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-rw-r--r--CMakeLists.txt2
-rw-r--r--meson.build1
-rw-r--r--src/crystfel_gui.c3
-rw-r--r--src/gui_ambi.c262
-rw-r--r--src/gui_ambi.h39
-rw-r--r--src/gui_project.c67
-rw-r--r--src/gui_project.h10
7 files changed, 380 insertions, 4 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index bdd31cb4..a698bfb1 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -397,7 +397,7 @@ if (GTK_FOUND)
src/gui_peaksearch.c src/gui_index.c src/gui_merge.c src/gui_backend_local.c
src/gui_project.c src/crystfelindexingopts.c src/crystfelmergeopts.c
src/crystfelsymmetryselector.c src/gtk-util-routines.c src/gui_fom.c
- src/gui_export.c)
+ src/gui_export.c src/gui_ambi.c)
if (HAVE_SLURM)
set(CRYSTFEL_GUI_SOURCES ${CRYSTFEL_GUI_SOURCES} src/gui_backend_slurm.c)
diff --git a/meson.build b/meson.build
index 21bfa2f6..ed68aa03 100644
--- a/meson.build
+++ b/meson.build
@@ -228,6 +228,7 @@ if gtkdep.found()
'src/gui_merge.c',
'src/gui_fom.c',
'src/gui_export.c',
+ 'src/gui_ambi.c',
'src/gui_backend_local.c',
'src/gui_project.c',
versionc]
diff --git a/src/crystfel_gui.c b/src/crystfel_gui.c
index e4151b43..f32153aa 100644
--- a/src/crystfel_gui.c
+++ b/src/crystfel_gui.c
@@ -50,6 +50,7 @@
#include "gui_merge.h"
#include "gui_fom.h"
#include "gui_export.h"
+#include "gui_ambi.h"
#include "gui_project.h"
#include "version.h"
@@ -857,7 +858,7 @@ static void add_task_buttons(GtkWidget *vbox, struct crystfelproject *proj)
add_button(vbox, "Determine unit cell", "applications-engineering",
G_CALLBACK(cell_explorer_sig), proj);
add_button(vbox, "Indexing ambiguity", "face-worried",
- G_CALLBACK(NULL), proj);
+ G_CALLBACK(ambi_sig), proj);
add_button(vbox, "Merge", "applications-science",
G_CALLBACK(merge_sig), proj);
add_button(vbox, "Figures of merit", "trophy-gold",
diff --git a/src/gui_ambi.c b/src/gui_ambi.c
new file mode 100644
index 00000000..666da6eb
--- /dev/null
+++ b/src/gui_ambi.c
@@ -0,0 +1,262 @@
+/*
+ * gui_ambi.c
+ *
+ * Resolve indexing ambiguities via CrystFEL GUI
+ *
+ * Copyright © 2021 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2021 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 <string.h>
+#include <gtk/gtk.h>
+#include <assert.h>
+
+#include "crystfelsymmetryselector.h"
+#include "gui_project.h"
+#include "crystfel_gui.h"
+#include "gtk-util-routines.h"
+
+
+struct ambi_window
+{
+ struct crystfelproject *proj;
+ GtkWidget *dataset;
+ GtkWidget *limit_res;
+ GtkWidget *min_res;
+ GtkWidget *max_res;
+ GtkWidget *niter;
+ GtkWidget *use_ncorr;
+ GtkWidget *ncorr;
+ GtkWidget *sym;
+ GtkWidget *source_sym;
+ GtkWidget *operator;
+ GtkWidget *use_source_sym;
+ GtkWidget *use_operator;
+};
+
+
+static char *get_sym(GtkWidget *w)
+{
+ return crystfel_symmetry_selector_get_group_symbol(CRYSTFEL_SYMMETRY_SELECTOR(w));
+}
+
+
+static char *get_str(GtkWidget *w)
+{
+ const char *text = gtk_entry_get_text(GTK_ENTRY(w));
+ if ( text == NULL ) return NULL;
+ if ( text[0] == '\0' ) return NULL;
+ return strdup(text);
+}
+
+
+static void ambi_response_sig(GtkWidget *dialog, gint resp,
+ struct ambi_window *win)
+{
+ int r = 0;
+
+ if ( resp == GTK_RESPONSE_ACCEPT ) {
+ win->proj->ambi_use_res = get_bool(win->limit_res);
+ win->proj->ambi_res_min = get_float(win->min_res);
+ win->proj->ambi_res_max = get_float(win->max_res);
+ win->proj->ambi_niter = get_uint(win->niter);
+ win->proj->ambi_use_ncorr = get_bool(win->use_ncorr);
