Framework for new unit cell comparison function

4 files changed, 87 insertions, 119 deletions

diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 141eaaab..20ede189 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -2341,10 +2341,9 @@ IntegerMatrix *reduce_g6(double *g, double eps)
  * \param tolerance: Pointer to tolerances for a,b,c (fractional), al,be,ga (radians)
  * \param pmb: Place to store pointer to matrix
  *
- * Compare \p cell_in with \p reference_in.  If they are the same,
- * within \p tolerance, taking into account possible permutations of the axes,
- * this function returns non-zero and stores the transformation which needs to
- * be applied to \p cell_in at \p pmb.
+ * Compare the \p cell_in with \p reference_in.  If they represent the same
+ * lattice, this function returns non-zero and stores the transformation which
+ * needs to be applied to \p cell_in at \p pmb.
  *
  * Subject to the tolerances, this function will find the transformation which
  * gives the best match to the reference cell, using the Euclidian norm in
@@ -2356,76 +2355,44 @@ IntegerMatrix *reduce_g6(double *g, double eps)
  * \returns non-zero if the cells match, zero for no match or error.
  *
  */
-int compare_permuted_cell_parameters(UnitCell *cell, UnitCell *reference,
-                                     double *tolerance, IntegerMatrix **pmb)
+int compare_lattices(UnitCell *cell_in, UnitCell *reference_in,
+                     double *tolerance, RationalMatrix **pmb)
 {
-	IntegerMatrix *m;
-	signed int i[9];
-	double a, b, c, al, be, ga;
-	double min_dist = +INFINITY;
-
-	m = intmat_new(3, 3);
-	cell_get_parameters(reference, &a, &b, &c, &al, &be, &ga);
-	*pmb = NULL;
-
-	for ( i[0]=-1; i[0]<=+1; i[0]++ ) {
-	for ( i[1]=-1; i[1]<=+1; i[1]++ ) {
-	for ( i[2]=-1; i[2]<=+1; i[2]++ ) {
-	for ( i[3]=-1; i[3]<=+1; i[3]++ ) {
-	for ( i[4]=-1; i[4]<=+1; i[4]++ ) {
-	for ( i[5]=-1; i[5]<=+1; i[5]++ ) {
-	for ( i[6]=-1; i[6]<=+1; i[6]++ ) {
-	for ( i[7]=-1; i[7]<=+1; i[7]++ ) {
-	for ( i[8]=-1; i[8]<=+1; i[8]++ ) {
-
-		UnitCell *test;
-		int j, k;
-		int l = 0;
-		signed int det;
-
-		for ( j=0; j<3; j++ )
-			for ( k=0; k<3; k++ )
-				intmat_set(m, j, k, i[l++]);
-
-		det = intmat_det(m);
-		if ( (det != +1) && (det != -1) ) continue;
-
-		test = cell_transform_intmat(cell, m);
-
-		if ( compare_cell_parameters(reference, test, tolerance) ) {
-
-			double at, bt, ct, alt, bet, gat;
-			double dist;
+	UnitCell *cell;
+	UnitCell *reference;
+	IntegerMatrix *CBint;
+	RationalMatrix *CiA;
+	RationalMatrix *CB;
+	IntegerMatrix *Mcell;
+	IntegerMatrix *Mref;
+	double eps;
+	double G6cell[6];
+	double G6ref[6];
 
-			cell_get_parameters(test, &at, &bt, &ct, &alt, &bet, &gat);
-			dist = g6_distance(at, bt, ct, alt, bet, gat,
-			                   a, b, c, al, be, ga);
-			if ( dist < min_dist ) {
-				min_dist = dist;
-				intmat_free(*pmb);
-				*pmb = intmat_copy(m);
-			}
+	/* Un-center both cells */
+	reference = uncenter_cell(reference_in, &CBint, NULL);
+	if ( reference == NULL ) return 0;
+	CB = rtnl_mtx_from_intmat(CBint);
+	intmat_free(CBint);
 
-		}
+	cell = uncenter_cell(cell_in, NULL, &CiA);
+	if ( cell == NULL ) return 0;
 
-		cell_free(test);
+	/* Calculate G6 components for both */
+	g6_components(G6cell, cell);
+	g6_components(G6ref, reference);
 
-	}
-	}
-	}
-	}
-	}
-	}
-	}
-	}
-	}
+	/* Convert both to reduced basis (stably) */
+	eps = pow(cell_get_volume(cell), 1.0/3.0) * 1e-5;
+	Mcell = reduce_g6(G6cell, eps);
+	eps = pow(cell_get_volume(reference), 1.0/3.0) * 1e-5;
+	Mref = reduce_g6(G6ref, eps);
 
