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
|
/*
* rejection.c
*
* Crystal rejection for scaling
*
* Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2015 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/>.
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <assert.h>
#include "crystal.h"
#include "reflist.h"
#include "rejection.h"
static double mean_intensity(RefList *list)
{
Reflection *refl;
RefListIterator *iter;
double total = 0.0;
int n = 0;
for ( refl = first_refl(list, &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
total += get_intensity(refl);
n++;
}
return total/n;
}
/* Reject really obvious outliers */
void early_rejection(Crystal **crystals, int n)
{
int i;
double m = 0.0;
double mean_m;
FILE *fh = fopen("reject.dat", "w");
int n_flag = 0;
for ( i=0; i<n; i++ ) {
double u;
RefList *list = crystal_get_reflections(crystals[i]);
u = mean_intensity(list);
m += u;
fprintf(fh, "%i %f\n", i, u);
}
mean_m = m/n;
for ( i=0; i<n; i++ ) {
double u;
RefList *list = crystal_get_reflections(crystals[i]);
u = mean_intensity(list);
if ( u/mean_m < 0.2 ) {
crystal_set_user_flag(crystals[i], 5);
n_flag++;
}
}
fclose(fh);
STATUS("Mean intensity/peak = %f ADU\n", m/n);
STATUS("%i crystals flagged\n", n_flag);
check_rejection(crystals, n);
}
void check_rejection(Crystal **crystals, int n)
{
int i;
int n_acc = 0;
for ( i=0; i<n; i++ ) {
if ( crystal_get_user_flag(crystals[i]) == 0 ) {
n_acc++;
if ( n_acc >= 2 ) break;
}
}
if ( n_acc < 2 ) {
ERROR("Not enough crystals left to proceed (%i). Sorry.\n",
n_acc);
exit(1);
}
}
|
