Solved problem concerning prof_radius and diff_lim calculation, prof_radius and diff_lim removed from sol file

4 files changed, 28 insertions, 29 deletions

diff --git a/libcrystfel/src/fromfile.c b/libcrystfel/src/fromfile.c
index 05262458..13044ebe 100644
--- a/libcrystfel/src/fromfile.c
+++ b/libcrystfel/src/fromfile.c
@@ -42,7 +42,7 @@
 /* There are 9 vector components, 
  * 2 detector shifts, 1 profile radius,
  *  1 resolution limit */
-#define NPARAMS_PER_LINE 13  
+#define NPARAMS_PER_LINE 11 
 /* The keys read from file 
  * are the filename, event */
 #define NKEYS_PER_LINE 2
@@ -326,7 +326,7 @@ int fromfile_index(struct image *image, void *mpriv, int crystal_number)
 	Crystal *cr;
 	UnitCell *cell;
 	float asx, asy, asz, bsx, bsy, bsz, csx, csy, csz;
-	float xshift, yshift, profile_radius, resolution_limit;
+	float xshift, yshift; 
 	struct fromfile_entries *item, *p, *pprime;
 	int ncryst = 0;
 	float *sol;
@@ -359,8 +359,6 @@ int fromfile_index(struct image *image, void *mpriv, int crystal_number)
 	csz = sol[8] * 1e9;
 	xshift = sol[9] * 1e-3;
 	yshift = sol[10] * 1e-3;
-	profile_radius = sol[11] * 1e9;
-	resolution_limit = sol[12] * 1e9;
 
 	cell = cell_new();
 	cell_set_reciprocal(cell, asx, asy, asz, bsx, bsy, bsz, csx, csy, csz);
@@ -371,8 +369,6 @@ int fromfile_index(struct image *image, void *mpriv, int crystal_number)
 	cr = crystal_new();
 	ncryst += 1;
 	crystal_set_cell(cr, cell);
-	crystal_set_profile_radius(cr, profile_radius);
-	crystal_set_resolution_limit(cr, resolution_limit);
 	crystal_set_det_shift(cr, xshift , yshift);
 	update_detector(image->det, xshift , yshift);
 	image_add_crystal(image, cr);
@@ -382,6 +378,8 @@ int fromfile_index(struct image *image, void *mpriv, int crystal_number)
 	HASH_FIND(hh,  dp->sol_hash, &item->key, 
 	          sizeof(struct fromfile_keys), pprime);
 
+	/* If a similar tag exist,
+	 * recursive call increasing the crystal_number by 1 */
     if ( pprime != NULL ) {
 		ncryst += fromfile_index(image, mpriv, crystal_number+1);
 	}
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index e0e8ff05..7b03ba3e 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -664,9 +664,7 @@ static int try_indexer(struct image *image, IndexingMethod indm,
 		Crystal *cr = image->crystals[this_crystal];
 
 		crystal_set_image(cr, image);
-		if ( indm != INDEXING_FILE){
-			crystal_set_profile_radius(cr, 0.02e9);
-		}
+		crystal_set_profile_radius(cr, 0.02e9);
 		crystal_set_mosaicity(cr, 0.0);
 
 		/* Pre-refinement unit cell check if requested */
@@ -877,12 +875,14 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 	if ( ipriv == NULL ) return;
 
-	map_all_peaks(image);
+	if ( ipriv->methods[0] != INDEXING_FILE){
+		map_all_peaks(image);
+		orig = image->features;
+	}
+	
 	image->crystals = NULL;
 	image->n_crystals = 0;
 
-	orig = image->features;
-
 	for ( n=0; n<ipriv->n_methods; n++ ) {
 
 		int done = 0;
@@ -890,7 +890,9 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 		int ntry = 0;
 		int success = 0;
 
-		image->features = sort_peaks(orig);
+		if ( ipriv->methods[0] != INDEXING_FILE){
+			image->features = sort_peaks(orig);
+		}
 
 		do {
 
@@ -906,7 +908,9 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 		} while ( !done );
 
-		image_feature_list_free(image->features);
+		if ( ipriv->methods[0] != INDEXING_FILE){
+			image_feature_list_free(image->features);
+		}
 
 		/* Stop now if the pattern is indexed (don't try again for more
 		 * crystals with a different indexing method) */
@@ -917,13 +921,19 @@ void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping,
 
 	}
 
+	if ( ipriv->methods[0] == INDEXING_FILE){
+		map_all_peaks(image);
+	}
+	else{
+		image->features = orig;
+	}
+
 	if ( n < ipriv->n_methods ) {
 		image->indexed_by = ipriv->methods[n];
 	} else {
 		image->indexed_by = INDEXING_NONE;
 	}
 
-	image->features = orig;
 }
 
 
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 8a3c581e..3d8258c1 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1687,14 +1687,9 @@ void integrate_all_5(struct image *image, IntegrationMethod meth,
 			                           saved_R * 5);
 		}
 
-		if ( image->indexed_by != INDEXING_FILE ){
-			res = estimate_resolution(crystal_get_cell(image->crystals[i]),
+		res = estimate_resolution(crystal_get_cell(image->crystals[i]),
 		                          image->features);
-			crystal_set_resolution_limit(image->crystals[i], res);
-		}
-		else{
-			res = crystal_get_resolution_limit(image->crystals[i]);
-		}
+		crystal_set_resolution_limit(image->crystals[i], res);
 
 		list = predict_to_res(image->crystals[i], res+push_res);
 		crystal_set_reflections(image->crystals[i], list);
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");
 			}
 		}
 	}