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imagejan/Invert_RGB.groovy

Created February 2, 2020 21:04
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  1. imagejan created this gist Feb 2, 2020.
    38 changes: 38 additions & 0 deletions Invert_RGB.groovy
    View file
    Original file line number Diff line number Diff line change
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    #@ Dataset input
    #@ OpService ops
    #@ DatasetService ds
    #@ ConvertService cs

    import net.imagej.axis.Axes
    import net.imglib2.IterableInterval
    import net.imglib2.type.numeric.integer.UnsignedShortType
    import ij.CompositeImage
    import ij.ImagePlus
    import ij.IJ

    // For each channel, get the average of the two other channels

    ch1 = ops.convert().uint16(ops.transform().hyperSliceView(input, input.dimensionIndex(Axes.CHANNEL), 0))
    ch2 = ops.convert().uint16(ops.transform().hyperSliceView(input, input.dimensionIndex(Axes.CHANNEL), 1))
    ch3 = ops.convert().uint16(ops.transform().hyperSliceView(input, input.dimensionIndex(Axes.CHANNEL), 2))

    nCh1 = ops.math().add(ch2, ch3 as IterableInterval)
    nCh2 = ops.math().add(ch1, ch3 as IterableInterval)
    nCh3 = ops.math().add(ch1, ch2 as IterableInterval)

    merged16 = ops.transform().stackView([nCh1, nCh2, nCh3])
    divided = ops.create().img(merged16)

    divideOp = ops.op("math.divide", nCh1.firstElement(), new UnsignedShortType(2))
    ops.map(divided, merged16, divideOp)

    merged = ops.create().img(input)
    ops.image().invert(merged, ops.convert().uint8(divided))

    // stuff needed for correct display in ImageJ1

    result = ds.create(merged)
    imp = cs.convert(result, ImagePlus.class)
    resultImage = new CompositeImage(imp.duplicate(), IJ.COMPOSITE)
    resultImage.setTitle(input.getName() + "_RGBinverted")
    resultImage.show()