aboutsummaryrefslogtreecommitdiff
path: root/src/mosflm.c
blob: 7b4253cbdda39263a4271c042ec19a0f174e5efe (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
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
/*
 * mosflm.c
 *
 * Invoke the DPS auto-indexing algorithm through MOSFLM
 *
 * (c) 2010 Richard Kirian <rkirian@asu.edu>
 * (c) 2006-2010 Thomas White <taw@physics.org>
 *
 * Part of CrystFEL - crystallography with a FEL
 *
 */

/* TODO:
 *
 * Properly read the newmat file (don't use fscanf-- spaces between numers
 *  are not guaranteed)
 *
 * "Success" is indicated by existence of NEWMAT file written by mosflm.
 *  Better to interact with mosflm directly in order to somehow verify success.
 *
 * Investigate how these keywords affect mosflms behavior:
 *
 *  MOSAICITY
 *  DISPERSION
 *  DIVERGENCE
 *  POLARISATION
 *  POSTREF BEAM
 *  POSTREF USEBEAM OFF
 *  PREREFINE ON
 *  EXTRA ON
 *  POSTREF ON
 *
 *  These did not seem to affect the results by my (Rick's) experience, probably
 *  because they are only used conjunction with image intensity data, but it's
 *  worth another look at the documentation.
 */

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


#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <unistd.h>
#include <assert.h>
#include <fcntl.h>
#include <errno.h>

#if HAVE_FORKPTY_LINUX
#include <pty.h>
#elif HAVE_FORKPTY_BSD
#include <util.h>
#endif


#include "image.h"
#include "mosflm.h"
#include "utils.h"
#include "sfac.h"
#include "peaks.h"


#define MOSFLM_VERBOSE 0


typedef enum {
	MOSFLM_INPUT_NONE,
	MOSFLM_INPUT_LINE,
	MOSFLM_INPUT_PROMPT
} MOSFLMInputType;


struct mosflm_data {

	/* MOSFLM auto-indexing low-level stuff */
	int                     pty;
	pid_t                   pid;
	char                    *rbuffer;
	int                     rbufpos;
	int                     rbuflen;

	/* MOSFLM high-level stuff */
	char                    newmatfile[128];
	char                    imagefile[128];
	char                    sptfile[128];
	int                     step;
	UnitCell                *target_cell;

};


static void mosflm_parseline(const char *line, struct image *image,
                             struct mosflm_data *dirax)
{
	#if MOSFLM_VERBOSE
	char *copy;
	int i;

	copy = strdup(line);
	for ( i=0; i<strlen(copy); i++ ) {
		if ( copy[i] == '\r' ) copy[i]='r';
		if ( copy[i] == '\n' ) copy[i]='\0';
	}
	STATUS("MOSFLM: %s\n", copy);
	free(copy);
	#endif
}


static int read_newmat(const char *filename, struct image *image)
{
	FILE * fh;
	float asx, asy, asz;
	float bsx, bsy, bsz;
	float csx, csy, csz;
	int n;
	double c;

	fh = fopen(filename, "r");
	if ( fh == NULL ) {
		STATUS("No NEWMAT file (autoindexing was unsuccessful).\n");
		return 1;
	}
	n  = fscanf(fh, "%f %f %f\n", &asx, &bsx, &csx);
	n += fscanf(fh, "%f %f %f\n", &asy, &bsy, &csy);
	n += fscanf(fh, "%f %f %f\n", &asz, &bsz, &csz);
	if ( n != 9 ) {
		STATUS("Fewer than 9 parameters found in NEWMAT file.\n");
		return 1;
	}
	fclose(fh);

	/* MOSFLM "A" matrix is multiplied by lambda, so fix this */
	c = 1/image->lambda;

	image->candidate_cells[0] = cell_new();

	cell_set_reciprocal(image->candidate_cells[0],
                            asz*c, asy*c, asx*c,
                            bsz*c, bsy*c, bsx*c,
                            csz*c, csy*c, csx*c);

        image->ncells = 1;

        return 0;
}


/* Need to sort mosflm peaks by intensity... */
struct sptline {
	double x; /* x coordinate of peak */
	double y; /* y coordinate of peak */
	double h; /* height of peak */
	double s; /* sigma of peak */
};


static int compare_vals(const void *ap, const void *bp)
{
	const struct sptline a = *(struct sptline *)ap;
	const struct sptline b = *(struct sptline *)bp;

