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

Arthur Glowacki · Arthur Glowacki · commit 27c180fb085f · 2025-08-26T09:09:25.000-05:00
diff --git a/src/data_struct/analysis_job.cpp b/src/data_struct/analysis_job.cpp
@@ -106,13 +106,13 @@ Analysis_Job<T_real>::~Analysis_Job()
 template<typename T_real>
 Detector<T_real>* Analysis_Job<T_real>::get_first_detector()
 {
-       Detector<T_real>* detector = nullptr;
-       for(auto &itr : detectors_meta_data)
-       {
-           detector = &(itr.second);
-           break;
-       }
-       return detector;
+    Detector<T_real>* detector = nullptr;
+    auto itr = detectors_meta_data.begin();
+    if (itr != detectors_meta_data.end())
+    {
+        detector = &(itr->second);
+    }
+    return detector;
 }
 
 //-----------------------------------------------------------------------------
diff --git a/src/data_struct/element_info.cpp b/src/data_struct/element_info.cpp
@@ -335,7 +335,6 @@ template<typename T_real>
 T_real Element_Info<T_real>::get_f2(T_real energy)
 {
     T_real f2 = 0.0;
-    T_real molecules_per_cc = 0.0;
    
     size_t low_e_idx = 0, high_e_idx = 0;
     bool found_indexes = false;
diff --git a/src/data_struct/fit_element_map.cpp b/src/data_struct/fit_element_map.cpp
@@ -362,7 +362,7 @@ 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
+bool Fit_Element_Map<T_real>::check_binding_energy(T_real incident_energy, size_t energy_ratio_idx) const
 {
 	if (_element_info != nullptr)
 	{
diff --git a/src/data_struct/fit_element_map.h b/src/data_struct/fit_element_map.h
@@ -193,7 +193,7 @@ class DLL_EXPORT Fit_Element_Map
 
     std::unordered_map<std::string, T_real> generate_roi_centers_per_shell();
 
-	bool check_binding_energy(T_real incident_energy, int energy_ratio_idx) const;
+	bool check_binding_energy(T_real incident_energy, size_t energy_ratio_idx) const;
 protected:
 
     void generate_energy_ratio(T_real energy, T_real ratio, Element_Param_Type et, const Element_Info<T_real> * const detector_element);
diff --git a/src/fitting/models/gaussian_model.cpp b/src/fitting/models/gaussian_model.cpp
@@ -470,7 +470,7 @@ const Spectra<T_real> Gaussian_Model<T_real>::model_spectrum_element(const Fit_P
     if (false == std::isfinite(pre_faktor))
     {
         logE << "Prefactor = " << pre_faktor << " for "<<element_to_fit->full_name()<<" . Log10 Value = "<< fitp->value(element_to_fit->full_name()) <<"\n";
-        spectra_model = (ArrayTr<T_real>)(spectra_model).unaryExpr([](T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
+        spectra_model = (ArrayTr<T_real>)(spectra_model).unaryExpr([]( [[maybe_unused]]  T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
         return spectra_model;
     }
 
@@ -655,7 +655,7 @@ const ArrayTr<T_real> Gaussian_Model<T_real>::elastic_peak(const Fit_Parameters<
     if(false == std::isfinite(sigma))
     {
         logE << "sigma = " << sigma << "\n";
-        counts = counts.unaryExpr([](T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
+        counts = counts.unaryExpr([]( [[maybe_unused]]  T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
         return counts;
     }
 	ArrayTr<T_real>delta_energy = ev - fitp->value(STR_COHERENT_SCT_ENERGY);
@@ -682,7 +682,7 @@ const ArrayTr<T_real> Gaussian_Model<T_real>::compton_peak(const Fit_Parameters<
     if(false == std::isfinite(sigma))
     {
         logE << "sigma = " << sigma << "\n";
-        counts = (ArrayTr<T_real>)(counts).unaryExpr([](T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
+        counts = (ArrayTr<T_real>)(counts).unaryExpr([]( [[maybe_unused]]  T_real v) { return  std::numeric_limits<T_real>::quiet_NaN(); });
         return counts;
     }
 
