diff options
Diffstat (limited to 'libcrystfel')
| -rw-r--r-- | libcrystfel/CMakeLists.txt | 12 | ||||
| -rw-r--r-- | libcrystfel/src/felix.c | 176 | ||||
| -rw-r--r-- | libcrystfel/src/felix.h | 17 | ||||
| -rw-r--r-- | libcrystfel/src/index.c | 1 | ||||
| -rw-r--r-- | libcrystfel/src/index.h | 2 | ||||
| -rw-r--r-- | libcrystfel/src/integration.c | 23 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.c | 166 | ||||
| -rw-r--r-- | libcrystfel/src/pinkindexer.h | 3 | ||||
| -rw-r--r-- | libcrystfel/src/taketwo.c | 104 | ||||
| -rw-r--r-- | libcrystfel/src/taketwo.h | 12 | ||||
| -rw-r--r-- | libcrystfel/src/utils.c | 2 | ||||
| -rw-r--r-- | libcrystfel/src/xgandalf.c | 159 | ||||
| -rw-r--r-- | libcrystfel/src/xgandalf.h | 12 |
13 files changed, 638 insertions, 51 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt index fdba725e..10e0584d 100644 --- a/libcrystfel/CMakeLists.txt +++ b/libcrystfel/CMakeLists.txt @@ -2,8 +2,6 @@ project(libcrystfel VERSION ${CRYSTFEL_SHORT_VERSION} LANGUAGES C) find_package(Curses) find_package(XGANDALF) -find_package(PINKINDEXER) -find_package(NBP) find_package(FDIP) find_package(ZLIB REQUIRED) find_package(FLEX REQUIRED) @@ -156,16 +154,6 @@ if (FDIP_FOUND) target_link_libraries(${PROJECT_NAME} PRIVATE ${FDIP_LIBRARIES}) endif (FDIP_FOUND) -if (PINKINDEXER_FOUND) - target_include_directories(${PROJECT_NAME} PRIVATE ${PINKINDEXER_INCLUDES}) - target_link_libraries(${PROJECT_NAME} PRIVATE ${PINKINDEXER_LIBRARIES}) -endif (PINKINDEXER_FOUND) - -if (NBP_FOUND) - target_include_directories(${PROJECT_NAME} PRIVATE ${NBP_INCLUDES}) - target_link_libraries(${PROJECT_NAME} PRIVATE ${NBP_LIBRARIES}) -endif (NBP_FOUND) - if (FFTW_FOUND) target_include_directories(${PROJECT_NAME} PRIVATE ${FFTW_INCLUDE_DIRS}) target_link_libraries(${PROJECT_NAME} PRIVATE ${FFTW_LDFLAGS}) diff --git a/libcrystfel/src/felix.c b/libcrystfel/src/felix.c index ea27093a..cac12410 100644 --- a/libcrystfel/src/felix.c +++ b/libcrystfel/src/felix.c @@ -70,6 +70,21 @@ #define FELIX_VERBOSE 0 +struct felix_options +{ + double ttmin; /* radians */ + double ttmax; /* radians */ + int min_visits; + double min_completeness; + double max_uniqueness; + int n_voxels; + double fraction_max_visits; + double sigma; + double domega; + double max_internal_angle; +}; + + /* Global private data, prepared once */ struct felix_private { @@ -789,3 +804,164 @@ const char *felix_probe(UnitCell *cell) if ( ok ) return "felix"; return NULL; } + + +static void show_help() +{ + printf("Parameters for the Felix indexing algorithm:\n" +" --felix-domega Degree range of omega (moscaicity) to consider.\n" +" Default: 2\n" +" --felix-fraction-max-visits\n" +" Cutoff for minimum fraction of the max visits.\n" +" Default: 0.75\n" +" --felix-max-internal-angle\n" +" Cutoff for maximum internal angle between observed\n" +" spots and predicted spots. Default: 0.25\n" +" --felix-max-uniqueness\n" +" Cutoff for maximum fraction of found spots which\n" +" can belong to other crystallites. Default: 0.5\n" +" --felix-min-completeness\n" +" Cutoff for minimum fraction of projected spots\n" +" found in the pattern. Default: 0.001\n" +" --felix-min-visits\n" +" Cutoff for minimum number of voxel visits.