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/*
* reflist.h
*
* Fast reflection/peak list
*
* Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2011-2020 Thomas White <taw@physics.org>
*
* 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 REFLIST_H
#define REFLIST_H
#define SERIAL(h, k, l) ((((h)+512)<<20) + (((k)+512)<<10) + ((l)+512))
#define GET_H(serial) ((((serial) & 0x3ff00000)>>20)-512)
#define GET_K(serial) ((((serial) & 0x000ffc00)>>10)-512)
#define GET_L(serial) (((serial) & 0x000003ff)-512)
/**
* \file reflist.h
* The fast reflection list stores reflections in an RB-tree indexed
* by the Miller indices h, k and l. Any reflection can be found in a
* length of time which scales logarithmically with the number of reflections in
* the list.
*
* A RefList can contain any number of reflections, and can store more than
* one reflection with a given set of indices, for example when two distinct
* reflections are to be stored according to their asymmetric indices.
*
* There are getters and setters which can be used to get and set values for an
* individual reflection. The reflection list does not calculate any values,
* only stores what it was given earlier. As such, you will need to carefully
* examine which fields your prior processing steps have filled in.
*/
/**
* A RefList represents a list of Bragg reflections.
*
* This data structure is opaque. You must use the available accessor functions
* to read and write its contents.
*
**/
typedef struct _reflist RefList;
/**
* A Reflection represents a single Bragg reflection.
*
* This data structure is opaque. You must use the available accessor functions
* to read and write its contents.
*
**/
typedef struct _reflection Reflection;
/**
* A RefListIterator is an opaque data type used when iterating over a
* RefList.
*
**/
typedef struct _reflistiterator RefListIterator;
#include "crystal.h"
#ifdef __cplusplus
extern "C" {
#endif
/* Structure representing the contributions to a merged reflection */
struct reflection_contributions
{
int n_contrib;
int max_contrib;
Reflection **contribs;
Crystal **contrib_crystals;
};
extern RefList *reflist_new(void);
extern void reflist_free(RefList *list);
extern Reflection *reflection_new(signed int h, signed int k, signed int l);
extern void reflection_free(Reflection *refl);
/* Search */
extern Reflection *find_refl(const RefList *list, signed int h, signed int k, signed int l);
extern Reflection *next_found_refl(Reflection *refl);
/* Get */
extern void get_detector_pos(const Reflection *refl, double *fs, double *ss);
extern int get_panel_number(const Reflection *refl);
extern double get_partiality(const Reflection *refl);
extern double get_khalf(const Reflection *refl);
extern double get_kpred(const Reflection *refl);
extern double get_exerr(const Reflection *refl);
extern double get_lorentz(const Reflection *refl);
extern void get_indices(const Reflection *refl,
signed int *h, signed int *k, signed int *l);
extern void get_symmetric_indices(const Reflection *refl,
signed int *hs, signed int *ks,
signed int *ls);
extern double get_intensity(const Reflection *refl);
extern int get_redundancy(const Reflection *refl);
extern double get_temp1(const Reflection *refl);
extern double get_temp2(const Reflection *refl);
extern double get_esd_intensity(const Reflection *refl);
extern double get_phase(const Reflection *refl, int *have_phase);
extern double get_peak(const Reflection *refl);
extern double get_mean_bg(const Reflection *refl);
extern int get_flag(const Reflection *refl);
extern struct reflection_contributions *get_contributions(const Reflection *refl);
/* Set */
extern void copy_data(Reflection *to, const Reflection *from);
extern void set_detector_pos(Reflection *refl, double fs, double ss);
extern void set_panel_number(Reflection *refl, int pn);
extern void set_kpred(Reflection *refl, double kpred);
extern void set_khalf(Reflection *refl, double khalf);
extern void set_exerr(Reflection *refl, double exerr);
extern void set_partiality(Reflection *refl, double p);
extern void set_lorentz(Reflection *refl, double L);
extern void set_intensity(Reflection *refl, double intensity);
extern void set_redundancy(Reflection *refl, int red);
extern void set_temp1(Reflection *refl, double temp);
extern void set_temp2(Reflection *refl, double temp);
extern void set_esd_intensity(Reflection *refl, double esd);
extern void set_phase(Reflection *refl, double phase);
extern void set_peak(Reflection *refl, double peak);
extern void set_mean_bg(Reflection *refl, double mean_bg);
extern void set_symmetric_indices(Reflection *refl,
signed int hs, signed int ks, signed int ls);
extern void set_flag(Reflection *refl, int flag);
extern void set_contributions(Reflection *refl,
struct reflection_contributions *contribs);
/* Insertion */
extern Reflection *add_refl(RefList *list,
signed int h, signed int k, signed int l);
extern void add_refl_to_list(Reflection *refl, RefList *list);
/* Iteration */
extern Reflection *first_refl(RefList *list, RefListIterator **piter);
extern Reflection *next_refl(Reflection *refl, RefListIterator *iter);
extern const Reflection *first_refl_const(const RefList *list, RefListIterator **piter);
extern const Reflection *next_refl_const(const Reflection *refl, RefListIterator *iter);
/* Misc */
extern int num_reflections(RefList *list);
extern int tree_depth(RefList *list);
extern void lock_reflection(Reflection *refl);
extern void unlock_reflection(Reflection *refl);
extern const char *reflist_get_notes(RefList *reflist);
extern void reflist_add_notes(RefList *reflist, const char *notes_add);
#ifdef __cplusplus
}
#endif
#endif /* REFLIST_H */
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