diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/indexamajig.c | 128 | ||||
| -rw-r--r-- | src/process_image.h | 2 |
2 files changed, 130 insertions, 0 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index bd159a9a..5770051a 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -204,6 +204,32 @@ static void show_help(const char *s) " All peaks are used for refinement.\n" " Default: 250\n" "\n" +" --pinkIndexer-considered-peaks-count Considered peaks count selector \n" +" [0-4] (veryFew to manyMany)\n" +" Default is 4 (manyMany)\n" +" --pinkIndexer-angle-resolution Angle resolution selector \n" +" [0-4] (extremelyLoose to extremelyDense)\n" +" Default is 2 (normal)\n" +" --pinkIndexer-refinement-type Refinement type \n" +" Default is 1\n" +" 0 = none\n" +" 1 = fixedLatticeParameters\n" +" 2 = variableLatticeParameters\n" +" 3 = firstFixedThenVariableLatticeParameters\n" +" 4 = firstFixedThenVariableLatticeParametersMultiSeed\n" +" 5 = firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed\n" +" --pinkIndexer-tolerance Relative tolerance of the lattice vectors.\n" +" Default is 0.06\n" +" --pinkIndexer-reflection-radius radius of the reflections in reciprocal space in 1/A.\n" +" Default is 2%% of a*.\n" +" Should be chosen ~0.002 for electrons.\n" +" --pinkIndexer-max-resolution-for-indexing Measured in 1/A\n" +" --pinkIndexer-multi Use pinkIndexers own multi indexing.\n" +" --pinkIndexer-thread-count thread count for internal parallelization \n" +" Default is 1\n" +" --pinkIndexer-no-check-indexed Leave the check whether a pattern is indexed completely to CrystFEL\n" +" useful for monochromatic and tweaking." +"\n" "\nIntegration options:\n\n" " --integration=<meth> Integration method (rings,prof2d)-(cen,nocen)\n" " Default: rings-nocen\n" @@ -253,6 +279,7 @@ static void add_geom_beam_stuff_to_field_list(struct imagefile_field_list *copym int main(int argc, char *argv[]) { int c; + unsigned int tmp_enum; char *filename = NULL; char *outfile = NULL; FILE *fh; @@ -360,6 +387,16 @@ int main(int argc, char *argv[]) iargs.xgandalf_opts.minLatticeVectorLength_A = 30; iargs.xgandalf_opts.maxLatticeVectorLength_A = 250; iargs.xgandalf_opts.maxPeaksForIndexing = 250; + iargs.pinkIndexer_opts.considered_peaks_count = 4; + iargs.pinkIndexer_opts.angle_resolution = 2; + iargs.pinkIndexer_opts.refinement_type = 1; + iargs.pinkIndexer_opts.tolerance = 0.06; + iargs.pinkIndexer_opts.maxResolutionForIndexing_1_per_A = FLT_MAX; + iargs.pinkIndexer_opts.thread_count = 1; + iargs.pinkIndexer_opts.multi = 0; + iargs.pinkIndexer_opts.no_check_indexed = 0; + iargs.pinkIndexer_opts.min_peaks = 2; + iargs.pinkIndexer_opts.reflectionRadius = -1; iargs.felix_opts.ttmin = -1.0; iargs.felix_opts.ttmax = -1.0; iargs.felix_opts.min_visits = 0; @@ -491,6 +528,21 @@ int main(int argc, char *argv[]) {"min-sq-gradient", 1, NULL, 359}, /* compat */ {"xgandalf-fast-execution", 0, NULL, 360}, {"xgandalf-max-peaks", 1, NULL, 361}, + {"pinkIndexer-considered-peaks-count", 1, NULL, 362}, + {"pinkIndexer-cpc", 1, NULL, 362}, + {"pinkIndexer-angle-resolution", 1, NULL, 363}, + {"pinkIndexer-ar", 1, NULL, 363}, + {"pinkIndexer-refinement-type", 1, NULL, 364}, + {"pinkIndexer-rt", 1, NULL, 364}, + {"pinkIndexer-thread-count", 1, NULL, 365}, + {"pinkIndexer-tc", 1, NULL, 365}, + {"pinkIndexer-max-resolution-for-indexing", 1, NULL, 366}, + {"pinkIndexer-mrfi", 1, NULL, 