bogovicj

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

	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

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

bogovicj

#@ 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

#@ 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)

bogovicj

/**
 * 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.*;

bogovicj

#!/bin/bash

isMac12 () {
    hasSwVers=$(command -v sw_vers)

    if [ ! -z $hasSwVers  ]
    then
        ver=$(sw_vers | grep -Eo '[0-9]+\.[0-9]+\.[0-9]+')
        if [[ $ver =~ ^12\..* ]]
        then

bogovicj

#@ Dataset source
#@ Dataset target

/**
 * Pads/crops the source image such that its field of view matches that target image,
 * respecting the target image origin.
 * 
 * Currently only supports pixel-length shifts, and ignores source origin.
 * 
 * see:

bogovicj

#@File lut

lut = ij.plugin.LutLoader.openLut( lut.getCanonicalPath() );
for( i in 0..<lut.getMapSize() )
{
	println( [lut.getRed( i ), lut.getGreen(i), lut.getBlue(i)].join(" ") )
}