/*--------------------------------------------------------------------
 *	$Id: grdrotater.c 18110 2017-05-03 01:29:16Z pwessel $
 *
 *   Copyright (c) 1999-2017 by P. Wessel
 *
 *   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.soest.hawaii.edu/pwessel
 *--------------------------------------------------------------------*/
/*
 * grdrotater will read a grid file, apply a finite rotation to the grid
 * coordinates, and then interpolate the old grid at the new coordinates.
 *
 * Author:	Paul Wessel
 * Date:	27-JAN-2006
 * Ver:		1
 */

#include "gmt_dev.h"
#include "spotter.h"

#define THIS_MODULE_NAME	"grdrotater"
#define THIS_MODULE_LIB		"spotter"
#define THIS_MODULE_PURPOSE	"Finite rotation reconstruction of geographic grid"
#define THIS_MODULE_KEYS	"<G{,FD(,GG},TD("
#define THIS_MODULE_NEEDS	"g"
#define THIS_MODULE_OPTIONS "-:>RVbdfghno" GMT_OPT("HMmQ")

#define PAD 3	/* Used to polish up a rotated grid by checking near neighbor nodes */

struct GRDROTATER_CTRL {	/* All control options for this program (except common args) */
	/* active is true if the option has been activated */
	struct In {
		bool active;
		char *file;
	} In;
	struct D {	/* -Drotpolfile or -Dtemplate */
		bool active;
		char *file;
	} D;
	struct E {	/* -E[+]rotfile, -E[+]<ID1>-<ID2>, or -E<lon/lat/angle> */
		bool active;
		struct SPOTTER_ROT rot;
	} E;
	struct F {	/* -Fpolfile */
		bool active;
		char *file;
	} F;
	struct G {	/* -Goutfile or -Gtemplate*/
		bool active;
		char *file;
	} G;
	struct N {	/* -N */
		bool active;
	} N;
	struct S {	/* -S */
		bool active;
	} S;
	struct T {	/* -T<time>, -T<start/stop/inc> or -T<tfile.txt> */
		bool active;
		unsigned int n_times;	/* Number of reconstruction times */
		double *value;	/* Array with one or more reconstruction times */
	} T;
};

GMT_LOCAL void *New_Ctrl (struct GMT_CTRL *GMT) {	/* Allocate and initialize a new control structure */
	struct GRDROTATER_CTRL *C;

	C = gmt_M_memory (GMT, NULL, 1, struct GRDROTATER_CTRL);

	return (C);
}

GMT_LOCAL void Free_Ctrl (struct GMT_CTRL *GMT, struct GRDROTATER_CTRL *C) {	/* Deallocate control structure */
	if (!C) return;
	gmt_M_str_free (C->In.file);	
	gmt_M_str_free (C->D.file);	
	gmt_M_str_free (C->E.rot.file);	
	gmt_M_str_free (C->F.file);	
	gmt_M_str_free (C->G.file);	
	gmt_M_str_free (C->T.value);	
	gmt_M_free (GMT, C);	
}

GMT_LOCAL int usage (struct GMTAPI_CTRL *API, int level) {
	gmt_show_name_and_purpose (API, THIS_MODULE_LIB, THIS_MODULE_NAME, THIS_MODULE_PURPOSE);
	if (level == GMT_MODULE_PURPOSE) return (GMT_NOERROR);
	GMT_Message (API, GMT_TIME_NONE, "usage: grdrotater <grid> %s -G<outgrid> [-F<polygontable>]\n", SPOTTER_E_OPT);
	GMT_Message (API, GMT_TIME_NONE, "\t[-D<rotoutline>] [-N] [%s] [-S] [-T<time(s)>] [%s]\n", GMT_Rgeo_OPT, GMT_V_OPT);
	GMT_Message (API, GMT_TIME_NONE, "\t[%s] [%s] [%s]\n\t[%s]\n\t[%s] [%s]\n\n", GMT_b_OPT, GMT_d_OPT, GMT_g_OPT, GMT_h_OPT, GMT_n_OPT, GMT_o_OPT);

	if (level == GMT_SYNOPSIS) return (GMT_MODULE_SYNOPSIS);

	GMT_Message (API, GMT_TIME_NONE, "\t<grid> is the gridded data file in geographic coordinates to be rotated.\n");
	GMT_Message (API, GMT_TIME_NONE, "\t-G Set output filename for the new, rotated grid.  The boundary of the\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   original grid (or a subset; see -F) after rotation is written to stdout (but see -D)\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   unless the grid is global.  If more than one reconstruction time is chosen\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   then -D is required unless -N is used and <outgrid> must be a filename template\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   containing a C-format specifier for formatting a double (for the variable time).\n");
	spotter_rot_usage (API, 'E');
	GMT_Message (API, GMT_TIME_NONE, "\t   Alternatively, specify a single finite rotation (in degrees) to be applied.\n");
	GMT_Message (API, GMT_TIME_NONE, "\n\tOPTIONS:\n");
	GMT_Message (API, GMT_TIME_NONE, "\t-D Write the rotated polygon or grid outline to <rotoutline> [stdout].\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   Required if more than one reconstruction time is chosen and -N is not set\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   and must then contain a C-format specifier for formatting a double (for the variable time).\n");
	GMT_Message (API, GMT_TIME_NONE, "\t-F Specify a multi-segment closed polygon table that describes the area of the grid\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   that should be projected [Default projects entire grid].\n");
	GMT_Message (API, GMT_TIME_NONE, "\t-N Do NOT output the rotated polygon or grid outlines.\n");
	GMT_Option (API, "Rg");
	GMT_Message (API, GMT_TIME_NONE, "\t-S Do NOT rotate the grid - just produce the rotated outlines (requires -D).\n");
	GMT_Message (API, GMT_TIME_NONE, "\t-T Set the time(s) of reconstruction.  Append a single time (-T<time>),\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   an equidistant range of times (-T<min>/<max>/<inc> or -T<min>/<max>/<npoints>+),\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   or the name of a file with a list of times (-T<tfile>).  If no -T is set\n");
	GMT_Message (API, GMT_TIME_NONE, "\t   then the reconstruction times equal the rotation times given in -E.\n");
	GMT_Option (API, "V,bi2,bo,d,g,h,n,:,.");

