aboutsummaryrefslogtreecommitdiff
path: root/libcrystfel/src/utils.c
blob: af0abedc3d3d4fb8de0d13affcb2053f99115ff3 (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
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
/*
 * utils.c
 *
 * Utility stuff
 *
 * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
 *                       a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2009-2014 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 <libgen.h>
#include <math.h>
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_eigen.h>

#include "utils.h"
#include "image.h"


/**
 * SECTION:utils
 * @short_description: Miscellaneous utilities
 * @title: Utilities
 * @section_id:
 * @see_also:
 * @include: "utils.h"
 * @Image:
 *
 * Wibble
 */

/**
 * show_matrix_eqn:
 * @M: A matrix
 * @v: A vector
 *
 * Displays a matrix equation of the form @M.a = @v.
 **/
void show_matrix_eqn(gsl_matrix *M, gsl_vector *v)
{
	int i, j;

	if ( M->size1 != v->size ) {
		ERROR("Matrix and vector sizes don't agree.\n");
		return;
	}

	for ( i=0; i<M->size1; i++ ) {
		STATUS("[ ");
		for ( j=0; j<M->size2; j++ ) {
			STATUS("%+9.3e ", gsl_matrix_get(M, i, j));
		}
		if ( i < M->size2 ) {
			STATUS("][ a%2i ] = [ %+9.3e ]\n", i,
			       gsl_vector_get(v, i));
		} else {
			STATUS("]        = [ +%9.3e ]\n", gsl_vector_get(v, i));
		}
	}
}


/**
 * show_matrix:
 * @M: A matrix
 *
 * Displays a matrix.
 **/
void show_matrix(gsl_matrix *M)
{
	int i, j;

	for ( i=0; i<M->size1; i++ ) {
		STATUS("[ ");
		for ( j=0; j<M->size2; j++ ) {
			STATUS("%+9.3e ", gsl_matrix_get(M, i, j));
		}
		STATUS("]\n");
	}
}


static int check_eigen(gsl_vector *e_val, int verbose)
{
	int i;
	double vmax, vmin;
	const int n = e_val->size;
	const double max_condition = 1e6;
	int n_filt = 0;

	if ( verbose ) STATUS("Eigenvalues:\n");
	vmin = +INFINITY;
	vmax = 0.0;
	for ( i=0; i<n; i++ ) {
		double val = gsl_vector_get(e_val, i);
		if ( verbose ) STATUS("%i: %e\n", i, val);
		if ( val > vmax ) vmax = val;
		if ( val < vmin ) vmin = val;
	}

	for ( i=0; i<n; i++ ) {
		double val = gsl_vector_get(e_val, i);
		if ( val < vmax/max_condition ) {
			gsl_vector_set(e_val, i, 0.0);
			n_filt++;
		}
	}

	vmin = +INFINITY;
	vmax = 0.0;
	for ( i=0; i<n; i++ ) {
		double val = gsl_vector_get(e_val, i);
		if ( val == 0.0 ) continue;
		if ( val > vmax ) vmax = val;
		if ( val < vmin ) vmin = val;
	}
	if ( verbose ) {
		STATUS("Condition number: %e / %e = %5.2f\n",
		       vmax, vmin, vmax/vmin);
		STATUS("%i out of %i eigenvalues filtered.\n", n_filt, n);
	}

	return n_filt;
}


/**
 * solve_svd:
 * v: a gsl_vector
 * M: a gsl_matrix
 * n_filt: pointer to store the number of filtered eigenvalues
 * verbose: flag for verbosity on the terminal
 *
 * Solves the matrix equation M.x = v, returning x.
 * Performs rescaling and eigenvalue filtering.
 **/
gsl_vector *solve_svd(gsl_vector *v, gsl_matrix *M, int *pn_filt, int verbose)
{
	gsl_matrix *s_vec;
	gsl_vector *s_val;
	int err, n;
	gsl_vector *shifts;
	gsl_vector *SB;
	gsl_vector *SinvX;
	gsl_matrix *S;  /* rescaling matrix due to Bricogne */
	gsl_matrix *AS;
	gsl_matrix *SAS;
	int i;
	int n_filt;
	gsl_matrix *SAS_copy;

	n = v->size;
	if ( v->size != M->size1 ) return NULL;
	if ( v->size != M->size2 ) return NULL;

	/* Calculate the rescaling matrix S */
	S = gsl_matrix_calloc(n, n);
	for ( i=0; i<n; i++ ) {
		double sii = pow(gsl_matrix_get(M, i, i), -0.5);
		gsl_matrix_set(S, i, i, sii);
	}