\n" +" Default: 15\n" +" --felix-num-voxels Number of voxels for Rodrigues space search\n" +" Default: 100\n" +" --felix-sigma The sigma of the 2theta, eta and omega angles.\n" +" Default: 0.2\n" +" --felix-tthrange-max Maximum 2theta to consider for indexing (degrees)\n" +" Default: 30\n" +" --felix-tthrange-min Minimum 2theta to consider for indexing (degrees)\n" +" Default: 0\n" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + struct felix_options **opts_ptr = state->input; + float tmp; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct felix_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->ttmin = -1.0; + (*opts_ptr)->ttmax = -1.0; + (*opts_ptr)->min_visits = 0; + (*opts_ptr)->min_completeness = -1.0; + (*opts_ptr)->max_uniqueness = -1.0; + (*opts_ptr)->n_voxels = 0; + (*opts_ptr)->fraction_max_visits = -1.0; + (*opts_ptr)->sigma = -1.0; + (*opts_ptr)->domega = -1.0; + (*opts_ptr)->max_internal_angle = -1.0; + break; + + case 1 : + show_help(); + return EINVAL; + + case 2 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-min\n"); + return EINVAL; + } + (*opts_ptr)->ttmin = deg2rad(tmp); + break; + + case 3 : + if ( sscanf(arg, "%f", &tmp) != 1 ) { + ERROR("Invalid value for --felix-tthrange-max\n"); + return EINVAL; + } + (*opts_ptr)->ttmax = deg2rad(tmp); + break; + + case 4 : + if ( sscanf(arg, "%d", &(*opts_ptr)->min_visits) != 1 ) { + ERROR("Invalid value for --felix-min-visits\n"); + return EINVAL; + } + break; + + case 5 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->min_completeness) != 1 ) { + ERROR("Invalid value for --felix-min-completeness\n"); + return EINVAL; + } + break; + + case 6 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_uniqueness) != 1 ) { + ERROR("Invalid value for --felix-max-uniqueness\n"); + return EINVAL; + } + break; + + case 7 : + if ( sscanf(arg, "%d", &(*opts_ptr)->n_voxels) != 1 ) { + ERROR("Invalid value for --felix-num-voxels\n"); + return EINVAL; + } + break; + + case 8 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->fraction_max_visits) != 1 ) { + ERROR("Invalid value for --felix-fraction-max-visits\n"); + return EINVAL; + } + break; + + case 9 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->sigma) != 1 ) { + ERROR("Invalid value for --felix-sigma\n"); + return EINVAL; + } + break; + + case 10 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->domega) != 1 ) { + ERROR("Invalid value for --felix-domega\n"); + return EINVAL; + } + break; + + case 11 : + if ( sscanf(arg, "%lf", &(*opts_ptr)->max_internal_angle) != 1 ) { + ERROR("Invalid value for --felix-max-internal-angle\n"); + return EINVAL; + } + break; + + default : + return ARGP_ERR_UNKNOWN; + + } + + return 0; +} + + +static struct argp_option options[] = { + + {"help-felix", 1, NULL, OPTION_NO_USAGE, + "Show options for Felix indexing algorithm", 99}, + {"felix-tthrange-min", 2, "2theta", OPTION_HIDDEN, NULL}, + {"felix-tthrange-max", 3, "2theta", OPTION_HIDDEN, NULL}, + {"felix-min-visits", 4, "n", OPTION_HIDDEN, NULL}, + {"felix-min-completeness", 5, "frac", OPTION_HIDDEN, NULL}, + {"felix-max-uniqueness", 6, "n", OPTION_HIDDEN, NULL}, + {"felix-num-voxels", 7, "n", OPTION_HIDDEN, NULL}, + {"felix-fraction-max-visits", 8, "n", OPTION_HIDDEN, NULL}, + {"felix-sigma", 