	return (GMT_MODULE_USAGE);

}

GMT_LOCAL int parse (struct GMT_CTRL *GMT, struct GRDROTATER_CTRL *Ctrl, struct GMT_OPTION *options) {
	/* This parses the options provided to grdrotater and sets parameters in CTRL.
	 * Any GMT common options will override values set previously by other commands.
	 * It also replaces any file names specified as input or output with the data ID
	 * returned when registering these sources/destinations with the API.
	 */

	unsigned int n_errors = 0, k, n_files = 0;
	uint64_t t = 0;
	bool gave_e = false;
	char txt_a[GMT_LEN256] = {""}, txt_b[GMT_LEN256] = {""}, txt_c[GMT_LEN256] = {""};
	struct GMT_OPTION *opt = NULL;
	struct GMTAPI_CTRL *API = GMT->parent;

	for (opt = options; opt; opt = opt->next) if (opt->option == 'E' || opt->option == 'e') gave_e = true;	/* Pre-check to see if GMT4 or newer syntax */

	for (opt = options; opt; opt = opt->next) {
		switch (opt->option) {

			case '<':	/* Input files */
				if (n_files++ > 0) break;
				if ((Ctrl->In.active = gmt_check_filearg (GMT, '<', opt->arg, GMT_IN, GMT_IS_GRID)) != 0)
					Ctrl->In.file = strdup (opt->arg);
				else
					n_errors++;
				break;

			/* Supplemental parameters */

			case 'C':	/* Now done automatically in spotter_init */
				if (gmt_M_compat_check (GMT, 4))
					GMT_Report (API, GMT_MSG_COMPAT, "Warning: -C is no longer needed as total reconstruction vs stage rotation is detected automatically.\n");
				else
					n_errors += gmt_default_error (GMT, opt->option);
				break;
			case 'D':
				Ctrl->D.active = true;
				Ctrl->D.file = strdup (opt->arg);
				break;
			case 'e':
				GMT_Report (API, GMT_MSG_COMPAT, "Warning: -e is deprecated and will be removed in 5.2.x. Use -E instead.\n");
				/* Fall-through on purpose */
			case 'E':	/* File with stage poles or a single rotation pole */
				Ctrl->E.active = true;
				n_errors += spotter_parse (GMT, opt->option, opt->arg, &(Ctrl->E.rot));
				break;
			case 'F':
				if ((Ctrl->F.active = gmt_check_filearg (GMT, 'F', opt->arg, GMT_IN, GMT_IS_DATASET)) != 0)
					Ctrl->F.file = strdup (opt->arg);
				else
					n_errors++;
				break;
			case 'G':
				if ((Ctrl->G.active = gmt_check_filearg (GMT, 'G', opt->arg, GMT_OUT, GMT_IS_GRID)) != 0)
					Ctrl->G.file = strdup (opt->arg);
				else
					n_errors++;
				break;
			case 'N':
				Ctrl->N.active = true;
				break;
			case 'S':
				Ctrl->S.active = true;
				break;
			case 'T':	/* New: -Tage, -Tmin/max/inc, -Tmin/max/n+, -Tfile; compat mode: -Tlon/lat/angle Finite rotation parameters */
				Ctrl->T.active = true;
				if (!gmt_access (GMT, opt->arg, R_OK)) {	/* Gave a file with times in first column */
					uint64_t seg, row;
					struct GMT_DATASET *T = NULL;
					struct GMT_DATASEGMENT *S = NULL;
					if ((T = GMT_Read_Data (API, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_NONE, GMT_READ_NORMAL, NULL, opt->arg, NULL)) == NULL) {
						GMT_Report (API, GMT_MSG_NORMAL, "Error reading file %s\n", opt->arg);
						n_errors++;
						continue;
					}
					/* Single table, build t array */
					Ctrl->T.n_times = (unsigned int)T->n_records;
					Ctrl->T.value = gmt_M_memory (GMT, NULL, Ctrl->T.n_times, double);
					for (seg = t = 0; seg < T->table[0]->n_segments; seg++) {
						S = T->table[0]->segment[seg];	/* Shorthand to current segment */
						for (row = 0; row < S->n_rows; seg++, t++)
							Ctrl->T.value[t] = S->data[GMT_X][row];
					}
					if (GMT_Destroy_Data (API, &T) != GMT_NOERROR)
						n_errors++;
					break;
				}
				/* Not a file */
				k = sscanf (opt->arg, "%[^/]/%[^/]/%s", txt_a, txt_b, txt_c);
				if (k == 3) {	/* Gave -Ttstart/tstop/tinc or possibly ancient -Tlon/lat/angle */
					if (gmt_M_compat_check (GMT, 4) && !gave_e) {	/* No -E|e so likely ancient syntax */
						GMT_Report (API, GMT_MSG_COMPAT, "Warning: -T<lon>/<lat>/<angle> is deprecated; use -E<lon>/<lat>/<angle> instead.\n");
						Ctrl->E.rot.single = Ctrl->E.active = true;
						Ctrl->T.active = false;
						Ctrl->E.rot.w = atof (txt_c);
						Ctrl->E.rot.age = GMT->session.d_NaN;
						n_errors += gmt_verify_expectations (GMT, GMT->current.io.col_type[GMT_IN][GMT_X], gmt_scanf_arg (GMT, txt_a, GMT->current.io.col_type[GMT_IN][GMT_X], &Ctrl->E.rot.lon), txt_a);
						n_errors += gmt_verify_expectations (GMT, GMT->current.io.col_type[GMT_IN][GMT_Y], gmt_scanf_arg (GMT, txt_b, GMT->current.io.col_type[GMT_IN][GMT_Y], &Ctrl->E.rot.lat), txt_b);
					}
					else {	/* Must be Ttstart/tstop/tinc */
						double min, max, inc;
						min = atof (txt_a);	max = atof (txt_b);	inc = atof (txt_c);
						if (opt->arg[strlen(opt->arg)-1] == '+')	/* Gave number of points instead; calculate inc */
							inc = (max - min) / (inc - 1.0);
						if (inc <= 0.0) {
							GMT_Report (API, GMT_MSG_NORMAL, "Syntax error -T option: Age increment must be positive\n");
							n_errors++;
						}
						else {
							Ctrl->T.n_times = lrint ((max - min) / inc) + 1;
							Ctrl->T.value = gmt_M_memory (GMT, NULL, Ctrl->T.n_times, double);
							for (t = 0; t < Ctrl->T.n_times; t++) Ctrl->T.value[t] = (t == (Ctrl->T.n_times-1)) ? max: min + t * inc;
						}
					}
				}
				else {	/* Got a single time */
					Ctrl->T.n_times = 1;
					Ctrl->T.value = gmt_M_memory (GMT, NULL, Ctrl->T.n_times, double);
					Ctrl->T.value[0] = atof (txt_a);
				}
				break;

