Difference between revisions of "FocalBlur"

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(angles as Fermat's spiral instead of random)
(Script)
Line 44: Line 44:
 
from shutil import rmtree
 
from shutil import rmtree
 
from math import sin,cos,pi,sqrt
 
from math import sin,cos,pi,sqrt
 
+
import subprocess
 +
 
def FocalBlur(aperture=2.0,samples=10,ray=0,width=0,height=0):
 
def FocalBlur(aperture=2.0,samples=10,ray=0,width=0,height=0):
 
     '''
 
     '''
 
DESCRIPTION
 
DESCRIPTION
 
+
 
     Creates fancy figures by introducing a focal blur to the image. The object
 
     Creates fancy figures by introducing a focal blur to the image. The object
 
     at the origin will be in focus.  
 
     at the origin will be in focus.  
 
+
 
AUTHOR
 
AUTHOR
 
+
 
     Jarl Underhaug
 
     Jarl Underhaug
 
     University of Bergen
 
     University of Bergen
 
     jarl_dot_underhaug_at_gmail_dot_com
 
     jarl_dot_underhaug_at_gmail_dot_com
  
 +
    Updates by Jason Vertrees and Thomas Holder
 +
 
USAGE
 
USAGE
 
+
 
     FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int
 
     FocalBlur aperture=float, samples=int, ray=0/1, width=int, height=int
     
+
 
EXAMPELS
 
EXAMPELS
 
+
 
     FocalBlur aperture=1, samples=100
 
     FocalBlur aperture=1, samples=100
 
     FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
 
     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)
 
     aperture, samples = float(aperture), int(samples)
     ray, width, height = int(ray), int(width), int(height)
+
     width, height = int(width), int(height)
 
+
 
     # Because of a bug, only custom sizes when raytracing
 
     # Because of a bug, only custom sizes when raytracing
     if not ray:
+
     #if not ray:
        width=0
+
    #    width=0
        height=0
+
    #    height=0
 
+
 
     # Create a temporary directory
 
     # Create a temporary directory
 
     tmpdir = mkdtemp()
 
     tmpdir = mkdtemp()
 
+
 
     # Get the orientation of the protein and the light
 
     # Get the orientation of the protein and the light
 
     light = cmd.get('light')[1:-1]
 
     light = cmd.get('light')[1:-1]
 
     light = [float(s) for s in light.split(',')]
 
     light = [float(s) for s in light.split(',')]
 
     view = cmd.get_view()
 
     view = cmd.get_view()
 
+
 
     # Rotate the protein and the light in order to create the blur
 
     # Rotate the protein and the light in order to create the blur
 
     for frame in range(samples):
 
     for frame in range(samples):
Line 93: Line 98:
 
         xr = x/180.0*pi
 
         xr = x/180.0*pi
 
         yr = y/180.0*pi
 
         yr = y/180.0*pi
 
+
 
         # Rotate the protein
 
         # Rotate the protein
 
         cmd.turn('x',x)
 
         cmd.turn('x',x)
 
         cmd.turn('y',y)
 
         cmd.turn('y',y)
 
+
 
         # Rotate the light
 
         # Rotate the light
 
         ly = light[1]*cos(xr)-light[2]*sin(xr)
 
         ly = light[1]*cos(xr)-light[2]*sin(xr)
Line 104: Line 109:
 
         lz = lz*cos(yr)-lx*sin(yr)
 
         lz = lz*cos(yr)-lx*sin(yr)
 
         cmd.set('light',[lx,ly,lz])
 
         cmd.set('light',[lx,ly,lz])
 +
 +
        curFile = "%s/frame-%04d.png" % (tmpdir,frame)
  
 
         # Save the image
 
         # Save the image
        cmd.png(tmpdir+'/frame-%04d.png' % (frame),width=width,height=height,ray=ray)
+
if ray:
       
+
        cmd.png(curFile,width=width,height=height,ray=ray,quiet=1)
 +
else:
 +
        cmd.png(curFile,quiet=1)
 +
 
         # Return the protein and the light to the original orientation
 
         # Return the protein and the light to the original orientation
 
         cmd.set('light',light)
 
         cmd.set('light',light)
 
         cmd.set_view(view)
 
         cmd.set_view(view)
 
+
 
     # Create a blured image of all the frames
 
     # Create a blured image of all the frames
     system('convert %s/frame-*.png +matte -average %s/blur.png' % (tmpdir,tmpdir))
+
     r = subprocess.call('convert %s/frame-*.png +matte -average %s/blur.png' % (tmpdir,tmpdir),shell=True)
 
 
    # Load the blured image
 
    cmd.load('%s/blur.png' % (tmpdir))
 
  
 +
 +
    # Load the blured image
 +
    print "load %s/blur.png" % tmpdir
 +
    cmd.load('%s/blur.png' % tmpdir)
 +
 
     # Delete the temporary files
 
     # Delete the temporary files
 
     rmtree(tmpdir)
 
     rmtree(tmpdir)
 
+
 
cmd.extend('FocalBlur', FocalBlur)
 
cmd.extend('FocalBlur', FocalBlur)
  

Revision as of 05:04, 9 June 2011

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
import subprocess
 
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)
 
    # 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])
 
        curFile = "%s/frame-%04d.png" % (tmpdir,frame)

        # Save the image
	if ray:
        	cmd.png(curFile,width=width,height=height,ray=ray,quiet=1)
	else:
        	cmd.png(curFile,quiet=1)
 
        # 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
    r = subprocess.call('convert %s/frame-*.png +matte -average %s/blur.png' % (tmpdir,tmpdir),shell=True)

 
    # Load the blured image
    print "load %s/blur.png" % tmpdir 
    cmd.load('%s/blur.png' % tmpdir)
 
    # Delete the temporary files
    rmtree(tmpdir)
 
cmd.extend('FocalBlur', FocalBlur)