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-rw-r--r--libcrystfel/src/cell-utils.c61
-rw-r--r--libcrystfel/src/cell-utils.h20
-rw-r--r--libcrystfel/src/index.c7
-rw-r--r--src/whirligig.c12
4 files changed, 52 insertions, 48 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index b78c4831..2580f3fb 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -1669,8 +1669,8 @@ double cell_get_volume(UnitCell *cell)
/**
- * \param cell1: A UnitCell
- * \param cell2: Another UnitCell
+ * \param cell: A UnitCell
+ * \param reference: Another UnitCell
* \param tolerance: Pointer to tolerances for a,b,c (fractional), al,be,ga (radians)
*
* Compare the two unit cells. If the real space parameters match to within
@@ -1684,17 +1684,17 @@ double cell_get_volume(UnitCell *cell)
* \returns non-zero if the cells match.
*
*/
-int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2, double *tolerance)
+int compare_cell_parameters(UnitCell *cell, UnitCell *reference, double *tolerance)
{
double a1, b1, c1, al1, be1, ga1;
double a2, b2, c2, al2, be2, ga2;
/* Centering must match: we don't arbitrarte primitive vs centered,
* different cell choices etc */
- if ( cell_get_centering(cell1) != cell_get_centering(cell2) ) return 0;
+ if ( cell_get_centering(cell) != cell_get_centering(reference) ) return 0;
- cell_get_parameters(cell1, &a1, &b1, &c1, &al1, &be1, &ga1);
- cell_get_parameters(cell2, &a2, &b2, &c2, &al2, &be2, &ga2);
+ cell_get_parameters(cell, &a1, &b1, &c1, &al1, &be1, &ga1);
+ cell_get_parameters(reference, &a2, &b2, &c2, &al2, &be2, &ga2);
if ( !within_tolerance(a1, a2, tolerance[0]*100.0) ) return 0;
if ( !within_tolerance(b1, b2, tolerance[1]*100.0) ) return 0;
@@ -1717,8 +1717,8 @@ static double moduli_check(double ax, double ay, double az,
/**
- * \param cell1: A UnitCell
- * \param cell2: Another UnitCell
+ * \param cell: A UnitCell
+ * \param reference: Another UnitCell
* \param ltl: Maximum allowable fractional difference in axis lengths
* \param atl: Maximum allowable difference in angles (in radians)
*
@@ -1730,27 +1730,27 @@ static double moduli_check(double ax, double ay, double az,
* If you just want to see if the parameters are the same, use
* compare_cell_parameters() instead.
*
- * The cells \p a and \p b must have the same centering. Otherwise, this function
- * always returns zero.
+ * \p cell and \p reference must have the same centering. Otherwise, this
+ * function always returns zero.
*
* \returns non-zero if the cells match.
*
*/
-int compare_cell_parameters_and_orientation(UnitCell *cell1, UnitCell *cell2,
+int compare_cell_parameters_and_orientation(UnitCell *cell, UnitCell *reference,
const double ltl, const double atl)
{
double ax1, ay1, az1, bx1, by1, bz1, cx1, cy1, cz1;
double ax2, ay2, az2, bx2, by2, bz2, cx2, cy2, cz2;
- if ( cell_get_centering(cell1) != cell_get_centering(cell2) ) return 0;
+ if ( cell_get_centering(cell) != cell_get_centering(reference) ) return 0;
- cell_get_cartesian(cell1, &ax1, &ay1, &az1,
- &bx1, &by1, &bz1,
- &cx1, &cy1, &cz1);
+ cell_get_cartesian(cell, &ax1, &ay1, &az1,
+ &bx1, &by1, &bz1,
+ &cx1, &cy1, &cz1);
- cell_get_cartesian(cell2, &ax2, &ay2, &az2,
- &bx2, &by2, &bz2,
- &cx2, &cy2, &cz2);
+ cell_get_cartesian(reference, &ax2, &ay2, &az2,
+ &bx2, &by2, &bz2,
+ &cx2, &cy2, &cz2);
if ( angle_between(ax1, ay1, az1, ax2, ay2, az2) > atl ) return 0;
if ( angle_between(bx1, by1, bz1, bx2, by2, bz2) > atl ) return 0;
@@ -1765,8 +1765,8 @@ int compare_cell_parameters_and_orientation(UnitCell *cell1, UnitCell *cell2,
/**
- * \param a: A UnitCell
- * \param b: Another UnitCell
+ * \param cell: A UnitCell
+ * \param reference: Another UnitCell
* \param ltl: Maximum allowable fractional difference in reciprocal axis lengths
* \param atl: Maximum allowable difference in reciprocal angles (in radians)
* \param pmb: Place to store pointer to matrix
@@ -1774,26 +1774,27 @@ int compare_cell_parameters_and_orientation(UnitCell *cell1, UnitCell *cell2,
* Compare the two unit cells. If, using any permutation of the axes, the
* axes can be made to match in length (to within fractional difference \p ltl)
* and the axes aligned to within \p atl radians, this function returns non-zero
- * and stores the transformation to map \p b onto \p a.
+ * and stores the transformation which must be applied to \p cell at \p pmb.
*
* Note that the orientations of the cells must match, not just the parameters.
* The comparison is done after reindexing using
* compare_cell_parameters_and_orientation().
*
- * The cells \p a and \p b must have the same centering. Otherwise, this function
- * always returns zero.
+ * \p cell and \p reference must have the same centering. Otherwise, this
+ * function always returns zero.