			default:	/* Report bad options */
				n_errors += gmt_default_error (GMT, opt->option);
				break;
		}
	}

        if (GMT->common.b.active[GMT_IN] && GMT->common.b.ncol[GMT_IN] == 0) GMT->common.b.ncol[GMT_IN] = 2;
	n_errors += gmt_M_check_condition (GMT, Ctrl->S.active && Ctrl->G.active, "Syntax error: No output grid file allowed with -S\n");
	n_errors += gmt_M_check_condition (GMT, Ctrl->S.active && Ctrl->N.active, "Syntax error: Cannot use -N with -S\n");
	n_errors += gmt_M_check_condition (GMT, !Ctrl->S.active && !Ctrl->In.file, "Syntax error: Must specify input file\n");
	n_errors += gmt_M_check_condition (GMT, !Ctrl->S.active && !Ctrl->G.file, "Syntax error -G: Must specify output file\n");
	n_errors += gmt_M_check_condition (GMT, Ctrl->S.active && Ctrl->N.active, "Syntax error: -N and -S cannot both be given\n");
	n_errors += gmt_M_check_condition (GMT, GMT->common.b.active[GMT_IN] && GMT->common.b.ncol[GMT_IN] < 3,
	                                 "Syntax error: Binary input data (-bi) must have at least 2 columns\n");
	n_errors += gmt_M_check_condition (GMT, Ctrl->D.active && Ctrl->N.active, "Syntax error: -N and -D cannot both be given\n");
	n_errors += gmt_M_check_condition (GMT, !Ctrl->E.active, "Syntax error: Option -E is required\n");

	return (n_errors ? GMT_PARSE_ERROR : GMT_NOERROR);
}

GMT_LOCAL struct GMT_DATASET *get_grid_path (struct GMT_CTRL *GMT, struct GMT_GRID_HEADER *h) {
	/* Return a single polygon that encloses this geographic grid exactly.
	 * It is used in the case when no particular clip polygon has been given.
	 * Note that the path is the same for pixel or grid-registered grids.
	 */

	unsigned int np = 0, add, col, row;
	uint64_t dim[GMT_DIM_SIZE] = {1, 1, 0, 2};
	struct GMT_DATASET *D = NULL;
	struct GMT_DATASEGMENT *S = NULL;

	if ((D = GMT_Create_Data (GMT->parent, GMT_IS_DATASET, GMT_IS_POLY, 0, dim, NULL, NULL, 0, 0, NULL)) == NULL)
		return (NULL);	/* An empty table with one segment, two cols */

