interacting with ImageJ from Python

gaussian_blur_movie.py

"""
Creates a movie of an image that starts off blurry and gradually comes into focus.
"""
from msl.loadlib import LoadLibrary

jar = LoadLibrary('ij.jar')
ij = jar.lib.ij


def make_movie(url=None, start_sigma=30, nframes=100, fps=24):
    if url is None:
        url = 'http://wsr.imagej.net/images/lena-std.tif'

    opener = ij.io.Opener()
    img = opener.openImage(url)
    stack = ij.ImageStack(img.getWidth(), img.getHeight())
    gb = ij.plugin.filter.GaussianBlur()

    sigmas = [start_sigma * i / float(nframes) for i in range(nframes, -1, -1)]
    for sig in sigmas:
        print('blurring with a sigma of {}'.format(sig))
        imp = img.duplicate().getChannelProcessor()
        gb.blurGaussian(imp, sig)
        stack.addSlice(imp)

    new_filename = '{}-{}-{}-{}'.format(img.getTitle().rsplit('.', 1)[0], start_sigma, nframes, fps)
    imp = ij.ImagePlus(new_filename, stack)
    print('Saving AVI...')
    ij.IJ.run(imp, 'AVI... ', 'compression=JPEG frame={} save={}.avi'.format(fps, new_filename))


make_movie()
jar.gateway.shutdown()