+ win->proj->ambi_ncorr = get_uint(win->ncorr);
+ win->proj->ambi_sym = get_sym(win->sym);
+ win->proj->ambi_source_sym = get_sym(win->source_sym);
+ win->proj->ambi_operator = get_str(win->operator);
+ }
+
+ if ( !r ) gtk_widget_destroy(dialog);
+}
+
+
+gint ambi_sig(GtkWidget *widget, struct crystfelproject *proj)
+{
+ GtkWidget *dialog;
+ GtkWidget *content_area;
+ GtkWidget *vbox;
+ GtkWidget *hbox;
+ GtkWidget *label;
+ struct ambi_window *win;
+ int i;
+ char tmp[64];
+
+ win = malloc(sizeof(struct ambi_window));
+ if ( win == NULL ) return 0;
+
+ win->proj = proj;
+
+ dialog = gtk_dialog_new_with_buttons("Resolve indexing ambiguity",
+ GTK_WINDOW(proj->window),
+ GTK_DIALOG_DESTROY_WITH_PARENT,
+ "Close", GTK_RESPONSE_CLOSE,
+ "Run", GTK_RESPONSE_ACCEPT,
+ NULL);
+
+ g_signal_connect(G_OBJECT(dialog), "response",
+ G_CALLBACK(ambi_response_sig),
+ win);
+
+ 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);
+ gtk_container_set_border_width(GTK_CONTAINER(vbox), 4);
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ label = gtk_label_new("Indexing result for input:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+ FALSE, FALSE, 4.0);
+ win->dataset = gtk_combo_box_text_new();
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->dataset),
+ FALSE, FALSE, 4.0);
+ for ( i=0; i<proj->n_results; i++ ) {
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(win->dataset),
+ proj->results[i].name,
+ proj->results[i].name);
+ }
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ label = gtk_label_new("Target ('real') point group:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+ FALSE, FALSE, 4.0);
+ win->sym = crystfel_symmetry_selector_new();
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->sym),
+ FALSE, FALSE, 4.0);
+ crystfel_symmetry_selector_set_group_symbol(CRYSTFEL_SYMMETRY_SELECTOR(win->sym),
+ proj->ambi_sym);
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ win->use_source_sym = gtk_radio_button_new_with_label(NULL, "Source ('twinned') point group:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->use_source_sym),
+ FALSE, FALSE, 4.0);
+ win->source_sym = crystfel_symmetry_selector_new();
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->source_sym),
+ FALSE, FALSE, 4.0);
+ crystfel_symmetry_selector_set_group_symbol(CRYSTFEL_SYMMETRY_SELECTOR(win->source_sym),
+ proj->ambi_source_sym);
+ g_signal_connect(G_OBJECT(win->use_source_sym), "toggled",
+ G_CALLBACK(i_maybe_disable), win->source_sym);
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ win->use_operator = gtk_radio_button_new_with_label_from_widget(GTK_RADIO_BUTTON(win->use_source_sym),
+ "Ambiguity operation:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->use_operator),
+ FALSE, FALSE, 4.0);
+ win->operator = gtk_entry_new();
+ gtk_entry_set_text(GTK_ENTRY(win->operator), proj->ambi_operator);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->operator),
+ FALSE, FALSE, 4.0);
+ g_signal_connect(G_OBJECT(win->use_operator), "toggled",
+ G_CALLBACK(i_maybe_disable), win->operator);
+
+ if ( proj->ambi_source_sym != NULL ) {
+ gtk_widget_set_sensitive(win->operator, FALSE);
+ set_active(win->use_source_sym, TRUE);
+ } else {
+ gtk_widget_set_sensitive(win->source_sym, FALSE);
+ set_active(win->use_operator, TRUE);
+ }
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ win->limit_res = gtk_check_button_new_with_label("Restrict resolution range:");
