ExtendView Op¶

In [1]:

//load ImageJ
%classpath config resolver scijava.public https://maven.scijava.org/content/groups/public
%classpath add mvn net.imagej imagej 2.0.0-rc-67

//create ImageJ object
ij = new net.imagej.ImageJ()

Added new repo: scijava.public

Out[1]:

net.imagej.ImageJ@7b00c550

This Op wraps the Views.extend() method of ImgLib2, removing the borders of any RandomAccessibleInterval (which transforms it into a RandomAccessible). Let's see how it is called:

In [2]:

ij.op().help('extendView')

Out[2]:

Available operations:
	(ExtendedRandomAccessibleInterval out) =
	net.imagej.ops.transform.extendView.DefaultExtendView(
		RandomAccessibleInterval in,
		OutOfBoundsFactory factory)

Note that this Op takes an OutOfBoundsFactory as input. The OutOfBoundsFactory gives extendValue a strategy for populating all of the new pixels outside of the original image. Most of the classes extending OutOfBoundsFactory already have their own transform.extend() Op, but this Op can be used if you define your own, or if you are not sure beforehand on which OutOfBoundsFactory to use. For this notebook, however, we will just use an OutOfBoundsFactory that is already defined, for simplicity.

In [3]:

input = ij.scifio().datasetIO().open("http://imagej.net/images/clown.png")

ij.notebook().display(input)

Out[3]:

Let's find a more interesting section instead of running the Op on the whole image:

In [4]:

import net.imglib2.FinalInterval
region = FinalInterval.createMinSize(30, 17, 0, 85, 78, 3)

eye = ij.op().run("crop", input, region)

ij.notebook().display(eye)

Out[4]:

Now that we have a smaller section, let's extend the border. We have to create an OutOfBoundsFactory, so let's use OutOfBoundsMirrorExpWindowingFactory, an OutOfBoundsFactory that mirrors the image like extendMirror, however after a given distance (the default is 6, but the constructor can take any int) the image fades to zero. We will also use pad so that we can see the new pixels:

In [5]:

def pad(image, extended, t, r, b, l) {
  min = new long[image.numDimensions()]
  max = new long[image.numDimensions()]
  image.min(min)
  image.max(max)
  min[0] -= l; min[1] -= t; max[0] += r; max[1] += b
  return ij.op().run("intervalView", extended, min, max)
}

import net.imglib2.outofbounds.OutOfBoundsMirrorExpWindowingFactory
factory = new OutOfBoundsMirrorExpWindowingFactory(20)

extended = ij.op().run("extendView", eye, factory)

//let's extend our image out 20 pixels on each side
padLength = 40
padded = pad(eye, extended, padLength, padLength, padLength, padLength)

ij.notebook().display(padded)

Out[5]: