aboutsummaryrefslogtreecommitdiff
path: root/src/stream.c
blob: 54c31050a628fd649f064269db70e854c0052d7f (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
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
/*
 * stream.c
 *
 * Stream tools
 *
 * (c) 2006-2011 Thomas White <taw@physics.org>
 * (c) 2011 Rick Kirian <rkirian@asu.edu>
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */

#ifdef HAVE_CONFIG_H
#include <config.h>
#endif


#include <stdlib.h>
#include <stdio.h>
#include <string.h>

#include "cell.h"
#include "utils.h"
#include "image.h"
#include "stream.h"
#include "reflist.h"
#include "reflist-utils.h"


#define CHUNK_START_MARKER "----- Begin chunk -----"
#define CHUNK_END_MARKER "----- End chunk -----"
#define PEAK_LIST_START_MARKER "Peaks from peak search"
#define PEAK_LIST_END_MARKER "End of peak list"
#define REFLECTION_START_MARKER "Reflections measured after indexing"
/* REFLECTION_END_MARKER is over in reflist-utils.h because it is also
 * used to terminate a standalone list of reflections */

static void exclusive(const char *a, const char *b)
{
	ERROR("The stream options '%s' and '%s' are mutually exclusive.\n",
	      a, b);
}


int parse_stream_flags(const char *a)
{
	int n, i;
	int ret = STREAM_NONE;
	char **flags;

	n = assplode(a, ",", &flags, ASSPLODE_NONE);

	for ( i=0; i<n; i++ ) {

		if ( strcmp(flags[i], "pixels") == 0) {
			if ( ret & STREAM_INTEGRATED ) {
				exclusive("pixels", "integrated");
				return -1;
			}
			ret |= STREAM_PIXELS;

		} else if ( strcmp(flags[i], "integrated") == 0) {
			if ( ret & STREAM_PIXELS ) {
				exclusive("pixels", "integrated");
				return -1;
			}
			ret |= STREAM_INTEGRATED;

		} else if ( strcmp(flags[i], "peaks") == 0) {
			if ( ret & STREAM_PEAKS_IF_INDEXED ) {
				exclusive("peaks", "peaksifindexed");
				return -1;
			}
			if ( ret & STREAM_PEAKS_IF_NOT_INDEXED ) {
				exclusive("peaks", "peaksifnotindexed");
				return -1;
			}
			ret |= STREAM_PEAKS;

		} else if ( strcmp(flags[i], "peaksifindexed") == 0) {
			if ( ret & STREAM_PEAKS ) {
				exclusive("peaks", "peaksifindexed");
				return -1;
			}
			if ( ret & STREAM_PEAKS_IF_NOT_INDEXED ) {
				exclusive("peaksifnotindexed",
				          "peaksifindexed");
				return -1;
			}
			ret |= STREAM_PEAKS_IF_INDEXED;

		} else if ( strcmp(flags[i], "peaksifnotindexed") == 0) {
			if ( ret & STREAM_PEAKS ) {
				exclusive("peaks", "peaksifnotindexed");
				return -1;
			}
			if ( ret & STREAM_PEAKS_IF_INDEXED ) {
				exclusive("peaksifnotindexed",
				          "peaksifindexed");
				return -1;
			}
			ret |= STREAM_PEAKS_IF_NOT_INDEXED;

		} else {
			ERROR("Unrecognised stream flag '%s'\n", flags[i]);
			return -1;
		}

		free(flags[i]);

	}
	free(flags);

	return ret;
}


int count_patterns(FILE *fh)
{
	char *rval;

	int n_total_patterns = 0;
	do {
		char line[1024];

		rval = fgets(line, 1023, fh);
		if ( rval == NULL ) continue;
		chomp(line);
		if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_total_patterns++;

	} while ( rval != NULL );

	if ( ferror(fh) ) {
		ERROR("Read error while counting patterns.\n");
		return 0;
	}

	return n_total_patterns;
}


static int read_peaks(FILE *fh, struct image *image)
{
	char *rval = NULL;
	int first = 1;

	image->features = image_feature_list_new();

	do {

		char line[1024];
		float x, y, d, intensity;
		int r;

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

		if ( strcmp(line, PEAK_LIST_END_MARKER) == 0 ) return 0;

		r = sscanf(line, "%f %f %f %f", &x, &y, &d, &intensity);
		if ( (r != 4) && (!first) ) {
			ERROR("Failed to parse peak list line.\n");
			ERROR("The failed line was: '%s'\n", line);
			return 1;
		}

		first = 0;
		if ( r == 4 ) {
			image_add_feature(image->features, x, y,
			                  image, intensity, NULL);
		}