-	intmat_free(m);
+	/* Compare cells (including nearby ones, possibly permuting
+	 * axes if close to equality) */
 
-	if ( isinf(min_dist) ) {
-		return 0;
-	}
-
-	/* Solution found */
-	return 1;
+	intmat_free(Mcell);
+	intmat_free(Mref);
+	cell_free(reference);
+	cell_free(cell);
 }
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index fa577269..e46d860b 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -90,9 +90,6 @@ extern double cell_get_volume(UnitCell *cell);
 extern int compare_cell_parameters(UnitCell *cell, UnitCell *reference,
                                    double *tolerance);
 
-extern int compare_permuted_cell_parameters(UnitCell *cell, UnitCell *reference,
-                                            double *tolerance, IntegerMatrix **pmb);
-
 extern int compare_cell_parameters_and_orientation(UnitCell *cell,
                                                    UnitCell *reference,
                                                    const double ltl,
@@ -108,6 +105,9 @@ extern int compare_reindexed_cell_parameters(UnitCell *cell, UnitCell *reference
                                              double *tolerance, int csl,
                                              RationalMatrix **pmb);
 
+extern int compare_lattices(UnitCell *cell_in, UnitCell *reference_in,
+                            double *tolerance, RationalMatrix **pmb);
+
 #ifdef __cplusplus
 }
 #endif
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index b07dd067..aa0cfb6a 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -547,26 +547,13 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
                       double *tolerance)
 {
 	UnitCell *out;
-	IntegerMatrix *im;
 	RationalMatrix *rm;
 
 	/* Check at all? */
 	if ( ! ((flags & INDEXING_CHECK_CELL_COMBINATIONS)
 	         || (flags & INDEXING_CHECK_CELL_AXES)) ) return 0;
 
-	if ( compare_permuted_cell_parameters(crystal_get_cell(cr), target,
-	                                      tolerance, &im) )
-	{
-		out = cell_transform_intmat(crystal_get_cell(cr), im);
-		cell_free(crystal_get_cell(cr));
-		crystal_set_cell(cr, out);
-		intmat_free(im);
-		return 0;
-	}
-
-	if ( (flags & INDEXING_CHECK_CELL_COMBINATIONS )
-	  && compare_reindexed_cell_parameters(crystal_get_cell(cr), target,
-	                                       tolerance, 0, &rm) )
+	if ( compare_lattices(crystal_get_cell(cr), target, tolerance, &rm) )
 	{
 		out = cell_transform_rational(crystal_get_cell(cr), rm);
 		cell_free(crystal_get_cell(cr));
@@ -576,7 +563,6 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
 	}
 
 	return 1;
-
 }
 
 
diff --git a/tests/cellcompare_check.c b/tests/cellcompare_check.c
index 48b7a9c5..0e98276c 100644
--- a/tests/cellcompare_check.c
+++ b/tests/cellcompare_check.c
@@ -116,29 +116,6 @@ static int check_ccp(UnitCell *cell, UnitCell *cref, double *tols,
 }
 
 
-static int check_cpcp(UnitCell *cell, UnitCell *cref, double *tols,
-                      int should_match)
-{
-	IntegerMatrix *m = NULL;
-	const char *a;
-	const char *b;
-
-	a = should_match ? "" : "NOT ";
-	b = " with compare_permuted_cell_parameters";
-
-	if ( compare_permuted_cell_parameters(cell, cref, tols, &m) != should_match )
-	{
-		complain(cell, cref, a, b);
-		STATUS("Matrix was:\n");
-		intmat_print(m);
-		intmat_free(m);
-		return 1;
-	}
-	intmat_free(m);
-	return 0;
-}
-
-
 static int check_ccpao(UnitCell *cell, UnitCell *cref, double *tols,
                        int should_match)
 {
@@ -206,6 +183,33 @@ static int check_crcp(UnitCell *cell, UnitCell *cref, double *tols,
 }
 
 
+static void yaro_test()
+{
+	UnitCell *cell;
+	UnitCell *reference;
+	UnitCell *cmatch;
+	float tols[] = {5, 5, 5, 1.5};
+
+	cell = cell_new_from_parameters(64.24e-10, 63.94e-10, 64.61e-10,
+	                                deg2rad(89.98), deg2rad(89.82), deg2rad(119.87));
+	cell_set_unique_axis(cell, 'c');
+	cell_set_lattice_type(cell, L_HEXAGONAL);
+
+	reference = cell_new_from_parameters(64.7e-10, 64.7e-10, 65.2e-10,
+	                                     deg2rad(90.0), deg2rad(90.0), deg2rad(120.0));
+	cell_set_unique_axis(reference, 'c');
+	cell_set_lattice_type(reference, L_HEXAGONAL);
+
+	cell_print(cell);
+	cell_print(reference);
+	cmatch = match_cell(cell, reference, 0, tols, 1);
+	cell_print(cmatch);
+}
+
+
+extern IntegerMatrix *reduce_g6(double *g, double eps);
+extern void g6_components(double *g6, UnitCell *cell);
+
 int main(int argc, char *argv[])
 {
 	UnitCell *cell, *cref;
@@ -216,13 +220,29 @@ int main(int argc, char *argv[])
 
 	rng = gsl_rng_alloc(gsl_rng_mt19937);
 
