Merge branch 'polar' of github.com:/aglowacki/XRF-Maps into polar

Author: Arthur Glowacki

src/core/main.cpp

@@ -179,7 +179,7 @@ void set_optimizer(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real>&
 // ----------------------------------------------------------------------------
 
 template <typename T_real>
-void set_mem_limit(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real>& analysis_job)
+void set_mem_limit(Command_Line_Parser& clp, [[maybe_unused]] data_struct::Analysis_Job<T_real>& analysis_job)
 {
     //check if we should set a ram memory limit
     if (clp.option_exists("--mem-limit"))
@@ -448,8 +448,8 @@ int set_dir_and_files(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real
                 continue;
             }
             logI<<dataset_dir << DIR_END_CHAR << itr << DIR_END_CHAR << "*.h5"<<"\n";
-            std::vector<std::string> flist = io::file::File_Scan::inst()->find_all_dataset_files_by_list(dataset_dir + DIR_END_CHAR + itr + DIR_END_CHAR, search_ext_h5_list);
-            for (const auto& fitr : flist)
+            std::vector<std::string> flist1 = io::file::File_Scan::inst()->find_all_dataset_files_by_list(dataset_dir + DIR_END_CHAR + itr + DIR_END_CHAR, search_ext_h5_list);
+            for (const auto& fitr : flist1)
             {
                 //logI<<fitr<<"\n";
                 analysis_job.dataset_files.push_back(itr + DIR_END_CHAR + fitr);
@@ -957,8 +957,8 @@ int main(int argc, char* argv[])
 
     // get location of where we are running from and use it to find ref files
     std::string exe_loc = std::string(argv[0]);
-    int prog_idx = exe_loc.find("xrf_maps");
-    if (prog_idx > 0)
+    size_t prog_idx = exe_loc.find("xrf_maps");
+    if (prog_idx != std::string::npos)
     {
         exe_loc = exe_loc.substr(0, prog_idx);
     }

src/core/process_whole.cpp

@@ -127,7 +127,7 @@ bool optimize_integrated_fit_params(data_struct::Analysis_Job<double> * analysis
             ret_val = false;
             break;
         }
-        io::file::save_optimized_fit_params(analysis_job->output_dir, save_filename, detector_num, result, &out_fitp, &int_spectra, &(params_override->elements_to_fit));
+        io::file::save_optimized_fit_params(analysis_job->output_dir, save_filename, (int)detector_num, result, &out_fitp, &int_spectra, &(params_override->elements_to_fit));
 
         delete fit_routine;
     }
@@ -142,7 +142,7 @@ void generate_optimal_params(data_struct::Analysis_Job<double>* analysis_job)
 {
     std::unordered_map<int, data_struct::Fit_Parameters<double>> fit_params_avgs;
     std::unordered_map<int, data_struct::Params_Override<double>*> params;
-    std::unordered_map<int, float> detector_file_cnt;
+    std::unordered_map<size_t, float> detector_file_cnt;
     data_struct::Params_Override<double>* params_override = nullptr;
     data_struct::Spectra<double> int_spectra;
 
@@ -463,7 +463,7 @@ bool perform_quantification(data_struct::Analysis_Job<double>* analysis_job, boo
         for(size_t detector_num : analysis_job->detector_num_arr)
         {
             data_struct::Detector<double>* detector = analysis_job->get_detector(detector_num);
-            data_struct::Params_Override<double>* override_params = &(detector->fit_params_override_dict);
+            //data_struct::Params_Override<double>* override_params = &(detector->fit_params_override_dict);
 
 
             load_and_fit_quatification_datasets(analysis_job, detector_num);
@@ -549,8 +549,8 @@ bool perform_quantification(data_struct::Analysis_Job<double>* analysis_job, boo
                 }
 
                 // check if esrf dataset and remove folder 
-                int didx = dataset_file.find(DIR_END_CHAR);
-                if (didx > -1)
+                size_t didx = dataset_file.find(DIR_END_CHAR);
+                if (didx != std::string::npos)
                 {
                     dataset_file = dataset_file.substr(didx + 1);
                 }
@@ -783,7 +783,7 @@ void optimize_single_roi(data_struct::Analysis_Job<double>& analysis_job,
     // int specs loaded from v10 version
     std::unordered_map<std::string, data_struct::Spectra<double> > int_specs;
 
-    int slen = roi_file_name.size();
+    size_t slen = roi_file_name.size();
     if (slen < 6)
     {
         logE << "Roi file name too short " << roi_file_name << ". Skipping file.\n";
@@ -804,7 +804,7 @@ void optimize_single_roi(data_struct::Analysis_Job<double>& analysis_job,
                     // search for detector in list of int specs loaded
                     for (const auto& spec_itr : int_specs)
                     {
-                        int slen = spec_itr.first.length();
+                        slen = spec_itr.first.length();
                         if (slen > 0 && spec_itr.first[slen - 1] == str_detector_num[0])
                         {
                             search_filename = spec_itr.first;

src/core/process_whole.h

@@ -320,7 +320,7 @@ DLL_EXPORT void proc_spectra(data_struct::Spectra_Volume<T_real>* spectra_volume
             cur_block++;
         }
 
