diff options
Diffstat (limited to 'libcrystfel/src/pinkindexer.c')
| -rw-r--r-- | libcrystfel/src/pinkindexer.c | 28 |
1 files changed, 26 insertions, 2 deletions
diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c index e3ecf5a9..22208885 100644 --- a/libcrystfel/src/pinkindexer.c +++ b/libcrystfel/src/pinkindexer.c @@ -55,6 +55,8 @@ struct pinkIndexer_private_data { int no_check_indexed; + float maxRefinementDisbalance; + IntegerMatrix *centeringTransformation; LatticeTransform_t latticeReductionTransform; }; @@ -95,15 +97,24 @@ int run_pinkIndexer(struct image *image, void *ipriv) Lattice_t indexedLattice[MAX_MULTI_LATTICE_COUNT]; float center_shift[MAX_MULTI_LATTICE_COUNT][2]; - float maxRefinementDisbalance = 0.4; + do { int peakCount = reciprocalPeaks_1_per_A->peakCount; int matchedPeaksCount = PinkIndexer_indexPattern(pinkIndexer_private_data->pinkIndexer, &(indexedLattice[indexed]), center_shift[indexed], reciprocalPeaks_1_per_A, intensities, - maxRefinementDisbalance, + pinkIndexer_private_data->maxRefinementDisbalance, pinkIndexer_private_data->threadCount); + if(matchedPeaksCount == -1){ + STATUS("WARNING: Indexing solution was rejected due to too large disbalance of the refinement." + "If you see this message often, check the documentation for the parameter " + "--pinkIndexer-max-refinement-disbalance\n"); + + matchedPeaksCount = 0; + } + + printf("matchedPeaksCount %d from %d\n",matchedPeaksCount,peakCount); if ((matchedPeaksCount >= 25 && matchedPeaksCount >= peakCount * 0.30) || matchedPeaksCount >= peakCount * 0.4 || matchedPeaksCount >= 70 @@ -181,6 +192,7 @@ void *pinkIndexer_prepare(IndexingMethod *indm, UnitCell *cell, pinkIndexer_private_data->multi = pinkIndexer_opts->multi; pinkIndexer_private_data->min_peaks = pinkIndexer_opts->min_peaks; pinkIndexer_private_data->no_check_indexed = pinkIndexer_opts->no_check_indexed; + pinkIndexer_private_data->maxRefinementDisbalance = pinkIndexer_opts->maxRefinementDisbalance; UnitCell* primitiveCell = uncenter_cell(cell, &pinkIndexer_private_data->centeringTransformation, NULL); @@ -412,6 +424,9 @@ static void show_help() " --pinkIndexer-no-check-indexed\n" " Disable internal check for correct indexing\n" " solutions\n" +" --pinkIndexer-max-refinement-disbalance=n\n" +" Maximum disbalance after refinement:\n" +" 0 (no disbalance) to 2 (extreme disbalance), default 0.4\n" " --pinkIndexer-override-photon-energy=ev\n" " Mean energy in eV to use for indexing.\n" " --pinkIndexer-override-bandwidth=n\n" @@ -447,6 +462,7 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) (*opts_ptr)->reflectionRadius = -1; (*opts_ptr)->customPhotonEnergy = -1; (*opts_ptr)->customBandwidth = -1; + (*opts_ptr)->maxRefinementDisbalance = 0.4; break; case 1 : @@ -548,6 +564,12 @@ static error_t parse_arg(int key, char *arg, struct argp_state *state) (*opts_ptr)->customBandwidth *= -1; } break; + case 14 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxRefinementDisbalance) != 1) + { + ERROR("Invalid value for --pinkIndexer-max-refinement-disbalance\n"); + return EINVAL; + } } return 0; @@ -589,6 +611,8 @@ static struct argp_option options[] = { {"pinkIndexer-override-visible-energy-range", 13, "overridenVisibleEnergyRange", OPTION_HIDDEN, NULL}, + {"pinkIndexer-max-refinement-disbalance", 14, "maxDisbalance", OPTION_HIDDEN, NULL}, + {0} }; |