added APRConverter to APR, and then included some calling methods, then you call apr.get_apr(), instead of using the converter

Author: cheesema

examples/Example_get_apr.cpp

@@ -45,33 +45,31 @@ int main(int argc, char **argv) {
     //the apr datastructure
     APR<uint16_t> apr;
 
-    APRConverter<uint16_t> apr_converter;
-
     //read in the command line options into the parameters file
-    apr_converter.par.Ip_th = options.Ip_th;
-    apr_converter.par.rel_error = options.rel_error;
-    apr_converter.par.lambda = options.lambda;
-    apr_converter.par.mask_file = options.mask_file;
-    apr_converter.par.min_signal = options.min_signal;
-    apr_converter.par.SNR_min = options.SNR_min;
-    apr_converter.par.normalized_input = options.normalize_input;
-    apr_converter.par.neighborhood_optimization = options.neighborhood_optimization;
-    apr_converter.par.output_steps = options.output_steps;
+    apr.parameters.Ip_th = options.Ip_th;
+    apr.parameters.rel_error = options.rel_error;
+    apr.parameters.lambda = options.lambda;
+    apr.parameters.mask_file = options.mask_file;
+    apr.parameters.min_signal = options.min_signal;
+    apr.parameters.SNR_min = options.SNR_min;
+    apr.parameters.normalized_input = options.normalize_input;
+    apr.parameters.neighborhood_optimization = options.neighborhood_optimization;
+    apr.parameters.output_steps = options.output_steps;
 
     //where things are
-    apr_converter.par.input_image_name = options.input;
-    apr_converter.par.input_dir = options.directory;
-    apr_converter.par.name = options.output;
-    apr_converter.par.output_dir = options.output_dir;
+    apr.parameters.input_image_name = options.input;
+    apr.parameters.input_dir = options.directory;
+    apr.parameters.name = options.output;
+    apr.parameters.output_dir = options.output_dir;
 
-    apr_converter.fine_grained_timer.verbose_flag = false;
-    apr_converter.method_timer.verbose_flag = false;
-    apr_converter.computation_timer.verbose_flag = false;
-    apr_converter.allocation_timer.verbose_flag = false;
-    apr_converter.total_timer.verbose_flag = true;
+    apr.apr_converter.fine_grained_timer.verbose_flag = false;
+    apr.apr_converter.method_timer.verbose_flag = false;
+    apr.apr_converter.computation_timer.verbose_flag = false;
+    apr.apr_converter.allocation_timer.verbose_flag = false;
+    apr.apr_converter.total_timer.verbose_flag = true;
 
     //Gets the APR
-    if(apr_converter.get_apr(apr)){
+    if(apr.get_apr()){
 
         //Below is IO and outputting of the Implied Resolution Function through the Particle Cell level.
 

examples/Example_get_apr.h

@@ -6,7 +6,6 @@
 
 #include "algorithm/APRParameters.hpp"
 #include "data_structures/Mesh/PixelData.hpp"
-#include "algorithm/APRConverter.hpp"
 #include "data_structures/APR/APR.hpp"
 
 

src/algorithm/APRConverter.hpp

@@ -27,6 +27,8 @@ template<typename ImageType>
 class APRConverter: public LocalIntensityScale, public ComputeGradient, public LocalParticleCellSet, public PullingScheme {
 
 public:
+
+
     APRParameters par;
     APRTimer fine_grained_timer;
     APRTimer method_timer;
@@ -52,20 +54,21 @@ class APRConverter: public LocalIntensityScale, public ComputeGradient, public L
         }
     };
 
-private:
     //get apr without setting parameters, and with an already loaded image.
     template<typename T>
     bool get_apr_method(APR<ImageType> &aAPR, PixelData<T> &input_image);
 
+    template<typename T>
+    void auto_parameters(const PixelData<T> &input_img);
+
+private:
+
     //pointer to the APR structure so member functions can have access if they need
     const APR<ImageType> *apr;
 
     template<typename T>
     void init_apr(APR<ImageType>& aAPR, PixelData<T>& input_image);
 
-    template<typename T>
-    void auto_parameters(const PixelData<T> &input_img);
-
     template<typename T>
     bool get_apr_method_from_file(APR<ImageType> &aAPR, const TiffUtils::TiffInfo &aTiffFile);
 
@@ -191,7 +194,7 @@ bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, PixelData<T>&
     fine_grained_timer.stop_timer();
 
 #ifndef APR_USE_CUDA
-    method_timer.verbose_flag = true;
+    //method_timer.verbose_flag = true;
     method_timer.start_timer("compute_gradient_magnitude_using_bsplines");
     get_gradient(image_temp, grad_temp, local_scale_temp, local_scale_temp2, bspline_offset, par);
     method_timer.stop_timer();
@@ -203,7 +206,7 @@ bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, PixelData<T>&
     method_timer.start_timer("compute_local_intensity_scale");
     get_local_intensity_scale(local_scale_temp, local_scale_temp2, par);
     method_timer.stop_timer();
-    method_timer.verbose_flag = false;
+    //method_timer.verbose_flag = false;
 
     if(par.output_steps){
         TiffUtils::saveMeshAsTiff(par.output_dir + "local_intensity_scale_step.tif", local_scale_temp);
@@ -305,7 +308,7 @@ void APRConverter<ImageType>::get_gradient(PixelData<ImageType> &image_temp, Pix
     //  Input: full sized image.
     //  Output: down-sampled by 2 gradient magnitude (Note, the gradient is calculated at pixel level then maximum down sampled within the loops below)
 
-    fine_grained_timer.verbose_flag = true;
+    //fine_grained_timer.verbose_flag = true;
 
     fine_grained_timer.start_timer("threshold");
 

src/data_structures/APR/APR.hpp

@@ -10,11 +10,12 @@
 #include "../../algorithm/APRParameters.hpp"
 #include "../../numerics/APRCompress.hpp"
 #include "../../numerics/APRReconstruction.hpp"
+#include "../../algorithm/APRConverter.hpp"
+
 #include "../../io/APRWriter.hpp"
 #include "APRAccess.hpp"
 #include "ExtraParticleData.hpp"
 
-
 template<typename ImageType>
 class APR {
 
@@ -26,8 +27,11 @@ class APR {
     APRWriter apr_writer;
     APRReconstruction apr_recon;
 
+
 public:
+
     APRAccess apr_access;
+    APRConverter<ImageType> apr_converter;
 
     ExtraParticleData<ImageType> particles_intensities;
     std::string name;
@@ -44,6 +48,24 @@ class APR {
 
     inline uint64_t total_number_particles() const { return (apr_access).total_number_particles; }
 
+    ///////////////////////////////////
+    ///
+    /// APR Generation Methods (Calls members of the APRConverter class)
+    ///
+    //////////////////////////////////
+
+    bool get_apr(){
+        //copy across parameters
+        this->apr_converter.par = parameters;
+        return this->apr_converter.get_apr(*this);
+    }
+
+    template<typename T>
+    bool get_apr(PixelData<T>& input_img){
+        this->apr_converter.par = parameters;
+        return this->apr_converter.get_apr_method(*this, input_img);
+    }
+
     ///////////////////////////////////
     ///
     /// APR IO Methods (Calls members of the APRWriter class)