# Generated by pandoc-plot 1.8.0
import matplotlib.pyplot as plt
import numpy as np

np.random.seed(2019)

from skued import diffread, align
from pathlib import Path

ref = diffread(Path("images") / "mnxc" / "Cr_1.tif")
im = diffread(Path("images") / "mnxc" / "Cr_2.tif")

mask = np.ones_like(ref, dtype=bool)
mask[0:1250, 950:1250] = False

shifted = align(image=im, reference=ref, mask=mask)

fig, ((ax1, ax2, ax3), (ax4, ax5, ax6)) = plt.subplots(nrows=2, ncols=3, figsize=(9, 6))
ax1.imshow(ref, vmin=0, vmax=200, cmap='inferno')
ax2.imshow(im, vmin=0, vmax=200, cmap='inferno')
ax3.imshow(ref - im, cmap="RdBu_r")
ax4.imshow(mask * im, vmin=0, vmax=200, cmap="inferno")
ax5.imshow(shifted, vmin=0, vmax=200, cmap='inferno')
ax6.imshow(ref - shifted, cmap="RdBu_r")

for ax in (ax1, ax2, ax3, ax4, ax5, ax6):
    ax.get_xaxis().set_visible(False)
    ax.get_yaxis().set_visible(False)

ax1.set_title("Reference")
ax2.set_title("Data")
ax3.set_title("Difference")
ax4.set_title("Masked image")
ax5.set_title("Aligned data")
ax6.set_title("Difference after shift")

plt.tight_layout()