Examples with IFilter ini.trakem2.imaging.filters.IFilter used on opensource projects

Example 1 with IFilter

use of ini.trakem2.imaging.filters.IFilter 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 2 with IFilter

use of ini.trakem2.imaging.filters.IFilter in project TrakEM2 by trakem2.

the class FilterEditor method GUI.

public static final void GUI(final Collection<Patch> patches, final Patch reference) {
    final ArrayList<FilterWrapper> filters = new ArrayList<FilterWrapper>();
    // Find out if all images have the exact same filters
    final StringBuilder sb = new StringBuilder();
    final Patch ref = (null == reference ? patches.iterator().next() : reference);
    final IFilter[] refFilters = ref.getFilters();
    if (null != refFilters) {
        // makes a copy of the IFilter
        for (final IFilter f : refFilters) filters.add(new FilterWrapper(f));
    }
    // 
    for (final Patch p : patches) {
        if (ref == p)
            continue;
        final IFilter[] fs = p.getFilters();
        // ok
        if (null == fs && null == refFilters)
            continue;
        if ((null != refFilters && null == fs) || (null == refFilters && null != fs) || (null != refFilters && null != fs && fs.length != refFilters.length)) {
            sb.append("WARNING: patch #" + p.getId() + " has a different number of filters than reference patch #" + ref.getId());
            continue;
        }
        // Compare each
        for (int i = 0; i < refFilters.length; ++i) {
            if (fs[i].getClass() != refFilters[i].getClass()) {
                sb.append("WARNING: patch #" + p.getId() + " has a different filters than reference patch #" + ref.getId());
                break;
            }
            // Does the filter have the same parameters?
            if (!filters.get(i).sameParameterValues(new FilterWrapper(fs[i]))) {
                sb.append("WARNING: patch #" + p.getId() + " has filter '" + fs[i].getClass().getSimpleName() + "' with different parameters than the reference patch #" + ref.getId());
            }
        }
    }
    if (sb.length() > 0) {
        final GenericDialog gd = new GenericDialog("WARNING", null == Display.getFront() ? IJ.getInstance() : Display.getFront().getFrame());
        gd.addMessage("Filters are not all the same for all images:");
        gd.addTextAreas(sb.toString(), null, 20, 30);
        final String[] s = new String[] { "Use the filters of the reference image", "Start from an empty list of filters" };
        gd.addChoice("Do:", s, s[0]);
        gd.showDialog();
        if (gd.wasCanceled())
            return;
        if (1 == gd.getNextChoiceIndex())
            filters.clear();
    }
    final TableChosenFilters tcf = new TableChosenFilters(filters);
    final TableParameters tp = new TableParameters(tcf);
    tcf.setupListener(tp);
    final TableAvailableFilters taf = new TableAvailableFilters(tcf);
    if (filters.size() > 0) {
        tcf.getSelectionModel().setSelectionInterval(0, 0);
    }
    final JFrame frame = new JFrame("Image filters");
    final JButton set = new JButton("Set");
    final JComboBox pulldown = new JComboBox(new String[] { "Selected images (" + patches.size() + ")", "All images in layer " + (ref.getLayer().getParent().indexOf(ref.getLayer()) + 1), "All images in layer range..." });
    final Component[] cs = new Component[] { set, pulldown, tcf, tp, taf };
    set.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(final ActionEvent e) {
            if (check(frame, filters)) {
                final ArrayList<Patch> ps = new ArrayList<Patch>();
                switch(pulldown.getSelectedIndex()) {
                    case 0:
                        ps.addAll(patches);
                        break;
                    case 1:
                        for (final Displayable d : ref.getLayer().getDisplayables(Patch.class)) {
                            ps.add((Patch) d);
                        }
                        break;
                    case 2:
                        final GenericDialog gd = new GenericDialog("Apply filters");
                        Utils.addLayerRangeChoices(ref.getLayer(), gd);
                        gd.addStringField("Image title matches:", "", 30);
                        gd.addCheckbox("Visible images only", true);
                        gd.showDialog();
                        if (gd.wasCanceled())
                            return;
                        final String regex = gd.getNextString();
                        final boolean visible_only = gd.getNextBoolean();
                        Pattern pattern = null;
                        if (0 != regex.length()) {
                            pattern = Pattern.compile(regex);
                        }
                        for (final Layer l : ref.getLayer().getParent().getLayers(gd.getNextChoiceIndex(), gd.getNextChoiceIndex())) {
                            for (final Displayable d : l.getDisplayables(Patch.class, visible_only)) {
                                if (null != pattern && !pattern.matcher(d.getTitle()).matches()) {
                                    continue;
                                }
                                ps.add((Patch) d);
                            }
                        }
                }
                apply(ps, filters, cs, false);
            }
        }
    });
    final JPanel buttons = new JPanel();
    final JLabel label = new JLabel("Push F1 for help");
    final GridBagConstraints c2 = new GridBagConstraints();
    final GridBagLayout gb2 = new GridBagLayout();
    buttons.setLayout(gb2);
    c2.anchor = GridBagConstraints.WEST;
    c2.gridx = 0;
    gb2.setConstraints(label, c2);
    buttons.add(label);
    c2.gridx = 1;
    c2.weightx = 1;
    final JPanel empty = new JPanel();
    gb2.setConstraints(empty, c2);
    buttons.add(empty);
    c2.gridx = 2;
    c2.weightx = 0;
    c2.anchor = GridBagConstraints.EAST;
    final JLabel a = new JLabel("Apply to:");
    gb2.setConstraints(a, c2);
    buttons.add(a);
    c2.gridx = 3;
    c2.insets = new Insets(4, 10, 4, 0);
    gb2.setConstraints(pulldown, c2);
    buttons.add(pulldown);
    c2.gridx = 4;
    gb2.setConstraints(set, c2);
    buttons.add(set);
    // 
    taf.setPreferredSize(new Dimension(350, 500));
    tcf.setPreferredSize(new Dimension(350, 250));
    tp.setPreferredSize(new Dimension(350, 250));
    // 
    final GridBagLayout gb = new GridBagLayout();
    final GridBagConstraints c = new GridBagConstraints();
    final JPanel all = new JPanel();
    all.setBackground(Color.white);
    all.setPreferredSize(new Dimension(700, 500));
    all.setLayout(gb);
    c.gridx = 0;
    c.gridy = 0;
    c.anchor = GridBagConstraints.NORTHWEST;
    c.fill = GridBagConstraints.BOTH;
    c.gridheight = 2;
    c.weightx = 0.5;
    final JScrollPane p1 = new JScrollPane(taf);
    p1.setPreferredSize(taf.getPreferredSize());
    gb.setConstraints(p1, c);
    all.add(p1);
    c.gridx = 1;
    c.gridy = 0;
    c.gridheight = 1;
    c.weighty = 0.7;
    final JScrollPane p2 = new JScrollPane(tcf);
    p2.setPreferredSize(tcf.getPreferredSize());
    gb.setConstraints(p2, c);
    all.add(p2);
    c.gridx = 1;
    c.gridy = 1;
    c.weighty = 0.3;
    final JScrollPane p3 = new JScrollPane(tp);
    p3.setPreferredSize(tp.getPreferredSize());
    gb.setConstraints(p3, c);
    all.add(p3);
    c.gridx = 0;
    c.gridy = 2;
    c.gridwidth = 2;
    c.weightx = 1;
    c.weighty = 0;
    gb.setConstraints(buttons, c);
    all.add(buttons);
    final KeyAdapter help = new KeyAdapter() {

        @Override
        public void keyPressed(final KeyEvent ke) {
            if (ke.getKeyCode() == KeyEvent.VK_F1) {
                final GenericDialog gd = new GenericDialog("Help :: image filters");
                gd.addMessage("In the table 'Available Filters':\n" + " - double-click a filter to add it to the table of 'Chosen Filters'\n \n" + "In the table 'Chosen Filters':\n" + " - double-click a filter to remove it.\n" + " - PAGE UP/DOWN keys move the filter up/down in the list.\n" + " - 'Delete' key removes the selected filter.\n \n" + "In the table of parameter names and values:\n" + " - double-click a value to edit it. Then push enter to set the new value.\n \n" + "What you need to know:\n" + " - filters are set and applied in order, so order matters.\n" + " - filters with parameters for which you entered a value of zero\nwill result in a warning message.\n" + " - when applying the filters, if you choose 'Selected images', these are the images\nthat were selected when the filter editor was opened.\n" + " - when applying the filters, if you want to filter for a regular expression pattern\nin the image name, use the 'All images in layer range...' option,\nwhere a range of one single layer is also possible.");
                gd.hideCancelButton();
                gd.setModal(false);
                gd.showDialog();
            }
        }
    };
    taf.addKeyListener(help);
    tcf.addKeyListener(help);
    tp.addKeyListener(help);
    all.addKeyListener(help);
    buttons.addKeyListener(help);
    empty.addKeyListener(help);
    a.addKeyListener(help);
    frame.getContentPane().add(all);
    frame.pack();
    frame.setVisible(true);
}

