Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 56 with ImagePlus

use of ij.ImagePlus in project bioformats by openmicroscopy.

the class LociFunctions method openThumbImage.

public void openThumbImage(String title, Double no) throws FormatException, IOException {
    ImporterOptions options = new ImporterOptions();
    options.setWindowless(true);
    options.setId(r.getCurrentFile());
    options.setCrop(true);
    options.setSpecifyRanges(true);
    options.setSeriesOn(r.getSeries(), true);
    int[] zct = r.getZCTCoords(no.intValue());
    options.setCBegin(r.getSeries(), zct[1]);
    options.setZBegin(r.getSeries(), zct[0]);
    options.setTBegin(r.getSeries(), zct[2]);
    options.setCEnd(r.getSeries(), zct[1]);
    options.setZEnd(r.getSeries(), zct[0]);
    options.setTEnd(r.getSeries(), zct[2]);
    ImportProcess process = new ImportProcess(options);
    process.execute();
    ImagePlusReader reader = new ImagePlusReader(process);
    final ImagePlus imp = reader.openThumbImagePlus()[0];
    Calibrator calibrator = new Calibrator(process);
    calibrator.applyCalibration(imp);
    process.getReader().close();
    imp.show();
}

Example 57 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class Cache method put.

/**
 * @param maxdim is max(width, height) of the Patch wrapping @param imp;
 *  that is, the dimensions of the mipmap image.
 */
public final void put(final long id, final ImagePlus imp, final int maxdim) {
    Pyramid p = pyramids.getValue(id);
    if (null == p) {
        p = new Pyramid(id, imp, maxdim);
        pyramids.put(id, p);
        append(p);
        // 
        // may be null, in which case it is not stored in imps
        final String path = getPath(imp);
        // u is null if path is null
        final ImagePlusUsers u = imps.getValue(path);
        if (null == u) {
            // AFTER adding it to the pyramids
            fit(Cache.size(imp));
            if (null != path)
                imps.put(path, new ImagePlusUsers(imp, id));
        } else {
            u.addUser(id);
        }
        // 
        count++;
    } else {
        update(p);
        final ImagePlus pyrimp = p.getImagePlus();
        if (null == pyrimp)
            count++;
        else if (imp != pyrimp) {
            // Remove from old
            final String path1 = getPath(pyrimp);
            final ImagePlusUsers u1 = imps.getValue(path1);
            u1.removeUser(id, path1);
            // Add to new, which may have to be created
            final String path2 = getPath(imp);
            final ImagePlusUsers u2 = imps.getValue(path2);
            if (null == u2) {
                if (null != path2) {
                    imps.put(path2, new ImagePlusUsers(imp, id));
                }
            } else {
                u2.addUser(id);
            }
        }
        fit(p.replace(imp));
    }
}

Example 58 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class Cache method removeImagePlus.

private final ImagePlus removeImagePlus(final Pyramid p) {
    if (null == p)
        return null;
    final ImagePlus pyrimp = p.getImagePlus();
    if (null == pyrimp)
        return null;
    final ImagePlus imp = pyrimp;
    p.setImagePlus(null);
    // 
    final String path = getPath(imp);
    final ImagePlusUsers u = imps.getValue(path);
    if (null != u) {
        u.removeUser(p.id, path);
    }
    if (null == u || u.users.isEmpty()) {
        // Reclaim space only if the ImagePlus is no longer referenced
        // (u is null if the ImagePlus was preprocessed)
        addBytes(p.replace(null));
        count--;
        // 
        if (0 == p.n_images) {
            p.interval.removeEntry(p.id);
            pyramids.removeEntry(p.id);
        }
    }
    return imp;
}

Example 59 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class Cache method get.

public final ImagePlus get(final long id) {
    final Pyramid p = pyramids.getValue(id);
    if (null == p)
        return null;
    final ImagePlus pyrimp = p.getImagePlus();
    if (null == pyrimp)
        return null;
    update(p);
    return pyrimp;
}

Example 60 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class Cache method removeAndFlushSome.

public final long removeAndFlushSome(int n) {
    long size = 0;
    while (intervals.size() > 0) {
        final TypedHashMap<Long, Pyramid> interval = intervals.getFirst();
        for (final Iterator<Pyramid> it = interval.values().iterator(); it.hasNext(); ) {
            final Pyramid p = it.next();
            final ImagePlus pyrimp = p.getImagePlus();
            if (null != pyrimp) {
                final String path = getPath(pyrimp);
                final ImagePlusUsers u = imps.getValue(path);
                if (null == path || null == u || 1 == u.users.size()) {
                    // 
                    imps.removeEntry(path);
                    // 
                    final long s = p.replace(null);
                    size -= s;
                    addBytes(s);
                    // the imp may need cleanup
                    p.replace(null);
                    n--;
                    count--;
                    if (0 == n) {
                        if (0 == p.n_images) {
                            pyramids.removeEntry(p.id);
                            it.remove();
                            if (interval.isEmpty())
                                intervals.removeFirst();
                        }
                        return size;
                    }
                }
            }
            for (int i = 0; i < p.images.length; i++) {
                if (null == p.images[i])
                    continue;
                final long s = p.replace(null, i);
                size -= s;
                addBytes(s);
                n--;
                count--;
                if (0 == n) {
                    if (0 == p.n_images) {
                        pyramids.removeEntry(p.id);
                        it.remove();
                        if (interval.isEmpty())
                            intervals.removeFirst();
                    }
                    return size;
                }
            }
            pyramids.removeEntry(p.id);
            // from the interval
            it.remove();
        }
        intervals.removeFirst();
    }
    return size;
}