diff options
| -rw-r--r-- | libcrystfel/src/cell-utils.c | 46 | ||||
| -rw-r--r-- | libcrystfel/src/cell-utils.h | 4 | ||||
| -rw-r--r-- | src/cell_tool.c | 20 |
3 files changed, 42 insertions, 28 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index f6e189ad..3f3ce252 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -1671,12 +1671,11 @@ double cell_get_volume(UnitCell *cell) /** * \param cell1: A UnitCell * \param cell2: Another UnitCell - * \param ltl: Maximum allowable fractional difference in axis lengths - * \param atl: Maximum allowable difference in reciprocal angles (in radians) + * \param tolerance: Pointer to tolerances for a,b,c (fractional), al,be,ga (radians) * * Compare the two unit cells. If the real space parameters match to within - * fractional difference \p ltl, and the inter-axial angles match within \p atl, - * and the centering matches, this function returns 1. Otherwise 0. + * the specified tolerances, and the centering matches, this function returns 1. + * Otherwise 0. * * This function considers the cell parameters and centering, but ignores the * orientation of the cell. If you want to compare the orientation as well, @@ -1685,8 +1684,7 @@ double cell_get_volume(UnitCell *cell) * \returns non-zero if the cells match. * */ -int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2, - float ltl, float atl) +int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2, double *tolerance) { double a1, b1, c1, al1, be1, ga1; double a2, b2, c2, al2, be2, ga2; @@ -1698,12 +1696,12 @@ int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2, cell_get_parameters(cell1, &a1, &b1, &c1, &al1, &be1, &ga1); cell_get_parameters(cell2, &a2, &b2, &c2, &al2, &be2, &ga2); - if ( !within_tolerance(a1, a2, ltl*100.0) ) return 0; - if ( !within_tolerance(b1, b2, ltl*100.0) ) return 0; - if ( !within_tolerance(c1, c2, ltl*100.0) ) return 0; - if ( fabs(al1-al2) > atl ) return 0; - if ( fabs(be1-be2) > atl ) return 0; - if ( fabs(ga1-ga2) > atl ) return 0; + if ( !within_tolerance(a1, a2, tolerance[0]*100.0) ) return 0; + if ( !within_tolerance(b1, b2, tolerance[1]*100.0) ) return 0; + if ( !within_tolerance(c1, c2, tolerance[2]*100.0) ) return 0; + if ( fabs(al1-al2) > tolerance[3] ) return 0; + if ( fabs(be1-be2) > tolerance[4] ) return 0; + if ( fabs(ga1-ga2) > tolerance[5] ) return 0; return 1; } @@ -1960,15 +1958,15 @@ static double g6_distance(double a1, double b1, double c1, /** * \param cell_in: A UnitCell * \param reference_in: Another UnitCell - * \param ltl: Maximum allowable fractional difference in direct-space axis lengths - * \param atl: Maximum allowable difference in direct-space angles (in radians) + * \param tolerance: Pointer to tolerances for a,b,c (fractional), al,be,ga (radians) * \param csl: Non-zero to look for coincidence site lattice relationships * \param pmb: Place to store pointer to matrix * * Compare the \p cell_in with \p reference_in. If \p cell is a derivative lattice - * of \p reference, within fractional axis length difference \p ltl and absolute angle - * difference \p atl (in radians), this function returns non-zero and stores the - * transformation which needs to be applied to \p cell_in at \p pmb. + * of \p reference, within fractional axis length differences \p tolerance[0..2] + * and absolute angle difference \p atl[3..5] (in radians), this function returns + * non-zero and stores the transformation which needs to be applied to + * \p cell_in at \p pmb. * * Note that the tolerances will be applied to the primitive unit cell. If * the reference cell is centered, a primitive unit cell will first be calculated. @@ -1989,7 +1987,7 @@ static double g6_distance(double a1, double b1, double c1, * */ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, - double ltl, double atl, int csl, + double *tolerance, int