Fixed AreaList mesh to acceptable situation.

[trakem2.git] / Register_Virtual_Stack_MT.java

/** Albert Cardona 2008. This work released under the terms of the General Public License in its latest edition. */
/** Greg Jefferis enhanced progress report and interaction with the user. */

import ij.IJ;
import ij.gui.GenericDialog;
import ij.plugin.PlugIn;
import ij.VirtualStack;
import ij.ImagePlus;
import ij.io.DirectoryChooser;
import ij.io.Opener;
import ij.io.FileSaver;

import ini.trakem2.ControlWindow;
import ini.trakem2.Project;
import ini.trakem2.display.Layer;
import ini.trakem2.display.Patch;
import ini.trakem2.imaging.StitchingTEM;
import ini.trakem2.imaging.Registration;
import ini.trakem2.persistence.Loader;
import ini.trakem2.utils.IJError;
import ini.trakem2.utils.Utils;
import mpi.fruitfly.general.MultiThreading;

import java.util.concurrent.atomic.AtomicInteger;
import java.util.ArrayList;
import java.util.Arrays;
import java.awt.geom.AffineTransform;
import java.awt.image.BufferedImage;
import java.awt.image.IndexColorModel;
import java.awt.Graphics2D;
import java.awt.Color;
import java.awt.Rectangle;
import java.io.File;
import java.io.FilenameFilter;

import java.util.Arrays;

/** Requires: a directory with images, all of the same dimensions
 *  Performs: registration of one image to the next, by phase- and cross-correlation or by SIFT
 *  Outputs: the list of new images, one for slice, into a target directory as .tif files.
 */
public class Register_Virtual_Stack_MT implements PlugIn {

        // Registration types
        static public final int PHASE_CORRELATION = 0;
        static public final int SIFT = 1;

        public void run(String arg) {

                GenericDialog gd = new GenericDialog("Options");
                String[] types = {"translation only (phase-correlation)",
                                  "translation and rotation (SIFT)"};
                gd.addChoice("Registration: ", types, types[0]);
                gd.addSlider("Scaling % (for performance): ", 1, 100, 25);
                gd.showDialog();
                if (gd.wasCanceled()) {
                        return;
                }
                final int registration_type = gd.getNextChoiceIndex();
                // parameter to scale down images (1.0 means no scaling)
                final float scale = (float)gd.getNextNumber() / 100.0f;

                final Registration.SIFTParameters sp = (1 == registration_type ? new Registration.SIFTParameters() : null );
                if (null != sp) {
                        sp.scale = scale;
                        sp.setup();
                }

                DirectoryChooser dc = new DirectoryChooser("Source images");
                String source_dir = dc.getDirectory();
                if (null == source_dir) return;
                source_dir = source_dir.replace('\\', '/');
                if (!source_dir.endsWith("/")) source_dir += "/";

                dc = new DirectoryChooser("Target folder");
                String target_dir = dc.getDirectory();
                if (null == target_dir) return;
                target_dir = target_dir.replace('\\', '/');
                if (!target_dir.endsWith("/")) target_dir += "/";

                if (source_dir.equals(target_dir)) {
                        IJ.showMessage("Source and target directories MUST be different\n or images would get overwritten.");
                        return;
                }
                exec(source_dir, target_dir, registration_type, sp, scale, StitchingTEM.DEFAULT_MIN_R);
        }

