Examples with Stack ini.trakem2.display.Stack used on opensource projects

Example 1 with Stack

use of ini.trakem2.display.Stack in project TrakEM2 by trakem2.

the class DBLoader method fetchImagePlus.

public ImagePlus fetchImagePlus(Patch p) {
    synchronized (db_lock) {
        long id = p.getId();
        // see if the ImagePlus is cached:
        ImagePlus imp = mawts.get(id);
        if (null != imp) {
            if (null != imp.getProcessor() && null != imp.getProcessor().getPixels()) {
                // may have been flushed by ImageJ, for example when making images from a stack
                return imp;
            } else {
                // can't hurt
                flush(imp);
            }
        }
        // connect if disconnected
        if (!connectToDatabase()) {
            return null;
        }
        releaseMemory2();
        InputStream i_stream = null;
        try {
            // StopWatch sw = new StopWatch();
            ResultSet r = connection.prepareStatement("SELECT tiff_working FROM ab_patches WHERE tiff_working IS NOT NULL AND id=" + id).executeQuery();
            boolean found = false;
            if (r.next()) {
                found = true;
                // sw.elapsed();
                i_stream = r.getBinaryStream("tiff_working");
                // sw.elapsed();
                imp = unzipTiff(i_stream, p.getTitle());
                // sw.elapsed();
                i_stream.close();
                mawts.put(id, imp, (int) Math.max(p.getWidth(), p.getHeight()));
            }
            r.close();
            // if the working is not there, fetch the original instead
            if (!found) {
                r = connection.prepareStatement("SELECT tiff_original FROM ab_patches WHERE id=" + id).executeQuery();
                if (r.next()) {
                    // sw.elapsed();
                    i_stream = r.getBinaryStream("tiff_original");
                    // sw.elapsed();
                    // will apply the preprocessor plugin to it as well
                    imp = unzipTiff(i_stream, p.getTitle());
                    // sw.elapsed();
                    i_stream.close();
                    mawts.put(id, imp, (int) Math.max(p.getWidth(), p.getHeight()));
                }
                r.close();
            }
            // non-destructive contrast: min and max
            if (null != imp) {
            // OBSOLETE and wrong -- but then this whole class is obsolete// p.putMinAndMax(imp);
            }
        } catch (Exception e) {
            IJError.print(e);
            if (null != i_stream) {
                try {
                    i_stream.close();
                } catch (Exception ie) {
                    IJError.print(ie);
                }
            }
            return null;
        }
        return imp;
    }
}

Example 2 with Stack

use of ini.trakem2.display.Stack in project TrakEM2 by trakem2.

the class PatchStack method createColor256Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createColor256Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    Loader loader = patch[0].getProject().getLoader();
    // the montage, in RGB
    patch[0].getProject().getLoader().releaseToFit(4 * patch.length * width * height);
    final ColorProcessor montage = new ColorProcessor(width * patch.length, height);
    for (int i = 0; i < patch.length; i++) {
        montage.insert(this.stack.getProcessor(i + 1), i * width, 0);
    }
    final MedianCut mc = new MedianCut(montage);
    loader.releaseToFit(patch.length * width * height);
    ImageProcessor m2 = mc.convertToByte(256);
    final ImageStack st = new ImageStack(width, height);
    for (int i = 0; i < patch.length; i++) {
        m2.setRoi(i * width, 0, width, height);
        loader.releaseToFit(width * height);
        st.addSlice(null, m2.crop());
    }
    ImagePlus imp = new ImagePlus("color256", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 3 with Stack

use of ini.trakem2.display.Stack in project TrakEM2 by trakem2.

the class PatchStack method createGray8Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createGray8Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    // compute minimum bounding box
    ImageStack st = new ImageStack(width, height);
    Loader loader = patch[0].getProject().getLoader();
    for (int i = 1; i < patch.length; i++) {
        loader.releaseToFit(width * height);
        st.addSlice(Integer.toString(i), this.stack.getProcessor(i).convertToByte(true));
    }
    ImagePlus imp = new ImagePlus("byte", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 4 with Stack

use of ini.trakem2.display.Stack in project TrakEM2 by trakem2.

the class ContrastEnhancerWrapper method apply.