	S = D->table[0]->segment[0];	/* Short hand */

	/* Add south border w->e */
	if (h->wesn[YLO] == -90.0) {	/* If at the S pole we just add it twice for end longitudes */
		add = 2;
		S->data[GMT_X] = gmt_M_memory (GMT, NULL, add, double);
		S->data[GMT_Y] = gmt_M_memory (GMT, NULL, add, double);
		S->data[GMT_X][0] = h->wesn[XLO];	S->data[GMT_X][1] = h->wesn[XHI];
		S->data[GMT_Y][0] = S->data[GMT_Y][1] = h->wesn[YLO];
	}
	else {				/* Loop along south border from west to east */
		add = h->n_columns - !h->registration;
		S->data[GMT_X] = gmt_M_memory (GMT, NULL, add, double);
		S->data[GMT_Y] = gmt_M_memory (GMT, NULL, add, double);
		for (col = 0; col < add; col++) {
			S->data[GMT_X][col] = gmt_M_col_to_x (GMT, col, h->wesn[XLO], h->wesn[XHI], h->inc[GMT_X], 0.0, h->n_columns);
			S->data[GMT_Y][col] = h->wesn[YLO];
		}
	}
	np += add;
	/* Add east border s->n */
	add = h->n_rows - !h->registration;
	S->data[GMT_X] = gmt_M_memory (GMT, S->data[GMT_X], add + np, double);
	S->data[GMT_Y] = gmt_M_memory (GMT, S->data[GMT_Y], add + np, double);
	for (row = 0; row < add; row++) {	/* Loop along east border from south to north */
		S->data[GMT_X][np+row] = h->wesn[XHI];
		S->data[GMT_Y][np+row] = gmt_M_row_to_y (GMT, h->n_rows - 1 - row, h->wesn[YLO], h->wesn[YHI], h->inc[GMT_Y], 0.0, h->n_rows);
	}
	np += add;
	/* Add north border e->w */
	if (h->wesn[YHI] == 90.0) {	/* If at the N pole we just add it twice for end longitudes */
		add = 2;
		S->data[GMT_X] = gmt_M_memory (GMT, S->data[GMT_X], add + np, double);
		S->data[GMT_Y] = gmt_M_memory (GMT, S->data[GMT_Y], add + np, double);
		S->data[GMT_X][np] = h->wesn[XHI];	S->data[GMT_X][np+1] = h->wesn[XLO];
		S->data[GMT_Y][np] = S->data[GMT_Y][np+1] = h->wesn[YHI];
	}
	else {			/* Loop along north border from east to west */
		add = h->n_columns - !h->registration;
		S->data[GMT_X] = gmt_M_memory (GMT, S->data[GMT_X], add + np, double);
		S->data[GMT_Y] = gmt_M_memory (GMT, S->data[GMT_Y], add + np, double);
		for (col = 0; col < add; col++) {
			S->data[GMT_X][np+col] = gmt_M_col_to_x (GMT, h->n_columns - 1 - col, h->wesn[XLO], h->wesn[XHI], h->inc[GMT_X], 0.0, h->n_columns);
			S->data[GMT_Y][np+col] = h->wesn[YHI];
		}
	}
	np += add;
	/* Add west border n->s */
	add = h->n_rows - !h->registration;
	S->data[GMT_X] = gmt_M_memory (GMT, S->data[GMT_X], add + np + 1, double);
	S->data[GMT_Y] = gmt_M_memory (GMT, S->data[GMT_Y], add + np + 1, double);
	for (row = 0; row < add; row++) {	/* Loop along west border from north to south */
		S->data[GMT_X][np+row] = h->wesn[XLO];
		S->data[GMT_Y][np+row] = gmt_M_row_to_y (GMT, row, h->wesn[YLO], h->wesn[YHI], h->inc[GMT_Y], 0.0, h->n_rows);
	}
	np += add;
	S->data[GMT_X][np] = S->data[GMT_X][0];	/* Close polygon explicitly */
	S->data[GMT_Y][np] = S->data[GMT_Y][0];
	np++;
	S->n_rows = np;
	S->n_columns = 2;
	S->min[GMT_X] = h->wesn[XLO];	S->max[GMT_X] = h->wesn[XHI];
	S->min[GMT_Y] = h->wesn[YLO];	S->max[GMT_Y] = h->wesn[YHI];
	S->pole = 0;
	S->alloc_mode = GMT_ALLOC_INTERNALLY;

	return (D);
}

GMT_LOCAL bool skip_if_outside (struct GMT_CTRL *GMT, struct GMT_DATATABLE *P, double lon, double lat) {
	/* Returns true if the selected point is outside the polygon */
	uint64_t seg;
	unsigned int inside = 0;
	for (seg = 0; seg < P->n_segments && !inside; seg++) {	/* Use degrees since function expects it */
		if (gmt_M_polygon_is_hole (P->segment[seg])) continue;	/* Holes are handled within gmt_inonout */
		inside = (gmt_inonout (GMT, lon, lat, P->segment[seg]) > 0);
	}
	return ((inside) ? false : true);	/* true if outside */
}

