Merge branch 'master' into simple-search

1 files changed, 56 insertions, 53 deletions

diff --git a/src/reflections.c b/src/reflections.c
index a589231..ce5f7a9 100644
--- a/src/reflections.c
+++ b/src/reflections.c
@@ -32,9 +32,9 @@ static void reflectionlist_init(ReflectionList *reflectionlist) {
 ReflectionList *reflectionlist_new() {
 
 	ReflectionList *reflectionlist = malloc(sizeof(ReflectionList));
-	
+
 	reflectionlist_init(reflectionlist);
-	
+
 	return reflectionlist;
 
 }
@@ -44,10 +44,10 @@ void reflectionlist_clear_markers(ReflectionList *reflectionlist) {
 	Reflection *reflection = reflectionlist->reflections;
 	Reflection *prev = NULL;
 	int del = 0;
-	
+
 	 while ( reflection ) {
 		Reflection *next = reflection->next;
-		
+
 		if ( (reflection->type == REFLECTION_MARKER) || (reflection->type == REFLECTION_GENERATED)
 		 || (reflection->type == REFLECTION_VECTOR_MARKER_1) || (reflection->type == REFLECTION_VECTOR_MARKER_2)
 		 || (reflection->type == REFLECTION_VECTOR_MARKER_3) ) {
@@ -61,14 +61,14 @@ void reflectionlist_clear_markers(ReflectionList *reflectionlist) {
 		} else {
 			prev = reflection;
 		}
-		
+
 		reflection = next;
-	
+
 	};
-	
+
 	reflectionlist->n_reflections -= del;
 	reflectionlist->last_reflection = prev;
-	
+
 }
 void reflectionlist_clear(ReflectionList *reflectionlist) {
 
@@ -78,7 +78,7 @@ void reflectionlist_clear(ReflectionList *reflectionlist) {
 		free(reflection);
 		reflection = next;
 	};
-	
+
 	reflectionlist_init(reflectionlist);
 
 }
@@ -92,27 +92,32 @@ Reflection *reflection_add(ReflectionList *reflectionlist, double x, double y, d
 
 	Reflection *new_reflection;
 	Reflection *nearest;
-	
+
 	if ( reflectionlist->list_capped ) return NULL;
-	
+
 	if ( reflectionlist->n_reflections > 1e7 ) {
 		fprintf(stderr, "More than 10 million reflections on list.  I think this is silly.\n");
 		fprintf(stderr, "No further reflections will be stored.  Go and fix the peak detection.\n");
 		reflectionlist->list_capped = 1;
 	}
-	
-	nearest = reflectionlist_find_nearest_type(reflectionlist, x, y, z, type);
-	if ( nearest && distance3d(x, y, z, nearest->x, nearest->y, nearest->z) < 0.1e9 ) return NULL;
-	
+
+//	nearest = reflectionlist_find_nearest_type(reflectionlist, x, y, z, type);
+//	if ( nearest && distance3d(x, y, z, nearest->x, nearest->y, nearest->z) < 0.1e9 ) {
+//	printf("Too close\n");
+//	return NULL;
+//}
 	new_reflection = malloc(sizeof(Reflection));
 	new_reflection->next = NULL;
 	new_reflection->x = x;
 	new_reflection->y = y;
 	new_reflection->z = z;
+	new_reflection->h = 999;
+	new_reflection->k = 333;
+	new_reflection->l = 111;
 	new_reflection->intensity = intensity;
 	new_reflection->type = type;
 	new_reflection->found = 0;
-	
+
 	if ( reflectionlist->last_reflection ) {
 		reflectionlist->last_reflection->next = new_reflection;
 		reflectionlist->last_reflection = new_reflection;
@@ -121,16 +126,16 @@ Reflection *reflection_add(ReflectionList *reflectionlist, double x, double y, d
 		reflectionlist->last_reflection = new_reflection;
 	}
 	reflectionlist->n_reflections++;
-	
+
 	return new_reflection;
-	
+
 }
 
 double reflectionlist_largest_g(ReflectionList *reflectionlist) {
 
 	double max = 0.0;
 	Reflection *reflection;
-	
+
 	reflection = reflectionlist->reflections;
 	while ( reflection ) {
 		if ( reflection->type == REFLECTION_NORMAL ) {
@@ -140,7 +145,7 @@ double reflectionlist_largest_g(ReflectionList *reflectionlist) {
 		}
 		reflection = reflection->next;
 	};
-	
+
 	return max;
 
 }
@@ -150,7 +155,7 @@ Reflection *reflectionlist_find_nearest(ReflectionList *reflectionlist, double x
 	double max = +INFINITY;
 	Reflection *reflection;
 	Reflection *best = NULL;
-	
+
 	reflection = reflectionlist->reflections;
 	while ( reflection ) {
 		if ( reflection->type == REFLECTION_NORMAL ) {
@@ -163,7 +168,7 @@ Reflection *reflectionlist_find_nearest(ReflectionList *reflectionlist, double x
 		}
 		reflection = reflection->next;
 	};
-	
+
 	return best;
 
