bogovicj

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;

bogovicj

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

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

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

#!/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

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

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

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

// @UIService ui
// @ImageDisplayService disp
// @DatasetService data
// @LogService log

import java.util.ArrayList;

import net.imagej.axis.Axes

import net.imglib2.view.Views;

bogovicj

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;