Pad a series of 2D images

brainsaw_pad.py

import numpy as np
import tifffile as tiff
from pathlib import Path

# Define the input and output directories
input_dir = Path('/home/adam/Desktop/blackcap/blackcap_stitched/2')
output_dir = Path('/home/adam/Desktop/blackcap/blackcap_stitched_padded/2')

# Ensure the output directory exists
output_dir.mkdir(parents=True, exist_ok=True)

# Define the padding size
pad_width = 25

# Process each file in the input directory
for file_path in input_dir.glob('*.tif*'):
    # Load the 2D TIFF file
    image = tiff.imread(file_path)

    if image.ndim == 2:  # Ensure it's a 2D image
        # Pad the image on the x and y axes (height and width)
        padded_image = np.pad(image, pad_width=((pad_width, pad_width),
                                                (pad_width, pad_width)),
                              mode='constant', constant_values=0)

        # Save the padded image to the output directory
        output_path = output_dir / file_path.name
        tiff.imwrite(output_path, padded_image)

        print(f"Processed and saved: {output_path}")
    else:
        print(f"Skipping non-2D image: {file_path}")

print("Processing complete.")