#define bailout(code) {gmt_M_free_options (mode); return (code);}
#define Return(code) {Free_Ctrl (GMT, Ctrl); gmt_end_module (GMT, GMT_cpy); bailout (code);}

int GMT_grdrotater (void *V_API, int mode, void *args) {
	int scol, srow, error = 0;	/* Signed row, col */
	int n_stages;
	bool not_global, global = false;
	unsigned int col, row, col_o, row_o, start_row, stop_row, start_col, stop_col;
	char gfile[GMT_BUFSIZ] = {""};

	uint64_t ij, ij_rot, seg, rec, t;

	double xx, yy, lon, P_original[3], P_rotated[3], R[3][3], plon, plat, pw;
	double *grd_x = NULL, *grd_y = NULL, *grd_yc = NULL;

	struct EULER *p = NULL;			/* Pointer to array of stage poles */
	struct GMT_DATASET *D = NULL, *Dr = NULL;
	struct GMT_DATATABLE *pol = NULL, *polr = NULL;
	struct GMT_DATASEGMENT *S = NULL, *Sr = NULL;
	struct GMT_OPTION *ptr = NULL;
	struct GMT_GRID *G = NULL, *G_rot = NULL;
	struct GRDROTATER_CTRL *Ctrl = NULL;
	struct GMT_CTRL *GMT = NULL, *GMT_cpy = NULL;
	struct GMT_OPTION *options = NULL;
	struct GMTAPI_CTRL *API = gmt_get_api_ptr (V_API);	/* Cast from void to GMTAPI_CTRL pointer */

	/*----------------------- Standard module initialization and parsing ----------------------*/

	if (API == NULL) return (GMT_NOT_A_SESSION);
	if (mode == GMT_MODULE_PURPOSE) return (usage (API, GMT_MODULE_PURPOSE));	/* Return the purpose of program */
	options = GMT_Create_Options (API, mode, args);	if (API->error) return (API->error);	/* Set or get option list */

	if (!options || options->option == GMT_OPT_USAGE) bailout (usage (API, GMT_USAGE));	/* Return the usage message */
	if (options->option == GMT_OPT_SYNOPSIS) bailout (usage (API, GMT_SYNOPSIS));	/* Return the synopsis */

	/* Parse the command-line arguments */

	if ((GMT = gmt_init_module (API, THIS_MODULE_LIB, THIS_MODULE_NAME, THIS_MODULE_KEYS, THIS_MODULE_NEEDS, &options, &GMT_cpy)) == NULL) bailout (API->error); /* Save current state */
	if ((ptr = GMT_Find_Option (API, 'f', options)) == NULL) gmt_parse_common_options (GMT, "f", 'f', "g"); /* Did not set -f, implicitly set -fg */
	if (GMT_Parse_Common (API, THIS_MODULE_OPTIONS, options)) Return (API->error);
	Ctrl = New_Ctrl (GMT);	/* Allocate and initialize a new control structure */
	if ((error = parse (GMT, Ctrl, options)) != 0) Return (error);

	/*---------------------------- This is the grdrotater main code ----------------------------*/

	gmt_set_pad (GMT, 2U);	/* Ensure space for BCs in case an API passed pad == 0 */

	/* Check limits and get data file */

	if (Ctrl->In.file) {	/* Provided an input grid */
		if ((G = GMT_Read_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_CONTAINER_ONLY, NULL, Ctrl->In.file, NULL)) == NULL) {	/* Get header only */
			Return (API->error);
		}

		if (!GMT->common.R.active[RSET]) gmt_M_memcpy (GMT->common.R.wesn, G->header->wesn, 4, double);	/* -R was not set so we use the grid domain */

		/* Determine the wesn to be used to read the Ctrl->In.file; or exit if file is outside -R */

		if (!gmt_grd_setregion (GMT, G->header, GMT->common.R.wesn, BCR_BILINEAR)) {
			GMT_Report (API, GMT_MSG_NORMAL, "No grid values inside selected region - aborting\n");
			Return (GMT_RUNTIME_ERROR);
		}
		global = (doubleAlmostEqual (GMT->common.R.wesn[XHI] - GMT->common.R.wesn[XLO], 360.0)
							&& doubleAlmostEqual (GMT->common.R.wesn[YHI] - GMT->common.R.wesn[YLO], 180.0));
		if (!GMT->common.R.active[RSET]) global = gmt_M_grd_is_global (GMT, G->header);
	}
	not_global = !global;

	if (!Ctrl->S.active) {	/* Read the input grid */
		GMT_Report (API, GMT_MSG_VERBOSE, "Allocates memory and read grid file\n");
		if (GMT_Read_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_DATA_ONLY, GMT->common.R.wesn, Ctrl->In.file, G) == NULL) {
			Return (API->error);
		}
	}

	if (Ctrl->F.active) {	/* Read the user's polygon file */
		if ((D = GMT_Read_Data (API, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_POLY, GMT_READ_NORMAL, NULL, Ctrl->F.file, NULL)) == NULL) {
			Return (API->error);
		}
		pol = D->table[0];	/* Since we know it is a single file */
	}
	else if (not_global) {	/* Make a single grid-outline polygon */
		if (!G) {
			GMT_Report (API, GMT_MSG_NORMAL, "No grid give so cannot determine grid outline path\n");
			Return (API->error);
		}
		if ((D = get_grid_path (GMT, G->header)) == NULL) Return (API->error);
		pol = D->table[0];	/* Since we know it is a single file */
	}
	if (pol) {
		Dr = GMT_Duplicate_Data (API, GMT_IS_DATASET, GMT_DUPLICATE_ALLOC, D);	/* Same table length as D */
		polr = Dr->table[0];	/* Since we know it is also a single file */
	}