-	cref = cell_new_from_parameters(50e-10, 55e-10, 70e-10,
-	                                deg2rad(67.0),
-	                                deg2rad(70.0),
-	                                deg2rad(77.0));
+	yaro_test();
+
+	cref = cell_new_from_parameters(3e-0, 5.196e-0, 2e-0,
+	                                deg2rad(103.9166666),
+	                                deg2rad(109.4666666),
+	                                deg2rad(134.8833333));
 	cell_set_centering(cref, 'P');
 	if ( cref == NULL ) return 1;
 
+	STATUS("The test cell:\n");
+	cell_print(cref);
+	double g[6];
+	g6_components(g, cref);
+	STATUS("G6: %e %e %e %e %e %e\n", g[0], g[1], g[2], g[3], g[4], g[5]);
+	double eps = pow(cell_get_volume(cref), 1.0/3.0) * 1e-5;
+	//eps = 1e-27;
+	IntegerMatrix *M = reduce_g6(g, eps);
+	STATUS("The transformation to reduce:\n");
+	intmat_print(M);
+	STATUS("The reduced cell:\n");
+	cell = cell_transform_intmat(cref, M);
+	cell_print(cell);
+
 	/* Just rotate cell */
 	for ( i=0; i<100; i++ ) {
 
@@ -230,7 +250,6 @@ int main(int argc, char *argv[])
 		if ( cell == NULL ) return 1;
 
 		if ( check_ccp(cell, cref, tols, 1) ) return 1;
-		if ( check_cpcp(cell, cref, tols, 1) ) return 1;
 		if ( check_ccpao(cell, cref, tols, 0) ) return 1;
 		if ( check_cpcpao(cell, cref, tols, 0) ) return 1;
 		if ( check_crcp(cell, cref, tols, NULL, 1) ) return 1;
@@ -248,7 +267,6 @@ int main(int argc, char *argv[])
 		cell = cell_transform_intmat(cref, tr);
 
 		if ( check_ccp(cell, cref, tols, intmat_is_identity(tr)) ) return 1;
-		if ( check_cpcp(cell, cref, tols, 1) ) return 1;
 		if ( check_ccpao(cell, cref, tols, intmat_is_identity(tr)) ) return 1;
 		if ( check_cpcpao(cell, cref, tols, 1) ) return 1;
 		if ( check_crcp(cell, cref, tols, NULL, 1) ) return 1;
@@ -272,7 +290,6 @@ int main(int argc, char *argv[])
 		cell_free(cell2);
 
 		if ( check_ccp(cell, cref, tols, intmat_is_identity(tr)) ) return 1;
-		if ( check_cpcp(cell, cref, tols, 1) ) return 1;
 		if ( check_ccpao(cell, cref, tols, 0) ) return 1;
 		if ( check_cpcpao(cell, cref, tols, 0) ) return 1;
 		if ( check_crcp(cell, cref, tols, NULL, 1) ) return 1;
@@ -301,7 +318,6 @@ int main(int argc, char *argv[])
 		 * cell_transform_rational doesn't set the unique axis (yet?) */
 
 		if ( check_ccp(cell, cref, tols, rtnl_mtx_is_identity(tr)) ) return 1;
-		if ( check_cpcp(cell, cref, tols, rtnl_mtx_is_perm(tr)) ) return 1;
 		if ( check_ccpao(cell, cref, tols, rtnl_mtx_is_identity(tr)) ) return 1;
 		if ( check_cpcpao(cell, cref, tols, rtnl_mtx_is_perm(tr)) ) return 1;
 		if ( check_crcp(cell, cref, tols, tr, 1) ) return 1;
@@ -332,7 +348,6 @@ int main(int argc, char *argv[])
 		cell_free(cell2);
 
 		if ( check_ccp(cell, cref, tols, rtnl_mtx_is_identity(tr)) ) return 1;
-		if ( check_cpcp(cell, cref, tols, rtnl_mtx_is_perm(tr)) ) return 1;
 		if ( check_ccpao(cell, cref, tols, 0) ) return 1;
 		if ( check_cpcpao(cell, cref, tols, 0) ) return 1;
 		if ( check_crcp(cell, cref, tols, tr, 1) ) return 1;