Examples with VirtualStack ij.VirtualStack used on opensource projects

Example 1 with VirtualStack

use of ij.VirtualStack in project TrakEM2 by trakem2.

the class FSLoader method importStackAsPatches.

/**
 * Returns the last Patch.
 */
protected Patch importStackAsPatches(final Project project, final Layer first_layer, final double x, final double y, final ImagePlus imp_stack, final boolean as_copy, final String filepath) {
    Utils.log2("FSLoader.importStackAsPatches filepath=" + filepath);
    String target_dir = null;
    if (as_copy) {
        DirectoryChooser dc = new DirectoryChooser("Folder to save images");
        target_dir = dc.getDirectory();
        // user canceled dialog
        if (null == target_dir)
            return null;
        if (IJ.isWindows())
            target_dir = target_dir.replace('\\', '/');
        if (target_dir.length() - 1 != target_dir.lastIndexOf('/')) {
            target_dir += "/";
        }
    }
    // Double.MAX_VALUE is a flag to indicate "add centered"
    double pos_x = Double.MAX_VALUE != x ? x : first_layer.getLayerWidth() / 2 - imp_stack.getWidth() / 2;
    double pos_y = Double.MAX_VALUE != y ? y : first_layer.getLayerHeight() / 2 - imp_stack.getHeight() / 2;
    final double thickness = first_layer.getThickness();
    final String title = Utils.removeExtension(imp_stack.getTitle()).replace(' ', '_');
    Utils.showProgress(0);
    Patch previous_patch = null;
    final int n = imp_stack.getStackSize();
    final ImageStack stack = imp_stack.getStack();
    final boolean virtual = stack.isVirtual();
    final VirtualStack vs = virtual ? (VirtualStack) stack : null;
    for (int i = 1; i <= n; i++) {
        Layer layer = first_layer;
        double z = first_layer.getZ() + (i - 1) * thickness;
        // will create new layer if not found
        if (i > 1)
            layer = first_layer.getParent().getLayer(z, thickness, true);
        if (null == layer) {
            Utils.log("Display.importStack: could not create new layers.");
            return null;
        }
        String patch_path = null;
        ImagePlus imp_patch_i = null;
        if (virtual) {
            // because we love inefficiency, every time all this is done again
            // VirtualStack vs = (VirtualStack)imp_stack.getStack();
            String vs_dir = vs.getDirectory().replace('\\', '/');
            if (!vs_dir.endsWith("/"))
                vs_dir += "/";
            String iname = vs.getFileName(i);
            patch_path = vs_dir + iname;
            Utils.log2("virtual stack: patch path is " + patch_path);
            releaseToFit(new File(patch_path).length() * 3);
            Utils.log2(i + " : " + patch_path);
            imp_patch_i = openImage(patch_path);
        } else {
            ImageProcessor ip = stack.getProcessor(i);
            if (as_copy)
                ip = ip.duplicate();
            imp_patch_i = new ImagePlus(title + "__slice=" + i, ip);
        }
        String label = stack.getSliceLabel(i);
        if (null == label)
            label = "";
        Patch patch = null;
        if (as_copy) {
            patch_path = target_dir + cleanSlashes(imp_patch_i.getTitle()) + ".zip";
            ini.trakem2.io.ImageSaver.saveAsZip(imp_patch_i, patch_path);
            patch = new Patch(project, label + " " + title + " " + i, pos_x, pos_y, imp_patch_i);
        } else if (virtual) {
            patch = new Patch(project, label, pos_x, pos_y, imp_patch_i);
        } else {
            patch_path = filepath + "-----#slice=" + i;
            // Utils.log2("path is "+ patch_path);
            final AffineTransform atp = new AffineTransform();
            atp.translate(pos_x, pos_y);
            patch = new Patch(project, getNextId(), label + " " + title + " " + i, imp_stack.getWidth(), imp_stack.getHeight(), imp_stack.getWidth(), imp_stack.getHeight(), imp_stack.getType(), false, imp_stack.getProcessor().getMin(), imp_stack.getProcessor().getMax(), atp);
            patch.addToDatabase();
        // Utils.log2("type is " + imp_stack.getType());
        }
        Utils.log2("B: " + i + " : " + patch_path);
        addedPatchFrom(patch_path, patch);
        if (!as_copy && !virtual) {
            if (// each slice separately
            virtual)
                // each slice separately
                cache(patch, imp_patch_i);
            else
                // uses the entire stack, shared among all Patch instances
                cache(patch, imp_stack);
        }
        // submit for regeneration
        if (isMipMapsRegenerationEnabled())
            regenerateMipMaps(patch);
        if (null != previous_patch)
            patch.link(previous_patch);
        layer.add(patch);
        previous_patch = patch;
        Utils.showProgress(i * (1.0 / n));
    }
    Utils.showProgress(1.0);
    // return the last patch
    return previous_patch;
}