 }
@@ -174,7 +179,7 @@ Reflection *reflectionlist_find_nearest_longer_unknown(ReflectionList *reflectio
 	double max = +INFINITY;
 	Reflection *reflection;
 	Reflection *best = NULL;
-	
+
 	reflection = reflectionlist->reflections;
 	while ( reflection ) {
 		if ( (reflection->type == REFLECTION_NORMAL) && (!reflection->found) ) {
@@ -187,7 +192,7 @@ Reflection *reflectionlist_find_nearest_longer_unknown(ReflectionList *reflectio
 		}
 		reflection = reflection->next;
 	};
-	
+
 	return best;
 
 }
@@ -198,7 +203,7 @@ Reflection *reflectionlist_find_nearest_type(ReflectionList *reflectionlist, dou
 	double max = +INFINITY;
 	Reflection *reflection;
 	Reflection *best = NULL;
-	
+
 	reflection = reflectionlist->reflections;
 	while ( reflection ) {
 		if ( reflection->type == type ) {
@@ -211,7 +216,7 @@ Reflection *reflectionlist_find_nearest_type(ReflectionList *reflectionlist, dou
 		}
 		reflection = reflection->next;
 	};
-	
+
 	return best;
 
 }
@@ -223,9 +228,9 @@ ReflectionList *reflection_list_from_cell(Basis *basis) {
 	double max_res;
 	signed int h, k, l;
 	int max_order_a, max_order_b, max_order_c;
-	
+
 	ordered = reflectionlist_new();
-	
+
 	max_res = 21e9;
 	do {
 		max_order_a = max_res/modulus(basis->a.x, basis->a.y, basis->a.z);
@@ -234,36 +239,35 @@ ReflectionList *reflection_list_from_cell(Basis *basis) {
 		max_res -= 1e9;
 	} while ( (max_order_a * max_order_b * max_order_c * 8) > 1e4 );
 	printf("Selected maximum resolution %8.5f nm^-1\n", max_res/1e9);
-	
+
 	for ( h=-max_order_a; h<=max_order_a; h++ ) {
 		for ( k=-max_order_b; k<=max_order_b; k++ ) {
 			for ( l=-max_order_c; l<=max_order_c; l++ ) {
 
 				double x, y, z;
-				
-				/* Test mode */
-				//if ( h != 0 ) continue;
-				
+
 				x = h*basis->a.x + k*basis->b.x + l*basis->c.x;
 				y = h*basis->a.y + k*basis->b.y + l*basis->c.y;
 				z = h*basis->a.z + k*basis->b.z + l*basis->c.z;
-				
+
 				if ( ( x*x + y*y + z*z ) <= max_res*max_res ) {
-					Reflection *ref;
-					ref = reflection_add(ordered, x, y, z, 1.0, REFLECTION_GENERATED);
-					if ( ref ) {	/* Check it's not NULL */
-						ref->h = h;	ref->k = k;	ref->l = l;
-					}
 					if ( (h!=0) || (k!=0) || (l!=0) ) {
-					//	reflection_add(ctx->reflectionlist, x, y, z, 1.0, REFLECTION_GENERATED);
-						reflection_add(ordered, x, y, z, 1.0, REFLECTION_GENERATED);
+						Reflection *ref;
+						ref = reflection_add(ordered,
+							x, y, z, 1.0,
+							REFLECTION_GENERATED);
+						if ( ref ) {
+							ref->h = h;
+							ref->k = k;
+							ref->l = l;
+						}
 					}
 				}
-				
+
 			}
 		}
 	}
-	
+
 	return ordered;
 
 }
@@ -271,19 +275,19 @@ ReflectionList *reflection_list_from_cell(Basis *basis) {
 void reflection_list_from_new_cell(ReflectionList *ordered, Basis *basis) {
 
 	Reflection *ref;
-	
+
 	ref = ordered->reflections;
-	
+
 	while ( ref ) {
-	
+
 		signed int h, k, l;
-		
+
 		h = ref->h;	k = ref->k;	l = ref->l;
-				
+
 		ref->x = h*basis->a.x + k*basis->b.x + l*basis->c.x;
 		ref->y = h*basis->a.y + k*basis->b.y + l*basis->c.y;
 		ref->z = h*basis->a.z + k*basis->b.z + l*basis->c.z;
-		
+
 		ref = ref->next;
 
 	}
@@ -296,7 +300,7 @@ int reflection_is_easy(Reflection *reflection) {
 	if ( reflection->h ) return !(reflection->k || reflection->l);
 	if ( reflection->k ) return !(reflection->h || reflection->l);
 	if ( reflection->l ) return !(reflection->h || reflection->k);
-	
+
 	return 0;	/* 000 */
 
 }
@@ -304,7 +308,7 @@ int reflection_is_easy(Reflection *reflection) {
 Reflection *reflectionlist_find(ReflectionList *reflectionlist, signed int h, signed int k, signed int l) {
 
 	Reflection *reflection;
-	
+
 	reflection = reflectionlist->reflections;
 	while ( reflection ) {
 		if ( (reflection->h==h) && (reflection->k==k) && (reflection->l==l) ) {
@@ -312,8 +316,7 @@ Reflection *reflectionlist_find(ReflectionList *reflectionlist, signed int h, si
 		}
 		reflection = reflection->next;
 	};
-	
+
 	return NULL;
 
 }
-