Compile a TIFF stack into a H.264 movie

tiffstack2movie.py

#!/usr/bin/env python
import argparse, os
from libtiff import TIFF
import moviepy.editor as mpy
import numpy as np
from skimage.color import gray2rgb

if __name__ == '__main__':
    ap = argparse.ArgumentParser()
    ap.add_argument('input_stack', help="Path to a tiff stack file")
    ap.add_argument('output_file', nargs='?', default=None, help="Path to the file that will be created")
    ap.add_argument('-i', '--input-rate', type=int, dest='input_rate', help="Frame rate of the input")
    ap.add_argument('-o', '--output-rate', type=int, dest='output_rate', help="Frame rate of the output")
    ap.add_argument('-c', '--hist-crop', nargs=2, type=float, default=[2, 98], dest='hist_crop', help="Low and high percentiles for normalizing intensity")
    ap.add_argument('-b', '--swap-bytes', action='store_true', default=False, dest='swap_bytes', help="Seems to be necessary for float (e.g. ratio) images, but not 16 bit uint tiffs")
    args = ap.parse_args()

    if not args.output_file:
        root, ext = os.path.splitext(args.input_stack)
        args.output_file = root + '_%0.1fx.mp4' % (args.output_rate / args.input_rate)

    tif = TIFF.open(args.input_stack, mode='r')
    stack_iter = tif.iter_images()
    stack_iter.next()
    test_frame = stack_iter.next().byteswap()
    low, high = np.percentile(test_frame, args.hist_crop[0]), np.percentile(test_frame, args.hist_crop[1])
    depth = 2**8 - 1

    def get_image(t):
        frame = stack_iter.next()
        if args.swap_bytes:
            frame = frame.byteswap()
        normed = np.clip(depth * (frame - low) / high, 0, depth)
        uint = np.uint8(normed)
        return gray2rgb(uint)

    clip = mpy.VideoClip(get_image, duration=60*5)

    clip.write_videofile(args.output_file, fps=args.output_rate, codec='libx264', audio=False, preset='fast', threads=4, ffmpeg_params=['-pix_fmt', 'yuv420p'])