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/*
* 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 <taw@physics.org>
* 2010 Richard Kirian
* 2012 Lorenzo Galli
* 2015 Kenneth Beyerlein <kenneth.beyerlein@desy.de>
*
* 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 <http://www.gnu.org/licenses/>.
*
*/
#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 asdf_options {
int fast_execution;
};
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 struct argp asdf_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,
struct asdf_options **asdf_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,
struct asdf_options *asdf_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 */
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