+ set_active(win->limit_res, proj->ambi_use_res);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->limit_res),
+ FALSE, FALSE, 4.0);
+ win->min_res = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(win->min_res), 6);
+ snprintf(tmp, 64, "%.2f", proj->ambi_res_min);
+ gtk_entry_set_text(GTK_ENTRY(win->min_res), tmp);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->min_res),
+ FALSE, FALSE, 4.0);
+ label = gtk_label_new("to");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+ FALSE, FALSE, 4.0);
+ win->max_res = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(win->max_res), 6);
+ snprintf(tmp, 64, "%.2f", proj->ambi_res_max);
+ gtk_entry_set_text(GTK_ENTRY(win->max_res), tmp);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->max_res),
+ FALSE, FALSE, 4.0);
+ label = gtk_label_new("Å");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+ FALSE, FALSE, 4.0);
+ g_signal_connect(G_OBJECT(win->limit_res), "toggled",
+ G_CALLBACK(i_maybe_disable), win->min_res);
+ g_signal_connect(G_OBJECT(win->limit_res), "toggled",
+ G_CALLBACK(i_maybe_disable), win->max_res);
+ gtk_widget_set_sensitive(win->min_res, proj->ambi_use_res);
+ gtk_widget_set_sensitive(win->max_res, proj->ambi_use_res);
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ win->use_ncorr = gtk_check_button_new_with_label("Limit number of correlations to:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->use_ncorr),
+ FALSE, FALSE, 4.0);
+ win->ncorr = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(win->ncorr), 6);
+ snprintf(tmp, 64, "%i", proj->ambi_ncorr);
+ gtk_entry_set_text(GTK_ENTRY(win->ncorr), tmp);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->ncorr),
+ FALSE, FALSE, 4.0);
+ g_signal_connect(G_OBJECT(win->use_ncorr), "toggled",
+ G_CALLBACK(i_maybe_disable), win->ncorr);
+ set_active(win->use_ncorr, proj->ambi_use_ncorr);
+ gtk_widget_set_sensitive(win->ncorr, proj->ambi_use_ncorr);
+
+ hbox = gtk_hbox_new(FALSE, 0.0);
+ gtk_box_pack_start(GTK_BOX(vbox), GTK_WIDGET(hbox),
+ FALSE, FALSE, 4.0);
+ label = gtk_label_new("Number of iterations:");
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(label),
+ FALSE, FALSE, 4.0);
+ win->niter = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(win->niter), 2);
+ snprintf(tmp, 64, "%i", proj->ambi_niter);
+ gtk_entry_set_text(GTK_ENTRY(win->niter), tmp);
+ gtk_box_pack_start(GTK_BOX(hbox), GTK_WIDGET(win->niter),
+ FALSE, FALSE, 4.0);
+
+ gtk_dialog_set_default_response(GTK_DIALOG(dialog),
+ GTK_RESPONSE_CLOSE);
+ gtk_widget_show_all(dialog);
+
+ return FALSE;
+}
diff --git a/src/gui_ambi.h b/src/gui_ambi.h
new file mode 100644
index 00000000..f63c29a0
--- /dev/null
+++ b/src/gui_ambi.h
@@ -0,0 +1,39 @@
+/*
+ * gui_ambi.h
+ *
+ * Resolve indexing ambiguities via CrystFEL GUI
+ *
+ * Copyright © 2021 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2021 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/>.
+ *
+ */
+
+#ifndef GUI_AMBI_H
+#define GUI_AMBI_H
+
+#include <gtk/gtk.h>
+
+#include "gui_project.h"
+
+extern gint ambi_sig(GtkWidget *widget,
+ struct crystfelproject *proj);
+
+#endif
diff --git a/src/gui_project.c b/src/gui_project.c
index 153fb55f..d89c66f9 100644
--- a/src/gui_project.c
+++ b/src/gui_project.c
@@ -312,6 +312,39 @@ static void add_metadata_to_copy(struct index_params *ip,
}
+static void parse_ambi_opt(const char *key, const char *val,
+ struct crystfelproject *proj)
+{
+ if ( strcmp(key, "ambi.min_res_A") == 0 ) {
