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-rw-r--r--src/crystfelindexingopts.c244
-rw-r--r--src/crystfelindexingopts.h38
2 files changed, 277 insertions, 5 deletions
diff --git a/src/crystfelindexingopts.c b/src/crystfelindexingopts.c
index eb717354..dd02ffa4 100644
--- a/src/crystfelindexingopts.c
+++ b/src/crystfelindexingopts.c
@@ -507,18 +507,129 @@ static GtkWidget *integration_parameters(CrystFELIndexingOpts *io)
static GtkWidget *advanced_parameters(CrystFELIndexingOpts *io)
{
GtkWidget *box;
+ GtkWidget *vbox;
+ GtkWidget *vvbox;
+ GtkWidget *hbox;
GtkWidget *expander;
GtkWidget *label;
+ GtkWidget *scale;
+ GtkWidget *combo;
+ GtkWidget *entry;
+ GtkWidget *check;
box = gtk_box_new(GTK_ORIENTATION_VERTICAL, 8);
gtk_container_set_border_width(GTK_CONTAINER(box), 8);
expander = gtk_expander_new("PinkIndexer");
gtk_box_pack_start(GTK_BOX(box), expander, FALSE, FALSE, 8);
- label = gtk_label_new("Advanced options for this indexing method are "
- "currently not available through the GUI.");
- gtk_label_set_line_wrap(GTK_LABEL(label), TRUE);
- gtk_container_add(GTK_CONTAINER(expander), label);
+ vbox = gtk_box_new(GTK_ORIENTATION_VERTICAL, 8);
+ gtk_container_add(GTK_CONTAINER(expander), vbox);
+
+ vvbox = gtk_box_new(GTK_ORIENTATION_VERTICAL, 0);
+ gtk_box_pack_start(GTK_BOX(vbox), vvbox, FALSE, FALSE, 8);
+ label = gtk_label_new("Number of peaks to consider in initial stage:");
+ gtk_misc_set_alignment(GTK_MISC(label), 0.0, 0.5);
+ gtk_box_pack_start(GTK_BOX(vvbox), label, FALSE, FALSE, 0);
+ scale = gtk_scale_new_with_range(GTK_ORIENTATION_HORIZONTAL,
+ 0.0, 4.0, 1.0);
+ gtk_scale_set_draw_value(GTK_SCALE(scale), TRUE);
+ gtk_scale_add_mark(GTK_SCALE(scale), 0.0, GTK_POS_TOP, "very few");
+ gtk_scale_add_mark(GTK_SCALE(scale), 1.0, GTK_POS_TOP, "few");
+ gtk_scale_add_mark(GTK_SCALE(scale), 2.0, GTK_POS_TOP, "medium");
+ gtk_scale_add_mark(GTK_SCALE(scale), 3.0, GTK_POS_TOP, "many");
+ gtk_scale_add_mark(GTK_SCALE(scale), 4.0, GTK_POS_TOP, "very many");
+ gtk_widget_set_margin_start(scale, 12);
+ gtk_box_pack_start(GTK_BOX(vvbox), scale, TRUE, TRUE, 0);
+ io->pinkindexer_cpeaks = scale;
+
+ hbox = gtk_box_new(GTK_ORIENTATION_HORIZONTAL, 4);
+ gtk_container_add(GTK_CONTAINER(vbox), hbox);
+ check = gtk_check_button_new_with_label("Exclude peaks with 1/d above");
+ gtk_box_pack_start(GTK_BOX(hbox), check, FALSE, FALSE, 0);
+ entry = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(entry), 5);
+ gtk_entry_set_input_purpose(GTK_ENTRY(entry), GTK_INPUT_PURPOSE_NUMBER);
+ gtk_box_pack_start(GTK_BOX(hbox), entry, FALSE, FALSE, 4);
+ label = gtk_label_new("Å^-1 from initial stage");
+ gtk_label_set_markup(GTK_LABEL(label), "Å<sup>-1</sup> from initial stage");
+ gtk_box_pack_start(GTK_BOX(hbox), label, FALSE, FALSE, 4);
+ i_disable_if_not(check, entry);
+ io->pinkindexer_use_max_res = check;
+ io->pinkindexer_max_res = entry;
+
+ vvbox = gtk_box_new(GTK_ORIENTATION_VERTICAL, 0);
+ gtk_box_pack_start(GTK_BOX(vbox), vvbox, FALSE, FALSE, 8);
+ label = gtk_label_new("Angular sampling density:");
+ gtk_misc_set_alignment(GTK_MISC(label), 0.0, 0.5);
+ gtk_box_pack_start(GTK_BOX(vvbox), label, FALSE, FALSE, 0);
+ scale = gtk_scale_new_with_range(GTK_ORIENTATION_HORIZONTAL,
+ 0.0, 4.0, 1.0);
