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gmt_nc.c
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gmt_nc.c
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/*--------------------------------------------------------------------
*
* Copyright (c) 1991-2022 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
* See LICENSE.TXT file for copying and redistribution conditions.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; version 3 or any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* Contact info: www.generic-mapping-tools.org
*--------------------------------------------------------------------*/
/*
*
* G M T _ N C . C R O U T I N E S
*
* Takes care of all grd input/output built on NCAR's NetCDF routines.
* This version is intended to provide more general support for reading
* NetCDF files that were not generated by GMT. At the same time, the grids
* written by these routines are intended to be more conform COARDS conventions.
* These routines are to eventually replace the older gmt_cdf_ routines.
*
* Most functions will return with error message if an internal error is returned.
* There functions are only called indirectly via the GMT_* grdio functions.
*
* Author: Remko Scharroo
* Date: 04-AUG-2005
* Version: 1
*
* Added support for chunked I/O, Florian Wobbe, June 2012.
*
* Functions include:
*
* gmt_nc_read_grd_info: Read header from file
* gmt_nc_read_grd: Read data set from file
* gmt_nc_update_grd_info: Update header in existing file
* gmt_nc_write_grd_info: Write header to new file
* gmt_nc_write_grd: Write header and data set to new file
* gmt_nc_read_cube_info: Read information from cube file
* gmt_nc_write_cube: rite header and cube to new file(s)
* gmtlib_is_nc_grid: Determine if we have a nc grid
*
* Private functions:
* gmtnc_setup_chunk_cache: Change the default HDF5 chunk cache settings
* gmtnc_pad_grid: Add padding to a grid
* gmtnc_unpad_grid: Remove padding from a grid
* gmtnc_padding_copy: Fill padding by replicating the border cells
* gmtnc_padding_zero: Fill padding with zeros
* gmtnc_n_chunked_rows_in_cache Determines how many chunks to read at once
* gmtnc_io_nc_grid Does the actual netcdf I/O
* gmtnc_netcdf_libvers returns the netCDF library version
* gmtnc_right_shift_grid
* gmtnc_set_optimal_chunksize Determines the optimal chunksize
* gmtnc_get_units
* gmtnc_put_units
* gmtnc_check_step
* gmtnc_grd_info
* gmtnc_grid_fix_repeat_col
* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/
#include "gmt_dev.h"
#include "gmt_internals.h"
#include <netcdf.h>
/* Declaration modifier for netcdf DLL support
* annoying: why can't netcdf.h do this on its own? */
#if defined WIN32 && ! defined NETCDF_STATIC
#define DLL_NETCDF
#endif
/* HDF5 chunk cache: reasonable defaults assuming min. chunk size of 128x128 and type byte */
#define NC_CACHE_SIZE 33554432 /* 32MiB */
#define NC_CACHE_NELEMS 2053 /* prime > NC_CACHE_SIZE / (128*128*1byte) */
#define NC_CACHE_PREEMPTION 0.75f
int gmt_cdf_grd_info (struct GMT_CTRL *GMT, int ncid, struct GMT_GRID_HEADER *header, char job);
int gmt_cdf_read_grd (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header, gmt_grdfloat *grid, double wesn[], unsigned int *pad, unsigned int complex_mode);
static int nc_libvers[] = {-1, -1, -1, -1}; /* holds the version of the netCDF library */
static char *regtype[2] = {"gridline", "pixel"};
GMT_LOCAL const int * gmtnc_netcdf_libvers (void) {
static bool inquired = false;
if (!inquired) {
const char *vers_string = nc_inq_libvers();
sscanf (vers_string, "%d.%d.%d.%d",
nc_libvers, nc_libvers+1, nc_libvers+2, nc_libvers+3);
inquired = true;
}
return nc_libvers; /* return pointer to version array */
}
/* netcdf I/O mode */
enum Netcdf_io_mode {
k_put_netcdf = 0,
k_get_netcdf
};
/* Wrapper around gmt_nc_put_vara_grdfloat and gmt_nc_get_vara_grdfloat */
static inline int gmtnc_vara_grdfloat (int ncid, int varid, const size_t *startp, const size_t *countp, gmt_grdfloat *fp, unsigned io_mode) {
if (io_mode == k_put_netcdf) /* write netcdf */
return gmt_nc_put_vara_grdfloat (ncid, varid, startp, countp, fp);
/* read netcdf */
return gmt_nc_get_vara_grdfloat (ncid, varid, startp, countp, fp);
}
/* Wrapper around gmt_nc_put_varm_grdfloat and gmt_nc_get_varm_grdfloat */
static inline int gmtnc_varm_grdfloat (int ncid, int varid, const size_t *startp, const size_t *countp, const ptrdiff_t *stridep, const ptrdiff_t *imapp, gmt_grdfloat *fp, unsigned io_mode) {
if (io_mode == k_put_netcdf) /* write netcdf */
return gmt_nc_put_varm_grdfloat (ncid, varid, startp, countp, stridep, imapp, fp);
/* read netcdf */
return gmt_nc_get_varm_grdfloat (ncid, varid, startp, countp, stridep, imapp, fp);
}
/* Get number of chunked rows that fit into cache (32MiB) */
GMT_LOCAL int gmtnc_n_chunked_rows_in_cache (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header, unsigned width, unsigned height, size_t *n_contiguous_chunk_rows, size_t *chunksize) {
struct GMT_GRID_HEADER_HIDDEN *HH = gmt_get_H_hidden (header);
nc_type z_type; /* type of z variable */
size_t z_size; /* size of z variable */
size_t z_bytes; /* Number of bytes */
size_t width_t = (size_t)width;
size_t height_t = (size_t)height;
unsigned yx_dim[2] = {HH->xy_dim[1], HH->xy_dim[0]}; /* because xy_dim not row major */
int err, storage_in;
gmt_M_err_trap (nc_inq_vartype(HH->ncid, HH->z_id, &z_type)); /* type of z */
gmt_M_err_trap (nc_inq_type(HH->ncid, z_type, NULL, &z_size)); /* size of z elements in bytes */
gmt_M_err_trap (nc_inq_var_chunking (HH->ncid, HH->z_id, &storage_in, chunksize));
if (storage_in != NC_CHUNKED) {
/* default if NC_CONTIGUOUS */
chunksize[yx_dim[0]] = 128; /* 128 rows */
chunksize[yx_dim[1]] = width_t; /* all columns */
}
z_bytes = height_t * height_t * z_size;
if (z_bytes > NC_CACHE_SIZE) {