366}, + {"pinkIndexer-tolerance", 1, NULL, 367}, + {"pinkIndexer-tol", 1, NULL, 367}, + {"pinkIndexer-multi", 0, NULL, 368}, + {"pinkIndexer-no-check-indexed", 0, NULL, 369}, + {"pinkIndexer-reflection-radius", 1, NULL, 370}, {0, 0, NULL, 0} }; @@ -689,6 +741,7 @@ int main(int argc, char *argv[]) case 331: iargs.min_peaks = atoi(optarg); + iargs.pinkIndexer_opts.min_peaks = iargs.min_peaks; break; case 332: @@ -922,6 +975,74 @@ int main(int argc, char *argv[]) } break; + case 362: + if (sscanf(optarg, "%u", &tmp_enum) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-considered-peaks-count\n"); + return 1; + } + iargs.pinkIndexer_opts.considered_peaks_count = tmp_enum; + break; + + case 363: + if (sscanf(optarg, "%u", &tmp_enum) != 1) + { + ERROR("Invalid value for --pinkIndexer-angle-resolution \n"); + return 1; + } + iargs.pinkIndexer_opts.angle_resolution = tmp_enum; + break; + + case 364: + if (sscanf(optarg, "%u", &tmp_enum) != 1) + { + ERROR("Invalid value for --pinkIndexer-refinement-type \n"); + return 1; + } + iargs.pinkIndexer_opts.refinement_type = tmp_enum; + break; + + case 365: + if (sscanf(optarg, "%d", &iargs.pinkIndexer_opts.thread_count) != 1) + { + ERROR("Invalid value for --pinkIndexer-thread-count \n"); + return 1; + } + break; + + case 366: + if (sscanf(optarg, "%f", &iargs.pinkIndexer_opts.maxResolutionForIndexing_1_per_A) != 1) + { + ERROR("Invalid value for --pinkIndexer-max-resolution-for-indexing \n"); + return 1; + } + break; + + case 367: + if (sscanf(optarg, "%f", &iargs.pinkIndexer_opts.tolerance) != 1) + { + ERROR("Invalid value for --pinkIndexer-tolerance \n"); + return 1; + } + break; + + case 368: + iargs.pinkIndexer_opts.multi = 1; + break; + + case 369: + iargs.pinkIndexer_opts.no_check_indexed = 1; + break; + + case 370: + if (sscanf(optarg, "%f", &iargs.pinkIndexer_opts.reflectionRadius) != 1) + { + ERROR("Invalid value for --pinkIndexer-reflection-radius \n"); + return 1; + } + break; + case 0 : break; @@ -1021,6 +1142,12 @@ int main(int argc, char *argv[]) return 1; } add_geom_beam_stuff_to_field_list(iargs.copyme, iargs.det, iargs.beam); + iargs.pinkIndexer_opts.beamEnergy = iargs.beam->photon_energy; + iargs.pinkIndexer_opts.beamBandwidth = iargs.beam->photon_energy_bandwidth; + iargs.pinkIndexer_opts.detectorDistance = iargs.det->panels[0].clen; + if(iargs.det->panels[0].clen_from != NULL){ + iargs.pinkIndexer_opts.detectorDistance = 0; + } /* If no peak path from geometry file, use these (but see later) */ if ( iargs.hdf5_peak_path == NULL ) { @@ -1263,6 +1390,7 @@ int main(int argc, char *argv[]) iargs.tols, flags, &iargs.taketwo_opts, &iargs.xgandalf_opts, + &iargs.pinkIndexer_opts, &iargs.felix_opts); if ( iargs.ipriv == NULL ) { ERROR("Failed to set up indexing system\n"); diff --git a/src/process_image.h b/src/process_image.h index 9a58a64f..ced3bcf2 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -46,6 +46,7 @@ struct index_args; #include "time-accounts.h" #include "taketwo.h" #include "xgandalf.h" +#include "../libcrystfel/src/pinkindexer.h" #include "felix.h" @@ -117,6 +118,7 @@ struct index_args int profile; /* Whether or not to do wall clock profiling */ struct taketwo_options taketwo_opts; struct xgandalf_options xgandalf_opts; + struct pinkIndexer_options pinkIndexer_opts; struct felix_options felix_opts; Spectrum *spectrum; signed int wait_for_file; /* -1 means wait forever */ |