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-rw-r--r--libcrystfel/src/cell-utils.c101
-rw-r--r--libcrystfel/src/cell.c15
-rw-r--r--libcrystfel/src/cell.h6
3 files changed, 91 insertions, 31 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 */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 10:18:45 +0000