9, "n", OPTION_HIDDEN, NULL}, + {"felix-domega", 10, "n", OPTION_HIDDEN, NULL}, + {"felix-max-internal-angle", 11, "ang", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp felix_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/felix.h b/libcrystfel/src/felix.h index 645adaeb..8cec9754 100644 --- a/libcrystfel/src/felix.h +++ b/libcrystfel/src/felix.h @@ -34,6 +34,8 @@ #include <config.h> #endif +#include <argp.h> + #include "cell.h" /** @@ -41,19 +43,8 @@ * Felix indexer interface */ -struct felix_options -{ - double ttmin; /* radians */ - double ttmax; /* radians */ - int min_visits; - double min_completeness; - double max_uniqueness; - int n_voxels; - double fraction_max_visits; - double sigma; - double domega; - double max_internal_angle; -}; +typedef struct felix_options FelixOptions; +extern struct argp felix_argp; extern void *felix_prepare(IndexingMethod *indm, UnitCell *cell, struct felix_options *opts); diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c index 440a5b97..049c3ba0 100644 --- a/libcrystfel/src/index.c +++ b/libcrystfel/src/index.c @@ -593,6 +593,7 @@ static int check_cell(IndexingFlags flags, Crystal *cr, UnitCell *target, tolerance, &rm); if ( out != NULL ) { + /* Replace crystal's cell with new one */ cell_free(crystal_get_cell(cr)); crystal_set_cell(cr, out); rtnl_mtx_free(rm); diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h index 4fc95b1d..5e9e40ad 100644 --- a/libcrystfel/src/index.h +++ b/libcrystfel/src/index.h @@ -125,7 +125,7 @@ typedef enum { INDEXING_CHECK_PEAKS = 32, /** Check that the unit cell agrees with the target cell */ - INDEXING_CHECK_CELL = 32, + INDEXING_CHECK_CELL = 64, } IndexingFlags; diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index 5270816b..a1655aab 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -1399,9 +1399,9 @@ static void integrate_prof2d(IntegrationMethod meth, } -static void integrate_rings_once(Reflection *refl, struct image *image, - struct intcontext *ic, UnitCell *cell, - pthread_mutex_t *term_lock) +static int integrate_rings_once(Reflection *refl, struct image *image, + struct intcontext *ic, UnitCell *cell, + pthread_mutex_t *term_lock) { double pfs, pss; struct peak_box *bx; @@ -1423,7 +1423,7 @@ static void integrate_rings_once(Reflection *refl, struct image *image, pn = panel_number(image->det, p); if ( pn == image->det->n_panels ) { ERROR("Couldn't find panel %p\n", p); - return; + return 1; } /* Explicit truncation of digits after the decimal point. @@ -1458,14 +1458,14 @@ static void integrate_rings_once(Reflection *refl, struct image *image, } if ( r ) { delete_box(ic, bx); - return; + return 1; } if ( saturated ) { ic->n_saturated++; if ( !(ic->meth & INTEGRATION_SATURATED) ) { delete_box(ic, bx); - return; + return 1; } } @@ -1509,7 +1509,10 @@ static void integrate_rings_once(Reflection *refl, struct image *image, if ( intensity < -5.0*sigma ) { ic->n_implausible++; set_redundancy(refl, 0); + return 1; } + + return 0; } @@ -1612,6 +1615,7 @@ static void integrate_rings(IntegrationMethod meth, RefListIterator *iter; UnitCell *cell; struct intcontext ic; + int n_rej = 0; list = crystal_get_reflections(cr); cell = crystal_get_cell(cr); @@ -1641,11 +1645,16 @@ static void integrate_rings(IntegrationMethod meth, refl != NULL; refl = next_refl(refl, iter) ) { - integrate_rings_once(refl, image, &ic, cell, term_lock); + n_rej += integrate_rings_once(refl, image, &ic, cell, term_lock); } free_intcontext(&ic); + if ( n_rej > 0 ) { + ERROR("WARNING: %i reflections could not be integrated\n", + n_rej); + } + crystal_set_num_saturated_reflections(cr, ic.n_saturated); crystal_set_num_implausible_reflections(cr, ic.n_implausible); } diff --git a/libcrystfel/src/pinkindexer.c b/libcrystfel/src/pinkindexer.c index eb8ec05e..811aa3c8 100644 --- a/libcrystfel/src/pinkindexer.c +++ b/libcrystfel/src/pinkindexer.c @@ -367,3 +367,169 @@ const char *pinkIndexer_probe(UnitCell *cell) } #endif /* HAVE_PINKINDEXER */ + +static void show_help() +{ + 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" +" --pinkIndexer-angle-resolution\n" +" Angle resolution, 0 (loosest) to 4 (most dense)\n" +" Default: 2\n" +" --pinkIndexer-refinement-type\n" +" Refinement type, 0 (none) to 5 (most accurate)\n" +" Default: 1\n" +" --pinkIndexer-tolerance\n" +" Relative tolerance of the lattice vectors.\n" +" Default 0.06\n" +" --pinkIndexer-reflection-radius\n" +" Radius of the reflections in reciprocal space.\n" +" Specified in 1/A. Default is 2%% of a*.\n" +" --pinkIndexer-max-resolution-for-indexing\n" +" Measured in 1/A\n" +" --pinkIndexer-multi Use pinkIndexers own multi indexing.\n" +" --pinkIndexer-thread-count\n" +" Thread count for internal parallelization \n" +" Default: 1\n" +" --pinkIndexer-no-check-indexed\n" +" Disable internal check for correct indexing\n" +" solutions\n" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + float tmp; + struct pinkIndexer_options **opts_ptr = state->input; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct pinkIndexer_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->considered_peaks_count = 4; + (*opts_ptr)->angle_resolution = 2; + (*opts_ptr)->refinement_type = 1; + (*opts_ptr)->tolerance = 0.06; + (*opts_ptr)->maxResolutionForIndexing_1_per_A = +INFINITY; + (*opts_ptr)->thread_count = 1; + (*opts_ptr)->multi = 0; + (*opts_ptr)->no_check_indexed = 0; + (*opts_ptr)->min_peaks = 2; + (*opts_ptr)->reflectionRadius = -1; + break; + + case 1 : + show_help(); + return EINVAL; + + case 2 : + if (sscanf(arg, "%u", &(*opts_ptr)->considered_peaks_count) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-considered-peaks-count\n"); + return EINVAL; + } + break; + + case 3 : + if (sscanf(arg, "%u", &(*opts_ptr)->angle_resolution) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-angle_resolution\n"); + return EINVAL; + } + break; + + case 4 : + if (sscanf(arg, "%u", &(*opts_ptr)->refinement_type) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-refinement-type\n"); + return EINVAL; + } + break; + + case 5 : + if (sscanf(arg, "%d", &(*opts_ptr)->thread_count) != 1) + { + ERROR("Invalid value for --pinkIndexer-thread-count\n"); + return EINVAL; + } + break; + + case 6 : + if (sscanf(arg, "%f", &(*opts_ptr)->maxResolutionForIndexing_1_per_A) != 1) + { + ERROR("Invalid value for " + "--pinkIndexer-max-resolution-for-indexing\n"); + return EINVAL; + } + break; + + case 7 : + if (sscanf(arg, "%f", &(*opts_ptr)->tolerance) != 