/* memory needed for subset exceeds the cache size */
unsigned int level;
size_t chunks_per_row = (size_t) ceil ((double)width / chunksize[yx_dim[1]]);
*n_contiguous_chunk_rows = NC_CACHE_SIZE / (width_t * z_size) / chunksize[yx_dim[0]];
#ifdef NC4_DEBUG
level = GMT_MSG_WARNING;
#else
level = GMT_MSG_DEBUG;
#endif
GMT_Report (GMT->parent, level,
"processing at most %" PRIuS " (%" PRIuS "x%" PRIuS ") chunks at a time (%.1lf MiB)...\n",
*n_contiguous_chunk_rows * chunks_per_row,
*n_contiguous_chunk_rows, chunks_per_row,
*n_contiguous_chunk_rows * z_size * width * chunksize[yx_dim[0]] / 1048576.0);
}
else
*n_contiguous_chunk_rows = 0; /* all chunks fit into cache */
return GMT_NOERROR;
}
/* Read and write classic or chunked netcdf files */
GMT_LOCAL int gmtnc_io_nc_grid (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header, unsigned dim[], unsigned origin[], size_t stride, unsigned io_mode, gmt_grdfloat* grid, bool cube) {
/* io_mode = k_get_netcdf: read a netcdf file to grid
* io_mode = k_put_netcdf: write a grid to netcdf */
int status = NC_NOERR;
unsigned int d_off = (cube) ? 1 : 0;
unsigned width = dim[1+d_off], height = dim[0+d_off];
unsigned yx_dim[2]; /* because xy_dim is not row major! */
size_t width_t = (size_t)width;
size_t height_t = (size_t)height;
size_t chunksize[5]; /* chunksize of z */
size_t start[5] = {0,0,0,0,0}, count[5] = {1,1,1,1,1};
size_t n_contiguous_chunk_rows = 0; /* that are processed at once, 0 = all */
ptrdiff_t imap[5] = {1,1,1,1,1}; /* mapping between dims of netCDF and in-memory grid */
const ptrdiff_t onestride[5] = {1,1,1,1,1}; /* Passing this instead of NULL bypasses netCDF bug in 4.6.2 */
struct GMT_GRID_HEADER_HIDDEN *HH = gmt_get_H_hidden (header);
/* catch illegal io_mode in debug */
assert (io_mode == k_put_netcdf || io_mode == k_get_netcdf);
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "%s n_columns:%u n_rows:%u x0:%u y0:%u y-order:%s\n",
io_mode == k_put_netcdf ? "writing," : "reading,",
dim[1+d_off], dim[0+d_off], origin[1], origin[0],
HH->row_order == k_nc_start_south ? "S->N" : "N->S");
#endif
/* set index of input origin */
yx_dim[0] = HH->xy_dim[1], yx_dim[1] = HH->xy_dim[0]; /* xy_dim not row major */
memcpy (start, HH->t_index, 3 * sizeof(size_t)); /* set lower dimensions first (e.g. layer) */
start[yx_dim[0]] = origin[0]; /* first row */
start[yx_dim[1]] = origin[1]; /* first col */
/* set mapping of complex grids or if reading a part of a grid */
imap[yx_dim[0]] = (stride == 0 ? width : stride); /* distance between each row */
imap[yx_dim[1]] = 1; /* distance between values in a row */
if (cube) imap[0] = header->nm; /* distance between values in a layer (?) */
/* determine how many chunks to process at once */
gmtnc_n_chunked_rows_in_cache (GMT, header, width, height, &n_contiguous_chunk_rows, chunksize);
if (n_contiguous_chunk_rows) {
/* read/write grid in chunks to keep memory footprint low */
size_t remainder;
#ifdef NC4_DEBUG
unsigned row_num = 0;
GMT_Report (GMT->parent, GMT_MSG_WARNING, "stride: %u width: %u\n",
stride, width);
#endif
/* adjust row count, so that it ends on the bottom of a chunk */
count[yx_dim[0]] = chunksize[yx_dim[0]] * n_contiguous_chunk_rows;
remainder = start[yx_dim[0]] % chunksize[yx_dim[0]];
count[yx_dim[0]] -= remainder;
count[yx_dim[1]] = width_t;
while ( (start[yx_dim[0]] + count[yx_dim[0]]) <= height_t && status == NC_NOERR) {
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "chunked row #%u start-y:%" PRIuS " height:%" PRIuS "\n",
++row_num, start[yx_dim[0]], count[yx_dim[0]]);
#endif
/* get/put chunked rows */
if (stride)
status = gmtnc_varm_grdfloat (HH->ncid, HH->z_id, start, count, onestride, imap, grid, io_mode);
else
status = gmtnc_vara_grdfloat (HH->ncid, HH->z_id, start, count, grid, io_mode);
/* advance grid location and set new origin */
grid += count[yx_dim[0]] * ((stride == 0 ? width_t : stride));
start[yx_dim[0]] += count[yx_dim[0]];
if (remainder) {
/* reset count to full chunk height */
count[yx_dim[0]] += remainder;
remainder = 0;
}
}
if ( start[yx_dim[0]] != height_t && status == NC_NOERR ) {
/* get/put last chunked row */
count[yx_dim[0]] = height_t - start[yx_dim[0]] + origin[0];
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "chunked row #%u start-y:%" PRIuS " height:%" PRIuS "\n",
++row_num, start[yx_dim[0]], count[yx_dim[0]]);
#endif
if (stride)
status = gmtnc_varm_grdfloat (HH->ncid, HH->z_id, start, count, onestride, imap, grid, io_mode);
else
status = gmtnc_vara_grdfloat (HH->ncid, HH->z_id, start, count, grid, io_mode);
}
}
else {
/* get/put whole grid contiguous */
count[yx_dim[0]] = height_t;
count[yx_dim[1]] = width_t;
if (stride)
status = gmtnc_varm_grdfloat (HH->ncid, HH->z_id, start, count, onestride, imap, grid, io_mode);
else
status = gmtnc_vara_grdfloat (HH->ncid, HH->z_id, start, count, grid, io_mode);
}
return status;
}
GMT_LOCAL void gmtnc_get_units (struct GMT_CTRL *GMT, int ncid, int varid, char *name_units) {
/* Get attributes long_name and units for given variable ID
* and assign variable name if attributes are not available.
* ncid, varid : as in nc_get_att_text
* nameunit : long_name and units in form "long_name [units]"
*/
char name[GMT_GRID_UNIT_LEN80], units[GMT_GRID_UNIT_LEN80];
if (gmtlib_nc_get_att_text (GMT, ncid, varid, "long_name", name, GMT_GRID_UNIT_LEN80))
nc_inq_varname (ncid, varid, name);
if (!gmtlib_nc_get_att_text (GMT, ncid, varid, "units", units, GMT_GRID_UNIT_LEN80) && units[0])
snprintf (name_units, GMT_GRID_UNIT_LEN80, "%s [%s]", name, units);
else
strncpy (name_units, name, GMT_GRID_UNIT_LEN80-1);
}
GMT_LOCAL void gmtnc_put_units (int ncid, int varid, char *name_units) {
/* Put attributes long_name and units for given variable ID based on
* string name_unit in the form "long_name [units]".
