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/*
* index.h
*
* Perform indexing (somehow)
*
* Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
* 2010-2017 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
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#define INDEXING_DEFAULTS_DIRAX (INDEXING_DIRAX | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_ASDF (INDEXING_ASDF | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_MOSFLM (INDEXING_MOSFLM | INDEXING_CHECK_PEAKS \
| INDEXING_CHECK_CELL_COMBINATIONS \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_FELIX (INDEXING_FELIX \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_RETRY | INDEXING_REFINE)
#define INDEXING_DEFAULTS_TAKETWO (INDEXING_TAKETWO | INDEXING_CHECK_PEAKS \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_USE_LATTICE_TYPE \
| INDEXING_RETRY | INDEXING_REFINE)
/* Axis check is needed for XDS, because it likes to permute the axes */
#define INDEXING_DEFAULTS_XDS (INDEXING_XDS | INDEXING_USE_LATTICE_TYPE \
| INDEXING_USE_CELL_PARAMETERS \
| INDEXING_CHECK_CELL_AXES \
| INDEXING_CHECK_PEAKS \
| INDEXING_RETRY | INDEXING_REFINE)
/**
* IndexingMethod:
* @INDEXING_NONE: No indexing to be performed
* @INDEXING_DIRAX: Invoke DirAx
* @INDEXING_MOSFLM: Invoke MOSFLM
* @INDEXING_FELIX: Invoke Felix
* @INDEXING_XDS: Invoke XDS
* @INDEXING_SIMULATION: Dummy value
* @INDEXING_DEBUG: Results injector for debugging
* @INDEXING_ASDF: Use in-built "asdf" indexer
* @INDEXING_TAKETWO: Use in-built "taketwo" indexer
* @INDEXING_CHECK_CELL_COMBINATIONS: Check linear combinations of unit cell
* axes for agreement with given cell.
* @INDEXING_CHECK_CELL_AXES: Check unit cell axes for agreement with given
* cell, and permute them if necessary.
* @INDEXING_CHECK_PEAKS: Check that the peaks can be explained by the indexing
* result.
* @INDEXING_USE_LATTICE_TYPE: Use lattice type and centering information to
* guide the indexing process.
* @INDEXING_USE_CELL_PARAMETERS: Use the unit cell parameters to guide the
* indexingprocess.
* @INDEXING_RETRY: If the indexer doesn't succeed, delete the weakest peaks
* and try again.
* @INDEXING_MULTI: If the indexer succeeds, delete the peaks explained by the
* lattice and try again in the hope of finding another crystal.
* @INDEXING_REFINE: Perform "prediction refinement" after indexing.
*
* An enumeration of all the available indexing methods. The dummy value
* @INDEXING_SIMULATION is used by partial_sim to indicate that no indexing was
* performed, and that the indexing results are just from simulation.
**/
typedef enum {
INDEXING_NONE = 0,
/* The core indexing methods themselves */
INDEXING_DIRAX = 1,
INDEXING_MOSFLM = 2,
INDEXING_FELIX = 4,
INDEXING_XDS = 5,
INDEXING_SIMULATION = 6,
INDEXING_DEBUG = 7,
INDEXING_ASDF = 8,
INDEXING_TAKETWO = 9,
/* Bits at the top of the IndexingMethod are flags which modify the
* behaviour of the indexer. */
INDEXING_CHECK_CELL_COMBINATIONS = 256,
INDEXING_CHECK_CELL_AXES = 512,
INDEXING_CHECK_PEAKS = 1024,
INDEXING_USE_LATTICE_TYPE = 2048,
INDEXING_USE_CELL_PARAMETERS = 4096,
INDEXING_RETRY = 8192,
INDEXING_MULTI = 16384,
INDEXING_REFINE = 32768,
} IndexingMethod;
/* This defines the bits in "IndexingMethod" which are used to represent the
* core of the indexing method */
#define INDEXING_METHOD_MASK (0xff)
/* Indexing flags which the indexing method does not need to know about */
#define INDEXING_CONTROL_FLAGS (INDEXING_RETRY | INDEXING_MULTI | INDEXING_REFINE)
#ifdef __cplusplus
extern "C" {
#endif
/**
* IndexingPrivate:
*
* This is an opaque data structure containing information needed by the
* indexing method.
**/
typedef void *IndexingPrivate;
extern IndexingMethod *build_indexer_list(const char *str);
extern char *indexer_str(IndexingMethod indm);
#include "detector.h"
#include "cell.h"
#include "image.h"
extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
struct detector *det, float *ltl,
const char *options);
extern void index_pattern(struct image *image,
IndexingMethod *indms, IndexingPrivate **iprivs);
extern void index_pattern_2(struct image *image, IndexingMethod *indms,
IndexingPrivate **iprivs, int *ping);
extern void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs);
#ifdef __cplusplus
}
#endif
#endif /* INDEX_H */
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