FocalBlur
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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.
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
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 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)