	} while ( rval != NULL );

	/* Got read error of some kind before finding PEAK_LIST_END_MARKER */
	return 1;
}


static void write_peaks(struct image *image, FILE *ofh)
{
	int i;

	fprintf(ofh, PEAK_LIST_START_MARKER"\n");
	fprintf(ofh, "  fs/px   ss/px  (1/d)/nm^-1   Intensity\n");

	for ( i=0; i<image_feature_count(image->features); i++ ) {

		struct imagefeature *f;
		struct rvec r;
		double q;

		f = image_get_feature(image->features, i);
		if ( f == NULL ) continue;

		r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
		q = modulus(r.u, r.v, r.w);

		fprintf(ofh, "%7.2f %7.2f   %10.2f  %10.2f\n",
		       f->fs, f->ss, q/1.0e9, f->intensity);

	}

	fprintf(ofh, PEAK_LIST_END_MARKER"\n");
}


void write_chunk(FILE *ofh, struct image *i, int f)
{
	double asx, asy, asz;
	double bsx, bsy, bsz;
	double csx, csy, csz;
	double a, b, c, al, be, ga;

	fprintf(ofh, CHUNK_START_MARKER"\n");

	fprintf(ofh, "Image filename: %s\n", i->filename);

	if ( i->indexed_cell != NULL ) {

		cell_get_parameters(i->indexed_cell, &a, &b, &c,
		                                         &al, &be, &ga);
		fprintf(ofh, "Cell parameters %7.5f %7.5f %7.5f nm,"
			     " %7.5f %7.5f %7.5f deg\n",
			     a*1.0e9, b*1.0e9, c*1.0e9,
			     rad2deg(al), rad2deg(be), rad2deg(ga));

		cell_get_reciprocal(i->indexed_cell, &asx, &asy, &asz,
			                  &bsx, &bsy, &bsz,
			                  &csx, &csy, &csz);
		fprintf(ofh, "astar = %+9.7f %+9.7f %+9.7f nm^-1\n",
			asx/1e9, asy/1e9, asz/1e9);
		fprintf(ofh, "bstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
			bsx/1e9, bsy/1e9, bsz/1e9);
		fprintf(ofh, "cstar = %+9.7f %+9.7f %+9.7f nm^-1\n",
		        csx/1e9, csy/1e9, csz/1e9);

	} else {

		fprintf(ofh, "No unit cell from indexing.\n");

	}

	if ( i->i0_available ) {
		fprintf(ofh, "I0 = %7.5f (arbitrary units)\n", i->i0);
	} else {
		fprintf(ofh, "I0 = invalid\n");
	}

	fprintf(ofh, "photon_energy_eV = %f\n",
	        J_to_eV(ph_lambda_to_en(i->lambda)));

	//FIXME:we're writing camera length from first panel only.
	//this should actually write camera length for all panels.
	fprintf(ofh, "camera_length = %f\n",i->det->panels[0].clen);

	if ( (f & STREAM_PEAKS)
	  || ((f & STREAM_PEAKS_IF_INDEXED) && (i->indexed_cell != NULL))
	  || ((f & STREAM_PEAKS_IF_NOT_INDEXED) && (i->indexed_cell == NULL)) )
	{
		fprintf(ofh, "\n");
		write_peaks(i, ofh);
	}

	if ( (f & STREAM_PIXELS) || (f & STREAM_INTEGRATED) ) {

		if ( i->reflections != NULL ) {

			fprintf(ofh, "\n");
			fprintf(ofh, REFLECTION_START_MARKER"\n");
			write_reflections_to_file(ofh, i->reflections,
			                               i->indexed_cell);
			fprintf(ofh, REFLECTION_END_MARKER"\n");

		}
	}

	fprintf(ofh, CHUNK_END_MARKER"\n\n");
}


static int find_start_of_chunk(FILE *fh)
{
	char *rval = NULL;
	char line[1024];

	do {

		rval = fgets(line, 1023, fh);

		/* Trouble? */
		if ( rval == NULL ) return 1;

		chomp(line);

	} while ( strcmp(line, CHUNK_START_MARKER) != 0 );

	return 0;
}


/* Read the next chunk from a stream and fill in 'image' */
int read_chunk(FILE *fh, struct image *image)
{
	char line[1024];
	char *rval = NULL;
	struct rvec as, bs, cs;
	int have_as = 0;
	int have_bs = 0;
	int have_cs = 0;
	int have_filename = 0;
	int have_cell = 0;
	int have_ev = 0;

	if ( find_start_of_chunk(fh) ) return 1;

	image->i0_available = 0;
	image->i0 = 1.0;
	image->lambda = -1.0;
	image->features = NULL;
	image->reflections = NULL;
	image->indexed_cell = NULL;

	do {

		float u, v, w;

		rval = fgets(line, 1023, fh);

