aboutsummaryrefslogtreecommitdiff
path: root/src/gui_peaksearch.c
blob: 3aa9c3f670d2c64c80569d846fddb48120ca0eb3 (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
/*
 * gui_peaksearch.c
 *
 * Peak search parts of GUI
 *
 * Copyright © 2020 Deutsches Elektronen-Synchrotron DESY,
 *                  a research centre of the Helmholtz Association.
 *
 * Authors:
 *   2020 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 <stdarg.h>
#include <stdio.h>
#include <getopt.h>
#include <string.h>
#include <gtk/gtk.h>
#include <gdk/gdkkeysyms-compat.h>
#include <assert.h>

#include <datatemplate.h>
#include <peaks.h>

#include "crystfel_gui.h"
#include "crystfelimageview.h"


void update_peaks(struct crystfelproject *proj)
{

	if ( proj->n_frames == 0 ) return;

	if ( proj->show_peaks ) {

		struct image *image;
		const DataTemplate *dtempl;

		image = crystfel_image_view_get_image_struct(CRYSTFEL_IMAGE_VIEW(proj->imageview));
		if ( image == NULL ) return;

		dtempl = crystfel_image_view_get_datatemplate(CRYSTFEL_IMAGE_VIEW(proj->imageview));
		image_feature_list_free(image->features);
		image->features = NULL;

		switch ( proj->peak_search_params.method ) {

		case PEAK_ZAEF:
			search_peaks(image,
			             proj->peak_search_params.threshold,
			             proj->peak_search_params.min_sq_gradient,
			             proj->peak_search_params.min_snr,
			             proj->peak_search_params.pk_inn,
			             proj->peak_search_params.pk_mid,
			             proj->peak_search_params.pk_out,
			             1);
			break;

		case PEAK_PEAKFINDER8:
			search_peaks_peakfinder8(image, 2048,
			                         proj->peak_search_params.threshold,
			                         proj->peak_search_params.min_snr,
			                         proj->peak_search_params.min_pix_count,
			                         proj->peak_search_params.max_pix_count,
			                         proj->peak_search_params.local_bg_radius,
			                         proj->peak_search_params.min_res,
			                         proj->peak_search_params.max_res,
			                         1);
			break;

		case PEAK_HDF5:
		case PEAK_CXI:
			image->features = image_read_peaks(dtempl,
			                                   image->filename,
			                                   image->ev,
			                                   proj->peak_search_params.half_pixel_shift);
			break;

		default:
			ERROR("This peak detection method not implemented!\n");
			break;

		}

		crystfel_image_view_set_peaks(CRYSTFEL_IMAGE_VIEW(proj->imageview),
		                              image->features, 0);

	} else {
		crystfel_image_view_set_peaks(CRYSTFEL_IMAGE_VIEW(proj->imageview),
		                              NULL, 0);
	}
}


struct param_callback_vals
{
	float *pfval;
	int *pival;
	struct crystfelproject *proj;
};


static void check_param_callback(GtkWidget *checkbox,
                                 struct param_callback_vals *vals)
{
	int val = gtk_toggle_button_get_active(GTK_TOGGLE_BUTTON(checkbox));
	*(vals->pival) = val;
	update_peaks(vals->proj);
}


static void int_param_callback(GtkWidget *entry,
                               struct param_callback_vals *cbvals)
{
	const char *text;
	int val;

	text = gtk_entry_get_text(GTK_ENTRY(entry));
	if (sscanf(text, "%i", &val) != 1) {
		ERROR("Invalid value\n");
		return;
	}

	*(cbvals->pival) = val;
	update_peaks(cbvals->proj);
}


static void float_param_callback(GtkWidget *entry,
                                 struct param_callback_vals *cbvals)
{
	const char *text;
	float val;

	text = gtk_entry_get_text(GTK_ENTRY(entry));
	if (sscanf(text, "%f", &val) != 1) {
		ERROR("Invalid value\n");
		return;
	}

