Merge pull request #140 from aglowacki/master

Bugfix in netcdf loading spectra volume times and io counts

CMakeLists.txt

@@ -276,7 +276,7 @@ set(XRF_IO_HEADERS
 	src/core/mem_info.h
 	src/support/mdautils-1.4.1/mda-load.h
 	src/io/file/mda_io.h
-        src/io/file/mca_io.h
+  src/io/file/mca_io.h
 	src/io/file/hdf5_io.h
 	src/io/file/netcdf_io.h
 	src/io/file/csv_io.h
@@ -292,13 +292,13 @@ set(XRF_IO_HEADERS
 	src/workflow/xrf/detector_sum_spectra_source.h
 	src/workflow/xrf/spectra_stream_saver.h
 	src/workflow/xrf/spectra_net_streamer.h
-    src/core/process_streaming.h
-    src/core/process_whole.h
-   )
+  src/core/process_streaming.h
+  src/core/process_whole.h
+  )
 
 set(XRF_IO_SOURCE
     ${VISUAL_INC}
-	src/core/mem_info.cpp
+	  src/core/mem_info.cpp
     src/support/zmq/zmq.hpp
     src/support/mdautils-1.4.1/mda_loader.c
     src/io/file/mda_io.cpp

src/core/process_whole.cpp

@@ -144,7 +144,7 @@ bool optimize_integrated_fit_params(data_struct::Analysis_Job* analysis_job,
 
     if (params_override != nullptr)
     {
-        //load the quantification standard dataset
+        //load the standard dataset
         if (false == io::load_and_integrate_spectra_volume(analysis_job->dataset_directory, dataset_filename, detector_num, &int_spectra, params_override))
         {
             logE << "In optimize_integrated_dataset loading dataset" << dataset_filename << " for detector" << detector_num << "\n";
@@ -332,7 +332,7 @@ void proc_spectra(data_struct::Spectra_Volume* spectra_volume,
         start = std::chrono::system_clock::now();
         if (override_params->elements_to_fit.size() < 1)
         {
-            logE<<"No elements to fit. Check  maps_fit_parameters_override.txt0 - 3 exist"<<"\n";
+            logE<<"No elements to fit. Check  maps_fit_parameters_override.txt0 - 7 exist"<<"\n";
             continue;
         }
 
@@ -848,13 +848,6 @@ bool perform_quantification(data_struct::Analysis_Job* analysis_job)
                {
                     fitting::routines::Base_Fit_Routine *fit_routine = fit_itr.second;
 
-                    // update e_cal_ratio for elements in standards by average value
-                    for (auto& s_itr : detector->quantification_standards)
-                    {
-                        Quantification_Standard* quantification_standard = &(s_itr.second);
-                        detector->update_element_quants(fit_itr.first, quant_itr.first, quantification_standard, &quantification_model, quant_itr.second);
-                    }
-
                     logI << Fitting_Routine_To_Str.at(fit_itr.first) << " "<< quant_itr.first  << "\n";
                     Fit_Parameters fit_params;
                     fit_params.add_parameter(Fit_Param("quantifier", 0.0, std::numeric_limits<real_t>::max(), 1.0, 0.1, E_Bound_Type::FIT));

src/data_struct/detector.cpp

@@ -171,8 +171,27 @@ void Detector::update_element_quants(Fitting_Routines routine,
 
                             real_t counts = standard->element_counts.at(routine).at(name);
                             real_t e_cal_factor = (eq_itr.weight * (ic_quantifier));
-                            real_t e_cal = e_cal_factor / counts;
-                            eq_itr.e_cal_ratio = (real_t)1.0 / e_cal;
+                            if (counts > 0.)
+                            {
+                                real_t e_cal = e_cal_factor / counts;
+                                if (eq_itr.e_cal_ratio == 0.)
+                                {
+                                    eq_itr.e_cal_ratio = (real_t)1.0 / e_cal;
+                                }
+                                else // else avg the two
+                                {
+                                    real_t second_cal_ratio = (real_t)1.0 / e_cal;
+                                    eq_itr.e_cal_ratio += second_cal_ratio;
+                                    eq_itr.e_cal_ratio *= 0.5;
+                                }
+                            }
+                            else
+                            {
+                                if (eq_itr.e_cal_ratio == 0.)
+                                {
+                                    eq_itr.e_cal_ratio = 1.0e-10;
+                                }
+                            }
                         }
                     }
                 }

src/data_struct/spectra.cpp

@@ -238,16 +238,5 @@ ArrayXr snip_background(const Spectra* const spectra,
 
 }
 
-void gen_energy_vector(real_t number_channels, real_t energy_offset, real_t energy_slope, std::vector<real_t> *out_vec)
-{
-
-    out_vec->resize(number_channels);
-    for(int i=0; i<number_channels; i++)
-    {
-        (*out_vec)[i] = (i * energy_slope) + energy_offset;
-    }
-
-}
-
 } //namespace data_struct
 

src/data_struct/spectra.h

@@ -229,8 +229,6 @@ DLL_EXPORT ArrayXr convolve1d(const ArrayXr& arr, const ArrayXr& boxcar);
 DLL_EXPORT ArrayXr snip_background(const Spectra * const spectra, real_t energy_offset, real_t energy_linear, real_t energy_quadratic, real_t width, real_t xmin, real_t xmax);
 
 
-DLL_EXPORT void gen_energy_vector(real_t number_channels, real_t energy_offset, real_t energy_slope, std::vector<real_t> *out_vec);
-
 typedef std::function<void(size_t, size_t, size_t, size_t, size_t, data_struct::Spectra*, void*)> IO_Callback_Func_Def;