diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 11 | ||||
| -rw-r--r-- | libcrystfel/src/peaks.c | 8 | ||||
| -rw-r--r-- | src/indexamajig.c | 8 |
3 files changed, 17 insertions, 10 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index ac443906..6d28fdc4 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -296,9 +296,18 @@ Run \fIn\fR analyses in parallel. Default: 1. 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 diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c index 88477190..cddb6069 100644 --- a/libcrystfel/src/peaks.c +++ b/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; diff --git a/src/indexamajig.c b/src/indexamajig.c index 281cac43..8c073e2c 100644 --- a/src/indexamajig.c +++ b/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}, |