diff --git a/src/fitting/optimizers/nlopt_optimizer.cpp b/src/fitting/optimizers/nlopt_optimizer.cpp
@@ -103,7 +103,7 @@ double residuals_nlopt(const std::vector<double> &x, [[maybe_unused]] std::vecto
         {
             (*ud->status_callback)(ud->cur_itr, ud->total_itr);
         }
-        catch (int e)
+        catch ([[maybe_unused]]  int e)
         {
             logI << "Cancel fitting" << std::endl;
             return -1;
diff --git a/src/fitting/routines/param_optimized_fit_routine.cpp b/src/fitting/routines/param_optimized_fit_routine.cpp
@@ -286,8 +286,8 @@ OPTIMIZER_OUTCOME Param_Optimized_Fit_Routine<T_real>::fit_spectra_parameters(co
 // ----------------------------------------------------------------------------
 
 template<typename T_real>
-void Param_Optimized_Fit_Routine<T_real>::initialize(models::Base_Model<T_real>* const model,
-                                                    const Fit_Element_Map_Dict<T_real>* const elements_to_fit,
+void Param_Optimized_Fit_Routine<T_real>::initialize([[maybe_unused]]  models::Base_Model<T_real>* const model,
+                                                    [[maybe_unused]]  const Fit_Element_Map_Dict<T_real>* const elements_to_fit,
                                                     const struct Range energy_range,
                                                     ArrayTr<T_real>* custom_background)
 {
diff --git a/src/io/file/hdf5_io.cpp b/src/io/file/hdf5_io.cpp
@@ -1201,12 +1201,12 @@ bool HDF5_IO::generate_stream_dataset(std::string dataset_directory,
 
 
 //-----------------------------------------------------------------------------
-
+/*
 bool HDF5_IO::close_dataset(size_t d_hash)
 {
     return false;
 }
-
+*/
 //-----------------------------------------------------------------------------
 
 void HDF5_IO::update_theta(std::string dataset_file, std::string theta_pv_str)
@@ -2094,7 +2094,7 @@ void HDF5_IO::add_v9_layout(std::string dataset_file)
 	std::string max_name = "/MAPS/Spectra/Integrated_Spectra/"+ STR_MAX_CHANNELS_INT_SPEC;
 	std::string max10_name = "/MAPS/Spectra/Integrated_Spectra/"+ STR_MAX10_INT_SPEC;
 	std::string v9_max_name = "/MAPS/max_chan_spec";
-	hid_t fit_int_id = -1, max_id = -1, max_10_id = -1, nnls_id = -1, back_id = -1, max_space = -1, max_type, v9_max_id = -1, v9_space = -1;
+	hid_t fit_int_id = -1, max_id = -1, max_10_id = -1, nnls_id = -1, back_id = -1, max_space = -1, max_type = -1, v9_max_id = -1, v9_space = -1;
 	
 	max_id = H5Dopen(file_id, max_name.c_str(), H5P_DEFAULT);
     if(max_id > -1)
@@ -2261,7 +2261,7 @@ void HDF5_IO::add_v9_layout(std::string dataset_file)
         
         hid_t chan_space = H5Dget_space(chan_names);
         _global_close_map.push({chan_space, H5O_DATASPACE });
-        int num_chan;
+        int num_chan = 0;
         if(chan_names > -1)
         {
             hsize_t chan_size = 1;
@@ -2277,7 +2277,7 @@ void HDF5_IO::add_v9_layout(std::string dataset_file)
         hsize_t unit_dims[2];
         hsize_t offset_dims[2] = { 0,0 };
         unit_dims[0] = 4;
-        unit_dims[1] =num_chan;
+        unit_dims[1] = num_chan;
         hid_t ch_unit_id, units_space;
             
