Merge pull request #238 from aglowacki/master

updates and bug fixes

Author: aglowacki

CMakeLists.txt

@@ -306,6 +306,7 @@ set(libxrf_fit_SOURCE
 set(XRF_IO_HEADERS
 	src/core/mem_info.h
 	src/support/mdautils-1.4.1/mda-load.h
+  src/io/file/file_scan.h
 	src/io/file/mda_io.h
     src/io/file/mca_io.h
 	src/io/file/hdf5_io.h
@@ -314,7 +315,6 @@ set(XRF_IO_HEADERS
 	src/io/file/aps/aps_fit_params_import.h
     src/io/file/aps/aps_roi.h
     src/io/file/esrf/edf_io.h
-    src/io/file/file_scan.h
 	src/io/file/hl_file_io.h
 	src/io/net/basic_serializer.h
 	src/workflow/source.h
@@ -333,12 +333,12 @@ set(XRF_IO_HEADERS
 set(XRF_IO_SOURCE
     ${VISUAL_INC}
 	  src/core/mem_info.cpp
+    src/io/file/file_scan.cpp
     src/support/mdautils-1.4.1/mda_loader.c
     src/io/file/aps/aps_fit_params_import.cpp
     src/io/file/mda_io.cpp
     src/io/file/hdf5_io.cpp
     src/io/file/netcdf_io.cpp
-    src/io/file/file_scan.cpp
     src/io/file/hl_file_io.cpp
     src/io/file/aps/aps_roi.cpp
     src/io/net/basic_serializer.cpp

src/core/defines.h

@@ -218,8 +218,10 @@ const std::string STR_SCAN_TYPE_TIME_BASED_2D_MAP = "TIME_BASED_XRF_MAPS";
 
 const std::string STR_SR_CURRENT = "SR_Current";
 const std::string STR_US_IC = "US_IC";
+const std::string STR_US_IC_FULL = "UPSTREAM_IONCHAMBER";
 const std::string STR_US_FM = "US_FM";
 const std::string STR_DS_IC = "DS_IC";
+const std::string STR_DS_IC_FULL = "DOWNSTREAM_IONCHAMBER";
 const std::string STR_CFG_2 = "CFG_2";
 const std::string STR_CFG_3 = "CFG_3";
 const std::string STR_CFG_4 = "CFG_4";
@@ -352,6 +354,16 @@ const std::string STR_MAP_ROI_INT_SPEC_FILENAME = "File_Name";
 const std::string STR_BNL_PARAM_DWELL = "param_dwell";
 const std::string STR_BNL_INCIDENT_ENERGY = "instrument_mono_incident_energy";
 
+//Xspress3 scaler names
+const std::string STR_ARRAY_COUNTER = "array_counter";
+const std::string STR_RESET_TICKS = "reset_ticks";
+const std::string STR_RESET_COUNT = "reset_count";
+const std::string STR_EVENT_WIDTH = "event_width";
+const std::string STR_WINDOW0 = "window0";
+const std::string STR_WINDOW1 = "window1";
+const std::string STR_DEADTIME_PERC = "dead_time_percent";
+const std::string STR_DEADTIME_FACT = "dead_time_factor";
+
 //}
 
 //}// namespace keys

src/core/main.cpp

@@ -464,7 +464,7 @@ int set_dir_and_files(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real
         }
 
         // search for h5 files in img.dat directory but filter out and mda files associated with them.
-        for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir + "img.dat" + DIR_END_CHAR, ".h5"))
+        for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files_by_ext(dataset_dir + "img.dat" + DIR_END_CHAR, ".h5"))
         {
             bool found = false;
             size_t idx = itr.find(".h5");

src/core/process_streaming.h

@@ -73,11 +73,11 @@ DLL_EXPORT data_struct::Stream_Block<T_real>* proc_spectra_block( data_struct::S
         {
             stream_block->fitting_blocks[itr.first].fit_counts[el_itr.first] = counts_dict[el_itr.first] / stream_block->spectra->elapsed_livetime();
         }
-        if(counts_dict.count(STR_NUM_ITR) > 0)
+        if(counts_dict.contains(STR_NUM_ITR))
         {
             stream_block->fitting_blocks[itr.first].fit_counts[STR_NUM_ITR] = counts_dict[STR_NUM_ITR];
         }
-        if(counts_dict.count(STR_RESIDUAL) > 0)
+        if(counts_dict.contains(STR_RESIDUAL))
         {
             stream_block->fitting_blocks[itr.first].fit_counts[STR_RESIDUAL] = counts_dict[STR_RESIDUAL];
         }

src/core/process_whole.cpp

@@ -222,7 +222,7 @@ DLL_EXPORT bool fit_single_spectra(fitting::routines::Base_Fit_Routine<T_real>*
         //save count / sec
         for (auto& itr : *out_fit_counts)
         {
-            if (counts_dict.count(itr.first) > 0)
+            if (counts_dict.contains(itr.first))
             {
                 itr.second(i, j) = counts_dict[itr.first] / spectra->elapsed_livetime();
             }
@@ -232,12 +232,12 @@ DLL_EXPORT bool fit_single_spectra(fitting::routines::Base_Fit_Routine<T_real>*
 