1) + { + ERROR("Invalid value for --pinkIndexer-tolerance\n"); + return EINVAL; + } + break; + + case 8 : + (*opts_ptr)->multi = 1; + break; + + case 9 : + (*opts_ptr)->no_check_indexed = 1; + break; + + case 10 : + if (sscanf(arg, "%f", &tmp) != 1) { + ERROR("Invalid value for --pinkIndexer-reflection-radius\n"); + return EINVAL; + } + (*opts_ptr)->reflectionRadius = tmp / 1e10; /* A^-1 to m^-1 */ + break; + + } + + return 0; +} + + +static struct argp_option options[] = { + + {"help-pinkindexer", 1, NULL, OPTION_NO_USAGE, + "Show options for PinkIndexer indexing algorithm", 99}, + + {"pinkIndexer-considered-peaks-count", 2, "n", OPTION_HIDDEN, NULL}, + {"pinkIndexer-cpc", 2, "n", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-angle-resolution", 3, "ang", OPTION_HIDDEN, NULL}, + {"pinkIndexer-ar", 3, "ang", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-refinement-type", 4, "t", OPTION_HIDDEN, NULL}, + {"pinkIndexer-rt", 4, "t", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-thread-count", 5, "n", OPTION_HIDDEN, NULL}, + {"pinkIndexer-tc", 5, "n", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-max-resolution-for-indexing", 6, "res", OPTION_HIDDEN, NULL}, + {"pinkIndexer-mrfi", 6, "res", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-tolerance", 7, "tol", OPTION_HIDDEN, NULL}, + {"pinkIndexer-tol", 7, "tol", OPTION_HIDDEN, NULL}, + + {"pinkIndexer-multi", 8, NULL, OPTION_HIDDEN, NULL}, + + {"pinkIndexer-no-check-indexed", 9, NULL, OPTION_HIDDEN, NULL}, + + {"pinkIndexer-reflection-radius", 10, "r", OPTION_HIDDEN, NULL}, + + {0} +}; + + +struct argp pinkIndexer_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/pinkindexer.h b/libcrystfel/src/pinkindexer.h index 1fcb3711..0169d028 100644 --- a/libcrystfel/src/pinkindexer.h +++ b/libcrystfel/src/pinkindexer.h @@ -33,6 +33,9 @@ #include <config.h> #endif +typedef struct pinkIndexer_options PinkIndexerOptions; +extern struct argp pinkIndexer_argp; + struct pinkIndexer_options { unsigned int considered_peaks_count; unsigned int angle_resolution; diff --git a/libcrystfel/src/taketwo.c b/libcrystfel/src/taketwo.c index ddbfe173..893791e4 100644 --- a/libcrystfel/src/taketwo.c +++ b/libcrystfel/src/taketwo.c @@ -100,6 +100,14 @@ #include "peaks.h" #include "symmetry.h" +struct taketwo_options +{ + int member_thresh; + double len_tol; + double angle_tol; + double trace_tol; +}; + /** * \param obsvec an observed vector between two spots * \param matches array of matching theoretical vectors from unit cell @@ -2241,6 +2249,7 @@ void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell) return tp; } + void taketwo_cleanup(IndexingPrivate *pp) { struct taketwo_private *tp = (struct taketwo_private *)pp; @@ -2257,3 +2266,98 @@ const char *taketwo_probe(UnitCell *cell) if ( cell_has_parameters(cell) ) return "taketwo"; return NULL; } + + +static void show_help() +{ + printf("Parameters for the TakeTwo indexing algorithm:\n" +" --taketwo-member-threshold\n" +" Minimum number of members in network\n" +" --taketwo-len-tolerance\n" +" Reciprocal space length tolerance (1/A)\n" +" --taketwo-angle-tolerance\n" +" Reciprocal space angle tolerance (in degrees)\n" +" --taketwo-trace-tolerance\n" +" Rotation