1 /* This file is part of the hkl library.
3 * The hkl library is free software: you can redistribute it and/or modify
4 * it under the terms of the GNU General Public License as published by
5 * the Free Software Foundation, either version 3 of the License, or
6 * (at your option) any later version.
8 * The hkl library is distributed in the hope that it will be useful,
9 * but WITHOUT ANY WARRANTY; without even the implied warranty of
10 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 * GNU General Public License for more details.
13 * You should have received a copy of the GNU General Public License
14 * along with the hkl library. If not, see <http://www.gnu.org/licenses/>.
16 * Copyright (C) 2003-2014 Synchrotron SOLEIL
17 * L'Orme des Merisiers Saint-Aubin
18 * BP 48 91192 GIF-sur-YVETTE CEDEX
20 * Authors: Picca Frédéric-Emmanuel <picca@synchrotron-soleil.fr>
24 #define _XOPEN_SOURCE 500
25 #include <gsl/gsl_errno.h> // for gsl_set_error_handler, etc
26 #include <gsl/gsl_multimin.h> // for gsl_multimin_function, etc
27 #include <gsl/gsl_nan.h> // for GSL_NAN
28 #include <gsl/gsl_vector_double.h> // for gsl_vector_get, etc
29 #include <math.h> // for M_PI, fabs
30 #include <stddef.h> // for size_t
31 #include <stdio.h> // for fprintf, FILE
32 #include <stdlib.h> // for free
33 #include <string.h> // for NULL, strdup
34 #include "hkl-detector-private.h" // for hkl_detector_new_copy, etc
35 #include "hkl-geometry-private.h" // for _HklGeometry, etc
36 #include "hkl-lattice-private.h" // for _HklLattice, etc
37 #include "hkl-macros-private.h" // for HKL_MALLOC
38 #include "hkl-matrix-private.h" // for hkl_matrix_init_from_euler, etc
39 #include "hkl-parameter-private.h" // for hkl_parameter_fprintf, etc
40 #include "hkl-quaternion-private.h" // for hkl_quaternion_conjugate, etc
41 #include "hkl-sample-private.h" // for _HklSample, etc
42 #include "hkl-source-private.h" // for hkl_source_compute_ki
43 #include "hkl-unit-private.h" // for hkl_unit_angle_deg, etc
44 #include "hkl-vector-private.h" // for HklVector, hkl_vector_angle, etc
45 #include "hkl.h" // for HklSample, etc
46 #include "hkl/ccan/darray/darray.h" // for darray_foreach, darray_item
47 #include "hkl/ccan/list/list.h" // for list_head, list_add_tail, etc
50 #define ITER_MAX 10000
53 static void hkl_sample_clear_all_reflections(HklSample
*self
)
55 HklSampleReflection
*reflection
;
56 HklSampleReflection
*next
;
58 list_for_each_safe(&self
->reflections
, reflection
, next
, list
){
59 list_del(&reflection
->list
);
60 hkl_sample_reflection_free(reflection
);
65 static void hkl_sample_copy_all_reflections(HklSample
*self
, const HklSample
*src
)
67 HklSampleReflection
*reflection
;
69 list_head_init(&self
->reflections
);
70 list_for_each(&src
->reflections
, reflection
, list
){
71 list_add_tail(&self
->reflections
,
72 &hkl_sample_reflection_new_copy(reflection
)->list
);
74 self
->n_reflections
= src
->n_reflections
;
78 static void hkl_sample_sample_set(HklSample
*self
, const HklSample
*src
)
82 self
->name
= strdup(src
->name
);
