Correction on DWImageClustering for Average processing

WaterDetect.ini

@@ -201,7 +201,7 @@ VEGETATION = no
 NOT_VEGETATED = no
 WATER = no
 UNCLASSIFIED = no
-CLOUD_MEDIUM_PROBABILITY = no
+CLOUD_MEDIUM_PROBABILITY = yes
 CLOUD_HIGH_PROBABILITY = yes
 THIN_CIRRUS = yes
 SNOW = no

runWaterDetect.py

@@ -126,10 +126,10 @@ def process_ext_masks():
                                                 'processed and copied manually into each image folder.',
                         default='S2_S2COR', type=str)
     parser.add_argument("-d", "--dilation", type=int, required=False, default=0,
-                        help='Size of the dilation kernel to be applied to the final mask. Default value is 0 '
-                             '(no dilation).')
+                        help='Size of the dilation kernel to be applied to the final mask in pixels. '
+                             'Default value is 0 (no dilation).')
     parser.add_argument("-f", "--flags", help="Values to be masked. Each value should be preceded by the -f "
-                                              "(ex. -f 2 -f 3 -f 15",
+                                              "(ex. -f 2 -f 3 -f 15)",
                         required=True, type=int, action='append')
 
     args = parser.parse_args()

waterdetect/Common.py

@@ -328,6 +328,16 @@ def bitwise_or(array, bit_values):
     def bitwise_and(array, bit_values):
         return np.bitwise_and(array, bit_values)
 
+    @staticmethod
+    def flatten(x):
+        result = []
+        for el in x:
+            if isinstance(el, list):
+                result.extend(DWutils.flatten(el))
+            else:
+                result.append(el)
+        return result
+
     @staticmethod
     def listify(lst, uniques=[]):
         # pdb.set_trace()

waterdetect/External_mask.py

@@ -92,7 +92,12 @@ def prepare_external_masks(imgs_dir: str, masks_dir: str, flags: list, img_type:
 
     # loop through the images. For each image, we will look for the corresponding mask
     for img in imgs:
-        mask = search_mask(img, masks_path, img_type)
-        if mask is not None:
-            print(f'Processing mask: {str(mask)}')
-            process_mask(mask, img, flags, dilation=dilation)
+        try:
+            mask = search_mask(img, masks_path, img_type)
+            if mask is not None:
+                print(f'Processing mask: {str(mask)}')
+                process_mask(mask, img, flags, dilation=dilation)
+
+        except Exception as e:
+            print(e)
+            print(f'Problem processing mask {mask.name}')

waterdetect/Image.py

@@ -32,8 +32,11 @@ def get_necessary_bands(self):
         Check the config file and all the parametrization to return a set of bands needed to run the algorithm
         """
 
+        # first we will flatten the bands_keys list (it can contain list of lists)
+        bands = DWutils.flatten(self.bands_keys)
+
         # create a set from the bands_keys
-        bands = set(self.bands_keys)
+        bands = set(bands)
 
         # include the reference band
         bands.add(self.config.reference_band)