Removed useless uses of struct. We have typedefs, why not use them? Changed fit_data variable name to just fit. Renamed fit() to fit_do() to avoid issues with fit(fit)...

Author: jaakkojulin

plugins/testplugin.c

@@ -35,6 +35,6 @@ void reaction_free(jabs_plugin_reaction *r) {
     free(r);
 }
 
-double testplugin_cs(const struct jabs_plugin_reaction *r, double theta, double E) {
+double testplugin_cs(const jabs_plugin_reaction *r, double theta, double E) {
     return jibal_cross_section_rbs(r->incident, r->target, theta, E, JIBAL_CS_RUTHERFORD); /* just a simple test */
 }

src/fit.c

@@ -76,7 +76,7 @@ int fit_detector(const jibal *jibal, const fit_data_det *fdd, const simulation *
 void fit_deriv_prepare_jspaces(const gsl_vector *x, fit_data *fit) {
     jacobian_space *space = fit->jspace;
     for(size_t j = 0; j < fit->fit_params->n_active; j++) { /* Make copies of sim (shallow) with deep copies of detector and sample. This way we can parallelize. */
-        struct jacobian_space *spc = &space[j];
+        jacobian_space *spc = &space[j];
         spc->n_spectra_calculated = 0;
         fit_variable *var = spc->var;
         double xj = gsl_vector_get(x, j);
@@ -105,7 +105,7 @@ void fit_deriv_prepare_jspaces(const gsl_vector *x, fit_data *fit) {
 void fit_deriv_cleanup_jspaces(fit_data *fit) {
     jacobian_space *space = fit->jspace;
     for(size_t j = 0; j <  fit->fit_params->n_active; j++) {
-        struct jacobian_space *spc = &space[j];
+        jacobian_space *spc = &space[j];
         fit_variable *var = spc->var;
         fit->stats.n_spectra_iter += spc->n_spectra_calculated;
         switch(var->type) {
@@ -122,7 +122,7 @@ void fit_deriv_cleanup_jspaces(fit_data *fit) {
 }
 
 int fit_deriv_function(const gsl_vector *x, void *params, gsl_matrix *J) {
-    struct fit_data *fit = (struct fit_data *) params;
+    fit_data *fit = (fit_data *) params;
     assert(fit->stats.iter_call >= 1); /* This function relies on data that was computed when iter_call == 1 */
     assert(fit->fdf->p == fit->fit_params->n_active);
 
@@ -138,7 +138,7 @@ int fit_deriv_function(const gsl_vector *x, void *params, gsl_matrix *J) {
 #pragma omp for schedule(dynamic)
     for(j = 0; j < n; j++) {
         //fprintf(stderr, "Thread id %i got %zu.\n", omp_get_thread_num(), j);
-        struct jacobian_space *spc = &fit->jspace[j];
+        jacobian_space *spc = &fit->jspace[j];
         fit_variable *var = spc->var;
         size_t i_start, i_stop;
         if(var->type == FIT_VARIABLE_DETECTOR) {
@@ -178,7 +178,7 @@ int fit_deriv_function(const gsl_vector *x, void *params, gsl_matrix *J) {
 }
 
 int fit_function(const gsl_vector *x, void *params, gsl_vector *f) {
-    struct fit_data *fit = (struct fit_data *) params;
+    fit_data *fit = (fit_data *) params;
     fit->stats.iter_call++;
     if(fit->stats.iter_call == 1) { /* Clear stored spectra from previous iteration */
         for(size_t i = 0; i < fit->n_det_spectra; i++) {
@@ -254,7 +254,7 @@ int fit_sanity_check(const fit_data *fit) {
     return GSL_SUCCESS;
 }
 
