From 0cc8a3db1a6e57f64275deab0da2b31a15fdbb69 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Fri, 12 Mar 2021 11:26:01 +0100
Subject: Clean up after merge

---
 libcrystfel/src/index.c | 14 ++++++++------
 libcrystfel/src/index.h |  2 +-
 src/indexamajig.c       |  9 ++++-----
 src/process_image.c     |  1 -
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index c2f79eff..341abf58 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -63,9 +63,9 @@
 
 #include "uthash.h"
 
-
 /** \file index.h */
 
+
 struct _indexingprivate
 {
 	IndexingFlags flags;
@@ -79,6 +79,7 @@ struct _indexingprivate
 	void **engine_private;
 };
 
+
 static const char *onoff(int a)
 {
 	if ( a ) return "on";
@@ -99,6 +100,7 @@ static void set_last_task(char *lt, const char *task)
 	strcpy(lt, task);
 }
 
+
 static void show_indexing_flags(IndexingFlags flags)
 {
 	STATUS("Indexing parameters:\n");
@@ -404,7 +406,7 @@ IndexingPrivate *setup_indexing(const char *method_list,
 		                                          pinkIndexer_opts,
 		                                          felix_opts,
 		                                          ttopts,
-                                                  filename);
+		                                          filename);
 
 		if ( ipriv->engine_private[i] == NULL ) return NULL;
 
@@ -639,8 +641,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 
 		case INDEXING_FILE :
 		set_last_task(last_task, "indexing:file");
-		int crystal_number = 0;
-		r = fromfile_index(image, mpriv, crystal_number);
+		r = fromfile_index(image, mpriv, 0);
 		break;
 
 		case INDEXING_FELIX :
@@ -942,7 +943,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 		int ntry = 0;
 		int success = 0;
 
-		if ( ipriv->methods[0] != INDEXING_FILE){
+		if ( ipriv->methods[0] != INDEXING_FILE ) {
 			image->features = sort_peaks(orig);
 		}
 
@@ -960,7 +961,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 		} while ( !done );
 
-		if ( ipriv->methods[0] != INDEXING_FILE){
+		if ( ipriv->methods[0] != INDEXING_FILE ) {
 			image_feature_list_free(image->features);
 		}
 
@@ -979,6 +980,7 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 		image->indexed_by = INDEXING_NONE;
 	}
 
+	image->features = orig;
 }
 
 
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 92406604..5cee29b2 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -73,7 +73,7 @@ typedef enum {
 	INDEXING_FELIX = 4,       /**< Invoke Felix program */
 	INDEXING_XDS = 5,         /**< Invoke XDS program (NB not nXDS) */
 	INDEXING_SIMULATION = 6,  /**< Dummy value for simulated data */
-	INDEXING_FILE = 7,       /**< Results injector for debugging */
+	INDEXING_FILE = 7,        /**< Results injector for debugging */
 	INDEXING_ASDF = 8,        /**< Use built-in ASDF algorithm */
 	INDEXING_TAKETWO = 9,     /**< Use built-in TakeTwo algorithm */
 	INDEXING_XGANDALF = 10,   /**< Use XGANDALF (via optional library) */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 4b12194c..7f73cef6 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -849,7 +849,6 @@ int main(int argc, char *argv[])
 		ERROR("Failed to open input file '%s'\n", args.filename);
 		return 1;
 	}
-	
 
 	/* Check prefix (if given) */
 	if ( args.check_prefix ) {
@@ -997,10 +996,10 @@ int main(int argc, char *argv[])
 		                                  xgandalf_opts,
 		                                  pinkindexer_opts,
 		                                  felix_opts,
-                                          args.filename);
-        
-        free(args.filename);
-        
+		                                  args.filename);
+
+		free(args.filename);
+
 		if ( args.iargs.ipriv == NULL ) {
 			ERROR("Failed to set up indexing system\n");
 			return 1;
diff --git a/src/process_image.c b/src/process_image.c
index d3355f38..825e57d9 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -381,7 +381,6 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		}
 	}
 
-
 	if ( iargs->fix_profile_r < 0.0 ) {
 		for ( i=0; i<image->n_crystals; i++ ) {
 			if ( refine_radius(image->crystals[i], image) ) {
-- 
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