diff options
Diffstat (limited to 'libcrystfel/src/pinkindexer.c')
-rw-r--r-- | libcrystfel/src/pinkindexer.c | 43 |
1 files changed, 38 insertions, 5 deletions
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c index 811aa3c8..b8833847 100644 --- a/libcrystfel/src/pinkindexer.c +++ b/libcrystfel/src/pinkindexer.c @@ -157,9 +157,9 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, struct pinkIndexer_options *pinkIndexer_opts, struct detector *det, struct beam_params *beam) { - if ( beam->photon_energy_from != NULL ) { + if ( beam->photon_energy_from != NULL && pinkIndexer_opts->overridenPhotonEnergy > 0) { ERROR("For pinkIndexer, the photon_energy must be defined as a " - "constant in the geometry file\n"); + "constant in the geometry file or a parameter\n"); return NULL; } if ( (det->panels[0].clen_from != NULL) && pinkIndexer_opts->refinement_type == @@ -201,13 +201,20 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, float beamEenergy_eV = beam->photon_energy; float nonMonochromaticity = beam->bandwidth; + if(pinkIndexer_opts->overridenPhotonEnergy > 0){ + beamEenergy_eV = pinkIndexer_opts->overridenPhotonEnergy; + } + if(pinkIndexer_opts->overridenBandwidth >= 0){ + nonMonochromaticity = pinkIndexer_opts->overridenBandwidth; + } + float reflectionRadius_1_per_A; if (pinkIndexer_opts->reflectionRadius < 0) { reflectionRadius_1_per_A = 0.02 * sqrt(lattice.ax * lattice.ax + lattice.ay * lattice.ay + lattice.az * lattice.az); } else { - reflectionRadius_1_per_A = pinkIndexer_opts->reflectionRadius; + reflectionRadius_1_per_A = pinkIndexer_opts->reflectionRadius * 1e10; /* m^-1 to A^-1*/ } float divergenceAngle_deg = 0.01; //fake @@ -370,7 +377,8 @@ const char *pinkIndexer_probe(UnitCell *cell) static void show_help() { - printf("Parameters for the PinkIndexer indexing algorithm:\n" + printf( +"Parameters for the PinkIndexer indexing algorithm:\n" " --pinkIndexer-considered-peaks-count\n" " Considered peaks count, 0 (fewest) to 4 (most)\n" " Default: 4\n" @@ -395,7 +403,11 @@ static void show_help() " --pinkIndexer-no-check-indexed\n" " Disable internal check for correct indexing\n" " solutions\n" -); +" --pinkIndexer-override-photon-energy\n" +" Mean wavelength in A to use for indexing.\n" +" --pinkIndexer-override-bandwidth\n" +" Bandwidth in (delta lambda)/(lambda) to use for indexing.\n" + ); } @@ -419,6 +431,8 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) (*opts_ptr)->no_check_indexed = 0; (*opts_ptr)->min_peaks = 2; (*opts_ptr)->reflectionRadius = -1; + (*opts_ptr)->overridenPhotonEnergy = -1; + (*opts_ptr)->overridenBandwidth = -1; break; case 1 : @@ -493,6 +507,21 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) (*opts_ptr)->reflectionRadius = tmp / 1e10; /* A^-1 to m^-1 */ break; + case 11 : + if (sscanf(arg, "%f", &(*opts_ptr)->overridenPhotonEnergy) != 1) + { + ERROR("Invalid value for --pinkIndexer-override-photon-energy\n"); + return EINVAL; + } + break; + + case 12 : + if (sscanf(arg, "%f", &(*opts_ptr)->overridenBandwidth) != 1) + { + ERROR("Invalid value for --pinkIndexer-override-bandwidth\n"); + return EINVAL; + } + break; } return 0; @@ -528,6 +557,10 @@ static struct argp_option options[] = { {"pinkIndexer-reflection-radius", 10, "r", OPTION_HIDDEN, NULL}, + {"pinkIndexer-override-photon-energy", 11, "overriddenPhotonEnergy", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-override-bandwidth", 12, "overridenBandwidth", OPTION_HIDDEN, NULL}, + {0} }; |