-int fit_parameters_set_from_vector(struct fit_data *fit, const gsl_vector *x) {
+int fit_parameters_set_from_vector(fit_data *fit, const gsl_vector *x) {
     DEBUGMSG("Fit iteration has %zu active parameters from a total of %zu possible.", fit->fit_params->n_active, fit->fit_params->n)
     for(size_t i = 0; i < fit->fit_params->n; i++) {
         fit_variable *var = &fit->fit_params->vars[i];
@@ -271,7 +271,7 @@ int fit_parameters_set_from_vector(struct fit_data *fit, const gsl_vector *x) {
     return GSL_SUCCESS;
 }
 
-void fit_iter_stats_update(struct fit_data *fit_data, const gsl_multifit_nlinear_workspace *w) {
+void fit_iter_stats_update(fit_data *fit_data, const gsl_multifit_nlinear_workspace *w) {
     gsl_vector *f = gsl_multifit_nlinear_residual(w);
     /* compute reciprocal condition number of J(x) */
     gsl_multifit_nlinear_rcond(&fit_data->stats.rcond, w);
@@ -283,20 +283,20 @@ void fit_iter_stats_update(struct fit_data *fit_data, const gsl_multifit_nlinear
     fit_data->stats.cputime_cumul += fit_data->stats.cputime_iter;
 }
 
-void fit_iter_stats_print(const struct fit_stats *stats) {
+void fit_iter_stats_print(const fit_stats *stats) {
     jabs_message(MSG_INFO, "%4zu | %10.2e | %14.7e | %12.7lf | %7zu | %7zu | %10.3lf | %13.1lf |\n",
                  stats->iter, 1.0 / stats->rcond, stats->norm,
                  stats->chisq_dof, stats->n_evals, stats->n_spectra,
                  stats->cputime_cumul, 1000.0 * stats->cputime_iter / stats->n_spectra_iter);
 }
 
-void fit_stats_print(const struct fit_stats *stats, jabs_msg_level msg_level) {
+void fit_stats_print(const fit_stats *stats, jabs_msg_level msg_level) {
     if(stats->chisq_dof > 0.0) {
         jabs_message(msg_level, "Final chisq/dof = %.7lf\n", stats->chisq_dof);
     }
 }
 
-int fit_data_fit_range_add(struct fit_data *fit_data, const struct roi *range) { /* Makes a deep copy */
+int fit_data_fit_range_add(fit_data *fit_data, const roi *range) { /* Makes a deep copy */
     if(range->low == 0 && range->high == 0) {
         return EXIT_FAILURE;
     }
@@ -314,7 +314,7 @@ int fit_data_fit_range_add(struct fit_data *fit_data, const struct roi *range) {
     return EXIT_SUCCESS;
 }
 
-void fit_data_fit_ranges_free(struct fit_data *fit_data) {
+void fit_data_fit_ranges_free(fit_data *fit_data) {
     if(!fit_data)
         return;
     free(fit_data->fit_ranges);
@@ -341,7 +341,7 @@ void fit_data_det_residual_vector_set(const fit_data_det *fdd, const jabs_histog
     DEBUGMSG("Set %zu elements of vector from %zu ranges.", i_vec, fdd->n_ranges);
 }
 fit_data *fit_data_new(const jibal *jibal, simulation *sim) {
-    struct fit_data *fit = calloc(1, sizeof(struct fit_data));
+    fit_data *fit = calloc(1, sizeof(fit_data));
     fit->jibal = jibal;
     fit->sim = sim;
     fit_data_exp_alloc(fit);
@@ -425,20 +425,20 @@ void fit_data_exp_reset(fit_data *fit) {
     }
 }
 
