FocalBlur

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Type Python Script
Download focal_blur.py
Author(s) Jarl Underhaug
License -
This code has been put under version control in the project Pymol-script-repo
StylizedFocalBlur.png


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=20,ray=1

or using python syntax:

FocalBlur(aperture=2.0,samples=20,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 aperture is related to the aperture on a camera, and is inversely proportional to the f-number.

Bugs

  • FocalBlur uses the Python Image Library (PIL), a necessary components of PIL is missing in the Windows version of PyMOL
  • There is a bug when not using ray tracing with the free version of PyMOL

Examples

Script

Load the script using the run command

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)