84 hkl_lattice_lattice_set(self
->lattice
, src
->lattice
);
88 hkl_parameter_init_copy(self
->ux
, src
->ux
, NULL
);
89 hkl_parameter_init_copy(self
->uy
, src
->uy
, NULL
);
90 hkl_parameter_init_copy(self
->uz
, src
->uz
, NULL
);
92 /* copy all the reflections */
93 hkl_sample_clear_all_reflections(self
);
94 hkl_sample_copy_all_reflections(self
, src
);
98 static void hkl_sample_reflection_update(HklSampleReflection
*self
)
106 /* compute the _hkl using only the axes of the geometry */
107 /* first Q from angles */
108 hkl_source_compute_ki(&self
->geometry
->source
, &ki
);
110 hkl_vector_rotated_quaternion(&self
->_hkl
,
111 &darray_item(self
->geometry
->holders
, self
->detector
->idx
)->q
);
112 hkl_vector_minus_vector(&self
->_hkl
, &ki
);
114 q
= darray_item(self
->geometry
->holders
, 0)->q
;
115 hkl_quaternion_conjugate(&q
);
116 hkl_vector_rotated_quaternion(&self
->_hkl
, &q
);
119 static void hkl_sample_compute_UxUyUz(HklSample
*self
)
125 hkl_matrix_to_euler(&self
->U
, &ux
, &uy
, &uz
);
126 hkl_parameter_value_set(self
->ux
, ux
, HKL_UNIT_DEFAULT
, NULL
);
127 hkl_parameter_value_set(self
->uy
, uy
, HKL_UNIT_DEFAULT
, NULL
);
128 hkl_parameter_value_set(self
->uz
, uz
, HKL_UNIT_DEFAULT
, NULL
);
131 static int hkl_sample_compute_UB(HklSample
*self
)
135 if (!hkl_lattice_get_B(self
->lattice
, &B
))
139 hkl_matrix_times_matrix(&self
->UB
, &B
);
145 * this structure is used by the minimization gsl algorithm.
146 * in the set_UB method
154 static int hkl_sample_init_from_gsl_vector(HklSample
*self
, const gsl_vector
*x
)
156 double euler_x
, euler_y
, euler_z
;
158 euler_x
= gsl_vector_get(x
, 0);
159 euler_y
= gsl_vector_get(x
, 1);
160 euler_z
= gsl_vector_get(x
, 2);
162 hkl_parameter_value_set(self
->ux
, euler_x
, HKL_UNIT_DEFAULT
, NULL
);
163 hkl_parameter_value_set(self
->uy
, euler_y
, HKL_UNIT_DEFAULT
, NULL
);
164 hkl_parameter_value_set(self
->uz
, euler_z
, HKL_UNIT_DEFAULT
, NULL
);
165 hkl_parameter_value_set(self
->lattice
->a
, gsl_vector_get(x
, 3), HKL_UNIT_DEFAULT
, NULL
);
166 hkl_parameter_value_set(self
->lattice
->b
, gsl_vector_get(x
, 4), HKL_UNIT_DEFAULT
, NULL
);
167 hkl_parameter_value_set(self
->lattice
->c
, gsl_vector_get(x
, 5), HKL_UNIT_DEFAULT
, NULL
);
168 hkl_parameter_value_set(self
->lattice
->alpha
, gsl_vector_get(x
, 6), HKL_UNIT_DEFAULT
, NULL
);
169 hkl_parameter_value_set(self
->lattice
->beta
, gsl_vector_get(x
, 7), HKL_UNIT_DEFAULT
, NULL
);
170 hkl_parameter_value_set(self
->lattice
->gamma
, gsl_vector_get(x
, 8), HKL_UNIT_DEFAULT
, NULL
);
172 hkl_matrix_init_from_euler(&self
->U
, euler_x
, euler_y
, euler_z
);
173 if (!hkl_sample_compute_UB(self
))
179 static void hkl_sample_to_gsl_vector(HklSample
*self
, gsl_vector
*x
)
181 gsl_vector_set (x
, 0, hkl_parameter_value_get(self
->ux
, HKL_UNIT_DEFAULT
));
182 gsl_vector_set (x
, 1, hkl_parameter_value_get(self
->uy
, HKL_UNIT_DEFAULT
));
183 gsl_vector_set (x
, 2, hkl_parameter_value_get(self
->uz
, HKL_UNIT_DEFAULT
));
184 gsl_vector_set (x
, 3, hkl_parameter_value_get(self
->lattice
->a
, HKL_UNIT_DEFAULT
