Merge pull request #204 from aglowacki/master

Bug fixes and clean up warnings

Author: aglowacki

CMakeLists.txt

@@ -142,7 +142,7 @@ IF (CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU"
     set(CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} -D__APPLE__")
   ENDIF()
   # Enable C++11 mode on C++ / Clang
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++1z -D__Unix__  -fPIC -g")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -D__Unix__  -fPIC -g")
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D__Unix__  -fPIC")
   IF(BUILD_FOR_PHI AND CMAKE_CXX_COMPILER_ID MATCHES "Intel" )
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xMIC-AVX512")
@@ -152,7 +152,7 @@ IF (CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID MATCHES "GNU"
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -march=native")
   ENDIF()
   #set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Wextra")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Waddress -Warray-bounds=1 -Wbool-compare -Wbool-operation -Wc++11-compat -Wc++14-compat -Wcatch-value -Wchar-subscripts -Wcomment -Wenum-compare -Wformat -Winit-self -Wlogical-not-parentheses -Wmain -Wmaybe-uninitialized -Wmemset-elt-size -Wmemset-transposed-args -Wmisleading-indentation -Wmissing-attributes -Wmissing-braces -Wmultistatement-macros -Wnarrowing -Wnonnull -Wnonnull-compare -Wopenmp-simd -Wparentheses -Wreorder -Wrestrict -Wreturn-type -Wsequence-point -Wsign-compare -Wsizeof-pointer-div -Wsizeof-pointer-memaccess -Wstrict-aliasing -Wstrict-overflow=1 -Wswitch -Wtautological-compare -Wtrigraphs -Wuninitialized -Wunknown-pragmas -Wunused-function -Wunused-label -Wunused-value -Wvolatile-register-var")
+  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Waddress -Warray-bounds=1 -Wbool-compare -Wbool-operation -Wc++17-compat -Wcatch-value -Wchar-subscripts -Wcomment -Wenum-compare -Wformat -Winit-self -Wlogical-not-parentheses -Wmain -Wmaybe-uninitialized -Wmemset-elt-size -Wmemset-transposed-args -Wmisleading-indentation -Wmissing-attributes -Wmissing-braces -Wmultistatement-macros -Wnarrowing -Wnonnull -Wnonnull-compare -Wopenmp-simd -Wparentheses -Wreorder -Wrestrict -Wreturn-type -Wsequence-point -Wsign-compare -Wsizeof-pointer-div -Wsizeof-pointer-memaccess -Wstrict-aliasing -Wstrict-overflow=1 -Wswitch -Wtautological-compare -Wtrigraphs -Wuninitialized -Wunknown-pragmas -Wunused-function -Wunused-label -Wunused-value -Wvolatile-register-var")
 ELSEIF(MSVC)
   IF(CMAKE_CXX_FLAGS MATCHES "/W[0-4]")
     string(REGEX REPLACE "/W[0-4]" "/W4" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")

src/core/process_whole.cpp

@@ -47,6 +47,7 @@ POSSIBILITY OF SUCH DAMAGE.
 
 #include "core/process_whole.h"
 #include <algorithm>
+#include <fitting/models/gaussian_model.h>
 
 using namespace std::placeholders; //for _1, _2,
 
@@ -396,12 +397,7 @@ void load_and_fit_quatification_datasets(data_struct::Analysis_Job<double>* anal
                     }
                 }
                 fitting::routines::Matrix_Optimized_Fit_Routine<double>* f_routine = (fitting::routines::Matrix_Optimized_Fit_Routine<double>*)fit_routine;
-                double energy_offset = fit_params.value(STR_ENERGY_OFFSET);
-                double energy_slope = fit_params.value(STR_ENERGY_SLOPE);
-                double energy_quad = fit_params.value(STR_ENERGY_QUADRATIC);
-
-                data_struct::ArrayTr<double> energy = data_struct::ArrayTr<double>::LinSpaced(energy_range.count(), energy_range.min, energy_range.max);
-                data_struct::ArrayTr<double> ev = energy_offset + (energy * energy_slope) + (Eigen::pow(energy, (double)2.0) * energy_quad);
+                const ArrayTr<double> ev = data_struct::generate_energy_array(energy_range, &fit_params);
                 data_struct::ArrayTr<double> sub_spectra = quantification_standard->integrated_spectra.segment(energy_range.min, energy_range.count());
 
                 std::string full_path = analysis_job->output_dir + DIR_END_CHAR + "output" + DIR_END_CHAR + "calib_" + fit_routine->get_name() + "_" + standard_itr.standard_filename;

