FocalBlur - Revision history

Bell: 16 revisions

2014-07-11T15:34:55Z

16 revisions

Jlec at 06:31, 4 July 2014

2014-07-04T06:31:02Z

Pyadmin: 1 revision

2014-03-28T02:16:24Z

1 revision

New page

[[Image:StylizedFocalBlur.png|550px|right]]

==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:
<source lang="python">
FocalBlur aperture=2.0,samples=20,ray=1
</source>
or using python syntax:
<source lang="python">
FocalBlur(aperture=2.0,samples=20,ray=1)
</source>

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===

<gallery perrow=3 widths=300 heights=240>
Image:FocalBlur_a1.0_r1.png|FocalBlur aperture=1,samples=100,ray=1
Image:FocalBlur_a2.0_r1.png|FocalBlur aperture=2,samples=100,ray=1
Image:FocalBlur_a4.0_r1.png|FocalBlur aperture=4,samples=400,ray=1
Image:FocalBlur_a4.0_r0.png|FocalBlur aperture=4,samples=400,ray=0
Image:Focal_blur _ex6.png
Image:Focal blur_ex_ap3.png
Image:Focal blur_ex_ap3_mode1.png
Image:Focal blur_ex_ap3_mode2.png
Image:Focal blur_ex_ap3_mode3.png
</gallery>

==Script==
Load the script using the [[run]] command

<source lang="python">
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)

</source>

[[Category:Script_Library]]

Jarl.Underhaug: /* Script */

2012-12-14T11:47:33Z

Script

Jarl.Underhaug at 14:30, 28 November 2012

2012-11-28T14:30:16Z

Jarl.Underhaug: /* Usage */

2012-11-28T14:29:47Z

Usage

Jarl.Underhaug at 14:29, 28 November 2012

2012-11-28T14:29:30Z

Jarl.Underhaug: /* Notes */

2012-11-28T14:26:07Z

Notes

Jarl.Underhaug: /* Script */

2012-11-28T14:25:00Z

Script

Jarl.Underhaug: /* Script */

2011-07-18T08:56:07Z

Script

← Older revision		Revision as of 06:31, 4 July 2014
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]]		[[Image:StylizedFocalBlur.png\|550px\|right]]

← Older revision	Revision as of 15:34, 11 July 2014
(No difference)

@@ Line 116: / Line 116: @@
          # Save the image to temporary directory
 	if ray:
-                 cmd.ray()
+                 cmd.ray(width,height)
                  cmd.png(curFile)
 	else:

@@ Line 26: / Line 26: @@
 * 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===

@@ Line 7: / Line 7: @@
 Load the script using the [[run]] command. Execute the script using PyMOL syntax:
 <source lang="python">
-FocalBlur aperture=2.0,samples=100,ray=1
+FocalBlur aperture=2.0,samples=20,ray=1
 </source>
 or using python syntax:
 <source lang="python">
-FocalBlur(aperture=2.0,samples=100,ray=1)
+FocalBlur(aperture=2.0,samples=20,ray=1)
 </source>

@@ Line 21: / Line 21: @@
 * 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.
 ===Examples===

@@ Line 43: / Line 43: @@
 <source lang="python">
 from pymol import cmd
 from tempfile import mkdtemp
 from shutil import rmtree
 from math import sin,cos,pi,sqrt
-from sys import exit
+from PIL import Image
 def FocalBlur(aperture=2.0,samples=10,ray=0,width=0,height=0):
@@ Line 74: / Line 72: @@
      FocalBlur aperture=2, samples=100, ray=1, width=600, height=400
      '''
      # Formalize the parameter types
@@ Line 85: / Line 77: @@
      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]
@@ Line 122: / Line 109: @@
          curFile = "%s/frame-%04d.png" % (tmpdir,frame)
-         # Save the image
+         # Save the image to temporary directory
 	if ray:
-        	cmd.png(curFile,width=width,height=height,ray=ray,quiet=1)
+                cmd.ray()
 	else:
          	cmd.png(curFile,quiet=1)
-−
          # Return the protein and the light to the original orientation
          cmd.set('light',light)
          cmd.set_view(view)
      # 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
      rmtree(tmpdir)
-−
 cmd.extend('FocalBlur', FocalBlur)