* ncid, varid : as is nc_put_att_text
* name_units : string in form "long_name [units]"
*/
bool copy = false;
int i = 0, j = 0;
char name[GMT_GRID_UNIT_LEN80], units[GMT_GRID_UNIT_LEN80];
strncpy (name, name_units, GMT_GRID_UNIT_LEN80-1);
units[0] = '\0';
for (i = 0; i < GMT_GRID_UNIT_LEN80 && name[i]; i++) {
if (name[i] == ']') copy = false, units[j] = '\0';
if (copy) units[j++] = name[i];
if (name[i] == '[') {
name[i] = '\0';
if (i > 0 && name[i-1] == ' ') name[i-1] = '\0';
copy = true;
}
}
if (name[0]) nc_put_att_text (ncid, varid, "long_name", strlen(name), name);
if (units[0]) nc_put_att_text (ncid, varid, "units", strlen(units), units);
if (strstr(units, "degrees_east")) {
nc_put_att_text (ncid, varid, "standard_name", 9, "longitude");
nc_put_att_text (ncid, varid, "axis", 1, "X");
}
else if (strstr(units, "degrees_north")) {
nc_put_att_text (ncid, varid, "standard_name", 8, "latitude");
nc_put_att_text (ncid, varid, "axis", 1, "Y");
}
}
GMT_LOCAL int gmtnc_check_step (struct GMT_CTRL *GMT, uint32_t n, double *x, char *varname, char *file, bool save_xy_array) {
/* Check if all steps in range are the same (within 0.1%). Returns 0 if OK and 1 if variable spacing */
double step, step_min, step_max;
uint32_t i;
unsigned int wlevel = (save_xy_array) ? GMT_MSG_INFORMATION : GMT_MSG_WARNING;
if (n < 2) return 0;
step_min = step_max = x[1]-x[0];
for (i = 2; i < n; i++) {
step = x[i]-x[i-1];
if (step < step_min) step_min = step;
if (step > step_max) step_max = step;
}
if (fabs (step_min-step_max)/(fabs (step_min)*0.5 + fabs (step_max)*0.5) > 0.001) {
GMT_Report (GMT->parent, wlevel,
"The step size of coordinate (%s) in grid %s is not constant.\n", varname, file);
GMT_Report (GMT->parent, wlevel,
"GMT will use a constant step size of %g; the original ranges from %g to %g.\n",
(x[n-1]-x[0])/(n-1), step_min, step_max);
return 1;
}
return 0;
}
GMT_LOCAL void gmtnc_set_optimal_chunksize (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header) {
/* For optimal performance, set the number of elements in a given chunk
* dimension (n) to be the ceiling of the number of elements in that
* dimension of the array variable (d) divided by a natural number N>1.
* That is, set n = ceil (d / N). Using a chunk size slightly larger than
* this value is also acceptable. For example: 129 = ceil (257 / 2).
* Do NOT set n = floor (d / N), for example 128 = floor (257 / 2). */
double chunksize[2] = {128, 128}; /* default min chunksize */
const size_t min_chunk_pixels = (size_t)(chunksize[0] * chunksize[1]); /* min pixel count per chunk */
if (GMT->current.setting.io_nc4_chunksize[0] == k_netcdf_io_classic)
/* no chunking with classic model */
return;
if (GMT->current.setting.io_nc4_chunksize[0] != k_netcdf_io_chunked_auto && (
header->n_rows >= GMT->current.setting.io_nc4_chunksize[0] ||
header->n_columns >= GMT->current.setting.io_nc4_chunksize[1])) {
/* if chunk size is smaller than grid size */
return;
}
/* here, chunk size is either k_netcdf_io_chunked_auto or the chunk size is
* larger than grid size */
if ( header->nm < min_chunk_pixels ) {
/* the grid dimension is too small for chunking to make sense. switch to
* classic model */
GMT->current.setting.io_nc4_chunksize[0] = k_netcdf_io_classic;
return;
}
/* adjust default chunk sizes for grids that have more than min_chunk_pixels
* cells but less than chunksize (default 128) cells in one dimension */
if (header->n_rows < chunksize[0]) {
chunksize[0] = header->n_rows;
chunksize[1] = floor (min_chunk_pixels / chunksize[0]);
}
else if (header->n_columns < chunksize[1]) {
chunksize[1] = header->n_columns;
chunksize[0] = floor (min_chunk_pixels / chunksize[1]);
}
/* determine optimal chunk size in the range [chunksize,2*chunksize) */
GMT->current.setting.io_nc4_chunksize[0] = (size_t) ceil (header->n_rows / floor (header->n_rows / chunksize[0]));
GMT->current.setting.io_nc4_chunksize[1] = (size_t) ceil (header->n_columns / floor (header->n_columns / chunksize[1]));
}
GMT_LOCAL bool gmtnc_not_obviously_global (double *we) {
/* If range is not 360 and boundaries are not 0, 180, 360 then we pass true */
if (!gmt_M_360_range (we[0], we[1])) return true;
if (!(doubleAlmostEqualZero (we[0], 0.0) || doubleAlmostEqual (we[0], -180.0))) return true;
return false;
}
GMT_LOCAL bool gmtnc_not_obviously_polar (double *se) {
/* If range is not 180 and boundaries are not -90/90 then we pass true */
if (!gmt_M_180_range (se[0], se[1])) return true;
if (!(doubleAlmostEqual (se[0], -90.0) && doubleAlmostEqual (se[1], 90.0))) return true;
return false;
}
GMT_LOCAL int gmtnc_put_xy_vectors (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header) {
/* Write the x and y vectors to the netCDF file */
int err = GMT_NOERROR;
/* Create enough memory to store the x- and y-coordinate values */
double *xy = gmt_M_memory (GMT, NULL, MAX (header->n_columns,header->n_rows), double);
unsigned int col, row;
struct GMT_GRID_HEADER_HIDDEN *HH = gmt_get_H_hidden (header);
if (xy == NULL) return (GMT_MEMORY_ERROR);
for (col = 0; col < header->n_columns; col++) xy[col] = gmt_M_grd_col_to_x (GMT, col, header);
gmt_M_err_trap (nc_put_var_double (HH->ncid, HH->xyz_id[GMT_X], xy));
/* Depending on row_order, write y-coordinate array bottom-to-top or top-to-bottom */
if (HH->row_order == k_nc_start_south) {
for (row = 0; row < header->n_rows; row++)
xy[row] = (double) gmt_M_col_to_x (GMT, row, header->wesn[YLO], header->wesn[YHI], header->inc[GMT_Y], 0.5 * header->registration, header->n_rows);
}
else {
for (row = 0; row < header->n_rows; row++)
xy[row] = (double) gmt_M_row_to_y (GMT, row, header->wesn[YLO], header->wesn[YHI], header->inc[GMT_Y], 0.5 * header->registration, header->n_rows);
}
gmt_M_err_trap (nc_put_var_double (HH->ncid, HH->xyz_id[GMT_Y], xy));
gmt_M_free (GMT, xy);
return GMT_NOERROR;
}
