indexamajig: Make --no-closer-peak the default

doc/man/indexamajig.1

@@ -295,10 +295,19 @@ Run \fIn\fR analyses in parallel.  Default: 1.
 .PD
 Don't attempt to correct the prefix (see \fB--prefix\fR) if it doesn't look correct.
 
+.PD 0
+.IP \fB--closer-peak\fR
+.PD
+If you use this option, indexamajig will integrate around the location of a detected peak instead of the predicted peak location if one is found close to the predicted position, within ten pixels.  \fBDon't use this option\fR, because
+there is currently no way to set the definition of 'nearby' to be appropriate
+for your data.
+
 .PD 0
 .IP \fB--no-closer-peak\fR
 .PD
-Normally, indexamajig will integrate around the location of a detected peak instead of the predicted peak location if one is found close to the predicted position.  This option disables this behaviour.  Normally it doesn't make much difference either way.
+This is the opposite of \fB--closer-peak\fR, and is provided for compatibility
+with old scripts because this option selects the behaviour which is now the
+default.
 
 .PD 0
 .IP \fB--insane\fR

libcrystfel/src/peaks.c

@@ -52,10 +52,6 @@
 #include "beam-parameters.h"
 
 
-/* How close a peak must be to an indexed position to be considered "close"
- * for the purposes of integration. */
-#define PEAK_REALLY_CLOSE (10.0)
-
 /* Degree of polarisation of X-ray beam */
 #define POL (1.0)
 
@@ -640,7 +636,9 @@ void integrate_reflections(struct image *image, int use_closer, int bgsub,
 			} else {
 				f = NULL;
 			}
-			if ( (f != NULL) && (d < PEAK_REALLY_CLOSE) ) {
+
+			/* FIXME: Horrible hardcoded value */
+			if ( (f != NULL) && (d < 10.0) ) {
 
 				pfs = f->fs;
 				pss = f->ss;

src/indexamajig.c

@@ -228,9 +228,8 @@ static void show_help(const char *s)
 "\n"
 "\nOptions you probably won't need:\n\n"
 "     --no-check-prefix    Don't attempt to correct the --prefix.\n"
-"     --no-closer-peak     Don't integrate from the location of a nearby peak\n"
-"                           instead of the position closest to the reciprocal\n"
-"                           lattice point.\n"
+"     --closer-peak        Don't integrate from the location of a nearby peak\n"
+"                           instead of the predicted spot.  Don't use.\n"
 "     --insane             Don't check that the reduced cell accounts for at\n"
 "                           least 10%% of the located peaks.\n"
 "     --no-bg-sub          Don't subtract local background estimates from\n"
@@ -561,7 +560,7 @@ int main(int argc, char *argv[])
 	int config_verbose = 0;
 	int config_satcorr = 1;
 	int config_checkprefix = 1;
-	int config_closer = 1;
+	int config_closer = 0;
 	int config_insane = 0;
 	int config_bgsub = 1;
 	int config_basename = 0;
@@ -630,6 +629,7 @@ int main(int argc, char *argv[])
 		{"threshold",          1, NULL,               't'},
 		{"no-check-prefix",    0, &config_checkprefix, 0},
 		{"no-closer-peak",     0, &config_closer,      0},
+		{"closer-peak",        0, &config_closer,      1},
 		{"insane",             0, &config_insane,      1},
 		{"image",              1, NULL,               'e'},
 		{"basename",           0, &config_basename,    1},