Commit cfbbdae0 authored by Thomas White's avatar Thomas White
Browse files

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

parent d7ff5c5a
......@@ -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
......
......@@ -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;
......
......@@ -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},
......
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