diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/partialator.c | 25 | ||||
| -rw-r--r-- | src/process_hkl.c | 34 |
2 files changed, 37 insertions, 22 deletions
diff --git a/src/partialator.c b/src/partialator.c index 68c886c9..ef6d0f80 100644 --- a/src/partialator.c +++ b/src/partialator.c @@ -325,6 +325,7 @@ static void show_help(const char *s) " -m, --model=<model> Specify partiality model.\n" " --min-measurements=<n> Minimum number of measurements to require.\n" " --no-polarisation Disable polarisation correction.\n" +" --polarisation=<p> Specify type of polarisation correction.\n" " --max-adu=<n> Saturation value of detector.\n" " --min-res=<n> Merge only crystals which diffract above <n> A.\n" " --push-res=<n> Merge higher than apparent resolution cutoff.\n" @@ -951,7 +952,7 @@ int main(int argc, char *argv[]) PartialityModel pmodel = PMODEL_XSPHERE; int min_measurements = 2; char *rval; - int polarisation = 1; + struct polarisation polarisation = {.fraction = 1.0, .angle= 0.0}; int start_after = 0; int stop_after = 0; double max_adu = +INFINITY; @@ -1005,14 +1006,14 @@ int main(int argc, char *argv[]) {"force-radius", 1, NULL, 11}, {"min-res", 1, NULL, 12}, {"force-lambda", 1, NULL, 13}, + {"polarisation", 1, NULL, 14}, + {"polarization", 1, NULL, 14}, /* compat */ + {"no-polarisation", 0, NULL, 15}, + {"no-polarization", 0, NULL, 15}, /* compat */ {"no-scale", 0, &no_scale, 1}, {"no-Bscale", 0, &no_Bscale, 1}, {"no-pr", 0, &no_pr, 1}, - {"no-polarisation", 0, &polarisation, 0}, - {"no-polarization", 0, &polarisation, 0}, /* compat */ - {"polarisation", 0, &polarisation, 1}, - {"polarization", 0, &polarisation, 1}, /* compat */ {"no-free", 0, &no_free, 1}, {"output-every-cycle", 0, &output_everycycle, 1}, {"no-logs", 0, &no_logs, 1}, @@ -1184,6 +1185,13 @@ int main(int argc, char *argv[]) force_lambda *= 1e-10; break; + case 14 : + polarisation = parse_polarisation(optarg); + break; + + case 15 : + polarisation.fraction = 0.5; + break; case 0 : break; @@ -1427,11 +1435,8 @@ int main(int argc, char *argv[]) cr_refl = apply_max_adu(cr_refl, max_adu); - if ( polarisation ) { - polarisation_correction(cr_refl, - crystal_get_cell(cr), - image); - } + polarisation_correction(cr_refl, crystal_get_cell(cr), + image->lambda, polarisation); if ( !no_free ) select_free_reflections(cr_refl, rng); diff --git a/src/process_hkl.c b/src/process_hkl.c index 393dc3e8..5e17f31c 100644 --- a/src/process_hkl.c +++ b/src/process_hkl.c @@ -80,7 +80,8 @@ static void show_help(const char *s) " model.\n" " --even-only Merge even numbered crystals only\n" " --odd-only Merge odd numbered crystals only\n" -" --no-polarisation Disable polarisation correction.\n" +" --no-polarisation Disable polarisation correction.\n" +" --polarisation=<p> Specify type of polarisation correction.\n" " --min-measurements=<n> Require at least <n> measurements before a\n" " reflection appears in the output. Default: 2\n" " --min-snr=<n> Require individual intensity measurements to\n" @@ -258,7 +259,7 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr, RefList *reference, const SymOpList *sym, double **hist_vals, signed int hist_h, signed int hist_k, signed int hist_l, int *hist_n, - int config_nopolar, double min_snr, double max_adu, + struct polarisation p, double min_snr, double max_adu, double push_res, double min_cc, int do_scale, FILE *stat) { @@ -270,9 +271,8 @@ static int merge_crystal(RefList *model, struct image *image, Crystal *cr, new_refl = crystal_get_reflections(cr); /* First, correct for polarisation */ - if ( !config_nopolar ) { - polarisation_correction(new_refl, crystal_get_cell(cr), image); - } + polarisation_correction(new_refl, crystal_get_cell(cr), + image->lambda, p); if ( reference != NULL ) { if ( do_scale ) { @@ -385,7 +385,7 @@ static int merge_all(Stream *st, RefList *model, RefList *reference, const SymOpList *sym, double **hist_vals, signed int hist_h, signed int hist_k, signed int hist_l, - int *hist_i, int config_nopolar, int min_measurements, + int *hist_i, struct polarisation p, int min_measurements, double min_snr, double max_adu, int start_after, int stop_after, double min_res, double push_res, double min_cc, int do_scale, int flag_even_odd, char *stat_output) @@ -435,7 +435,7 @@ static int merge_all(Stream *st, RefList *model, RefList *reference, r = merge_crystal(model, &image, cr, reference, sym, hist_vals, hist_h, hist_k, hist_l, - hist_i, config_nopolar, + hist_i, p, min_snr, max_adu, push_res, min_cc, do_scale, stat); if ( r == 0 ) n_crystals_used++; @@ -506,7 +506,7 @@ int main(int argc, char *argv[]) int hist_i; int space_for_hist = 0; char *histo_params = NULL; - int config_nopolar = 0; + struct polarisation polarisation = {.fraction = 1.0, .angle= 0.0}; char *rval; int min_measurements = 2; int r; @@ -530,8 +530,6 @@ int main(int argc, char *argv[]) {"scale", 0, &config_scale, 1}, {"even-only", 0, &config_evenonly, 1}, {"odd-only", 0, &config_oddonly, 1}, - {"no-polarisation", 0, &config_nopolar, 1}, - {"no-polarization", 0, &config_nopolar, 1}, {"symmetry", 1, NULL, 'y'}, {"histogram", 1, NULL, 'g'}, {"hist-parameters", 1, NULL, 'z'}, @@ -544,6 +542,10 @@ int main(int argc, char *argv[]) {"version", 0, NULL, 7}, {"min-cc", 1, NULL, 8}, {"stat", 1, NULL, 9}, + {"polarisation", 1, NULL, 10}, + {"polarization", 1, NULL, 10}, /* compat */ + {"no-polarisation", 0, NULL, 11}, + {"no-polarization", 0, NULL, 11}, /* compat */ {0, 0, NULL, 0} }; @@ -671,6 +673,14 @@ int main(int argc, char *argv[]) twopass = 1; break; + case 10 : + polarisation = parse_polarisation(optarg); + break; + + case 11 : + polarisation.fraction = 0.5; + break; + case 0 : break; @@ -760,7 +770,7 @@ int main(int argc, char *argv[]) hist_i = 0; r = merge_all(st, model, NULL, sym, &hist_vals, hist_h, hist_k, hist_l, - &hist_i, config_nopolar, min_measurements, min_snr, + &hist_i, polarisation, min_measurements, min_snr, max_adu, start_after, stop_after, min_res, push_res, min_cc, config_scale, flag_even_odd, stat_output); fprintf(stderr, "\n"); @@ -795,7 +805,7 @@ int main(int argc, char *argv[]) r = merge_all(st, model, reference, sym, &hist_vals, hist_h, hist_k, hist_l, &hist_i, - config_nopolar, min_measurements, min_snr, + polarisation, min_measurements, min_snr, max_adu, start_after, stop_after, min_res, push_res, min_cc, config_scale, flag_even_odd, stat_output); |