));
185 gsl_vector_set (x
, 4, hkl_parameter_value_get(self
->lattice
->b
, HKL_UNIT_DEFAULT
));
186 gsl_vector_set (x
, 5, hkl_parameter_value_get(self
->lattice
->c
, HKL_UNIT_DEFAULT
));
187 gsl_vector_set (x
, 6, hkl_parameter_value_get(self
->lattice
->alpha
, HKL_UNIT_DEFAULT
));
188 gsl_vector_set (x
, 7, hkl_parameter_value_get(self
->lattice
->beta
, HKL_UNIT_DEFAULT
));
189 gsl_vector_set (x
, 8, hkl_parameter_value_get(self
->lattice
->gamma
, HKL_UNIT_DEFAULT
));
193 static double set_UB_fitness(const gsl_vector
*x
, void *params
)
197 struct set_UB_t
*parameters
= params
;
198 HklSample
*sample
= parameters
->sample
;
200 if (!hkl_sample_init_from_gsl_vector(sample
, x
))
205 double tmp
= parameters
->UB
.data
[i
][j
] - sample
->UB
.data
[i
][j
];
206 fitness
+= tmp
* tmp
;
209 fprintf(stderr
, "fitness: %f\n", fitness
);
214 static double mono_crystal_fitness(const gsl_vector
*x
, void *params
)
218 HklSample
*sample
= params
;
219 HklSampleReflection
*reflection
;
221 if (!hkl_sample_init_from_gsl_vector(sample
, x
))
225 list_for_each(&sample
->reflections
, reflection
, list
){
226 if(reflection
->flag
){
229 UBh
= reflection
->hkl
;
230 hkl_matrix_times_vector(&sample
->UB
, &UBh
);
233 double tmp
= UBh
.data
[j
] - reflection
->_hkl
.data
[j
];
234 fitness
+= tmp
* tmp
;
241 static int minimize(HklSample
*sample
,
242 double (* f
) (const gsl_vector
* x
, void * params
),
243 void *params
, GError
**error
)
246 gsl_multimin_fminimizer_type
const *T
= gsl_multimin_fminimizer_nmsimplex
;
247 gsl_multimin_fminimizer
*s
= NULL
;
249 gsl_multimin_function minex_func
;
255 hkl_error (error
== NULL
|| *error
== NULL
);
257 /* save the sample state */
258 saved
= hkl_sample_new_copy(sample
);
261 x
= gsl_vector_alloc (9);
262 hkl_sample_to_gsl_vector(sample
, x
);
264 /* Set initial step sizes to 1 */
265 ss
= gsl_vector_alloc (9);
266 gsl_vector_set (ss
, 0, sample
->ux
->fit
);
267 gsl_vector_set (ss
, 1, sample
->uy
->fit
);
268 gsl_vector_set (ss
, 2, sample
->uz
->fit
);
269 gsl_vector_set (ss
, 3, sample
->lattice
->a
->fit
);
270 gsl_vector_set (ss
, 4, sample
->lattice
->b
->fit
);
271 gsl_vector_set (ss
, 5, sample
->lattice
->c
->fit
);
272 gsl_vector_set (ss
, 6, sample
->lattice
->alpha
->fit
);
273 gsl_vector_set (ss
, 7, sample
->lattice
->beta
->fit
);
274 gsl_vector_set (ss
, 8, sample
->lattice
->gamma
->fit
);
276 /* Initialize method and iterate */
279 minex_func
.params
= params
;
280 s
= gsl_multimin_fminimizer_alloc (T
, 9);
281 gsl_set_error_handler_off();
282 gsl_multimin_fminimizer_set (s
, &minex_func
, x
, ss
);
285 status
= gsl_multimin_fminimizer_iterate(s
);
287 fprintf(stderr
, "status iterate: %d (%d): %s\n", status
, iter
, gsl_strerror(status
));
291 size
= gsl_multimin_fminimizer_size (s
);
292 status
= gsl_multimin_test_size (size
, HKL_EPSILON
/ 2.);
294 fprintf(stderr
, "status test: %d size: %f :%s\n", status
, size
, gsl_strerror(status
));
295 fprintf(stderr
, " x:");
296 for(int i
=0; i
<9; ++i
)
297 fprintf(stderr
, " %f", gsl_vector_get(s
->x
, i
));
298 fprintf(stderr
