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/*
* integration.h
*
* Integration of intensities
*
* Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2020 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 INTEGRATION_H
#define INTEGRATION_H
#include "geometry.h"
/**
* \file integration.h
* Integration of reflections
*/
/**
* An IntDiag describes the condition under which the integration subsystem
* should display diagnostic information to the user.
**/
typedef enum {
/** Never show diagnostics */
INTDIAG_NONE,
/** Show diagnostics for a randomly selected 1% of reflections */
INTDIAG_RANDOM,
/** Show diagnostics for all reflections */
INTDIAG_ALL,
/** Show diagnostics when the Miller indices of the reflection are the
* ones specified */
INTDIAG_INDICES,
/** Show diagnostics when the measured intensity is less than minus
* three times its estimated error. */
INTDIAG_NEGATIVE,
/** Show diagnostics when the measured intensity is less than minus five
* times its estimated error. */
INTDIAG_IMPLAUSIBLE,
/** Show diagnostics when the measured intensity is more than three
* times its estimated error. */
INTDIAG_STRONG
} IntDiag;
#define INTEGRATION_DEFAULTS_RINGS (INTEGRATION_RINGS)
#define INTEGRATION_DEFAULTS_PROF2D (INTEGRATION_PROF2D | INTEGRATION_CENTER)
/**
* An enumeration of all the available integration methods. The first items
* are the actual integration methods. The later ones are flags which can be
* ORed with the method to affect its behaviour.
*/
typedef enum {
/** No integration at all */
INTEGRATION_NONE = 0,
/** Summation of pixel values inside ring, minus background */
INTEGRATION_RINGS = 1,
/** Two dimensional profile fitting */
INTEGRATION_PROF2D = 2,
/** Integrate saturated reflections */
INTEGRATION_SATURATED = 256,
/** Center the peak in the box prior to integration */
INTEGRATION_CENTER = 512,
/* 1024 was INTEGRATION_RESCUT, which is no longer used */
/** Fit a gradient to the background */
INTEGRATION_GRADIENTBG = 2048,
} IntegrationMethod;
/** This defines the bits in \ref IntegrationMethod which are used to represent the
* core of the integration method. */
#define INTEGRATION_METHOD_MASK (0xff)
#ifdef __cplusplus
extern "C" {
#endif
struct intcontext;
extern IntegrationMethod integration_method(const char *t, int *err);
extern char *str_integration_method(IntegrationMethod m);
extern struct intcontext *intcontext_new(struct image *image,
UnitCell *cell,
IntegrationMethod meth,
int ir_inn, int ir_mid, int ir_out,
int **masks);
extern int integrate_rings_once(Reflection *refl,
struct intcontext *ic,
pthread_mutex_t *term_lock);
extern void intcontext_free(struct intcontext *ic);
extern void integrate_all(struct image *image, IntegrationMethod meth,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl);
extern void integrate_all_2(struct image *image, IntegrationMethod meth,
double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl);
extern void integrate_all_3(struct image *image, IntegrationMethod meth,
PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl);
extern void integrate_all_4(struct image *image, IntegrationMethod meth,
PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
pthread_mutex_t *term_lock);
extern void integrate_all_5(struct image *image, IntegrationMethod meth,
PartialityModel pmodel, double push_res,
double ir_inn, double ir_mid, double ir_out,
IntDiag int_diag,
signed int idh, signed int idk, signed int idl,
pthread_mutex_t *term_lock, int overpredict);
#ifdef __cplusplus
}
#endif
#endif /* INTEGRATION_H */
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