-void fit_data_roi_print(const struct fit_data *fit_data, const struct roi *roi) {
-    if(!fit_data) {
+void fit_data_roi_print(const fit_data *fit, const struct roi *roi) {
+    if(!fit) {
         return;
     }
-    jabs_histogram *histo_sim = fit_data_histo_sum(fit_data, roi->i_det);
-    jabs_histogram *histo_exp = fit_data_exp(fit_data, roi->i_det);
-    jabs_histogram *histo_ref = fit_data->ref;
+    jabs_histogram *histo_sim = fit_data_histo_sum(fit, roi->i_det);
+    jabs_histogram *histo_exp = fit_data_exp(fit, roi->i_det);
+    jabs_histogram *histo_ref = fit->ref;
     size_t n_sim = jabs_histogram_channels_in_range(histo_sim, roi->low, roi->high);
     size_t n_exp = jabs_histogram_channels_in_range(histo_exp, roi->low, roi->high);
     size_t n_ref = jabs_histogram_channels_in_range(histo_ref, roi->low, roi->high);
     double sim_cts = jabs_histogram_roi(histo_sim, roi->low, roi->high);
     double exp_cts = jabs_histogram_roi(histo_exp, roi->low, roi->high);
     double ref_cts = jabs_histogram_roi(histo_ref, roi->low, roi->high);
-    const detector *det = sim_det(fit_data->sim, roi->i_det);
+    const detector *det = sim_det(fit->sim, roi->i_det);
 
     jabs_message(MSG_INFO, "          low = %12zu\n", roi->low);
     jabs_message(MSG_INFO, "         high = %12zu\n", roi->high);
@@ -677,7 +677,7 @@ void fit_data_exp_free(fit_data *fit) {
     fit->n_exp = 0;
 }
 
-int fit_data_load_exp(struct fit_data *fit, size_t i_det, const char *filename) {
+int fit_data_load_exp(fit_data *fit, size_t i_det, const char *filename) {
     jabs_histogram *h = spectrum_read_detector(filename, sim_det(fit->sim, i_det));
     if(!h) {
         jabs_message(MSG_ERROR, "Reading spectrum from file \"%s\" was not successful.\n", filename);
@@ -756,7 +756,7 @@ void fit_data_spectra_free(fit_data *fit) {
     fit->n_det_spectra = 0;
 }
 
-int fit_data_add_det(struct fit_data *fit, detector *det) {
+int fit_data_add_det(fit_data *fit, detector *det) {
     if(!fit || !det)
         return EXIT_FAILURE;
     if(sim_det_add(fit->sim, det)) {
@@ -775,11 +775,11 @@ fit_data_det *fit_data_fdd(const fit_data *fit, size_t i_det) {
 }
 
 
-size_t fit_data_ranges_calculate_number_of_channels(const struct fit_data *fit_data) {
+size_t fit_data_ranges_calculate_number_of_channels(const fit_data *fit) {
     size_t sum = 0;
-    for(size_t i = 0; i < fit_data->n_fit_ranges; i++) {
-        roi *r = &fit_data->fit_ranges[i];
-        detector *det = sim_det(fit_data->sim, r->i_det);
+    for(size_t i = 0; i < fit->n_fit_ranges; i++) {
+        roi *r = &fit->fit_ranges[i];
+        detector *det = sim_det(fit->sim, r->i_det);
         if(!det) {
             continue;
         }
@@ -792,8 +792,8 @@ size_t fit_data_ranges_calculate_number_of_channels(const struct fit_data *fit_d
     return sum;
 }
 
-struct fit_stats fit_stats_init(void) {
-    struct fit_stats s;
+fit_stats fit_stats_init(void) {
+    fit_stats s;
     s.n_evals = 0;
     s.n_evals_iter = 0;
     s.n_spectra = 0;
@@ -869,31 +869,30 @@ int multifit_nlinear_print_jacobian(const gsl_multifit_nlinear_workspace *w, con
     return EXIT_SUCCESS;
 }
 
