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-rw-r--r--libcrystfel/src/cell-utils.c13
-rw-r--r--libcrystfel/src/cell.c81
-rw-r--r--libcrystfel/src/cell.h1
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 */