aboutsummaryrefslogtreecommitdiff
path: root/src/detector.c
blob: 97e6220232d3f6a699f0c7432b6307d9accc8437 (plain)
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
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
/*
 * 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;
	double max_tt = 0.0;

	/* 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 = 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);
		}

		if ( image->twotheta[x + image->width*y] > max_tt ) {
			max_tt = image->twotheta[x + image->width*y];
		}

	}
	progress_bar(x, image->width-1, "Post-processing");
	}

	STATUS("Max 2theta = %.2f deg, min d = %.2f nm\n",
	        rad2deg(max_tt), (image->lambda/(2.0*sin(max_tt/2.0)))/1e-9);

	double tt_side = image->twotheta[512+image->width*0];
	STATUS("At 512,0: %.2f deg, min d = %.2f nm\n",
	        rad2deg(tt_side), (image->lambda/(2.0*sin(tt_side/2.0)))/1e-9);

	tt_side = image->twotheta[0+image->width*512];
	STATUS("At 0,512: %.2f deg, min d = %.2f nm\n",
	        rad2deg(tt_side), (image->lambda/(2.0*sin(tt_side/2.0)))/1e-9);

	STATUS("Halve the d values to get the voxel size for a synthesis.\n");
}


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;
}


struct detector *get_detector_geometry(const char *filename)
{
	FILE *fh;
	struct detector *det;
	char *rval;
	char **bits;
	int i;

	fh = fopen(filename, "r");
	if ( fh == NULL ) return NULL;

	det = malloc(sizeof(struct detector));
	if ( det == NULL ) {
		fclose(fh);
		return NULL;
	}
	det->n_panels = -1;

	do {

		int n1, n2;
		char **path;
		char line[1024];
		int np;

		rval = fgets(line, 1023, fh);
		if ( rval == NULL ) break;
		chomp(line);

		n1 = assplode(line, " \t", &bits, ASSPLODE_NONE);
		if ( n1 < 3 ) {
			for ( i=0; i<n1; i++ ) free(bits[i]);
			free(bits);
			continue;
		}

		if ( bits[1][0] != '=' ) {
			for ( i=0; i<n1; i++ ) free(bits[i]);
			free(bits);
			continue;
		}

		if ( strcmp(bits[0], "n_panels") == 0 ) {
			if ( det->n_panels != -1 ) {
				ERROR("Duplicate n_panels statement.\n");
				fclose(fh);
				free(det);
				for ( i=0; i<n1; i++ ) free(bits[i]);
				free(bits);
				return NULL;
			}
			det->n_panels = atoi(bits[2]);
			det->panels = malloc(det->n_panels
			                      * sizeof(struct panel));
			for ( i=0; i<n1; i++ ) free(bits[i]);
			free(bits);
			continue;
		}

		n2 = assplode(bits[0], "/\\.", &path, ASSPLODE_NONE);

		np = atoi(path[0]);

		if ( strcmp(path[1], "min_x") == 0 ) {
			det->panels[np].min_x = atof(bits[2]);
		} else if ( strcmp(path[1], "max_x") == 0 ) {
			det->panels[np].max_x = atof(bits[2]);
		} else if ( strcmp(path[1], "min_y") == 0 ) {
			det->panels[np].min_y = atof(bits[2]);
		} else if ( strcmp(path[1], "max_y") == 0 ) {
			det->panels[np].max_y = atof(bits[2]);
		} else if ( strcmp(path[1], "cx") == 0 ) {
			det->panels[np].cx = atof(bits[2]);
		} else if ( strcmp(path[1], "cy") == 0 ) {
			det->panels[np].cy = atof(bits[2]);
		} else if ( strcmp(path[1], "clen") == 0 ) {
			det->panels[np].clen = atof(bits[2]);
		} else if ( strcmp(path[1], "res") == 0 ) {
			det->panels[np].res = atof(bits[2]);
		} else if ( strcmp(path[1], "badrow_direction") == 0 ) {
			det->panels[np].badrow = bits[2][0];
			if ( (det->panels[np].badrow != 'x')
			  && (det->panels[np].badrow != 'y') ) {
				ERROR("badrow_direction must be 'x' or 'y'\n");
				ERROR("Assuming 'x'\n.");
				det->panels[np].badrow = 'x';
			}
		} else {
			ERROR("Unrecognised field '%s'\n", path[1]);
		}

		for ( i=0; i<n1; i++ ) free(bits[i]);
		for ( i=0; i<n2; i++ ) free(path[i]);
		free(bits);
		free(path);

	} while ( rval != NULL );

	if ( det->n_panels == -1 ) {
		ERROR("No panel descriptions in geometry file.\n");
		fclose(fh);
		free(det->panels);
		free(det);
		return NULL;
	}

	for ( i=0; i<det->n_panels; i++ ) {
		STATUS("Panel %i, min_x = %i\n", i, det->panels[i].min_x);
		STATUS("Panel %i, max_x = %i\n", i, det->panels[i].max_x);
		STATUS("Panel %i, min_y = %i\n", i, det->panels[i].min_y);
		STATUS("Panel %i, max_y = %i\n", i, det->panels[i].max_y);
		STATUS("Panel %i, cx = %f\n", i, det->panels[i].cx);
		STATUS("Panel %i, cy = %f\n", i, det->panels[i].cy);
		STATUS("Panel %i, clen = %f\n", i, det->panels[i].clen);
		STATUS("Panel %i, res = %f\n", i, det->panels[i].res);
	}

	fclose(fh);

	return det;
}