	if (Ctrl->E.rot.single) {	/* Got a single rotation, create a rotation table with one entry */
		Ctrl->T.n_times = n_stages = 1;
		p = gmt_M_memory (GMT, NULL, n_stages, struct EULER);
		p[0].lon = Ctrl->E.rot.lon; p[0].lat = Ctrl->E.rot.lat; p[0].omega = Ctrl->E.rot.w;
		if (gmt_M_is_dnan (Ctrl->E.rot.age)) {	/* No age, use fake age = 1 everywhere */
			Ctrl->T.value = gmt_M_memory (GMT, NULL, Ctrl->T.n_times, double);
			Ctrl->T.value[0] = p[0].t_start = 1.0;
		}
		spotter_setrot (GMT, &(p[0]));
	}
	else {	/* Got a rotation file with multiple rotations in total reconstruction format */
		double t_max = 0.0;
		n_stages = spotter_init (GMT, Ctrl->E.rot.file, &p, false, true, Ctrl->E.rot.invert, &t_max);
		gmt_set_segmentheader (GMT, GMT_OUT, true);
	}

	if (!Ctrl->T.active && !Ctrl->E.rot.single) {	/* Gave no time to go with the rotations, use rotation times */
		GMT_Report (API, GMT_MSG_VERBOSE, "No reconstruction times specified; using %d reconstruction times from rotation table\n", n_stages);
		Ctrl->T.n_times = n_stages;
		Ctrl->T.value = gmt_M_memory (GMT, NULL, Ctrl->T.n_times, double);
		for (t = 0; t < Ctrl->T.n_times; t++) Ctrl->T.value[t] = p[t].t_start;
	}

	if (Ctrl->T.n_times > 1) {	/* Requires that template names be given */
		if (!Ctrl->N.active) {	/* Did not give -N so require -D template */
			if (!Ctrl->D.file || !strchr (Ctrl->D.file, '%')) {	/* No file given or filename without C-format specifiers */
				GMT_Report (API, GMT_MSG_VERBOSE, "Multiple output times requires a template name via -D (unless -N is set)\n");
				Return (API->error);
			}
		}
		if (!Ctrl->S.active && !strchr (Ctrl->G.file, '%')) {	/* Grid filename without C-format specifiers */
			GMT_Report (API, GMT_MSG_VERBOSE, "Multiple output times requires a template gridfile name via -G\n");
			Return (API->error);
		}
	}

	for (t = 0; t < Ctrl->T.n_times; t++) {	/* For each reconstruction time */
		if (Ctrl->E.rot.single) {
			plon = Ctrl->E.rot.lon;	plat = Ctrl->E.rot.lat;	pw = Ctrl->E.rot.w;
			GMT_Report (API, GMT_MSG_VERBOSE, "Using rotation (%g, %g, %g)\n", plon, plat, pw);
		}
		else {	/* Extract rotation for given time */
			if (Ctrl->T.value[t] < p[0].t_stop || Ctrl->T.value[t] > p[n_stages-1].t_start) {
				GMT_Report (API, GMT_MSG_NORMAL, "Requested a reconstruction time outside range of rotation table - skipped\n");
				continue;
			}
			spotter_get_rotation (GMT, p, n_stages, Ctrl->T.value[t], &plon, &plat, &pw);
			GMT_Report (API, GMT_MSG_VERBOSE, "Time %g Ma: Using rotation (%g, %g, %g)\n", Ctrl->T.value[t], plon, plat, pw);
		}
		gmt_make_rot_matrix (GMT, plon, plat, pw, R);	/* Make rotation matrix from rotation parameters */

		if (Ctrl->E.rot.single)
			GMT_Report (API, GMT_MSG_VERBOSE, "Reconstruct polygon outline\n");
		else
			GMT_Report (API, GMT_MSG_VERBOSE, "Reconstruct polygon outline for time %g\n", Ctrl->T.value[t]);