, "\n");
300 } while (status
== GSL_CONTINUE
&& iter
< ITER_MAX
);
303 gsl_multimin_fminimizer_free(s
);
304 gsl_set_error_handler (NULL
);
306 if (status
== GSL_CONTINUE
){
307 hkl_sample_sample_set(sample
, saved
); /* restore the saved sample */
310 HKL_SAMPLE_ERROR_MINIMIZED
,
311 "Minimization failed after %d iterations.",
316 hkl_sample_free(saved
);
333 HklSample
* hkl_sample_new(const char *name
)
335 HklSample
*self
= NULL
;
337 /* check parameters */
341 self
= HKL_MALLOC(HklSample
);
343 self
->name
= strdup(name
);
344 self
->lattice
= hkl_lattice_new_default();
345 hkl_matrix_init(&self
->U
,1, 0, 0, 0, 1, 0, 0, 0, 1);
346 hkl_matrix_init(&self
->UB
,1, 0, 0, 0, 1, 0, 0, 0, 1);
348 self
->ux
= hkl_parameter_new("ux", "the sample rotation around $\vec{x}$",
352 &hkl_unit_angle_deg
);
353 self
->uy
= hkl_parameter_new("uy", "the sample rotation around $\vec{y}$",
357 &hkl_unit_angle_deg
);
358 self
->uz
= hkl_parameter_new("uz", "the sample rotation around $\vec{z}$",
362 &hkl_unit_angle_deg
);
364 hkl_sample_compute_UB(self
);
365 list_head_init(&self
->reflections
);
366 self
->n_reflections
= 0;
372 * hkl_sample_new_copy: (skip)
379 HklSample
*hkl_sample_new_copy(const HklSample
*self
)
381 HklSample
*dup
= NULL
;
383 /* check parameters */
387 dup
= HKL_MALLOC(HklSample
);
389 dup
->name
= strdup(self
->name
);
390 dup
->lattice
= hkl_lattice_new_copy(self
->lattice
);
393 dup
->ux
= hkl_parameter_new_copy(self
->ux
);
394 dup
->uy
= hkl_parameter_new_copy(self
->uy
);
395 dup
->uz
= hkl_parameter_new_copy(self
->uz
);
397 hkl_sample_copy_all_reflections(dup
, self
);
403 * hkl_sample_free: (skip)
408 void hkl_sample_free(HklSample
*self
)
414 hkl_lattice_free(self
->lattice
);
415 hkl_parameter_free(self
->ux
);
416 hkl_parameter_free(self
->uy
);
417 hkl_parameter_free(self
->uz
);
418 hkl_sample_clear_all_reflections(self
);
423 * hkl_sample_name_get:
424 * @self: the this ptr
426 * Return value: the name of the sample
428 const char *hkl_sample_name_get(const HklSample
*self
)
434 * hkl_sample_name_set:
435 * @self: the this ptr
436 * @name: the new name to set
438 * set the name of the sample
440 void hkl_sample_name_set(HklSample
*self
, const char *name
)
444 self
->name
= strdup(name
);
448 * hkl_sample_lattice_get:
449 * @self: the this ptr
451 * Return value: the lattice parameters of the sample.
453 const HklLattice
*hkl_sample_lattice_get(HklSample
*self
)
455 return self
->lattice
;
459 * hkl_sample_lattice_set:
460 * @self: the this ptr
461 * @lattice: the lattice to set
463 void hkl_sample_lattice_set(HklSample
*self
, const HklLattice
*lattice
)
465 hkl_lattice_lattice_set(self
->lattice
, lattice
);
466 hkl_sample_compute_UB(self
);
471 * @self: the this ptr
473 * Return value: the ux part of the U matrix.
475 const HklParameter
*hkl_sample_ux_get(const HklSample
*self
)
482 * @self: the this ptr
484 * Return value: the uy part of the U matrix.
486 const HklParameter
*hkl_sample_uy_get(const HklSample
*self
)
493 * @self: the this ptr
495 * Return value: the uz part of the U matrix.