*
* \returns non-zero if the cells match.
*
*/
-int compare_reindexed_cell_parameters_and_orientation(UnitCell *a, UnitCell *b,
- double ltl, double atl,
- IntegerMatrix **pmb)
+int compare_permuted_cell_parameters_and_orientation(UnitCell *cell,
+ UnitCell *reference,
+ double ltl, double atl,
+ IntegerMatrix **pmb)
{
IntegerMatrix *m;
int i[9];
- if ( cell_get_centering(a) != cell_get_centering(b) ) return 0;
+ if ( cell_get_centering(cell) != cell_get_centering(reference) ) return 0;
m = intmat_new(3, 3);
@@ -1817,9 +1818,11 @@ int compare_reindexed_cell_parameters_and_orientation(UnitCell *a, UnitCell *b,
if ( intmat_det(m) != +1 ) continue;
- nc = cell_transform_intmat(b, m);
+ nc = cell_transform_intmat(cell, m);
- if ( compare_cell_parameters_and_orientation(a, nc, ltl, atl) ) {
+ if ( compare_cell_parameters_and_orientation(nc, reference,
+ ltl, atl) )
+ {
if ( pmb != NULL ) *pmb = m;
cell_free(nc);
return 1;
diff --git a/libcrystfel/src/cell-utils.h b/libcrystfel/src/cell-utils.h
index a489a6d8..fa577269 100644
--- a/libcrystfel/src/cell-utils.h
+++ b/libcrystfel/src/cell-utils.h
@@ -87,27 +87,27 @@ extern int forbidden_reflection(UnitCell *cell,
extern double cell_get_volume(UnitCell *cell);
-extern int compare_cell_parameters(UnitCell *cell1, UnitCell *cell2,
+extern int compare_cell_parameters(UnitCell *cell, UnitCell *reference,
double *tolerance);
+extern int compare_permuted_cell_parameters(UnitCell *cell, UnitCell *reference,
+ double *tolerance, IntegerMatrix **pmb);
-extern int compare_cell_parameters_and_orientation(UnitCell *cell1,
- UnitCell *cell2,
+extern int compare_cell_parameters_and_orientation(UnitCell *cell,
+ UnitCell *reference,
const double ltl,
const double atl);
-extern int compare_reindexed_cell_parameters_and_orientation(UnitCell *a,
- UnitCell *b,
- double ltl,
- double atl,
- IntegerMatrix **pmb);
+extern int compare_permuted_cell_parameters_and_orientation(UnitCell *cell,
+ UnitCell *reference,
+ double ltl,
+ double atl,
+ IntegerMatrix **pmb);
extern int compare_reindexed_cell_parameters(UnitCell *cell, UnitCell *reference,
double *tolerance, int csl,
RationalMatrix **pmb);
-extern int compare_permuted_cell_parameters(UnitCell *cell, UnitCell *reference,
- double *tolerance, IntegerMatrix **pmb);
#ifdef __cplusplus
}
#endif
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index b187e119..b07dd067 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -542,6 +542,7 @@ void map_all_peaks(struct image *image)
}
+/* Return 0 for cell OK, 1 for cell incorrect */
static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
double *tolerance)
{
@@ -708,9 +709,9 @@ static int try_indexer(struct image *image, IndexingMethod indm,
/* Don't do similarity check against bad crystals */
if ( crystal_get_user_flag(that_cr) ) continue;
- if ( compare_reindexed_cell_parameters_and_orientation(crystal_get_cell(cr),
- crystal_get_cell(that_cr),
- 0.1, deg2rad(0.5), NULL) )
+ if ( compare_permuted_cell_parameters_and_orientation(crystal_get_cell(cr),
+ crystal_get_cell(that_cr),
+ 0.1, deg2rad(0.5), NULL) )
{
crystal_set_user_flag(cr, 1);
}
diff --git a/src/whirligig.c b/src/whirligig.c
index cc2b531e..a144e769 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -309,9 +309,9 @@ static IntegerMatrix *try_all(struct window *win, int n1, int n2,
for ( i=0; i<i1->n_crystals; i++ ) {
for ( j=0; j<i2->n_crystals; j++ ) {
- if ( compare_reindexed_cell_parameters_and_orientation(crystal_get_cell(i1->crystals[i]),
- crystal_get_cell(i2->crystals[j]),
- 0.1, deg2rad(5.0), &m) )
+ if ( compare_permuted_cell_parameters_and_orientation(crystal_get_cell(i1->crystals[i]),
+ crystal_get_cell(i2->crystals[j]),
+ 0.1, deg2rad(5.0), &m) )
{
if ( !crystal_used(win, n1, i)
&& !crystal_used(win, n2, j) )
@@ -374,9 +374,9 @@ static int try_join(struct window *win, int sn)
for ( j=0; j<win->img[win->join_ptr].n_crystals; j++ ) {
Crystal *cr2;
cr2 = win->img[win->join_ptr].crystals[j];
- if ( compare_reindexed_cell_parameters_and_orientation(ref, crystal_get_cell(cr2),
- 0.1, deg2rad(5.0),
- &win->mat[sn][win->join_ptr]) )
+ if ( compare_permuted_cell_parameters_and_orientation(ref, crystal_get_cell(cr2),
+ 0.1, deg2rad(5.0),
+ &win->mat[sn][win->join_ptr]) )
{
win->ser[sn][win->join_ptr] = j;
cell_free(ref);
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-16 08:21:28 +0000