		/* First reconstruct the polygon outline */

		for (seg = 0; pol && seg < pol->n_segments; seg++) {
			S = pol->segment[seg];		/* Shorthand for current original segment */
			Sr = polr->segment[seg];	/* Shorthand for current rotated segment */
			for (rec = 0; rec < pol->segment[seg]->n_rows; rec++) {
				Sr->data[GMT_X][rec] = S->data[GMT_X][rec];
				Sr->data[GMT_Y][rec] = gmt_lat_swap (GMT, S->data[GMT_Y][rec], GMT_LATSWAP_G2O);	/* Convert to geocentric */
				gmt_geo_to_cart (GMT, Sr->data[GMT_Y][rec], Sr->data[GMT_X][rec], P_original, true);	/* Convert to a Cartesian x,y,z vector; true since we have degrees */
				gmt_matrix_vect_mult (GMT, 3U, R, P_original, P_rotated);				/* Rotate the vector */
				gmt_cart_to_geo (GMT, &Sr->data[GMT_Y][rec], &Sr->data[GMT_X][rec], P_rotated, true);	/* Recover lon lat representation; true to get degrees */
				Sr->data[GMT_Y][rec] = gmt_lat_swap (GMT, Sr->data[GMT_Y][rec], GMT_LATSWAP_O2G);	/* Convert back to geodetic */
			}
			gmt_set_seg_polar (GMT, Sr);	/* Determine if it is a polar cap */
		}
		gmt_set_tbl_minmax (GMT, GMT_IS_POLY, polr);	/* Update table domain */
		if (!Ctrl->N.active && not_global) {
			char dfile[GMT_BUFSIZ] = {""}, *file = NULL;
			if (Ctrl->T.n_times > 1) {
				sprintf (dfile, Ctrl->D.file, Ctrl->T.value[t]);
				file = dfile;
			}
			else
				file = Ctrl->D.file;
			if (!Ctrl->E.rot.single) {	/* Add a segment header with the age via -Z */
				char txt[BUFSIZ] = {""};
				sprintf (txt, "-Z%g", Ctrl->T.value[t]);
				for (seg = 0; seg < polr->n_segments; seg++) {
					Sr = polr->segment[seg];	/* Shorthand for current rotated segment */
					gmt_M_str_free (Sr->header);
					Sr->header = strdup (txt);
				}
			}
			if (GMT_Write_Data (API, GMT_IS_DATASET, GMT_IS_FILE, GMT_IS_POLY, GMT_WRITE_SET, NULL, file, Dr) != GMT_NOERROR) {
				Return (API->error);
			}
		}
		if (Ctrl->S.active) /* No grids will be rotated */
			continue;

		/* Then, find min/max of reconstructed outline */

		if (global)
			gmt_M_memcpy (GMT->common.R.wesn, G->header->wesn, 4, double);
		else {
			GMT->common.R.wesn[XLO] = floor (polr->min[GMT_X] * G->header->r_inc[GMT_X]) * G->header->inc[GMT_X];
			GMT->common.R.wesn[XHI] = ceil  (polr->max[GMT_X] * G->header->r_inc[GMT_X]) * G->header->inc[GMT_X];
			GMT->common.R.wesn[YLO] = floor (polr->min[GMT_Y] * G->header->r_inc[GMT_Y]) * G->header->inc[GMT_Y];
			GMT->common.R.wesn[YHI] = ceil  (polr->max[GMT_Y] * G->header->r_inc[GMT_Y]) * G->header->inc[GMT_Y];
			/* Adjust longitude range, as indicated by FORMAT_GEO_OUT */
			gmt_lon_range_adjust (GMT->current.io.geo.range, &GMT->common.R.wesn[XLO]);
			gmt_lon_range_adjust (GMT->current.io.geo.range, &GMT->common.R.wesn[XHI]);
			if (GMT->common.R.wesn[XLO] >= GMT->common.R.wesn[XHI]) GMT->common.R.wesn[XHI] += 360.0;
		}
		GMT->common.R.active[RSET] = true;

		if ((G_rot = GMT_Create_Data (API, GMT_IS_GRID, GMT_IS_SURFACE, GMT_CONTAINER_AND_DATA, NULL, NULL, G->header->inc, \
			GMT_GRID_DEFAULT_REG, GMT_NOTSET, NULL)) == NULL) Return (API->error);

		/* Precalculate node coordinates in both degrees and radians */
		grd_x = gmt_grd_coord (GMT, G_rot->header, GMT_X);
		grd_y = gmt_grd_coord (GMT, G_rot->header, GMT_Y);
		grd_yc = gmt_M_memory (GMT, NULL, G_rot->header->n_rows, double);
		for (row = 0; row < G_rot->header->n_rows; row++) grd_yc[row] = gmt_lat_swap (GMT, grd_y[row], GMT_LATSWAP_G2O);

		/* Loop over all nodes in the new rotated grid and find those inside the reconstructed polygon */

		if (Ctrl->E.rot.single)
			GMT_Report (API, GMT_MSG_VERBOSE, "Interpolate reconstructed grid\n");
		else
			GMT_Report (API, GMT_MSG_VERBOSE, "Interpolate reconstructed grid for time %g\n", Ctrl->T.value[t]);

		gmt_make_rot_matrix (GMT, plon, plat, -pw, R);	/* Make inverse rotation using negative angle */

		gmt_M_grd_loop (GMT, G_rot, row, col, ij_rot) {
			G_rot->data[ij_rot] = GMT->session.f_NaN;
			if (not_global && skip_if_outside (GMT, polr, grd_x[col], grd_y[row])) continue;	/* Outside rotated polygon */

			/* Here we are inside; get the coordinates and rotate back to original grid coordinates */

			gmt_geo_to_cart (GMT, grd_yc[row], grd_x[col], P_rotated, true);	/* Convert degree lon,lat to a Cartesian x,y,z vector */
			gmt_matrix_vect_mult (GMT, 3U, R, P_rotated, P_original);	/* Rotate the vector */
			gmt_cart_to_geo (GMT, &yy, &xx, P_original, true);		/* Recover degree lon lat representation */
			yy = gmt_lat_swap (GMT, yy, GMT_LATSWAP_O2G);			/* Convert back to geodetic */
			xx -= 360.0;
			while (xx < G->header->wesn[XLO]) xx += 360.0;	/* Make sure we deal with 360 issues */
			G_rot->data[ij_rot] = (float)gmt_bcr_get_z (GMT, G, xx, yy);
		}