        /** @param source_dir Directory to read all images from, where each image is a slice in a sequence. Their names must be bit-sortable, i.e. if numbered, they must be padded with zeros.
         *  @param target_fir Directory to store registered slices into.
         *  @param registration_type Either PHASE_CORRELATION or SIFT (0 or 1)
         *  @param sp The ini.trakem2.imaging.Registration.SIFTParameters class instance containing all SIFT parameters. Can be null only if not using SIFT as @param registration_type.
         *  @param scale The scale at which phase-correlation should be executed.
         *  @param min_R The minimal acceptable cross-correlation score, from 0 to 1, to evaluate the goodness of a phase-correlation.
         */
        static public void exec(final String source_dir, final String target_dir, final int registration_type, final Registration.SIFTParameters sp, final float scale, final float min_R) {
                if (SIFT == registration_type && null == sp) {
                        System.out.println("Can't use a null sp.");
                        return;
                }
                // get file listing
                final String exts = ".tif.jpg.png.gif.tiff.jpeg.bmp.pgm";
                final String[] names = new File(source_dir).list(new FilenameFilter() {
                        public boolean accept(File dir, String name) {
                                int idot = name.lastIndexOf('.');
                                if (-1 == idot) return false;
                                return exts.contains(name.substring(idot).toLowerCase());
                        }
                });
                Arrays.sort(names);

                try {
                        // disable TrakEM2 windows
                        ControlWindow.setGUIEnabled(false);
                        // create temporary host project
                        final Project project = Project.newFSProject("blank", null, source_dir);
                        final Loader loader = project.getLoader();
                        // disable mipmaps
                        loader.setMipMapsRegeneration(false);
                        // create a layer to work on
                        // no need //Layer layer = project.getRootLayerSet().getLayer(0, 1, true);

                        if (null != sp) sp.project = project;

                        // Open first image
                        ImagePlus first = new Opener().openImage(source_dir + names[0]);
                        final int width = first.getWidth();
                        final int height = first.getHeight();
                        final int type = first.getType();
                        final double min = first.getProcessor().getMin();
                        final double max = first.getProcessor().getMax();
                        final boolean color = (type == ImagePlus.COLOR_RGB);
                        first = null; // don't interfere with memory management

                        // create all patches. Images are NOT loaded
                        IJ.showStatus("Loading Image Patches ...");
                        final ArrayList<Patch> pa = new ArrayList<Patch>();

                        for (int i=0; i<names.length; i++) {
                                if (!new File(source_dir + names[i]).exists()) {
                                        System.out.println("Ignoring image " + names[i]);
                                        continue;
                                }
                                Patch patch = new Patch(project, loader.getNextId(), names[i], width, height, type, false, min, max, new AffineTransform());
                                loader.addedPatchFrom(source_dir + names[i], patch);
                                pa.add(patch);
                        }

                        // find out the affine transform of each slice to the previous
                        final AffineTransform[] affine = new AffineTransform[pa.size()];
                        affine[0] = new AffineTransform(); // first slice doesn't move

                        final Thread[] threads = MultiThreading.newThreads();
                        final AtomicInteger ai = new AtomicInteger(1); // start at second slice
                        final AtomicInteger finished = new AtomicInteger(0);

                        for (int ithread = 0; ithread < threads.length; ++ithread) {
                                threads[ithread] = new Thread() { public void run() { setPriority(Thread.NORM_PRIORITY);

                                        for (int i = ai.getAndIncrement(); i < affine.length; i = ai.getAndIncrement()) {
                                                IJ.showStatus("Computing transform for slice (" + i + "/" + affine.length + ")");
                                                if (IJ.debugMode) IJ.log("Computing transform for slice (" + i + "/" + affine.length + ")");
                                                IJ.showProgress(finished.get(), affine.length);

                                                Patch prev = pa.get(i-1);
                                                Patch next = pa.get(i);
                                                // will load images on its own (only once for each, guaranteed)
                                                loader.releaseToFit(width * height * (ImagePlus.GRAY8 == type ? 1 : 5) * threads.length * 6);
                                                if ( 0 == registration_type ) {
                                                        double[] c = StitchingTEM.correlate(prev, next, 1.0f, scale, StitchingTEM.TOP_BOTTOM, 0, 0, min_R);
                                                        affine[i] = new AffineTransform();
                                                        affine[i].translate(c[0], c[1]);
                                                } else if ( 1 == registration_type ) {
                                                        Object[] result = Registration.registerWithSIFTLandmarks(prev, next, sp, null, false, true);
                                                        affine[i] = (null == result ? new AffineTransform() : (AffineTransform)result[2]);
                                                }
                                                IJ.showProgress(finished.incrementAndGet(), affine.length);
                                        }