	/* Calculate the matrix SAS, which we will be (not) inverting */
	AS = gsl_matrix_calloc(n, n);
	SAS = gsl_matrix_calloc(n, n);
	gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, M, S, 0.0, AS);
	gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, S, AS, 0.0, SAS);
	gsl_matrix_free(AS);

	/* Calculate the vector SB, which is the RHS of the equation */
	SB = gsl_vector_calloc(n);
	gsl_blas_dgemv(CblasNoTrans, 1.0, S, v, 0.0, SB);

	if ( verbose ) {
		STATUS("The equation after rescaling:\n");
		show_matrix_eqn(SAS, SB);
	}

	SAS_copy = gsl_matrix_alloc(SAS->size1, SAS->size2);
	gsl_matrix_memcpy(SAS_copy, SAS);

	for ( i=0; i<n; i++ ) {
		int j;
		if ( isnan(gsl_vector_get(SB, i)) ) gsl_vector_set(SB, i, 0.0);
		for ( j=0; j<n; j++ ) {
			if ( isnan(gsl_matrix_get(SAS, i, j)) ) {
					gsl_matrix_set(SAS, i, j, 0.0);
			}
		}
	}

	/* Do the SVD */
	s_val = gsl_vector_calloc(n);
	s_vec = gsl_matrix_calloc(n, n);
	err = gsl_linalg_SV_decomp_jacobi(SAS, s_vec, s_val);
	if ( err ) {
		if ( verbose ) ERROR("SVD failed: %s\n", gsl_strerror(err));
		gsl_matrix_free(s_vec);
		gsl_vector_free(s_val);
		gsl_matrix_free(SAS);
		gsl_matrix_free(S);
		return NULL;
	}
	/* "SAS" is now "U" */

	/* Filter the eigenvalues */
	n_filt = check_eigen(s_val, verbose);
	if ( pn_filt != NULL ) *pn_filt = n_filt;

	gsl_matrix_free(SAS_copy);

	/* Solve the equation SAS.SinvX = SB */
	SinvX = gsl_vector_calloc(n);
	err = gsl_linalg_SV_solve(SAS, s_vec, s_val, SB, SinvX);
	gsl_vector_free(SB);
	gsl_matrix_free(SAS);
	gsl_matrix_free(s_vec);
	gsl_vector_free(s_val);

	if ( err ) {
		ERROR("Matrix solution failed: %s\n", gsl_strerror(err));
		gsl_matrix_free(S);
		gsl_vector_free(SinvX);
		return NULL;
	}

	/* Calculate S.SinvX to get X, the shifts */
	shifts = gsl_vector_calloc(n);
	gsl_blas_dgemv(CblasNoTrans, 1.0, S, SinvX, 0.0, shifts);

	gsl_matrix_free(S);
	gsl_vector_free(SinvX);

	return shifts;
}


size_t notrail(char *s)
{
	ssize_t i;
	size_t munched = 0;

	for ( i=strlen(s)-1; i>=0; i-- ) {
		if ( (s[i] == ' ') || (s[i] == '\t') ) {
			s[i] = '\0';
			munched++;
		} else {
			return munched;
		}
	}

	return munched;
}


void chomp(char *s)
{
	size_t i;

	if ( !s ) return;

	for ( i=0; i<strlen(s); i++ ) {
		if ( (s[i] == '\n') || (s[i] == '\r') ) {
			s[i] = '\0';
			return;
		}
	}
}


void progress_bar(int val, int total, const char *text)
{
	double frac;
	int n, i;
	char s[1024];
	const int width = 50;

	if ( total == 0 ) return;

	if ( !isatty(STDERR_FILENO) ) return;
	if ( tcgetpgrp(STDERR_FILENO) != getpgrp() ) return;

	frac = (double)val/total;
	n = (int)(frac*width);

	for ( i=0; i<n; i++ ) s[i] = '=';
	for ( i=n; i<width; i++ ) s[i] = '.';
	s[width] = '\0';

	pthread_mutex_lock(&stderr_lock);
	fprintf(stderr, "\r%s: |%s|", text, s);
	if ( val == total ) fprintf(stderr, "\n");
	pthread_mutex_unlock(&stderr_lock);

	fflush(stdout);
}


double random_flat(gsl_rng *rng, double max)
{
	return max * gsl_rng_uniform(rng);
}


double flat_noise(gsl_rng *rng, double expected, double width)
{
	double noise = random_flat(rng, 2.0*width);
	return expected+noise-width;
}


double gaussian_noise(gsl_rng *rng, double expected, double stddev)
{
	double x1, x2, noise;

	/* Generate two uniformly distributed random numbers between 0 and 1,
	 * including 1 but not 0. */
	x1 = 1.0 - gsl_rng_uniform(rng);
	x2 = 1.0 - gsl_rng_uniform(rng);

	noise = sqrt(-2.0*log(x1)) * cos(2.0*M_PI*x2);

	return expected + noise*stddev;
}


static int fake_poisson_noise(gsl_rng *rng, double expected)
{
	double rf = gaussian_noise(rng, expected, sqrt(expected));
	return (int)rf;
}


int poisson_noise(gsl_rng *rng, double expected)
{
	double L;
	int k = 0;
	double p = 1.0;

	/* For large values of the mean, we get big problems with arithmetic.
	 * In such cases, fall back on a Gaussian with the right variance. */
	if ( expected > 100.0 ) return fake_poisson_noise(rng, expected);

	L = exp(-expected);

	do {

		double r;

		k++;
		r = gsl_rng_uniform(rng);
		p *= r;

	} while ( p > L );

	return k - 1;
}


/**
 * SECTION:quaternion
 * @short_description: Simple quaternion handling
 * @title: Quaternion
 * @section_id:
 * @see_also:
 * @include: "utils.h"
 * @Image:
 *
 * There is a simple quaternion structure in CrystFEL.  At the moment, it is
 * only used when simulating patterns, as an argument to cell_rotate() to
 * orient the unit cell.
 */

/**
 * quaternion_modulus:
 * @q: A %quaternion
 *
 * If a quaternion represents a pure rotation, its modulus should be unity.
 *
 * Returns: the modulus of the given quaternion.
 **/
double quaternion_modulus(struct quaternion q)
{
	return sqrt(q.w*q.w + q.x*q.x + q.y*q.y + q.z*q.z);
}


/**
 * normalise_quaternion:
 * @q: A %quaternion
 *
 * Rescales the quaternion such that its modulus is unity.
 *
 * Returns: the normalised version of @q
 **/
struct quaternion normalise_quaternion(struct quaternion q)
{
	double mod;
	struct quaternion r;

	mod = quaternion_modulus(q);

	r.w = q.w / mod;
	r.x = q.x / mod;
	r.y = q.y / mod;
	r.z = q.z / mod;

	return r;
}


/**
 * random_quaternion:
 * @rng: A GSL random number generator to use
 *
 * Returns: a randomly generated, normalised, quaternion.
 **/
struct quaternion random_quaternion(gsl_rng *rng)
{
	struct quaternion q;

	q.w = 2.0*gsl_rng_uniform(rng) - 1.0;
	q.x = 2.0*gsl_rng_uniform(rng) - 1.0;
	q.y = 2.0*gsl_rng_uniform(rng) - 1.0;
	q.z = 2.0*gsl_rng_uniform(rng) - 1.0;
	q = normalise_quaternion(q);

	return q;
}


/**
 * quaternion_valid:
 * @q: A %quaternion
 *
 * Checks if the given quaternion is normalised.
 *
 * This function performs a nasty floating point comparison of the form
 * <code>(modulus > 0.999) && (modulus < 1.001)</code>, and so should not be
 * relied upon to spot anything other than the most obvious input error.
 *
 * Returns: 1 if the quaternion is normalised, 0 if not.
 **/
int quaternion_valid(struct quaternion q)
{
	double qmod;

	qmod = quaternion_modulus(q);

	/* Modulus = 1 to within some tolerance?
	 * Nasty allowance for floating-point accuracy follows... */
	if ( (qmod > 0.999) && (qmod < 1.001) ) return 1;

	return 0;
}


/**
 * quat_rot
 * @q: A vector (in the form of a "struct rvec")
 * @z: A %quaternion
 *
 * Rotates a vector according to a quaternion.
 *
 * Returns: A rotated version of @p.
 **/
struct rvec quat_rot(struct rvec q, struct quaternion z)
{
	struct rvec res;
	double t01, t02, t03, t11, t12, t13, t22, t23, t33;

	t01 = z.w*z.x;
	t02 = z.w*z.y;
	t03 = z.w*z.z;
	t11 = z.x*z.x;
	t12 = z.x*z.y;
	t13 = z.x*z.z;
	t22 = z.y*z.y;
	t23 = z.y*z.z;
	t33 = z.z*z.z;

	res.u = (1.0 - 2.0 * (t22 + t33)) * q.u
	            + (2.0 * (t12 + t03)) * q.v
	            + (2.0 * (t13 - t02)) * q.w;

