Update the preprocessing with the new API

pipeline/feature-preprocessing/pipeline_preprocessing.m

@@ -11,9 +11,14 @@
 z_size = 1024;
 
 % Define a fix sigma value 
+method_denoising = 'bm3d';
 sigma = 190. / 255.;
 
+% Define the method for flattening
+method_flattening = 'srinivasan-2014';
+
 % Define the parameters for the cropping
+method_cropping = 'srinivasan-2014';
 h_over_rpe = 325;
 h_under_rpe = 30;
 width_crop = 340;
@@ -41,14 +46,15 @@
         vol = vol / max( vol(:) );
 
         % Apply the preprocessing
-        vol_denoised = denoising_volume( vol, sigma );
+        vol_denoised = denoising_volume( vol, method_denoising, sigma );
         disp( [ 'Image ', directory_info(idx_file).name, ' denoised' ] ...
              );
         [ baseline_vol, vol_flattened ] = flattening_volume( ...
-            vol_denoised );
+            vol_denoised, method_flattening );
         disp( [ 'Image ', directory_info(idx_file).name, ' flattened' ] ...
              );
-        vol_cropped = crop_volume( vol_flattened, baseline_vol, h_over_rpe, ...
+        vol_cropped = crop_volume( vol_flattened, method_cropping, ...
+                                   baseline_vol, h_over_rpe, ...
                                    h_under_rpe, width_crop );
         disp( [ 'Image ', directory_info(idx_file).name, ' cropped' ] ...
              );