From 4b3ffa51ec169406185a76016a29833bc9637264 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 31 Aug 2012 16:20:21 +0200 Subject: WIP on cell transformations --- libcrystfel/src/cell-utils.c | 81 ++++++++++++++++++++++++++++++++------------ libcrystfel/src/cell-utils.h | 4 ++- libcrystfel/src/cell.c | 54 +++++++++++++++++++++++++++++ libcrystfel/src/cell.h | 15 ++++++++ 4 files changed, 131 insertions(+), 23 deletions(-) (limited to 'libcrystfel') diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 508b70e5..776526aa 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -83,7 +83,7 @@ UnitCell *cell_rotate(UnitCell *in, struct quaternion quat) } -static const char *str_lattice(LatticeType l) +const char *str_lattice(LatticeType l) { switch ( l ) { @@ -253,17 +253,19 @@ int bravais_lattice(UnitCell *cell) if ( lattice == L_HEXAGONAL ) return 1; return 0; + case 'R' : + if ( lattice == L_RHOMBOHEDRAL ) return 1; + return 0; + default : return 0; } } -/* Turn any cell into a primitive one, e.g. for comparison purposes */ -UnitCell *uncenter_cell(UnitCell *in) +static UnitCellTransformation *uncentering_transformation(UnitCell *in) { - UnitCell *cell; - + UnitCellTransformation *t; double ax, ay, az; double bx, by, bz; double cx, cy, cz; @@ -276,34 +278,29 @@ UnitCell *uncenter_cell(UnitCell *in) LatticeType lt; char ua, cen; - if ( !bravais_lattice(in) ) { - ERROR("Cannot uncenter: not a Bravais lattice.\n"); - return NULL; - } - cell_get_cartesian(in, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz); lt = cell_get_lattice_type(in); ua = cell_get_unique_axis(in); cen = cell_get_centering(in); - if ( ua == 'a' ) { + if ( (ua == 'a') || (cen == 'A') ) { double tx, ty, tz; tx = ax; ty = ay; tz = az; ax = cx; ay = cy; az = cz; - cx = tx; cy = ty; cz = tz; + cx = -tx; cy = -ty; cz = -tz; if ( cen == 'A' ) cen = 'C'; + ua = 'c'; } - if ( ua == 'b' ) { + if ( (ua == 'b') || (cen == 'B') ) { double tx, ty, tz; tx = bx; ty = by; tz = bz; - ax = cx; ay = cy; az = cz; - cx = tx; cy = ty; cz = tz; + bx = cx; by = cy; bz = cz; + cx = -tx; cy = -ty; cz = -tz; if ( cen == 'B' ) cen = 'C'; + ua = 'c'; } - cell = cell_new(); - switch ( cen ) { case 'P' : @@ -392,9 +389,39 @@ UnitCell *uncenter_cell(UnitCell *in) } - cell_set_cartesian(cell, nax, nay, naz, nbx, nby, nbz, ncx, ncy, ncz); - return cell; +} + + +/** + * uncenter_cell: + * @in: A %UnitCell + * @t: Location at which to store the transformation which was used. + * + * Turns any cell into a primitive one, e.g. for comparison purposes. The + * transformation which was used is stored at @t, which can be NULL if the + * transformation is not required. + * + * Returns: a primitive version of @in in a conventional (unique axis c) + * setting. + * + */ +UnitCell *uncenter_cell(UnitCell *in, UnitCellTransformation **t) +{ + UnitCell *cell; + UnitCellTransformation *tt; + + if ( !bravais_lattice(in) ) { + ERROR("Cannot uncenter: not a Bravais lattice.\n"); + return NULL; + } + + tt = uncentering_transformation(in); + if ( tt == NULL ) return NULL; + + if ( t != NULL ) *t = tt; + + return cell_transform(in, tt); } @@ -455,9 +482,15 @@ UnitCell *match_cell(UnitCell *cell_in, UnitCell *template_in, int verbose, float angtol = deg2rad(tols[3]); UnitCell *cell; UnitCell *template; + UnitCellTransformation *to_given_cell; + UnitCell *new_cell_trans; - cell = uncenter_cell(cell_in); - template = uncenter_cell(template_in); + /* "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); if ( cell_get_reciprocal(template, &asx, &asy, &asz, &bsx, &bsy, &bsz, @@ -638,7 +671,11 @@ UnitCell *match_cell(UnitCell *cell_in, UnitCell *template_in, int verbose, free(cand[1]); free(cand[2]); - return new_cell; + /* Reverse the de-centering transformation */ + new_cell_trans = cell_transform_inverse(new_cell, to_given_cell); + cell_free(new_cell); + + return new_cell_trans; } diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h index b2cb7b67..8acf2f85 100644 --- a/libcrystfel/src/cell-utils.h +++ b/libcrystfel/src/cell-utils.h @@ -55,10 +55,12 @@ extern int cell_is_sensible(UnitCell *cell); extern void validate_cell(UnitCell *cell); -extern UnitCell *uncenter_cell(UnitCell *in); +extern UnitCell *uncenter_cell(UnitCell *in, UnitCellTransformation **tr); extern int bravais_lattice(UnitCell *cell); extern int right_handed(UnitCell *cell); +extern const char *str_lattice(LatticeType l); + #endif /* CELL_UTILS_H */ diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c index 37e201e3..e2617dfc 100644 --- a/libcrystfel/src/cell.c +++ b/libcrystfel/src/cell.c @@ -599,3 +599,57 @@ const char *cell_rep(UnitCell *cell) return "unknown"; } + + +static UnitCellTransformation *inverse_transformation(UnitCellTransformation *t) +{ + /* FIXME: Implementation */ + return NULL; +} + + +/** + * cell_transform: + * @cell: A %UnitCell. + * @t: A %UnitCellTransformation. + * + * Applies @t to @cell. + * + * Returns: Transformed copy of @cell. + * + */ +UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t) +{ + UnitCell *out; + + if ( t == NULL ) return NULL; + + out = cell_new(); + if ( out == NULL ) return NULL; + + /* FIXME: Implementation */ + + return out; +} + + +/** + * cell_transform: + * @cell: A %UnitCell. + * @t: A %UnitCellTransformation. + * + * Applies the inverse of @t to @cell. + * + * Returns: Transformed copy of @cell. + * + */ +UnitCell *cell_transform_inverse(UnitCell *cell, UnitCellTransformation *t) +{ + return cell_transform(cell, inverse_transformation(t)); +} + + +void cell_transformation_print(UnitCellTransformation *t) +{ + +} diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h index 4e90a8ad..625884e1 100644 --- a/libcrystfel/src/cell.h +++ b/libcrystfel/src/cell.h @@ -68,6 +68,15 @@ typedef enum **/ typedef struct _unitcell UnitCell; + +/** + * UnitCellTransformation: + * + * This opaque data structure represents a tranformation of a unit cell, such + * as a rotation or a centering operation. + **/ +typedef struct _unitcelltransformation UnitCellTransformation; + extern UnitCell *cell_new(void); extern UnitCell *cell_new_from_cell(UnitCell *orig); extern void cell_free(UnitCell *cell); @@ -127,4 +136,10 @@ extern void cell_set_unique_axis(UnitCell *cell, char unique_axis); extern const char *cell_rep(UnitCell *cell); +extern UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t); +extern UnitCell *cell_transform_inverse(UnitCell *cell, + UnitCellTransformation *t); + +extern void cell_transformation_print(UnitCellTransformation *t); + #endif /* CELL_H */ -- cgit v1.2.3