Example 3 with IFilter

use of ini.trakem2.imaging.filters.IFilter in project TrakEM2 by trakem2.

the class Patch method exportXML.

/**
 * Opens and closes the tag and exports data. The image is saved in the directory provided in @param any as a String.
 */
@Override
public void exportXML(final StringBuilder sb_body, final String indent, final XMLOptions options) {
    // TODO the Loader should handle the saving of images, not this class.
    final String in = indent + "\t";
    String path = null;
    String path2 = null;
    if (options.export_images) {
        path = options.patches_dir + title;
        // save image without overwriting, and add proper extension (.zip)
        path2 = project.getLoader().exportImage(this, path, false);
    // path2 will be null if the file exists already
    }
    sb_body.append(indent).append("<t2_patch\n");
    String rel_path = null;
    if (null != path && path.equals(path2)) {
        // this happens when a DB project is exported. It may be a different path when it's a FS loader
        // Utils.log2("p id=" + id + "  path==path2");
        rel_path = path2;
        // TrakEM2 uses paths that always have '/' and never '\', so using java.io.File.separatorChar would be an error.
        int i_slash = rel_path.lastIndexOf('/');
        if (i_slash > 0) {
            i_slash = rel_path.lastIndexOf('/', i_slash - 1);
            if (-1 != i_slash) {
                rel_path = rel_path.substring(i_slash + 1);
            }
        }
    } else {
        // Utils.log2("Setting rel_path to " + path2);
        rel_path = path2;
    }
    // For FSLoader projects, saving a second time will save images as null unless calling it
    if (null == rel_path) {
        // Utils.log2("path2 was null");
        final Object ob = project.getLoader().getPath(this);
        path2 = null == ob ? null : (String) ob;
        if (null == path2) {
            // Utils.log2("ERROR: No path for Patch id=" + id + " and title: " + title);
            // at least some clue for recovery
            rel_path = title;
        } else {
            rel_path = path2;
        }
    }
    // Utils.log("Patch path is: " + rel_path);
    super.exportXML(sb_body, in, options);
    final String[] RGB = Utils.getHexRGBColor(color);
    int type = this.type;
    if (-1 == this.type) {
        Utils.log2("Retrieving type for p = " + this);
        final ImagePlus imp = project.getLoader().fetchImagePlus(this);
        if (null != imp)
            type = imp.getType();
    }
    sb_body.append(in).append("type=\"").append(type).append("\"\n").append(in).append("file_path=\"").append(rel_path).append("\"\n").append(in).append("style=\"fill-opacity:").append(alpha).append(";stroke:#").append(RGB[0]).append(RGB[1]).append(RGB[2]).append(";\"\n").append(in).append("o_width=\"").append(o_width).append("\"\n").append(in).append("o_height=\"").append(o_height).append("\"\n");
    if (null != original_path) {
        sb_body.append(in).append("original_path=\"").append(original_path).append("\"\n");
    }
    sb_body.append(in).append("min=\"").append(min).append("\"\n");
    sb_body.append(in).append("max=\"").append(max).append("\"\n");
    final String pps = getPreprocessorScriptPath();
    if (null != pps)
        sb_body.append(in).append("pps=\"").append(project.getLoader().makeRelativePath(pps)).append("\"\n");
    sb_body.append(in).append("mres=\"").append(meshResolution).append("\"\n");
    if (hasCoordinateTransform()) {
        sb_body.append(in).append("ct_id=\"").append(ct_id).append("\"\n");
    }
    if (hasAlphaMask()) {
        sb_body.append(in).append("alpha_mask_id=\"").append(alpha_mask_id).append("\"\n");
    }
    sb_body.append(indent).append(">\n");
    if (hasCoordinateTransform()) {
        if (options.include_coordinate_transform) {
            // Write an XML entry for the CoordinateTransform
            char[] ct_chars = null;
            try {
                ct_chars = readCoordinateTransformFile();
            } catch (final Exception e) {
                IJError.print(e);
            }
            if (null != ct_chars) {
                sb_body.append(ct_chars).append('\n');
            } else {
                Utils.log("ERROR: could not write the CoordinateTransform to the XML file!");
            }
        }
    }
    if (null != filters && filters.length > 0) {
        // specify their own line termination
        for (final IFilter f : filters) sb_body.append(f.toXML(in));
    }
    super.restXML(sb_body, in, options);
    sb_body.append(indent).append("</t2_patch>\n");
}