matrix equivalence tolerance (in degrees)\n" +); +} + + +static error_t parse_arg(int key, char *arg, struct argp_state *state) +{ + struct taketwo_options **opts_ptr = state->input; + float tmp; + + switch ( key ) { + + case ARGP_KEY_INIT : + *opts_ptr = malloc(sizeof(struct taketwo_options)); + if ( *opts_ptr == NULL ) return ENOMEM; + (*opts_ptr)->member_thresh = -1.0; + (*opts_ptr)->len_tol = -1.0; + (*opts_ptr)->angle_tol = -1.0; + (*opts_ptr)->trace_tol = -1.0; + break; + + case 1 : + show_help(); + return EINVAL; + + case 2 : + if ( sscanf(arg, "%i", &(*opts_ptr)->member_thresh) != 1 ) + { + ERROR("Invalid value for --taketwo-member-threshold\n"); + return EINVAL; + } + break; + + case 3 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-len-tol\n"); + return EINVAL; + } + (*opts_ptr)->len_tol = tmp * 1e10; /* Convert to m^-1 */ + break; + + case 4 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-angle-tol\n"); + return EINVAL; + } + (*opts_ptr)->angle_tol = deg2rad(tmp); + break; + + case 5 : + if ( sscanf(arg, "%f", &tmp) != 1 ) + { + ERROR("Invalid value for --taketwo-trace-tol\n"); + return EINVAL; + } + (*opts_ptr)->trace_tol = deg2rad(tmp); + break; + + default : + return ARGP_ERR_UNKNOWN; + + } + + return 0; +} + + +static struct argp_option options[] = { + + {"help-taketwo", 1, NULL, OPTION_NO_USAGE, + "Show options for TakeTwo indexing algorithm", 99}, + + {"taketwo-member-threshold", 2, "n", OPTION_HIDDEN, NULL}, + {"taketwo-len-tolerance", 3, "one_over_A", OPTION_HIDDEN, NULL}, + {"taketwo-angle-tolerance", 4, "deg", OPTION_HIDDEN, NULL}, + {"taketwo-trace-tolerance", 5, "deg", OPTION_HIDDEN, NULL}, + {0} +}; + + +struct argp taketwo_argp = { options, parse_arg, NULL, NULL, NULL, NULL, NULL }; diff --git a/libcrystfel/src/taketwo.h b/libcrystfel/src/taketwo.h index 6960446d..c489228f 100644 --- a/libcrystfel/src/taketwo.h +++ b/libcrystfel/src/taketwo.h @@ -31,19 +31,15 @@ #ifndef TAKETWO_H #define TAKETWO_H +#include <argp.h> + #include "cell.h" #include "index.h" /** \file taketwo.h */ -struct taketwo_options -{ - int member_thresh; - double len_tol; - double angle_tol; - double trace_tol; -}; - +typedef struct taketwo_options TakeTwoOptions; +extern struct argp taketwo_argp; extern void *taketwo_prepare(IndexingMethod *indm, UnitCell *cell); extern const char *taketwo_probe(UnitCell *cell); diff --git a/libcrystfel/src/utils.c b/libcrystfel/src/utils.c index a2ba2c60..ba6f44c3 100644 --- a/libcrystfel/src/utils.c +++ b/libcrystfel/src/utils.c @@ -469,6 +469,8 @@ char *check_prefix(char *prefix) char *new; size_t len; + if ( prefix[0] == '\0' ) return prefix; + /* Is "prefix" a directory? */ r = stat(prefix, &statbuf); if ( r != 0 ) { 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 }; diff --git a/libcrystfel/src/xgandalf.h b/libcrystfel/src/xgandalf.h index 23c5c1b0..7cc85388 100644 --- a/libcrystfel/src/xgandalf.h +++ b/libcrystfel/src/xgandalf.h @@ -34,21 +34,15 @@ #endif #include <stddef.h> +#include <argp.h> /** * \file xgandalf.h * XGANDALF indexer interface */ -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; -}; +typedef struct xgandalf_options XGandalfOptions; +extern struct argp xgandalf_argp; #include "index.h" |