replace std::cout calls with info()

src/include/stir/Scanner.h

@@ -87,8 +87,7 @@ class Succeeded;
           coincidence window then the reconstruction will essential be nonTOF but the
             projector will restrict the size of the LOR to the size of the coincidence window.
       \li \c The scanner will be classified as TOF enabled when the numer of TOF bins and
-TOF bin size are  >1 and >0, respectively. If the timing resolution is not set that will be fine
-as long as the final TOF possitions is 1. Then we just restict the size of the LOR.
+TOF bin size are  >1 and >0, respectively. If the timing resolution is not set, we will attempt to handle this if the number TOF positions is 1 (the projector will then just use the bin-size to restrict the size of the LOR).
 
       A further complication is that some scanners (including many Siemens scanners)
       insert virtual crystals in the sinogram data (corresponding to gaps between

src/recon_buildblock/ML_estimate_component_based_normalisation.cxx

@@ -94,7 +94,7 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
 
   FanProjData model_fan_data;
   FanProjData fan_data;
-  std::cout << "Allocating ..." << std::endl;
+  info("Allocating memory ...", 3);
   DetectorEfficiencies data_fan_sums(IndexRange2D(num_physical_rings, num_physical_detectors_per_ring));
   DetectorEfficiencies efficiencies(IndexRange2D(num_physical_rings, num_physical_detectors_per_ring));
 
@@ -151,9 +151,8 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
       model_fan_data_sum += *local_model_fan_data_sum[i];
 
     local_model_fan_data_sum.clear();
-    std::cout << "Model sum: " << model_fan_data_sum << std::endl;
+    info("Model sum of fan data: " + std::to_string(model_fan_data_sum), 3);
   }
-  std::cout << ">>><<<: " << std::endl;
   {
     // next could be local if KL is not computed below
     FanProjData measured_fan_data;
@@ -196,16 +195,16 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
           // to avoid divisions by zero.
           data_fan_sum = make_all_fan_data_from_cache(measured_fan_data, measured_data, model_fan_data);
           float dd = data_fan_sums.find_max();
-          std::cout << "Data fan sum max " << dd << std::endl;
+          info("Data fan sum max: " + std::to_string(dd), 3);
           threshold_for_KL =dd / 100000000.F;
 
-          std::cout << "1. Making fan sum data .. " << std::endl;
+          info("1. Making fan sum data .. ", 3);
           make_fan_sum_data(data_fan_sums, measured_fan_data);
-          std::cout << "fan sum data min/max " <<  data_fan_sums.find_min() << " " << data_fan_sums.find_max() << std::endl;
+          info("fan sum data min/max " + std::to_string(data_fan_sums.find_min()) + "/" + std::to_string(data_fan_sums.find_max()), 3);
 
-          std::cout << "2. Making fan geo data .. " << std::endl;
+          info("2. Making fan geo data .. ", 3);
           make_geo_data(measured_geo_data, measured_fan_data);
-          std::cout << "measured_geo_data min/max " <<  measured_geo_data.find_min() << " " << measured_geo_data.find_max() << std::endl;
+           info("measured_geo_data min/max " + std::to_string(measured_geo_data.find_min()) + "/" + std::to_string(measured_geo_data.find_max()), 3);;
         }
       if (do_display && do_block)
         display(measured_block_data, "raw block data from measurements");
@@ -239,32 +238,31 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
         std::cout << "Iteration number: " << iter_num << std::endl;
         if (iter_num == 1)
           {
-            std::cout << "Calculating sums: " << std::endl;
+            info("Calculating sums om fan_data ...", 3);
             float value = sqrt(data_fan_sum / model_fan_data_sum);
-            std::cout << "Ratio: " << value << std::endl;
+            info("Ratio: " + std::to_string(value), 3);
             efficiencies.fill(value);
-            std::cout << "Finished sums." << std::endl;
             norm_geo_data.fill(1);
             norm_block_data.fill(1);
           }
         // efficiencies
         {
-          std::cout << "Copying model to fan_data..." << std::endl;
+          info("Copying model to fan_data...", 3);
           fan_data = model_fan_data;
-          std::cout << "Applying geo norm..." << std::endl;
+          info("Applying geo norm...", 3);
           apply_geo_norm(fan_data, norm_geo_data);
           if (do_block)
             {
-              std::cout << "Applying block norm..." << std::endl;
+              info("Applying block norm...", 3);
               apply_block_norm(fan_data, norm_block_data);
             }
           if (do_display)
             display(fan_data, "model*geo*block");
           for (int eff_iter_num = 1; eff_iter_num <= num_eff_iterations; ++eff_iter_num)
             {
-              std::cout << "Efficiency iteration number: " << iter_num << std::endl;
+              info("Efficiency iteration number: " + std::to_string(iter_num), 3);
               iterate_efficiencies(efficiencies, data_fan_sums, fan_data);
-              std::cout << "Finished efficiency iteration number: " << iter_num << std::endl;
+              info("Finished efficiency iteration", 3);
               {
                 char* out_filename = new char[out_filename_prefix.size() + 30];
                 sprintf(out_filename, "%s_%s_%d_%d.out", out_filename_prefix.c_str(), "eff", iter_num, eff_iter_num);
@@ -274,7 +272,7 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
               }
               if (do_KL)
                 {
-                  std::cout << "Calculating KL" << std::endl;
+                  info("Calculating KL", 3);
                   apply_efficiencies(fan_data, efficiencies);
                   std::cerr << "measured*norm min " << measured_fan_data.find_min() << " ,max " << measured_fan_data.find_max()
                             << std::endl;
@@ -302,8 +300,8 @@ ML_estimate_component_based_normalisation(const std::string& out_filename_prefix
             }
         } // end efficiencies
 
-        std::cout << "geo norm" << std::endl;
-        std::cout << "Copying model to fan_data..." << std::endl;
+        info("Starting geo norm", 3);
+        info("Copying model to fan_data...", 3);
         fan_data = model_fan_data;
         apply_efficiencies(fan_data, efficiencies);
         if (do_block)

src/utilities/construct_fanProjData_fromProjData.cxx

@@ -4,7 +4,7 @@
   \file
   \ingroup utilities
 
-\brief Construct FanProjData from ProjData
+\brief Construct stir::FanProjData from stir::ProjData
 
 \author Nikos Efthimiou