GMT_LOCAL int gmtnc_grd_info (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *header, char job, bool cube, uint64_t n_layers) {
/* Used when reading and writing 2-D grids and when writing 3-D data cubes */
int j, err, has_vector, has_range, registration, var_spacing = 0;
int old_fill_mode, status;
unsigned int d_off = (cube) ? 1 : 0;
size_t len;
double dummy[2], min, max;
char dimname[GMT_GRID_UNIT_LEN80], coord[GMT_LEN8];
nc_type z_type;
bool save_xy_array = !strncmp (GMT->init.module_name, "grd2xyz", 7U);
struct GMT_GRID_HEADER_HIDDEN *HH = gmt_get_H_hidden (header);
/* Dimension ids, variable ids, etc.. */
int i, ncid, z_id = GMT_NOTSET, ids[5] = {-1,-1,-1,-1,-1}, gm_id = GMT_NOTSET, dims[5], nvars, ndims = 0;
size_t lens[5], item[2];
/* If not yet determined, attempt to get the layer IDs from the variable name */
int n_t_index_by_value = 0;
double t_value[3];
if (HH->varname[0]) {
char *c = strpbrk (HH->varname, "(["); /* find first occurrence of ( or [ */
if (c != NULL && *c == '(') {
n_t_index_by_value = sscanf (c+1, "%lf,%lf,%lf", &t_value[0], &t_value[1], &t_value[2]);
*c = '\0';
/* t_index will be determined later from t_value when the nc-file is opened */
}
else if (c != NULL && *c == '[') {
sscanf (c+1, "%" PRIuS ",%" PRIuS ",%" PRIuS "", &HH->t_index[0], &HH->t_index[1], &HH->t_index[2]);
*c = '\0';
}
}
/* Open NetCDF file */
if (!strcmp (HH->name,"=")) return (GMT_GRDIO_NC_NO_PIPE);
switch (job) {
case 'r':
gmt_M_err_trap (gmt_nc_open (GMT, HH->name, NC_NOWRITE, &ncid));
break;
case 'u':
gmt_M_err_trap (gmt_nc_open (GMT, HH->name, NC_WRITE, &ncid));
gmt_M_err_trap (nc_set_fill (ncid, NC_NOFILL, &old_fill_mode));
break;
default:
/* create new nc-file */
gmtnc_set_optimal_chunksize (GMT, header);
if (GMT->current.setting.io_nc4_chunksize[0] != k_netcdf_io_classic) {
/* create chunked nc4 file */
gmt_M_err_trap (gmt_nc_create (GMT, HH->name, NC_NETCDF4, &ncid));
HH->is_netcdf4 = true;
}
else {
/* create nc using classic data model */
gmt_M_err_trap (gmt_nc_create (GMT, HH->name, NC_CLOBBER, &ncid));
HH->is_netcdf4 = false;
}
gmt_M_err_trap (nc_set_fill (ncid, NC_NOFILL, &old_fill_mode));
break;
}
/* Retrieve or define dimensions and variables */
if (job == 'r' || job == 'u') {
int kind;
/* determine netCDF data model */
gmt_M_err_trap (nc_inq_format(ncid, &kind));
HH->is_netcdf4 = (kind == NC_FORMAT_NETCDF4 || kind == NC_FORMAT_NETCDF4_CLASSIC);
/* First see if this is an old NetCDF formatted file */
if (!nc_inq_dimid (ncid, "xysize", &i)) return (gmt_cdf_grd_info (GMT, ncid, header, job));
/* Find first 2-dimensional (z) variable or specified variable */
if (!HH->varname[0]) { /* No specific named variable was requested; search for suitable matrix */
int ID = GMT_NOTSET, dim = 0;
gmt_M_err_trap (nc_inq_nvars (ncid, &nvars));
i = 0;
while (i < nvars && z_id < 0) { /* Look for first 2D grid, with fallback to first higher-dimension (3-4D) grid if 2D not found */
gmt_M_err_trap (nc_inq_varndims (ncid, i, &ndims));
if (ndims == 2) /* Found the first 2-D grid */
z_id = i;
else if (ID == GMT_NOTSET && ndims > 2 && ndims < 5) { /* Also look for higher-dim grid in case no 2-D */
ID = i;
dim = ndims;
}
i++;
}
if (z_id < 0) { /* No 2-D grid found, check if we found a higher dimension cube */
if (ID == GMT_NOTSET) return (GMT_GRDIO_NO_2DVAR); /* No we didn't */
z_id = ID; /* Pick the higher dimensioned cube instead, get its name, and warn */
ndims = dim; /* Recall the dimensions of this ID */
nc_inq_varname (ncid, z_id, HH->varname);
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "No 2-D array in file %s. Selecting first 2-D slice in the %d-D array %s\n", HH->name, dim, HH->varname);
}
}
else if (nc_inq_varid (ncid, HH->varname, &z_id) == NC_NOERR) { /* Gave a named variable that exist, is it 2-4 D? */
gmt_M_err_trap (nc_inq_varndims (ncid, z_id, &ndims));
if (ndims < 2 || ndims > 5) return (GMT_GRDIO_BAD_DIM);
}
else /* No such named variable in the grid */
return (GMT_GRDIO_NO_VAR);
if (z_id < 0) return (GMT_GRDIO_NO_2DVAR);
/* Get the z data type and determine its dimensions */
gmt_M_err_trap (nc_inq_vartype (ncid, z_id, &z_type));
gmt_M_err_trap (nc_inq_vardimid (ncid, z_id, dims));
switch (z_type) {
case NC_UBYTE: header->type = GMT_GRID_IS_NB; HH->orig_datatype = GMT_UCHAR; break;
case NC_BYTE: header->type = GMT_GRID_IS_NB; HH->orig_datatype = GMT_CHAR; break;
case NC_SHORT: header->type = GMT_GRID_IS_NS; HH->orig_datatype = GMT_SHORT; break;
case NC_INT: header->type = GMT_GRID_IS_NI; HH->orig_datatype = GMT_INT; break;
case NC_FLOAT: header->type = GMT_GRID_IS_NF; HH->orig_datatype = GMT_FLOAT; break;
case NC_DOUBLE: header->type = GMT_GRID_IS_ND; HH->orig_datatype = GMT_DOUBLE; break;
default: header->type = k_grd_unknown_fmt; break;
}
/* Get the ids of the x and y (and depth and time) coordinate variables */
for (i = 0; i < ndims; i++) {
gmt_M_err_trap (nc_inq_dim (ncid, dims[i], dimname, &lens[i]));
//if (nc_inq_varid (ncid, dimname, &ids[i])) return (GMT_GRDIO_NC_NOT_COARDS);
if ((status = nc_inq_varid (ncid, dimname, &ids[i])) != NC_NOERR)
GMT_Report (GMT->parent, GMT_MSG_WARNING, "\"%s\", %s\n\tIf something bad happens later, try importing via GDAL.\n",
dimname, nc_strerror(status));
}
HH->xy_dim[0] = ndims-1;
HH->xy_dim[1] = ndims-2;
HH->xyz_id[GMT_X] = ids[1];
HH->xyz_id[GMT_Y] = ids[0];
/* Check if LatLon variable exists, then we may need to flip x and y */
if (nc_inq_varid (ncid, "LatLon", &i) == NC_NOERR) nc_get_var_int (ncid, i, HH->xy_dim);
header->n_columns = (uint32_t) lens[HH->xy_dim[0]];
header->n_rows = (uint32_t) lens[HH->xy_dim[1]];
/* Check if the spatial_ref attribute exists, first via the z_id variable, and if not then via a global attribute */
if (nc_inq_attlen (ncid, z_id, "grid_mapping", &len) == NC_NOERR) { /* The data layer has an attribute with the name of the variable that has the spatial_ref */
char *v_name = gmt_M_memory (GMT, NULL, len+1, char); /* Allocate the needed space for the variable name */
