diff options
Diffstat (limited to 'libcrystfel/src/xgandalf.c')
| -rw-r--r-- | libcrystfel/src/xgandalf.c | 159 |
1 files changed, 158 insertions, 1 deletions
diff --git a/libcrystfel/src/xgandalf.c b/libcrystfel/src/xgandalf.c index 6a8ba4d5..2b5bd512 100644 --- a/libcrystfel/src/xgandalf.c +++ b/libcrystfel/src/xgandalf.c @@ -28,19 +28,32 @@ #include "xgandalf.h" -#ifdef HAVE_XGANDALF #include <stdlib.h> #include "utils.h" #include "cell-utils.h" #include "peaks.h" +#ifdef HAVE_XGANDALF #include "xgandalf/adaptions/crystfel/Lattice.h" #include "xgandalf/adaptions/crystfel/ExperimentSettings.h" #include "xgandalf/adaptions/crystfel/IndexerPlain.h" +#endif /** \file xgandalf.h */ +struct xgandalf_options { + unsigned int sampling_pitch; + unsigned int grad_desc_iterations; + float tolerance; + unsigned int no_deviation_from_provided_cell; + float minLatticeVectorLength_A; + float maxLatticeVectorLength_A; + int maxPeaksForIndexing; +}; + +#ifdef HAVE_XGANDALF + struct xgandalf_private_data { IndexerPlain *indexer; reciprocalPeaks_1_per_A_t reciprocalPeaks_1_per_A; @@ -332,3 +345,147 @@ const char *xgandalf_probe(UnitCell *cell) } #endif // HAVE_XGANDALF + +static void show_help() +{ + printf("Parameters for the TakeTwo indexing algorithm:\n" +" --xgandalf-sampling-pitch\n" +" Sampling pitch: 0 (loosest) to 4 (most dense)\n" +" or with secondary Miller indices: 5 (loosest) to\n" +" 7 (most dense). Default: 6\n" +" --xgandalf-grad-desc-iterations\n" +" Gradient descent iterations: 0 (few) to 5 (many)\n" +" Default: 4\n" +" --xgandalf-fast-execution Shortcut to set\n" +" --xgandalf-sampling-pitch=2\n" +" --xgandalf-grad-desc-iterations=3\n" +" --xgandalf-tolerance Relative tolerance of the lattice vectors.\n" +" Default is 0.02\n" +" --xgandalf-no-deviation-from-provided-cell\n" +" Force the fitted cell to have the same lattice\n" +" parameters as the provided one\n" +" --xgandalf-min-lattice-vector-length\n" +" Minimum possible lattice vector length in A.\n" +" Default: 30 A\n" +" --xgandalf-max-lattice-vector-length\n" +" Maximum possible lattice vector length in A.\n" +" Default: 250 A\n" +" --xgandalf-max-peaks\n" +" Maximum number of peaks used for indexing.\n" +" All peaks are used for refinement.\n" +" Default: 250\n" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + struct xgandalf_options **opts_ptr = state->input; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct xgandalf_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->sampling_pitch = 6; + (*opts_ptr)->grad_desc_iterations = 4; + (*opts_ptr)->tolerance = 0.02; + (*opts_ptr)->no_deviation_from_provided_cell = 0; + (*opts_ptr)->minLatticeVectorLength_A = 30; + (*opts_ptr)->maxLatticeVectorLength_A = 250; + (*opts_ptr)->maxPeaksForIndexing = 250; + break; + + case 1 : + show_help(); + return EINVAL; + + case 2 : + if (sscanf(arg, "%u", &(*opts_ptr)->sampling_pitch) != 1) { + ERROR("Invalid value for --xgandalf-sampling-pitch\n"); + return EINVAL; + } + break; + + case 3 : + if (sscanf(arg, "%u", &(*opts_ptr)->grad_desc_iterations) != 1) { + ERROR("Invalid value for --xgandalf-grad-desc-iterations\n"); + return EINVAL; + } + break; + + case 4 : + if (sscanf(arg, "%f", &(*opts_ptr)->tolerance) != 1) { + ERROR("Invalid value for --xgandalf-tolerance\n"); + return EINVAL; + } + break; + + case 5 : + (*opts_ptr)->no_deviation_from_provided_cell = 1; + break; + + case 6 : + if (sscanf(arg, "%f", &(*opts_ptr)->minLatticeVectorLength_A) != 1) { + ERROR("Invalid value for --xgandalf-min-lattice-vector-length\n"); + return EINVAL; + } + break; + + case 7 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxLatticeVectorLength_A) != 1) { + ERROR("Invalid value for --xgandalf-max-lattice-vector-length\n"); + return EINVAL; + } + break; + + case 8 : + (*opts_ptr)->sampling_pitch = 2; + (*opts_ptr)->grad_desc_iterations = 3; + break; + + case 9 : + if (sscanf(arg, "%i", &(*opts_ptr)->maxPeaksForIndexing) != 1) { + ERROR("Invalid value for --xgandalf-max-peaks\n"); + return EINVAL; + } + break; + + } + + return 0; +} + + +static struct argp_option options[] = { + + {"help-xgandalf", 1, NULL, OPTION_NO_USAGE, + "Show options for XGANDALF indexing algorithm", 99}, + + {"xgandalf-sampling-pitch", 2, "pitch", OPTION_HIDDEN, NULL}, + {"xgandalf-sps", 2, "pitch", OPTION_HIDDEN, NULL}, + + {"xgandalf-grad-desc-iterations", 3, "n", OPTION_HIDDEN, NULL}, + {"xgandalf-gdis", 3, "n", OPTION_HIDDEN, NULL}, + + {"xgandalf-tolerance", 4, "t", OPTION_HIDDEN, NULL}, + {"xgandalf-tol", 4, "t", OPTION_HIDDEN, NULL}, + + {"xgandalf-no-deviation-from-provided-cell", 5, NULL, OPTION_HIDDEN, NULL}, + {"xgandalf-ndfpc", 5, NULL, OPTION_HIDDEN, NULL}, + + {"xgandalf-min-lattice-vector-length", 6, "len", OPTION_HIDDEN, NULL}, + {"xgandalf-min-lvl", 6, "len", OPTION_HIDDEN, NULL}, + + {"xgandalf-max-lattice-vector-length", 7, "len", OPTION_HIDDEN, NULL}, + {"xgandalf-max-lvl", 7, "len", OPTION_HIDDEN, NULL}, + + {"xgandalf-fast-execution", 8, NULL, OPTION_HIDDEN, NULL}, + + {"xgandalf-max-peaks", 9, "n", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp xgandalf_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; |