+ gtk_scale_set_draw_value(GTK_SCALE(scale), TRUE);
+ gtk_scale_add_mark(GTK_SCALE(scale), 0.0, GTK_POS_TOP, "very loose");
+ gtk_scale_add_mark(GTK_SCALE(scale), 1.0, GTK_POS_TOP, "loose");
+ gtk_scale_add_mark(GTK_SCALE(scale), 2.0, GTK_POS_TOP, "medium");
+ gtk_scale_add_mark(GTK_SCALE(scale), 3.0, GTK_POS_TOP, "dense");
+ gtk_scale_add_mark(GTK_SCALE(scale), 4.0, GTK_POS_TOP, "very dense");
+ gtk_widget_set_margin_start(scale, 12);
+ gtk_box_pack_start(GTK_BOX(vvbox), scale, TRUE, TRUE, 0);
+ io->pinkindexer_angle_density = scale;
+
+ hbox = gtk_box_new(GTK_ORIENTATION_HORIZONTAL, 0);
+ gtk_container_add(GTK_CONTAINER(vbox), hbox);
+ label = gtk_label_new("Refinement type");
+ gtk_box_pack_start(GTK_BOX(hbox), label, FALSE, FALSE, 0);
+ combo = gtk_combo_box_text_new();
+ gtk_box_pack_start(GTK_BOX(hbox), combo, FALSE, FALSE, 4);
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "0",
+ "None");
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "1",
+ "Fixed lattice parameters");
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "2",
+ "Variable lattice parameters");
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "3",
+ "Fixed, then variable parameters");
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "4",
+ "Fixed, then variable, multiseed");
+ gtk_combo_box_text_append(GTK_COMBO_BOX_TEXT(combo), "5",
+ "Fixed, then variable, multiseed, center refinement");
+ io->pinkindexer_refinement_type = combo;
+
+ hbox = gtk_box_new(GTK_ORIENTATION_HORIZONTAL, 0);
+ gtk_container_add(GTK_CONTAINER(vbox), hbox);
+ label = gtk_label_new("Relative tolerance for lattice vectors:");
+ gtk_box_pack_start(GTK_BOX(hbox), label, FALSE, FALSE, 0);
+ entry = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(entry), 5);
+ gtk_entry_set_input_purpose(GTK_ENTRY(entry), GTK_INPUT_PURPOSE_NUMBER);
+ gtk_box_pack_start(GTK_BOX(hbox), entry, FALSE, FALSE, 4);
+ io->pinkindexer_tolerance = entry;
+
+ hbox = gtk_box_new(GTK_ORIENTATION_HORIZONTAL, 0);
+ gtk_container_add(GTK_CONTAINER(vbox), hbox);
+ check = gtk_check_button_new_with_label("Manually set the estimated reflection radius to");
+ gtk_box_pack_start(GTK_BOX(hbox), check, FALSE, FALSE, 0);
+ entry = gtk_entry_new();
+ gtk_entry_set_width_chars(GTK_ENTRY(entry), 5);
+ gtk_entry_set_input_purpose(GTK_ENTRY(entry), GTK_INPUT_PURPOSE_NUMBER);
+ gtk_box_pack_start(GTK_BOX(hbox), entry, FALSE, FALSE, 4);
+ label = gtk_label_new("Å^-1");
+ gtk_label_set_markup(GTK_LABEL(label), "Å<sup>-1</sup>");
+ gtk_box_pack_start(GTK_BOX(hbox), label, FALSE, FALSE, 4);
+ i_disable_if_not(check, entry);
+ io->pinkindexer_use_refl_radius = check;
+ io->pinkindexer_refl_radius = entry;
+
+ vvbox = gtk_box_new(GTK_ORIENTATION_VERTICAL, 0);
+ gtk_box_pack_start(GTK_BOX(vbox), vvbox, FALSE, FALSE, 8);
+ label = gtk_label_new("Maximum allowable refinement imbalance:");
+ gtk_misc_set_alignment(GTK_MISC(label), 0.0, 0.5);
+ gtk_box_pack_start(GTK_BOX(vvbox), label, FALSE, FALSE, 0);
+ scale = gtk_scale_new_with_range(GTK_ORIENTATION_HORIZONTAL,
+ 0.0, 2.0, 0.1);
+ gtk_scale_set_draw_value(GTK_SCALE(scale), TRUE);
+ gtk_widget_set_margin_start(scale, 12);
+ gtk_box_pack_start(GTK_BOX(vvbox), scale, TRUE, TRUE, 0);
+ io->pinkindexer_max_imbalance = scale;
expander = gtk_expander_new("XGandalf");