497 const HklParameter
*hkl_sample_uz_get(const HklSample
*self
)
504 * @self: the this ptr
505 * @ux: the ux parameter to set
506 * @error: return location for a GError, or NULL
508 * set the ux part of the U matrix.
510 * Returns: TRUE on success, FALSE if an error occurred
512 int hkl_sample_ux_set(HklSample
*self
,
513 const HklParameter
*ux
,
516 hkl_error (error
== NULL
|| *error
== NULL
);
518 if(!hkl_parameter_init_copy(self
->ux
, ux
, error
)){
519 g_assert (error
== NULL
|| *error
!= NULL
);
522 g_assert (error
== NULL
|| *error
== NULL
);
524 hkl_matrix_init_from_euler(&self
->U
,
525 hkl_parameter_value_get(self
->ux
, HKL_UNIT_DEFAULT
),
526 hkl_parameter_value_get(self
->uy
, HKL_UNIT_DEFAULT
),
527 hkl_parameter_value_get(self
->uz
, HKL_UNIT_DEFAULT
));
528 hkl_sample_compute_UB(self
);
535 * @self: the this ptr
536 * @uy: the uy parameter to set
537 * @error: return location for a GError, or NULL
539 * set the uy part of the U matrix.
541 * Returns: TRUE on success, FALSE if an error occurred
543 int hkl_sample_uy_set(HklSample
*self
, const HklParameter
*uy
,
546 hkl_error (error
== NULL
|| *error
== NULL
);
548 if(!hkl_parameter_init_copy(self
->uy
, uy
, error
)){
549 g_assert (error
== NULL
|| *error
!= NULL
);
552 g_assert (error
== NULL
|| *error
== NULL
);
554 hkl_matrix_init_from_euler(&self
->U
,
555 hkl_parameter_value_get(self
->ux
, HKL_UNIT_DEFAULT
),
556 hkl_parameter_value_get(self
->uy
, HKL_UNIT_DEFAULT
),
557 hkl_parameter_value_get(self
->uz
, HKL_UNIT_DEFAULT
));
558 hkl_sample_compute_UB(self
);
563 * @self: the this ptr
564 * @uz: the uz parameter to set
565 * @error: return location for a GError, or NULL
567 * set the uz part of the U matrix.
569 * Returns: TRUE on success, FALSE if an error occurred
571 int hkl_sample_uz_set(HklSample
*self
, const HklParameter
*uz
,
574 hkl_error (error
== NULL
|| *error
== NULL
);
576 if(!hkl_parameter_init_copy(self
->uz
, uz
, error
)){
577 g_assert (error
== NULL
|| *error
!= NULL
);
580 g_assert (error
== NULL
|| *error
== NULL
);
582 hkl_matrix_init_from_euler(&self
->U
,
583 hkl_parameter_value_get(self
->ux
, HKL_UNIT_DEFAULT
),
584 hkl_parameter_value_get(self
->uy
, HKL_UNIT_DEFAULT
),
585 hkl_parameter_value_get(self
->uz
, HKL_UNIT_DEFAULT
));
586 hkl_sample_compute_UB(self
);
591 * @self: the this ptr
593 * Return value: the U matrix of the sample
595 const HklMatrix
*hkl_sample_U_get(const HklSample
*self
)
601 * TODO implemente the error
603 void hkl_sample_U_set(HklSample
*self
, const HklMatrix
*U
, GError
**error
)
607 hkl_matrix_matrix_set(&self
->U
, U
);
608 hkl_sample_compute_UB(self
);
609 hkl_matrix_to_euler(&self
->U
, &x
, &y
, &z
);
610 hkl_parameter_value_set(self
->ux
, x
, HKL_UNIT_DEFAULT
, NULL
);
611 hkl_parameter_value_set(self
->uy
, y
, HKL_UNIT_DEFAULT
, NULL
);
612 hkl_parameter_value_set(self
->uz
, z
, HKL_UNIT_DEFAULT
, NULL
);
617 * @self: the this ptr.
