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Update DeconWithGrid.groovy #37

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merged 2 commits into from
Feb 15, 2024
Merged

Update DeconWithGrid.groovy #37

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Update DeconWithGrid.groovy
andmccall Feb 9, 2024
e242153
Update DeconWithGrid.groovy
andmccall Feb 14, 2024
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33 changes: 13 additions & 20 deletions src/main/resources/script_templates/Deconvolution/DeconWithGrid.groovy
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Original file line number Diff line number Diff line change
@@ -1,46 +1,39 @@
#@ OpService ops
#@ UIService ui
#@ ConvertService convert
#@ DatasetService data

import net.imglib2.type.numeric.real.FloatType;
import net.imagej.ops.Op
import net.imglib2.outofbounds.OutOfBoundsConstantValueFactory
import net.imagej.ops.deconvolve.RichardsonLucyF
import net.imglib2.util.Util

// create the sample image
base = ops.run("create.img", [150, 100], new FloatType())
formula = "p[0]^2 * p[1]"
ops.image().equation(base, formula)

ui.show(base);
ui.show("input image", base);

// create kernel
kernel_small = ops.run("create.img", [3,3], new FloatType())
kernel_big = ops.run("create.img", [20,20], new FloatType())

ops.image().equation(kernel_small, "p[0]")
ops.image().equation(kernel_big, "p[0]")

// convolve with large and small kernel
convolved_small = ops.filter().convolve(base, kernel_small)
// convolve with large kernel
convolved_big = ops.filter().convolve(base, kernel_big)

ui.show(convolved_small);
ui.show(convolved_big);
ui.show("convolved", convolved_big);

base_deconvolved = ops.run(RichardsonLucyF.class, convolved_small, kernel_small, null, new OutOfBoundsConstantValueFactory<>(Util.getTypeFromInterval(kernel_small).createVariable()), 10)
// deconvolve with Richardson Lucy
base_deconvolved_big=ops.create().img(convolved_big, new FloatType())
base_deconvolved_big = ops.deconvolve().richardsonLucy(base_deconvolved_big, convolved_big, kernel_big, null, new OutOfBoundsConstantValueFactory<>(Util.getTypeFromInterval(kernel_big).createVariable()), 10)

// 50 iterations richardson lucy
base_deconvolved_big = ops.run(RichardsonLucyF.class, convolved_big, kernel_big, 50);
// deconvolve with non-circulant Richardson Lucy
base_deconvolved_big_noncirc=ops.create().img(convolved_big, new FloatType())
base_deconvolved_big_noncirc = ops.deconvolve().richardsonLucy(base_deconvolved_big_noncirc, convolved_big, kernel_big, null, null, null, null, null, 50, true, false)

// 50 iterations non-circulant richardson lucy
base_deconvolved_big_noncirc = ops.run(RichardsonLucyF.class, convolved_big, kernel_big, null, null,null, null, null,50,true,false );

// 50 iterations non-circulant accelerated richardson lucy
base_deconvolved_big_acc_noncirc = ops.run(RichardsonLucyF.class, convolved_big, kernel_big, null, null,null, null, null, 50, true, true)
// deconvolve with accelerated non-circulalant Richardson LUcy
base_deconvolved_big_acc_noncirc=ops.create().img(convolved_big, new FloatType())
base_deconvolved_big_acc_noncirc = ops.deconvolve().richardsonLucy(base_deconvolved_big_acc_noncirc, convolved_big, kernel_big, null, null, null, null, null, 50, true, true)

ui.show("RL",base_deconvolved_big)
ui.show("RLNon-Circ",base_deconvolved_big_noncirc)
ui.show("RL Acc/Non-Circ",base_deconvolved_big_acc_noncirc)
ui.show("RL Acc/Non-Circ",base_deconvolved_big_acc_noncirc)
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