Be clear about whether functions need rational or integer transformations

4 files changed, 75 insertions, 31 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;