Example 4 with IFilter

use of ini.trakem2.imaging.filters.IFilter in project TrakEM2 by trakem2.

the class TMLHandler method endElement.

public void endElement(String namespace_URI, String local_name, String qualified_name) {
    if (null == loader)
        return;
    if (skip) {
        // reset
        skip = false;
        return;
    }
    String orig_qualified_name = qualified_name;
    // Utils.log2("endElement: " + qualified_name);
    // iterate over all open things and find the one that matches the qualified_name, and set it closed (pop it out of the list):
    qualified_name = qualified_name.toLowerCase().trim();
    if (0 == qualified_name.indexOf("t2_")) {
        qualified_name = qualified_name.substring(3);
    }
    for (int i = al_open.size() - 1; i > -1; i--) {
        Thing thing = al_open.get(i);
        if (thing.getType().toLowerCase().equals(qualified_name)) {
            al_open.remove(i);
            break;
        }
    }
    if (null != last_annotation && null != last_displayable) {
        last_displayable.setAnnotation(last_annotation.toString().trim().replaceAll("&lt;", "<"));
        last_annotation = null;
    }
    // terminate non-single clause objects
    if (orig_qualified_name.equals("t2_node")) {
        // Remove one node from the stack
        nodes.removeLast();
        taggables.removeLast();
    } else if (orig_qualified_name.equals("t2_connector")) {
        if (null != last_connector) {
            tree_root_nodes.put(last_connector, last_root_node);
            last_root_node = null;
            last_connector = null;
            last_tree = null;
            nodes.clear();
        }
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_area_list")) {
        last_area_list = null;
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_area")) {
        if (null != reca) {
            if (null != last_area_list) {
                // it's local
                last_area_list.addArea(last_area_list_layer_id, reca.getArea());
            } else {
                ((AreaTree.AreaNode) nodes.getLast()).setData(reca.getArea());
            }
            reca = null;
        }
    } else if (orig_qualified_name.equals("ict_transform_list")) {
        ct_list_stack.remove(ct_list_stack.size() - 1);
    } else if (orig_qualified_name.equals("t2_patch")) {
        if (last_patch_filters.size() > 0) {
            last_patch.setFilters(last_patch_filters.toArray(new IFilter[last_patch_filters.size()]));
        }
        if (null != last_ct) {
            last_patch.setCoordinateTransformSilently(last_ct);
            last_ct = null;
        } else if (!last_patch.checkCoordinateTransformFile()) {
            Utils.log("ERROR: could not find a file for the coordinate transform #" + last_patch.getCoordinateTransformId() + " of Patch #" + last_patch.getId());
        }
        if (!last_patch.checkAlphaMaskFile()) {
            Utils.log("ERROR: could not find a file for the alpha mask #" + last_patch.getAlphaMaskId() + " of Patch #" + last_patch.getId());
        }
        last_patch = null;
        last_patch_filters.clear();
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_ball")) {
        last_ball = null;
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_dissector")) {
        last_dissector = null;
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_treeline")) {
        if (null != last_treeline) {
            // old format:
            if (null == last_root_node && null != last_treeline_data && last_treeline_data.length() > 0) {
                last_root_node = parseBranch(Utils.trim(last_treeline_data));
                last_treeline_data = null;
            }
            // new
            tree_root_nodes.put(last_treeline, last_root_node);
            last_root_node = null;
            // always:
            last_treeline = null;
            last_tree = null;
            nodes.clear();
        }
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_areatree")) {
        if (null != last_areatree) {
            tree_root_nodes.put(last_areatree, last_root_node);
            last_root_node = null;
            last_areatree = null;
            last_tree = null;
            // the absence of this line would have made the nodes list grow with all nodes of all areatrees, which is ok but consumes memory
            nodes.clear();
        }
        last_displayable = null;
    } else if (orig_qualified_name.equals("t2_stack")) {
        if (null != last_ict) {
            last_stack.setInvertibleCoordinateTransformSilently(last_ict);
            last_ict = null;
        }
        last_stack = null;
        last_displayable = null;
    } else if (in(orig_qualified_name, all_displayables)) {
        last_displayable = null;
    }
}

