indexamajig: Hooks for Mille

4 files changed, 59 insertions, 11 deletions

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index 02b01757..e3512b4a 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -591,7 +591,8 @@ static float real_time()
 
 /* Return non-zero for "success" */
 static int try_indexer(struct image *image, IndexingMethod indm,
-                       IndexingPrivate *ipriv, void *mpriv, char *last_task)
+                       IndexingPrivate *ipriv, void *mpriv, char *last_task,
+                       Mille *mille)
 {
 	int i, r;
 	int n_bad = 0;
@@ -719,7 +720,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		{
 			int r;
 			profile_start("refine");
-			r = refine_prediction(image, cr);
+			r = refine_prediction(image, cr, mille);
 			profile_end("refine");
 			if ( r ) {
 				crystal_set_user_flag(cr, 1);
@@ -920,19 +921,26 @@ static int finished_retry(IndexingMethod indm, IndexingFlags flags,
 
 void index_pattern(struct image *image, IndexingPrivate *ipriv)
 {
-	index_pattern_3(image, ipriv, NULL, NULL);
+	index_pattern_4(image, ipriv, NULL, NULL, NULL);
 }
 
 
 void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping)
 {
-	index_pattern_3(image, ipriv, ping, NULL);
+	index_pattern_4(image, ipriv, ping, NULL, NULL);
 }
 
 
 void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
                      char *last_task)
 {
+	index_pattern_4(image, ipriv, ping, last_task, NULL);
+}
+
+
+void index_pattern_4(struct image *image, IndexingPrivate *ipriv, int *ping,
+                     char *last_task, Mille *mille)
+{
 	int n = 0;
 	ImageFeatureList *orig;
 
@@ -982,7 +990,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 			r = try_indexer(image, ipriv->methods[n],
 			                ipriv, ipriv->engine_private[n],
-			                last_task);
+			                last_task, mille);
 			success += r;
 			ntry++;
 			done = finished_retry(ipriv->methods[n], ipriv->flags,
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 94018904..fa371276 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -3,13 +3,13 @@
  *
  * Perform indexing (somehow)
  *
- * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2021 Thomas White <taw@physics.org>
+ *   2010-2023 Thomas White <taw@physics.org>
  *   2010      Richard Kirian
  *   2012      Lorenzo Galli
  *   2015      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
@@ -210,6 +210,7 @@ extern char *base_indexer_str(IndexingMethod indm);
 #include "cell.h"
 #include "image.h"
 #include "datatemplate.h"
+#include "predict-refine.h"
 
 extern struct argp felix_argp;
 extern struct argp pinkIndexer_argp;
@@ -251,6 +252,9 @@ extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv,
 extern void index_pattern_3(struct image *image, IndexingPrivate *ipriv,
                             int *ping, char *last_task);
 
+extern void index_pattern_4(struct image *image, IndexingPrivate *ipriv,
+                            int *ping, char *last_task, Mille *mille);
+
 extern void cleanup_indexing(IndexingPrivate *ipriv);
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/predict-refine.c b/libcrystfel/src/predict-refine.c
index 19c689cd..d45388b9 100644
--- a/libcrystfel/src/predict-refine.c
+++ b/libcrystfel/src/predict-refine.c
@@ -3,11 +3,11 @@
  *
  * Prediction refinement
  *
- * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2020 Thomas White <taw@physics.org>
+ *   2010-2023 Thomas White <taw@physics.org>
  *   2016      Valerio Mariani
  *
  * This file is part of CrystFEL.
@@ -37,6 +37,11 @@
 #include "image.h"
 #include "geometry.h"
 #include "cell-utils.h"
+#include "predict-refine.h"
+
+#ifdef HAVE_MILLEPEDE
+#include <mille_c_wrap.h>
+#endif
 
 
 /** \file predict-refine.h */
@@ -569,7 +574,7 @@ static void free_rps_noreflist(struct reflpeak *rps, int n)
 }
 
 
-int refine_prediction(struct image *image, Crystal *cr)
+int refine_prediction(struct image *image, Crystal *cr, Mille *mille)
 {
 	int n;
 	int i;
@@ -654,5 +659,29 @@ int refine_prediction(struct image *image, Crystal *cr)
 		return 1;
 	}
 
+	if ( mille != NULL ) {
+		printf("Mille mode!\n");
+	}
+
 	return 0;
 }
+
+
+Mille *crystfel_mille_new(const char *outFileName,
+                          int asBinary,
+                          int writeZero)
+{
+	#ifdef HAVE_MILLEPEDE
+	return mille_new(outFileName, asBinary, writeZero);
+	#else
+	return NULL;
+	#endif
+}
+
+
+void crystfel_mille_free(Mille *m)
+{
+	#ifdef HAVE_MILLEPEDE
+	mille_free(m);
+	#endif
+}
diff --git a/libcrystfel/src/predict-refine.h b/libcrystfel/src/predict-refine.h
index 5607e356..91b44e07 100644
--- a/libcrystfel/src/predict-refine.h
+++ b/libcrystfel/src/predict-refine.h
@@ -33,12 +33,19 @@
 
 struct image;
 
+typedef void *Mille;
+
 /**
  * \file predict-refine.h
  * Prediction refinement: refinement of indexing solutions before integration.
  */
 
-extern int refine_prediction(struct image *image, Crystal *cr);
+extern Mille *crystfel_mille_new(const char *outFileName,
+                                 int asBinary,
+                                 int writeZero);
+extern void crystfel_mille_free(Mille *m);
+
+extern int refine_prediction(struct image *image, Crystal *cr, Mille *mille);
 extern int refine_radius(Crystal *cr, struct image *image);