 2 ) cdf_redef(fileID); int xtype = cdfDefDatatype(dtype, streamptr->filetype); if ( xtype == NC_BYTE && missval > 127 && missval < 256 ) xtype = NC_INT; if ( lcheck == 0 || streamptr->ncmode != 2 || streamptr->filetype == CDI_FILETYPE_NC || streamptr->filetype == CDI_FILETYPE_NC2 ) cdf_put_att_double(fileID, ncvarid, "_FillValue", (nc_type) xtype, 1, &missval); cdf_put_att_double(fileID, ncvarid, "missing_value", (nc_type) xtype, 1, &missval); if ( lcheck && streamptr->ncmode == 2 ) cdf_enddef(fileID); streamptr->vars[varID].defmiss = true; } } static void cdfDefInstitut(stream_t *streamptr) { int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; int instID = vlistInqInstitut(vlistID); if ( instID != CDI_UNDEFID ) { const char *longname = institutInqLongnamePtr(instID); if ( longname ) { size_t len = strlen(longname); if ( len > 0 ) { if ( streamptr->ncmode == 2 ) cdf_redef(fileID); cdf_put_att_text(fileID, NC_GLOBAL, "institution", len, longname); if ( streamptr->ncmode == 2 ) cdf_enddef(fileID); } } } } static void cdfDefSource(stream_t *streamptr) { int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; int modelID = vlistInqModel(vlistID); if ( modelID != CDI_UNDEFID ) { const char *longname = modelInqNamePtr(modelID); if ( longname ) { size_t len = strlen(longname); if ( len > 0 ) { if ( streamptr->ncmode == 2 ) cdf_redef(fileID); cdf_put_att_text(fileID, NC_GLOBAL, "source", len, longname); if ( streamptr->ncmode == 2 ) cdf_enddef(fileID); } } } } static inline void *resizeBuf(void **buf, size_t *bufSize, size_t reqSize) { if ( reqSize > *bufSize ) { *buf = Realloc(*buf, reqSize); *bufSize = reqSize; } return *buf; } void cdfDefineAttributes(int cdiID, int varID, int fileID, int ncvarID) { int atttype, attlen; size_t len; char attname[CDI_MAX_NAME+1]; void *attBuf = NULL; size_t attBufSize = 0; int natts; cdiInqNatts(cdiID, varID, &natts); for ( int iatt = 0; iatt < natts; ++iatt ) { cdiInqAtt(cdiID, varID, iatt, attname, &atttype, &attlen); if ( attlen == 0 ) continue; if ( atttype == CDI_DATATYPE_TXT ) { size_t attSize = (size_t)attlen*sizeof(char); char *atttxt = (char *)resizeBuf(&attBuf, &attBufSize, attSize); cdiInqAttTxt(cdiID, varID, attname, attlen, atttxt); len = (size_t)attlen; cdf_put_att_text(fileID, ncvarID, attname, len, atttxt); } else if ( atttype == CDI_DATATYPE_INT8 || atttype == CDI_DATATYPE_UINT8 || atttype == CDI_DATATYPE_INT16 || atttype == CDI_DATATYPE_UINT16 || atttype == CDI_DATATYPE_INT32 || atttype == CDI_DATATYPE_UINT32 ) { size_t attSize = (size_t)attlen*sizeof(int); int *attint = (int *)resizeBuf(&attBuf, &attBufSize, attSize); cdiInqAttInt(cdiID, varID, attname, attlen, &attint[0]); len = (size_t)attlen; nc_type xtype = (atttype == CDI_DATATYPE_INT8) ? NC_BYTE : (atttype == CDI_DATATYPE_INT16) ? NC_SHORT : #if defined (HAVE_NETCDF4) (atttype == CDI_DATATYPE_UINT8) ? NC_UBYTE : (atttype == CDI_DATATYPE_UINT16) ? NC_USHORT : (atttype == CDI_DATATYPE_UINT32) ? NC_UINT : #endif NC_INT; cdf_put_att_int(fileID, ncvarID, attname, xtype, len, attint); } else if ( atttype == CDI_DATATYPE_FLT32 || atttype == CDI_DATATYPE_FLT64 ) { size_t attSize = (size_t)attlen * sizeof(double); double *attflt = (double *)resizeBuf(&attBuf, &attBufSize, attSize); cdiInqAttFlt(cdiID, varID, attname, attlen, attflt); len = (size_t)attlen; if ( atttype == CDI_DATATYPE_FLT32 ) { float attflt_sp[len]; for ( size_t i = 0; i < len; ++i ) attflt_sp[i] = (float)attflt[i]; cdf_put_att_float(fileID, ncvarID, attname, NC_FLOAT, len, attflt_sp); } else cdf_put_att_double(fileID, ncvarID, attname, NC_DOUBLE, len, attflt); } } Free(attBuf); } static void cdfDefGlobalAtts(stream_t *streamptr) { if ( streamptr->globalatts ) return; int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; cdfDefSource(streamptr); cdfDefInstitut(streamptr); int