Merge branch 'tom/deltacchalf'

4 files changed, 80 insertions, 9 deletions

diff --git a/libcrystfel/src/reflist-utils.c b/libcrystfel/src/reflist-utils.c
index 54c467b3..70548994 100644
--- a/libcrystfel/src/reflist-utils.c
+++ b/libcrystfel/src/reflist-utils.c
@@ -3,11 +3,11 @@
  *
  * Utilities to complement the core reflist.c
  *
- * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2011-2017 Thomas White <taw@physics.org>
+ *   2011-2018 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *
  * This file is part of CrystFEL.
@@ -648,6 +648,30 @@ RefList *copy_reflist(RefList *list)
 }
 
 
+/**
+ * free_contribs:
+ * @list: A %RefList
+ *
+ * Goes through @list and frees all the reflection contribution structures.
+ **/
+void free_contribs(RefList *list)
+{
+	Reflection *refl;
+	RefListIterator *iter;
+
+	for ( refl = first_refl(list, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) )
+	{
+		struct reflection_contributions *c;
+		c = get_contributions(refl);
+		free(c->contribs);
+		free(c->contrib_crystals);
+		free(c);
+	}
+}
+
+
 static char *full_command_line(int argc, char *argv[])
 {
 	int i;
diff --git a/libcrystfel/src/reflist-utils.h b/libcrystfel/src/reflist-utils.h
index f64e9f51..c955491a 100644
--- a/libcrystfel/src/reflist-utils.h
+++ b/libcrystfel/src/reflist-utils.h
@@ -3,11 +3,11 @@
  *
  * Utilities to complement the core reflist.c
  *
- * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2011-2017 Thomas White <taw@physics.org>
+ *   2011-2018 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *
  * This file is part of CrystFEL.
@@ -69,6 +69,8 @@ extern RefList *res_cutoff(RefList *list, UnitCell *cell,
 
 extern RefList *copy_reflist(RefList *list);
 
+extern void free_contribs(RefList *list);
+
 extern void reflist_add_command_and_version(RefList *list,
                                             int argcv, char *argv[]);
 
diff --git a/libcrystfel/src/reflist.c b/libcrystfel/src/reflist.c
index a35aa575..f1d759ea 100644
--- a/libcrystfel/src/reflist.c
+++ b/libcrystfel/src/reflist.c
@@ -3,11 +3,11 @@
  *
  * Fast reflection/peak list
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2011-2016 Thomas White <taw@physics.org>
+ *   2011-2018 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -100,6 +100,9 @@ struct _refldata {
 	double peak;
 	double mean_bg;
 
+	/* Contributions */
+	struct reflection_contributions *contribs;
+
 	/* User-specified temporary values */
 	double temp1;
 	double temp2;
@@ -587,6 +590,18 @@ int get_flag(const Reflection *refl)
 }
 
 
+/**
+ * get_contributions:
+ * @refl: A %Reflection
+ *
+ * Returns: the reflection's contribution list
+ *
+ **/
+struct reflection_contributions *get_contributions(const Reflection *refl)
+{
+	return refl->data.contribs;
+}
+
 /********************************** Setters ***********************************/
 
 /**
@@ -634,6 +649,7 @@ void set_panel(Reflection *refl, struct panel *p)
 	refl->data.panel = p;
 }
 
+
 /**
  * set_khalf:
  * @refl: A %Reflection
@@ -647,7 +663,6 @@ void set_khalf(Reflection *refl, double khalf)
 }
 
 
-
 /**
  * set_kpred:
  * @refl: A %Reflection
@@ -848,6 +863,21 @@ void set_flag(Reflection *refl, int flag)
 }
 
 
+/**
+ * set_contributions:
+ * @refl: A %Reflection
+ * @contribs: Pointer to the contribution list
+ *
+ * Note that the pointer will be stored, not the contents of the structure.
+ *
+ **/
+void set_contributions(Reflection *refl,
+                       struct reflection_contributions *contribs)
+{
+	refl->data.contribs = contribs;
+}
+
+
 /********************************* Insertion **********************************/
 
 static Reflection *rotate_once(Reflection *refl, int dir)
diff --git a/libcrystfel/src/reflist.h b/libcrystfel/src/reflist.h
index 9f494474..f2fadb8b 100644
--- a/libcrystfel/src/reflist.h
+++ b/libcrystfel/src/reflist.h
@@ -3,11 +3,11 @@
  *
  * Fast reflection/peak list
  *
- * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2011-2017 Thomas White <taw@physics.org>
+ *   2011-2018 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -38,6 +38,7 @@
 #define GET_K(serial) ((((serial) & 0x000ffc00)>>10)-512)
 #define GET_L(serial) (((serial) & 0x000003ff)-512)
 
+
 /**
  * RefList:
  *
@@ -73,6 +74,17 @@ typedef struct _reflistiterator RefListIterator;
 extern "C" {
 #endif
 
+typedef struct _crystal Crystal;
+
+/* Structure representing the contributions to a merged reflection */
+struct reflection_contributions
+{
+	int          n_contrib;
+	int          max_contrib;
+	Reflection **contribs;
+	Crystal    **contrib_crystals;
+};
+
 /* Creation/deletion */
 extern RefList *reflist_new(void);
 extern void reflist_free(RefList *list);
@@ -105,6 +117,7 @@ extern double get_phase(const Reflection *refl, int *have_phase);
 extern double get_peak(const Reflection *refl);
 extern double get_mean_bg(const Reflection *refl);
 extern int get_flag(const Reflection *refl);
+extern struct reflection_contributions *get_contributions(const Reflection *refl);
 
 /* Set */
 extern void copy_data(Reflection *to, const Reflection *from);
@@ -126,6 +139,8 @@ extern void set_mean_bg(Reflection *refl, double mean_bg);
 extern void set_symmetric_indices(Reflection *refl,
                                   signed int hs, signed int ks, signed int ls);
 extern void set_flag(Reflection *refl, int flag);
+extern void set_contributions(Reflection *refl,
+                              struct reflection_contributions *contribs);
 
 /* Insertion */
 extern Reflection *add_refl(RefList *list,