diff options
Diffstat (limited to 'src/indexamajig.c')
| -rw-r--r-- | src/indexamajig.c | 94 |
1 files changed, 64 insertions, 30 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index ae610063..faee01fc 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -91,6 +91,9 @@ struct static_index_args struct beam_params *beam; const char *element; const char *hdf5_peak_path; + double ir_inn; + double ir_mid; + double ir_out; /* Output stream */ pthread_mutex_t *output_mutex; /* Protects the output stream */ @@ -178,34 +181,34 @@ static void show_help(const char *s) "The default is '--record=integrated'.\n" "\n\n" "For more control over the process, you might need:\n\n" -" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n" -" none : no matching, just use the raw cell.\n" -" reduce : full cell reduction.\n" -" compare : match by at most changing the order of\n" -" the indices.\n" -" compare_ab : compare 'a' and 'b' lengths only.\n" -" --tolerance=<a,b,c,angl> Set the tolerance for a,b,c axis (in %%)\n" -" and for the angles (in deg) when reducing\n" -" or comparing (default is 5%% and 1.5deg)\n" -" --filter-cm Perform common-mode noise subtraction on images\n" -" before proceeding. Intensities will be extracted\n" -" from the image as it is after this processing.\n" -" --filter-noise Apply an aggressive noise filter which sets all\n" -" pixels in each 3x3 region to zero if any of them\n" -" have negative values. Intensity measurement will\n" -" be performed on the image as it was before this.\n" -" --no-sat-corr Don't correct values of saturated peaks using a\n" -" table included in the HDF5 file.\n" -" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n" -" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n" -" Default: 100,000.\n" -" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" -" Default: 5.\n" -" --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n" -" during integration. Default: -infinity.\n" -" -e, --image=<element> Use this image from the HDF5 file.\n" -" Example: /data/data0.\n" -" Default: The first one found.\n" +" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n" +" none : no matching, just use the raw cell.\n" +" reduce : full cell reduction.\n" +" compare : match by at most changing the order of\n" +" the indices.\n" +" compare_ab : compare 'a' and 'b' lengths only.\n" +" --tolerance=<tol> Set the tolerances for cell reduction.\n" +" Default: 5,5,5,1.5.\n" +" --filter-cm Perform common-mode noise subtraction on images\n" +" before proceeding. Intensities will be extracted\n" +" from the image as it is after this processing.\n" +" --filter-noise Apply an aggressive noise filter which sets all\n" +" pixels in each 3x3 region to zero if any of them\n" +" have negative values. Intensity measurement will\n" +" be performed on the image as it was before this.\n" +" --no-sat-corr Don't correct values of saturated peaks using a\n" +" table included in the HDF5 file.\n" +" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n" +" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n" +" Default: 100,000.\n" +" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" +" Default: 5.\n" +" --min-integration-snr=<n> Minimum signal-to-noise ratio for peaks\n" +" during integration. Default: -infinity.\n" +" --int-radius=<r> Set the integration radii. Default: 4,5,7.\n" +"-e, --image=<element> Use this image from the HDF5 file.\n" +" Example: /data/data0.\n" +" Default: The first one found.\n" "\n" "\nFor time-resolved stuff, you might want to use:\n\n" " --copy-hdf5-field <f> Copy the value of field <f> into the stream. You\n" @@ -353,7 +356,10 @@ static void process_image(void *pp, int cookie) case PEAK_ZAEF : search_peaks(&image, pargs->static_args.threshold, pargs->static_args.min_gradient, - pargs->static_args.min_snr); + pargs->static_args.min_snr, + pargs->static_args.ir_inn, + pargs->static_args.ir_mid, + pargs->static_args.ir_out); break; } @@ -382,7 +388,10 @@ static void process_image(void *pp, int cookie) integrate_reflections(&image, pargs->static_args.config_closer, pargs->static_args.config_bgsub, - pargs->static_args.min_int_snr); + pargs->static_args.min_int_snr, + pargs->static_args.ir_inn, + pargs->static_args.ir_mid, + pargs->static_args.ir_out); } @@ -587,6 +596,10 @@ int main(int argc, char *argv[]) char *endptr; char *hdf5_peak_path = NULL; struct copy_hdf5_field *copyme; + char *intrad = NULL; + float ir_inn = 4.0; + float ir_mid = 5.0; + float ir_out = 7.0; copyme = new_copy_hdf5_field_list(); if ( copyme == NULL ) { @@ -631,6 +644,7 @@ int main(int argc, char *argv[]) {"min-snr", 1, NULL, 11}, {"min-integration-snr",1, NULL, 12}, {"tolerance", 1, NULL, 13}, + {"int-radius", 1, NULL, 14}, {0, 0, NULL, 0} }; @@ -762,6 +776,10 @@ int main(int argc, char *argv[]) toler = strdup(optarg); break; + case 14 : + intrad = strdup(optarg); + break; + case 0 : break; @@ -900,6 +918,19 @@ int main(int argc, char *argv[]) } } + if ( intrad != NULL ) { + int r; + r = sscanf(intrad, "%f,%f,%f", &ir_inn, &ir_mid, &ir_out); + if ( r != 3 ) { + ERROR("Invalid parameters for '--int-radius'\n"); + return 1; + } + } else { + STATUS("WARNING: You did not specify --int-radius.\n"); + STATUS("WARNING: I will use the default values, which are" + " probably not appropriate for your patterns.\n"); + } + if ( geometry == NULL ) { ERROR("You need to specify a geometry file with --geometry\n"); return 1; @@ -994,6 +1025,9 @@ int main(int argc, char *argv[]) qargs.static_args.stream_flags = stream_flags; qargs.static_args.hdf5_peak_path = hdf5_peak_path; qargs.static_args.copyme = copyme; + qargs.static_args.ir_inn = ir_inn; + qargs.static_args.ir_mid = ir_mid; + qargs.static_args.ir_out = ir_out; qargs.fh = fh; qargs.prefix = prefix; |