gtk_box_pack_start(GTK_BOX(box), expander, FALSE, FALSE, 8);
@@ -977,6 +1088,60 @@ double crystfel_indexing_opts_get_fixed_divergence(CrystFELIndexingOpts *opts)
}
+int crystfel_indexing_opts_get_pinkindexer_cpeaks(CrystFELIndexingOpts *opts)
+{
+ return gtk_range_get_value(GTK_RANGE(opts->pinkindexer_cpeaks));
+}
+
+
+int crystfel_indexing_opts_get_pinkindexer_use_max_res(CrystFELIndexingOpts *opts)
+{
+ return get_bool(opts->pinkindexer_use_max_res);
+}
+
+
+double crystfel_indexing_opts_get_pinkindexer_max_res(CrystFELIndexingOpts *opts)
+{
+ return get_float(opts->pinkindexer_max_res);
+}
+
+
+int crystfel_indexing_opts_get_pinkindexer_angle_density(CrystFELIndexingOpts *opts)
+{
+ return gtk_range_get_value(GTK_RANGE(opts->pinkindexer_angle_density));
+}
+
+
+int crystfel_indexing_opts_get_pinkindexer_refinement_type(CrystFELIndexingOpts *opts)
+{
+ return atoi(get_combo_id(opts->pinkindexer_refinement_type));
+}
+
+
+double crystfel_indexing_opts_get_pinkindexer_tolerance(CrystFELIndexingOpts *opts)
+{
+ return get_float(opts->pinkindexer_tolerance);
+}
+
+
+int crystfel_indexing_opts_get_pinkindexer_use_refl_radius(CrystFELIndexingOpts *opts)
+{
+ return get_bool(opts->pinkindexer_use_refl_radius);
+}
+
+
+double crystfel_indexing_opts_get_pinkindexer_refl_radius(CrystFELIndexingOpts *opts)
+{
+ return get_float(opts->pinkindexer_refl_radius);
+}
+
+
+double crystfel_indexing_opts_get_pinkindexer_max_imbalance(CrystFELIndexingOpts *opts)
+{
+ return gtk_range_get_value(GTK_RANGE(opts->pinkindexer_max_imbalance));
+}
+
+
/********************** Setters *************************/
@@ -1255,3 +1420,74 @@ void crystfel_indexing_opts_set_fixed_divergence(CrystFELIndexingOpts *opts,
snprintf(tmp, 63, "%.3f", val*1e3);
gtk_entry_set_text(GTK_ENTRY(opts->fix_divergence), tmp);
}
+
+
+void crystfel_indexing_opts_set_pinkindexer_cpeaks(CrystFELIndexingOpts *opts,
+ int val)
+{
+ gtk_range_set_value(GTK_RANGE(opts->pinkindexer_cpeaks), val);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_use_max_res(CrystFELIndexingOpts *opts,
+ int val)
+{
+ set_active(opts->pinkindexer_use_max_res, val);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_max_res(CrystFELIndexingOpts *opts,
+ double val)
+{
+ char tmp[64];
+ snprintf(tmp, 63, "%.3f", val);
+ gtk_entry_set_text(GTK_ENTRY(opts->pinkindexer_max_res), tmp);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_angle_density(CrystFELIndexingOpts *opts,
+ int val)
+{
+ gtk_range_set_value(GTK_RANGE(opts->pinkindexer_angle_density), val);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_refinement_type(CrystFELIndexingOpts *opts,
+ int val)
+{
+ char tmp[64];
+ snprintf(tmp, 63, "%i", val);
+ set_combo_id(opts->pinkindexer_refinement_type, tmp);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_tolerance(CrystFELIndexingOpts *opts,
+ double val)
+{
+ char tmp[64];
+ snprintf(tmp, 63, "%.3f", val);
+ gtk_entry_set_text(GTK_ENTRY(opts->pinkindexer_tolerance), tmp);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_use_refl_radius(CrystFELIndexingOpts *opts,
+ int val)
+{
+ set_active(opts->pinkindexer_use_refl_radius, val);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_refl_radius(CrystFELIndexingOpts *opts,
+ double val)
+{
+ char tmp[64];
+ snprintf(tmp, 63, "%.3f", val);
