partialator: Add B-factor scaling and rejection

1 files changed, 83 insertions, 0 deletions

diff --git a/src/rejection.c b/src/rejection.c
new file mode 100644
index 00000000..d413666f
--- /dev/null
+++ b/src/rejection.c
@@ -0,0 +1,83 @@
+/*
+ * rejection.c
+ *
+ * Crystal rejection for scaling
+ *
+ * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ *   2010-2015 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdlib.h>
+#include <assert.h>
+
+#include "crystal.h"
+#include "reflist.h"
+
+
+static double mean_intensity(RefList *list)
+{
+	Reflection *refl;
+	RefListIterator *iter;
+	double total = 0.0;
+	int n = 0;
+
+	for ( refl = first_refl(list, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) )
+	{
+		total += get_intensity(refl);
+		n++;
+	}
+
+	return total/n;
+}
+
+
+/* Reject really obvious outliers */
+void early_rejection(Crystal **crystals, int n)
+{
+	int i;
+	double m = 0.0;
+	FILE *fh = fopen("reject.dat", "w");
+	int n_flag = 0;
+
+	for ( i=0; i<n; i++ ) {
+		double u;
+		RefList *list = crystal_get_reflections(crystals[i]);
+		u = mean_intensity(list);
+		m += u;
+		fprintf(fh, "%i %f\n", i, u);
+		if ( u < 100.0 ) {
+			crystal_set_user_flag(crystals[i], 5);
+			n_flag++;
+		}
+	}
+	fclose(fh);
+
+	STATUS("Mean intensity/peak = %f ADU\n", m/n);
+	STATUS("%i crystals flagged\n", n_flag);
+}