+ proj->ambi_res_min = parse_float(val);
+ }
+ if ( strcmp(key, "ambi.max_res_A") == 0 ) {
+ proj->ambi_res_max = parse_float(val);
+ }
+ if ( strcmp(key, "ambi.use_res") == 0 ) {
+ proj->ambi_use_res = parse_int(val);
+ }
+ if ( strcmp(key, "ambi.niter") == 0 ) {
+ proj->ambi_niter = parse_int(val);
+ }
+ if ( strcmp(key, "ambi.ncorr") == 0 ) {
+ proj->ambi_ncorr = parse_int(val);
+ }
+ if ( strcmp(key, "ambi.use_ncorr") == 0 ) {
+ proj->ambi_use_ncorr = parse_int(val);
+ }
+ if ( strcmp(key, "ambi.sym") == 0 ) {
+ proj->ambi_sym = strdup(val);
+ }
+ if ( strcmp(key, "ambi.source_sym") == 0 ) {
+ proj->ambi_source_sym = strdup(val);
+ }
+ if ( strcmp(key, "ambi.operator") == 0 ) {
+ proj->ambi_operator = strdup(val);
+ }
+}
+
+
static void parse_fom_opt(const char *key, const char *val,
struct crystfelproject *proj)
{
@@ -460,6 +493,10 @@ static void handle_var(const char *key, const char *val,
parse_fom_opt(key, val, proj);
}
+ if ( strncmp(key, "ambi.", 4) == 0 ) {
+ parse_ambi_opt(key, val, proj);
+ }
+
if ( strncmp(key, "stream.", 7) == 0 ) {
parse_stream_opt(key, val, &proj->indexing_params);
} else if ( strcmp(key, "stream") == 0 ) {
@@ -871,6 +908,22 @@ int save_project(struct crystfelproject *proj)
}
}
+ fprintf(fh, "ambi.min_res_A %f\n", proj->ambi_res_min);
+ fprintf(fh, "ambi.max_res_A %f\n", proj->ambi_res_max);
+ fprintf(fh, "ambi.use_res %i\n", proj->ambi_use_res);
+ fprintf(fh, "ambi.niter %i\n", proj->ambi_niter);
+ fprintf(fh, "ambi.ncorr %i\n", proj->ambi_ncorr);
+ fprintf(fh, "ambi.use_ncorr %i\n", proj->ambi_use_ncorr);
+ if ( proj->ambi_sym != NULL ) {
+ fprintf(fh, "ambi.sym %s\n", proj->ambi_sym);
+ }
+ if ( proj->ambi_source_sym != NULL ) {
+ fprintf(fh, "ambi.source_sym %s\n", proj->ambi_source_sym);
+ }
+ if ( proj->ambi_operator != NULL ) {
+ fprintf(fh, "ambi.operator %s\n", proj->ambi_operator);
+ }
+
fprintf(fh, "merging.model %s\n",
proj->merging_params.model);
fprintf(fh, "merging.symmetry %s\n",
@@ -1045,6 +1098,16 @@ void default_project(struct crystfelproject *proj)
proj->indexing_params.metadata_to_copy = NULL;
proj->indexing_params.n_metadata = 0;
+ proj->ambi_use_res = 1;
+ proj->ambi_res_min = 20; /* Angstroms */
+ proj->ambi_res_max = 4; /* Angstroms */
+ proj->ambi_niter = 4;
+ proj->ambi_use_ncorr = 0;
+ proj->ambi_ncorr = 1000;
+ proj->ambi_sym = NULL;
+ proj->ambi_source_sym = NULL;
+ proj->ambi_operator = NULL;
+
proj->merging_params.model = strdup("unity");
proj->merging_params.symmetry = strdup("1");
proj->merging_params.scale = 1;
@@ -1066,8 +1129,8 @@ void default_project(struct crystfelproject *proj)
proj->merge_results = NULL;
proj->n_merge_results = 0;
- proj->fom_res_min = 100.0;
- proj->fom_res_max = 5.0;
+ proj->fom_res_min = 100.0; /* Angstroms */
+ proj->fom_res_max = 5.0; /* Angstroms */
proj->fom_nbins = 20;
proj->fom_min_snr = -INFINITY;
proj->fom_min_meas = 1;
diff --git a/src/gui_project.h b/src/gui_project.h
index 4d2e75c3..37307d3b 100644
--- a/src/gui_project.h
+++ b/src/gui_project.h
@@ -277,6 +277,16 @@ struct crystfelproject {
double export_res_min;
double export_res_max;
+
+ int ambi_use_res;
+ double ambi_res_min; /* Angstroms */
+ double ambi_res_max; /* Angstroms */
+ int ambi_niter;
+ int ambi_use_ncorr;
+ int ambi_ncorr;
+ char *ambi_sym;
+ char *ambi_source_sym;
+ char *ambi_operator;
};
extern enum match_type_id decode_matchtype(const char *type_id);
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 19:28:55 +0000