if (nc_get_att_text (ncid, z_id, "grid_mapping", v_name) == NC_NOERR) { /* Get the name of the variable */
if (nc_inq_varid (ncid, v_name, &i) == NC_NOERR) /* Got the id of this variable */
gm_id = i;
}
gmt_M_free (GMT, v_name);
}
else if (nc_inq_varid (ncid, "grid_mapping", &i) == NC_NOERR) /* A global variable has it */
gm_id = i;
} /* if (job == 'r' || job == 'u') */
else {
/* Define dimensions of z variable */
ndims = (cube) ? 3 : 2;
HH->xy_dim[0] = 1 + d_off;
HH->xy_dim[1] = 0 + d_off;
strcpy (coord, (gmt_M_x_is_lon (GMT, GMT_OUT)) ? "lon" : (gmt_M_type (GMT, GMT_OUT, GMT_X) & GMT_IS_RATIME) ? "time" : "x");
gmt_M_err_trap (nc_def_dim (ncid, coord, (size_t) header->n_columns, &dims[1+d_off]));
gmt_M_err_trap (nc_def_var (ncid, coord, NC_DOUBLE, 1, &dims[1+d_off], &ids[1+d_off]));
HH->xyz_id[GMT_X] = ids[1+d_off];
strcpy (coord, (gmt_M_y_is_lat (GMT, GMT_OUT)) ? "lat" : (gmt_M_type (GMT, GMT_OUT, GMT_Y) & GMT_IS_RATIME) ? "time" : "y");
gmt_M_err_trap (nc_def_dim (ncid, coord, (size_t) header->n_rows, &dims[0+d_off]));
gmt_M_err_trap (nc_def_var (ncid, coord, NC_DOUBLE, 1, &dims[0+d_off], &ids[0+d_off]));
HH->xyz_id[GMT_Y] = ids[0+d_off];
if (cube) { /* Allow for cube expansion by setting layer dimension to 0 (NC_UNLIMITED) */
strcpy (coord, (gmt_M_type (GMT, GMT_OUT, GMT_Z) & GMT_IS_RATIME) ? "time" : "z");
gmt_M_err_trap (nc_def_dim (ncid, coord, (size_t) n_layers, &dims[0]));
gmt_M_err_trap (nc_def_var (ncid, coord, NC_DOUBLE, 1, &dims[0], &HH->xyz_id[GMT_Z]));
}
switch (header->type) {
case GMT_GRID_IS_NB: z_type = NC_BYTE; break;
case GMT_GRID_IS_NS: z_type = NC_SHORT; break;
case GMT_GRID_IS_NI: z_type = NC_INT; break;
case GMT_GRID_IS_NF: z_type = NC_FLOAT; break;
case GMT_GRID_IS_ND: z_type = NC_DOUBLE; break;
default: z_type = NC_NAT;
}
/* Variable name is given, or defaults to "z" (or "cube" under cube) */
if (!HH->varname[0])
strcpy (HH->varname, (cube) ? "cube" : "z");
gmt_M_err_trap (nc_def_var (ncid, HH->varname, z_type, (cube) ? 3 : 2, dims, &z_id));
/* set deflation and chunking */
if (GMT->current.setting.io_nc4_chunksize[0] != k_netcdf_io_classic) {
/* set chunk size */
size_t nc4_chunksize[3] = {0, 0, 0};
gmt_M_memcpy (&nc4_chunksize[cube], GMT->current.setting.io_nc4_chunksize, 2U, size_t);
gmt_M_err_trap (nc_def_var_chunking (ncid, z_id, NC_CHUNKED, nc4_chunksize));
/* set deflation level and shuffle for x, y[, z], and z[|w] variable */
if (GMT->current.setting.io_nc4_deflation_level) {
gmt_M_err_trap (nc_def_var_deflate (ncid, HH->xyz_id[GMT_X], true, true, GMT->current.setting.io_nc4_deflation_level));
gmt_M_err_trap (nc_def_var_deflate (ncid, HH->xyz_id[GMT_Y], true, true, GMT->current.setting.io_nc4_deflation_level));
if (cube && n_layers == 0) gmt_M_err_trap (nc_def_var_deflate (ncid, HH->xyz_id[GMT_Z], true, true, GMT->current.setting.io_nc4_deflation_level));
gmt_M_err_trap (nc_def_var_deflate (ncid, z_id, true, true, GMT->current.setting.io_nc4_deflation_level));
}
} /* GMT->current.setting.io_nc4_chunksize[0] != k_netcdf_io_classic */
} /* if (job == 'r' || job == 'u') */
HH->z_id = z_id;
HH->ncid = ncid;
/* Query or assign attributes */
if (job == 'u') gmt_M_err_trap (nc_redef (ncid));
if (job == 'r') {
bool set_reg = true;
double dx = 0, dy = 0, threshold = 0.0;
/* Create enough memory to store the x- and y-coordinate values */
double *xy = gmt_M_memory (GMT, NULL, MAX (header->n_columns,header->n_rows), double);
if (xy == NULL) return (GMT_MEMORY_ERROR);
/* Get global information */
if (gmtlib_nc_get_att_vtext (GMT, ncid, NC_GLOBAL, "title", header, header->title, GMT_GRID_TITLE_LEN80))
gmtlib_nc_get_att_vtext (GMT, ncid, z_id, "long_name", header, header->title, GMT_GRID_TITLE_LEN80);
if (gmtlib_nc_get_att_vtext (GMT, ncid, NC_GLOBAL, "history", header, header->command, GMT_GRID_COMMAND_LEN320))
gmtlib_nc_get_att_vtext (GMT, ncid, NC_GLOBAL, "source", header, header->command, GMT_GRID_COMMAND_LEN320);
gmtlib_nc_get_att_vtext (GMT, ncid, NC_GLOBAL, "description", header, header->remark, GMT_GRID_REMARK_LEN160);
header->registration = GMT_GRID_NODE_REG;
if (!nc_get_att_int (ncid, NC_GLOBAL, "node_offset", &i)) { /* GMT wrote the registration in the grid */
header->registration = i;
set_reg = false; /* Do not update it below since we know the registration */
}
if (gm_id != GMT_NOTSET && nc_inq_attlen (ncid, gm_id, "spatial_ref", &len) == NC_NOERR) { /* Good to go */
char *attrib = NULL;
gmt_M_str_free (header->ProjRefWKT); /* Make sure we didn't have a previously allocated one */
attrib = gmt_M_memory (GMT, NULL, len+1, char); /* and allocate the needed space */
gmt_M_err_trap (nc_get_att_text (ncid, gm_id, "spatial_ref", attrib));
header->ProjRefWKT = strdup (attrib); /* Turn it into a strdup allocation to be compatible with other instances elsewhere */
gmt_M_free (GMT, attrib);
}
/* Explanation for the logic below: Not all netCDF grids are proper COARDS grids and hence we sometime must guess
* regarding the settings. The x and y coordinates may be written as arrays, which reflect the positions of the
* nodes. There may also be the attributes actual_range which specifies the x range. These will differ if the
* grid is pixel registered, hence when both are present we use this difference to detect a pixel grid. However,
* some external tools such as xarray may slice a grid but not update the attributes. In this case the actual_range
* may have an initial range that is no longer the case. We have added a check if these differ by more than a
* half grid increment. If not then we can trust it. If actual_range is missing then we have to guess the registration
* which we do by checking if the start coordinate is an integer multiple of the increment. If not, we guess pixel registration
* but cannot know if this is the case unless the adjusted coordinates in x has a range of 360 and in y a range of 180.
* Finally, if there is no array just the actual_range, then we cannot tell the registration from the range but try
* and leave it as gridline registration. */
/* Get information about x variable */
gmtnc_get_units (GMT, ncid, ids[HH->xy_dim[0]], header->x_units);
/* Set default range to number of nodes in case nothing is found further down */
dummy[0] = 0.0, dummy[1] = (double) header->n_columns-1; /* Default */
registration = GMT_GRID_NODE_REG;
/* Look for the x-coordinate vector */
if ((has_vector = !nc_get_var_double (ncid, ids[HH->xy_dim[0]], xy)) && header->n_columns > 1) {
var_spacing = gmtnc_check_step (GMT, header->n_columns, xy, header->x_units, HH->name, save_xy_array);
if (save_xy_array && var_spacing) {
if (GMT->current.io.nc_xarray) gmt_M_free (GMT, GMT->current.io.nc_xarray);
GMT->current.io.nc_xarray = gmt_M_memory (GMT, NULL, header->n_columns, double);
gmt_M_memcpy (GMT->current.io.nc_xarray, xy, header->n_columns, double);
HH->var_spacing[GMT_X] = var_spacing;
}
dx = fabs (xy[1] - xy[0]); /* Grid spacing in x */
}
if (has_vector && header->n_columns == 1) has_vector = false; /* One coordinate does not a vector make */
/* Look for the x-coordinate range attributes */
has_range = (!nc_get_att_double (ncid, ids[HH->xy_dim[0]], "actual_range", dummy) ||
!nc_get_att_double (ncid, ids[HH->xy_dim[0]], "valid_range", dummy) ||
!(nc_get_att_double (ncid, ids[HH->xy_dim[0]], "valid_min", &dummy[0]) +
nc_get_att_double (ncid, ids[HH->xy_dim[0]], "valid_max", &dummy[1])));
if (has_vector && has_range) { /* Has both so we can do a basic sanity check */
threshold = (0.5+GMT_CONV5_LIMIT) * dx;
min = xy[0]; max = xy[header->n_columns-1];
if (min > max) gmt_M_double_swap (min, max); /* Got it backwards in the array */
if (fabs (dummy[0] - min) > threshold || fabs (dummy[1] - max) > threshold) {
if (gmtnc_not_obviously_global (dummy)) {
GMT_Report (GMT->parent, GMT_MSG_WARNING, "The x-coordinates and range attribute are in conflict; must rely on coordinates only\n");
dummy[0] = xy[0], dummy[1] = xy[header->n_columns-1];
has_range = false; /* Since useless information */
/* For registration, we have to assume that the actual range is an integer multiple of increment.
* If so, then if the coordinates are off by 0.5*dx then we assume we have pixel registration */
threshold = (0.5-GMT_CONV5_LIMIT) * dx;
if (set_reg && fabs (fmod (dummy[0], dx)) > threshold) { /* Pixel registration */
registration = header->registration = GMT_GRID_PIXEL_REG;
dummy[0] -= 0.5 * dx; dummy[1] += 0.5 * dx;
if (gmt_M_360_range (dummy[0], dummy[1]))
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "Grid x-coordinates after pixel registration adjustment have exactly 360 range\n");
}
}
else { /* Got clean global longitude range, stick with that information and ignore xy */
GMT_Report (GMT->parent, GMT_MSG_WARNING, "The x-coordinates and range attribute are in conflict but range is exactly 360; we rely on this range\n");
if (set_reg && (header->n_columns%2) == 0) { /* Pixel registration */
registration = header->registration = GMT_GRID_PIXEL_REG;
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "Global longitudes, guessing registration to be %s since nx is odd\n", regtype[header->registration]);
}
}
}
else { /* Data seems OK; determine registration */
dummy[0] = xy[0], dummy[1] = xy[header->n_columns-1];
if (set_reg && (fabs(dummy[1] - dummy[0]) / fabs(xy[header->n_columns-1] - xy[0]) - 1.0 > 0.5 / (header->n_columns - 1)))
registration = header->registration = GMT_GRID_PIXEL_REG;
}
}
else if (has_vector) { /* No attribute for range, use coordinates */
dummy[0] = xy[0], dummy[1] = xy[header->n_columns-1];
threshold = (0.5-GMT_CONV5_LIMIT) * dx;
if (set_reg && fabs (fmod (dummy[0], dx)) > threshold) { /* Most likely pixel registration since off by dx/2 */
registration = header->registration = GMT_GRID_PIXEL_REG;
dummy[0] -= 0.5 * dx; dummy[1] += 0.5 * dx;
if (gmt_M_360_range (dummy[0], dummy[1]))
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "Grid x-coordinates after pixel registration adjustment have exactly 360 range\n");
}
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "No range attribute, guessing registration to be %s\n", regtype[header->registration]);
}
else { /* Only has the valid_range settings. If no registration set, and no dx available, guess based on nx */
if (set_reg && (header->n_columns%2) == 0) { /* Pixel registration */
registration = header->registration = GMT_GRID_PIXEL_REG;
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "No x-coordinates, guessing registration to be %s since nx is odd\n", regtype[header->registration]);
}
}
/* Determine grid step */
header->inc[GMT_X] = gmt_M_get_inc (GMT, dummy[0], dummy[1], header->n_columns, registration);
if (gmt_M_is_dnan(header->inc[GMT_X]) || gmt_M_is_zero (header->inc[GMT_X])) header->inc[GMT_X] = 1.0;
if (header->n_columns == 1) registration = GMT_GRID_PIXEL_REG; /* The only way to have a grid like that */
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "x registration: %u\n", header->registration);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "x dummy: %g %g\n", dummy[0], dummy[1]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "x[0] x[nx-1]: %g %g\n", xy[0], xy[header->n_columns-1]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "xinc: %g %g\n", header->inc[GMT_X]);
#endif
/* Extend x boundaries by half if we found pixel registration */
if (registration == GMT_GRID_NODE_REG && header->registration == GMT_GRID_PIXEL_REG)
header->wesn[XLO] = dummy[0] - header->inc[GMT_X] / 2.0,
header->wesn[XHI] = dummy[1] + header->inc[GMT_X] / 2.0;
else /* Use as is */
header->wesn[XLO] = dummy[0], header->wesn[XHI] = dummy[1];
/* Get information about y variable */
gmtnc_get_units (GMT, ncid, ids[HH->xy_dim[1]], header->y_units);
/* Set default range to number of nodes in case nothing is found further down */
dummy[0] = 0.0, dummy[1] = (double) header->n_rows-1; /* Default */
registration = GMT_GRID_NODE_REG;
/* Read the y-coordinate vector (if available), otherwise just look for range attributes */
if ((has_vector = !nc_get_var_double (ncid, ids[HH->xy_dim[1]], xy)) && header->n_rows > 1) {
var_spacing = gmtnc_check_step (GMT, header->n_rows, xy, header->y_units, HH->name, save_xy_array);
if (save_xy_array && var_spacing) {
if (GMT->current.io.nc_yarray) gmt_M_free (GMT, GMT->current.io.nc_yarray);
GMT->current.io.nc_yarray = gmt_M_memory (GMT, NULL, header->n_rows, double);
gmt_M_memcpy (GMT->current.io.nc_yarray, xy, header->n_rows, double);
HH->var_spacing[GMT_Y] = var_spacing;
/* Flip-ud y-array since row = 0 is the last value */
gmt_grd_flip_vertical (GMT->current.io.nc_yarray, 1, header->n_rows, 0, sizeof(double));
}
dummy[0] = xy[0], dummy[1] = xy[header->n_rows-1];
dy = fabs (xy[1] - xy[0]); /* Grid spacing in y */
}
if (has_vector && header->n_rows == 1) has_vector = false; /* One coordinate does not a vector make */
has_range = (!nc_get_att_double (ncid, ids[HH->xy_dim[1]], "actual_range", dummy) ||
!nc_get_att_double (ncid, ids[HH->xy_dim[1]], "valid_range", dummy) ||
!(nc_get_att_double (ncid, ids[HH->xy_dim[1]], "valid_min", &dummy[0]) +
nc_get_att_double (ncid, ids[HH->xy_dim[1]], "valid_max", &dummy[1])));
if (has_vector && has_range) { /* Has both so we can do a basic sanity check */
threshold = (0.5+GMT_CONV5_LIMIT) * dy;
min = xy[0]; max = xy[header->n_rows-1];
if (min > max) gmt_M_double_swap (min, max); /* Got it backwards in the array */
if (fabs (dummy[0] - min) > threshold || fabs (dummy[1] - max) > threshold) {
if (gmtnc_not_obviously_polar (dummy)) {
GMT_Report (GMT->parent, GMT_MSG_WARNING, "The y-coordinates and range attribute are in conflict; must rely on coordinates only\n");
dummy[0] = xy[0], dummy[1] = xy[header->n_rows-1];
has_range = false; /* Since useless information */
/* Registration was set using x values, so here we just check that we get the same result.