         (*out_fit_counts)[STR_RESIDUAL](i, j) = counts_dict[STR_RESIDUAL];
         // add total fluorescense yield
-        if (out_fit_counts->count(STR_TOTAL_FLUORESCENCE_YIELD))
+        if (out_fit_counts->contains(STR_TOTAL_FLUORESCENCE_YIELD))
         {
             (*out_fit_counts)[STR_TOTAL_FLUORESCENCE_YIELD](i, j) = spectra->sum() / spectra->elapsed_livetime();
         }
         // add sum coherent and compton
-        if (out_fit_counts->count(STR_SUM_ELASTIC_INELASTIC_AMP) > 0 && counts_dict.count(STR_COHERENT_SCT_AMPLITUDE) > 0 && counts_dict.count(STR_COMPTON_AMPLITUDE) > 0)
+        if (out_fit_counts->contains(STR_SUM_ELASTIC_INELASTIC_AMP)  && counts_dict.contains(STR_COHERENT_SCT_AMPLITUDE)  && counts_dict.contains(STR_COMPTON_AMPLITUDE) )
         {
             (*out_fit_counts)[STR_SUM_ELASTIC_INELASTIC_AMP](i, j) = counts_dict[STR_COHERENT_SCT_AMPLITUDE] + counts_dict[STR_COMPTON_AMPLITUDE];
         }
@@ -448,7 +448,7 @@ void find_quantifier_scalers(std::unordered_map<std::string, double>& pv_map, Qu
     for (auto& itr : pv_map)
     {
         double multiplier = (T_real)1.0;
-        if(pv_map.count(itr.first+"_SCALE_FACTOR") > 0)
+        if(pv_map.contains(itr.first+"_SCALE_FACTOR"))
         {
             multiplier = pv_map.at(itr.first+"_SCALE_FACTOR");
         }
@@ -464,7 +464,7 @@ void find_quantifier_scalers(std::unordered_map<std::string, double>& pv_map, Qu
             T_real summed_val = 0.0;
             for (const auto& sitr : itr.scalers_to_sum)
             {
-                if (pv_map.count(sitr) > 0)
+                if (pv_map.contains(sitr))
                 {
                     summed_val += pv_map.at(sitr);
                 }
@@ -479,15 +479,15 @@ void find_quantifier_scalers(std::unordered_map<std::string, double>& pv_map, Qu
         {
             quantification_standard->sr_current = itr.second;
         }
-        else if (itr.first == STR_US_IC)
+        else if (itr.first == STR_US_IC || itr.first == STR_US_IC_FULL)
         {
             quantification_standard->US_IC = itr.second;
         }
         else if (itr.first == STR_US_FM)
         {
             quantification_standard->US_FM = itr.second;
         }
-        else if (itr.first == STR_DS_IC)
+        else if (itr.first == STR_DS_IC || itr.first == STR_DS_IC_FULL)
         {
             quantification_standard->DS_IC = itr.second;
         }
@@ -702,7 +702,7 @@ DLL_EXPORT void iterate_datasets_and_update(data_struct::Analysis_Job<T_real>& a
 
 
         // Can scan for all hdf5 files in img.dat but will have to do it for multiple ext and filter out by detector num and avg
-        //for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(analysis_job.output_dir + "img.dat", ".hdf5"))
+        //for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files_by_ext(analysis_job.output_dir + "img.dat", ".hdf5"))
         //{
         //    hdf5_dataset_list.push_back(analysis_job.output_dir + "img.dat" + DIR_END_CHAR + itr);
         //}

src/core/process_whole.h

@@ -121,7 +121,7 @@ template<typename T_real>
 Detector<T_real>* Analysis_Job<T_real>::get_detector(int detector_num)
 {
        Detector<T_real>* detector = nullptr;
-       if(detectors_meta_data.count(detector_num) > 0)
+       if(detectors_meta_data.contains(detector_num))
        {
             detector = &(detectors_meta_data.at(detector_num));
        }

src/data_struct/analysis_job.cpp

@@ -103,7 +103,7 @@ Detector<T_real>::~Detector()
 template<typename T_real>
 void Detector<T_real>::append_element(Fitting_Routines routine, std::string quant_scaler, std::string name, T_real weight)
 {
-    if (fitting_quant_map.count(routine) == 0)
+    if (fitting_quant_map.contains(routine) == false)
     {
         fitting_quant_map[routine] = Fitting_Quantification_Struct<T_real>();
     }
@@ -114,7 +114,7 @@ void Detector<T_real>::append_element(Fitting_Routines routine, std::string quan
         data_struct::Electron_Shell shell = get_shell_by_name(name);
         fitting_quant_map.at(routine).update_weight_if_greater(shell, element->number, weight);
 
