Displaying data from binary file in python

Numpy is quite handy for reading in simple binary file formats.

From the sound of it, you have a large binary file of uin16's that you want to read into a 3D array and visualize. We don't have to load it all into memory, but for this example, we will.

Here's a basic idea of what the code would look like:

import numpy as np
import matplotlib.pyplot as plt

def main():
    data = read_data('test.dat', 512, 512)
    visualize(data)

def read_data(filename, width, height):
    with open(filename, 'r') as infile:
        # Skip the header
        infile.seek(512)
        data = np.fromfile(infile, dtype=np.uint16)
    # Reshape the data into a 3D array. (-1 is a placeholder for however many
    # images are in the file... E.g. 2000)
    return data.reshape((width, height, -1))

def visualize(data):
    # There are better ways to do this, but let's keep it simple
    plt.ion()
    fig, ax = plt.subplots()
    im = ax.imshow(data[:,:,0], cmap=plt.cm.gray)
    for i in xrange(data.shape[-1]):
        image = data[:,:,i]
        im.set(data=image, clim=[image.min(), image.max()])
        fig.canvas.draw()

main()