* If the coordinates are off by 0.5*dy then we assume we have pixel registration */
threshold = (0.5-GMT_CONV5_LIMIT) * dy;
if (fabs (fmod (dummy[0], dy)) > threshold) { /* Pixel registration? */
if (header->registration == GMT_GRID_NODE_REG) /* No, somehow messed up now */
GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
else { /* Pixel registration confirmed */
dummy[0] -= 0.5 * dy; dummy[1] += 0.5 * dy;
registration = GMT_GRID_PIXEL_REG;
if (gmt_M_180_range (dummy[0], dummy[1]))
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "Grid y-coordinates after pixel registration adjustment have exactly 180 range\n");
}
}
}
else {
GMT_Report (GMT->parent, GMT_MSG_WARNING, "The y-coordinates and range attribute are in conflict but range is exactly 180; we rely on this range\n");
if ((header->n_rows%2) == 1 && header->registration == GMT_GRID_NODE_REG) /* Pixel registration? */
GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
else
registration = header->registration;
}
}
else { /* Data seems OK; determine registration and set dummy from data coordinates */
dummy[0] = xy[0], dummy[1] = xy[header->n_rows-1];
if ((fabs(dummy[1] - dummy[0]) / fabs(xy[header->n_rows-1] - xy[0]) - 1.0 > 0.5 / (header->n_rows - 1)) && header->registration == GMT_GRID_NODE_REG)
GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
}
}
else if (has_vector) { /* No attribute for range, use coordinates */
threshold = (0.5-GMT_CONV5_LIMIT) * dy;
dummy[0] = xy[0], dummy[1] = xy[header->n_rows-1];
if (fabs (fmod (dummy[0], dy)) > threshold) { /* Most likely pixel registration since off by dy/2 */
if (header->registration == GMT_GRID_NODE_REG) /* No, somehow messed up now */
GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
else { /* Pixel registration confirmed */
if (dummy[0] > dummy[1]) { /* Check for reverse order of y-coordinate */
gmt_M_double_swap (dummy[0], dummy[1]);
HH->row_order = k_nc_start_north;
}
dummy[0] -= 0.5 * dy; dummy[1] += 0.5 * dy;
registration = GMT_GRID_PIXEL_REG;
if (gmt_M_180_range (dummy[0], dummy[1]))
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "Grid y-coordinates after pixel registration adjustment have exactly 180 range\n");
}
}
}
else { /* Only has the valid_range settings. If no registration set, and no dy available, guess based on ny */
if ((header->n_rows%2) == 1 && header->registration == GMT_GRID_NODE_REG) /* Pixel registration? */
GMT_Report (GMT->parent, GMT_MSG_WARNING, "Guessing of registration in conflict between x and y, using %s\n", regtype[header->registration]);
}
/* Check for reverse order of y-coordinate */
if (dummy[0] > dummy[1]) {
HH->row_order = k_nc_start_north;
gmt_M_double_swap (dummy[0], dummy[1]);
}
else if (has_vector && (xy[0] > xy[header->n_rows-1]) && (dummy[0] > dummy[1])) /* Here the lat vector is top-down but range is bottum-up */
HH->row_order = k_nc_start_north;
else if (HH->row_order != k_nc_start_north) /* If not already set to north in an above test */
HH->row_order = k_nc_start_south;
/* Determine grid step */
header->inc[GMT_Y] = gmt_M_get_inc (GMT, dummy[0], dummy[1], header->n_rows, registration);
if (gmt_M_is_dnan(header->inc[GMT_Y]) || gmt_M_is_zero (header->inc[GMT_Y])) header->inc[GMT_Y] = 1.0;
if (header->n_rows == 1) registration = GMT_GRID_PIXEL_REG; /* The only way to have a grid like that */
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "y registration: %u\n", header->registration);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "y dummy: %g %g\n", dummy[0], dummy[1]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "y[0] y[ny-1]: %g %g\n", xy[0], xy[header->n_rows-1]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "xinc: %g %g\n", header->inc[GMT_Y]);
#endif
/* Extend y boundaries by half if we found pixel registration */
if (registration == GMT_GRID_NODE_REG && header->registration == GMT_GRID_PIXEL_REG)
header->wesn[YLO] = dummy[0] - header->inc[GMT_Y] / 2.0,
header->wesn[YHI] = dummy[1] + header->inc[GMT_Y] / 2.0;
else /* Use as is */
header->wesn[YLO] = dummy[0], header->wesn[YHI] = dummy[1];
gmt_M_free (GMT, xy); /* Done with the array */
/* Get information about z variable */
gmtnc_get_units (GMT, ncid, z_id, header->z_units);
if (nc_get_att_double (ncid, z_id, "scale_factor", &header->z_scale_factor)) header->z_scale_factor = 1.0;
if (nc_get_att_double (ncid, z_id, "add_offset", &header->z_add_offset)) header->z_add_offset = 0.0;
#ifdef DOUBLE_PRECISION_GRID
if (nc_get_att_double (ncid, z_id, "_FillValue", &header->nan_value))
nc_get_att_double (ncid, z_id, "missing_value", &header->nan_value);
#else
if (nc_get_att_float (ncid, z_id, "_FillValue", &header->nan_value))
nc_get_att_float (ncid, z_id, "missing_value", &header->nan_value);
#endif
if (!nc_get_att_double (ncid, z_id, "actual_range", dummy)) {
/* z-limits need to be converted from actual to internal grid units. */
header->z_min = (dummy[0] - header->z_add_offset) / header->z_scale_factor;
header->z_max = (dummy[1] - header->z_add_offset) / header->z_scale_factor;
}
else if (!nc_get_att_double (ncid, z_id, "valid_range", dummy) ||
!(nc_get_att_double (ncid, ids[HH->xy_dim[1]], "valid_min", &dummy[0]) +
nc_get_att_double (ncid, ids[HH->xy_dim[1]], "valid_max", &dummy[1]))) {
/* Valid range is already in packed units, so do not convert */
header->z_min = dummy[0], header->z_max = dummy[1];
}
