This is a read-only mirror of pymolwiki.org

Difference between revisions of "FocalBlur"

From PyMOL Wiki
Jump to navigation Jump to search
m (16 revisions)
 
(9 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 +
{{Infobox script-repo
 +
|type      = script
 +
|filename  = focal_blur.py
 +
|author    = [[User:Jarl.Underhaug|Jarl Underhaug]]
 +
|license  = -
 +
}}
 +
 +
[[Image:StylizedFocalBlur.png|550px|right]]
 +
 +
 +
 
==Description==
 
==Description==
  
Line 7: Line 18:
 
Load the script using the [[run]] command. Execute the script using PyMOL syntax:
 
Load the script using the [[run]] command. Execute the script using PyMOL syntax:
 
<source lang="python">
 
<source lang="python">
−
FocalBlur aperture=2.0,samples=100,ray=1
+
FocalBlur aperture=2.0,samples=20,ray=1
 
</source>
 
</source>
 
or using python syntax:
 
or using python syntax:
 
<source lang="python">
 
<source lang="python">
−
FocalBlur(aperture=2.0,samples=100,ray=1)
+
FocalBlur(aperture=2.0,samples=20,ray=1)
 
</source>
 
</source>
  
Line 20: Line 31:
  
 
* When using raytracing, the image creation will take ''n'' times longer than normal, where ''n'' is the number of samples.
 
* When using raytracing, the image creation will take ''n'' times longer than normal, where ''n'' is the number of samples.
−
* [http://www.imagemagick.org/ ImageMagick] is required for the script to work.
+
* The aperture is related to the aperture on a camera.
−
* 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.
+
===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===
 
===Examples===
Line 43: Line 57:
 
<source lang="python">
 
<source lang="python">
 
from pymol import cmd
 
from pymol import cmd
−
from os import system
 
 
from tempfile import mkdtemp
 
from tempfile import mkdtemp
 
from shutil import rmtree
 
from shutil import rmtree
 
from math import sin,cos,pi,sqrt
 
from math import sin,cos,pi,sqrt
−
from sys import exit
+
from PIL import Image
−
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):
Line 74: Line 86:
 
     FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
 
     FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
 
     '''
 
     '''
−
    # Check if Imagemagick is installed
 
−
    try:
 
−
        subprocess.call(['convert','-version'])
 
−
    except OSError, e:
 
−
        if e[0]==2: print('Error - ImageMagick is probably not installed')
 
−
        sys.exit()
 
  
 
     # Formalize the parameter types
 
     # Formalize the parameter types
Line 85: Line 91:
 
     aperture, samples = float(aperture), int(samples)
 
     aperture, samples = float(aperture), int(samples)
 
     width, height = int(width), int(height)
 
     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
 
     # 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]
Line 122: Line 123:
 
   
 
   
 
         curFile = "%s/frame-%04d.png" % (tmpdir,frame)
 
         curFile = "%s/frame-%04d.png" % (tmpdir,frame)
 +
        print "Created frame %i/%i (%0.0f%%)" % (frame+1,samples,100*(frame+1)/samples)
  
−
         # Save the image
+
         # Save the image to temporary directory
 
if ray:
 
if ray:
−
        cmd.png(curFile,width=width,height=height,ray=ray,quiet=1)
+
                cmd.ray(width,height)
 +
                cmd.png(curFile)
 
else:
 
else:
 
         cmd.png(curFile,quiet=1)
 
         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
 
         # 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
 
−
    r = subprocess.call('convert %s/frame-*.png +matte -average %s/blur.png' % (tmpdir,tmpdir),shell=True)
 
−
 
 
   
 
   
 
     # Load the blured image
 
     # Load the blured image
−
     print "load %s/blur.png" % tmpdir  
+
     avg.save('%s/avg.png' % (tmpdir))
−
     cmd.load('%s/blur.png' % tmpdir)
+
     cmd.load('%s/avg.png' % (tmpdir))
 
   
 
   
 
     # Delete the temporary files
 
     # Delete the temporary files
 
     rmtree(tmpdir)
 
     rmtree(tmpdir)
−
+
 
 
cmd.extend('FocalBlur', FocalBlur)
 
cmd.extend('FocalBlur', FocalBlur)
  

Latest revision as of 15:34, 11 July 2014

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.

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

  • Focal blur ex6.png
  • Focal blur ex ap3.png
  • Focal blur ex ap3 mode1.png
  • Focal blur ex ap3 mode2.png
  • Focal blur ex ap3 mode3.png

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)
Retrieved from "http://wiki.pymol.org/index.php?title=FocalBlur&oldid=11995"