indexamajig: Hooks for Mille

8 files changed, 91 insertions, 20 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);
 
 
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index a91c6a87..c3f2ca70 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -69,6 +69,7 @@
 #include "im-zmq.h"
 #include "profile.h"
 #include "im-asapo.h"
+#include "predict-refine.h"
 
 
 struct sandbox
@@ -340,6 +341,7 @@ static int run_work(const struct index_args *iargs, Stream *st,
 	int allDone = 0;
 	struct im_zmq *zmqstuff = NULL;
 	struct im_asapo *asapostuff = NULL;
+	Mille *mille;
 
 	if ( sb->profile ) {
 		profile_init();
@@ -363,6 +365,14 @@ static int run_work(const struct index_args *iargs, Stream *st,
 		}
 	}
 
+	if ( iargs->mille ) {
+		char tmp[64];
+		snprintf(tmp, 63, "mille-data-%i.bin", cookie);
+		mille = crystfel_mille_new(tmp, 1, 0);
+	} else {
+		mille = NULL;
+	}
+
 	while ( !allDone ) {
 
 		struct pattern_args pargs;
@@ -519,7 +529,7 @@ static int run_work(const struct index_args *iargs, Stream *st,
 			profile_start("process-image");
 			process_image(iargs, &pargs, st, cookie, tmpdir, ser,
 			              sb->shared, sb->shared->last_task[cookie],
-			              asapostuff);
+			              asapostuff, mille);
 			profile_end("process-image");
 		}
 
@@ -536,6 +546,8 @@ static int run_work(const struct index_args *iargs, Stream *st,
 		free(pargs.event);
 	}
 
+	crystfel_mille_free(mille);
+
 	/* These are both no-ops if argument is NULL */
 	im_zmq_shutdown(zmqstuff);
 	im_asapo_shutdown(asapostuff);
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 57e1e5fb..7f5504cd 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -3,13 +3,13 @@
  *
  * Index patterns, output hkl+intensity etc.
  *
- * Copyright © 2012-2022 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:
- *   2010-2022 Thomas White <taw@physics.org>
+ *   2010-2023 Thomas White <taw@physics.org>
  *   2011      Richard Kirian
  *   2012      Lorenzo Galli
  *   2012      Chunhong Yoon
@@ -722,6 +722,10 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state)
 		}
 		break;
 
+		case 416 :
+		args->iargs.mille = 1;
+		break;
+
 		/* ---------- Integration ---------- */
 
 		case 501 :
@@ -966,6 +970,7 @@ int main(int argc, char *argv[])
 	args.iargs.clen_estimate = NAN;
 	args.iargs.n_threads = 1;
 	args.iargs.data_format = DATA_SOURCE_TYPE_UNKNOWN;
+	args.iargs.mille = 0;
 
 	argp_program_version_hook = show_version;
 
@@ -1085,6 +1090,8 @@ int main(int argc, char *argv[])
 		        "Maximum number of threads allowed for indexing engines."},
 		{"camera-length-estimate", 415, "metres", 0,
 		        "Estimate of the camera length, in metres."},
+		{"mille", 416, NULL, 0,
+		        "Generate data for detector geometry refinement using Millepede"},
 
 		{NULL, 0, 0, OPTION_DOC, "Integration options:", 5},
 		{"integration", 501, "method", OPTION_NO_USAGE, "Integration method"},
diff --git a/src/process_image.c b/src/process_image.c
index 8acd3e86..4763646a 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -178,7 +178,8 @@ static struct image *file_wait_open_read(const char *filename,
 void process_image(const struct index_args *iargs, struct pattern_args *pargs,
                    Stream *st, int cookie, const char *tmpdir,
                    int serial, struct sb_shm *sb_shared,
-                   char *last_task, struct im_asapo *asapostuff)
+                   char *last_task, struct im_asapo *asapostuff,
+                   Mille *mille)
 {
 	struct image *image;
 	int i;
@@ -414,8 +415,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	/* Index the pattern */
 	set_last_task(last_task, "indexing");
 	profile_start("index");
-	index_pattern_3(image, iargs->ipriv, &sb_shared->pings[cookie],
-	                last_task);
+	index_pattern_4(image, iargs->ipriv, &sb_shared->pings[cookie],
+	                last_task, mille);
 	profile_end("index");
 
 	r = chdir(rn);
diff --git a/src/process_image.h b/src/process_image.h
index cca2f7d2..eabd425a 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -3,11 +3,11 @@
  *
  * The processing pipeline for one image
  *
- * Copyright © 2012-2022 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2023 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2022 Thomas White <taw@physics.org>
+ *   2010-2023 Thomas White <taw@physics.org>
  *   2014-2017 Valerio Mariani <valerio.mariani@desy.de>
  *   2017-2018 Yaroslav Gevorkov <yaroslav.gevorkov@desy.de>
  *
@@ -46,6 +46,7 @@ struct index_args;
 #include "peaks.h"
 #include "image.h"
 #include "im-asapo.h"
+#include "predict-refine.h"
 
 
 /* Information about the indexing process which is common to all patterns */
@@ -73,6 +74,7 @@ struct index_args
 	float wavelength_estimate;
 	float clen_estimate;
 	int n_threads;
+	int mille;
 
 	/* Integration */
 	IntegrationMethod int_meth;
@@ -115,7 +117,8 @@ extern void process_image(const struct index_args *iargs,
                           struct pattern_args *pargs, Stream *st,
                           int cookie, const char *tmpdir, int serial,
                           struct sb_shm *sb_shared, char *last_task,
-                          struct im_asapo *asapostuff);
+                          struct im_asapo *asapostuff,
+                          Mille *mille);
 
 
 #endif	/* PROCESS_IMAGE_H */