natts; cdiInqNatts(vlistID, CDI_GLOBAL, &natts); if ( natts > 0 && streamptr->ncmode == 2 ) cdf_redef(fileID); cdfDefineAttributes(vlistID, CDI_GLOBAL, fileID, NC_GLOBAL); if ( natts > 0 && streamptr->ncmode == 2 ) cdf_enddef(fileID); streamptr->globalatts = 1; } static void cdfDefLocalAtts(stream_t *streamptr) { int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; if ( streamptr->localatts ) return; if ( vlistInqInstitut(vlistID) != CDI_UNDEFID ) return; streamptr->localatts = 1; if ( streamptr->ncmode == 2 ) cdf_redef(fileID); for ( int varID = 0; varID < streamptr->nvars; varID++ ) { int instID = vlistInqVarInstitut(vlistID, varID); if ( instID != CDI_UNDEFID ) { int ncvarid = streamptr->vars[varID].ncvarid; const char *name = institutInqNamePtr(instID); if ( name ) { size_t len = strlen(name); cdf_put_att_text(fileID, ncvarid, "institution", len, name); } } } if ( streamptr->ncmode == 2 ) cdf_enddef(fileID); } static void cdf_get_gmapvarname(int gridID, char *gmapvarname) { int pgridID = gridID; char mapping[CDI_MAX_NAME]; mapping[0] = 0; cdiGridInqKeyStr(pgridID, CDI_KEY_MAPNAME, CDI_MAX_NAME, mapping); if ( !mapping[0] ) { int projID = gridInqProj(gridID); if ( projID != CDI_UNDEFID ) { pgridID = projID; cdiGridInqKeyStr(pgridID, CDI_KEY_MAPNAME, CDI_MAX_NAME, mapping); } } if ( mapping[0] ) cdiGridInqKeyStr(pgridID, CDI_KEY_MAPPING, CDI_MAX_NAME, gmapvarname); } static int nc_grid_index(stream_t *streamptr, int gridID) { int index = 0; int vlistID = streamptr->vlistID; int ngrids = vlistNgrids(vlistID); for ( index = 0; index < ngrids; ++index ) if ( streamptr->ncgrid[index].gridID == gridID ) break; assert(index < ngrids); return index; } static int cdfDefVar(stream_t *streamptr, int varID) { int ncvarid = -1; int xid = CDI_UNDEFID, yid = CDI_UNDEFID; size_t xsize = 0, ysize = 0; int dims[4]; size_t chunks[4] = {0,0,0,0}; int ndims = 0; int tablenum; int dimorder[3]; size_t iax = 0; char axis[5]; int ensID, ensCount, forecast_type; int fileID = streamptr->fileID; if ( CDI_Debug ) Message("streamID = %d, fileID = %d, varID = %d", streamptr->self, fileID, varID); if ( streamptr->vars[varID].ncvarid != CDI_UNDEFID ) return streamptr->vars[varID].ncvarid; int vlistID = streamptr->vlistID; int gridID = vlistInqVarGrid(vlistID, varID); int zaxisID = vlistInqVarZaxis(vlistID, varID); int tsteptype = vlistInqVarTsteptype(vlistID, varID); int code = vlistInqVarCode(vlistID, varID); int param = vlistInqVarParam(vlistID, varID); int pnum, pcat, pdis; cdiDecodeParam(param, &pnum, &pcat, &pdis); int chunktype = vlistInqVarChunkType(vlistID, varID); vlistInqVarDimorder(vlistID, varID, &dimorder); size_t gridsize = (size_t)(gridInqSize(gridID)); bool lchunk = (gridsize >= 16); int gridtype = gridInqType(gridID); int gridindex = nc_grid_index(streamptr, gridID); if ( gridtype != GRID_TRAJECTORY ) { xid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_X]; yid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_Y]; if ( xid != CDI_UNDEFID ) cdf_inq_dimlen(fileID, xid, &xsize); if ( yid != CDI_UNDEFID ) cdf_inq_dimlen(fileID, yid, &ysize); } int zaxisindex = vlistZaxisIndex(vlistID, zaxisID); int zid = streamptr->zaxisID[zaxisindex]; bool zaxis_is_scalar = false; if ( zid == CDI_UNDEFID ) zaxis_is_scalar = zaxisInqScalar(zaxisID) > 0; if ( dimorder[0] != 3 ) lchunk = false; /* ZYX and ZXY */ if ( ((dimorder[0]>0)+(dimorder[1]>0)+(dimorder[2]>0)) < ((xid!=CDI_UNDEFID)+(yid!=CDI_UNDEFID)+(zid!