         if (false == _open_h5_dataset("/MAPS/channel_units", filetype, file_id, 2, &unit_dims[0], &unit_dims[0], ch_unit_id, units_space))
diff --git a/src/io/file/hdf5_io.h b/src/io/file/hdf5_io.h
@@ -1861,9 +1861,9 @@ class DLL_EXPORT HDF5_IO
     bool _load_spectra_line_xspress3(hid_t file_id, size_t detector_num, data_struct::Spectra_Line<T_real>* spec_row)
     {
         std::stack<std::pair<hid_t, H5_OBJECTS> > close_map;
-        hid_t  dset_id, dataspace_id, maps_grp_id, scaler_grp_id, scaler2_grp_id, memoryspace_id, memoryspace_meta_id = -1;
-        hid_t dset_lt_id, dset_rt_id, dset_outcnt_id = -1;
-        hid_t    dataspace_lt_id, dataspace_rt_id, dataspace_outcnt_id = -1;
+        hid_t  dset_id = -1, dataspace_id = -1, maps_grp_id = -1, scaler_grp_id = -1, scaler2_grp_id = -1, memoryspace_id = -1, memoryspace_meta_id = -1;
+        hid_t dset_lt_id = -1, dset_rt_id = -1, dset_outcnt_id = -1;
+        hid_t    dataspace_lt_id = -1, dataspace_rt_id = -1, dataspace_outcnt_id = -1;
       
         herr_t   error = -1;
         std::string detector_path;
@@ -3639,7 +3639,7 @@ class DLL_EXPORT HDF5_IO
 
             //  read scaler names and search for elt1, ert1, incnt1, outcnt1
             hsize_t dims_out[1];
-            unsigned int status_n = H5Sget_simple_extent_dims(dataspace_scaler_names, &dims_out[0], nullptr);
+            H5Sget_simple_extent_dims(dataspace_scaler_names, &dims_out[0], nullptr);
             char tmp_name[256] = { 0 };
             memoryspace_1 = H5Screate_simple(1, count, nullptr);
             for (hsize_t idx = 0; idx < dims_out[0]; idx++)
@@ -4277,7 +4277,7 @@ class DLL_EXPORT HDF5_IO
             logE << "Error getting rank for /MAPS/Scalers/Values\n";
         }
         hsize_t* dims_out = new hsize_t[rank];
-        unsigned int status_n = H5Sget_simple_extent_dims(counts_dspace_id, &dims_out[0], nullptr);
+        H5Sget_simple_extent_dims(counts_dspace_id, &dims_out[0], nullptr);
 
         filetype = H5Tcopy(H5T_C_S1);
         H5Tset_size(filetype, 256);
@@ -5419,7 +5419,7 @@ class DLL_EXPORT HDF5_IO
     }
 
     //-----------------------------------------------------------------------------
-
+    /*
     template<typename T_real>
     bool save_stream_row(size_t d_hash, size_t detector_num, size_t row, std::vector< data_struct::Spectra<T_real>* >  *spectra_row)
     {
@@ -5433,11 +5433,11 @@ class DLL_EXPORT HDF5_IO
     {
         return false;
     }
-
+    
     //-----------------------------------------------------------------------------
 
     bool close_dataset(size_t d_hash);
-
+    */
     bool start_save_seq(const std::string filename, bool force_new_file=false, bool open_file_only=false);
 
     bool start_save_seq(bool force_new_file=false){ return start_save_seq(_cur_filename, force_new_file, false);}
diff --git a/src/quantification/models/quantification_model.cpp b/src/quantification/models/quantification_model.cpp
@@ -88,7 +88,7 @@ void Quantification_Model<T_real>::init_element_quant(Element_Quant<T_real>& ele
                                             T_real detector_chip_thickness,
                                             T_real beryllium_window_thickness,
                                             T_real germanium_dead_layer,
-                                            size_t z_number)
+                                            int z_number)
 {
     //incident_E(incident_energy) == COHERENT_SCT_ENERGY: Maps_fit_params
     //fit_t_be == BE_WINDOW_THICKNESS * 1000
diff --git a/src/quantification/models/quantification_model.h b/src/quantification/models/quantification_model.h
@@ -90,7 +90,7 @@ class DLL_EXPORT Quantification_Model
                             T_real detector_chip_thickness,
                             T_real beryllium_window_thickness,
                             T_real germanium_dead_layer,
-                            size_t z_number);
+                            int z_number);
 