	*(cbvals->pfval) = val;
	update_peaks(cbvals->proj);
}


static void free_callback_params(gpointer cbvals,
                                 GClosure *closure)
{
	free(cbvals);
}


static void add_int_param(GtkWidget *params_box, const char *labeltext,
                          int *pval, struct crystfelproject *proj)
{
	GtkWidget *hbox;
	GtkWidget *label;
	GtkWidget *entry;
	struct param_callback_vals *cbvals;
	char tmp[64];

	hbox = gtk_hbox_new(FALSE, 0.0);
	gtk_box_pack_start(GTK_BOX(params_box),
	                   GTK_WIDGET(hbox), FALSE, FALSE, 8.0);
	label = gtk_label_new(labeltext);
	gtk_misc_set_alignment(GTK_MISC(label), 1.0, 0.5);
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
	                   FALSE, FALSE, 2.0);
	entry = gtk_entry_new();
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(entry),
	                   TRUE, TRUE, 2.0);
	snprintf(tmp, 63, "%i", *pval);
	gtk_entry_set_text(GTK_ENTRY(entry), tmp);

	cbvals = malloc(sizeof(struct param_callback_vals));
	if ( cbvals != NULL ) {
		cbvals->proj = proj;
		cbvals->pival = pval;
		g_signal_connect_data(G_OBJECT(entry), "activate",
		                      G_CALLBACK(int_param_callback),
		                      cbvals, free_callback_params, 0);
	} else {
		ERROR("Failed to connect parameter callback\n");
	}
}


static void add_float_param(GtkWidget *params_box, const char *labeltext,
                            float *pval, struct crystfelproject *proj)
{
	GtkWidget *hbox;
	GtkWidget *label;
	GtkWidget *entry;
	struct param_callback_vals *cbvals;
	char tmp[64];

	hbox = gtk_hbox_new(FALSE, 0.0);
	gtk_box_pack_start(GTK_BOX(params_box),
	                   GTK_WIDGET(hbox), FALSE, FALSE, 8.0);
	label = gtk_label_new(labeltext);
	gtk_misc_set_alignment(GTK_MISC(label), 1.0, 0.5);
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
	                   FALSE, FALSE, 2.0);
	entry = gtk_entry_new();
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(entry),
	                   TRUE, TRUE, 2.0);
	snprintf(tmp, 63, "%.2f", *pval);
	gtk_entry_set_text(GTK_ENTRY(entry), tmp);

	cbvals = malloc(sizeof(struct param_callback_vals));
	if ( cbvals != NULL ) {
		cbvals->proj = proj;
		cbvals->pfval = pval;
		g_signal_connect_data(G_OBJECT(entry), "activate",
		                      G_CALLBACK(float_param_callback),
		                      cbvals, free_callback_params, 0);
	} else {
		ERROR("Failed to connect parameter callback\n");
	}
}


static void add_check_param(GtkWidget *params_box, const char *labeltext,
                            int *pval, struct crystfelproject *proj)
{
	GtkWidget *checkbox;
	struct param_callback_vals *cbvals;

	checkbox = gtk_check_button_new_with_label(labeltext);
	gtk_box_pack_start(GTK_BOX(params_box),
	                   GTK_WIDGET(checkbox), FALSE, FALSE, 8.0);
	gtk_toggle_button_set_active(GTK_TOGGLE_BUTTON(checkbox),
	                             *pval);

	cbvals = malloc(sizeof(struct param_callback_vals));
	if ( cbvals != NULL ) {
		cbvals->proj = proj;
		cbvals->pival = pval;
		g_signal_connect_data(G_OBJECT(checkbox), "toggled",
		                      G_CALLBACK(check_param_callback),
		                      cbvals, free_callback_params, 0);
	} else {
		ERROR("Failed to connect parameter callback\n");
	}
}


static void peaksearch_algo_changed(GtkWidget *combo,
                                    struct crystfelproject *proj)
{
	const char *algo_id;

	if ( proj->peak_params != NULL ) {
		gtk_container_remove(GTK_CONTAINER(proj->peak_vbox),
		                     proj->peak_params);
		proj->peak_params = NULL;
	}

	proj->peak_params = gtk_vbox_new(FALSE, 0.0);
	gtk_box_pack_start(GTK_BOX(proj->peak_vbox),
	                   GTK_WIDGET(proj->peak_params),
	                   FALSE, FALSE, 8.0);

	algo_id = gtk_combo_box_get_active_id(GTK_COMBO_BOX(combo));

	if ( strcmp(algo_id, "zaef") == 0 ) {

		proj->peak_search_params.method = PEAK_ZAEF;

		add_float_param(proj->peak_params, "Threshold:",
		                &proj->peak_search_params.threshold, proj);
		add_float_param(proj->peak_params, "Minimum squared gradient:",
		                &proj->peak_search_params.min_sq_gradient, proj);
		add_float_param(proj->peak_params, "Minimum signal/noise ratio:",
		                &proj->peak_search_params.min_snr, proj);