-int jabs_gsl_multifit_nlinear_driver(const size_t maxiter, const double xtol, const double chisq_tol, struct fit_data *fit_data, gsl_multifit_nlinear_workspace *w) {
+int jabs_gsl_multifit_nlinear_driver(const size_t maxiter, const double xtol, const double chisq_tol, fit_data *fit, gsl_multifit_nlinear_workspace *w) {
     int status = 0;
-    size_t iter;
     double chisq_dof_old;
     jabs_message(MSG_INFO, "iter |   cond(J)  |     |f(x)|     |   chisq/dof  |   evals | spectra | time cumul | time/spectrum |\n");
     jabs_message(MSG_INFO, "     |            |                |              |  cumul. |  cumul. |          s |            ms |\n");
-    for(iter = 0; iter <= maxiter; iter++) {
-        fit_data->stats.iter_call = 0;
-        fit_data->stats.iter = iter;
+    for(size_t iter = 0; iter <= maxiter; iter++) {
+        fit->stats.iter_call = 0;
+        fit->stats.iter = iter;
         if(iter) {
-            chisq_dof_old = fit_data->stats.chisq_dof;
-            fit_data->stats.cputime_iter = 0.0;
-            fit_data->stats.n_evals_iter = 0;
-            fit_data->stats.n_spectra_iter = 0;
+            chisq_dof_old = fit->stats.chisq_dof;
+            fit->stats.cputime_iter = 0.0;
+            fit->stats.n_evals_iter = 0;
+            fit->stats.n_spectra_iter = 0;
             status = gsl_multifit_nlinear_iterate(w);
             DEBUGMSG("Iteration status %i (%s)", status, gsl_strerror(status));
         }
-        if(fit_data->stats.error) {
-            return fit_data->stats.error;
+        if(fit->stats.error) {
+            return fit->stats.error;
         }
         if(status == GSL_ENOPROG && iter == 1) {
             return FIT_ERROR_NO_PROGRESS;
         }
-        fit_iter_stats_update(fit_data, w);
-        fit_iter_stats_print(&fit_data->stats);
+        fit_iter_stats_update(fit, w);
+        fit_iter_stats_print(&fit->stats);
 #ifdef DEBUG
         if(fit_data->stats.phase > FIT_PHASE_FAST) {
             char *jacobian_filename;
@@ -904,8 +903,8 @@ int jabs_gsl_multifit_nlinear_driver(const size_t maxiter, const double xtol, co
             }
         }
 #endif
-        if(fit_data->fit_iter_callback) {
-            if(fit_data->fit_iter_callback(fit_data->stats)) {
+        if(fit->fit_iter_callback) {
+            if(fit->fit_iter_callback(fit->stats)) {
                 return FIT_ERROR_ABORTED;
             }
         }
@@ -916,8 +915,8 @@ int jabs_gsl_multifit_nlinear_driver(const size_t maxiter, const double xtol, co
         if(status == GSL_SUCCESS) {
             return FIT_SUCCESS_DELTA;
         }
-        double chisq_change = 1.0 - fit_data->stats.chisq_dof / chisq_dof_old;
-        if(fit_data->stats.chisq_dof > chisq_dof_old) {
+        double chisq_change = 1.0 - fit->stats.chisq_dof / chisq_dof_old;
+        if(fit->stats.chisq_dof > chisq_dof_old) {
             jabs_message(MSG_WARNING, "Chisq increased, this probably shouldn't happen.\n");
         }
         if(chisq_change < chisq_tol) {
@@ -1055,8 +1054,8 @@ int fit_uncertainty_spectra(const fit_data *fit, const gsl_matrix *J, const gsl_
     return EXIT_SUCCESS;
 }
 
-int fit(fit_data *fit) {
-    struct fit_params *fit_params = fit->fit_params;
+int fit_do(fit_data *fit) {
+    fit_params *fit_params = fit->fit_params;
     if(!fit_params || fit_params->n_active == 0) {
         jabs_message(MSG_ERROR, "No parameters to fit.\n");
         return EXIT_FAILURE;
@@ -1280,7 +1279,7 @@ int fit_set_roi_from_string(roi *r, const char *str) {
     return EXIT_SUCCESS;
 }
 
-double fit_emin(struct fit_data *fit, size_t i_det) {
+double fit_emin(fit_data *fit, size_t i_det) {
     double emin = fit->sim->beam_E;
     for(size_t i_range = 0; i_range < fit->n_fit_ranges; i_range++) {
         const roi *r = &(fit->fit_ranges[i_range]);

src/fit.h

@@ -55,7 +55,7 @@ typedef enum fit_phase {
         FIT_PHASE_SLOW = 2
 } fit_phase;
 
