From 6b18fa18fbdc1f272e65f81d04b22d973acafa1e Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Tue, 30 Apr 2013 18:01:07 +0200
Subject: partialator: Add --min-measurements

---
 src/hrs-scaling.c |  4 ++--
 src/hrs-scaling.h |  3 ++-
 src/partialator.c | 19 +++++++++++++++++--
 3 files changed, 21 insertions(+), 5 deletions(-)

(limited to 'src')

diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
index 46590f7e..c249ef46 100644
--- a/src/hrs-scaling.c
+++ b/src/hrs-scaling.c
@@ -493,12 +493,12 @@ static void calculate_esds(Crystal **crystals, int n, RefList *full,
 
 /* Scale the stack of images */
 RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
-                           int n_threads, int noscale, PartialityModel pmodel)
+                           int n_threads, int noscale, PartialityModel pmodel,
+                           int min_redundancy)
 {
 	int i;
 	double max_corr;
 	RefList *full = NULL;
-	const int min_redundancy = 2;
 
 	for ( i=0; i<n; i++ ) crystal_set_osf(crystals[i], 1.0);
 
diff --git a/src/hrs-scaling.h b/src/hrs-scaling.h
index 8ae12380..0979bb98 100644
--- a/src/hrs-scaling.h
+++ b/src/hrs-scaling.h
@@ -41,7 +41,8 @@
 
 extern RefList *scale_intensities(Crystal **crystals, int n,
                                   RefList *reference, int n_threads,
-                                  int noscale, PartialityModel pmodel);
+                                  int noscale, PartialityModel pmodel,
+                                  int min_redundancy);
 
 
 #endif	/* HRS_SCALING_H */
diff --git a/src/partialator.c b/src/partialator.c
index 58025b96..cfa3a6ba 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -80,6 +80,8 @@ static void show_help(const char *s)
 "                              instead of taking the mean of the intensity\n"
 "                              estimates.\n"
 "  -m, --model=<model>        Specify partiality model.\n"
+"      --min-measurements=<n> Require at least <n> measurements before a\n"
+"                             reflection appears in the output.  Default: 2\n"
 "\n"
 "  -j <n>                     Run <n> analyses in parallel.\n");
 }
@@ -323,6 +325,8 @@ int main(int argc, char *argv[])
 	Crystal **crystals;
 	char *pmodel_str = NULL;
 	PartialityModel pmodel = PMODEL_SPHERE;
+	int min_measurements = 2;
+	char *rval;
 
 	/* Long options */
 	const struct option longopts[] = {
@@ -336,6 +340,7 @@ int main(int argc, char *argv[])
 		{"no-scale",           0, &noscale,            1},
 		{"reference",          1, NULL,               'r'},
 		{"model",              1, NULL,               'm'},
+		{"min-measurements",   1, NULL,                2},
 
 		{0, 0, NULL, 0}
 	};
@@ -398,6 +403,15 @@ int main(int argc, char *argv[])
 			reference_file = strdup(optarg);
 			break;
 
+			case 2 :
+			errno = 0;
+			min_measurements = strtod(optarg, &rval);
+			if ( *rval != '\0' ) {
+				ERROR("Invalid value for --min-measurements.\n");
+				return 1;
+			}
+			break;
+
 			case 0 :
 			break;
 
@@ -583,7 +597,7 @@ int main(int argc, char *argv[])
 	STATUS("Performing initial scaling.\n");
 	if ( noscale ) STATUS("Scale factors fixed at 1.\n");
 	full = scale_intensities(crystals, n_crystals, reference,
-	                         nthreads, noscale, pmodel);
+	                         nthreads, noscale, pmodel, min_measurements);
 
 	sr = sr_titlepage(crystals, n_crystals, "scaling-report.pdf",
 	                  infile, cmdline);
@@ -621,7 +635,8 @@ int main(int argc, char *argv[])
 		/* Re-estimate all the full intensities */
 		reflist_free(full);
 		full = scale_intensities(crystals, n_crystals,
-		                         reference, nthreads, noscale, pmodel);
+		                         reference, nthreads, noscale, pmodel,
+		                         min_measurements);
 
 		sr_iteration(sr, i+1, crystals, n_crystals, full);
 
-- 
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