if (gmtlib_nc_get_att_vtext (GMT, ncid, z_id, "cpt", header, NULL, 0) == NC_NOERR) /* Found cpt attribute */
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "netCDF grid %s has a default CPT %s.\n", HH->name, HH->cpt);
else
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "netCDF grid %s has no default CPT.\n", HH->name);
if (gmt_M_is_dnan (header->z_min) && gmt_M_is_dnan (header->z_max)) {
GMT_Report (GMT->parent, GMT_MSG_INFORMATION, "netCDF grid %s information has zmin = zmax = NaN. Reset to 0/0.\n", HH->name);
header->z_min = header->z_max = 0.0;
}
{ /* Get deflation and chunking info */
int storage_mode, shuffle = 0, deflate = 0, deflate_level = 0;
size_t chunksize[5]; /* chunksize of z */
gmt_M_err_trap (nc_inq_var_chunking (ncid, z_id, &storage_mode, chunksize));
if (storage_mode == NC_CHUNKED) {
HH->z_chunksize[0] = chunksize[dims[0]]; /* chunk size in vertical dimension */
HH->z_chunksize[1] = chunksize[dims[1]]; /* chunk size in horizontal dimension */
}
else { /* NC_CONTIGUOUS */
HH->z_chunksize[0] = HH->z_chunksize[1] = 0;
}
if (HH->is_netcdf4) gmt_M_err_trap (nc_inq_var_deflate (ncid, z_id, &shuffle, &deflate, &deflate_level));
HH->z_shuffle = shuffle ? true : false; /* if shuffle filter is turned on */
HH->z_deflate_level = deflate ? deflate_level : 0; /* if deflate filter is in use */
}
/* Determine t_index from t_value */
item[0] = 0;
for (i = 0; i < n_t_index_by_value; i++) {
item[1] = lens[i]-1;
if (nc_get_att_double (ncid, ids[i], "actual_range", dummy)) {
gmt_M_err_trap (nc_get_var1_double (ncid, ids[i], &item[0], &dummy[0]));
gmt_M_err_trap (nc_get_var1_double (ncid, ids[i], &item[1], &dummy[1]));
}
if (item[1] != 0 && dummy[0] != dummy[1]) { /* avoid dvision by 0 */
double index = (t_value[i] - dummy[0]) / (dummy[1] - dummy[0]) * item[1];
if (index > 0)
HH->t_index[i] = (size_t)index;
}
}
#ifdef NC4_DEBUG
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->wesn: %g %g %g %g\n",
header->wesn[XLO], header->wesn[XHI], header->wesn[YLO], header->wesn[YHI]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->registration:%u\n", header->registration);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->row_order: %s\n",
HH->row_order == k_nc_start_south ? "S->N" : "N->S");
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->n_columns: %3d head->n_rows:%3d\n", header->n_columns, header->n_rows);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->inc: %g %g\n", header->inc[GMT_X], header->inc[GMT_Y]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->mx: %3d head->my:%3d\n", header->mx, header->my);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->nm: %3d head->size:%3d\n", header->nm, header->size);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->t-index %d,%d,%d\n",
HH->t_index[0], HH->t_index[1], HH->t_index[2]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->pad xlo:%u xhi:%u ylo:%u yhi:%u\n",
header->pad[XLO], header->pad[XHI], header->pad[YLO], header->pad[YHI]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->BC xlo:%u xhi:%u ylo:%u yhi:%u\n",
HH->BC[XLO], HH->BC[XHI], HH->BC[YLO], HH->BC[YHI]);
GMT_Report (GMT->parent, GMT_MSG_WARNING, "head->grdtype:%u %u\n", HH->grdtype, GMT_GRID_GEOGRAPHIC_EXACT360_REPEAT);
#endif
}
else { /* Here we are writing */
/* Store global attributes */
const int *nc_vers = gmtnc_netcdf_libvers();
GMT_Report (GMT->parent, GMT_MSG_DEBUG, "netCDF Library version: %d\n", *nc_vers);
gmt_M_err_trap (nc_put_att_text (ncid, NC_GLOBAL, "Conventions", strlen(GMT_NC_CONVENTION), GMT_NC_CONVENTION));
gmt_M_err_trap (gmtlib_nc_put_att_vtext (GMT, ncid, "title", header));
gmt_M_err_trap (gmtlib_nc_put_att_vtext (GMT, ncid, "history", header));
gmt_M_err_trap (gmtlib_nc_put_att_vtext (GMT, ncid, "description", header));
gmt_M_err_trap (nc_put_att_text (ncid, NC_GLOBAL, "GMT_version", strlen(GMT_VERSION), (const char *) GMT_VERSION));
if (header->registration == GMT_GRID_PIXEL_REG) {
int reg = header->registration;
gmt_M_err_trap (nc_put_att_int (ncid, NC_GLOBAL, "node_offset", NC_LONG, 1U, ®));
}
else
nc_del_att (ncid, NC_GLOBAL, "node_offset");
/* If we have projection information create a container variable named "grid_mapping" with an attribute
"spatial_ref" that will hold the projection info in WKT format. GDAL and Mirone know use this info */
if ((header->ProjRefWKT != NULL) || (header->ProjRefPROJ4 != NULL)) {
int id[1], dim[1];
if (header->ProjRefWKT == NULL || !header->ProjRefWKT[0]) { /* Must convert from proj4 string to WKT */
OGRSpatialReferenceH hSRS = OSRNewSpatialReference(NULL);
if (header->ProjRefPROJ4 && (!strncmp(header->ProjRefPROJ4, "+unavailable", 4) || strlen(header->ProjRefPROJ4) <= 5)) { /* Silently jump out of here */
OSRDestroySpatialReference(hSRS);
goto L100;
}
GMT_Report(GMT->parent, GMT_MSG_INFORMATION, "Proj4 string to be converted to WKT:\n\t%s\n", header->ProjRefPROJ4);
if (OSRImportFromProj4(hSRS, header->ProjRefPROJ4) == CE_None) {
char *pszPrettyWkt = NULL;
OSRExportToPrettyWkt(hSRS, &pszPrettyWkt, false);
header->ProjRefWKT = strdup(pszPrettyWkt);
CPLFree(pszPrettyWkt);
GMT_Report(GMT->parent, GMT_MSG_INFORMATION, "WKT converted from proj4 string:\n%s\n", header->ProjRefWKT);
}
else {
header->ProjRefWKT = NULL;
GMT_Report(GMT->parent, GMT_MSG_WARNING, "gmtnc_grd_info failed to convert the proj4 string\n%s\n to WKT\n",
header->ProjRefPROJ4);