+ gtk_entry_set_text(GTK_ENTRY(opts->pinkindexer_refl_radius), tmp);
+}
+
+
+void crystfel_indexing_opts_set_pinkindexer_max_imbalance(CrystFELIndexingOpts *opts,
+ double val)
+{
+ gtk_range_set_value(GTK_RANGE(opts->pinkindexer_max_imbalance), val);
+}
diff --git a/src/crystfelindexingopts.h b/src/crystfelindexingopts.h
index fe5f4ccd..567bdb8e 100644
--- a/src/crystfelindexingopts.h
+++ b/src/crystfelindexingopts.h
@@ -83,6 +83,16 @@ struct _crystfelindexingopts
GtkWidget *fix_profile_radius;
GtkWidget *fix_divergence;
+ GtkWidget *pinkindexer_cpeaks;
+ GtkWidget *pinkindexer_use_max_res;
+ GtkWidget *pinkindexer_max_res;
+ GtkWidget *pinkindexer_angle_density;
+ GtkWidget *pinkindexer_refinement_type;
+ GtkWidget *pinkindexer_tolerance;
+ GtkWidget *pinkindexer_use_refl_radius;
+ GtkWidget *pinkindexer_refl_radius;
+ GtkWidget *pinkindexer_max_imbalance;
+
GtkWidget *exclude_nonhits;
GtkWidget *no_peaks_in_stream;
GtkWidget *no_refls_in_stream;
@@ -127,7 +137,15 @@ extern double crystfel_indexing_opts_get_fixed_profile_radius(CrystFELIndexingOp
int *active);
extern double crystfel_indexing_opts_get_fixed_divergence(CrystFELIndexingOpts *opts);
-
+extern int crystfel_indexing_opts_get_pinkindexer_cpeaks(CrystFELIndexingOpts *opts);
+extern int crystfel_indexing_opts_get_pinkindexer_use_max_res(CrystFELIndexingOpts *opts);
+extern double crystfel_indexing_opts_get_pinkindexer_max_res(CrystFELIndexingOpts *opts);
+extern int crystfel_indexing_opts_get_pinkindexer_angle_density(CrystFELIndexingOpts *opts);
+extern int crystfel_indexing_opts_get_pinkindexer_refinement_type(CrystFELIndexingOpts *opts);
+extern double crystfel_indexing_opts_get_pinkindexer_tolerance(CrystFELIndexingOpts *opts);
+extern int crystfel_indexing_opts_get_pinkindexer_use_refl_radius(CrystFELIndexingOpts *opts);
+extern double crystfel_indexing_opts_get_pinkindexer_refl_radius(CrystFELIndexingOpts *opts);
+extern double crystfel_indexing_opts_get_pinkindexer_max_imbalance(CrystFELIndexingOpts *opts);
@@ -179,5 +197,23 @@ extern void crystfel_indexing_opts_set_fixed_profile_radius(CrystFELIndexingOpts
extern void crystfel_indexing_opts_set_fixed_divergence(CrystFELIndexingOpts *opts,
double val);
+extern void crystfel_indexing_opts_set_pinkindexer_cpeaks(CrystFELIndexingOpts *opts,
+ int val);
+extern void crystfel_indexing_opts_set_pinkindexer_use_max_res(CrystFELIndexingOpts *opts,
+ int val);
+extern void crystfel_indexing_opts_set_pinkindexer_max_res(CrystFELIndexingOpts *opts,
+ double val);
+extern void crystfel_indexing_opts_set_pinkindexer_angle_density(CrystFELIndexingOpts *opts,
+ int val);
+extern void crystfel_indexing_opts_set_pinkindexer_refinement_type(CrystFELIndexingOpts *opts,
+ int val);
+extern void crystfel_indexing_opts_set_pinkindexer_tolerance(CrystFELIndexingOpts *opts,
+ double val);
+extern void crystfel_indexing_opts_set_pinkindexer_use_refl_radius(CrystFELIndexingOpts *opts,
+ int val);
+extern void crystfel_indexing_opts_set_pinkindexer_refl_radius(CrystFELIndexingOpts *opts,
+ double val);
+extern void crystfel_indexing_opts_set_pinkindexer_max_imbalance(CrystFELIndexingOpts *opts,
+ double val);
#endif /* CRYSTFELINDEXINGOPTS_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-16 14:04:45 +0000