619 * Return value: get the UB matrix of the sample
621 const HklMatrix
*hkl_sample_UB_get(const HklSample
*self
)
628 * @self: the sample to modify
629 * @UB: the UB matrix to set
630 * @error: error set in case of impossibility
632 * Set the UB matrix using an external UB matrix. In fact you give
633 * the UB matrix but only the U matrix of the sample is affected by
634 * this operation. We keep the B matrix constant.
635 * U * B = UB -> U = UB * B^-1
636 * TODO implemente the error
638 int hkl_sample_UB_set(HklSample
*self
, const HklMatrix
*UB
,
641 struct set_UB_t params
= {
646 return minimize(self
, set_UB_fitness
, ¶ms
, error
);
650 * hkl_sample_n_reflections_get: (skip)
651 * @self: the this ptr
653 * return the number of reflections of the sample
657 size_t hkl_sample_n_reflections_get(const HklSample
*self
)
659 return self
->n_reflections
;
663 * hkl_sample_reflections_first_get: (skip)
664 * @self: the this ptr
666 * Return value: the first HklSampleReflection of the sample.
668 HklSampleReflection
*hkl_sample_reflections_first_get(HklSample
*self
)
670 return list_top(&self
->reflections
, HklSampleReflection
, list
);
674 * hkl_sample_reflections_next_get: (skip)
675 * @self: the this ptr
676 * @reflection: the current reflection
678 * Return value: (allow-none): the next reflection or NULL if no more reflection
680 HklSampleReflection
*hkl_sample_reflections_next_get(HklSample
*self
,
681 HklSampleReflection
*reflection
)
683 return list_next(&self
->reflections
, reflection
, list
);
687 * hkl_sample_add_reflection:
688 * @self: the this ptr
689 * @reflection: The reflection to add
691 * add a reflection to the sample, if the reflection is already part
692 * of the sample reflection list, this method does nothing.
694 void hkl_sample_add_reflection(HklSample
*self
,
695 HklSampleReflection
*reflection
)
697 HklSampleReflection
*ref
;
699 list_for_each(&self
->reflections
, ref
, list
){
700 if (ref
== reflection
)
704 list_add_tail(&self
->reflections
, &reflection
->list
);
705 self
->n_reflections
++;
709 * hkl_sample_del_reflection:
710 * @self: the this ptr
711 * @reflection: the reflection to remove.
713 * remove an HklSampleRefelction from the reflections list.
715 void hkl_sample_del_reflection(HklSample
*self
,
716 HklSampleReflection
*reflection
)
718 list_del(&reflection
->list
);
719 hkl_sample_reflection_free(reflection
);
720 self
->n_reflections
--;
724 * hkl_sample_compute_UB_busing_levy:
725 * @self: the this ptr
726 * @r1: the first #HklsampleReflection
727 * @r2: the second #HklSampleReflection
729 * compute the UB matrix using the Busing and Levy method
732 * Returns: 0 or 1 if it succeed
734 int hkl_sample_compute_UB_busing_levy(HklSample
*self
,
735 const HklSampleReflection
*r1
,
736 const HklSampleReflection
*r2
,
740 hkl_error (error
== NULL
|| *error
== NULL
);
742 if (!hkl_vector_is_colinear(&r1
->hkl
, &r2
->hkl
)) {
748 /* Compute matrix Tc from r1 and r2. */
751 hkl_lattice_get_B(self
->lattice
, &B
);
752 hkl_matrix_times_vector(&B
, &h1c
);
753 hkl_matrix_times_vector(&B
, &h2c
);
754 hkl_matrix_init_from_two_vector(&Tc
, &h1c
, &h2c
);
755 hkl_matrix_transpose(&Tc
);
758 hkl_matrix_init_from_two_vector(&self
->U
,
759 &r1
->_hkl
, &r2
->_hkl
);
760 hkl_matrix_times_matrix(&self
