Copy Op (for RandomAccessibleIntervals)¶
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@df84528
This notebook looks at copying RandomAccessibleIntervals. This Op exists for the times that copy.img() just doesn't work:
In [2]:
ij.op().help("copy.rai")
Out[2]:
Available operations: (RandomAccessibleInterval out?) = net.imagej.ops.copy.CopyRAI( RandomAccessibleInterval out?, RandomAccessibleInterval in)
In [3]:
import net.imglib2.FinalInterval
import net.imglib2.img.Img
import net.imglib2.IterableInterval
import net.imglib2.RandomAccessibleInterval
import net.imglib2.type.numeric.integer.UnsignedByteType
import net.imglib2.view.Views
dims = new FinalInterval(200, 150)
input1 = ij.op().create().img(dims, new UnsignedByteType())
equation1 = "127 * Math.sin(p[0] / 4) + 128"
ij.op().run("equation", input1, equation1)
input2 = ij.op().create().img(dims, new UnsignedByteType())
equation2 = "127 * Math.cos(p[1] / 4) + 128"
ij.op().run("equation", input2, equation2)
stack = Views.stack(input1, input2)
println(stack instanceof RandomAccessibleInterval)
println(stack instanceof IterableInterval)
println(stack instanceof Img)
ij.notebook().display(stack)
true false false
Out[3]:
Copying the Img is easy enough. All we need is the input we just made and an output image:
In [4]:
//Remember that output comes before input
copyRAI = ij.op().copy().rai(stack)
ij.notebook().display(copyRAI)
java.lang.ClassCastException: net.imglib2.view.StackView cannot be cast to net.imglib2.IterableInterval at net.imagej.ops.map.MapUnaryComputers$IIToIIParallel.compute(MapUnaryComputers.java:87) at net.imagej.ops.copy.CopyRAI.compute(CopyRAI.java:90) at net.imagej.ops.copy.CopyRAI.compute(CopyRAI.java:54) at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61) at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71) at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97) at org.scijava.command.CommandModule.run(CommandModule.java:199) at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:944) at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:156) at net.imagej.ops.copy.CopyNamespace.rai(CopyNamespace.java:156) at net.imagej.ops.copy.CopyNamespace$rai.call(Unknown Source) at this cell line 2 at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.runScript(GroovyCodeRunner.java:94) at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.call(GroovyCodeRunner.java:59) at com.twosigma.beakerx.groovy.evaluator.GroovyCodeRunner.call(GroovyCodeRunner.java:32)
There also exist Ops to copy Imgs and IterableIntervals, which you can find by accessing these links.