John Bogovic bogovicj

bogovicj / concatOpenImages.groovy

Last active August 21, 2018 14:39

concatOpenImages.groovy

bogovicj / trakem2_exportAreaLists-asMasks.bsh

Last active March 4, 2018 17:50

trakem2_exportAreaLists-asMasks.bsh

	import java.awt.Color;
	import java.awt.Graphics2D;
	import java.awt.Rectangle;
	import java.awt.geom.AffineTransform;
	import java.awt.geom.Area;
	import java.awt.image.BufferedImage;
	import java.awt.image.DataBufferByte;
	import java.io.File;
	import java.util.ArrayList;
	import java.util.Collections;

bogovicj / trakem2_exportAreaLists.bsh

Created February 23, 2018 17:33

trakem2_exportAreaLists.bsh

	import ij.IJ;
	import ij.ImagePlus;

	import java.util.ArrayList;

	import ini.trakem2.Project;
	import ini.trakem2.tree.ProjectThing;

	import ini.trakem2.display.Display;
	import ini.trakem2.display.AreaList;

bogovicj / ResaveVolume.java

Created June 23, 2017 19:05

Convert image to nii with mipav

	package mipavProject;

	import java.io.File;
	import java.io.IOException;

	import gov.nih.mipav.model.file.FileIO;
	import gov.nih.mipav.model.file.FileNIFTI;
	import gov.nih.mipav.model.file.FileUtility;
	import gov.nih.mipav.model.file.FileWriteOptions;
	import gov.nih.mipav.model.structures.ModelImage;

bogovicj / bashParameterExpansion.sh

Last active July 25, 2017 12:34

bashParameterExpansion.sh

	#!/bin/bash
	# See
	# https://www.gnu.org/software/bash/manual/html_node/Shell-Parameter-Expansion.html#Shell-Parameter-Expansion

	# ${parameter:-word} substitutes word if parameter is unset
	echo '${parameter:-word}'
	dog="dog"
	echo "${dog:-"cow"}" # Prints "dog"
	echo "${cow:-"cow"}" # Prints "cow"
	echo "${cow}" # Prints nothing (cow is unset)

bogovicj / DownsampleGaussian.java

Created February 28, 2017 14:55

Downsample after gaussian blurring

	package process;

	import java.util.Arrays;

	import org.janelia.utility.parse.ParseUtils;

	import com.beust.jcommander.JCommander;
	import com.beust.jcommander.Parameter;

	import bdv.util.Bdv;

bogovicj / SpaceToContinueExample.java

Last active January 3, 2017 17:18

ImageJ Keypress example

	import java.awt.event.KeyEvent;
	import java.awt.event.KeyListener;

	import ij.IJ;
	import ij.ImageJ;
	import ij.ImagePlus;

	public class SpaceToContinueExample implements KeyListener {

	final ImageJ ij;

bogovicj / maskingRai.java

Last active July 21, 2016 14:47

Masking a RandomAccessibleInterval

	public static <T extends RealType<T>, M extends RealType<M>> void maskToValue(
	RandomAccessibleInterval<T> img,
	RandomAccessibleInterval<M> mask,
	RandomAccessibleInterval<T> out,
	T val )
	{

	Cursor< M > maskC = Views.flatIterable( mask ).cursor();
	RandomAccess< T > ira = img.randomAccess();
	RandomAccess< T > ora = out.randomAccess();

bogovicj / ImageJNiiReadExample.java

Last active March 11, 2016 15:02

Reading a 3d Nifti image into an ImageJ ImagePlus

	import java.io.IOException;

	import loci.formats.FormatException;
	import loci.formats.in.NiftiReader;
	import loci.plugins.util.ImageProcessorReader;
	import ij.IJ;
	import ij.ImageJ;
	import ij.ImagePlus;
	import ij.ImageStack;