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-rw-r--r--libcrystfel/src/cell-utils.c8
-rw-r--r--libcrystfel/src/cell.c88
-rw-r--r--libcrystfel/src/cell.h8
-rw-r--r--libcrystfel/src/xgandalf.c2
-rw-r--r--src/cell_tool.c4
-rw-r--r--src/whirligig.c2
-rw-r--r--tests/transformation_check.c6
7 files changed, 81 insertions, 37 deletions
diff --git a/libcrystfel/src/cell-utils.c b/libcrystfel/src/cell-utils.c
index 507d4cc2..da1e6fd5 100644
--- a/libcrystfel/src/cell-utils.c
+++ b/libcrystfel/src/cell-utils.c
@@ -500,7 +500,7 @@ UnitCell *uncenter_cell(UnitCell *in, IntegerMatrix **t)
tt = centering_transformation(in, &new_centering, &new_latt, &new_ua);
if ( tt == NULL ) return NULL;
- out = cell_transform_inverse(in, tt);
+ out = cell_transform_intmat_inverse(in, tt);
if ( out == NULL ) return NULL;
cell_set_lattice_type(out, new_latt);
@@ -776,7 +776,7 @@ UnitCell *match_cell(UnitCell *cell_in, UnitCell *template_in, int verbose,
/* Reverse the de-centering transformation */
if ( new_cell != NULL ) {
- new_cell_trans = cell_transform(new_cell, centering);
+ new_cell_trans = cell_transform_intmat(new_cell, centering);
cell_free(new_cell);
cell_set_lattice_type(new_cell_trans,
cell_get_lattice_type(template_in));
@@ -905,7 +905,7 @@ UnitCell *match_cell_ab(UnitCell *cell_in, UnitCell *template_in)
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);
+ new_cell_trans = cell_transform_intmat_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));
@@ -1770,7 +1770,7 @@ int compare_reindexed_cell_parameters_and_orientation(UnitCell *a, UnitCell *b,
if ( intmat_det(m) != +1 ) continue;
- nc = cell_transform(b, m);
+ nc = cell_transform_intmat(b, m);
if ( compare_cell_parameters_and_orientation(a, nc, ltl, atl) ) {
if ( pmb != NULL ) *pmb = m;
diff --git a/libcrystfel/src/cell.c b/libcrystfel/src/cell.c
index 242094f6..5eb13349 100644
--- a/libcrystfel/src/cell.c
+++ b/libcrystfel/src/cell.c
@@ -688,16 +688,16 @@ UnitCell *cell_transform_gsl_reciprocal(UnitCell *in, gsl_matrix *m)
/**
- * cell_transform:
+ * cell_transform_rational:
* @cell: A %UnitCell.
- * @t: An %IntegerMatrix.
+ * @t: A %RationalMatrix.
*
* Applies @t to @cell.
*
* Returns: Transformed copy of @cell.
*
*/
-UnitCell *cell_transform(UnitCell *cell, IntegerMatrix *m)
+UnitCell *cell_transform_rational(UnitCell *cell, RationalMatrix *m)
{
UnitCell *out;
gsl_matrix *tm;
@@ -709,15 +709,15 @@ UnitCell *cell_transform(UnitCell *cell, IntegerMatrix *m)
return NULL;
}
- gsl_matrix_set(tm, 0, 0, intmat_get(m, 0, 0));
- gsl_matrix_set(tm, 0, 1, intmat_get(m, 0, 1));
- gsl_matrix_set(tm, 0, 2, intmat_get(m, 0, 2));
- gsl_matrix_set(tm, 1, 0, intmat_get(m, 1, 0));
- gsl_matrix_set(tm, 1, 1, intmat_get(m, 1, 1));
- gsl_matrix_set(tm, 1, 2, intmat_get(m, 1, 2));
- gsl_matrix_set(tm, 2, 0, intmat_get(m, 2, 0));
- gsl_matrix_set(tm, 2, 1, intmat_get(m, 2, 1));
- gsl_matrix_set(tm, 2, 2, intmat_get(m, 2, 2));
+ gsl_matrix_set(tm, 0, 0, rtnl_as_double(rtnl_mtx_get(m, 0, 0)));
+ gsl_matrix_set(tm, 0, 1, rtnl_as_double(rtnl_mtx_get(m, 0, 1)));
+ gsl_matrix_set(tm, 0, 2, rtnl_as_double(rtnl_mtx_get(m, 0, 2)));
+ gsl_matrix_set(tm, 1, 0, rtnl_as_double(rtnl_mtx_get(m, 1, 0)));
+ gsl_matrix_set(tm, 1, 1, rtnl_as_double(rtnl_mtx_get(m, 1, 1)));
+ gsl_matrix_set(tm, 1, 2, rtnl_as_double(rtnl_mtx_get(m, 1, 2)));
+ gsl_matrix_set(tm, 2, 0, rtnl_as_double(rtnl_mtx_get(m, 2, 0)));
+ gsl_matrix_set(tm, 2, 1, rtnl_as_double(rtnl_mtx_get(m, 2, 1)));
+ gsl_matrix_set(tm, 2, 2, rtnl_as_double(rtnl_mtx_get(m, 2, 2)));
out = cell_transform_gsl_direct(cell, tm);
@@ -730,16 +730,36 @@ UnitCell *cell_transform(UnitCell *cell, IntegerMatrix *m)
/**
- * cell_transform_inverse:
+ * cell_transform_intmat:
* @cell: A %UnitCell.
- * @m: An %IntegerMatrix
+ * @t: An %IntegerMatrix.
+ *
+ * Applies @t to @cell.
+ *
+ * Returns: Transformed copy of @cell.
+ *
+ */
+UnitCell *cell_transform_intmat(UnitCell *cell, IntegerMatrix *m)
+{
+ UnitCell *ans;
+ RationalMatrix *mtx = rtnl_mtx_from_intmat(m);
+ ans = cell_transform_rational(cell, mtx);
+ rtnl_mtx_free(mtx);
+ return ans;
+}
+
+
+/**
+ * cell_transform_rational_inverse:
+ * @cell: A %UnitCell.
+ * @m: A %RationalMatrix
*
* Applies the inverse of @m to @cell.
*
* Returns: Transformed copy of @cell.
*
*/
-UnitCell *cell_transform_inverse(UnitCell *cell, IntegerMatrix *m)
+UnitCell *cell_transform_rational_inverse(UnitCell *cell, RationalMatrix *m)
{
UnitCell *out;
gsl_matrix *tm;
@@ -754,15 +774,15 @@ UnitCell *cell_transform_inverse(UnitCell *cell, IntegerMatrix *m)
return NULL;
}
- gsl_matrix_set(tm, 0, 0, intmat_get(m, 0, 0));
- gsl_matrix_set(tm, 0, 1, intmat_get(m, 0, 1));
- gsl_matrix_set(tm, 0, 2, intmat_get(m, 0, 2));
- gsl_matrix_set(tm, 1, 0, intmat_get(m, 1, 0));
- gsl_matrix_set(tm, 1, 1, intmat_get(m, 1, 1));
- gsl_matrix_set(tm, 1, 2, intmat_get(m, 1, 2));
- gsl_matrix_set(tm, 2, 0, intmat_get(m, 2, 0));
- gsl_matrix_set(tm, 2, 1, intmat_get(m, 2, 1));
- gsl_matrix_set(tm, 2, 2, intmat_get(m, 2, 2));
+ gsl_matrix_set(tm, 0, 0, rtnl_as_double(rtnl_mtx_get(m, 0, 0)));
+ gsl_matrix_set(tm, 0, 1, rtnl_as_double(rtnl_mtx_get(m, 0, 1)));
+ gsl_matrix_set(tm, 0, 2, rtnl_as_double(rtnl_mtx_get(m, 0, 2)));
+ gsl_matrix_set(tm, 1, 0, rtnl_as_double(rtnl_mtx_get(m, 1, 0)));
+ gsl_matrix_set(tm, 1, 1, rtnl_as_double(rtnl_mtx_get(m, 1, 1)));
+ gsl_matrix_set(tm, 1, 2, rtnl_as_double(rtnl_mtx_get(m, 1, 2)));
+ gsl_matrix_set(tm, 2, 0, rtnl_as_double(rtnl_mtx_get(m, 2, 0)));
+ gsl_matrix_set(tm, 2, 1, rtnl_as_double(rtnl_mtx_get(m, 2, 1)));
+ gsl_matrix_set(tm, 2, 2, rtnl_as_double(rtnl_mtx_get(m, 2, 2)));
perm = gsl_permutation_alloc(3);
if ( perm == NULL ) {
@@ -796,3 +816,23 @@ UnitCell *cell_transform_inverse(UnitCell *cell, IntegerMatrix *m)
return out;
}
+
+
+/**
+ * cell_transform_intmat_inverse:
+ * @cell: A %UnitCell.
+ * @m: An %IntegerMatrix
+ *
+ * Applies the inverse of @m to @cell.
+ *
+ * Returns: Transformed copy of @cell.