src/core/process_whole.h

@@ -302,7 +302,7 @@ DLL_EXPORT void proc_spectra(data_struct::Spectra_Volume<T_real>* spectra_volume
             {
                 dataset_fullpath.replace(sidx, 7, "output"); // 7 = sizeof("img.dat")
                 std::string str_path = dataset_fullpath + "_" + fit_routine->get_name() + ".png";
-                data_struct::ArrayTr<T_real> ev = data_struct::gen_energy_vector(matrix_fit->energy_range(), override_params->fit_params);
+                data_struct::ArrayTr<T_real> ev = data_struct::generate_energy_array(matrix_fit->energy_range(), &(override_params->fit_params));
                 Spectra<T_real> int_spec = spectra_volume->integrate();
                 int_spec = int_spec.sub_spectra(matrix_fit->energy_range().min, matrix_fit->energy_range().count());
                 #ifdef _BUILD_WITH_QT

src/data_struct/fit_parameters.h

@@ -276,8 +276,6 @@ DLL_EXPORT Range get_energy_range(const T_real min_energy, const T_real max_ener
 {
 
     struct Range energy_range;
-
-    //data_struct::ArrayTr<double> ev = energy_offset + (energy * energy_slope) + (Eigen::pow(energy, (double)2.0) * energy_quad);
     energy_range.min = static_cast<size_t>(round((min_energy - energy_offset) / energy_slope));
     energy_range.max = static_cast<size_t>(round((max_energy - energy_offset) / energy_slope));
     //if (xmax > used_chan - 1) or (xmax <= np.amin([xmin, used_chan / 20.])):
@@ -305,19 +303,59 @@ DLL_EXPORT Range get_energy_range(const size_t spectra_size, const Fit_Parameter
         params->value(STR_ENERGY_SLOPE));
 }
 
-//-----------------------------------------------------------------------------
+// ----------------------------------------------------------------------------
 
 template<typename T_real>
-DLL_EXPORT const ArrayTr<T_real> gen_energy_vector(const Range& energy_range, const Fit_Parameters<T_real>& params)
+ArrayTr<T_real> generate_energy_array(const Range energy_range, const T_real energy_offset, const T_real energy_slope, const T_real energy_quad)
 {
-    const T_real energy_offset = params.value(STR_ENERGY_OFFSET);
-    const T_real energy_slope = params.value(STR_ENERGY_SLOPE);
-    const T_real energy_quad = params.value(STR_ENERGY_QUADRATIC);
-    ArrayTr<T_real> energy = ArrayTr<T_real>::LinSpaced(energy_range.count(), energy_range.min, energy_range.max);
-    ArrayTr<T_real> ev = energy_offset + (energy * energy_slope) + (Eigen::pow(energy, (T_real)2.0) * energy_quad);
+    const ArrayTr<T_real>energy = ArrayTr<T_real>::LinSpaced(energy_range.count(), energy_range.min, energy_range.max);
+    const ArrayTr<T_real>ev = energy_offset + (energy * energy_slope) + (Eigen::pow(energy, (T_real)2.0) * energy_quad);
     return ev;
 }
 
+
+// ----------------------------------------------------------------------------
+
+template<typename T_real>
+ArrayTr<T_real> generate_energy_array(const Range energy_range, const Fit_Parameters<T_real> * const fit_params)
+{
+    T_real energy_offset = 0.0;
+    T_real energy_slope = 0.0;
+    T_real energy_quad = 0.0;
+    if(fit_params != nullptr)
+    {
+        if (fit_params->contains(STR_ENERGY_OFFSET))
+        {
+            energy_offset = fit_params->value(STR_ENERGY_OFFSET);
+        }
+        else
+        {
+            logW<< "Missing fit parameter "<<STR_ENERGY_OFFSET<<"\n";
+        }
+        if (fit_params->contains(STR_ENERGY_SLOPE))
+        {
+            energy_slope = fit_params->value(STR_ENERGY_SLOPE);
+        }
+        else
+        {
+            logW<< "Missing fit parameter "<<STR_ENERGY_SLOPE<<"\n";
+        }
+        if (fit_params->contains(STR_ENERGY_QUADRATIC))
+        {
+            energy_quad = fit_params->value(STR_ENERGY_QUADRATIC);
+        }
+        else
+        {
+            logW<< "Missing fit parameter "<<STR_ENERGY_QUADRATIC<<"\n";
+        }
+    }
+    else
+    {
+        logW<< "fit parameters is "<<STR_ENERGY_QUADRATIC<<"\n";
+    }
+    return generate_energy_array(energy_range, energy_offset, energy_slope, energy_quad);
+}
+
 //-----------------------------------------------------------------------------
 
 } //namespace data_struct