->U
, &Tc
);
761 hkl_sample_compute_UxUyUz(self
);
762 hkl_sample_compute_UB(self
);
766 HKL_SAMPLE_ERROR_COMPUTE_UB_BUSING_LEVY
,
767 "It is not possible to compute the UB matrix when the given reflections are colinear");
771 g_assert (error
== NULL
|| *error
== NULL
);
778 * @self: the this ptr
782 * Returns: the fitness of the affined #HklSample
784 int hkl_sample_affine(HklSample
*self
, GError
**error
)
786 return minimize(self
, mono_crystal_fitness
, self
, error
);
790 * hkl_sample_get_reflection_measured_angle:
791 * @self: the this ptr
792 * @r1: the first #HklSampleReflection
793 * @r2: the second #HklSampleReflection
795 * get the measured angles between two #HklSampleReflection
797 * Returns: the measured angle beetween them
799 double hkl_sample_get_reflection_measured_angle(const HklSample
*self
,
800 const HklSampleReflection
*r1
,
801 const HklSampleReflection
*r2
)
803 return hkl_vector_angle(&r1
->_hkl
,
808 * hkl_sample_get_reflection_theoretical_angle:
809 * @self: the this ptr
810 * @r1: the first #HklSampleReflection
811 * @r2: the second #HklSampleReflection
813 * get the theoretical angles between two #HklSampleReflection
815 * Returns: the theoretical angle beetween them
817 double hkl_sample_get_reflection_theoretical_angle(const HklSample
*self
,
818 const HklSampleReflection
*r1
,
819 const HklSampleReflection
*r2
)
826 hkl_matrix_times_vector(&self
->UB
, &hkl1
);
827 hkl_matrix_times_vector(&self
->UB
, &hkl2
);
829 return hkl_vector_angle(&hkl1
, &hkl2
);
833 * hkl_sample_fprintf: (skip)
837 * print to a file a sample
839 void hkl_sample_fprintf(FILE *f
, const HklSample
*self
)
844 fprintf(f
, "\nSample name: \"%s\"", self
->name
);
846 fprintf(f
, "\nLattice parameters:");
848 hkl_parameter_fprintf(f
, self
->lattice
->a
);
850 hkl_parameter_fprintf(f
, self
->lattice
->b
);
852 hkl_parameter_fprintf(f
, self
->lattice
->c
);
854 hkl_parameter_fprintf(f
, self
->lattice
->alpha
);
856 hkl_parameter_fprintf(f
, self
->lattice
->beta
);
858 hkl_parameter_fprintf(f
, self
->lattice
->gamma
);
860 hkl_parameter_fprintf(f
, self
->ux
);
862 hkl_parameter_fprintf(f
, self
->uy
);
864 hkl_parameter_fprintf(f
, self
->uz
);
865 fprintf(f
, "\nUB:\n");
866 hkl_matrix_fprintf(f
, &self
->UB
);
868 if (!list_empty(&self
->reflections
)){
869 HklSampleReflection
*reflection
;
872 reflection
= list_top(&self
->reflections
, HklSampleReflection
, list
);
874 fprintf(f
, "Reflections:");
876 fprintf(f
, "%-10.6s %-10.6s %-10.6s", "h", "k", "l");
877 darray_foreach(axis
, reflection
->geometry
->axes
){
878 fprintf(f
, " %-10.6s", (*axis
)->name
);
881 list_for_each(&self
->reflections
, reflection
, list
){
882 fprintf(f
, "\n%-10.6f %-10.6f %-10.6f",
883 reflection
->hkl
.data
[0],
884 reflection
->hkl
.data
[1],
885 reflection
->hkl
.data
[2]);
886 darray_foreach(axis
, reflection
->geometry
->axes
){
887 fprintf(f
, " %-10.6f", hkl_parameter_value_get(*axis
, HKL_UNIT_USER
));
893 /***********************/
894 /* HklSampleReflection */
895 /***********************/
898 * hkl_sample_reflection_new:
909 HklSampleReflection
*hkl_sample_reflection_new(const HklGeometry
*geometry
,
910 const HklDetector
*detector
,
911 double h
, double k
, double l
,
914 HklSampleReflection
*self
;
916 if (!geometry
|| !detector
