diff options
Diffstat (limited to 'libcrystfel/src')
-rw-r--r-- | libcrystfel/src/cell-utils.c | 13 | ||||
-rw-r--r-- | libcrystfel/src/cell.c | 81 | ||||
-rw-r--r-- | libcrystfel/src/cell.h | 1 |
3 files changed, 86 insertions, 9 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c index 6c711642..9b65cae3 100644 --- a/libcrystfel/src/cell-utils.c +++ b/libcrystfel/src/cell-utils.c @@ -47,6 +47,19 @@ #include "image.h" +/** + * SECTION:cell-utils + * @short_description: Unit cell utilities + * @title: Unit cell utilities + * @section_id: + * @see_also: + * @include: "cell-utils.h" + * @Image: + * + * There are some utility functions associated with the core %UnitCell. + **/ + + /* Weighting factor of lengths relative to angles */ #define LWEIGHT (10.0e-9) diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c index beaa341a..7a62f51c 100644 --- a/libcrystfel/src/cell.c +++ b/libcrystfel/src/cell.c @@ -607,33 +607,55 @@ struct _unitcelltransformation }; +/** + * tfn_inverse: + * @t: A %UnitCellTransformation. + * + * Calculates the inverse of @t. That is, if you apply cell_transform() to a + * %UnitCell using @t, and then apply cell_transform() to the result using + * tfn_inverse(@t) instead of @t, you will recover the same lattice vectors + * (but note that the lattice type, centering and unique axis information will + * be lost). + * + * Returns: The inverse of @t. + * + */ UnitCellTransformation *tfn_inverse(UnitCellTransformation *t) { int s; + gsl_matrix *m; gsl_matrix *inv; gsl_permutation *perm; UnitCellTransformation *out; + m = gsl_matrix_alloc(3, 3); + if ( m == NULL ) return NULL; + out = tfn_identity(); - if ( out == NULL ) return NULL; + if ( out == NULL ) { + gsl_matrix_free(m); + return NULL; + } - perm = gsl_permutation_alloc(t->m->size1); + gsl_matrix_memcpy(m, t->m); + + perm = gsl_permutation_alloc(m->size1); if ( perm == NULL ) { ERROR("Couldn't allocate permutation\n"); return NULL; } - inv = gsl_matrix_alloc(t->m->size1, t->m->size2); + inv = gsl_matrix_alloc(m->size1, m->size2); if ( inv == NULL ) { ERROR("Couldn't allocate inverse\n"); gsl_permutation_free(perm); return NULL; } - if ( gsl_linalg_LU_decomp(t->m, perm, &s) ) { + if ( gsl_linalg_LU_decomp(m, perm, &s) ) { ERROR("Couldn't decompose matrix\n"); gsl_permutation_free(perm); return NULL; } - if ( gsl_linalg_LU_invert(t->m, perm, inv) ) { + if ( gsl_linalg_LU_invert(m, perm, inv) ) { ERROR("Couldn't invert matrix\n"); gsl_permutation_free(perm); return NULL; @@ -641,6 +663,7 @@ UnitCellTransformation *tfn_inverse(UnitCellTransformation *t) gsl_permutation_free(perm); gsl_matrix_free(out->m); + gsl_matrix_free(m); out->m = inv; return out; } @@ -651,7 +674,8 @@ UnitCellTransformation *tfn_inverse(UnitCellTransformation *t) * @cell: A %UnitCell. * @t: A %UnitCellTransformation. * - * Applies @t to @cell. + * Applies @t to @cell. Note that the lattice type, centering and unique axis + * information will not be preserved. * * Returns: Transformed copy of @cell. * @@ -675,7 +699,7 @@ UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t) &cx, &cy, &cz); m = gsl_matrix_alloc(3,3); - a = gsl_matrix_alloc(3,3); + a = gsl_matrix_calloc(3,3); if ( (m == NULL) || (a == NULL) ) { cell_free(out); return NULL; @@ -722,7 +746,13 @@ UnitCell *cell_transform(UnitCell *cell, UnitCellTransformation *t) */ UnitCell *cell_transform_inverse(UnitCell *cell, UnitCellTransformation *t) { - return cell_transform(cell, tfn_inverse(t)); + UnitCellTransformation *inv; + UnitCell *out; + + inv = tfn_inverse(t); + out = cell_transform(cell, inv); + tfn_free(inv); + return out; } @@ -769,7 +799,7 @@ void tfn_combine(UnitCellTransformation *t, double *na, double *nb, double *nc) gsl_matrix *n; n = gsl_matrix_alloc(3, 3); - a = gsl_matrix_alloc(3, 3); + a = gsl_matrix_calloc(3, 3); if ( (n == NULL) || (a == NULL) ) { return; } @@ -795,6 +825,18 @@ void tfn_combine(UnitCellTransformation *t, double *na, double *nb, double *nc) } +/** + * tfn_vector: + * @a: Amount of "a" to include in new vector + * @b: Amount of "b" to include in new vector + * @c: Amount of "c" to include in new vector + * + * This is a convenience function to use when sending vectors to tfn_combine(): + * tfn_combine(tfn, tfn_vector(1,0,0), + * tfn_vector(0,2,0), + * tfn_vector(0,0,1)); + * + */ double *tfn_vector(double a, double b, double c) { double *vec = malloc(3*sizeof(double)); @@ -804,6 +846,13 @@ double *tfn_vector(double a, double b, double c) } +/** + * tfn_print: + * @t: A %UnitCellTransformation + * + * Prints information about @t to stderr. + * + */ void tfn_print(UnitCellTransformation *t) { gsl_permutation *perm; @@ -842,3 +891,17 @@ void tfn_print(UnitCellTransformation *t) STATUS("Transformation determinant = %.2f\n", gsl_linalg_LU_det(lu, s)); } + + +/** + * tfn_free: + * @t: A %UnitCellTransformation + * + * Frees all resources associated with @t. + * + */ +void tfn_free(UnitCellTransformation *t) +{ + gsl_matrix_free(t->m); + free(t); +} diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h index ac1bd555..c7b8f8d6 100644 --- a/libcrystfel/src/cell.h +++ b/libcrystfel/src/cell.h @@ -146,5 +146,6 @@ extern void tfn_combine(UnitCellTransformation *t, extern void tfn_print(UnitCellTransformation *t); extern UnitCellTransformation *tfn_inverse(UnitCellTransformation *t); extern double *tfn_vector(double a, double b, double c); +extern void tfn_free(UnitCellTransformation *t); #endif /* CELL_H */ |