From f1a24d0e4c32735fa016cbb262b61a1cce5960fc Mon Sep 17 00:00:00 2001
From: Pascal Hogan-Lamarre <pascal.hogan@gmail.com>
Date: Thu, 9 Jul 2020 14:38:19 +0200
Subject: unit cell vectors are correct, space group missing

---
 src/indexamajig.c | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

(limited to 'src')

diff --git a/src/indexamajig.c b/src/indexamajig.c
index a03955ba..bfeb2960 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -848,7 +848,7 @@ int main(int argc, char *argv[])
 		ERROR("Failed to open input file '%s'\n", args.filename);
 		return 1;
 	}
-	free(args.filename);
+	
 
 	/* Check prefix (if given) */
 	if ( args.check_prefix ) {
@@ -1007,7 +1007,11 @@ int main(int argc, char *argv[])
 		                                  taketwo_opts,
 		                                  xgandalf_opts,
 		                                  pinkindexer_opts,
-		                                  felix_opts);
+		                                  felix_opts,
+                                          args.filename);
+        
+        free(args.filename);
+        
 		if ( args.iargs.ipriv == NULL ) {
 			ERROR("Failed to set up indexing system\n");
 			return 1;
-- 
cgit v1.2.3


From c97685fbeca127373ffb0a6cc1f2222e12a91f1e Mon Sep 17 00:00:00 2001
From: Pascal Hogan-Lamarre <pascal.hogan@gmail.com>
Date: Wed, 16 Sep 2020 22:35:42 -0400
Subject: if-conditions that prevent modification of the profile_radius read
 from file

---
 src/process_image.c | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

(limited to 'src')

diff --git a/src/process_image.c b/src/process_image.c
index 1e6bb814..003886c4 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -430,15 +430,20 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		}
 	} else {
 		for ( i=0; i<image.n_crystals; i++ ) {
-			crystal_set_profile_radius(image.crystals[i], 0.02e9);
+			if ( image.indexed_by != INDEXING_FILE){
+				crystal_set_profile_radius(image.crystals[i], 0.02e9);
+			}
 			crystal_set_mosaicity(image.crystals[i], 0.0);
 		}
 	}
 
+
 	if ( iargs->fix_profile_r < 0.0 ) {
 		for ( i=0; i<image.n_crystals; i++ ) {
-			if ( refine_radius(image.crystals[i], &image) ) {
-				ERROR("WARNING: Radius determination failed\n");
+			if ( image.indexed_by != INDEXING_FILE){
+				if ( refine_radius(image.crystals[i], &image) ) {
+					ERROR("WARNING: Radius determination failed\n");
+				}
 			}
 		}
 	}
-- 
cgit v1.2.3


From f937b91c7c9016665efd0c38af1e0a5d21d41c99 Mon Sep 17 00:00:00 2001
From: Pascal Hogan-Lamarre <pascal.hogan@gmail.com>
Date: Sun, 4 Oct 2020 20:57:30 -0400
Subject: Solved problem concerning prof_radius and diff_lim calculation,
 prof_radius and diff_lim removed from sol file

---
 src/process_image.c | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

(limited to 'src')

diff --git a/src/process_image.c b/src/process_image.c
index 003886c4..b785705a 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -430,9 +430,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 		}
 	} else {
 		for ( i=0; i<image.n_crystals; i++ ) {
-			if ( image.indexed_by != INDEXING_FILE){
-				crystal_set_profile_radius(image.crystals[i], 0.02e9);
-			}
+			crystal_set_profile_radius(image.crystals[i], 0.02e9);
 			crystal_set_mosaicity(image.crystals[i], 0.0);
 		}
 	}
@@ -440,10 +438,8 @@ 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 ( image.indexed_by != INDEXING_FILE){
-				if ( refine_radius(image.crystals[i], &image) ) {
-					ERROR("WARNING: Radius determination failed\n");
-				}
+			if ( refine_radius(image.crystals[i], &image) ) {
+				ERROR("WARNING: Radius determination failed\n");
 			}
 		}
 	}
-- 
cgit v1.2.3