		/* Also loop over original node locations to make sure the nearest nodes are set */

		for (seg = 0; not_global && seg < pol->n_segments; seg++) {
			for (rec = 0; rec < pol->segment[seg]->n_rows; rec++) {
				lon = pol->segment[seg]->data[GMT_X][rec];
				while (lon < G_rot->header->wesn[XLO]) lon += 360.0;
				scol = (int)gmt_M_grd_x_to_col (GMT, lon, G_rot->header);
				srow = (int)gmt_M_grd_y_to_row (GMT, pol->segment[seg]->data[GMT_Y][rec], G_rot->header);
				/* Visit the PAD * PAD number of cells centered on col, row and make sure they have been set */
				start_row = (srow > PAD) ? srow - PAD : 0;
				stop_row  = ((srow + PAD) >= 0) ? srow + PAD : 0;
				start_col = (scol > PAD) ? scol - PAD : 0;
				stop_col  = ((scol + PAD) >= 0) ? scol + PAD : 0;
				for (row = start_row; row <= stop_row; row++) {
					if (row >= G_rot->header->n_rows) continue;
					for (col = start_col; col <= stop_col; col++) {
						if (col >= G_rot->header->n_columns) continue;
						ij_rot = gmt_M_ijp (G_rot->header, row, col);
						if (!gmt_M_is_fnan (G_rot->data[ij_rot])) continue;	/* Already done this */
						if (not_global && skip_if_outside (GMT, pol, grd_x[col], grd_yc[row])) continue;	/* Outside input polygon */
						gmt_geo_to_cart (GMT, grd_yc[row], grd_x[col], P_rotated, true);	/* Convert degree lon,lat to a Cartesian x,y,z vector */
						gmt_matrix_vect_mult (GMT, 3U, R, P_rotated, P_original);	/* Rotate the vector */
						gmt_cart_to_geo (GMT, &xx, &yy, P_original, true);	/* Recover degree lon lat representation */
						yy = gmt_lat_swap (GMT, yy, GMT_LATSWAP_O2G);		/* Convert back to geodetic */
						scol = (int)gmt_M_grd_x_to_col (GMT, xx, G->header);
						if (scol < 0) continue;
						col_o = scol;	if (col_o >= G->header->n_columns) continue;
						srow = (int)gmt_M_grd_y_to_row (GMT, yy, G->header);
						if (srow < 0) continue;
						row_o = srow;	if (row_o >= G->header->n_rows) continue;
						ij = gmt_M_ijp (G->header, row_o, col_o);
						G_rot->data[ij_rot] = G->data[ij];
					}
				}
			}
		}

		/* Now write rotated grid */

		if (Ctrl->E.rot.single)
			GMT_Report (API, GMT_MSG_VERBOSE, "Write reconstructed grid\n");
		else
			GMT_Report (API, GMT_MSG_VERBOSE, "Write reconstructed grid for time %g\n", Ctrl->T.value[t]);

		gmt_set_pad (GMT, API->pad);	/* Reset to session default pad before output */

		if (Ctrl->E.rot.single)
			snprintf (G_rot->header->remark, GMT_GRID_REMARK_LEN160, "Grid reconstructed using R[lon lat omega] = %g %g %g", plon, plat, pw);
		else
			snprintf (G_rot->header->remark, GMT_GRID_REMARK_LEN160, "Grid reconstructed using R[lon lat omega] = %g %g %g for time %g", plon, plat, pw, Ctrl->T.value[t]);
		if (GMT_Set_Comment (API, GMT_IS_GRID, GMT_COMMENT_IS_OPTION | GMT_COMMENT_IS_COMMAND, options, G_rot)) Return (API->error);
		if (Ctrl->T.n_times > 1)	/* Use template to create name */
			sprintf (gfile, Ctrl->G.file, Ctrl->T.value[t]);
		else
			strcpy (gfile, Ctrl->G.file);
		if (GMT_Write_Data (API, GMT_IS_GRID, GMT_IS_FILE, GMT_IS_SURFACE, GMT_CONTAINER_AND_DATA, NULL, gfile, G_rot) != GMT_NOERROR) {
			Return (API->error);
		}
		if (G_rot && GMT_Destroy_Data (API, &G_rot) != GMT_NOERROR)
			Return (API->error);

		gmt_M_free (GMT, grd_x);
		gmt_M_free (GMT, grd_y);
		gmt_M_free (GMT, grd_yc);
	} /* End of loop over reconstruction times */

	gmt_M_free (GMT, p);

	if (Ctrl->S.active) {
		if (Ctrl->F.active && GMT_Destroy_Data (API, &D) != GMT_NOERROR) {
			Return (API->error);
		}
		else if (not_global)
			gmt_free_dataset (GMT, &D);
	}
	gmt_M_free (GMT, Ctrl->T.value);
	if (D && GMT_Destroy_Data (API, &D) != GMT_NOERROR)
		Return (API->error);
	if (Dr && GMT_Destroy_Data (API, &Dr) != GMT_NOERROR)
		Return (API->error);

	GMT_Report (API, GMT_MSG_VERBOSE, "Done!\n");

	Return (GMT_NOERROR);
}
