ASPIRE Image Class

This tutorial demonstrates some methods of the ASPIRE Image class

import os

import numpy as np

from aspire.image import Image
from aspire.operators import CTFFilter

file_path = os.path.join(os.path.dirname(os.getcwd()), "data", "monuments.npy")
img_data = np.load(file_path)
print(img_data.shape, img_data.dtype)

(4, 600, 600) uint8

Create an Image Instance

# Create an ASPIRE Image instance from the data
#   We'll tell it to convert to floating point data as well.
im = Image(img_data, dtype=np.float64)

Plot the Image Stack

# Plot the Image stack
im.show()

Apply a Uniform Shift

# Apply a single shift to each image.
shifts = np.array([100, 30])
im.shift(shifts).show()

Apply Image-wise Shifts

# Or apply shifts corresponding to to each image.
shifts = np.array([[300 * i, 100 * i] for i in range(1, im.n_images + 1)])
im.shift(shifts).show()

Downsampling

im.downsample(80).show()

CTF Filter

# pixel_size/defous_u/defocus_v in angstrom, voltage in kV
filter = CTFFilter(pixel_size=1, voltage=100, defocus_u=1500, defocus_v=2000)
im.filter(filter).show()