diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 6 | ||||
| -rw-r--r-- | src/indexamajig.c | 31 | ||||
| -rw-r--r-- | src/process_image.c | 6 | ||||
| -rw-r--r-- | src/process_image.h | 3 |
4 files changed, 41 insertions, 5 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index b151438c..01c07330 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -210,6 +210,12 @@ Read the unit cell for comparison from the CRYST1 line of the PDB file called \f Get the image data to display from \fIpath\fR inside the HDF5 file. For example: \fI/data/rawdata\fR. If this is not specified, the default behaviour is to use the first two-dimensional dataset with both dimensions greater than 64. .PD 0 +.IP \fB--peak-radius=\fR\fIinner,middle,outer\fR +.PD +Set the inner, middle and outer radii for three-ring integration during the peak search. See the section about \fBPEAK INTEGRATION\fR, above, for details of how to determine +these. The default is to use the same values as for \fB--int-radius\fR. + +.PD 0 .IP \fB--int-radius=\fR\fIinner,middle,outer\fR .PD Set the inner, middle and outer radii for three-ring integration. See the diff --git a/src/indexamajig.c b/src/indexamajig.c index 607e8b0c..d75e24be 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -124,6 +124,7 @@ static void show_help(const char *s) " --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n" " Default: 5.\n" " --check-hdf5-snr Check SNR for peaks from --peaks=hdf5.\n" +" --peak-radius=<r> Integration radii for peak search.\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" @@ -192,6 +193,7 @@ int main(int argc, char *argv[]) int n_proc = 1; struct index_args iargs; char *intrad = NULL; + char *pkrad = NULL; char *int_str = NULL; char *tempdir = NULL; char *int_diag = NULL; @@ -215,6 +217,9 @@ int main(int argc, char *argv[]) iargs.element = NULL; iargs.hdf5_peak_path = strdup("/processing/hitfinder/peakinfo"); iargs.copyme = NULL; + iargs.pk_inn = -1.0; + iargs.pk_mid = -1.0; + iargs.pk_out = -1.0; iargs.ir_inn = 4.0; iargs.ir_mid = 5.0; iargs.ir_out = 7.0; @@ -249,7 +254,7 @@ int main(int argc, char *argv[]) {"image", 1, NULL, 'e'}, /* Long-only options with no arguments */ - {"version", 0, NULL, 20}, + {"version", 0, NULL, 99}, {"filter-noise", 0, &iargs.noisefilter, 1}, {"no-check-prefix", 0, &config_checkprefix, 0}, {"basename", 0, &config_basename, 1}, @@ -285,6 +290,7 @@ int main(int argc, char *argv[]) {"int-diag", 1, NULL, 18}, {"push-res", 1, NULL, 19}, {"res-push", 1, NULL, 19}, /* compat */ + {"peak-radius", 1, NULL, 20}, {0, 0, NULL, 0} }; @@ -299,7 +305,7 @@ int main(int argc, char *argv[]) show_help(argv[0]); return 0; - case 20 : + case 99 : printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n"); printf(CRYSTFEL_BOILERPLATE"\n"); return 0; @@ -430,6 +436,10 @@ int main(int argc, char *argv[]) iargs.push_res *= 1e9; /* nm^-1 -> m^-1 */ break; + case 20 : + pkrad = strdup(optarg); + break; + case 0 : break; @@ -551,6 +561,23 @@ int main(int argc, char *argv[]) " probably not appropriate for your patterns.\n"); } + if ( pkrad != NULL ) { + int r; + r = sscanf(pkrad, "%f,%f,%f", + &iargs.pk_inn, &iargs.pk_mid, &iargs.pk_out); + if ( r != 3 ) { + ERROR("Invalid parameters for '--peak-radius'\n"); + return 1; + } + free(pkrad); + } + + if ( iargs.pk_inn < 0.0 ) { + iargs.pk_inn = iargs.ir_inn; + iargs.pk_mid = iargs.ir_mid; + iargs.pk_out = iargs.ir_out; + } + if ( iargs.det == NULL ) { ERROR("You need to provide a geometry file (please read the" " manual for more details).\n"); diff --git a/src/process_image.c b/src/process_image.c index ba68021a..4751073b 100644 --- a/src/process_image.c +++ b/src/process_image.c @@ -127,8 +127,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, } if ( !iargs->no_revalidate ) { validate_peaks(&image, iargs->min_snr, - iargs->ir_inn, iargs->ir_mid, - iargs->ir_out, iargs->use_saturated, + iargs->pk_inn, iargs->pk_mid, + iargs->pk_out, iargs->use_saturated, iargs->check_hdf5_snr); } break; @@ -136,7 +136,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs, case PEAK_ZAEF: search_peaks(&image, iargs->threshold, iargs->min_gradient, iargs->min_snr, - iargs->ir_inn, iargs->ir_mid, iargs->ir_out, + iargs->pk_inn, iargs->pk_mid,iargs->pk_out, iargs->use_saturated); break; diff --git a/src/process_image.h b/src/process_image.h index b8ded1ed..1a8a9ff3 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -63,6 +63,9 @@ struct index_args struct beam_params *beam; char *element; char *hdf5_peak_path; + float pk_inn; + float pk_mid; + float pk_out; float ir_inn; float ir_mid; float ir_out; |