Created
April 24, 2013 21:32
-
-
Save acardona/5455754 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Albert Cardona 2012-09-06 | |
# Animate an Orthoslice view of an image volume in the 3D Viewer | |
# and record it into an ImageStack. | |
# Assumes that the Orthoslice view is already present in the 3D Viewer | |
# and then the scripts limits itself to iterating through the slices in a specific axis | |
# and to rotate when desired. | |
from ij3d import Image3DUniverse | |
from math import radians | |
univ = Image3DUniverse.universes[0] | |
univ.select(None) | |
c = univ.getContents().iterator().next() | |
print c | |
orthogroup = c.getContent() | |
print orthogroup | |
renderer = orthogroup.getRenderer() | |
print renderer | |
width = 282 | |
height = 319 | |
depth = 1189 | |
dims = univ.getCanvas().getBounds() | |
print dims | |
stack = ImageStack(dims.width, dims.height) | |
# adjust Z | |
renderer.setSlice(2, 174) | |
renderer.setSlice(0, 0) | |
def snapshot(univ) | |
return univ.takeSnapshot().getProcessor().convertToByte() | |
def record(univ, renderer, stack, axis, first, last): | |
"""From first to last, inclusive, recorded into stack.""" | |
if first < last: | |
for i in xrange(first, last + 1): | |
renderer.setSlice(axis, i) | |
stack.addSlice(str(i), snapshot(univ)) | |
else: | |
for i in xrange(first, last -1, -1): | |
renderer.setSlice(axis, i) | |
stack.addSlice(str(i), snapshot(univ)) | |
# Acquire movie from X=0 to X=214 | |
record(univ, renderer, stack, 0, 0, 214) | |
# Rotate and acquire movie | |
#for i in xrange(40): | |
# univ.rotateY(radians(-1)) | |
# stack.addSlice(str(i), snapshot(univ)) | |
# Acquire movie from Z=174 to 0 | |
record(univ, renderer, stack, 2, 174, 0) | |
# Acquire movie from Z=0 to Z=1188 while rotating for the first 800 slices | |
for i in xrange(0, 1188 + 1): | |
renderer.setSlice(2, i) | |
if i < 500: | |
univ.rotateY(radians(-1 * (40 / 500.0))) | |
else: | |
univ.rotateY(radians(-1 * (20 / 688.0))) | |
stack.addSlice(str(i), snapshot(univ)) | |
ImagePlus("Movie", stack).show() |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment