/* \file \internal Variables for the diskless API. Copyright 2011, University Corporation for Atmospheric Research. See COPYRIGHT file for copying and redistribution conditions. */ #include #include "ncddispatch.h" #include /* Min and max deflate levels tolerated by HDF5. */ #define MIN_DEFLATE_LEVEL 0 #define MAX_DEFLATE_LEVEL 9 /* This is to track opened HDF5 objects to make sure they are * closed. */ #ifdef EXTRA_TESTS extern int num_plists; #endif /* EXTRA_TESTS */ /* One meg is the minimum buffer size. */ #define ONE_MEG 1048576 /* Szip options. */ #define NC_SZIP_EC_OPTION_MASK 4 #define NC_SZIP_NN_OPTION_MASK 32 #define NC_SZIP_MAX_PIXELS_PER_BLOCK 32 int nc4_get_default_fill_value(NC_TYPE_INFO_T *type_info, void *fill_value); /* Set chunk cache size for a variable. */ int NCD_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems, float preemption) { return NC_EINVAL; } /* Get chunk cache size for a variable. */ int NCD_get_var_chunk_cache(int ncid, int varid, size_t *sizep, size_t *nelemsp, float *preemptionp) { return NC_EINVAL; } /* Create a new variable to hold user data. This is what it's all * about baby! */ int NCD_def_var(int ncid, const char *name, nc_type xtype, int ndims, const int *dimidsp, int *varidp) { NC_FILE_INFO_T *nc; LOG((2, "NCD_def_var: ncid 0x%x name %s xtype %d ndims %d", ncid, name, xtype, ndims)); /* If there are dimensions, I need their ids. */ if (ndims && !dimidsp) return NC_EINVAL; /* Find metadata for this file. */ if (!(nc = nc4_find_nc_file(ncid))) return NC_EBADID; /* Netcdf-3 cases handled by dispatch layer. */ assert(nc->nc4_info); /* Handle netcdf-4 cases. */ { NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; NC_DIM_INFO_T *dim; NC_HDF5_FILE_INFO_T *h5; NC_TYPE_INFO_T *type_info; char norm_name[NC_MAX_NAME + 1]; int new_varid = 0; int num_unlim = 0; int d; size_t num_values = 1; int retval; /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_grp_h5(ncid, &grp, &h5))) return retval; assert(grp && h5); /* If it's not in define mode, strict nc3 files error out, * otherwise switch to define mode. */ if (!(h5->flags & NC_INDEF)) { if (h5->cmode & NC_CLASSIC_MODEL) return NC_ENOTINDEFINE; if ((retval = NCD_redef(ncid))) return retval; } /* Check and normalize the name. */ if ((retval = nc4_check_name(name, norm_name))) return retval; /* Not a Type is, well, not a type.*/ if (xtype == NC_NAT) return NC_EBADTYPE; /* For classic files, only classic types are allowed. */ if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE) return NC_ESTRICTNC3; /* If this is a user defined type, find it. */ if (xtype > NC_STRING) if ((retval = nc4_find_type(grp->file->nc4_info, xtype, &type_info))) return NC_EBADTYPE; /* cast needed for braindead systems with signed size_t */ if((unsigned long) ndims > X_INT_MAX) /* Backward compat */ return NC_EINVAL; /* Classic model files have a limit on number of vars. */ if(h5->cmode & NC_CLASSIC_MODEL && h5->nvars >= NC_MAX_VARS) return NC_EMAXVARS; /* Check that this name is not in use as a var, grp, or type. */ if ((retval = nc4_check_dup_name(grp, norm_name))) return retval; /* Get the new varid. */ for (var = grp->var; var; var = var->next) new_varid++; /* Check all the dimids to make sure they exist. */ for (d = 0; d < ndims; d++) { if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, NULL))) return retval; if (dim->unlimited) num_unlim++; else num_values *= dim->len; } /* These degrubbing messages sure are handy! */ LOG((3, "nc_def_var_nc4: name %s type %d ndims %d", norm_name, xtype, ndims)); #ifdef LOGGING { int dd; for (dd = 0; dd < ndims; dd++) LOG((4, "dimid[%d] %d", dd, dimidsp[dd])); } #endif /* Add the var to the end of the list. */ if ((retval = nc4_var_list_add(&grp->var, &var))) return retval; /* Now fill in the values in the var info structure. */ if (!(var->name = malloc((strlen(norm_name) + 1) * sizeof(char)))) return NC_ENOMEM; strcpy(var->name, norm_name); var->varid = grp->nvars++; var->xtype = xtype; var->ndims = ndims; var->dirty++; /* If this is a user-defined type, there is a type_info stuct with * all the type information. For atomic types, fake up a type_info * struct. */ if (xtype > NC_STRING) var->type_info = type_info; else { if (!(var->type_info = calloc(1, sizeof(NC_TYPE_INFO_T)))) return NC_ENOMEM; var->type_info->nc_typeid = xtype; if ((retval = nc4_get_hdf_typeid(h5, var->xtype, &var->type_info->hdf_typeid, var->type_info->endianness))) return retval; if ((var->type_info->native_typeid = H5Tget_native_type(var->type_info->hdf_typeid, H5T_DIR_DEFAULT)) < 0) return NC_EHDFERR; if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, &var->type_info->size))) return retval; } if (!num_unlim) var->contiguous = 1; /* Allocate space for dimension information. */ if (ndims) { if (!(var->dim = calloc(ndims, sizeof(NC_DIM_INFO_T *)))) return NC_ENOMEM; if (!(var->dimids = calloc(ndims, sizeof(int)))) return NC_ENOMEM; } /* Allocate space for the data. */ if (!(var->diskless_data = malloc(num_values * var->type_info->size))) return NC_ENOMEM; /* At the same time, check to see if this is a coordinate * variable. If so, it will have the same name as one of its * dimensions. If it is a coordinate var, is it a coordinate var in * the same group as the dim? */ for (d = 0; d < ndims; d++) { NC_GRP_INFO_T *dim_grp; if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp))) return retval; if (strcmp(dim->name, norm_name) == 0 && dim_grp == grp && d == 0) { var->dimscale++; dim->coord_var = var; dim->coord_var_in_grp++; } var->dimids[d] = dimidsp[d]; var->dim[d] = dim; } /* If the user names this variable the same as a dimension, but * doesn't use that dimension first in its list of dimension ids, * is not a coordinate variable. I need to change its HDF5 name, * because the dimension will cause a HDF5 dataset to be created, * and this var has the same name. */ for (dim = grp->dim; dim; dim = dim->next) if (!strcmp(dim->name, norm_name) && (!var->ndims || dimidsp[0] != dim->dimid)) { /* Set a different hdf5 name for this variable to avoid name * clash. */ if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME) return NC_EMAXNAME; if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) + strlen(norm_name) + 1) * sizeof(char)))) return NC_ENOMEM; sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name); } /* If this is a coordinate var, it is marked as a HDF5 dimension * scale. (We found dim above.) Otherwise, allocate space to * remember whether dimension scales have been attached to each * dimension. */ if (!var->dimscale && ndims) if (ndims && !(var->dimscale_attached = calloc(ndims, sizeof(int)))) return NC_ENOMEM; /* Return the varid. */ if (varidp) *varidp = var->varid; LOG((4, "new varid %d", var->varid)); } return NC_NOERR; } /* Get all the information about a variable. Pass NULL for whatever * you don't care about. This is an internal function, not exposed to * the user. */ int NCD_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp, int *shufflep, int *deflatep, int *deflate_levelp, int *fletcher32p, int *contiguousp, size_t *chunksizesp, int *no_fill, void *fill_valuep, int *endiannessp, int *options_maskp, int *pixels_per_blockp) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; NC_ATT_INFO_T *att; int natts=0; size_t type_size; int d; int retval; LOG((2, "nc_inq_var_all: ncid 0x%x varid %d", ncid, varid)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; assert(nc && grp && h5); /* Walk through the list of vars, and return the info about the one with a matching varid. If the varid is -1, find the global atts and call it a day. */ if (varid == NC_GLOBAL) { if (nattsp) { for (att = grp->att; att; att = att->next) natts++; *nattsp = natts; } return NC_NOERR; } /* Find the var. */ for (var = grp->var; var; var = var->next) if (var->varid == varid) break; /* Oh no! Maybe we couldn't find it (*sob*)! */ if (!var) return NC_ENOTVAR; /* Copy the data to the user's data buffers. */ if (name) strcpy(name, var->name); if (xtypep) *xtypep = var->xtype; if (ndimsp) *ndimsp = var->ndims; if (dimidsp) for (d = 0; d < var->ndims; d++) dimidsp[d] = var->dimids[d]; if (nattsp) { for (att = var->att; att; att = att->next) natts++; *nattsp = natts; } /* Chunking stuff. */ if (!var->contiguous && chunksizesp) for (d = 0; d < var->ndims; d++) { chunksizesp[d] = var->chunksizes[d]; LOG((4, "chunksizesp[%d]=%d", d, chunksizesp[d])); } if (contiguousp) *contiguousp = var->contiguous ? NC_CONTIGUOUS : NC_CHUNKED; /* Filter stuff. */ if (deflatep) *deflatep = var->deflate; if (deflate_levelp) *deflate_levelp = var->deflate_level; if (shufflep) *shufflep = var->shuffle; if (fletcher32p) *fletcher32p = var->fletcher32; if (options_maskp) *options_maskp = var->options_mask; if (pixels_per_blockp) *pixels_per_blockp = var->pixels_per_block; /* Fill value stuff. */ if (no_fill) *no_fill = var->no_fill; /* Don't do a thing with fill_valuep if no_fill mode is set for * this var, or if fill_valuep is NULL. */ if (!var->no_fill && fill_valuep) { /* Do we have a fill value for this var? */ if (var->fill_value) { if ((retval = nc4_get_typelen_mem(grp->file->nc4_info, var->xtype, 0, &type_size))) return retval; memcpy(fill_valuep, var->fill_value, type_size); } else { if ((retval = nc4_get_default_fill_value(var->type_info, fill_valuep))) return retval; } } /* Does the user want the endianness of this variable? */ if (endiannessp) *endiannessp = var->type_info->endianness; return NC_NOERR; } /* This functions sets extra stuff about a netCDF-4 variable which must be set before the enddef but after the def_var. This is an internal function, deliberately hidden from the user so that we can change the prototype of this functions without changing the API. */ static int nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate, int *deflate_level, int *fletcher32, int *contiguous, const size_t *chunksizes, int *no_fill, const void *fill_value, int *endianness, int *options_mask, int *pixels_per_block) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; NC_DIM_INFO_T *dim; size_t type_size; int d; int retval; LOG((2, "nc_def_var_extra: ncid 0x%x varid %d", ncid, varid)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; /* Attempting to do any of these things on a netCDF-3 file produces * an error. */ if (!h5) return NC_ENOTNC4; assert(nc && grp && h5); /* Find the var. */ for (var = grp->var; var; var = var->next) if (var->varid == varid) break; /* Oh no! Maybe we couldn't find it (*sob*)! */ if (!var) return NC_ENOTVAR; /* Can't turn on contiguous and deflate/fletcher32/szip. */ if (contiguous) if ((*contiguous != NC_CHUNKED && deflate) || (*contiguous != NC_CHUNKED && fletcher32) || (*contiguous != NC_CHUNKED && options_mask)) return NC_EINVAL; /* If the HDF5 dataset has already been created, then it is too * late to set all the extra stuff. */ if (var->created) return NC_ELATEDEF; /* Check compression options. */ if ((deflate && options_mask) || (deflate && !deflate_level) || (options_mask && !pixels_per_block)) return NC_EINVAL; /* Valid deflate level? */ if (deflate && deflate_level) { if (*deflate) if (*deflate_level < MIN_DEFLATE_LEVEL || *deflate_level > MAX_DEFLATE_LEVEL) return NC_EINVAL; if (var->options_mask) return NC_EINVAL; /* For scalars, just ignore attempt to deflate. */ if (!var->ndims) return NC_NOERR; /* Well, if we couldn't find any errors, I guess we have to take * the users settings. Darn! */ var->contiguous = 0; var->deflate = *deflate; if (*deflate) var->deflate_level = *deflate_level; LOG((3, "nc_def_var_extra: *deflate_level %d", *deflate_level)); } /* Szip in use? */ if (options_mask) { #ifndef USE_SZIP return NC_EINVAL; #endif if (var->deflate) return NC_EINVAL; if ((*options_mask != NC_SZIP_EC_OPTION_MASK) && (*options_mask != NC_SZIP_NN_OPTION_MASK)) return NC_EINVAL; if ((*pixels_per_block > NC_SZIP_MAX_PIXELS_PER_BLOCK) || (var->type_info->nc_typeid >= NC_STRING)) return NC_EINVAL; var->options_mask = *options_mask; var->pixels_per_block = *pixels_per_block; var->contiguous = 0; } /* Shuffle filter? */ if (shuffle) { var->shuffle = *shuffle; var->contiguous = 0; } /* Fltcher32 checksum error protection? */ if (fletcher32) { var->fletcher32 = *fletcher32; var->contiguous = 0; } /* Does the user want a contiguous dataset? Not so fast! Make sure * that there are no unlimited dimensions, and no filters in use * for this data. */ if (contiguous && *contiguous) { if (var->deflate || var->fletcher32 || var->shuffle || var->options_mask) return NC_EINVAL; for (d = 0; d < var->ndims; d++) { if ((retval = nc4_find_dim(grp, var->dimids[d], &dim, NULL))) return retval; if (dim->unlimited) return NC_EINVAL; } var->contiguous = NC_CONTIGUOUS; } /* Chunksizes anyone? */ if (contiguous && *contiguous == NC_CHUNKED) { var->contiguous = 0; } /* Are we setting a fill modes? */ if (no_fill) { if (*no_fill) var->no_fill = 1; else var->no_fill = 0; } /* Are we setting a fill value? */ if (fill_value && !var->no_fill) { /* If fill value hasn't been set, allocate space. */ if ((retval = nc4_get_typelen_mem(h5, var->xtype, 0, &type_size))) return retval; if (!var->fill_value) if (!(var->fill_value = malloc(type_size))) return NC_ENOMEM; /* Copy the fill_value. */ LOG((4, "Copying fill value into metadata for variable %s", var->name)); memcpy(var->fill_value, fill_value, type_size); /* If there's a _FillValue attribute, delete it. */ retval = nc_del_att(ncid, varid, _FillValue); if (retval && retval != NC_ENOTATT) return retval; /* Create a _FillValue attribute. */ if ((retval = nc_put_att(ncid, varid, _FillValue, var->xtype, 1, fill_value))) return retval; } /* Is the user setting the endianness? */ if (endianness) var->type_info->endianness = *endianness; return NC_NOERR; } /* Set the deflate level for a var, lower is faster, higher is * better. Must be called after nc_def_var and before nc_enddef or any * functions which writes data to the file. */ int NCD_def_var_deflate(int ncid, int varid, int shuffle, int deflate, int deflate_level) { return nc_def_var_extra(ncid, varid, &shuffle, &deflate, &deflate_level, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL); } /* Set checksum for a var. This must be called after the nc_def_var * but before the nc_enddef. */ int NCD_def_var_fletcher32(int ncid, int varid, int fletcher32) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, &fletcher32, NULL, NULL, NULL, NULL, NULL, NULL, NULL); } /* Define chunking stuff for a var. This must be done after nc_def_var and before nc_enddef. Chunking is required in any dataset with one or more unlimited dimension in HDF5, or any dataset using a filter. Where chunksize is a pointer to an array of size ndims, with the chunksize in each dimension. */ int NCD_def_var_chunking(int ncid, int varid, int contiguous, const size_t *chunksizesp) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, &contiguous, chunksizesp, NULL, NULL, NULL, NULL, NULL); } /* Define fill value behavior for a variable. This must be done after nc_def_var and before nc_enddef. */ int NCD_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, NULL, &no_fill, fill_value, NULL, NULL, NULL); } /* Define the endianness of a variable. */ int NCD_def_var_endian(int ncid, int varid, int endianness) { return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, &endianness, NULL, NULL); } /* Get var id from name. */ int NCD_inq_varid(int ncid, const char *name, int *varidp) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; char norm_name[NC_MAX_NAME + 1]; int retval; if (!name) return NC_EINVAL; if (!varidp) return NC_NOERR; LOG((2, "nc_inq_varid: ncid 0x%x name %s", ncid, name)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; /* Handle netcdf-3. */ assert(h5); /* Normalize name. */ if ((retval = nc4_normalize_name(name, norm_name))) return retval; /* Find var of this name. */ for (var = grp->var; var; var = var->next) if (!(strcmp(var->name, norm_name))) { *varidp = var->varid; return NC_NOERR; } return NC_ENOTVAR; } /* Rename a var to "bubba," for example. According to the netcdf-3.5 docs: If the new name is longer than the old name, the netCDF dataset must be in define mode. */ int NCD_rename_var(int ncid, int varid, const char *name) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_HDF5_FILE_INFO_T *h5; NC_VAR_INFO_T *var; int retval = NC_NOERR; LOG((2, "nc_rename_var: ncid 0x%x varid %d name %s", ncid, varid, name)); /* Find info for this file and group, and set pointer to each. */ if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5))) return retval; /* Take care of netcdf-3 files. */ assert(h5); /* Is the new name too long? */ if (strlen(name) > NC_MAX_NAME) return NC_EMAXNAME; /* Trying to write to a read-only file? No way, Jose! */ if (h5->no_write) return NC_EPERM; /* Check name validity, if strict nc3 rules are in effect for this * file. */ if ((retval = NC_check_name(name))) return retval; /* Is name in use? */ for (var = grp->var; var; var = var->next) if (!strncmp(var->name, name, NC_MAX_NAME)) return NC_ENAMEINUSE; /* Find the var. */ for (var = grp->var; var; var = var->next) if (var->varid == varid) break; if (!var) return NC_ENOTVAR; /* If we're not in define mode, new name must be of equal or less size, if strict nc3 rules are in effect for this . */ if (!(h5->flags & NC_INDEF) && strlen(name) > strlen(var->name) && (h5->cmode & NC_CLASSIC_MODEL)) return NC_ENOTINDEFINE; /* Change the HDF5 file, if this var has already been created there. */ if (var->created) { if (H5Gmove(grp->hdf_grpid, var->name, name) < 0) BAIL(NC_EHDFERR); } /* Now change the name in our metadata. */ free(var->name); if (!(var->name = malloc((strlen(name) + 1) * sizeof(char)))) return NC_ENOMEM; strcpy(var->name, name); exit: return retval; } int NCD_var_par_access(int ncid, int varid, int par_access) { return NC_ENOPAR; } int NCD_put_vara(int ncid, int varid, const size_t *startp, const size_t *countp, const void *op, int memtype) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; void *copy_point = NULL; size_t num_values = 1, num_values_to_start = 0; int d, retval; if (!(nc = nc4_find_nc_file(ncid))) return NC_EBADID; assert(nc->nc4_info); /* Find our metadata for this file, group, and var. */ assert(nc); if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) return retval; assert(grp && nc->nc4_info && var && var->name); /* Where do I start? */ if (var->ndims) { num_values_to_start = 1; for (d = 0; d < var->ndims; d++) num_values_to_start *= (startp[d] * var->dim[d]->len); } copy_point = (void *)((char *)var->diskless_data + num_values_to_start * var->type_info->size); /* How many values do I copy? */ if (var->ndims) for (d = 0; d < var->ndims; d++) num_values *= countp[d]; /* Copy the data to memory. */ memcpy(copy_point, op, num_values * var->type_info->size); return NC_NOERR; } /** \internal Read an array of values from a diskless file. */ int NCD_get_vara(int ncid, int varid, const size_t *startp, const size_t *countp, void *ip, int memtype) { NC_FILE_INFO_T *nc; NC_GRP_INFO_T *grp; NC_VAR_INFO_T *var; void *copy_point = NULL; size_t num_values = 1, num_values_to_start = 0; int d, retval; if (!(nc = nc4_find_nc_file(ncid))) return NC_EBADID; /* Find our metadata for this file, group, and var. */ assert(nc); if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var))) return retval; assert(grp && nc->nc4_info && var && var->name); /* Where do I start reading this data? */ if (var->ndims) { num_values_to_start = 1; for (d = 0; d < var->ndims; d++) num_values_to_start *= (startp[d] * var->dim[d]->len); } copy_point = (void *)((char *)var->diskless_data + num_values_to_start * var->type_info->size); /* How many values do I copy? */ if (var->ndims) for (d = 0; d < var->ndims; d++) num_values *= countp[d]; /* Copy the data to memory. */ memcpy(ip, copy_point, num_values * var->type_info->size); return NC_NOERR; }