=CDI_UNDEFID)) ) { printf("zid=%d yid=%d xid=%d\n", zid, yid, xid); Error("Internal problem, dimension order missing!"); } int tid = streamptr->basetime.ncdimid; if ( !CDI_reduce_dim && tsteptype != TSTEP_CONSTANT ) { if ( tid == CDI_UNDEFID ) Error("Internal problem, time undefined!"); chunks[ndims] = 1; dims[ndims++] = tid; axis[iax++] = 'T'; } /* if ( zid != CDI_UNDEFID ) axis[iax++] = 'Z'; if ( zid != CDI_UNDEFID ) chunks[ndims] = 1; if ( zid != CDI_UNDEFID ) dims[ndims++] = zid; if ( yid != CDI_UNDEFID ) chunks[ndims] = ysize; if ( yid != CDI_UNDEFID ) dims[ndims++] = yid; if ( xid != CDI_UNDEFID ) chunks[ndims] = xsize; if ( xid != CDI_UNDEFID ) dims[ndims++] = xid; */ size_t chunk_size_max = 65536; for ( int id = 0; id < 3; ++id ) { if ( dimorder[id] == 3 && zid != CDI_UNDEFID ) { axis[iax++] = 'Z'; chunks[ndims] = 1; dims[ndims] = zid; ndims++; } else if ( dimorder[id] == 2 && yid != CDI_UNDEFID ) { if ( chunktype == CDI_CHUNK_AUTO ) chunks[ndims] = (chunk_size_max > gridsize) ? ysize : chunk_size_max/xsize; else chunks[ndims] = (chunktype == CDI_CHUNK_LINES) ? 1 : ysize; dims[ndims] = yid; ndims++; } else if ( dimorder[id] == 1 && xid != CDI_UNDEFID ) { if ( chunktype == CDI_CHUNK_AUTO && yid == CDI_UNDEFID ) chunks[ndims] = (chunk_size_max > xsize) ? xsize : chunk_size_max; else chunks[ndims] = xsize; dims[ndims] = xid; ndims++; } } if ( CDI_Debug ) fprintf(stderr, "chunktype %d chunks %d %d %d %d\n", chunktype, (int)chunks[0], (int)chunks[1], (int)chunks[2], (int)chunks[3]); char varname[CDI_MAX_NAME]; char name[CDI_MAX_NAME]; name[0] = 0; char longname[CDI_MAX_NAME]; longname[0] = 0; char stdname[CDI_MAX_NAME]; stdname[0] = 0; char units[CDI_MAX_NAME]; units[0] = 0; if ( vlistInqVarNamePtr(vlistID, varID) ) vlistInqVarName(vlistID, varID, name); vlistInqVarLongname(vlistID, varID, longname); vlistInqVarStdname(vlistID, varID, stdname); vlistInqVarUnits(vlistID, varID, units); int tableID = vlistInqVarTable(vlistID, varID); if ( !name[0] ) tableInqEntry(tableID, code, -1, name, longname, units); if ( name[0] ) { sprintf(varname, "%s", name); bool checkname = true; int iz = 0; while ( checkname ) { if ( iz ) sprintf(varname, "%s_%d", name, iz+1); int status = nc_inq_varid(fileID, varname, &ncvarid); if ( status != NC_NOERR ) checkname = false; if ( checkname ) iz++; if ( iz >= CDI_MAX_NAME ) Error("Double entry of variable name '%s'!", name); } if ( strcmp(name, varname) != 0 ) { if ( iz == 1 ) Warning("Changed double entry of variable name '%s' to '%s'!", name, varname); else Warning("Changed multiple entry of variable name '%s' to '%s'!", name, varname); } strcpy(name, varname); } else { if ( code < 0 ) code = -code; if ( pnum < 0 ) pnum = -pnum; if ( pdis == 255 ) sprintf(varname, "var%d", code); else sprintf(varname, "param%d.%d.%d", pnum, pcat, pdis); char *varname2 = varname+strlen(varname); bool checkname = true; int iz = 0; while ( checkname ) { if ( iz ) sprintf(varname2, "_%d", iz+1); int status = nc_inq_varid(fileID, varname, &ncvarid); if ( status != NC_NOERR ) checkname = false; if ( checkname ) iz++; if ( iz >= CDI_MAX_NAME ) break; } strcpy(name, varname); code = 0; pdis = 255; } /* if ( streamptr->ncmode == 2 ) cdf_redef(fileID); */ int dtype = vlistInqVarDatatype(vlistID, varID); int xtype = cdfDefDatatype(dtype, streamptr->filetype); cdf_def_var(fileID, name, (nc_type) xtype, ndims, dims, &ncvarid); #if defined (HAVE_NETCDF4) if ( lchunk && (streamptr->filetype == CDI_FILETYPE_NC4 || streamptr->filetype == CDI_FILETYPE_NC4C) ) cdf_def_var_chunking(fileID, ncvarid, NC_CHUNKED, chunks); #endif if ( streamptr->comptype == CDI_COMPRESS_ZIP ) { if ( lchunk && (streamptr->filetype == CDI_FILETYPE_NC4 || streamptr->filetype == CDI_FILETYPE_NC4C) ) { cdfDefVarDeflate(fileID, ncvarid, streamptr->complevel); } else { if ( lchunk ) { static bool lwarn = true; if ( lwarn ) { lwarn = false; Warning("Deflate compression is only available for NetCDF4!"); } } } } if ( *stdname ) cdf_put_att_text(fileID, ncvarid, "standard_name", strlen(stdname), stdname); if ( *longname ) cdf_put_att_text(fileID, ncvarid, "long_name", strlen(longname), longname); if ( *units ) cdf_put_att_text(fileID, ncvarid, "units", strlen(units), units); if ( code > 0 && pdis == 255 ) cdf_put_att_int(fileID, ncvarid, "code", NC_INT, 1, &code); if ( pdis != 255 ) { char paramstr[32]; cdiParamToString(param, paramstr, sizeof(paramstr)); cdf_put_att_text(fileID, ncvarid, "param", strlen(paramstr), paramstr); } if ( tableID != CDI_UNDEFID ) { tablenum = tableInqNum(tableID); if ( tablenum > 0 ) cdf_put_att_int(fileID, ncvarid, "table", NC_INT, 1, &tablenum); } char coordinates[CDI_MAX_NAME]; coordinates[0] = 0; if ( zaxis_is_scalar || zaxisInqType(zaxisID) == ZAXIS_CHAR ) { int nczvarID = streamptr->nczvarID[zaxisindex]; if ( nczvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, nczvarID, coordinates+len); } } if ( gridtype != GRID_GENERIC && gridtype != GRID_LONLAT && gridtype != GRID_GAUSSIAN && gridtype != GRID_PROJECTION && gridtype != GRID_CURVILINEAR && gridtype != GRID_CHARXY ) { size_t len = strlen(gridNamePtr(gridtype)); if ( len > 0 ) cdf_put_att_text(fileID, ncvarid, "CDI_grid_type", len, gridNamePtr(gridtype)); } char gmapvarname[CDI_MAX_NAME]; gmapvarname[0] = 0; cdf_get_gmapvarname(gridID, gmapvarname); if ( gmapvarname[0] ) cdf_put_att_text(fileID, ncvarid, "grid_mapping", strlen(gmapvarname), gmapvarname); if ( gridtype == GRID_TRAJECTORY ) { cdf_put_att_text(fileID, ncvarid, "coordinates", 9, "tlon tlat" ); } else if ( gridtype == GRID_LONLAT && xid == CDI_UNDEFID && yid == CDI_UNDEFID && gridsize == 1 ) { int ncxvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_X]; int ncyvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_Y]; if ( ncyvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncyvarID, coordinates+len); } if ( ncxvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncxvarID, coordinates+len); } } else if ( gridtype == GRID_UNSTRUCTURED || gridtype == GRID_CURVILINEAR ) { char cellarea[CDI_MAX_NAME] = "area: "; int ncxvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_X]; int ncyvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_Y]; int ncavarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_A]; // CMOR order: coordinates = "lat lon" if ( cdiCoordinatesLonLat ) { if ( ncxvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncxvarID, coordinates+len); } if ( ncyvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncyvarID, coordinates+len); } } else { if ( ncyvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncyvarID, coordinates+len); } if ( ncxvarID != CDI_UNDEFID ) { size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncxvarID, coordinates+len); } } if ( ncavarID != CDI_UNDEFID ) { size_t len = strlen(cellarea); cdf_inq_varname(fileID, ncavarID, cellarea+len); len = strlen(cellarea); cdf_put_att_text(fileID, ncvarid, "cell_measures", len, cellarea); } if ( gridtype == GRID_UNSTRUCTURED ) { int position = gridInqPosition(gridID); if ( position > 0 ) cdf_put_att_int(fileID, ncvarid, "number_of_grid_in_reference", NC_INT, 1, &position); } } else if ( gridtype == GRID_SPECTRAL || gridtype == GRID_FOURIER ) { int gridTruncation = gridInqTrunc(gridID); axis[iax++] = '-'; axis[iax++] = '-'; cdf_put_att_text(fileID, ncvarid, "axis", iax, axis); cdf_put_att_int(fileID, ncvarid, "truncation", NC_INT, 1, &gridTruncation); } else if ( gridtype == GRID_CHARXY ) { if ( gridInqXIsc(gridID) ) { int ncxvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_X]; size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncxvarID, coordinates+len); } else if ( gridInqYIsc(gridID) ) { int ncyvarID = streamptr->ncgrid[gridindex].ncIDs[CDF_VARID_Y]; size_t len = strlen(coordinates); if ( len ) coordinates[len++] = ' '; cdf_inq_varname(fileID, ncyvarID, coordinates+len); } } size_t len = strlen(coordinates); if ( len ) cdf_put_att_text(fileID, ncvarid, "coordinates", len, coordinates); /* if ( xtype == NC_BYTE || xtype == NC_SHORT || xtype == NC_INT ) */ { int astype = NC_DOUBLE; double addoffset = vlistInqVarAddoffset(vlistID, varID); double scalefactor = vlistInqVarScalefactor(vlistID, varID); bool laddoffset = IS_NOT_EQUAL(addoffset, 0); bool lscalefactor = IS_NOT_EQUAL(scalefactor, 1); if ( laddoffset || lscalefactor ) { if ( IS_EQUAL(addoffset, (double) ((float) addoffset)) && IS_EQUAL(scalefactor, (double) ((float) scalefactor)) ) { astype = NC_FLOAT; } if ( xtype == (int) NC_FLOAT ) astype = NC_FLOAT; cdf_put_att_double(fileID, ncvarid, "add_offset", (nc_type) astype, 1, &addoffset); cdf_put_att_double(fileID, ncvarid, "scale_factor", (nc_type) astype, 1, &scalefactor); } } if ( dtype == CDI_DATATYPE_UINT8 && xtype == NC_BYTE ) { int validrange[2] = {0, 255}; cdf_put_att_int(fileID, ncvarid, "valid_range", NC_SHORT, 2, validrange); cdf_put_att_text(fileID, ncvarid, "_Unsigned", 4, "true"); } streamptr->vars[varID].ncvarid = ncvarid; if ( vlistInqVarMissvalUsed(vlistID, varID) ) cdfDefVarMissval(streamptr, varID, vlistInqVarDatatype(vlistID, varID), 0); if ( zid == -1 ) { if ( zaxisInqType(zaxisID) == ZAXIS_CLOUD_BASE || zaxisInqType(zaxisID) == ZAXIS_CLOUD_TOP || zaxisInqType(zaxisID) == ZAXIS_ISOTHERM_ZERO || zaxisInqType(zaxisID) == ZAXIS_TOA || zaxisInqType(zaxisID) == ZAXIS_SEA_BOTTOM || zaxisInqType(zaxisID) == ZAXIS_LAKE_BOTTOM || zaxisInqType(zaxisID) == ZAXIS_SEDIMENT_BOTTOM || zaxisInqType(zaxisID) == ZAXIS_SEDIMENT_BOTTOM_TA || zaxisInqType(zaxisID) == ZAXIS_SEDIMENT_BOTTOM_TW || zaxisInqType(zaxisID) == ZAXIS_MIX_LAYER || zaxisInqType(zaxisID) == ZAXIS_ATMOSPHERE ) { zaxisInqName(zaxisID, varname); cdf_put_att_text(fileID, ncvarid, "level_type", strlen(varname), varname); } } if ( vlistInqVarEnsemble( vlistID, varID, &ensID, &ensCount, &forecast_type ) ) { /* void cdf_put_att_int( int ncid, int varid, const char *name, nc_type xtype, size_t len, const int *ip ) */ cdf_put_att_int(fileID, ncvarid, "realization", NC_INT, 1, &ensID); cdf_put_att_int(fileID, ncvarid, "ensemble_members", NC_INT, 1, &ensCount); cdf_put_att_int(fileID, ncvarid, "forecast_init_type", NC_INT, 1, &forecast_type); } /* Attributes */ cdfDefineAttributes(vlistID, varID, fileID, ncvarid); /* if ( streamptr->ncmode == 2 ) cdf_enddef(fileID); */ return ncvarid; } void cdfEndDef(stream_t *streamptr) { cdfDefGlobalAtts(streamptr); cdfDefLocalAtts(streamptr); if ( streamptr->accessmode == 0 ) { int fileID = streamptr->fileID; if ( streamptr->ncmode == 2 ) cdf_redef(fileID); int nvars = streamptr->nvars; for ( int varID = 0; varID < nvars; varID++ ) cdfDefVar(streamptr, varID); if ( streamptr->ncmode == 2 ) { if ( CDI_netcdf_hdr_pad == 0UL ) cdf_enddef(fileID); else cdf__enddef(fileID, CDI_netcdf_hdr_pad); } streamptr->accessmode = 1; } } static void cdfWriteGridTraj(stream_t *streamptr, int gridID) { int gridindex = nc_grid_index(streamptr, gridID); int lonID = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_X]; int latID = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_Y]; double xlon = gridInqXval(gridID, 0); double xlat = gridInqYval(gridID, 0); int tsID = streamptr->curTsID; size_t index = (size_t)tsID; int fileID = streamptr->fileID; cdf_put_var1_double(fileID, lonID, &index, &xlon); cdf_put_var1_double(fileID, latID, &index, &xlat); } static void cdf_write_var_data(int fileID, int vlistID, int varID, int ncvarid, int dtype, size_t nvals, size_t xsize, size_t ysize, bool swapxy, size_t *start, size_t *count, int memtype, const void *data, int nmiss) { const double *pdata_dp = (const double *) data; double *mdata_dp = NULL; double *sdata_dp = NULL; const float *pdata_sp = (const float *) data; float *mdata_sp = NULL; float *sdata_sp = NULL; /* if ( dtype == CDI_DATATYPE_INT8 || dtype == CDI_DATATYPE_INT16 || dtype == CDI_DATATYPE_INT32 ) */ { double missval = vlistInqVarMissval(vlistID, varID); double addoffset = vlistInqVarAddoffset(vlistID, varID); double scalefactor = vlistInqVarScalefactor(vlistID, varID); bool laddoffset = IS_NOT_EQUAL(addoffset, 0); bool lscalefactor = IS_NOT_EQUAL(scalefactor, 1); if ( laddoffset || lscalefactor ) { if ( memtype == MEMTYPE_FLOAT ) { mdata_sp = (float *) Malloc(nvals*sizeof(float)); memcpy(mdata_sp, pdata_sp, nvals*sizeof(float)); pdata_sp = mdata_sp; if ( nmiss > 0 ) { for ( size_t i = 0; i < nvals; i++ ) { double temp = mdata_sp[i]; if ( !DBL_IS_EQUAL(temp, missval) ) { if ( laddoffset ) temp -= addoffset; if ( lscalefactor ) temp /= scalefactor; mdata_sp[i] = (float)temp; } } } else { for ( size_t i = 0; i < nvals; i++ ) { double temp = mdata_sp[i]; if ( laddoffset ) temp -= addoffset; if ( lscalefactor ) temp /= scalefactor; mdata_sp[i] = (float)temp; } } } else { mdata_dp = (double *) Malloc(nvals*sizeof(double)); memcpy(mdata_dp, pdata_dp, nvals*sizeof(double)); pdata_dp = mdata_dp; if ( nmiss > 0 ) { for ( size_t i = 0; i < nvals; i++ ) { if ( !DBL_IS_EQUAL(mdata_dp[i], missval) ) { if ( laddoffset ) mdata_dp[i] -= addoffset; if ( lscalefactor ) mdata_dp[i] /= scalefactor; } } } else { for ( size_t i = 0; i < nvals; i++ ) { if ( laddoffset ) mdata_dp[i] -= addoffset; if ( lscalefactor ) mdata_dp[i] /= scalefactor; } } } } if ( dtype == CDI_DATATYPE_UINT8 || dtype == CDI_DATATYPE_INT8 || dtype == CDI_DATATYPE_INT16 || dtype == CDI_DATATYPE_INT32 ) { if ( memtype == MEMTYPE_FLOAT ) { if ( mdata_sp == NULL ) { mdata_sp = (float *) Malloc(nvals*sizeof(float)); memcpy(mdata_sp, pdata_sp, nvals*sizeof(float)); pdata_sp = mdata_sp; } for ( size_t i = 0; i < nvals; i++ ) mdata_sp[i] = roundf(mdata_sp[i]); if ( dtype == CDI_DATATYPE_UINT8 ) { nc_type xtype; cdf_inq_vartype(fileID, ncvarid, &xtype); if ( xtype == NC_BYTE ) { for ( size_t i = 0; i < nvals; ++i ) if ( mdata_sp[i] > 127 ) mdata_sp[i] -= 256; } } } else { if ( mdata_dp == NULL ) { mdata_dp = (double *) Malloc(nvals*sizeof(double)); memcpy(mdata_dp, pdata_dp, nvals*sizeof(double)); pdata_dp = mdata_dp; } for ( size_t i = 0; i < nvals; i++ ) mdata_dp[i] = round(mdata_dp[i]); if ( dtype == CDI_DATATYPE_UINT8 ) { nc_type xtype; cdf_inq_vartype(fileID, ncvarid, &xtype); if ( xtype == NC_BYTE ) { for ( size_t i = 0; i < nvals; ++i ) if ( mdata_dp[i] > 127 ) mdata_dp[i] -= 256; } } } } if ( CDF_Debug && memtype != MEMTYPE_FLOAT ) { double fmin = 1.0e200; double fmax = -1.0e200; for ( size_t i = 0; i < nvals; ++i ) { if ( !DBL_IS_EQUAL(pdata_dp[i], missval) ) { if ( pdata_dp[i] < fmin ) fmin = pdata_dp[i]; if ( pdata_dp[i] > fmax ) fmax = pdata_dp[i]; } } Message("nvals = %zu, nmiss = %d, missval = %g, minval = %g, maxval = %g", nvals, nmiss, missval, fmin, fmax); } } if ( swapxy ) // implemented only for cdf_write_var_slice() { size_t gridsize = xsize*ysize; if ( memtype == MEMTYPE_FLOAT ) { sdata_sp = (float *) Malloc(gridsize*sizeof(float)); for ( size_t j = 0; j < ysize; ++j ) for ( size_t i = 0; i < xsize; ++i ) sdata_sp[i*ysize+j] = pdata_sp[j*xsize+i]; pdata_sp = sdata_sp; } else { sdata_dp = (double *) Malloc(gridsize*sizeof (double)); for ( size_t j = 0; j < ysize; ++j ) for ( size_t i = 0; i < xsize; ++i ) sdata_dp[i*ysize+j] = pdata_dp[j*xsize+i]; pdata_dp = sdata_dp; } } if ( memtype == MEMTYPE_FLOAT ) cdf_put_vara_float(fileID, ncvarid, start, count, pdata_sp); else cdf_put_vara_double(fileID, ncvarid, start, count, pdata_dp); if ( mdata_dp ) Free(mdata_dp); if ( sdata_dp ) Free(sdata_dp); if ( mdata_sp ) Free(mdata_sp); if ( sdata_sp ) Free(sdata_sp); } void cdf_write_var(stream_t *streamptr, int varID, int memtype, const void *data, int nmiss) { if ( streamptr->accessmode == 0 ) cdfEndDef(streamptr); // if ( streamptr->ncmode == 0 ) { cdfEndDef(streamptr); streamptr->ncmode = 2; } size_t xsize = 0, ysize = 0; size_t size; size_t start[5]; size_t count[5]; bool swapxy = false; size_t ndims = 0; if ( CDI_Debug ) Message("streamID = %d varID = %d", streamptr->self, varID); int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; long ntsteps = streamptr->ntsteps; if ( CDI_Debug ) Message("ntsteps = %ld", ntsteps); if ( vlistHasTime(vlistID) ) cdfDefTime(streamptr); int ncvarid = cdfDefVar(streamptr, varID); int gridID = vlistInqVarGrid(vlistID, varID); int zaxisID = vlistInqVarZaxis(vlistID, varID); int tsteptype = vlistInqVarTsteptype(vlistID, varID); int xid = CDI_UNDEFID, yid = CDI_UNDEFID; if ( gridInqType(gridID) == GRID_TRAJECTORY ) { cdfWriteGridTraj(streamptr, gridID); } else { int gridindex = nc_grid_index(streamptr, gridID); xid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_X]; yid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_Y]; } int zaxisindex = vlistZaxisIndex(vlistID, zaxisID); int zid = streamptr->zaxisID[zaxisindex]; if ( tsteptype != TSTEP_CONSTANT ) { start[ndims] = (size_t)ntsteps - 1; count[ndims] = 1; ndims++; } if ( zid != CDI_UNDEFID ) { start[ndims] = 0; count[ndims] = (size_t)zaxisInqSize(zaxisID); ndims++; } if ( yid != CDI_UNDEFID ) { start[ndims] = 0; cdf_inq_dimlen(fileID, yid, &size); /* count[ndims] = gridInqYsize(gridID); */ count[ndims] = size; ndims++; } if ( xid != CDI_UNDEFID ) { start[ndims] = 0; cdf_inq_dimlen(fileID, xid, &size); /* count[ndims] = gridInqXsize(gridID); */ count[ndims] = size; ndims++; } if ( CDI_Debug ) for (size_t idim = 0; idim < ndims; idim++) Message("dim = %d start = %d count = %d", idim, start[idim], count[idim]); if ( streamptr->ncmode == 1 ) { cdf_enddef(fileID); streamptr->ncmode = 2; } int dtype = vlistInqVarDatatype(vlistID, varID); if ( nmiss > 0 ) cdfDefVarMissval(streamptr, varID, dtype, 1); size_t nvals = (size_t)(gridInqSize(gridID)) * (size_t)(zaxisInqSize(zaxisID)); cdf_write_var_data(fileID, vlistID, varID, ncvarid, dtype, nvals, xsize, ysize, swapxy, start, count, memtype, data, nmiss); } void cdf_write_var_chunk(stream_t *streamptr, int varID, int memtype, const int rect[][2], const void *data, int nmiss) { if ( streamptr->accessmode == 0 ) cdfEndDef(streamptr); // if ( streamptr->ncmode == 0 ) { cdfEndDef(streamptr); streamptr->ncmode = 2; } int xid = CDI_UNDEFID, yid = CDI_UNDEFID; size_t xsize = 0, ysize = 0; size_t start[5]; size_t count[5]; bool swapxy = false; size_t ndims = 0; int streamID = streamptr->self; if ( CDI_Debug ) Message("streamID = %d varID = %d", streamID, varID); int vlistID = streamInqVlist(streamID); int fileID = streamInqFileID(streamID); long ntsteps = streamptr->ntsteps; if ( CDI_Debug ) Message("ntsteps = %ld", ntsteps); if ( vlistHasTime(vlistID) ) cdfDefTime(streamptr); int ncvarid = cdfDefVar(streamptr, varID); int gridID = vlistInqVarGrid(vlistID, varID); int zaxisID = vlistInqVarZaxis(vlistID, varID); int tsteptype = vlistInqVarTsteptype(vlistID, varID); if ( gridInqType(gridID) == GRID_TRAJECTORY ) { cdfWriteGridTraj(streamptr, gridID); } else { int gridindex = nc_grid_index(streamptr, gridID); xid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_X]; yid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_Y]; } int zaxisindex = vlistZaxisIndex(vlistID, zaxisID); int zid = streamptr->zaxisID[zaxisindex]; if ( tsteptype != TSTEP_CONSTANT ) { start[ndims] = (size_t)ntsteps - 1; count[ndims] = 1; ndims++; } if ( zid != CDI_UNDEFID ) { int size = zaxisInqSize(zaxisID); xassert(rect[2][0] >= 0 && rect[2][0] <= rect[2][1] && rect[2][1] <= size); start[ndims] = (size_t)rect[2][0]; count[ndims] = (size_t)rect[2][1] - (size_t)rect[2][0] + 1; ndims++; } if ( yid != CDI_UNDEFID ) { size_t size; cdf_inq_dimlen(fileID, yid, &size); xassert(rect[1][0] >= 0 && rect[1][0] <= rect[1][1] && (size_t)rect[1][1] <= size); start[ndims] = (size_t)rect[1][0]; count[ndims] = (size_t)rect[1][1] - (size_t)rect[1][0] + 1; ndims++; } if ( xid != CDI_UNDEFID ) { size_t size; cdf_inq_dimlen(fileID, xid, &size); xassert(rect[0][0] >= 0 && rect[0][0] <= rect[0][1] && (size_t)rect[0][1] <= size); start[ndims] = (size_t)rect[0][0]; count[ndims] = (size_t)rect[0][1] - (size_t)rect[0][0] + 1; ndims++; } if ( CDI_Debug ) for (size_t idim = 0; idim < ndims; idim++) Message("dim = %d start = %d count = %d", idim, start[idim], count[idim]); if ( streamptr->ncmode == 1 ) { cdf_enddef(fileID); streamptr->ncmode = 2; } int dtype = vlistInqVarDatatype(vlistID, varID); if ( nmiss > 0 ) cdfDefVarMissval(streamptr, varID, dtype, 1); size_t nvals = (size_t)(gridInqSize(gridID)) * (size_t)(zaxisInqSize(zaxisID)); cdf_write_var_data(fileID, vlistID, varID, ncvarid, dtype, nvals, xsize, ysize, swapxy, start, count, memtype, data, nmiss); } void cdf_write_var_slice(stream_t *streamptr, int varID, int levelID, int memtype, const void *data, int nmiss) { if ( streamptr->accessmode == 0 ) cdfEndDef(streamptr); // if ( streamptr->ncmode == 0 ) { streamptr->ncmode = 2; cdfEndDef(streamptr); } size_t xsize = 0, ysize = 0; size_t start[5]; size_t count[5]; int dimorder[3]; int xid = CDI_UNDEFID, yid = CDI_UNDEFID; if ( CDI_Debug ) Message("streamID = %d varID = %d", streamptr->self, varID); int vlistID = streamptr->vlistID; int fileID = streamptr->fileID; long ntsteps = streamptr->ntsteps; if ( CDI_Debug ) Message("ntsteps = %ld", ntsteps); if ( vlistHasTime(vlistID) ) cdfDefTime(streamptr); int ncvarid = cdfDefVar(streamptr, varID); int gridID = vlistInqVarGrid(vlistID, varID); int zaxisID = vlistInqVarZaxis(vlistID, varID); int tsteptype = vlistInqVarTsteptype(vlistID, varID); vlistInqVarDimorder(vlistID, varID, &dimorder); if ( gridInqType(gridID) == GRID_TRAJECTORY ) { cdfWriteGridTraj(streamptr, gridID); } else { int gridindex = nc_grid_index(streamptr, gridID); xid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_X]; yid = streamptr->ncgrid[gridindex].ncIDs[CDF_DIMID_Y]; } int zaxisindex = vlistZaxisIndex(vlistID, zaxisID); int zid = streamptr->zaxisID[zaxisindex]; bool swapxy = (dimorder[2] == 2 || dimorder[0] == 1) && xid != CDI_UNDEFID && yid != CDI_UNDEFID; size_t ndims = 0; if ( tsteptype != TSTEP_CONSTANT ) { start[ndims] = (size_t)ntsteps - 1; count[ndims] = 1; ndims++; } for ( int id = 0; id < 3; ++id ) { if ( dimorder[id] == 3 && zid != CDI_UNDEFID ) { start[ndims] = (size_t)levelID; count[ndims] = 1; ndims++; } else if ( dimorder[id] == 2 && yid != CDI_UNDEFID ) { start[ndims] = 0; cdf_inq_dimlen(fileID, yid, &ysize); count[ndims] = ysize; ndims++; } else if ( dimorder[id] == 1 && xid != CDI_UNDEFID ) { start[ndims] = 0; cdf_inq_dimlen(fileID, xid, &xsize); count[ndims] = xsize; ndims++; } } if ( CDI_Debug ) for (size_t idim = 0; idim < ndims; idim++) Message("dim = %d start = %d count = %d", idim, start[idim], count[idim]); int dtype = vlistInqVarDatatype(vlistID, varID); if ( nmiss > 0 ) cdfDefVarMissval(streamptr, varID, dtype, 1); size_t nvals = (size_t)(gridInqSize(gridID)); cdf_write_var_data(fileID, vlistID, varID, ncvarid, dtype, nvals, xsize, ysize, swapxy, start, count, memtype, data, nmiss); } void cdf_write_record(stream_t *streamptr, int memtype, const void *data, int nmiss) { int varID = streamptr->record->varID; int levelID = streamptr->record->levelID; cdf_write_var_slice(streamptr, varID, levelID, memtype, data, nmiss); } #endif /* * Local Variables: * c-file-style: "Java" * c-basic-offset: 2 * indent-tabs-mode: nil * show-trailing-whitespace: t * require-trailing-newline: t * End: */