-struct fit_stats {
+typedef struct fit_stats {
     fit_phase phase;
     size_t n_evals;
     size_t n_evals_iter; /* Number of function evaluations per iteration */
@@ -71,7 +71,7 @@ struct fit_stats {
     size_t iter;
     size_t iter_call;
     int error;
-};
+} fit_stats;
 
 typedef struct roi {
     size_t i_det; /* detector sim->det[i_det] */
@@ -122,7 +122,7 @@ typedef struct fit_data {
     fit_stats stats; /* Fit statistics, updated as we iterate */
     int phase_start; /* Fit phase to start from (see FIT_PHASE -defines) */
     int phase_stop; /* Inclusive */
-    int (*fit_iter_callback)(struct fit_stats stats);
+    int (*fit_iter_callback)(fit_stats stats);
     gsl_vector *f_iter;
     double h_df;
     jacobian_space *jspace;
@@ -138,38 +138,38 @@ void fit_data_free(fit_data *fit); /* Doesn't free everything in fit, like sm, j
 void fit_data_reset(fit_data *fit);
 void fit_data_exp_reset(fit_data *fit);
 void fit_data_print(const fit_data *fit, jabs_msg_level msg_level);
-void fit_data_roi_print(const struct fit_data *fit_data, const struct roi *roi);
+void fit_data_roi_print(const fit_data *fit, const roi *roi);
 jabs_histogram *fit_data_exp(const fit_data *fit, size_t i_det);
 jabs_histogram *fit_data_ref(const fit_data *fit_data);
 fit_params *fit_params_all(fit_data *fit);
 int fit_data_fdd_init(fit_data *fit);
 void fit_data_fdd_free(fit_data *fit);
 void fit_data_exp_alloc(fit_data *fit);
 void fit_data_exp_free(fit_data *fit);
-int fit_data_load_exp(struct fit_data *fit, size_t i_det, const char *filename);
+int fit_data_load_exp(fit_data *fit, size_t i_det, const char *filename);
 int fit_data_set_sample_model(fit_data *fit, sample_model *sm_new); /* Sets sample model of the fit (copies pointer), freeing the old model. Resets reactions. */
 jabs_histogram *fit_data_histo_sum(const fit_data *fit, size_t i_det);
 void fit_data_spectra_copy_to_spectra_from_ws(result_spectra *s, const detector *det, const jabs_histogram *exp, const sim_workspace *ws); /* Makes deep copies of histograms */
 int fit_data_spectra_alloc(fit_data *fit);
 void fit_data_spectra_free(fit_data *fit);
-int fit_data_add_det(struct fit_data *fit, detector *det);
+int fit_data_add_det(fit_data *fit, detector *det);
 fit_data_det *fit_data_fdd(const fit_data *fit, size_t i_det);
-size_t fit_data_ranges_calculate_number_of_channels(const struct fit_data *fit_data);
-struct fit_stats fit_stats_init(void);
-int fit(fit_data *fit);
+size_t fit_data_ranges_calculate_number_of_channels(const fit_data *fit);
+fit_stats fit_stats_init(void);
+int fit_do(fit_data *fit);
 void fit_correlation_print(const gsl_matrix *covar, jabs_msg_level msg_level);
 int fit_uncertainty_spectra(const fit_data *fit, const gsl_matrix *J, const gsl_matrix *covar, const gsl_vector *f, const gsl_vector *w, const char *filename); /* Calculates +/- uncertainty spectra and copies them to fit. If filename is not null, writes (debug) output in it. */
-int fit_parameters_set_from_vector(struct fit_data *fit, const gsl_vector *x); /* Updates values in fit params as they are varied by the fit algorithm. */
+int fit_parameters_set_from_vector(fit_data *fit, const gsl_vector *x); /* Updates values in fit params as they are varied by the fit algorithm. */
 int fit_function(const gsl_vector *x, void *params, gsl_vector *f);
 int fit_determine_active_detectors(fit_data *fit);
 int fit_sanity_check(const fit_data *fit);
-void fit_iter_stats_update(struct fit_data *params, const gsl_multifit_nlinear_workspace *w);
-void fit_iter_stats_print(const struct fit_stats *stats);
-void fit_stats_print(const struct fit_stats *stats, jabs_msg_level msg_level);
-int fit_data_fit_range_add(struct fit_data *fit_data, const struct roi *range); /* Makes a deep copy */
-void fit_data_fit_ranges_free(struct fit_data *fit_data);
+void fit_iter_stats_update(fit_data *params, const gsl_multifit_nlinear_workspace *w);
+void fit_iter_stats_print(const fit_stats *stats);
+void fit_stats_print(const fit_stats *stats, jabs_msg_level msg_level);
+int fit_data_fit_range_add(fit_data *fit_data, const roi *range); /* Makes a deep copy */
+void fit_data_fit_ranges_free(fit_data *fit_data);
 int fit_set_roi_from_string(roi *r, const char *str); /* Parses only low and high from "[low:high]". */
-double fit_emin(struct fit_data *fit, size_t i_det); /* Returns lowest energy of fit ranges for detector i_det. Detectors, calibrations and fit ranges must be set before calling. */
+double fit_emin(fit_data *fit, size_t i_det); /* Returns lowest energy of fit ranges for detector i_det. Detectors, calibrations and fit ranges must be set before calling. */
 const char *fit_error_str(int error);
 int fit_range_compare(const void *a, const void *b);
 const char *fit_phase_to_str(const fit_phase phase);

