From 5911a4b627e1c6676c5522a8ecd61a2a834f544e Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Wed, 12 Sep 2012 17:57:38 +0200
Subject: More work on transformations

---
 libcrystfel/src/cell-utils.c | 13 +++++++
 libcrystfel/src/cell.c       | 81 +++++++++++++++++++++++++++++++++++++++-----
 libcrystfel/src/cell.h       |  1 +
 3 files changed, 86 insertions(+), 9 deletions(-)

(limited to 'libcrystfel/src')

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 */
-- 
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