)
919 self
= HKL_MALLOC(HklSampleReflection
);
921 self
->geometry
= hkl_geometry_new_copy(geometry
);
922 self
->detector
= hkl_detector_new_copy(detector
);
923 self
->hkl
.data
[0] = h
;
924 self
->hkl
.data
[1] = k
;
925 self
->hkl
.data
[2] = l
;
928 hkl_sample_reflection_update(self
);
934 * hkl_sample_reflection_new_copy: (skip)
941 HklSampleReflection
*hkl_sample_reflection_new_copy(const HklSampleReflection
*self
)
943 HklSampleReflection
*dup
= NULL
;
945 dup
= HKL_MALLOC(HklSampleReflection
);
947 dup
->geometry
= hkl_geometry_new_copy(self
->geometry
);
948 dup
->detector
= hkl_detector_new_copy(self
->detector
);
949 dup
->hkl
= self
->hkl
;
950 dup
->_hkl
= self
->_hkl
;
951 dup
->flag
= self
->flag
;
957 * hkl_sample_reflection_free: (skip)
962 void hkl_sample_reflection_free(HklSampleReflection
*self
)
964 hkl_geometry_free(self
->geometry
);
965 hkl_detector_free(self
->detector
);
970 * hkl_sample_reflection_hkl_get:
971 * @self: the this ptr
972 * @h: (out caller-allocates): the h-coordinate of the #HklSampleReflection
973 * @k: (out caller-allocates): the k-coordinate of the #HklSampleReflection
974 * @l: (out caller-allocates): the l-coordinate of the #HklSampleReflection
976 * get the hkl coordinates of the #HklSampleReflection
978 void hkl_sample_reflection_hkl_get(const HklSampleReflection
*self
,
979 double *h
, double *k
, double *l
)
981 *h
= self
->hkl
.data
[0];
982 *k
= self
->hkl
.data
[1];
983 *l
= self
->hkl
.data
[2];
987 * hkl_sample_reflection_hkl_set:
988 * @self: the this ptr
989 * @h: the h-coordinate of the #HklSampleReflection
990 * @k: the k-coordinate of the #HklSampleReflection
991 * @l: the l-coordinate of the #HklSampleReflection
992 * @error: return location for a GError, or NULL
994 * set the hkl coordinates of the #HklSampleReflection
996 * Returns: TRUE on success, FALSE if an error occurred
998 int hkl_sample_reflection_hkl_set(HklSampleReflection
*self
,
999 double h
, double k
, double l
,
1002 hkl_error (error
== NULL
|| *error
== NULL
);
1004 if((fabs(h
) + fabs(k
) + fabs(l
) < HKL_EPSILON
)){
1006 HKL_SAMPLE_REFLECTION_ERROR
,
1007 HKL_SAMPLE_REFLECTION_ERROR_HKL_SET
,
1008 "it is not allow to set a null hkl reflection\n");
1012 self
->hkl
.data
[0] = h
;
1013 self
->hkl
.data
[1] = k
;
1014 self
->hkl
.data
[2] = l
;
1020 * hkl_sample_reflection_flag_get: (skip)
1023 * get the flag of the reflection
1025 int hkl_sample_reflection_flag_get(const HklSampleReflection
*self
)
1031 * hkl_sample_reflection_flag_set: (skip)
1035 * set the flag of the reglection
1037 void hkl_sample_reflection_flag_set(HklSampleReflection
*self
, int flag
)
1043 * hkl_sample_reflection_geometry_get: (skip)
1046 * set the geometry of the reflection
1048 const HklGeometry
*hkl_sample_reflection_geometry_get(HklSampleReflection
*self
)
1050 return self
->geometry
;
1054 * hkl_sample_reflection_geometry_set: (skip)
1058 * set the geometry of the reflection
1060 void hkl_sample_reflection_geometry_set(HklSampleReflection
*self
,
1061 const HklGeometry
*geometry
)
1064 if(self
->geometry
!= geometry
){
1065 hkl_geometry_free(self
->geometry
);
1066 self
->geometry
= hkl_geometry_new_copy(geometry
);
1069 self
->geometry
= hkl_geometry_new_copy(geometry
);
1071 hkl_sample_reflection_update(self
);