                                }};
                        }
                        // wait until all threads finished
                        MultiThreading.startAndJoin(threads);

                        IJ.showProgress(0);

                        // determine maximum canvas, make affines global by concatenation
                        final Rectangle box = new Rectangle(0, 0, width, height);
                        final Rectangle one = new Rectangle(0, 0, width, height);

                        for (int i=1; i<affine.length; i++) {
                                affine[i].concatenate(affine[i-1]);
                                box.add(affine[i].createTransformedShape(one).getBounds());
                                // reset
                                one.setRect(0, 0, width, height);
                        }
                        box.width = box.width - box.x;
                        box.height = box.height - box.y;
                        final AffineTransform trans = new AffineTransform();
                        trans.translate(-box.x, -box.y);
                        box.x = box.y = 0;

                        // fix stupid java defaults for indexed images, which are not purely grayscale
                        final byte[] r = new byte[256];
                        final byte[] g = new byte[256];
                        final byte[] b = new byte[256];
                        for (int i=0; i<256; i++) {
                                r[i]=(byte)i;
                                g[i]=(byte)i;
                                b[i]=(byte)i;
                        }
                        final IndexColorModel icm = new IndexColorModel(8, 256, r, g, b);

                        // output images as 8-bit or RGB
                        final Thread[] threads2 = MultiThreading.newThreads();
                        final AtomicInteger ai2 = new AtomicInteger(0);

                        final String[] tiffnames = new String[affine.length];

                        for (int ithread = 0; ithread < threads2.length; ++ithread) {
                                threads2[ithread] = new Thread() { public void run() { setPriority(Thread.NORM_PRIORITY);

                                        for (int i = ai2.getAndIncrement(); i < affine.length; i = ai2.getAndIncrement()) {
                                                affine[i].concatenate(trans);
                                                // ensure enough free memory
                                                loader.releaseToFit(width * height * (ImagePlus.GRAY8 == type ? 1 : 5) * threads2.length * 6); // 3: 1 processor + 1 image + 1 for safety , times 2 ...
                                                BufferedImage bi;
                                                Graphics2D g;
                                                if (color) {
                                                        bi = new BufferedImage(box.width, box.height, BufferedImage.TYPE_INT_ARGB);
                                                        g = bi.createGraphics();
                                                        g.setColor(Color.black);
                                                        g.fillRect(0, 0, box.width, box.height);
                                                } else {
                                                        bi = new BufferedImage(box.width, box.height, BufferedImage.TYPE_BYTE_INDEXED, icm);
                                                        g = bi.createGraphics();
                                                }
                                                Patch patch = pa.get(i);
                                                g.drawImage(loader.fetchImage(patch, 1.0), affine[i], null);
                                                ImagePlus imp = new ImagePlus(patch.getTitle(), bi);
                                                // Trim off file extension
                                                String slice_name = patch.getTitle();
                                                int idot = slice_name.lastIndexOf('.');
                                                if (idot > 0) slice_name = slice_name.substring(0, idot);
                                                tiffnames[i] = slice_name + ".tif";
                                                new FileSaver(imp).saveAsTiff(target_dir + tiffnames[i]);

                                                if (0 == i % threads.length) {
                                                        IJ.showStatus("Saving slice ("+i+"/"+affine.length+")");
                                                        IJ.showProgress(i, affine.length);
                                                }
                                        }
                                }};
                        }
                        // wait until all threads finished
                        MultiThreading.startAndJoin(threads2);

                        IJ.showStatus("done.");
                        IJ.showProgress(1.0);

                        project.destroy();

                        // open virtual stack
                        VirtualStack vs = new VirtualStack(box.width, box.height, icm, target_dir);
                        for (int i=0; i<tiffnames.length; i++) vs.addSlice(tiffnames[i]);
                        new ImagePlus("Registered", vs).show();

                } catch (Exception e) {
                        IJError.print(e);
                } finally {
                        ControlWindow.setGUIEnabled(false);
                        IJ.showProgress(0);
                }
        }
}