def dropSlices(img, nth):
""" Drop every nth slice. Calibration is to be multipled by nth for Z.
Counts slices 1-based so as to preserve the first slice (index zero).
"""
return Views.stack([Views.hyperSlice(img, 2, i)
for i in xrange(img.dimension(2)) if 0 == (i+1) % nth])
# Grap the current image
img = IL.wrap(IJ.getImage())
# Cut out a cube
img1 = Views.zeroMin(Views.interval(img, [39, 49, 0],
[39 + 378 -1, 49 + 378 -1, 378 -1]))
# Rotate the cube on the Y axis to the left
img2 = Views.zeroMin(Views.rotate(img1, 2, 0)) # zeroMin is CRITICAL
# Rotate the cube on the X axis to the top
img3 = Views.zeroMin(Views.rotate(img1, 2, 1))
# Reduce Z resolution: make them anisotropic but in a different direction
nth = 2
img1 = dropSlices(img1, nth)
img2 = dropSlices(img2, nth)
img3 = dropSlices(img3, nth)
# The sequence of images to transform, each relative to the previous
images = [img1, img2, img3]
IL.wrap(Views.stack(images), "unregistered").show()
from ij import IJ
from net.imglib2.algorithm.math import ImgMath, ImgSource
from net.imglib2.img.array import ArrayImgs
from net.imglib2.realtransform import RealViews, AffineTransform3D
from net.imglib2.interpolation.randomaccess import NLinearInterpolatorFactory
from net.imglib2.util import Intervals
img = IL.wrap(IJ.getImage())
# Cut out a cube
img1 = Views.zeroMin(
Views.interval(img, [39, 49, 0], [39 + 378 - 1, 49 + 378 - 1, 378 - 1]))
print[img1.dimension(d) for d in xrange(img1.numDimensions())]
# Rotate the cube on the Y axis to the left
img2 = Views.rotate(img1, 2, 0)
# copy into ArrayImg
img1a = ArrayImgs.unsignedShorts([378, 378, 378])
ImgMath.compute(ImgSource(img1)).into(img1a)
img2a = ArrayImgs.unsignedShorts([378, 378, 378])
ImgMath.compute(ImgSource(img2)).into(img2a)
img1 = img1a
img2 = img2a
IL.wrap(img1, "cube").show()
IL.wrap(img2, "cube rotated").show()
# Now register them
fi = FileInfo()
fi.offset = 1024 # header size in bytes
fi.width = 128
fi.height = 128
fi.nImages = 128
baseDir = "/home/albert/lab/scripts/data/cim.mcgill.ca-shape-benchmark/"
bird = IL.wrap(Raw.open(baseDir + "/birdsIm/b21.im", fi))
airplane = IL.wrap(Raw.open(baseDir + "/airplanesIm/b14.im", fi))
# Rotate bird
# Starts with posterior view
# Rotate 180 degrees around Y axis
# Set to dorsal up: 180 degrees
birdY90 = Views.rotate(bird, 2, 0) # 90
birdY180 = Views.rotate(birdY90, 2, 0) # 90 again: 180
c1 = Views.iterable(birdY180).cursor()
img1 = ArrayImgs.unsignedBytes(Intervals.dimensionsAsLongArray(birdY180))
c2 = img1.cursor()
while c2.hasNext():
c2.next().set(c1.next())
# Rotate airplane
# Starts with dorsal view, anterior down
# Set to: coronal view, but dorsal is down
airplaneC = Views.rotate(airplane, 2, 1)
# Set to dorsal up: 180 degrees
airplaneC90 = Views.rotate(airplaneC, 0, 1) # 90
airplaneC180 = Views.rotate(airplaneC90, 0, 1) # 90 again: 180