src/jabs.c

@@ -550,7 +550,7 @@ int assign_stopping_Z1_Z2(jibal_gsto *gsto, int Z1, int Z2) {
 
 int assign_stopping(jibal_gsto *gsto, const simulation *sim) {
     /* TODO: simplify this by finding all possible Z1, Z2 combinations, considering target elements, beam and reactions before attempting to assign stopping/straggling (GSTO) */
-    struct sample *sample = sim->sample;
+    sample *sample = sim->sample;
     if(!sample) {
         jabs_message(MSG_ERROR, "Could not assign stopping, because sample is not set!\n");
         return 1;

src/reaction.c

@@ -312,9 +312,9 @@ reaction *r33_file_to_reaction(const jibal_isotope *isotopes, const r33_file *rf
     }
     /* TODO: copy and convert data (check units etc) */
     r->n_cs_table = rfile->n_data;
-    r->cs_table = calloc(r->n_cs_table, sizeof(struct reaction_point));
+    r->cs_table = calloc(r->n_cs_table, sizeof(reaction_point));
     for(size_t i = 0; i < rfile->n_data; i++) {
-        struct reaction_point *rp = &r->cs_table[i];
+        reaction_point *rp = &r->cs_table[i];
         rp->E = rfile->data[i][0] * rfile->enfactors[0] * C_KEV; /* TODO: other factors? */
         if(rfile->unit == R33_UNIT_RR) {
             rp->sigma = rfile->data[i][2] * rfile->sigfactors[0] * jibal_cross_section_rbs(r->incident, r->target, r->theta, rp->E, JIBAL_CS_RUTHERFORD);

src/reaction.h

@@ -37,10 +37,10 @@ typedef enum {
     REACTION_PLUGIN = 5
 } reaction_type;
 
-struct reaction_point {
+typedef struct reaction_point {
     double E;
     double sigma;
-};
+} reaction_point;
 
 typedef enum jabs_reaction_cs {
     JABS_CS_NONE = 0,
@@ -80,7 +80,7 @@ typedef struct reaction {
     jabs_plugin *plugin; /* for REACTION_PLUGIN */
     jabs_plugin_reaction *plugin_r; /* for REACTION_PLUGIN */
 #endif
-    struct reaction_point *cs_table; /* for REACTION_FILE */
+    reaction_point *cs_table; /* for REACTION_FILE */
     size_t n_cs_table;
     double theta; /* For REACTION_FILE */
     double Q;