		/* Trouble? */
		if ( rval == NULL ) break;

		chomp(line);

		if ( strncmp(line, "Image filename: ", 16) == 0 ) {
			image->filename = strdup(line+16);
			have_filename = 1;
		}

		if ( strncmp(line, "camera_length = ",16) == 0 ) {
			//FIXME: assuming here that we have loaded detector
			//geometry into image prior to calling this routine.
			//otherise, we don't know how many panels there are!
			if ( !( image->det == NULL ) ) {
				int k;
				double clen;
				clen = atof( line+16 );
				for ( k=0; k< image->det->n_panels; k++ ) {
					image->det->panels[k].clen = clen;
				}
			}
		}

		if ( strncmp(line, "I0 = ", 5) == 0 ) {
			image->i0 = atof(line+5);
			image->i0_available = 1;
		}

		if ( sscanf(line, "astar = %f %f %f", &u, &v, &w) == 3 ) {
			as.u = u*1e9;  as.v = v*1e9;  as.w = w*1e9;
			have_as = 1;
		}

		if ( sscanf(line, "bstar = %f %f %f", &u, &v, &w) == 3 ) {
			bs.u = u*1e9;  bs.v = v*1e9;  bs.w = w*1e9;
			have_bs = 1;
		}

		if ( sscanf(line, "cstar = %f %f %f", &u, &v, &w) == 3 ) {
			cs.u = u*1e9;  cs.v = v*1e9;  cs.w = w*1e9;
			have_cs = 1;
		}

		if ( have_as && have_bs && have_cs ) {
			if ( image->indexed_cell != NULL ) {
				ERROR("Duplicate cell found in stream!\n");
				cell_free(image->indexed_cell);
			}
			image->indexed_cell = cell_new_from_reciprocal_axes(as,
			                                                    bs,
			                                                    cs);
			have_cell = 1;
			have_as = 0;  have_bs = 0;  have_cs = 0;
		}

		if ( strncmp(line, "photon_energy_eV = ", 19) == 0 ) {
			image->lambda = ph_en_to_lambda(eV_to_J(atof(line+19)));
			have_ev = 1;
		}

		if ( strcmp(line, PEAK_LIST_START_MARKER) == 0 ) {
			if ( read_peaks(fh, image) ) {
				ERROR("Failed while reading peaks\n");
				return 1;
			}
		}

		if ( strcmp(line, REFLECTION_START_MARKER) == 0 ) {
			image->reflections = read_reflections_from_file(fh);
			if ( image->reflections == NULL ) {
				ERROR("Failed while reading reflections\n");
				return 1;
			}
		}

		if ( strcmp(line, CHUNK_END_MARKER) == 0 ) {
			if ( have_filename && have_ev ) return 0;
			ERROR("Incomplete chunk found in input file.\n");
			return 1;
		}

	} while ( 1 );

	return 1;  /* Either error or EOF, don't care because we will complain
	            * on the terminal if it was an error. */
}


void write_stream_header(FILE *ofh, int argc, char *argv[])
{
	int i;

	fprintf(ofh, "CrystFEL stream format 2.0\n");
	fprintf(ofh, "Command line:");
	for ( i=0; i<argc; i++ ) {
		fprintf(ofh, " %s", argv[i]);
	}
	fprintf(ofh, "\n");
	fflush(ofh);
}


int skip_some_files(FILE *fh, int n)
{
	char *rval = NULL;
	int n_patterns = 0;

	do {

		char line[1024];

		if ( n_patterns == n ) return 0;

		rval = fgets(line, 1023, fh);
		if ( rval == NULL ) continue;
		if ( strcmp(line, CHUNK_END_MARKER) == 0 ) n_patterns++;

	} while ( rval != NULL );

	return 1;
}

int is_stream(const char *filename) {
	FILE *fh;
	char line[1024];
	char *rval = NULL;
	fh = fopen(filename, "r");
	rval = fgets(line, 1023, fh);
	fclose(fh);
	if ( rval == NULL ) {
		return -1;
	}
	if ( strncmp(line, "CrystFEL stream format 2.0", 26) == 0 ) {
		return 1;
	}
	else {
		return 0;
	}
	return -1;
}