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package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.GenericDialog;
import ij.util.ThreadUtil;
import ij.plugin.RGBStackMerge;
import ij.gui.*;
import java.util.concurrent.atomic.AtomicInteger;
/*
* This plugin implements most of the 3D filters in the Process/Filters submenu.
* @author Thomas Boudier
*/
public class Filters3D implements PlugIn {
public final static int MEAN=10, MEDIAN=11, MIN=12, MAX=13, VAR=14, MAXLOCAL=15;
private static float xradius = 2, yradius = 2, zradius = 2;
public void run(String arg) {
String name = null;
int filter = 0;
if (arg.equals("mean")) {
name = "3D Mean";
filter = MEAN;
} else if (arg.equals("median")) {
name = "3D Median";
filter = MEDIAN;
} else if (arg.equals("min")) {
name = "3D Minimum";
filter = MIN;
} else if (arg.equals("max")) {
name = "3D Maximum";
filter = MAX;
} else if (arg.equals("var")) {
name = "3D Variance";
filter = VAR;
} else
return;
ImagePlus imp = IJ.getImage();
if (imp.isComposite() && imp.getNChannels()==imp.getStackSize()) {
IJ.error(name, "Composite color images not supported");
return;
}
if (!showDialog(name))
return;
imp.startTiming();
run(imp, filter, xradius, yradius, zradius);
IJ.showTime(imp, imp.getStartTime(), "", imp.getStackSize());
}
private boolean showDialog(String name) {
GenericDialog gd = new GenericDialog(name);
gd.addNumericField("X radius:", xradius, 1);
gd.addNumericField("Y radius:", yradius, 1);
gd.addNumericField("Z radius:", zradius, 1);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
xradius = (float) gd.getNextNumber();
yradius = (float) gd.getNextNumber();
zradius = (float) gd.getNextNumber();
return true;
}
private void run(ImagePlus imp, int filter, float radX, float radY, float radZ) {
if (imp.isHyperStack()) {
filterHyperstack(imp, filter, radX, radY, radZ);
return;
}
ImageStack res = filter(imp.getStack(), filter, radX, radY, radZ);
imp.setStack(res);
}
public static ImageStack filter(ImageStack stackorig, int filter, float vx, float vy, float vz) {
if (stackorig.getBitDepth()==24)
return filterRGB(stackorig, filter, vx, vy, vz);
// get stack info
final ImageStack stack = stackorig;
final float voisx = vx;
final float voisy = vy;
final float voisz = vz;
final int width= stack.getWidth();
final int height= stack.getHeight();
final int depth= stack.getSize();
ImageStack res = null;
if ((filter==MEAN) || (filter==MEDIAN) || (filter==MIN) || (filter==MAX) || (filter==VAR)) {
if (filter==VAR)
res = ImageStack.create(width, height, depth, 32);
else
res = ImageStack.create(width, height, depth, stackorig.getBitDepth());
IJ.showStatus("3D filtering...");
// PARALLEL
final ImageStack out = res;
final AtomicInteger ai = new AtomicInteger(0);
final int n_cpus = Prefs.getThreads();
final int f = filter;
final int dec = (int) Math.ceil((double) stack.getSize() / (double) n_cpus);
Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
StackProcessor processor = new StackProcessor(stack);
for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
processor.filter3D(out, voisx, voisy, voisz, dec * k, dec * (k + 1), f);
}
}
};
}
ThreadUtil.startAndJoin(threads);
}
return res;
}
private static void filterHyperstack(ImagePlus imp, int filter, float vx, float vy, float vz) {
if (imp.getNDimensions()>4) {
IJ.error("5D hyperstacks are currently not supported");
return;
}
if (imp.getNChannels()==1) {
ImageStack stack = filter(imp.getStack(), filter, vx, vy, vz);
imp.setStack(stack);
return;
}
ImagePlus[] channels = ChannelSplitter.split(imp);
int n = channels.length;
for (int i=0; i<n; i++) {
ImageStack stack = filter(channels[i].getStack(), filter, vx, vy, vz);
channels[i].setStack(stack);
}
ImagePlus imp2 = RGBStackMerge.mergeChannels(channels, false);
imp.setImage(imp2);
imp.setC(1);
}
private static ImageStack filterRGB(ImageStack rgb_in, int filter, float vx, float vy, float vz) {
ImageStack[] channels = ChannelSplitter.splitRGB(rgb_in, false);
ImageStack red = filter(channels[0], filter, vx, vy, vz);
ImageStack green = filter(channels[1], filter, vx, vy, vz);
ImageStack blue = filter(channels[2], filter, vx, vy, vz);
return RGBStackMerge.mergeStacks(red, green, blue, false);
}
}
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