Image Alignment

In case of displacement of the detector component, i.e. scintilator, the open beam (background) image can not be used for normalization of the sample (signal) image without alignment.

Here is a simple image position shifting solution.

from pathlib import Path

ob_image = Path('background.tiff')
misaligned_image = Path('misaligned_sample.tiff')

# load tiff image
from PIL import Image

ob = Image.open(ob_image)
misaligned = Image.open(misaligned_image)

import numpy as np

ob_normalized = (ob / np.max(ob) * 255).astype(np.uint8)
misaligned_normalized = (misaligned / np.max(misaligned) * 255).astype(np.uint8)

def shift_pixels(image: np.ndarray, shift_x: int = 0, shift_y: int = 0) -> np.ndarray:
    """Shifts the pixels of an image by ``shift_x`` and ``shift_y``.

    Image size will remain the same, shifted pixels will
    be cropped and empty pixels will be filled with zeros.
    """
    rows, cols = image.shape
    empty_image = np.zeros(image.shape, dtype=np.uint8)
    cropping_point = (
        (max(0, -shift_y), min(rows, rows - shift_y)),
        (max(0, -shift_x), min(cols, cols - shift_x)),
    )
    placing_point = (
        (max(0, shift_y), min(rows, rows + shift_y)),
        (max(0, shift_x), min(cols, cols + shift_x)),
    )
    empty_image[
        placing_point[1][0] : placing_point[1][1],
        placing_point[0][0] : placing_point[0][1],
    ] = image[
        cropping_point[1][0] : cropping_point[1][1],
        cropping_point[0][0] : cropping_point[0][1],
    ]
    return empty_image

import matplotlib.pyplot as plt

fig, ax = plt.subplots(2, 2, figsize=(15, 10))
im = ax[0, 0].imshow(ob_normalized)
ax[0, 1].imshow(misaligned_normalized, cmap=im.cmap)
ax[1, 0].imshow(misaligned_normalized - (ob_normalized), cmap=im.cmap)
ax[1, 1].imshow(
    shift_pixels(misaligned_normalized, 6, 3) - (ob_normalized), cmap=im.cmap
)

ax[0, 0].set_title('Open Beam (Background)')
ax[0, 1].set_title('Misaligned Sample')
ax[1, 0].set_title('Misaligned Sample - Open Beam')
ax[1, 1].set_title('Shifted Misaligned Sample - Open Beam')

for ax_ in ax:
    plt.colorbar(im, ax=ax_)
    for ax__ in ax_:
        ax__.set_xlabel('pixel numbers')
        ax__.set_ylabel('pixel numbers')

Here is the sample image that is included in the misaligned image: