/*-
* #%L
* Scenery-backed 3D visualization package for ImageJ.
* %%
* Copyright (C) 2016 - 2018 SciView developers.
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
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* this list of conditions and the following disclaimer.
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package sc.iview.commands.demo;
import graphics.scenery.volumes.Volume;
import io.scif.services.DatasetIOService;
import net.imagej.mesh.Mesh;
import net.imagej.ops.OpService;
import net.imagej.ops.geom.geom3d.mesh.BitTypeVertexInterpolator;
import net.imglib2.Cursor;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.RealPoint;
import net.imglib2.algorithm.labeling.ConnectedComponents;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.roi.labeling.ImgLabeling;
import net.imglib2.roi.labeling.LabelRegion;
import net.imglib2.roi.labeling.LabelRegions;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.view.Views;
import org.joml.Vector3f;
import org.scijava.command.Command;
import org.scijava.command.CommandService;
import org.scijava.log.LogService;
import org.scijava.plugin.Menu;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.iview.SciView;
import sc.iview.process.MeshConverter;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Random;
import static sc.iview.commands.MenuWeights.DEMO;
import static sc.iview.commands.MenuWeights.DEMO_VOLUME_RENDER;
/**
* A demo of rendering meshes
*
* @author Kyle Harrington
*/
@Plugin(type = Command.class, label = "Show segmentation", menuRoot = "SciView", //
menu = { @Menu(label = "Demo", weight = DEMO), //
@Menu(label = "Show segmentation", weight = DEMO_VOLUME_RENDER) })
public class ShowSegmentationDemo implements Command {
@Parameter
private DatasetIOService datasetIO;
@Parameter
private LogService log;
@Parameter
private OpService ops;
@Parameter
private SciView sciView;
@Parameter
private int numSegments = 20;
private Random rng = new Random();
@Override
public void run() {
sciView.getFloor().setVisible(false);
RandomAccessibleInterval<UnsignedByteType> inputImage = generateDemo(100, 100, 100, numSegments);
Volume v = (Volume) sciView.addVolume( inputImage, new float[] { 1, 1, 1 } );
v.setPixelToWorldRatio(0.05f);
v.setName( "Segmentation Viz Demo" );
v.setNeedsUpdate(true);
ImgLabeling<Integer, IntType> labeling = ops.labeling().cca(inputImage, ConnectedComponents.StructuringElement.FOUR_CONNECTED);
LabelRegions<Integer> regions = new LabelRegions<>(labeling);
for( LabelRegion region : regions ) {
// Generate the mesh with imagej-ops
Mesh m = ops.geom().marchingCubes( region, 1, new BitTypeVertexInterpolator() );
// Convert the mesh into a scenery mesh for visualization
graphics.scenery.Mesh isoSurfaceMesh = MeshConverter.toScenery(m,false);
// Name the mesh after the segment label
isoSurfaceMesh.setName( "region " + region );
// Make a random color and assign it
Vector3f c = new Vector3f(rng.nextFloat(), rng.nextFloat(), rng.nextFloat());
isoSurfaceMesh.getMaterial().setDiffuse(c);
isoSurfaceMesh.getMaterial().setAmbient(c);
isoSurfaceMesh.getMaterial().setSpecular(c);
// Make the segmentation mesh a child of the parent
v.addChild(isoSurfaceMesh);
}
sciView.centerOnNode(v);
}
// Generate a demo image with a bunch of spheres at random positions
private RandomAccessibleInterval<UnsignedByteType> generateDemo(int w, int h, int d, int numSegments) {
double radiusSq = 36;
List<RealPoint> points = new ArrayList<>();
for( int k = 0; k < numSegments; k++ ) {
points.add( new RealPoint(rng.nextFloat() * w, rng.nextFloat() * h, rng.nextFloat() * d) );
}
long[] pos = new long[3];
RandomAccessibleInterval<UnsignedByteType> img = ArrayImgs.unsignedBytes(w, h, d);
Cursor<UnsignedByteType> cur = Views.iterable(img).cursor();
while(cur.hasNext()) {
cur.fwd();
cur.localize(pos);
cur.get().set(0);
for( int k = 0; k < points.size(); k++ ) {
double dt = dist(pos, points.get(k));
//System.out.println(dt + " " + Arrays.toString(pos) + " " + points.get(k));
if( dt < radiusSq ) {
cur.get().set(k+1);
}
}
}
return img;
}
private double dist(long[] pos, RealPoint realPoint) {
return ( pos[0] - realPoint.getDoublePosition(0) ) * ( pos[0] - realPoint.getDoublePosition(0) ) +
( pos[1] - realPoint.getDoublePosition(1) ) * ( pos[1] - realPoint.getDoublePosition(1) ) +
( pos[2] - realPoint.getDoublePosition(2) ) * ( pos[2] - realPoint.getDoublePosition(2) );
}
public static void main(String... args) throws Exception {
SciView sv = SciView.create();
CommandService command = sv.getScijavaContext().getService(CommandService.class);
HashMap<String, Object> argmap = new HashMap<String, Object>();
command.run(ShowSegmentationDemo.class, true, argmap);
}
}