	if ( a.h < b.h ) return 1;
	if ( a.h > b.h ) return -1;
	return 0;
}


/* Write .spt file for mosflm */
static void write_spt(struct image *image, const char *filename)
{
	FILE *fh;
	int i;
	double fclen=67.8;  /* fake camera length in mm */
	double fpix=0.075;  /* fake pixel size in mm */
	double pix;
	double height=100;
	double sigma=1;
	int nPeaks = image_feature_count(image->features);
	struct sptline *sptlines;

	fh = fopen(filename, "w");
	if ( !fh ) {
		ERROR("Couldn't open temporary file '%s'\n", filename);
		return;
	}

	fprintf(fh, "%10d %10d %10.8f %10.6f %10.6f\n", 1, 1, fpix, 1.0, 0.0);
	fprintf(fh, "%10d %10d\n", 1, 1);
	fprintf(fh, "%10.5f %10.5f\n", 0.0, 0.0);

	sptlines = malloc(sizeof(struct sptline)*nPeaks);

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

		struct imagefeature *f;

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

		struct panel *pan;
		pan = find_panel(image->det, f->x, f->y);
		if ( pan == NULL ) continue;

		pix = 1000/pan->res; /* pixel size in mm */
		height = f->intensity;

		sptlines[i].x = (f->y - pan->cy)*pix*fclen/pan->clen/1000;
		sptlines[i].y = -(f->x - pan->cx)*pix*fclen/pan->clen/1000;
		sptlines[i].h = height;
		sptlines[i].s = sigma;

	}

	qsort(sptlines, nPeaks, sizeof(struct sptline), compare_vals);

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

		fprintf(fh, "%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
		        sptlines[i].x, sptlines[i].y,
		        0.0, 0.0,
		        sptlines[i].h, sptlines[i].s);

	}

	free(sptlines);

	fprintf(fh,"%10.2f %10.2f %10.2f %10.2f %10.2f %10.2f\n",
	           -999.0,-999.0,-999.0,-999.0,-999.0,-999.0);
	fclose(fh);
}


/* Write a dummy 1x1 pixel image file for MOSFLM.  Without post refinement,
 * MOSFLM will ignore this, but it must be present. */
static void write_img(struct image *image, const char *filename)
{
	FILE *fh;
	unsigned short int *intimage;

	intimage = malloc(sizeof(unsigned short int));
	intimage[0] = 1;

	fh = fopen(filename, "w");
	if ( !fh ) {
		ERROR("Couldn't open temporary file '%s'\n", filename);
		return;
	}

	/* Write header */
	fprintf(fh, "{\nHEADER_BYTES=512;\n");
	fprintf(fh, "BYTE_ORDER=little_endian;\n");
	fprintf(fh, "TYPE=unsigned_short;\n");
	fprintf(fh, "DIM=2;\n");
	fprintf(fh, "SIZE1=1;\n");
	fprintf(fh, "SIZE2=1;\n");
	fprintf(fh, "}\n");

	/* Header padding */
	while ( ftell(fh) < 512 ) fprintf(fh," ");

	fwrite(intimage, sizeof(unsigned short int), 1, fh);
	free(intimage);
	fclose(fh);
}


static void mosflm_sendline(const char *line, struct mosflm_data *mosflm)
{
	#if MOSFLM_VERBOSE
	char *copy;
	int i;

	copy = strdup(line);
	for ( i=0; i<strlen(copy); i++ ) {
		if ( copy[i] == '\r' ) copy[i]='\0';
		if ( copy[i] == '\n' ) copy[i]='\0';
	}
	STATUS("To MOSFLM: '%s'\n", copy);
	free(copy);
	#endif

	write(mosflm->pty, line, strlen(line));
}


static void mosflm_send_next(struct image *image, struct mosflm_data *mosflm)
{
	char tmp[256];
	char symm[32];
	const char *sg;
	double wavelength;
	double a, b, c, alpha, beta, gamma;
	int i, j;

	switch ( mosflm->step ) {

	case 1 :
		mosflm_sendline("DETECTOR ROTATION HORIZONTAL"
		                " ANTICLOCKWISE ORIGIN LL FAST HORIZONTAL"
		                " RECTANGULAR\n", mosflm);
		break;

