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
138
139
140
141
142
143
144
145
146
147
148
149
150
151
|
/*
* detector.c
*
* Detector properties
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include "image.h"
#include "utils.h"
#include "diffraction.h"
#include "detector.h"
#include "parameters-lcls.tmp"
/* x,y in pixels relative to image origin */
int map_position(struct image *image, double dx, double dy,
double *rx, double *ry, double *rz)
{
double d;
double twotheta, psi;
const double k = 1.0 / image->lambda;
struct panel *p;
double x = 0.0;
double y = 0.0;
p = find_panel(&image->det, dx, dy);
if ( p == NULL ) return 1;
x = ((double)dx - p->cx);
y = ((double)dy - p->cy);
/* Convert pixels to metres */
x /= p->res;
y /= p->res; /* Convert pixels to metres */
d = sqrt((x*x) + (y*y));
twotheta = atan2(d, p->clen);
psi = atan2(y, x);
*rx = k*sin(twotheta)*cos(psi);
*ry = k*sin(twotheta)*sin(psi);
*rz = k - k*cos(twotheta);
return 0;
}
void record_image(struct image *image, int do_poisson)
{
int x, y;
double total_energy, energy_density;
double ph_per_e;
double area;
/* How many photons are scattered per electron? */
area = M_PI*pow(BEAM_RADIUS, 2.0);
total_energy = FLUENCE * ph_lambda_to_en(image->lambda);
energy_density = total_energy / area;
ph_per_e = (FLUENCE/area) * pow(THOMSON_LENGTH, 2.0);
STATUS("Fluence = %8.2e photons, "
"Energy density = %5.3f kJ/cm^2, "
"Total energy = %5.3f microJ\n",
FLUENCE, energy_density/1e7, total_energy*1e6);
for ( x=0; x<image->width; x++ ) {
for ( y=0; y<image->height; y++ ) {
double counts;
double cf;
double intensity, sa;
double pix_area, Lsq;
double dsq, proj_area;
struct panel *p;
intensity = (double)image->data[x + image->width*y];
if ( isinf(intensity) ) {
ERROR("Infinity at %i,%i\n", x, y);
}
if ( intensity < 0.0 ) {
ERROR("Negative at %i,%i\n", x, y);
}
if ( isnan(intensity) ) {
ERROR("NaN at %i,%i\n", x, y);
}
p = find_panel(&image->det, x, y);
/* Area of one pixel */
pix_area = pow(1.0/p->res, 2.0);
Lsq = pow(p->clen, 2.0);
/* Area of pixel as seen from crystal (approximate) */
proj_area = pix_area * cos(image->twotheta[x + image->width*y]);
/* Calculate distance from crystal to pixel */
dsq = pow(((double)x - p->cx) / p->res, 2.0);
dsq += pow(((double)y - p->cy) / p->res, 2.0);
/* Projected area of pixel divided by distance squared */
sa = proj_area / (dsq + Lsq);
if ( do_poisson ) {
counts = poisson_noise(intensity * ph_per_e * sa * DQE);
} else {
cf = intensity * ph_per_e * sa * DQE;
counts = rint(cf);
}
image->data[x + image->width*y] = counts * DETECTOR_GAIN;
if ( isinf(image->data[x+image->width*y]) ) {
ERROR("Processed infinity at %i,%i\n", x, y);
}
if ( isnan(image->data[x+image->width*y]) ) {
ERROR("Processed NaN at %i,%i\n", x, y);
}
if ( image->data[x+image->width*y] < 0.0 ) {
ERROR("Processed negative at %i,%i %f\n", x, y, counts);
}
}
progress_bar(x, image->width-1, "Post-processing");
}
}
struct panel *find_panel(struct detector *det, int x, int y)
{
int p;
for ( p=0; p<det->n_panels; p++ ) {
if ( (x >= det->panels[p].min_x)
&& (x <= det->panels[p].max_x)
&& (y >= det->panels[p].min_y)
&& (y <= det->panels[p].max_y) ) {
return &det->panels[p];
}
}
ERROR("No mapping found for %i,%i\n", x, y);
return NULL;
}
|
