Merge pull request #28 from MortenTabaka/Improve_segmentation_with_po…

…st_processing

Improve segmentation by implementing post-processing using SLIC algorithm for super pixels. 
Best enhancement is visible in boundaries post-processing.
Further research in best parameters are needed.

dockerfile-requirements.txt

@@ -10,3 +10,4 @@ tqdm
 requests
 PyYAML
 typer
+scikit-image

models/scripts/run_prediction_on_folder.py

@@ -1,5 +1,5 @@
-from pathlib import Path
 from enum import Enum
+from pathlib import Path
 
 import typer
 
@@ -22,13 +22,32 @@ def main(
     model_revision: AvailableRevisions = typer.Option(
         default=AvailableRevisions.version_5_10_2,
         help="Choose model revision for predictions.",
-        show_choices=True
+        show_choices=True,
     ),
     weights: TypeOfWeightsToLoad = typer.Option(
         default=TypeOfWeightsToLoad.miou,
         help="Pick which weights load",
-        show_choices=True
+        show_choices=True,
+    ),
+    sp_post_processing: bool = typer.Option(False),
+    sp_count: int = typer.Option(200, min=0),
+    sp_compactness: float = typer.Option(10, min=0),
+    sp_thresh: float = typer.Option(0.7, min=0, max=1),
+    border_sp: bool = typer.Option(
+        True, help="If should post-process tile boundaries with SuperPixels algorithm"
+    ),
+    border_sp_count: int = typer.Option(
+        50, min=0, help="Will be multiplied by number of borders in single strip"
     ),
+    border_compactness: float = typer.Option(10, min=0),
+    border_sp_thresh: float = typer.Option(0.3, min=0, max=1),
+    border_sp_class_balance: bool = typer.Option(False),
+    border_sp_pixel_range: int = typer.Option(
+        50,
+        min=1,
+        help="Strip width in single direction. Stripe width will be double of the value.",
+    ),
+    clear_cache: bool = typer.Option(True),
     input_folder: Path = typer.Option(
         get_absolute_path_to_project_location("models/custom_data/input"),
         help='Default: "models/custom_data/input". '
@@ -44,14 +63,22 @@ def main(
         dir_okay=True,
         show_default=False,
     ),
-    clear_cache: bool = typer.Option(True),
 ) -> None:
-
     PredictionPipeline(
         model_revision=model_revision,
         input_folder=input_folder,
         output_folder=output_folder,
-        which_metric_best_weights_to_load=weights
+        which_metric_best_weights_to_load=weights,
+        tiles_superpixel_postprocessing=sp_post_processing,
+        number_of_superpixels=sp_count,
+        compactness=sp_compactness,
+        superpixel_threshold=sp_thresh,
+        border_sp=border_sp,
+        border_sp_count=border_sp_count,
+        border_compactness=border_compactness,
+        border_sp_thresh=border_sp_thresh,
+        border_sp_class_balance=border_sp_class_balance,
+        border_sp_pixel_range=border_sp_pixel_range,
     ).process(clear_cache)