John Bogovic bogovicj
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bogovicj
/ composeDfields.groovy
Created
December 22, 2022 21:45
ImageJ2 script to compose displacement fields
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| #@ Dataset da | |
| #@ Dataset db | |
| dap = Views.moveAxis( da, 2, 0 ); | |
| dbp = Views.moveAxis( da, 2, 0 ); | |
| spacing = [1, 1, 1] as double[]; | |
| dfA = new DisplacementFieldTransform( dap, spacing ); | |
| dfB = new DisplacementFieldTransform( dbp, spacing ); |
bogovicj
/ WorldCup2022.ipynb
Created
November 20, 2022 17:06
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bogovicj
/ zarrQuantization.ipynb
Created
September 29, 2022 18:29
Quantizing and compressing with zarr.
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bogovicj
/ ConditionBenchmark.java
Created
September 1, 2022 19:30
How expensive is an addition if statement
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| package net.imglib2.benchmarks; | |
| import java.util.concurrent.TimeUnit; | |
| import org.openjdk.jmh.annotations.Benchmark; | |
| import org.openjdk.jmh.annotations.BenchmarkMode; | |
| import org.openjdk.jmh.annotations.Fork; | |
| import org.openjdk.jmh.annotations.Level; | |
| import org.openjdk.jmh.annotations.Mode; | |
| import org.openjdk.jmh.annotations.OutputTimeUnit; |
bogovicj
/ RealPointIteratorConverter.java
Created
September 1, 2022 18:54
create an interator over a real interval using an imgli2 converter
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| public static IterableInterval< RealPoint > usingConverters( RealInterval interval, int... numSteps ) | |
| { | |
| final int nd = interval.numDimensions(); | |
| final double[] steps = stepsFromSamples( interval, fillWithLast( nd, numSteps ) ); | |
| final RandomAccessibleInterval< Localizable > samples = Localizables.randomAccessibleInterval( | |
| new FinalInterval( Arrays.stream( steps ).mapToLong( x -> (long)x ).toArray() )); | |
| RandomAccessibleInterval< RealPoint > positions = Converters.convert2( samples, (x,y) -> { | |
| for( int i = 0; i < nd; i++ ) | |
| y.setPosition( |
bogovicj
/ Hemi2Fafb.java
Last active
August 29, 2022 20:38
Visualize the hemibrain and fafb together
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| import java.io.IOException; | |
| import java.util.Arrays; | |
| import java.util.Collections; | |
| import org.janelia.saalfeldlab.n5.N5DatasetDiscoverer; | |
| import org.janelia.saalfeldlab.n5.N5FSReader; | |
| import org.janelia.saalfeldlab.n5.N5Reader; | |
| import org.janelia.saalfeldlab.n5.N5TreeNode; | |
| import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader; | |
| import org.janelia.saalfeldlab.n5.ij.N5Importer; |
bogovicj
/ fitGaussianToCosine.ipynb
Last active
August 30, 2022 20:45
What sigma makes a gaussian most similar to a cosine?
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bogovicj
/ rigid_slice_align.groovy
Created
July 21, 2022 17:05
Rigidly align slices using landmarks (ImageJ2)
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| #@ ImagePlus imp | |
| #@ UIService ui | |
| /** | |
| * Rigidly align slices with point rois. | |
| * | |
| * Usage: | |
| * 1) Click at least 3 point landmarks in every slice of your image. | |
| * There must be an equal number of landmarks in each slice. | |
| * Landmarks must be clicked in the same order in each slice. |
bogovicj
/ piDay2022.groovy
Created
March 14, 2022 17:01
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| #@ UIService ui | |
| #@ DatasetService ds | |
| /* | |
| * Happy Pi Day 2022 | |
| * | |
| * This visualizes the bifurcation diagram for the "standard circle map" | |
| * https://en.wikipedia.org/wiki/Arnold_tongue#Standard_circle_map | |
| * | |
| * (and its parameters are expressed in terms of pi) |