John Bogovic bogovicj
bogovicj
/ composeDfields.groovy
Created
December 22, 2022 21:45
ImageJ2 script to compose displacement fields
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@ 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
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
bogovicj
/ zarrQuantization.ipynb
Created
September 29, 2022 18:29
Quantizing and compressing with zarr.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
bogovicj
/ ConditionBenchmark.java
Created
September 1, 2022 19:30
How expensive is an addition if statement
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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?
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
bogovicj
/ rigid_slice_align.groovy
Created
July 21, 2022 17:05
Rigidly align slices using landmarks (ImageJ2)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@ 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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@ 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) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /** | |
| * Happy Valentine's day 2022 | |
| * | |
| * author: John Bogovic | |
| */ | |
| import net.imglib2.*; | |
| import net.imglib2.view.*; | |
| import net.imglib2.img.array.*; | |
| import net.imglib2.img.imageplus.*; |