updated stain detection to use concrete post-filter

main.py

@@ -3,7 +3,7 @@
 from datetime import datetime
 
 # Define flags for processing
-concrete_pre_filter = False
+concrete_mask = True
 process_crack = True
 process_stain = True
 process_spall = True  # if crack is not processed, spall won't be processed.
@@ -40,9 +40,9 @@ def main():  # sourcery skip: extract-duplicate-method
     log_message("Create raw, mask, overlay, mvs folders in run_timestamp folder.")
     call_in_conda_env("python UpdateRawMaskOverlayConfigs.py")
 
-    # if concrete_pre_filter:
-    #     log_message("Running concrete mask...")
-    #     call_in_conda_env("python concretemask.py")
+    if concrete_mask:
+        log_message("Running concrete mask...")
+        call_in_conda_env("python concretemask.py")
 
     #     log_message("Running filter raw...")
     #     call_in_conda_env("python filterRaw.py")
@@ -54,13 +54,13 @@ def main():  # sourcery skip: extract-duplicate-method
         log_message("Running crack segmentation...")
         call_in_conda_env("python cracksegmentation.py")
 
-        log_message("Running concrete mask...")
-        call_in_conda_env("python concretemask.py")
-
-        log_message("Running concrete post filter...")
-        call_in_conda_env("python concretePostFilter.py")
-
-        exit()
+        # log_message("Running concrete mask...")
+        # call_in_conda_env("python concretemask.py")
+        if concrete_post_filter:
+            log_message("Running concrete post filter...")
+            call_in_conda_env("python concretePostFilter.py")
+            
+
 
         log_message("Converting crack masks to 3 categories according to directions...")
         call_in_conda_env("python crack23directions.py")

stainoverlay.py

@@ -8,9 +8,9 @@
 
 # Paths for the mask images, raw images, and output images
 # Read from the INI file
-mask_dir = config["StainSegmentation"]["mask_directory"]
+mask_dir = config["StainSegmentation"]["mask_directory"].replace("stainmask", "filteredStainMasks")
 raw_dir = config["Settings"]["image_path"]
-output_dir = config["StainOverlay"]["overlay_directory"]
+output_dir = config["StainOverlay"]["overlay_directory"].replace("stainoverlay", "filteredStainOverlays")
 
 # Ensure the output directory exists
 if not os.path.exists(output_dir):
@@ -19,7 +19,7 @@
 # Iterate over the files in the mask directory
 for mask_name in os.listdir(mask_dir):
     # Extract the image name from the filename
-    raw_name = mask_name.split(".")[0] + ".JPG"
+    raw_name = mask_name.split(".")[0] + ".jpg"
 
     # Load the mask and raw images
     mask = cv2.imread(os.path.join(mask_dir, mask_name), cv2.IMREAD_GRAYSCALE)