/*
 * cell_tool.c
 *
 * Unit cell tool
 *
 * Copyright © 2018 Deutsches Elektronen-Synchrotron DESY,
 *                  a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2012-2018 Thomas White <taw@physics.org>
 *
 * This file is part of CrystFEL.
 *
 * CrystFEL is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * CrystFEL 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
 *
 */


#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <assert.h>

#include "cell.h"
#include "cell-utils.h"
#include "reflist-utils.h"
#include "reflist.h"


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Unit cell manipulation tool.\n"
"\n"
" -h, --help                 Display this help message.\n"
" -p, --pdb=<file>           Get unit cell from <file> (PDB or CrystFEL format).\n"
"\n"
"  Actions:\n"
"     --find-ambi            Find indexing ambiguities for the cell.\n"
"     --uncenter             Calculate a primitive cell.\n"
"     --rings                Calculate powder ring positions.\n"
"     --compare-cell <file>  Compare unit cell with cell from <file>.\n"
"\n"
" -y <pointgroup>            Real point group of the structure.\n"
"     --tolerance=<tol>      Set the tolerances for cell reduction.\n"
"                             Default: 5,5,5,1.5.\n"
);
}


static int cells_are_similar(UnitCell *cell1, UnitCell *cell2, float *tols)
{
	double a1, b1, c1, al1, be1, ga1;
	double a2, b2, c2, al2, be2, ga2;
	UnitCellTransformation *tfn1, *tfn2;
	UnitCell *pcell1, *pcell2;

	/* Compare primitive cells, not centered */
	pcell1 = uncenter_cell(cell1, &tfn1);
	pcell2 = uncenter_cell(cell2, &tfn2);

	cell_get_parameters(pcell1, &a1, &b1, &c1, &al1, &be1, &ga1);
	cell_get_parameters(pcell2, &a2, &b2, &c2, &al2, &be2, &ga2);

	cell_free(pcell1);
	cell_free(pcell2);

	if ( !within_tolerance(a1, a2, tols[0]) ) return 0;
	if ( !within_tolerance(b1, b2, tols[1]) ) return 0;
	if ( !within_tolerance(c1, c2, tols[2]) ) return 0;
	if ( !within_tolerance(al1, al2, tols[3]) ) return 0;
	if ( !within_tolerance(be1, be2, tols[3]) ) return 0;
	if ( !within_tolerance(ga1, ga2, tols[3]) ) return 0;

	return 1;
}


static int find_ambi(UnitCell *cell, SymOpList *sym, float *tols)
{
	SymOpList *amb;
	SymOpList *ops;
	signed int i[9];
	const int maxorder = 3;

	ops = get_pointgroup("1");
	if ( ops == NULL ) return 1;
	set_symmetry_name(ops, "Observed");

	STATUS("Looking for ambiguities up to 3x each lattice length.\n");
	STATUS("This will take about 30 seconds.  Please wait...\n");

	for ( i[0]=-maxorder; i[0]<=+maxorder; i[0]++ ) {
	for ( i[1]=-maxorder; i[1]<=+maxorder; i[1]++ ) {
	for ( i[2]=-maxorder; i[2]<=+maxorder; i[2]++ ) {
	for ( i[3]=-maxorder; i[3]<=+maxorder; i[3]++ ) {
	for ( i[4]=-maxorder; i[4]<=+maxorder; i[4]++ ) {
	for ( i[5]=-maxorder; i[5]<=+maxorder; i[5]++ ) {
	for ( i[6]=-maxorder; i[6]<=+maxorder; i[6]++ ) {
	for ( i[7]=-maxorder; i[7]<=+maxorder; i[7]++ ) {
	for ( i[8]=-maxorder; i[8]<=+maxorder; i[8]++ ) {

