From 19f977c6d62ffca9f13bcdefef32b5b27a326b7a Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 26 Jun 2014 11:22:24 +0200
Subject: Rationalise counting of filtered eigenvalues

---
 src/partialator.c     | 11 ++++++++++-
 src/post-refinement.c | 14 ++++++++++----
 src/post-refinement.h |  1 +
 src/scaling-report.c  |  3 ---
 src/scaling-report.h  |  7 ++++---
 5 files changed, 25 insertions(+), 11 deletions(-)

(limited to 'src')

diff --git a/src/partialator.c b/src/partialator.c
index 8823990f..2ef01dba 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -129,7 +129,10 @@ static void done_image(void *vqargs, void *task)
 	struct refine_args *pargs = task;
 
 	qargs->n_done++;
-	qargs->srdata->n_filtered += pargs->prdata.n_filtered;
+	if ( pargs->prdata.refined ) {
+		qargs->srdata->n_refined += pargs->prdata.refined;
+		qargs->srdata->n_filtered += pargs->prdata.n_filtered;
+	}
 
 	progress_bar(qargs->n_done, qargs->n_crystals, "Refining");
 	free(task);
@@ -150,6 +153,7 @@ static void refine_all(Crystal **crystals, int n_crystals,
 	task_defaults.full = full;
 	task_defaults.crystal = NULL;
 	task_defaults.pmodel = pmodel;
+	task_defaults.prdata.refined = 0;
 	task_defaults.prdata.n_filtered = 0;
 
 	qargs.task_defaults = task_defaults;
@@ -164,6 +168,10 @@ static void refine_all(Crystal **crystals, int n_crystals,
 
 	run_threads(nthreads, refine_image, get_image, done_image,
 	            &qargs, n_crystals, 0, 0, 0);
+
+	STATUS("%5.2f eigenvalues filtered on final iteration per successfully "
+	       "refined crystal\n",
+	       (double)srdata->n_filtered/srdata->n_refined);
 }
 
 
@@ -462,6 +470,7 @@ int main(int argc, char *argv[])
 	srdata.n = n_crystals;
 	srdata.full = full;
 	srdata.n_filtered = 0;
+	srdata.n_refined = 0;
 
 	sr = sr_titlepage(crystals, n_crystals, "scaling-report.pdf",
 	                  infile, cmdline);
diff --git a/src/post-refinement.c b/src/post-refinement.c
index 535f7cff..5de8a246 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -469,7 +469,7 @@ static gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M, int *n_filt,
 
 /* Perform one cycle of post refinement on 'image' against 'full' */
 static double pr_iterate(Crystal *cr, const RefList *full,
-                         PartialityModel pmodel, struct prdata *prdata)
+                         PartialityModel pmodel, int *n_filtered)
 {
 	gsl_matrix *M;
 	gsl_vector *v;
@@ -482,6 +482,8 @@ static double pr_iterate(Crystal *cr, const RefList *full,
 	int nref = 0;
 	const int verbose = 0;
 
+	*n_filtered = 0;
+
 	reflections = crystal_get_reflections(cr);
 
 	M = gsl_matrix_calloc(NUM_PARAMS, NUM_PARAMS);
@@ -574,7 +576,7 @@ static double pr_iterate(Crystal *cr, const RefList *full,
 	}
 
 	max_shift = 0.0;
-	shifts = solve_svd(v, M, &prdata->n_filtered, verbose);
+	shifts = solve_svd(v, M, n_filtered, verbose);
 	if ( shifts != NULL ) {
 
 		for ( param=0; param<NUM_PARAMS; param++ ) {
@@ -698,6 +700,7 @@ struct prdata pr_refine(Crystal *cr, const RefList *full,
 	struct prdata prdata;
 	double mean_p_change = 0.0;
 
+	prdata.refined = 0;
 	prdata.n_filtered = 0;
 
 	/* Don't refine crystal if scaling was bad */
@@ -727,8 +730,7 @@ struct prdata pr_refine(Crystal *cr, const RefList *full,
 		cell_get_reciprocal(crystal_get_cell(cr), &asx, &asy, &asz,
 			               &bsx, &bsy, &bsz, &csx, &csy, &csz);
 
-		prdata.n_filtered = 0;
-		pr_iterate(cr, full, pmodel, &prdata);
+		pr_iterate(cr, full, pmodel, &prdata.n_filtered);
 
 		update_partialities_2(cr, pmodel, &n_gained, &n_lost,
 		                      &mean_p_change);
@@ -755,5 +757,9 @@ struct prdata pr_refine(Crystal *cr, const RefList *full,
 
 	free_backup_crystal(backup);
 
+	if ( crystal_get_user_flag(cr) == 0 ) {
+		prdata.refined = 1;
+	}
+
 	return prdata;
 }
diff --git a/src/post-refinement.h b/src/post-refinement.h
index abf2364b..e419c51d 100644
--- a/src/post-refinement.h
+++ b/src/post-refinement.h
@@ -63,6 +63,7 @@ enum {
 
 struct prdata
 {
+	int refined;
 	int n_filtered;
 };
 
diff --git a/src/scaling-report.c b/src/scaling-report.c
index 351d2dbd..ca4c5cbc 100644
--- a/src/scaling-report.c
+++ b/src/scaling-report.c
@@ -888,9 +888,6 @@ void sr_iteration(SRContext *sr, int iteration, struct srdata *d)
 		cairo_restore(sr->cr);
 
 	}
-
-	STATUS("%i filtered total, %5.2f filtered per crystal\n",
-	       d->n_filtered, (double)d->n_filtered / d->n);
 }
 
 
diff --git a/src/scaling-report.h b/src/scaling-report.h
index 5f6e2cb4..55037038 100644
--- a/src/scaling-report.h
+++ b/src/scaling-report.h
@@ -3,11 +3,11 @@
  *
  * Write a nice PDF of scaling parameters
  *
- * Copyright © 2012 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2011-2012 Thomas White <taw@physics.org>
+ *   2011-2014 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -46,6 +46,7 @@ struct srdata
 	RefList *full;
 
 	int n_filtered;
+	int n_refined;
 };
 
 #if defined(HAVE_CAIRO) && defined(HAVE_PANGO) && defined(HAVE_PANGOCAIRO)
-- 
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