     T_real transmission(T_real thickness, T_real beta, T_real llambda) const;
 
diff --git a/src/support/eigen-git-mirror b/src/support/eigen-git-mirror
@@ -1 +1 @@
-Subproject commit 6dbbf0a843ec3c76c8877e420ba0684bb07e6daa
+Subproject commit 454f89af9d6f3525b1df5f9ef9c86df58bf2d4d3
diff --git a/src/support/pybind11 b/src/support/pybind11
@@ -1 +1 @@
-Subproject commit ed5057ded698e305210269dafa57574ecf964483
+Subproject commit 68322895df3d02c94deba6f3a3f531dd5b566cee
diff --git a/src/workflow/xrf/spectra_stream_saver.cpp b/src/workflow/xrf/spectra_stream_saver.cpp
@@ -59,7 +59,7 @@ namespace xrf
 template<typename T_real>
 Spectra_Stream_Saver<T_real>::Spectra_Stream_Saver() : Sink<data_struct::Stream_Block<T_real>*>()
 {
-    this->_callback_func = std::bind(&Spectra_Stream_Saver<T_real>::save_stream, this, std::placeholders::_1);
+    //this->_callback_func = std::bind(&Spectra_Stream_Saver<T_real>::save_stream, this, std::placeholders::_1);
 }
 
 //-----------------------------------------------------------------------------
@@ -71,7 +71,7 @@ Spectra_Stream_Saver<T_real>::~Spectra_Stream_Saver()
 }
 
 // ----------------------------------------------------------------------------
-
+/*
 template<typename T_real>
 void Spectra_Stream_Saver<T_real>::save_stream(data_struct::Stream_Block<T_real>* stream_block)
 {
@@ -141,7 +141,7 @@ void Spectra_Stream_Saver<T_real>::save_stream(data_struct::Stream_Block<T_real>
         }
     }
 }
-
+*/
 // ----------------------------------------------------------------------------
 
 template<typename T_real>
@@ -172,7 +172,7 @@ void Spectra_Stream_Saver<T_real>::_new_detector(Dataset_Save *dataset, data_str
 }
 
 // ----------------------------------------------------------------------------
-
+/*
 template<typename T_real>
 void Spectra_Stream_Saver<T_real>::_finalize_dataset(Dataset_Save* dataset)
 {
@@ -195,7 +195,7 @@ void Spectra_Stream_Saver<T_real>::_finalize_dataset(Dataset_Save* dataset)
         delete dataset;
     }
 }
-
+*/
 // ----------------------------------------------------------------------------
 
 TEMPLATE_CLASS_DLL_EXPORT Spectra_Stream_Saver<float>;
diff --git a/src/workflow/xrf/spectra_stream_saver.h b/src/workflow/xrf/spectra_stream_saver.h
@@ -74,7 +74,7 @@ class DLL_EXPORT Spectra_Stream_Saver : public Sink<data_struct::Stream_Block<T_
 
     virtual ~Spectra_Stream_Saver();
 
-    void save_stream(data_struct::Stream_Block<T_real>* stream_block);
+    //void save_stream(data_struct::Stream_Block<T_real>* stream_block);
 
     virtual void set_function([[maybe_unused]] std::function<void (data_struct::Stream_Block<T_real>*)> func) { }
 
@@ -138,7 +138,7 @@ class DLL_EXPORT Spectra_Stream_Saver : public Sink<data_struct::Stream_Block<T_
 
     void _new_detector(Dataset_Save *dataset, data_struct::Stream_Block<T_real>* stream_block);
 
-    void _finalize_dataset(Dataset_Save *dataset);
+    //void _finalize_dataset(Dataset_Save *dataset);
 
     //by detector_dir + dataset hash
     std::map<size_t, Dataset_Save*> _dataset_map;
diff --git a/vcpkg b/vcpkg
@@ -1 +1 @@
-Subproject commit d8ad13c401b30c2836d00b8923c9127f05f591c7
+Subproject commit 89f00b3b8611028566a5264afce725cdfdfddbb4