	case 2 :
		if ( mosflm->target_cell != NULL ) {
			cell_get_parameters(mosflm->target_cell, &a, &b, &c,
				            &alpha, &beta, &gamma);
			snprintf(tmp, 255,
			         "CELL %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f\n",
		                 a*1e10, b*1e10, c*1e10,
		                 rad2deg(alpha), rad2deg(beta), rad2deg(gamma));
			mosflm_sendline(tmp, mosflm);
		} else {
			mosflm_sendline("# Do nothing\n", mosflm);
		}
		break;

	case 3 :
		if ( mosflm->target_cell != NULL ) {
			sg = cell_get_spacegroup(mosflm->target_cell);
			/* Remove white space from space group */
			j = 0;
			for ( i=0; i<strlen(sg); i++ ) {
				if (sg[i] != ' ') {
					symm[j++] = sg[i];
				}
			}
			symm[j] = '\0';
			snprintf(tmp, 255, "SYMM %s\n", symm);
			mosflm_sendline(tmp, mosflm);
		} else {
			mosflm_sendline("SYMM P1\n", mosflm);
		}
		break;

	case 4 :
		mosflm_sendline("DISTANCE 67.8\n", mosflm);
		break;

	case 5 :
		mosflm_sendline("BEAM 0.0 0.0\n", mosflm);
		break;

	case 6 :
		wavelength = image->lambda*1e10;
		snprintf(tmp, 255, "WAVELENGTH %10.5f\n", wavelength);
		mosflm_sendline(tmp, mosflm);
		break;

	case 7 :
		snprintf(tmp, 255, "NEWMAT %s\n", mosflm->newmatfile);
		mosflm_sendline(tmp, mosflm);
		break;

	case 8 :
		snprintf(tmp, 255, "IMAGE %s phi 0 0\n", mosflm->imagefile);
		mosflm_sendline(tmp, mosflm);
		break;

	case 9 :
		snprintf(tmp, 255, "AUTOINDEX DPS FILE %s IMAGE 1\n",
		         mosflm->sptfile);
		mosflm_sendline(tmp, mosflm);
		break;

	case 10 :
		mosflm_sendline("GO\n", mosflm);
		break;

	default:
		mosflm_sendline("exit\n", mosflm);
		return;

	}

	mosflm->step++;
}


static int mosflm_readable(struct image *image, struct mosflm_data *mosflm)
{
	int rval;
	int no_string = 0;

	rval = read(mosflm->pty, mosflm->rbuffer+mosflm->rbufpos,
	            mosflm->rbuflen-mosflm->rbufpos);

	if ( (rval == -1) || (rval == 0) ) return 1;

	mosflm->rbufpos += rval;
	assert(mosflm->rbufpos <= mosflm->rbuflen);

	while ( (!no_string) && (mosflm->rbufpos > 0) ) {

		int i;
		int block_ready = 0;
		MOSFLMInputType type = MOSFLM_INPUT_NONE;

		/* See if there's a full line in the buffer yet */
		for ( i=0; i<mosflm->rbufpos-1; i++ ) {
			/* Means the last value looked at is rbufpos-2 */

			/* Is there a prompt in the buffer? */
			if ( (i+10 <= mosflm->rbufpos)
			  && (!strncmp(mosflm->rbuffer+i, "MOSFLM => ", 10)) ) {
				block_ready = 1;
				type = MOSFLM_INPUT_PROMPT;
				break;
			}

			if ( (mosflm->rbuffer[i] == '\r')
			  && (mosflm->rbuffer[i+1] == '\n') ) {
				block_ready = 1;
				type = MOSFLM_INPUT_LINE;
				break;
			}

		}

		if ( block_ready ) {

			unsigned int new_rbuflen;
			unsigned int endbit_length;
			char *block_buffer = NULL;

			switch ( type ) {

			case MOSFLM_INPUT_LINE :

				block_buffer = malloc(i+1);
				memcpy(block_buffer, mosflm->rbuffer, i);
				block_buffer[i] = '\0';

				if ( block_buffer[0] == '\r' ) {
					memmove(block_buffer, block_buffer+1, i);
				}

				mosflm_parseline(block_buffer, image, mosflm);
				free(block_buffer);
				endbit_length = i+2;
				break;

			case MOSFLM_INPUT_PROMPT :

				mosflm_send_next(image, mosflm);
				endbit_length = i+7;
				break;

			default :

