diff options
| -rw-r--r-- | libcrystfel/src/cell-utils.c | 101 | ||||
| -rw-r--r-- | libcrystfel/src/cell.c | 15 | ||||
| -rw-r--r-- | libcrystfel/src/cell.h | 6 | ||||
| -rw-r--r-- | tests/centering_check.c | 2 |
4 files changed, 92 insertions, 32 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index f0c6328f..6c711642 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -263,7 +263,9 @@ int bravais_lattice(UnitCell *cell) } -static UnitCellTransformation *uncentering_transformation(UnitCell *in) +static UnitCellTransformation *uncentering_transformation(UnitCell *in, + char *new_centering, + LatticeType *new_latt) { UnitCellTransformation *t; const double OT = 1.0/3.0; @@ -280,12 +282,16 @@ static UnitCellTransformation *uncentering_transformation(UnitCell *in) if ( t == NULL ) return NULL; if ( (ua == 'a') || (cen == 'A') ) { - tfn_combine(t, v(0,0,1), v(0,1,0), v(-1,0,0)); + tfn_combine(t, tfn_vector(0,0,1), + tfn_vector(0,1,0), + tfn_vector(-1,0,0)); if ( cen == 'A' ) cen = 'C'; } if ( (ua == 'b') || (cen == 'B') ) { - tfn_combine(t, v(1,0,0), v(0,0,1), v(0,-1,0)); + tfn_combine(t, tfn_vector(1,0,0), + tfn_vector(0,0,1), + tfn_vector(0,-1,0)); if ( cen == 'B' ) cen = 'C'; } @@ -296,42 +302,50 @@ static UnitCellTransformation *uncentering_transformation(UnitCell *in) break; case 'I' : - tfn_combine(t, v(-H,H,H), v(H,-H,H), v(H,H,-H)); + tfn_combine(t, tfn_vector(-H,H,H), + tfn_vector(H,-H,H), + tfn_vector(H,H,-H)); /* FIXME: How to handle the change of lattice type? */ if ( lt == L_CUBIC ) { - cell_set_lattice_type(cell, L_RHOMBOHEDRAL); - cell_set_centering(cell, 'R'); + *new_latt = L_RHOMBOHEDRAL; + *new_centering = 'R'; } else { /* Tetragonal or orthorhombic */ - cell_set_lattice_type(cell, L_TRICLINIC); - cell_set_centering(cell, 'P'); + *new_latt = L_TRICLINIC; + *new_centering = 'P'; } break; case 'F' : - tfn_combine(t, v(0,H,H), v(H,0,H), v(H,H,0)); + tfn_combine(t, tfn_vector(0,H,H), + tfn_vector(H,0,H), + tfn_vector(H,H,0)); if ( lt == L_CUBIC ) { - cell_set_lattice_type(cell, L_RHOMBOHEDRAL); - cell_set_centering(cell, 'R'); + *new_latt = L_RHOMBOHEDRAL; + *new_centering = 'R'; } else { assert(lt == L_ORTHORHOMBIC); - cell_set_lattice_type(cell, L_TRICLINIC); - cell_set_centering(cell, 'P'); + *new_latt = L_TRICLINIC; + *new_centering = 'P'; } break; case 'C' : - tfn_combine(t, v(H,H,0), v(-H,H,0), v(0,0,1)); - cell_set_lattice_type(cell, L_MONOCLINIC); - cell_set_centering(cell, 'P'); + tfn_combine(t, tfn_vector(H,H,0), + tfn_vector(-H,H,0), + tfn_vector(0,0,1)); + *new_latt = L_MONOCLINIC; + *new_centering = 'P'; break; case 'H' : - tfn_combine(t, v(TT,OT,OT), v(-OT,OT,OT), v(-OT,-TT,OT)); + tfn_combine(t, tfn_vector(TT,OT,OT), + tfn_vector(-OT,OT,OT), + tfn_vector(-OT,-TT,OT)); assert(lt == L_HEXAGONAL); - cell_set_lattice_type(cell, L_RHOMBOHEDRAL); - cell_set_centering(cell, 'R'); + *new_latt = L_RHOMBOHEDRAL; + *new_centering = 'R'; break; default : @@ -341,12 +355,16 @@ static UnitCellTransformation *uncentering_transformation(UnitCell *in) } if ( ua == 'a' ) { - tfn_combine(t, v(0,0,-1), v(0,1,0), v(1,0,0)); + tfn_combine(t, tfn_vector(0,0,-1), + tfn_vector(0,1,0), + tfn_vector(1,0,0)); if ( cen == 'C' ) cen = 'A'; } if ( ua == 'b' ) { - tfn_combine(t, v(1,0,0), v(0,0,-1), v(0,1,0)); + tfn_combine(t, tfn_vector(1,0,0), + tfn_vector(0,0,-1), + tfn_vector(0,1,0)); if ( cen == 'C' ) cen = 'B'; } @@ -370,18 +388,27 @@ static UnitCellTransformation *uncentering_transformation(UnitCell *in) UnitCell *uncenter_cell(UnitCell *in, UnitCellTransformation **t) { UnitCellTransformation *tt; + char new_centering; + LatticeType new_latt; + UnitCell *out; if ( !bravais_lattice(in) ) { ERROR("Cannot uncenter: not a Bravais lattice.\n"); return NULL; } - tt = uncentering_transformation(in); + tt = uncentering_transformation(in, &new_centering, &new_latt); if ( tt == NULL ) return NULL; if ( t != NULL ) *t = tt; - return cell_transform(in, tt); + out = cell_transform(in, tt); + if ( out == NULL ) return NULL; + + cell_set_lattice_type(out, new_latt); + cell_set_centering(out, new_centering); + + return out; } @@ -634,12 +661,15 @@ UnitCell *match_cell(UnitCell *cell_in, UnitCell *template_in, int verbose, /* Reverse the de-centering transformation */ new_cell_trans = cell_transform_inverse(new_cell, to_given_cell); cell_free(new_cell); + cell_set_lattice_type(new_cell, cell_get_lattice_type(template_in)); + cell_set_centering(new_cell, cell_get_centering(template_in)); + cell_set_unique_axis(new_cell, cell_get_unique_axis(template_in)); return new_cell_trans; } -UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template) +UnitCell *match_cell_ab(UnitCell *cell_in, UnitCell *template_in) { double ax, ay, az; double bx, by, bz; @@ -654,6 +684,18 @@ UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template) int have_real_a; int have_real_b; int have_real_c; + UnitCell *cell; + UnitCell *template; + UnitCellTransformation *to_given_cell; + UnitCell *new_cell; + UnitCell *new_cell_trans; + + /* "Un-center" the template unit cell to make the comparison easier */ + template = uncenter_cell(template_in, &to_given_cell); + + /* The candidate cell is also uncentered, because it might be centered + * if it came from (e.g.) MOSFLM */ + cell = uncenter_cell(cell_in, NULL); /* Get the lengths to match */ if ( cell_get_cartesian(template, &ax, &ay, &az, @@ -731,7 +773,16 @@ UnitCell *match_cell_ab(UnitCell *cell, UnitCell *template) real_c.w = -real_c.w; } - return cell_new_from_direct_axes(real_a, real_b, real_c); + new_cell = cell_new_from_direct_axes(real_a, real_b, real_c); + + /* Reverse the de-centering transformation */ + new_cell_trans = cell_transform_inverse(new_cell, to_given_cell); + cell_free(new_cell); + cell_set_lattice_type(new_cell, cell_get_lattice_type(template_in)); + cell_set_centering(new_cell, cell_get_centering(template_in)); + cell_set_unique_axis(new_cell, cell_get_unique_axis(template_in)); + + return new_cell_trans; } diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c index 53b0436d..ca0fb9cd 100644 --- a/libcrystfel/src/cell.c +++ b/libcrystfel/src/cell.c @@ -601,6 +601,12 @@ const char *cell_rep(UnitCell *cell) } +struct _unitcelltransformation +{ + +}; + + static UnitCellTransformation *inverse_transformation(UnitCellTransformation *t) { /* FIXME: Implementation */ @@ -655,7 +661,7 @@ UnitCell *cell_transform_inverse(UnitCell *cell, UnitCellTransformation *t) * Returns: A %UnitCellTransformation corresponding to an identity operation. * */ -static UnitCellTransformation *tfn_identity() +UnitCellTransformation *tfn_identity() { } @@ -672,13 +678,12 @@ static UnitCellTransformation *tfn_identity() * Likewise, a = nba*a + nbb*b + nbc*c and c = nca*a + ncb*b + ncc*c. * */ -static void tfn_combine(UnitCellTransformation *t, - double *na, double *nb, double *nc) +void tfn_combine(UnitCellTransformation *t, double *na, double *nb, double *nc) { } -static double *v(double a, double b, double c) +double *tfn_vector(double a, double b, double c) { double *vec = malloc(3*sizeof(double)); if ( vec == NULL ) return NULL; @@ -687,7 +692,7 @@ static double *v(double a, double b, double c) } -void cell_transformation_print(UnitCellTransformation *t) +void tfn_print(UnitCellTransformation *t) { } diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h index 625884e1..e5c98ace 100644 --- a/libcrystfel/src/cell.h +++ b/libcrystfel/src/cell.h @@ -140,6 +140,10 @@ extern UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t); extern UnitCell *cell_transform_inverse(UnitCell *cell, UnitCellTransformation *t); -extern void cell_transformation_print(UnitCellTransformation *t); +extern UnitCellTransformation *tfn_identity(void); +extern void tfn_combine(UnitCellTransformation *t, + double *na, double *nb, double *nc); +extern void tfn_print(UnitCellTransformation *t); +extern double *tfn_vector(double a, double b, double c); #endif /* CELL_H */ diff --git a/tests/centering_check.c b/tests/centering_check.c index 96326d21..bfee2806 100644 --- a/tests/centering_check.c +++ b/tests/centering_check.c @@ -89,7 +89,7 @@ static int check_centering(double a, double b, double c, } STATUS("Transformation was:\n"); - cell_transformation_print(t); + tfn_print(t); if ( fail ) ERROR("\n"); |