Merge pull request #31 from MortenTabaka/Experiment_with_SuperPixels_…

…and_update_README Experiment with super pixels and slightly improve output folder structure
MortenTabaka · May 7, 2023 · b8556aa · b8556aa
2 parents 3cdf429 + beab3e0
commit b8556aa
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Showing 2 changed files with 40 additions and 14 deletions.
diff --git a/models/scripts/run_prediction_on_folder.py b/models/scripts/run_prediction_on_folder.py
@@ -41,7 +41,7 @@ def main(
         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_thresh: float = typer.Option(0.5, min=0, max=1),
     border_sp_class_balance: bool = typer.Option(False),
     border_sp_pixel_range: int = typer.Option(
         50,

diff --git a/src/pipelines/prediction_processor.py b/src/pipelines/prediction_processor.py
@@ -8,6 +8,7 @@
 import numpy as np
 import tensorflow as tf
 from cv2 import addWeighted, imread, imwrite
+from datetime import datetime
 from tensorflow.compat.v1 import ConfigProto, InteractiveSession
 from tensorflow_addons.image import blend
 from tqdm import tqdm
@@ -96,19 +97,36 @@ def __init__(
         self.border_sp_class_balance = border_sp_class_balance
         self.border_sp_pixel_range = border_sp_pixel_range
 
+        current_datetime = datetime.now().strftime("%Y-%m-%d--%H:%M:%S")
         self.output_folder_image_mask_overlays = (
-            self.output_folder / "prediction_image_mask_overlays"
+            self.output_folder
+            / model_revision
+            / current_datetime
+            / "overlays_mask_image"
         )
         self.output_folder_image_mask_overlays_with_marked_SP = (
             self.output_folder
-            / "prediction_image_mask_overlays_with_marked_SuperPixels"
+            / model_revision
+            / current_datetime
+            / "overlays_mask_image_with_marked_SuperPixels"
+        )
+        self.output_folder_prediction_masks = (
+            self.output_folder
+            / model_revision
+            / current_datetime
+            / "prediction_masks_no_borders_post_processed"
         )
-        self.output_folder_prediction_masks = self.output_folder / "prediction_masks"
         self.output_folder_superpixels_prediction_masks = (
-            self.output_folder / "prediction_masks_SuperPixels_postprocessing"
+            self.output_folder
+            / model_revision
+            / current_datetime
+            / "prediction_masks_borders_post_processed"
         )
         self.output_folder_raw_image_marked_borders = (
-            self.output_folder / "raw_images_marked_borders"
+            self.output_folder
+            / model_revision
+            / current_datetime
+            / "images_marked_borders_SuperPixels"
         )
         os.makedirs(self.output_folder_image_mask_overlays, exist_ok=True)
         os.makedirs(
@@ -174,17 +192,25 @@ def __postprocess_tiles_boundaries_in_concatenated_image(self):
             DataMode.NUMPY_TENSOR,
         ).concatenate_all_tiles()
 
+        all_input_images = self.__get_full_size_raw_images
+        all_numpy_tensors = sorted(
+            glob(path.join(self.output_folder_superpixels_prediction_masks, "*.npy"))
+        )
+        all_numpy_tensors = [
+            item
+            for item in all_numpy_tensors
+            if any(
+                f"{os.path.splitext(os.path.basename(filepath))[0]}.npy" in item
+                for filepath in all_input_images
+            )
+        ]
+
         for raw_image_filepath, raw_mask_filepath in zip(
-            self.__get_full_size_raw_images,
-            sorted(
-                glob(
-                    path.join(self.output_folder_superpixels_prediction_masks, "*.npy")
-                )
-            ),
+            all_input_images, all_numpy_tensors
         ):
             raw_image = imread(raw_image_filepath)
             raw_mask = np.load(raw_mask_filepath)
-            base_name = os.path.basename(raw_image_filepath)
+            base_name = os.path.splitext(os.path.basename(raw_image_filepath))[0]
             (
                 raw_processed_mask,
                 raw_image_with_boundaries,
@@ -218,7 +244,7 @@ def __postprocess_tiles_boundaries_in_concatenated_image(self):
             imwrite(
                 os.path.join(
                     self.output_folder_image_mask_overlays_with_marked_SP,
-                    f"{filename}.tiff",
+                    f"{filename}.jpg",
                 ),
                 blended_img_with_marked_borders,
             )