Original file line number	Diff line number	Diff line change
`@@ -335,7 +335,6 @@ template<typename T_real>`
`335`	`335`	`T_real Element_Info<T_real>::get_f2(T_real energy)`
`336`	`336`	`{`
`337`	`337`	`T_real f2 = 0.0;`
`338`		`- T_real molecules_per_cc = 0.0;`
`339`	`338`
`340`	`339`	`size_t low_e_idx = 0, high_e_idx = 0;`
`341`	`340`	`bool found_indexes = false;`
Original file line number	Diff line number	Diff line change
`@@ -362,7 +362,7 @@ void Fit_Element_Map<T_real>::set_as_pileup(std::string name, Element_Info<T_rea`
`362`	`362`	`//-----------------------------------------------------------------------------`
`363`	`363`
`364`	`364`	`template<typename T_real>`
`365`		`-bool Fit_Element_Map<T_real>::check_binding_energy(T_real incident_energy, int energy_ratio_idx) const`
	`365`	`+bool Fit_Element_Map<T_real>::check_binding_energy(T_real incident_energy, size_t energy_ratio_idx) const`
`366`	`366`	`{`
`367`	`367`	`if (_element_info != nullptr)`
`368`	`368`	`{`
Original file line number	Diff line number	Diff line change
`@@ -470,7 +470,7 @@ const Spectra<T_real> Gaussian_Model<T_real>::model_spectrum_element(const Fit_P`
`470`	`470`	`if (false == std::isfinite(pre_faktor))`
`471`	`471`	`{`
`472`	`472`	`logE << "Prefactor = " << pre_faktor << " for "<<element_to_fit->full_name()<<" . Log10 Value = "<< fitp->value(element_to_fit->full_name()) <<"\n";`
`473`		`- spectra_model = (ArrayTr<T_real>)(spectra_model).unaryExpr([](T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
	`473`	`+ spectra_model = (ArrayTr<T_real>)(spectra_model).unaryExpr([]( [[maybe_unused]] T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
`474`	`474`	`return spectra_model;`
`475`	`475`	`}`
`476`	`476`
`@@ -655,7 +655,7 @@ const ArrayTr<T_real> Gaussian_Model<T_real>::elastic_peak(const Fit_Parameters<`
`655`	`655`	`if(false == std::isfinite(sigma))`
`656`	`656`	`{`
`657`	`657`	`logE << "sigma = " << sigma << "\n";`
`658`		`- counts = counts.unaryExpr([](T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
	`658`	`+ counts = counts.unaryExpr([]( [[maybe_unused]] T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
`659`	`659`	`return counts;`
`660`	`660`	`}`
`661`	`661`	`ArrayTr<T_real>delta_energy = ev - fitp->value(STR_COHERENT_SCT_ENERGY);`
`@@ -682,7 +682,7 @@ const ArrayTr<T_real> Gaussian_Model<T_real>::compton_peak(const Fit_Parameters<`
`682`	`682`	`if(false == std::isfinite(sigma))`
`683`	`683`	`{`
`684`	`684`	`logE << "sigma = " << sigma << "\n";`
`685`		`- counts = (ArrayTr<T_real>)(counts).unaryExpr([](T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
	`685`	`+ counts = (ArrayTr<T_real>)(counts).unaryExpr([]( [[maybe_unused]] T_real v) { return std::numeric_limits<T_real>::quiet_NaN(); });`
`686`	`686`	`return counts;`
`687`	`687`	`}`
`688`	`688`
Original file line number	Diff line number	Diff line change
`@@ -103,7 +103,7 @@ double residuals_nlopt(const std::vector<double> &x, [[maybe_unused]] std::vecto`
`103`	`103`	`{`
`104`	`104`	`(*ud->status_callback)(ud->cur_itr, ud->total_itr);`
`105`	`105`	`}`
`106`		`- catch (int e)`
	`106`	`+ catch ([[maybe_unused]] int e)`
`107`	`107`	`{`
`108`	`108`	`logI << "Cancel fitting" << std::endl;`
`109`	`109`	`return -1;`
Original file line number	Diff line number	Diff line change
`@@ -88,7 +88,7 @@ void Quantification_Model<T_real>::init_element_quant(Element_Quant<T_real>& ele`
`88`	`88`	`T_real detector_chip_thickness,`
`89`	`89`	`T_real beryllium_window_thickness,`
`90`	`90`	`T_real germanium_dead_layer,`
`91`		`- size_t z_number)`
	`91`	`+ int z_number)`
`92`	`92`	`{`
`93`	`93`	`//incident_E(incident_energy) == COHERENT_SCT_ENERGY: Maps_fit_params`
`94`	`94`	`//fit_t_be == BE_WINDOW_THICKNESS * 1000`