				/* Obviously, this never happens :) */
				ERROR("Unrecognised MOSFLM input mode! "
				      "I don't know how to understand MOSFLM\n");
				return 1;

			}

			/* Now the block's been parsed, it should be
			 * forgotten about */
			memmove(mosflm->rbuffer,
			        mosflm->rbuffer + endbit_length,
			        mosflm->rbuflen - endbit_length);

			/* Subtract the number of bytes removed */
			mosflm->rbufpos = mosflm->rbufpos
			                       - endbit_length;
			new_rbuflen = mosflm->rbuflen - endbit_length;
			if ( new_rbuflen == 0 ) new_rbuflen = 256;
			mosflm->rbuffer = realloc(mosflm->rbuffer,
			                               new_rbuflen);
			mosflm->rbuflen = new_rbuflen;

		} else {

			if ( mosflm->rbufpos==mosflm->rbuflen ) {

				/* More buffer space is needed */
				mosflm->rbuffer = realloc(
				                    mosflm->rbuffer,
				                    mosflm->rbuflen + 256);
				mosflm->rbuflen = mosflm->rbuflen
				                                          + 256;
				/* The new space gets used at the next
				 * read, shortly... */

			}
			no_string = 1;

		}

	}

	return 0;
}


void run_mosflm(struct image *image, UnitCell *cell)
{
	int fail;
	struct mosflm_data *mosflm;
	unsigned int opts;
	int status;
	int rval;

	mosflm = malloc(sizeof(struct mosflm_data));
	if ( mosflm == NULL ) {
		ERROR("Couldn't allocate memory for MOSFLM data.\n");
		return;
	}

	mosflm->target_cell = cell;

	snprintf(mosflm->imagefile, 127, "xfel-%i_001.img", image->id);
	write_img(image, mosflm->imagefile); /* Dummy image */

	snprintf(mosflm->sptfile, 127, "xfel-%i_001.spt", image->id);
	write_spt(image, mosflm->sptfile);

	snprintf(mosflm->newmatfile, 127, "xfel-%i.newmat", image->id);

	mosflm->pid = forkpty(&mosflm->pty, NULL, NULL, NULL);
	if ( mosflm->pid == -1 ) {
		ERROR("Failed to fork for MOSFLM\n");
		return;
	}
	if ( mosflm->pid == 0 ) {

		/* Child process: invoke MOSFLM */
		struct termios t;

		/* Turn echo off */
		tcgetattr(STDIN_FILENO, &t);
		t.c_lflag &= ~(ECHO | ECHOE | ECHOK | ECHONL);
		tcsetattr(STDIN_FILENO, TCSANOW, &t);

		execlp("ipmosflm", "", (char *)NULL);
		ERROR("Failed to invoke MOSFLM.\n");
		_exit(0);

	}

	mosflm->rbuffer = malloc(256);
	mosflm->rbuflen = 256;
	mosflm->rbufpos = 0;

	/* Set non-blocking */
	opts = fcntl(mosflm->pty, F_GETFL);
	fcntl(mosflm->pty, F_SETFL, opts | O_NONBLOCK);

	mosflm->step = 1;	/* This starts the "initialisation" procedure */

	do {

		fd_set fds;
		struct timeval tv;
		int sval;

		FD_ZERO(&fds);
		FD_SET(mosflm->pty, &fds);

		tv.tv_sec = 10;
		tv.tv_usec = 0;

		sval = select(mosflm->pty+1, &fds, NULL, NULL, &tv);

		if ( sval == -1 ) {
			int err = errno;
			ERROR("select() failed: %s\n", strerror(err));
			rval = 1;
		} else if ( sval != 0 ) {
			rval = mosflm_readable(image, mosflm);
		} else {
			ERROR("No response from MOSFLM..\n");
			rval = 1;
		}

	} while ( !rval );

	close(mosflm->pty);
	free(mosflm->rbuffer);
	waitpid(mosflm->pid, &status, __WNOTHREAD);

	/* Read the mosflm NEWMAT file and set cell candidate *
	 * Existence of this file means possible success. Pretty shady. */
	fail = read_newmat(mosflm->newmatfile, image);
	if ( fail ) {
		ERROR("Failed to read MOSFLM's NEWMAT file.\n");
		return;
	}

	free(mosflm);
}