-        std::chrono::time_point<std::chrono::system_clock> end = std::chrono::system_clock::now();
+        end = std::chrono::system_clock::now();
         std::chrono::duration<double> elapsed_seconds = end - start;
         logI << "Fitting [ " << fit_routine->get_name() << " ] elapsed time: " << elapsed_seconds.count() << "s" << "\n";
 
@@ -342,8 +342,8 @@ DLL_EXPORT void proc_spectra(data_struct::Spectra_Volume<T_real>* spectra_volume
             }
             // save png 
             std::string dataset_fullpath = io::file::HDF5_IO::inst()->get_filename();
-            int sidx = dataset_fullpath.find("img.dat");
-            if (dataset_fullpath.length() > 0 && sidx > 0) 
+            size_t sidx = dataset_fullpath.find("img.dat");
+            if (dataset_fullpath.length() > 0 && sidx != std::string::npos) 
             {
                 dataset_fullpath.replace(sidx, 7, "output"); // 7 = sizeof("img.dat")
                 std::string str_path = dataset_fullpath + "_" + fit_routine->get_name() + ".png";
@@ -362,11 +362,10 @@ DLL_EXPORT void proc_spectra(data_struct::Spectra_Volume<T_real>* spectra_volume
         if (itr.first == data_struct::Fitting_Routines::GAUSS_MATRIX)
         {
             fitting::routines::Matrix_Optimized_Fit_Routine<T_real>* matrix_fit = (fitting::routines::Matrix_Optimized_Fit_Routine<T_real>*)fit_routine;
-            io::file::HDF5_IO::inst()->save_max_10_spectra(fit_routine->get_name(),
-                matrix_fit->energy_range(),
-                matrix_fit->max_integrated_spectra(),
-                matrix_fit->max_10_integrated_spectra(),
-                matrix_fit->fitted_integrated_background());
+            io::file::HDF5_IO::inst()->save_max_10_spectra(matrix_fit->energy_range(),
+                                                            matrix_fit->max_integrated_spectra(),
+                                                            matrix_fit->max_10_integrated_spectra(),
+                                                            matrix_fit->fitted_integrated_background());
         }
 
         delete fit_job_queue;

src/data_struct/element_info.cpp

@@ -58,7 +58,7 @@ namespace data_struct
 
 Electron_Shell get_shell_by_name(std::string element_name)
 {
-    int idx = element_name.find_last_of("_") + 1;
+    size_t idx = element_name.find_last_of("_") + 1;
     std::string shell_type = element_name.substr(idx);
     if (idx == 0)
     {
@@ -457,11 +457,11 @@ T_real Element_Info_Map<T_real>::calc_compound_beta(std::string compound_name, T
     T_real atwt = 0.0;
     T_real f2 = 0;
     //"N:78.08,O:20.95,Ar:0.93"
-    int idx = compound_name.find(",");
-    while (idx > -1 || compound_name.length() > 0)
+    size_t idx = compound_name.find(",");
+    while (std::string::npos != idx || compound_name.length() > 0)
     {
         std::string sub_compound;
-        if (idx > -1)
+        if (std::string::npos != idx)
         {
             sub_compound = compound_name.substr(0, idx);
             compound_name = compound_name.substr(idx + 1);
@@ -473,8 +473,8 @@ T_real Element_Info_Map<T_real>::calc_compound_beta(std::string compound_name, T
         }
 
 
-        int idx2 = sub_compound.find(":");
-        if (idx2 > -1)
+        size_t idx2 = sub_compound.find(":");
+        if (std::string::npos != idx2)
         {
             std::string el_symb = sub_compound.substr(0, idx2);
             std::string str_amt = sub_compound.substr(idx2+1);

src/data_struct/fit_element_map.cpp

@@ -73,7 +73,7 @@ Fit_Element_Map<T_real>::Fit_Element_Map(std::string name, Element_Info<T_real>*
 
     size_t num_ratios = 1;
 
-    int idx = _full_name.find_last_of("_") + 1;
+    size_t idx = _full_name.find_last_of("_") + 1;
     if(idx == 0)
     {
         _shell_type = Electron_Shell::K_SHELL;
@@ -341,7 +341,7 @@ void Fit_Element_Map<T_real>::set_as_pileup(std::string name, Element_Info<T_rea
 {
     if(_pileup_element_info == nullptr)
     {
-        int idx = name.find_last_of("_") + 1;
+        size_t idx = name.find_last_of("_") + 1;
         if(idx == 0)
         {
             _pileup_shell_type = "K";
@@ -364,7 +364,6 @@ void Fit_Element_Map<T_real>::set_as_pileup(std::string name, Element_Info<T_rea
 template<typename T_real>
 bool Fit_Element_Map<T_real>::check_binding_energy(T_real incident_energy, int energy_ratio_idx) const
 {
-	T_real binding_e;
 	if (_element_info != nullptr)
 	{
         if( _pileup_element_info != nullptr)