Example 2 with VirtualStack

use of ij.VirtualStack in project TrakEM2 by trakem2.

the class DNDInsertImage method importImageFile.

private boolean importImageFile(File f, String path, Point point) throws Exception {
    if (f.exists()) {
        final Layer layer = display.getLayer();
        Bureaucrat burro = null;
        if (f.isDirectory()) {
            // ask:
            GenericDialog gd = new GenericDialog("Import directory");
            String[] choice = new String[] { "Stack", "Grid", "Sequence as grid" };
            gd.addChoice("Directory as: ", choice, choice[0]);
            gd.showDialog();
            if (gd.wasCanceled()) {
                // the user cancel it, so all is ok.
                return true;
            }
            display.getLayerSet().addLayerContentStep(layer);
            switch(gd.getNextChoiceIndex()) {
                case // as stack
                0:
                    // if importing image sequence as a stack:
                    // don't filter by name  "^[^\\.].*[\\.][a-zA-Z1-9_]{3,4}$"
                    String[] names = f.list(new ImageFileFilter());
                    Utils.log2("stack size: " + names.length);
                    for (int i = 0; i < names.length; i++) {
                        Utils.log2(names[i]);
                    }
                    Arrays.sort(names);
                    // I don't care about the dimensions
                    VirtualStack stack = new VirtualStack(10, 10, null, f.getAbsolutePath().replace('\\', '/'));
                    for (int k = 0; k < names.length; k++) {
                        IJ.redirectErrorMessages();
                        // ignore trakem2 files
                        if (names[k].toLowerCase().endsWith(".xml"))
                            continue;
                        stack.addSlice(names[k]);
                    }
                    if (stack.getSize() > 0) {
                        burro = display.getProject().getLoader().importStack(layer, point.x, point.y, new ImagePlus("stack", stack), true, path, false);
                    }
                    break;
                case // as grid
                1:
                    burro = display.getProject().getLoader().importGrid(layer, path);
                    break;
                case // sequence as grid
                2:
                    burro = display.getProject().getLoader().importSequenceAsGrid(layer, path);
                    break;
            }
        } else {
            layer.getParent().addLayerContentStep(layer);
            // single image file (single image or a stack)
            burro = display.getProject().getLoader().importImage(layer, point.x, point.y, path, false);
        }
        if (null != burro) {
            burro.addPostTask(new Runnable() {

                public void run() {
                    // The current state
                    layer.getParent().addLayerContentStep(layer);
                }
            });
        }
        return true;
    } else {
        Utils.log("File not found: " + path);
        return false;
    }
}

Example 3 with VirtualStack

use of ij.VirtualStack in project TrakEM2 by trakem2.

the class Loader method createFlyThrough.

/**
 * Returns an ImageStack, one slice per region.
 */
public <I> ImagePlus createFlyThrough(final List<? extends Region<I>> regions, final double magnification, final int type, final String dir) {
    final ExecutorService ex = Utils.newFixedThreadPool(Runtime.getRuntime().availableProcessors(), "fly-through");
    final List<Future<ImagePlus>> fus = new ArrayList<Future<ImagePlus>>();
    for (final Region<I> r : regions) {
        fus.add(ex.submit(new Callable<ImagePlus>() {

            @Override
            public ImagePlus call() {
                return getFlatImage(r.layer, r.r, magnification, 0xffffffff, type, Displayable.class, null, true, Color.black);
            }
        }));
    }
    final Region<I> r = regions.get(0);
    final int w = (int) (r.r.width * magnification), h = (int) (r.r.height * magnification), size = regions.size();
    final ImageStack stack = null == dir ? new ImageStack(w, h) : new VirtualStack(w, h, null, dir);
    final int digits = Integer.toString(size).length();
    for (int i = 0; i < size; i++) {
        try {
            if (Thread.currentThread().isInterrupted()) {
                ex.shutdownNow();
                return null;
            }
            if (null == dir) {
                stack.addSlice(regions.get(i).layer.toString(), fus.get(i).get().getProcessor());
            } else {
                final StringBuilder name = new StringBuilder().append(i);
                while (name.length() < digits) name.insert(0, '0');
                name.append(".png");
                final String filename = name.toString();
                new FileSaver(fus.get(i).get()).saveAsPng(dir + filename);
                ((VirtualStack) stack).addSlice(filename);
            }
        } catch (final Throwable t) {
            IJError.print(t);
        }
    }
    ex.shutdown();
    return new ImagePlus("Fly-Through", stack);
}