	} else if ( strcmp(algo_id, "peakfinder8") == 0 ) {

		proj->peak_search_params.method = PEAK_PEAKFINDER8;

		add_float_param(proj->peak_params, "Threshold:",
		                &proj->peak_search_params.threshold, proj);
		add_float_param(proj->peak_params, "Minimum signal/noise ratio:",
		                &proj->peak_search_params.min_snr, proj);
		add_int_param(proj->peak_params, "Minimum number of pixels:",
		              &proj->peak_search_params.min_pix_count, proj);
		add_int_param(proj->peak_params, "Maximum number of pixels:",
		              &proj->peak_search_params.max_pix_count, proj);
		add_int_param(proj->peak_params, "Local background radius:",
		              &proj->peak_search_params.local_bg_radius, proj);
		add_int_param(proj->peak_params, "Minimum resolution (pixels):",
		              &proj->peak_search_params.min_res, proj);
		add_int_param(proj->peak_params, "Maximum resolution (pixels):",
		              &proj->peak_search_params.max_res, proj);

	} else if ( strcmp(algo_id, "hdf5") == 0 ) {

		proj->peak_search_params.method = PEAK_HDF5;

		add_check_param(proj->peak_params, "Half pixel shift",
		                &proj->peak_search_params.half_pixel_shift,
		                proj);

	} else if ( strcmp(algo_id, "cxi") == 0 ) {
		ERROR("algo_id should be hdf5, not cxi\n");

	} else {
		ERROR("Unrecognised peak search '%s'\n", algo_id);
	}

	/* FIXME: Radii */

	gtk_widget_show_all(proj->peak_vbox);
	update_peaks(proj);
}


static void peaksearch_response_sig(GtkWidget *dialog, gint resp,
                                    struct crystfelproject *proj)
{

	if ( (resp == GTK_RESPONSE_DELETE_EVENT)
	  || (resp == GTK_RESPONSE_CANCEL) )
	{
		proj->peak_search_params = proj->original_params;
		update_peaks(proj);
	}

	gtk_widget_destroy(dialog);
	proj->peak_vbox = NULL;
	proj->peak_params = NULL;
}


gint peaksearch_sig(GtkWidget *widget, struct crystfelproject *proj)
{
	GtkWidget *dialog;
	GtkWidget *content_area;
	GtkWidget *vbox;
	GtkWidget *hbox;
	GtkWidget *label;
	GtkWidget *combo;
	GtkWidget *w;

	if ( proj->peak_params != NULL ) return FALSE;

	proj->show_peaks = 1;

	w =  gtk_ui_manager_get_widget(proj->ui, "/ui/mainwindow/view/peaks");
	gtk_check_menu_item_set_active(GTK_CHECK_MENU_ITEM(w), 1);

	/* Take a copy of the original parameters, for reverting */
	proj->original_params = proj->peak_search_params;

	dialog = gtk_dialog_new_with_buttons("Peak search",
	                                     GTK_WINDOW(proj->window),
	                                     GTK_DIALOG_DESTROY_WITH_PARENT,
	                                     "Discard changes", GTK_RESPONSE_CANCEL,
	                                     "Confirm", GTK_RESPONSE_ACCEPT,
	                                     NULL);

	g_signal_connect(G_OBJECT(dialog), "response",
	                 G_CALLBACK(peaksearch_response_sig), proj);

	vbox = gtk_vbox_new(FALSE, 0.0);
	content_area = gtk_dialog_get_content_area(GTK_DIALOG(dialog));
	gtk_container_add(GTK_CONTAINER(content_area), vbox);
	gtk_container_set_border_width(GTK_CONTAINER(content_area), 8);
	proj->peak_vbox = vbox;

	hbox = gtk_hbox_new(FALSE, 0.0);
	gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox), FALSE, FALSE, 8.0);
	label = gtk_label_new("Peak search algorithm");
	gtk_misc_set_alignment(GTK_MISC(label), 1.0, 0.5);
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label), FALSE, FALSE, 2.0);
	combo = gtk_combo_box_text_new();
	gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(combo), TRUE, TRUE, 2.0);
	gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "zaef",
	                "Zaefferer gradient search (zaef)");
	gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "hdf5",
	                "Use the peak lists in the data files (hdf5/cxi)");
	gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "peakfinder8",
	                "Radial background estimation (peakfinder8)");
	#ifdef HAVE_FDIP
	gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "peakfinder9",
	                "Local background estimation (peakfinder9)");
	#endif
	g_signal_connect(G_OBJECT(combo), "changed",
	                 G_CALLBACK(peaksearch_algo_changed), proj);
	gtk_combo_box_set_active_id(GTK_COMBO_BOX(combo),
	                            str_peaksearch(proj->peak_search_params.method));
	proj->type_combo = combo;

	gtk_widget_show_all(dialog);

	return FALSE;
}