		UnitCellTransformation *tfn;
		UnitCell *nc;
		IntegerMatrix *m;
		int j, k;
		int l = 0;

		m = intmat_new(3, 3);
		for ( j=0; j<3; j++ ) {
		for ( k=0; k<3; k++ ) {
			intmat_set(m, j, k, i[l++]);
		}
		}

		if ( intmat_det(m) != +1 ) continue;

		tfn = tfn_from_intmat(m);
		nc = cell_transform(cell, tfn);

		if ( cells_are_similar(cell, nc, tols) ) {
			if ( !intmat_is_identity(m) ) add_symop(ops, m);
			STATUS("-----------------------------------------------"
			       "-------------------------------------------\n");
			cell_print(nc);
			intmat_print(m);
		} else {
			intmat_free(m);
		}

		tfn_free(tfn);
		cell_free(nc);

	}
	}
	}
	}
	}
	}
	}
	}
	}

	STATUS("Observed symmetry operations:\n");
	describe_symmetry(ops);

	amb = get_ambiguities(ops, sym);
	if ( amb == NULL ) {
		STATUS("No ambiguities (or error calculating them)\n");
	} else {
		STATUS("Ambiguity operations:\n");
		describe_symmetry(amb);
		free_symoplist(amb);
	}

	free_symoplist(ops);

	return 0;
}


enum {
	CT_NOTHING,
	CT_FINDAMBI,
	CT_UNCENTER,
	CT_RINGS,
	CT_COMPARE,
	CT_CHOICES,
};


int main(int argc, char *argv[])
{
	int c;
	char *cell_file = NULL;
	UnitCell *cell;
	char *toler = NULL;
	float tols[4] = {5.0, 5.0, 5.0, 1.5}; /* a,b,c,angles (%,%,%,deg) */
	char *sym_str = NULL;
	SymOpList *sym;
	int mode = CT_NOTHING;
	char *comparecell = NULL;

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"pdb",                1, NULL,               'p'},
		{"tolerance",          1, NULL,                2},

		/* Modes of operation */
		{"find-ambi",          0, &mode,               CT_FINDAMBI},
		{"uncenter",           0, &mode,               CT_UNCENTER},
		{"uncentre",           0, &mode,               CT_UNCENTER},
		{"rings",              0, &mode,               CT_RINGS},
		{"compare-cell",       1, NULL,                3},
		{"highres",            1, NULL,                5},

		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hp:y:",
	                        longopts, NULL)) != -1) {

		switch (c) {

			case 'h' :
			show_help(argv[0]);
			return 0;

			case 'p' :
			cell_file = strdup(optarg);
			break;

			case 'y' :
			sym_str = strdup(optarg);
			break;

			case 2 :
			toler = strdup(optarg);
			break;

			case 3 :
			comparecell = strdup(optarg);
			mode = CT_COMPARE;
			break;

			case 0 :
			break;

			default :
			return 1;

		}

	}

	if ( cell_file == NULL ) {
		ERROR("You must give a filename for the unit cell PDB file.\n");
		return 1;
	}
	cell = load_cell_from_file(cell_file);
	if ( cell == NULL ) {
		ERROR("Failed to load cell from '%s'\n", cell_file);
		return 1;
	}
	free(cell_file);

	if ( toler != NULL ) {
		int ttt;
		ttt = sscanf(toler, "%f,%f,%f,%f",
		             &tols[0], &tols[1], &tols[2], &tols[3] );
		if ( ttt != 4 ) {
			ERROR("Invalid parameters for '--tolerance'\n");
			return 1;
		}
		free(toler);
	}

	STATUS("Input unit cell:\n");
	cell_print(cell);

	if ( validate_cell(cell) ) {
		ERROR("Cell is invalid.\n");
		return 1;
	}

	if ( sym_str == NULL ) {
		ERROR("Please specify the point group of the structure.\n");
		return 1;
	}

	sym = get_pointgroup(sym_str);
	if ( sym == NULL ) return 1;
	free(sym_str);

	if ( mode == CT_NOTHING ) {
		ERROR("Please specify mode of operation (see --help)\n");
		return 1;
	}

	if ( mode == CT_FINDAMBI ) return find_ambi(cell, sym, tols);

	/* FIXME: Everything else */
	ERROR("Sorry, this mode of operation is not yet implemented.\n");
	return 1;
}