focal_blur.py

from __future__ import print_function
from pymol import cmd
from tempfile import mkdtemp
from shutil import rmtree
from math import sin, cos, pi, sqrt
from PIL import Image


def FocalBlur(aperture=2.0, samples=10, ray=0, width=0, height=0):
    '''
DESCRIPTION

    Creates fancy figures by introducing a focal blur to the image. The object
    at the origin will be in focus.

AUTHOR

    Jarl Underhaug
    University of Bergen
    jarl_dot_underhaug_at_gmail_dot_com

    Updates by Jason Vertrees and Thomas Holder

USAGE

    FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int

EXAMPELS

    FocalBlur aperture=1, samples=100
    FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
    '''

    # Formalize the parameter types
    ray = (ray in ("True", "true", 1, "1"))
    aperture, samples = float(aperture), int(samples)
    width, height = int(width), int(height)

    # Create a temporary directory
    tmpdir = mkdtemp()

    # Get the orientation of the protein and the light
    light = cmd.get('light')[1:-1]
    light = [float(s) for s in light.split(',')]
    view = cmd.get_view()

    # Rotate the protein and the light in order to create the blur
    for frame in range(samples):
        # Angles to rotate protein and light
        # Populate angles as Fermat's spiral
        theta = frame * pi * 110.0 / 144.0
        radius = 0.5 * aperture * sqrt(frame / float(samples - 1))
        x = cos(theta) * radius
        y = sin(theta) * radius
        xr = x / 180.0 * pi
        yr = y / 180.0 * pi

        # Rotate the protein
        cmd.turn('x', x)
        cmd.turn('y', y)

        # Rotate the light
        ly = light[1] * cos(xr) - light[2] * sin(xr)
        lz = light[2] * cos(xr) + light[1] * sin(xr)
        lx = light[0] * cos(yr) + lz * sin(yr)
        lz = lz * cos(yr) - lx * sin(yr)
        cmd.set('light', [lx, ly, lz])

        curFile = "%s/frame-%04d.png" % (tmpdir, frame)
        print("Created frame %i/%i (%0.0f%%)" % (frame + 1, samples, 100 * (frame + 1) / samples))

        # Save the image to temporary directory
        if ray:
            cmd.ray(width, height)
            cmd.png(curFile)
        else:
            cmd.png(curFile, quiet=1)

        # Create the average/blured image
        try:
            avg = Image.blend(avg, Image.open(curFile), 1.0 / (frame + 1))
        except:
            avg = Image.open(curFile)

        # Return the protein and the light to the original orientation
        cmd.set('light', light)
        cmd.set_view(view)

    # Load the blured image
    avg.save('%s/avg.png' % (tmpdir))
    cmd.load('%s/avg.png' % (tmpdir))

    # Delete the temporary files
    rmtree(tmpdir)

cmd.extend('FocalBlur', FocalBlur)