-        if (fitting_quant_map.at(routine).quant_scaler_map.count(quant_scaler) > 0)
+        if (fitting_quant_map.at(routine).quant_scaler_map.contains(quant_scaler))
         {
             all_element_quants[routine][quant_scaler][name] = &(fitting_quant_map.at(routine).quant_scaler_map.at(quant_scaler).curve_quant_map[shell][element->number - 1]);
         }
@@ -134,9 +134,9 @@ void Detector<T_real>::update_element_quants(Fitting_Routines routine,
                                     Quantification_Model<T_real>* quantification_model,
                                     T_real ic_quantifier)
 {
-    if (fitting_quant_map.count(routine) > 0)
+    if (fitting_quant_map.contains(routine))
     {
-        if (fitting_quant_map.at(routine).quant_scaler_map.count(quantifier_scaler) > 0)
+        if (fitting_quant_map.at(routine).quant_scaler_map.contains(quantifier_scaler) )
         {
             for (const auto& shell_itr : Shells_Quant_List)
             {
@@ -170,7 +170,7 @@ void Detector<T_real>::update_element_quants(Fitting_Routines routine,
                             name += "_M";
                         }
                         // with 2 standards we can have weights from another standard so we have to check if we have counts
-                        if (standard->element_counts.at(routine).count(name) > 0)
+                        if (standard->element_counts.at(routine).contains(name))
                         {
                             if (ic_quantifier == 0.0)
                             {
@@ -216,9 +216,9 @@ void Detector<T_real>::avg_element_quants(Fitting_Routines routine,
                                         std::string quantifier_scaler,
                                         std::unordered_map<int, float>& element_amt_dict)
 {
-    if (fitting_quant_map.count(routine) > 0)
+    if (fitting_quant_map.contains(routine))
     {
-        if (fitting_quant_map.at(routine).quant_scaler_map.count(quantifier_scaler) > 0)
+        if (fitting_quant_map.at(routine).quant_scaler_map.contains(quantifier_scaler))
         {
             for (const auto& shell_itr : Shells_Quant_List)
             {
@@ -346,9 +346,9 @@ void Detector<T_real>::update_calibration_curve(Fitting_Routines routine,
                                         Quantification_Model<T_real>* quantification_model,
                                         T_real val)
 {
-    if (fitting_quant_map.count(routine) > 0)
+    if (fitting_quant_map.contains(routine))
     {
-        if (fitting_quant_map.at(routine).quant_scaler_map.count(quantifier_scaler) > 0)
+        if (fitting_quant_map.at(routine).quant_scaler_map.contains(quantifier_scaler))
         {
             fitting_quant_map.at(routine).quantifier_map[quantifier_scaler] = val;
             for (const auto& shell_itr : Shells_Quant_List)

src/data_struct/detector.cpp

@@ -428,11 +428,11 @@ template<typename T_real>
 T_real Element_Info_Map<T_real>::calc_beta(std::string element_name, T_real density, T_real energy)
 {
     T_real beta = 0.0;
-    if (_name_element_info_map.count(element_name) > 0)
+    if (_name_element_info_map.contains(element_name))
     {
         beta = _name_element_info_map.at(element_name)->calc_beta(density, energy);
     }
-    else if(Henke_Compound_Density_Map<T_real>.count(element_name) > 0)
+    else if(Henke_Compound_Density_Map<T_real>.contains(element_name) )
     {
         beta = calc_compound_beta(element_name, density, energy);
     }
@@ -484,7 +484,7 @@ T_real Element_Info_Map<T_real>::calc_compound_beta(std::string compound_name, T
                 //beta += element_info->calc_beta(density, energy);
 
                 T_real amt = std::atof(str_amt.c_str());
-                if (amt > 0 && Element_Weight<T_real>.count(element_info->number) > 0)
+                if (amt > 0 && Element_Weight<T_real>.contains(element_info->number) )
                 {
                     T_real weight = Element_Weight<T_real>.at(element_info->number);
                     atwt += (amt * weight);
@@ -533,7 +533,7 @@ template<typename T_real>
 bool Element_Info_Map<T_real>::is_element(std::string element_name)
 {
     bool ret = false;
-    if (_name_element_info_map.count(element_name) > 0)
+    if (_name_element_info_map.contains(element_name) )
         ret = true;
     return ret;
 }

src/data_struct/element_info.cpp

@@ -138,7 +138,7 @@ class DLL_EXPORT Element_Info_Map
 
     //void set_energies(float* energy_arr, int num_energies);
 
-    bool contains(std::string element_name) {return _name_element_info_map.count(element_name) > 0 ? true : false; }
+    bool contains(std::string element_name) {return _name_element_info_map.contains(element_name); }
 
     std::vector<float> _energies;