public boolean apply(final Collection<Displayable> patches_) {
    if (null == patches_)
        return false;
    // Create appropriate patch list
    ArrayList<Patch> patches = new ArrayList<Patch>();
    for (final Displayable d : patches_) {
        if (d.getClass() == Patch.class)
            patches.add((Patch) d);
    }
    if (0 == patches.size())
        return false;
    // Check that all images are of the same size and type
    Patch firstp = (Patch) patches.get(0);
    final int ptype = firstp.getType();
    final double pw = firstp.getOWidth();
    final double ph = firstp.getOHeight();
    for (final Patch p : patches) {
        if (p.getType() != ptype) {
            // can't continue
            Utils.log("Can't homogenize histograms: images are not all of the same type.\nFirst offending image is: " + p);
            return false;
        }
        if (!equalize && 0 == stats_mode && p.getOWidth() != pw || p.getOHeight() != ph) {
            Utils.log("Can't homogenize histograms: images are not all of the same size.\nFirst offending image is: " + p);
            return false;
        }
    }
    try {
        if (equalize) {
            for (final Patch p : patches) {
                if (Thread.currentThread().isInterrupted())
                    return false;
                p.appendFilters(new IFilter[] { new EqualizeHistogram() });
                /*
					p.getProject().getLoader().releaseToFit(p.getOWidth(), p.getOHeight(), p.getType(), 3);
					ImageProcessor ip = p.getImageProcessor().duplicate(); // a throw-away copy
					if (this.from_existing_min_and_max) {
						ip.setMinAndMax(p.getMin(), p.getMax());
					}
					ce.equalize(ip);
					p.setMinAndMax(ip.getMin(), ip.getMax());
					*/
                // submit for regeneration
                p.getProject().getLoader().decacheImagePlus(p.getId());
                regenerateMipMaps(p);
            }
            return true;
        }
        // Else, call stretchHistogram with an appropriate stats object
        final ImageStatistics stats;
        if (1 == stats_mode) {
            // use each image independent stats
            stats = null;
        } else if (0 == stats_mode) {
            // use stack statistics
            final ArrayList<Patch> sub = new ArrayList<Patch>();
            if (use_full_stack) {
                sub.addAll(patches);
            } else {
                // build stack statistics, ordered by stdDev
                final SortedMap<Stats, Patch> sp = Collections.synchronizedSortedMap(new TreeMap<Stats, Patch>());
                Process.progressive(patches, new TaskFactory<Patch, Stats>() {

                    public Stats process(final Patch p) {
                        if (Thread.currentThread().isInterrupted())
                            return null;
                        ImagePlus imp = p.getImagePlus();
                        p.getProject().getLoader().releaseToFit(p.getOWidth(), p.getOHeight(), p.getType(), 2);
                        Stats s = new Stats(imp.getStatistics());
                        sp.put(s, p);
                        return s;
                    }
                });
                if (Thread.currentThread().isInterrupted())
                    return false;
                final ArrayList<Patch> a = new ArrayList<Patch>(sp.values());
                final int count = a.size();
                if (count < 3) {
                    sub.addAll(a);
                } else if (3 == count) {
                    // the middle one
                    sub.add(a.get(1));
                } else if (4 == count) {
                    sub.addAll(a.subList(1, 3));
                } else if (count > 4) {
                    int first = (int) (count / 4.0 + 0.5);
                    int last = (int) (count / 4.0 * 3 + 0.5);
                    sub.addAll(a.subList(first, last));
                }
            }
            stats = new StackStatistics(new PatchStack(sub.toArray(new Patch[sub.size()]), 1));
        } else {
            stats = reference_stats;
        }
        final Calibration cal = patches.get(0).getLayer().getParent().getCalibrationCopy();
        Process.progressive(patches, new TaskFactory<Patch, Object>() {

            public Object process(final Patch p) {
                if (Thread.currentThread().isInterrupted())
                    return null;
                p.getProject().getLoader().releaseToFit(p.getOWidth(), p.getOHeight(), p.getType(), 3);
                // a throw-away copy
                ImageProcessor ip = p.getImageProcessor().duplicate();
                if (ContrastEnhancerWrapper.this.from_existing_min_and_max) {
                    ip.setMinAndMax(p.getMin(), p.getMax());
                }
                ImageStatistics st = stats;
                if (null == stats) {
                    Utils.log2("Null stats, using image's self");
                    st = ImageStatistics.getStatistics(ip, Measurements.MIN_MAX, cal);
                }
                ce.stretchHistogram(ip, saturated, st);
                // This is all we care about from stretching the histogram:
                p.setMinAndMax(ip.getMin(), ip.getMax());
                regenerateMipMaps(p);
                return null;
            }
        });
    } catch (Exception e) {
        IJError.print(e);
        return false;
    }
    return true;
}

Example 5 with Stack

use of ini.trakem2.display.Stack in project TrakEM2 by trakem2.

the class LayerStack method getProcessor.

/**
 * Returns an ImageProcessor for the specified slice,
 *		where {@code 1<=n<=nslices}. Returns null if the stack is empty.
 */
@Override
public ImageProcessor getProcessor(int n) {
    if (n < 1 || n > layers.size())
        return null;
    // Create a flat image on the fly with everything on it, and return its processor.
    final Layer layer = layers.get(n - 1);
    final Loader loader = layer.getProject().getLoader();
    Long cid;
    synchronized (id_cache) {
        cid = id_cache.get(layer.getId());
        if (null == cid) {
            cid = loader.getNextTempId();
            id_cache.put(layer.getId(), cid);
        }
    }
    ImageProcessor ip;
    synchronized (cid) {
        ImagePlus imp = loader.getCachedImagePlus(cid);
        if (null == imp || null == imp.getProcessor() || null == imp.getProcessor().getPixels()) {
            ip = loader.getFlatImage(layer, this.roi, this.scale, this.c_alphas, this.type, this.clazz, null).getProcessor();
            if (invert)
                ip.invert();
            loader.cacheImagePlus(cid, new ImagePlus("", ip));
        } else
            ip = imp.getProcessor();
    }
    return ip;
}