diff options
Diffstat (limited to 'src/partialator.c')
| -rw-r--r-- | src/partialator.c | 127 |
1 files changed, 92 insertions, 35 deletions
diff --git a/src/partialator.c b/src/partialator.c index e5f965ed..0f0c2631 100644 --- a/src/partialator.c +++ b/src/partialator.c @@ -3,11 +3,11 @@ * * Scaling and post refinement for coherent nanocrystallography * - * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: - * 2010-2013 Thomas White <taw@physics.org> + * 2010-2015 Thomas White <taw@physics.org> * * This file is part of CrystFEL. * @@ -55,6 +55,7 @@ #include "post-refinement.h" #include "hrs-scaling.h" #include "scaling-report.h" +#include "rejection.h" static void show_help(const char *s) @@ -192,11 +193,29 @@ static void display_progress(int n_images, int n_crystals) static const char *str_flags(Crystal *cr) { - if ( crystal_get_user_flag(cr) ) { - return "N"; - } + switch ( crystal_get_user_flag(cr) ) { + + case 0 : + return "OK"; + + case 1 : + return "bad scaling"; + + case 2 : + return "not enough reflections"; + + case 3 : + return "PR solve failed"; - return "-"; + case 4 : + return "PR lost too many reflections"; + + case 5 : + return "Early rejection"; + + default : + return "Unknown flag"; + } } @@ -225,6 +244,62 @@ static RefList *apply_max_adu(RefList *list, double max_adu) } +static void show_duds(Crystal **crystals, int n_crystals) +{ + int j; + int n_dud = 0; + int n_noscale = 0; + int n_noref = 0; + int n_solve = 0; + int n_lost = 0; + int n_early = 0; + + for ( j=0; j<n_crystals; j++ ) { + int flag; + flag = crystal_get_user_flag(crystals[j]); + if ( flag != 0 ) n_dud++; + switch ( flag ) { + + case 0: + break; + + case 1: + n_noscale++; + break; + + case 2: + n_noref++; + break; + + case 3: + n_solve++; + break; + + case 4: + n_lost++; + break; + + case 5: + n_early++; + break; + + default: + STATUS("Unknown flag %i\n", flag); + break; + } + } + + if ( n_dud ) { + STATUS("%i bad crystals:\n", n_dud); + STATUS(" %i scaling failed.\n", n_noscale); + STATUS(" %i not enough reflections.\n", n_noref); + STATUS(" %i solve failed.\n", n_solve); + STATUS(" %i lost too many reflections.\n", n_lost); + STATUS(" %i early rejection.\n", n_early); + } +} + + int main(int argc, char *argv[]) { int c; @@ -462,6 +537,7 @@ int main(int argc, char *argv[]) as = asymmetric_indices(cr_refl, sym); crystal_set_reflections(cr, as); + crystal_set_user_flag(cr, 0); reflist_free(cr_refl); n_crystals++; @@ -499,6 +575,10 @@ int main(int argc, char *argv[]) } } + /* Make a first pass at cutting out crap */ + STATUS("Checking patterns.\n"); + early_rejection(crystals, n_crystals); + /* Make initial estimates */ STATUS("Performing initial scaling.\n"); if ( noscale ) STATUS("Scale factors fixed at 1.\n"); @@ -515,14 +595,10 @@ int main(int argc, char *argv[]) infile, cmdline); sr_iteration(sr, 0, &srdata); + show_duds(crystals, n_crystals); + /* Iterate */ for ( i=0; i<n_iter; i++ ) { - int n_noscale = 0; - int n_noref = 0; - int n_solve = 0; - int n_lost = 0; - int n_dud = 0; - int j; STATUS("Post refinement cycle %i of %i\n", i+1, n_iter); @@ -532,29 +608,8 @@ int main(int argc, char *argv[]) refine_all(crystals, n_crystals, full, nthreads, pmodel, &srdata); - for ( j=0; j<n_crystals; j++ ) { - int flag; - flag = crystal_get_user_flag(crystals[j]); - if ( flag != 0 ) n_dud++; - if ( flag == 1 ) { - n_noscale++; - } else if ( flag == 2 ) { - n_noref++; - } else if ( flag == 3 ) { - n_solve++; - } else if ( flag == 4 ) { - n_lost++; - } - } + show_duds(crystals, n_crystals); - if ( n_dud ) { - STATUS("%i crystals could not be refined this cycle.\n", - n_dud); - STATUS("%i scaling failed.\n", n_noscale); - STATUS("%i not enough reflections.\n", n_noref); - STATUS("%i solve failed.\n", n_solve); - STATUS("%i lost too many reflections.\n", n_lost); - } /* Re-estimate all the full intensities */ reflist_free(full); full = scale_intensities(crystals, n_crystals, nthreads, @@ -577,9 +632,11 @@ int main(int argc, char *argv[]) if ( fh == NULL ) { ERROR("Couldn't open partialator.params!\n"); } else { + fprintf(fh, " cr OSF relB div flag\n"); for ( i=0; i<n_crystals; i++ ) { - fprintf(fh, "%4i %5.2f %8.5e %s\n", i, + fprintf(fh, "%4i %10.5f %10.2f %8.5e %s\n", i, crystal_get_osf(crystals[i]), + crystal_get_Bfac(crystals[i])*1e20, crystal_get_image(crystals[i])->div, str_flags(crystals[i])); } |