	res.v =       (2.0 * (t12 - t03)) * q.u
	      + (1.0 - 2.0 * (t11 + t33)) * q.v
	            + (2.0 * (t01 + t23)) * q.w;

	res.w =       (2.0 * (t02 + t13)) * q.u
	            + (2.0 * (t23 - t01)) * q.v
	      + (1.0 - 2.0 * (t11 + t22)) * q.w;

	return res;
}


/* Return non-zero if c is in delims */
static int assplode_isdelim(const char c, const char *delims)
{
	size_t i;
	for ( i=0; i<strlen(delims); i++ ) {
		if ( c == delims[i] ) return 1;
	}
	return 0;
}


static int assplode_extract(char ***pbits, int n, size_t n_captured,
                            size_t start, const char *a)
{
	char **bits = *pbits;
	bits = realloc(bits, sizeof(char *)*(n+1));
	bits[n] = malloc(n_captured+1);
	memcpy(bits[n], a+start, n_captured);
	bits[n][n_captured] = '\0';
	n++;
	*pbits = bits;
	return n;
}


/* Split the string 'a' using 'delims' as a zero-terminated list of
 *  deliminators.
 * Store each segment in bits[0...n] where n is the number of segments and is
 *  the return value.  pbits = &bits
 * Each segment needs to be freed with free() when finished with.
 * The array of bits also needs to be freed with free() when finished with,
 *  unless n=0 in which case bits==NULL
 */
int assplode(const char *a, const char *delims, char ***pbits,
             AssplodeFlag flags)
{
	size_t i, start, n_captured;
	int n, last_was_delim;
	char **bits;

	n = 0;
	i = 0;
	n_captured = 0;
	start = 0;
	last_was_delim = 0;
	bits = NULL;
	while ( i < strlen(a) ) {

		if ( assplode_isdelim(a[i], delims) ) {

			if ( n_captured > 0 ) {
				/* This is a deliminator after a sequence of
				 * non-deliminator chars */
				n = assplode_extract(&bits, n, n_captured,
				                     start, a);
			}

			n_captured = 0;
			if ( (flags & ASSPLODE_DUPS) && last_was_delim ) {
				n = assplode_extract(&bits, n, 0, start, a);
			}
			last_was_delim = 1;

		} else {

			if ( n_captured == 0 ) {
				/* No characters currently found, so this is the
				 * start */
				start = i;
			}
			n_captured++;
			last_was_delim = 0;

		}

		i++;

	}
	/* Left over characters at the end? */
	if ( n_captured > 0 ) {
		n = assplode_extract(&bits, n, n_captured, start, a);
	}

	*pbits = bits;
	return n;
}


char *check_prefix(char *prefix)
{
	int r;
	struct stat statbuf;
	char *new;
	size_t len;

	/* Is "prefix" a directory? */
	r = stat(prefix, &statbuf);
	if ( r != 0 ) {
		/* "prefix" probably doesn't exist.  This is fine - assume
		 * the user knows what they're doing, and that "prefix"
		 * suffixed with the actual filename will produce something
		 * sensible. */
		return prefix;
	}

	if ( !S_ISDIR(statbuf.st_mode) ) {
		/* Also fine, as above. */
		return prefix;
	}

	/* Does the prefix end in a slash? */
	if ( prefix[strlen(prefix)-1] == '/' ) {
		/* This looks sensible. */
		return prefix;
	}

	STATUS("Your prefix ('%s') is a directory, but doesn't end"
	       " with a slash.  I'm going to add it for you.\n", prefix);
	STATUS("If this isn't what you want, run with --no-check-prefix.\n");
	len = strlen(prefix)+2;
	new = malloc(len);
	snprintf(new, len, "%s/", prefix);
	free(prefix);
	return new;
}


char *safe_basename(const char *in)
{
	int i;
	char *cpy;
	char *res;

	cpy = strdup(in);

	/* Get rid of any trailing slashes */
	for ( i=strlen(cpy)-1; i>0; i-- ) {
		if ( cpy[i] == '/' ) {
			cpy[i] = '\0';
		} else {
			break;
		}
	}

	/* Find the base name */
	for ( i=strlen(cpy)-1; i>0; i-- ) {
		if ( cpy[i] == '/' ) {
			i++;
			break;
		}
	}

	res = strdup(cpy+i);
	/* If we didn't find a previous slash, i==0 so res==cpy */

	free(cpy);

	return res;
}


/* Force the linker to bring in CBLAS to make GSL happy */
void utils_fudge_gslcblas()
{
        STATUS("%p\n", cblas_sgemm);
}