stainoverlay_transparent.py

import cv2
import os
import configparser

import numpy as np

# Load the INI file and parse it
config = configparser.ConfigParser()
config.read("config.ini")  # Replace with the actual path to your INI file

# Paths for the mask images, raw images, and output images
# Read from the INI file
stain_mask_dir = config["StainSegmentation"]["mask_directory"]
filtered_mask_dir = stain_mask_dir.replace("stainmask", "filteredStainMasks")
raw_dir = config["Settings"]["image_path"]
stain_output_dir = config["StainOverlay"]["overlay_directory"]
filtered_output_dir = stain_output_dir.replace("stainoverlay", "filteredStainOverlays")

# Function to process masks
def process_masks(mask_dir, output_dir):
    # Ensure the directories exist
    for directory in [mask_dir, output_dir]:
        if not os.path.exists(directory):
            print(f"Creating directory: {directory}")
            os.makedirs(directory)

    # Check if the mask directory is empty
    if not os.listdir(mask_dir):
        print(f"Warning: Mask directory '{mask_dir}' is empty. No files to process.")
        return

    # 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"
        if not os.path.isfile(os.path.join(raw_dir, raw_name)):
            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)
        raw = cv2.imread(os.path.join(raw_dir, raw_name))

        if mask is None or raw is None:
            print(f"Error reading {mask_name} or {raw_name}. Skipping...")
            continue

        print(raw.shape)
        print(mask.shape)

        # Create an empty weight map with the same dimensions as the raw image
        weight_map = np.zeros_like(raw)  

        # Set pixels where mask == 38 to the color [0, 0, 255] (blue)
        weight_map[mask == 38] = [0, 0, 100] 

        # Overlay the weight map onto the original image
        overlay = cv2.addWeighted(raw, 1, weight_map, 0.5, 0) 
        
        # Save the intermediate results
        # cv2.imwrite(os.path.join(output_dir, f"{raw_name}_mask.jpg"), mask)
        # # cv2.imwrite(os.path.join(output_dir, f"{raw_name}_binary_mask.jpg"), binary_mask)
        # cv2.imwrite(os.path.join(output_dir, f"{raw_name}_weight_map.jpg"), weight_map)


        # Save the overlaid image to the output directory
        output_name = os.path.join(output_dir, raw_name)
        cv2.imwrite(output_name, overlay)
        print(f"Saved {output_name}")

        print(f"Processed {mask_name}")

# Process stainmasks
print("Processing stainmasks...")
process_masks(stain_mask_dir, stain_output_dir)

# Process filteredStainMasks
print("Processing filteredStainMasks...")
process_masks(filtered_mask_dir, filtered_output_dir)

print("All processing complete!")