+ *
+ */
+UnitCell *cell_transform_intmat_inverse(UnitCell *cell, IntegerMatrix *m)
+{
+ UnitCell *ans;
+ RationalMatrix *mtx = rtnl_mtx_from_intmat(m);
+ ans = cell_transform_rational_inverse(cell, mtx);
+ rtnl_mtx_free(mtx);
+ return ans;
+}
diff --git a/libcrystfel/src/cell.h b/libcrystfel/src/cell.h
index e6ccbdf7..8e6809b5 100644
--- a/libcrystfel/src/cell.h
+++ b/libcrystfel/src/cell.h
@@ -150,8 +150,12 @@ extern const char *cell_rep(UnitCell *cell);
extern UnitCell *cell_transform_gsl_direct(UnitCell *in, gsl_matrix *m);
extern UnitCell *cell_transform_gsl_reciprocal(UnitCell *in, gsl_matrix *m);
-extern UnitCell *cell_transform(UnitCell *cell, IntegerMatrix *m);
-extern UnitCell *cell_transform_inverse(UnitCell *cell, IntegerMatrix *m);
+
+extern UnitCell *cell_transform_rational(UnitCell *cell, RationalMatrix *m);
+extern UnitCell *cell_transform_rational_inverse(UnitCell *cell, RationalMatrix *m);
+
+extern UnitCell *cell_transform_intmat(UnitCell *cell, IntegerMatrix *m);
+extern UnitCell *cell_transform_intmat_inverse(UnitCell *cell, IntegerMatrix *m);
#ifdef __cplusplus
}
diff --git a/libcrystfel/src/xgandalf.c b/libcrystfel/src/xgandalf.c
index e6618560..b122cb4c 100644
--- a/libcrystfel/src/xgandalf.c
+++ b/libcrystfel/src/xgandalf.c
@@ -114,7 +114,7 @@ int run_xgandalf(struct image *image, void *ipriv)
if(xgandalf_private_data->cellTemplate != NULL){
restoreCell(uc, &xgandalf_private_data->latticeReductionTransform);
- UnitCell *new_cell_trans = cell_transform(uc, xgandalf_private_data->centeringTransformation);
+ UnitCell *new_cell_trans = cell_transform_intmat(uc, xgandalf_private_data->centeringTransformation);
cell_free(uc);
uc = new_cell_trans;
diff --git a/src/cell_tool.c b/src/cell_tool.c
index 12a00192..20e156a1 100644
--- a/src/cell_tool.c
+++ b/src/cell_tool.c
@@ -119,7 +119,7 @@ static int comparecells(UnitCell *cell, const char *comparecell,
if ( intmat_det(m) < 1 ) continue;
- nc = cell_transform(cell, m);
+ nc = cell_transform_intmat(cell, m);
if ( compare_cell_parameters(cell2, nc, ltl, atl) ) {
STATUS("-----------------------------------------------"
@@ -294,7 +294,7 @@ static int find_ambi(UnitCell *cell, SymOpList *sym, double ltl, double atl)
if ( intmat_det(m) != +1 ) continue;
- nc = cell_transform(cell, m);
+ nc = cell_transform_intmat(cell, m);
if ( compare_cell_parameters(cell, nc, ltl, atl) ) {
if ( !intmat_is_identity(m) ) add_symop(ops, m);
diff --git a/src/whirligig.c b/src/whirligig.c
index 7d50141a..209e7fbe 100644
--- a/src/whirligig.c
+++ b/src/whirligig.c
@@ -369,7 +369,7 @@ static int try_join(struct window *win, int sn)
/* Get the appropriately transformed cell from the last crystal in this
* series */
cr = win->img[sp].crystals[win->ser[sn][sp]];
- ref = cell_transform(crystal_get_cell(cr), win->mat[sn][sp]);
+ ref = cell_transform_intmat(crystal_get_cell(cr), win->mat[sn][sp]);
for ( j=0; j<win->img[win->join_ptr].n_crystals; j++ ) {
Crystal *cr2;
diff --git a/tests/transformation_check.c b/tests/transformation_check.c
index 2eb01aa6..c5dad16c 100644
--- a/tests/transformation_check.c
+++ b/tests/transformation_check.c
@@ -176,11 +176,11 @@ static int check_transformation(UnitCell *cell, IntegerMatrix *tfn,
STATUS("-----------------------\n");
if ( ct == NULL ) {
- cnew = cell_transform(cell, tfn);
+ cnew = cell_transform_intmat(cell, tfn);
} else {
cnew = ct;
}
- cback = cell_transform_inverse(cnew, tfn);
+ cback = cell_transform_intmat_inverse(cnew, tfn);
STATUS("----> Before transformation:\n");
cell_print(cell);
@@ -257,7 +257,7 @@ static int check_identity(UnitCell *cell, IntegerMatrix *tfn)
STATUS("-----------------------\n");
- cnew = cell_transform(cell, tfn);
+ cnew = cell_transform_intmat(cell, tfn);
STATUS("----> Before identity transformation:\n");
cell_print(cell);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-18 09:53:38 +0000