FocalBlur

Description

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

Usage

Load the script using the run command. Execute the script using PyMOL syntax:

FocalBlur aperture=2.0,samples=100,ray=1

or using python syntax:

FocalBlur(aperture=2.0,samples=100,ray=1)

For additional options, see the script comments.

Notes

• When using raytracing, the image creation will take n times longer than normal, where n is the number of samples.
• The script uses ImageMagick for creating the blured image. It has only been tested on Linux
• The aperture is a purely arbitrary value and not related to f stops on a camera.
• There is a bug preventing custom image sizes when not using raytracing.

Examples

FocalBlur aperture=1,samples=100,ray=1	FocalBlur aperture=2,samples=100,ray=1
FocalBlur aperture=4,samples=400,ray=1	FocalBlur aperture=4,samples=400,ray=0

Script

Load the script using the run command

from pymol import cmd
from os import system
from tempfile import mkdtemp
from shutil import rmtree
from math import sin,cos,pi,sqrt

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

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
    '''
    aperture, samples = float(aperture), int(samples)
    ray, width, height = int(ray), int(width), int(height)

    # Because of a bug, only custom sizes when raytracing
    if not ray:
        width=0
        height=0

    # 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])

        # Save the image
        cmd.png(tmpdir+'/frame-%04d.png' % (frame),width=width,height=height,ray=ray)
        
        # Return the protein and the light to the original orientation
        cmd.set('light',light)
        cmd.set_view(view)

    # Create a blured image of all the frames
    system('convert %s/frame-*.png +matte -average %s/blur.png' % (tmpdir,tmpdir))

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

    # Delete the temporary files
    rmtree(tmpdir)

cmd.extend('FocalBlur', FocalBlur)