/* * index.h * * Perform indexing (somehow) * * Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * Copyright © 2012 Richard Kirian * Copyright © 2012 Lorenzo Galli * * Authors: * 2010-2021 Thomas White * 2010 Richard Kirian * 2012 Lorenzo Galli * 2015 Kenneth Beyerlein * * This file is part of CrystFEL. * * CrystFEL is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * CrystFEL is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with CrystFEL. If not, see . * */ #ifndef INDEX_H #define INDEX_H /** * \file index.h * The indexing subsystem */ #define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX) #define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_USE_CELL_PARAMETERS) #define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_USE_LATTICE_TYPE \ | INDEXING_USE_CELL_PARAMETERS) #define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX | INDEXING_USE_LATTICE_TYPE \ | INDEXING_USE_CELL_PARAMETERS) #define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO \ | INDEXING_USE_CELL_PARAMETERS \ | INDEXING_USE_LATTICE_TYPE) #define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \ | INDEXING_USE_CELL_PARAMETERS) #define INDEXING_DEFAULTS_XGANDALF (INDEXING_XGANDALF | INDEXING_USE_CELL_PARAMETERS) #define INDEXING_DEFAULTS_PINKINDEXER (INDEXING_PINKINDEXER | INDEXING_USE_CELL_PARAMETERS) /** * An enumeration of all the available indexing methods. **/ typedef enum { INDEXING_NONE = 0, /**< No indexing to be performed */ INDEXING_DIRAX = 1, /**< Invoke DirAx program */ INDEXING_MOSFLM = 2, /**< Invoke MOSFLM program */ INDEXING_FELIX = 4, /**< Invoke Felix program */ INDEXING_XDS = 5, /**< Invoke XDS program (NB not nXDS) */ INDEXING_SIMULATION = 6, /**< Dummy value for simulated data */ INDEXING_FILE = 7, /**< Results injector for debugging */ INDEXING_ASDF = 8, /**< Use built-in ASDF algorithm */ INDEXING_TAKETWO = 9, /**< Use built-in TakeTwo algorithm */ INDEXING_XGANDALF = 10, /**< Use XGANDALF (via optional library) */ INDEXING_PINKINDEXER = 11,/**< Use PinkIndexer (via optional library) */ INDEXING_ERROR = 255, /**< Special value for unrecognised indexing * engine */ /** \name Bits which can be set to modify the behaviour of the above * indexing methods */ /**@{*/ /** Use lattice type and centering information */ INDEXING_USE_LATTICE_TYPE = 2048, /** Use the cell parameters themselves */ INDEXING_USE_CELL_PARAMETERS = 4096, /**@}*/ } IndexingMethod; /** This defines the bits in "IndexingMethod" which are used to represent the * core of the indexing method */ #define INDEXING_METHOD_MASK (0xff) /** * Flags affecting how the indexing system processes the results from the * indexing engine */ typedef enum { /** Retry indexing if it doesn't work */ INDEXING_RETRY = 1, /** Attempt to index remaining peaks to find more lattices */ INDEXING_MULTI = 2, /** Refine the indexing solution */ INDEXING_REFINE = 4, /* 8, 16 reserved (formerly INDEXING_CHECK_CELL_COMBINATIONS and * INDEXING_CHECK_CELL_AXES respectively) */ /** Check that the peaks agree with the indexing solution */ INDEXING_CHECK_PEAKS = 32, /** Check that the unit cell agrees with the target cell */ INDEXING_CHECK_CELL = 64, } IndexingFlags; /** * Indexer-specific "private" options */ struct pinkindexer_options { unsigned int considered_peaks_count; unsigned int angle_resolution; unsigned int refinement_type; float maxResolutionForIndexing_1_per_A; float tolerance; float reflectionRadius; /* In m^-1 */ float customBandwidth; float maxRefinementDisbalance; }; 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; }; struct taketwo_options { int member_thresh; double len_tol; double angle_tol; double trace_tol; }; struct fromfile_options { char *filename; }; 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; }; #ifdef __cplusplus extern "C" { #endif /** * This is an opaque data structure containing information needed by the * indexing system. **/ typedef struct _indexingprivate IndexingPrivate; /* Convert indexing methods to/from text */ extern char *indexer_str(IndexingMethod indm); extern IndexingMethod get_indm_from_string(const char *method); extern IndexingMethod get_indm_from_string_2(const char *method, int *err); extern IndexingMethod *parse_indexing_methods(const char *method_list, int *pn); extern char *base_indexer_str(IndexingMethod indm); #include "cell.h" #include "image.h" #include "datatemplate.h" extern struct argp felix_argp; extern struct argp pinkIndexer_argp; extern struct argp taketwo_argp; extern struct argp xgandalf_argp; extern struct argp fromfile_argp; extern void default_method_options(struct taketwo_options **ttopts, struct xgandalf_options **xgandalf_opts, struct pinkindexer_options **pinkIndexer_opts, struct felix_options **felix_opts, struct fromfile_options **fromfile_opts); extern IndexingPrivate *setup_indexing(const char *methods, UnitCell *cell, float *ltl, IndexingFlags flags, double wavelength_estimate, double clen_estimate, int n_threads, struct taketwo_options *ttopts, struct xgandalf_options *xgandalf_opts, struct pinkindexer_options *pinkIndexer_opts, struct felix_options *felix_opts, struct fromfile_options *fromfile_opts); extern const IndexingMethod *indexing_methods(IndexingPrivate *p, int *n); extern char *detect_indexing_methods(UnitCell *cell); extern void index_pattern(struct image *image, IndexingPrivate *ipriv); extern void index_pattern_2(struct image *image, IndexingPrivate *ipriv, int *ping); extern void index_pattern_3(struct image *image, IndexingPrivate *ipriv, int *ping, char *last_task); extern void cleanup_indexing(IndexingPrivate *ipriv); #ifdef __cplusplus } #endif #endif /* INDEX_H */