Added a parameter to fit whether to calculate confidence limits at all (fit->cl, default: false, "set cl true" can be used to change). Changed plotting and saving defaults of confidence limits to true, so if they are calculated then by default they are also shown and saved.

Author: jaakkojulin

qjabs/mainwindow.cpp

@@ -132,7 +132,7 @@ void MainWindow::readPlotSettings()
     ui->widget->setLegendVisible(settings.value("showLegend", QVariant(true)).toBool());
     ui->widget->setLegendOutside(settings.value("legendOutside", QVariant(false)).toBool());
     ui->widget->setEnergyAxis(settings.value("energyAxis", QVariant(false)).toBool());
-    confidenceLimits = settings.value("confidenceLimits", QVariant(false)).toBool();
+    confidenceLimits = settings.value("confidenceLimits", QVariant(true)).toBool();
     plotSession();
 }
 

qjabs/plotdialog.cpp

@@ -47,7 +47,7 @@ void PlotDialog::readSettings()
     }
     ui->showlegendCheckBox->setChecked(settings.value("showLegend", QVariant(true)).toBool());
     ui->legendOutsideCheckBox->setChecked(settings.value("legendOutside", QVariant(false)).toBool());
-    ui->confidencelimitsCheckBox->setChecked(settings.value("confidenceLimits", QVariant(false)).toBool());
+    ui->confidencelimitsCheckBox->setChecked(settings.value("confidenceLimits", QVariant(true)).toBool());
 }
 
 void PlotDialog::saveSettings()

qjabs/plotdialog.ui

@@ -6,7 +6,7 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>270</width>
+    <width>316</width>
     <height>196</height>
    </rect>
   </property>
@@ -61,7 +61,10 @@
      <item>
       <widget class="QCheckBox" name="confidencelimitsCheckBox">
        <property name="text">
-        <string>Show confidence limits (BETA)</string>
+        <string>Show confidence limits if calculated (BETA)</string>
+       </property>
+       <property name="checked">
+        <bool>true</bool>
        </property>
       </widget>
      </item>

src/fit.c

@@ -356,6 +356,7 @@ void fit_data_defaults(fit_data *f) {
     f->chisq_fast_tol = FIT_FAST_CHISQ_TOL;
     f->phase_start = FIT_PHASE_FAST;
     f->phase_stop = FIT_PHASE_SLOW;
+    f->cl = FALSE;
 }
 
 int fit_data_jspace_init(fit_data *fit, size_t n_channels_in_fit) {
@@ -1221,12 +1222,14 @@ int fit(fit_data *fit) {
         fit_params_print_final(fit_params);
         fit_correlation_print(fit->covar, MSG_VERBOSE);
         fit_data_print(fit, MSG_VERBOSE);
+        if(fit->cl) { /* Calculate confidence limits */
 #ifdef DEBUG
-        const char *f_uncertainty = "errors.dat";
+            const char *f_uncertainty = "errors.dat";
 #else
-        const char *f_uncertainty = NULL;
+            const char *f_uncertainty = NULL;
 #endif
-        fit_uncertainty_spectra(fit, J, fit->covar, f, &wts.vector, f_uncertainty);
+            fit_uncertainty_spectra(fit, J, fit->covar, f, &wts.vector, f_uncertainty);
+        }
     }
     gsl_multifit_nlinear_free(w);
     gsl_vector_free(fit->f_iter);

src/fit.h

@@ -113,6 +113,7 @@ typedef struct fit_data {
     double xtol; /* Tolerance of step size */
     double chisq_tol; /* Chi squared relative change tolerance */
     double chisq_fast_tol; /* Chi squared relative change tolerance (fast phase) */
+    int cl; /* Calculate confidence limits */
     gsl_multifit_nlinear_fdf *fdf;
     size_t dof; /* Degrees of freedom (calculated) */
     struct fit_stats stats; /* Fit statistics, updated as we iterate */

src/script_command.c

@@ -286,21 +286,15 @@ script_command_status script_save_spectra(script_session *s, int argc, char *con
     size_t i_det = 0;
     struct fit_data *fit = s->fit;
     const int argc_orig = argc;
-    int cl = FALSE;
-    if(argc && strcmp(argv[0], "cl") == 0) {
-        cl = TRUE;
-        argc--;
-        argv++;
-    }
     if(script_get_detector_number(fit->sim, TRUE, &argc, &argv, &i_det) || argc < 1) {
-        jabs_message(MSG_ERROR, "Usage: save spectra {cl} {<detector>} <file>\n");
+        jabs_message(MSG_ERROR, "Usage: save spectra {<detector>} <file>\n");
         return SCRIPT_COMMAND_FAILURE;
     }
     if(argc < 1) {
         jabs_message(MSG_ERROR, "Not enough arguments for save spectra.\n");
         return SCRIPT_COMMAND_FAILURE;
     }
-    if(sim_workspace_print_spectra(fit->spectra, argv[0], cl)) {
+    if(sim_workspace_print_spectra(fit->spectra, argv[0], fit->cl)) {
         jabs_message(MSG_ERROR,
                      "Could not save spectra of detector %zu to file \"%s\"! There should be %zu detector(s).\n",
                      i_det + 1, argv[0], fit->sim->n_det);
@@ -1313,6 +1307,7 @@ script_command *script_commands_create(struct script_session *s) {
             {JIBAL_CONFIG_VAR_DOUBLE, "xtolerance",                    0,     0,                               &fit->xtol,                                  NULL},
             {JIBAL_CONFIG_VAR_DOUBLE, "chisq_tolerance",               0,     0,                               &fit->chisq_tol,                             NULL},
             {JIBAL_CONFIG_VAR_DOUBLE, "chisq_fast_tolerance",          0,     0,                               &fit->chisq_fast_tol,                        NULL},
+            {JIBAL_CONFIG_VAR_BOOL,   "cl",                            0,     0,                               &fit->cl,                                    NULL},
             {JIBAL_CONFIG_VAR_SIZE,   "n_bricks_max",                  0,     0,                               &sim->params->n_bricks_max,                  NULL},
             {JIBAL_CONFIG_VAR_BOOL,   "ds",                            0,     0,                               &sim->params->ds,                            NULL},
             {JIBAL_CONFIG_VAR_BOOL,   "rk4",                           0,     0,                               &sim->params->rk4,                           NULL},