1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
|
/*
* integration.h
*
* Integration of intensities
*
* Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2014 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
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "geometry.h"
/**
* IntDiag:
* @INTDIAG_NONE: Never show diagnostics
* @INTDIAG_RANDOM: Show diagnostics for a randomly selected 1% of reflections
* @INTDIAG_ALL: Show diagnostics for all reflections
* @INTDIAG_INDICES: Show diagnostics when the Miller indices of the reflection
* are the ones specified
* @INTDIAG_NEGATIVE: Show diagnostics when the measured intensity is less than
* minus three times its estimated error.
* @INTDIAG_IMPLAUSIBLE: Show diagnostics when the measured intensity is les
* than minus five times its estimated error.
* @INTDIAG_STRONG: Show diagnostics when the measured intensity is more than
* three times its estimated error.
*
* An %IntDiag describes the condition under which the integration subsystem
* should display diagnostic information to the user.
**/
typedef enum {
INTDIAG_NONE,
INTDIAG_RANDOM,
INTDIAG_ALL,
INTDIAG_INDICES,
INTDIAG_NEGATIVE,
INTDIAG_IMPLAUSIBLE,
INTDIAG_STRONG
} IntDiag;
#define INTEGRATION_DEFAULTS_RINGS (INTEGRATION_RINGS)
#define INTEGRATION_DEFAULTS_PROF2D (INTEGRATION_PROF2D | INTEGRATION_CENTER)
/**
* IntegrationMethod:
* @INTEGRATION_NONE: No integration at all
* @INTEGRATION_RINGS: Summation of pixel values inside ring, minus background
* @INTEGRATION_PROF2D: Two dimensional profile fitting
* @INTEGRATION_SATURATED: Integrate saturated reflections
* @INTEGRATION_CENTER: Center the peak in the box prior to integration
* @INTEGRATION_RESCUT: Stop integrating at the diffraction limit of the crystal
*
* An enumeration of all the available integration methods.
**/
typedef enum {
INTEGRATION_NONE = 0,
/* The core integration methods themselves */
INTEGRATION_RINGS = 1,
INTEGRATION_PROF2D = 2,
/* Bits at the top of the IntegrationMethod are flags which modify the
* behaviour of the integration. */
INTEGRATION_SATURATED = 256,
INTEGRATION_CENTER = 512,
INTEGRATION_RESCUT = 1024,
} IntegrationMethod;
/* This defines the bits in "IntegrationMethod" which are used to represent the
* core of the integration method */
#define INTEGRATION_METHOD_MASK (0xff)
#ifdef __cplusplus
extern "C" {
#endif
extern IntegrationMethod integration_method(const char *t, int *err);
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,
int results_pipe);
#ifdef __cplusplus
}
#endif
#endif /* INTEGRATION_H */
|