Example 5 with IFilter

use of ini.trakem2.imaging.filters.IFilter in project TrakEM2 by trakem2.

the class Loader method preProcess.

protected final void preProcess(final Patch p, ImagePlus imp, final long image_n_bytes) {
    if (null == p)
        return;
    try {
        final String path = preprocessors.get(p);
        boolean update = false;
        if (null != path) {
            final File f = new File(path);
            if (!f.exists()) {
                Utils.log("ERROR: preprocessor script file does NOT exist: " + path);
                return;
            } else if (!f.canRead()) {
                Utils.log("ERROR: can NOT read preprocessor script file at: " + path);
                return;
            }
            if (null == imp) {
                // uninitialized: the script may generate its data
                imp = new ImagePlus();
            } else {
                // Prepare image for pre-processing
                // for 8-bit and RGB images, your problem: setting min and max will expand the range.
                imp.getProcessor().setMinAndMax(p.getMin(), p.getMax());
            }
            // Free 10 times the memory taken by the image, as a gross estimate of memory consumption by the script
            releaseToFit(Math.min(10 * image_n_bytes, MAX_MEMORY / 4));
            // Run the script
            ini.trakem2.scripting.PatchScript.run(p, imp, path);
            // Update Patch image properties:
            if (null != imp.getProcessor() && null != imp.getProcessor().getPixels() && imp.getWidth() > 0 && imp.getHeight() > 0) {
                update = true;
            } else {
                Utils.log("ERROR: preprocessor script failed to create a valid image:" + "\n  ImageProcessor: " + imp.getProcessor() + "\n  pixel array: " + (null == imp.getProcessor() ? null : imp.getProcessor().getPixels()) + "\n  width: " + imp.getWidth() + "\n  height: " + imp.getHeight());
            }
        }
        // Now apply the Patch filters, if any
        final IFilter[] fs = p.getFilters();
        if (null != fs && fs.length > 0) {
            ImageProcessor ip = imp.getProcessor();
            for (final IFilter filter : fs) {
                ip = filter.process(ip);
            }
            if (ip != imp.getProcessor()) {
                imp.setProcessor(ip);
            }
            update = true;
        }
        // Now apply intensity correction if available
        update |= mapIntensities(p, imp);
        if (update) {
            // 1: Tag the ImagePlus as altered (misuses fileFormat field, which is unused in any case)
            final FileInfo fi = imp.getOriginalFileInfo();
            // otherwise, the null original FileInfo is a valid tag by itself in the persistence.Cache
            if (null != fi)
                fi.fileFormat = Loader.PREPROCESSED;
            // 2: cache
            cache(p, imp);
            // 3: update properties of the Patch
            p.updatePixelProperties(imp);
        }
    } catch (final Exception e) {
        IJError.print(e);
    }
}