src/data_struct/fit_parameters.cpp

@@ -208,7 +208,7 @@ void Fit_Parameters<T_real>::from_array_d(const std::vector<double> &arr)
 {
     for(auto& itr : _params)
     {
-        if (itr.second.opt_array_index > -1 && itr.second.opt_array_index < (int)arr.size())
+        if (itr.second.opt_array_index != -1 && itr.second.opt_array_index < (int)arr.size())
         {
             itr.second.value = arr[itr.second.opt_array_index];
         }
@@ -224,7 +224,7 @@ void Fit_Parameters<T_real>::from_array(const T_real* arr, size_t arr_size)
     //logit_s<<"\n";
     for(auto& itr : _params)
     {
-        if (itr.second.opt_array_index > -1 && itr.second.opt_array_index < (int)arr_size)
+        if (itr.second.opt_array_index != -1 && itr.second.opt_array_index < (int)arr_size)
         {
             itr.second.value = arr[itr.second.opt_array_index];
         }
@@ -397,7 +397,7 @@ void Fit_Parameters<T_real>::print()
     for(const auto& itr : _params)
     {
         // 22 is len of longest name COHERENT_SCT_AMPLITUDE 
-        int spaces = 24 - itr.first.length();
+        size_t spaces = 24 - itr.first.length();
         std::string name = itr.first;
         name.append(spaces, ' ');
         std::string value = std::to_string(itr.second.value);

src/data_struct/fit_parameters.h

@@ -112,7 +112,7 @@ struct DLL_EXPORT Fit_Param
         value = std::numeric_limits<T_real>::quiet_NaN();
         step_size = std::numeric_limits<T_real>::quiet_NaN();
         bound_type = E_Bound_Type::NOT_INIT;
-        opt_array_index = -1;
+        opt_array_index = (size_t)-1;
     }
 
     Fit_Param(const Fit_Param& param)
@@ -134,7 +134,7 @@ struct DLL_EXPORT Fit_Param
         value = std::numeric_limits<T_real>::quiet_NaN();
         step_size = std::numeric_limits<T_real>::quiet_NaN();
         bound_type = E_Bound_Type::NOT_INIT;
-        opt_array_index = -1;
+        opt_array_index = (size_t)-1;
     }
 
     Fit_Param(std::string name_, T_real val_)
@@ -145,7 +145,7 @@ struct DLL_EXPORT Fit_Param
         step_size = (T_real)0.000001;
         value = val_;
         bound_type = E_Bound_Type::FIXED;
-        opt_array_index = -1;
+        opt_array_index = (size_t)-1;
     }
 
 	Fit_Param(std::string name_, T_real val_, E_Bound_Type b_type)
@@ -156,7 +156,7 @@ struct DLL_EXPORT Fit_Param
 		step_size = (T_real)0.000001;
 		value = val_;
 		bound_type = b_type;
-		opt_array_index = -1;
+		opt_array_index = (size_t)-1;
 	}
 
     Fit_Param(std::string name_, T_real min_, T_real max_, T_real val_, T_real step_size_, E_Bound_Type b_type)
@@ -167,7 +167,7 @@ struct DLL_EXPORT Fit_Param
         value = val_;
         bound_type = b_type;
         step_size = step_size_;
-        opt_array_index = -1;
+        opt_array_index = (size_t)-1;
     }
 
     const std::string bound_type_str() const; 
@@ -178,7 +178,7 @@ struct DLL_EXPORT Fit_Param
     T_real value;
     T_real step_size;
     E_Bound_Type bound_type;
-    int opt_array_index;
+    size_t opt_array_index;
 };
 
 //-----------------------------------------------------------------------------

src/data_struct/spectra.h

@@ -306,14 +306,14 @@ DLL_EXPORT ArrayTr<T_real> convolve1d(const ArrayTr<T_real>& arr, const ArrayTr<
     out.setZero(n);
     for (size_t i = 0; i < n; ++i)
     {
-        for (int j(min_v.size() - 1), k(i); j >= 0; --j)
+        for (size_t j(min_v.size() - 1), k(i); j >= 0; --j)
         {
             out[i] += min_v[j] * max_v[k];
             ++k;
         }
     }
     T_real norm = 1 / T_real(boxcar.size());
-    int j = min_v.size() / 2;
+    size_t j = min_v.size() / 2;
     for (size_t i = 0; i < n; i++)
     {
         new_background[j] = out[i] * norm;

src/data_struct/stream_block.cpp

@@ -218,7 +218,7 @@ size_t Stream_Block<T_real>::dataset_hash()
     {
         return std::hash<std::string> {} ((*dataset_directory) + (*dataset_name)) + _detector;
     }
-    return -1;
+    return (size_t)-1;
 }
 
 //-----------------------------------------------------------------------------

src/fitting/models/base_model.h

@@ -124,7 +124,7 @@ class DLL_EXPORT Base_Model
 
     virtual void reset_to_default_fit_params() = 0;
 
-    virtual void update_fit_params_values(const Fit_Parameters<T_real> *fit_params) = 0;
+    virtual void update_fit_params_values(const Fit_Parameters<T_real> * const fit_params) = 0;
 
     virtual void print_fit_params() = 0;