csl, RationalMatrix **pmb) { UnitCell *cell; @@ -2026,9 +2024,9 @@ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, &cv[0], &cv[1], &cv[2]); /* Find vectors in 'cell' with lengths close to a, b and c */ - cand_a = find_candidates(a, av, bv, cv, ltl, csl, &ncand_a); - cand_b = find_candidates(b, av, bv, cv, ltl, csl, &ncand_b); - cand_c = find_candidates(c, av, bv, cv, ltl, csl, &ncand_c); + cand_a = find_candidates(a, av, bv, cv, tolerance[0], csl, &ncand_a); + cand_b = find_candidates(b, av, bv, cv, tolerance[1], csl, &ncand_b); + cand_c = find_candidates(c, av, bv, cv, tolerance[2], csl, &ncand_c); if ( (ncand_a==0) || (ncand_b==0) || (ncand_c==0) ) { *pmb = NULL; @@ -2065,7 +2063,7 @@ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, test = cell_transform_rational(cell, M); cell_get_parameters(test, &at, &bt, &ct, &alt, &bet, &gat); cell_free(test); - if ( fabs(gat - ga) > atl ) continue; + if ( fabs(gat - ga) > tolerance[5] ) continue; /* Gamma OK, now look for place for c axis */ for ( ic=0; ic<ncand_c; ic++ ) { @@ -2091,11 +2089,11 @@ int compare_reindexed_cell_parameters(UnitCell *cell_in, UnitCell *reference_in, cell_free(test); continue; } - if ( fabs(alt - al) > atl ) { + if ( fabs(alt - al) > tolerance[3] ) { cell_free(test); continue; } - if ( fabs(bet - be) > atl ) { + if ( fabs(bet - be) > tolerance[4] ) { cell_free(test); continue; } diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h index be878c10..42e7214b 100644 --- a/libcrystfel/src/cell-utils.h +++ b/libcrystfel/src/cell-utils.h @@ -88,7 +88,7 @@ extern int forbidden_reflection(UnitCell *cell, extern double cell_get_volume(UnitCell *cell); extern int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2, - float ltl, float atl); + double *tolerance); extern int compare_cell_parameters_and_orientation(UnitCell *cell1, @@ -103,7 +103,7 @@ extern int compare_reindexed_cell_parameters_and_orientation(UnitCell *a, IntegerMatrix **pmb); extern int compare_reindexed_cell_parameters(UnitCell *cell, UnitCell *reference, - double ltl, double atl, int csl, + double *tolerance, int csl, RationalMatrix **pmb); #ifdef __cplusplus diff --git a/src/cell_tool.c b/src/cell_tool.c index cd457f25..a1755f42 100644 --- a/src/cell_tool.c +++ b/src/cell_tool.c @@ -77,6 +77,7 @@ static int comparecells(UnitCell *cell, const char *comparecell, { UnitCell *cell2; RationalMatrix *m; + double tolerance[6]; cell2 = load_cell_from_file(comparecell); if ( cell2 == NULL ) { @@ -90,8 +91,15 @@ static int comparecells(UnitCell *cell, const char *comparecell, STATUS("------------------> The reference unit cell:\n"); cell_print(cell2); + tolerance[0] = ltl; + tolerance[1] = ltl; + tolerance[2] = ltl; + tolerance[3] = atl; + tolerance[4] = atl; + tolerance[5] = atl; + STATUS("------------------> The comparison results:\n"); - if ( !compare_reindexed_cell_parameters(cell, cell2, ltl, atl, csl, &m) ) { + if ( !compare_reindexed_cell_parameters(cell, cell2, tolerance, csl, &m) ) { STATUS("No relationship found between lattices.\n"); return 0; } else { @@ -227,6 +235,14 @@ static int find_ambi(UnitCell *cell, SymOpList *sym, double ltl, double atl) SymOpList *ops; signed int i[9]; const int maxorder = 3; + double tolerance[6]; + + tolerance[0] = ltl; + tolerance[1] = ltl; + tolerance[2] = ltl; + tolerance[3] = atl; + tolerance[4] = atl; + tolerance[5] = atl; ops = get_pointgroup("1"); if ( ops == NULL ) return 1; @@ -265,7 +281,7 @@ static int find_ambi(UnitCell *cell, SymOpList *sym, double ltl, double atl) nc = cell_transform_intmat(cell, m); - if ( compare_cell_parameters(cell, nc, ltl, atl) ) { + if ( compare_cell_parameters(cell, nc, tolerance) ) { if ( !intmat_is_identity(m) ) add_symop(ops, m); STATUS("-----------------------------------------------" "-------------------------------------------\n"); |