added remove_outlier_pixels method to image readers

takes care of pixels where the sensor malfunctions and creates an
anomolous bright spot

src/base/DICe.h

@@ -172,6 +172,8 @@ const char* const compute_image_gradients = "compute_image_gradients";
 /// String parameter name
 const char* const filter_failed_cine_pixels = "filter_failed_cine_pixels";
 /// String parameter name
+const char* const remove_outlier_pixels = "remove_outlier_pixels";
+/// String parameter name
 const char* const convert_cine_to_8_bit = "convert_cine_to_8_bit";
 /// String parameter name
 const char* const initial_condition_file = "initial_condition_file";
@@ -1233,12 +1235,17 @@ const Correlation_Parameter filter_failed_cine_pixels_param(filter_failed_cine_p
   BOOL_PARAM,
   false,
   "Filter out any pixels that failed during cine acquisition");
+/// Correlation parameter and properties
+const Correlation_Parameter remove_outlier_pixels_param(remove_outlier_pixels,
+  BOOL_PARAM,
+  false,
+  "Remove outlier pixel intensities (usually due to failed pixels)");
 
 
 // TODO don't forget to update this when adding a new one
 /// The total number of valid correlation parameters
 /// Vector of valid parameter names
-const int_t num_valid_correlation_params = 88;
+const int_t num_valid_correlation_params = 89;
 /// Vector oIf valid parameter names
 const Correlation_Parameter valid_correlation_params[num_valid_correlation_params] = {
   correlation_routine_param,
@@ -1317,6 +1324,7 @@ const Correlation_Parameter valid_correlation_params[num_valid_correlation_param
   rotate_def_image_270_param,
   levenberg_marquardt_regularization_factor_param,
   filter_failed_cine_pixels_param,
+  remove_outlier_pixels_param,
   time_average_cine_ref_frame_param,
   global_regularization_alpha_param,
   global_stabilization_tau_param,

src/utils/src/DICe_ImageIO.cpp

@@ -290,6 +290,9 @@ void read_image(const char * file_name,
   }
   // apply any post processing of the images as requested
   if(params!=Teuchos::null){
+    if(params->get<bool>(remove_outlier_pixels,false)){
+      remove_outliers(width,height,intensities);
+    }
     if(params->get<bool>(spread_intensity_histogram,false)){
       spread_histogram(width,height,intensities);
     }
@@ -313,6 +316,31 @@ void round_intensities(const int_t width,
   }
 }
 
+
+DICE_LIB_DLL_EXPORT
+void remove_outliers(const int_t width,
+  const int_t height,
+  intensity_t * intensities){
+
+  std::vector<intensity_t> sorted_intensities(width*height,0.0);
+  for(int_t i=0;i<width*height;++i)
+    sorted_intensities[i] = intensities[i];
+  std::sort(sorted_intensities.begin(),sorted_intensities.end());
+  const intensity_t outlier_intens = 0.98 * sorted_intensities[width*height-1];
+  intensity_t replacement_intens = 0.0;
+  for(int_t i=0;i<width*height;++i){
+    if(sorted_intensities[width*height-i-1] < outlier_intens){
+      replacement_intens = sorted_intensities[width*height-i-1];
+      break;
+    }
+  }
+  DEBUG_MSG("utils::remove_outliers(): outlier intensity value: " << outlier_intens << " to be replaced with intensity: " << replacement_intens);
+  for(int_t i=0;i<width*height;++i){
+      if(intensities[i]>=outlier_intens)
+        intensities[i] = replacement_intens;
+  }
+}
+
 DICE_LIB_DLL_EXPORT
 void floor_intensities(const int_t width,
   const int_t height,

src/utils/src/DICe_ImageIO.h

@@ -137,6 +137,16 @@ void round_intensities(const int_t width,
   const int_t height,
   intensity_t * intensities);
 
+/// Set the intensity value for outlier pixels (the ones with the highest intensity value) to the second highest value
+/// This is helpful in removing failed cine pixels
+/// \param width
+/// \param height
+/// \param intensities
+DICE_LIB_DLL_EXPORT
+void remove_outliers(const int_t width,
+  const int_t height,
+  intensity_t * intensities);
+
 /// Round the image intensity values to the nearest integer value
 /// \param width
 /// \param height

tools/DICe_CineToTiff.cpp

@@ -138,7 +138,8 @@ int main(int argc, char *argv[]) {
 
   // filter out failed cine pixels
   Teuchos::RCP<Teuchos::ParameterList> params = Teuchos::rcp(new Teuchos::ParameterList());
-  params->set(filter_failed_cine_pixels,true);
+  params->set(remove_outlier_pixels,true);
+  params->set(spread_intensity_histogram,true);
 
   for(int_t i=start_frame;i<=end_frame;++i){
     int_t num_digits_total = 0;