From fd363c300c1767681ac6b03f05132d9e6d8a6884 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 19 Jan 2024 12:59:47 +0100
Subject: Fix incorrect uses of cell_free

This also gets rid of crystal_copy_deep.  From now on, all crystal_copy
calls also copy the UnitCell.
---
 libcrystfel/src/crystal.c           | 28 ++--------------------------
 libcrystfel/src/crystal.h           |  1 -
 libcrystfel/src/image.c             |  6 +-----
 libcrystfel/src/index.c             |  1 -
 libcrystfel/src/indexers/fromfile.c |  2 +-
 5 files changed, 4 insertions(+), 34 deletions(-)

(limited to 'libcrystfel/src')

diff --git a/libcrystfel/src/crystal.c b/libcrystfel/src/crystal.c
index a21283f9..f0022fcc 100644
--- a/libcrystfel/src/crystal.c
+++ b/libcrystfel/src/crystal.c
@@ -88,41 +88,17 @@ Crystal *crystal_new()
 }
 
 
-/**
- * \param cryst: A \ref Crystal to copy.
- *
- * Creates a new \ref Crystal which is a copy of \p cryst.  The copy is a "shallow
- * copy", which means that copies are NOT made of the data structures which
- * \p cryst contains references to, for example its \ref RefList.
- *
- * \returns A (shallow) copy of \p cryst, or NULL on failure.
- *
- */
-Crystal *crystal_copy(const Crystal *cryst)
-{
-	Crystal *c;
-
-	c = crystal_new();
-	if ( c == NULL ) return NULL;
-
-	memcpy(c, cryst, sizeof(Crystal));
-	if ( c->notes != NULL ) c->notes = cfstrdup(c->notes);
-
-	return c;
-}
-
-
 /**
  * \param cryst: A \ref Crystal to copy.
  *
  * Creates a new \ref Crystal which is a copy of \p cryst.  The copy is a "deep
  * copy", which means that copies ARE made of the data structures which
- * \p cryst contains references to, for example its \ref RefList.
+ * \p cryst contains references to, for example its \ref UnitCell.
  *
  * \returns A (deep) copy of \p cryst, or NULL on failure.
  *
  */
-Crystal *crystal_copy_deep(const Crystal *cryst)
+Crystal *crystal_copy(const Crystal *cryst)
 {
 	Crystal *c;
 
diff --git a/libcrystfel/src/crystal.h b/libcrystfel/src/crystal.h
index 3f19386c..7147111f 100644
--- a/libcrystfel/src/crystal.h
+++ b/libcrystfel/src/crystal.h
@@ -49,7 +49,6 @@ extern "C" {
 
 extern Crystal *crystal_new(void);
 extern Crystal *crystal_copy(const Crystal *cryst);
-extern Crystal *crystal_copy_deep(const Crystal *cryst);
 extern void crystal_free(Crystal *cryst);
 
 extern UnitCell *crystal_get_cell(Crystal *cryst);
diff --git a/libcrystfel/src/image.c b/libcrystfel/src/image.c
index 142598e3..3b4e04df 100644
--- a/libcrystfel/src/image.c
+++ b/libcrystfel/src/image.c
@@ -352,9 +352,7 @@ int remove_flagged_crystals(struct image *image)
 	for ( i=0; i<image->n_crystals; i++ ) {
 		if ( crystal_get_user_flag(image->crystals[i].cr) ) {
 			int j;
-			Crystal *deleteme = image->crystals[i].cr;
-			cell_free(crystal_get_cell(deleteme));
-			crystal_free(deleteme);
+			crystal_free(image->crystals[i].cr);
 			reflist_free(image->crystals[i].refls);
 			for ( j=i; j<image->n_crystals-1; j++ ) {
 				image->crystals[j] = image->crystals[j+1];
@@ -375,8 +373,6 @@ void free_all_crystals(struct image *image)
 	int i;
 	if ( image->crystals == NULL ) return;
 	for ( i=0; i<image->n_crystals; i++ ) {
-		Crystal *cr = image->crystals[i].cr;
-		cell_free(crystal_get_cell(cr));
 		crystal_free(image->crystals[i].cr);
 		reflist_free(image->crystals[i].refls);
 	}
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 7aea3b59..2a2542f5 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -552,7 +552,6 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target,
 	if ( out != NULL ) {
 
 		/* Replace crystal's cell with new one */
-		cell_free(crystal_get_cell(cr));
 		crystal_set_cell(cr, out);
 		rtnl_mtx_free(rm);
 		if ( !right_handed(out) ) STATUS("WARNING: left handed\n");
diff --git a/libcrystfel/src/indexers/fromfile.c b/libcrystfel/src/indexers/fromfile.c
index c7f1d1ba..30305b21 100644
--- a/libcrystfel/src/indexers/fromfile.c
+++ b/libcrystfel/src/indexers/fromfile.c
@@ -337,7 +337,7 @@ int fromfile_index(struct image *image, void *mpriv)
 
 	for ( i=0; i<p->n_crystals; i++ ) {
 		Crystal *cr;
-		cr = crystal_copy_deep(p->crystals[i]);
+		cr = crystal_copy(p->crystals[i]);
 		image_add_crystal(image, cr);
 	}
 
-- 
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