diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 14 | ||||
| -rw-r--r-- | src/indexamajig.c | 5 | ||||
| -rw-r--r-- | src/process_image.h | 1 |
3 files changed, 0 insertions, 20 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index ae71a571..124ee459 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -288,20 +288,6 @@ 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 -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--no-use-saturated\fR .PD Normally, peaks which contain one or more pixels above max_adu (defined in the detector geometry file) will be used for indexing (but not used in the final integration - see the section on peak integration above). Using this option causes saturated peaks to be ignored completely. The opposite is \fB--use-saturated\fR, which is the default. diff --git a/src/indexamajig.c b/src/indexamajig.c index b411b901..ab148a0b 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -138,8 +138,6 @@ 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" -" --closer-peak Don't integrate from the location of a nearby peak\n" -" instead of the predicted spot. Don't use.\n" " --no-use-saturated During the initial peak search, reject\n" " peaks which contain pixels above max_adu.\n" " --no-revalidate Don't re-integrate and check HDF5 peaks for\n" @@ -205,7 +203,6 @@ int main(int argc, char *argv[]) iargs.noisefilter = 0; iargs.median_filter = 0; iargs.satcorr = 1; - iargs.closer = 0; iargs.tols[0] = 5.0; iargs.tols[1] = 5.0; iargs.tols[2] = 5.0; @@ -256,7 +253,6 @@ int main(int argc, char *argv[]) /* Long-only options with no arguments */ {"filter-noise", 0, &iargs.noisefilter, 1}, {"no-check-prefix", 0, &config_checkprefix, 0}, - {"closer-peak", 0, &iargs.closer, 1}, {"basename", 0, &config_basename, 1}, {"no-peaks-in-stream", 0, &iargs.stream_peaks, 0}, {"no-refls-in-stream", 0, &iargs.stream_refls, 0}, @@ -268,7 +264,6 @@ int main(int argc, char *argv[]) /* Long-only options which don't actually do anything */ {"no-sat-corr", 0, &iargs.satcorr, 0}, {"sat-corr", 0, &iargs.satcorr, 1}, - {"no-closer-peak", 0, &iargs.closer, 0}, {"no-check-hdf5-snr", 0, &iargs.check_hdf5_snr, 0}, {"use-saturated", 0, &iargs.use_saturated, 1}, diff --git a/src/process_image.h b/src/process_image.h index 7fedc51b..b8ded1ed 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -51,7 +51,6 @@ struct index_args int noisefilter; int median_filter; int satcorr; - int closer; float threshold; float min_gradient; float min_snr; |