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

Example 46 with Patch

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

the class ImageJCommandListener method commandExecuting.

// I know, I could create a hashtable and then map methods of this class to each command key ... this is just easier, and performance-wise nobody cares
// Or even a hastable with String command keys and then a number as value, and use a gigantic switch block. So much pain to write. WHAT I REALLY WANT is a switch that takes a String and is fast because it has its own hash setup.
public String commandExecuting(final String command) {
    // Utils.log2("Command: " + command);
    // 1 - check source
    ImagePlus current = WindowManager.getCurrentImage();
    // not a trakem2 display: continue happily
    if (!(current instanceof FakeImagePlus))
        return command;
    // 2 - identify project
    final FakeImagePlus fimp = (FakeImagePlus) current;
    final Display display = fimp.getDisplay();
    final LayerSet layer_set = display.getLayer().getParent();
    final Project project = display.getProject();
    final ProjectTree ptree = project.getProjectTree();
    final Displayable active = display.getActive();
    final Selection selection = display.getSelection();
    // FILE menu
    if (command.equals("Save")) {
        project.save();
        return null;
    } else // EDIT menu
    if (command.equals("Undo")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Cut")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Copy")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Copy to System")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Paste")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Clear")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Clear Outside")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Fill")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Draw")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Invert")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else // EDIT - SELECTION menu
    if (command.equals("Select All")) {
        if (ProjectToolbar.SELECT == Toolbar.getToolId()) {
            selection.selectAll();
            return null;
        }
        return command;
    } else if (command.equals("Select None")) {
        if (ProjectToolbar.SELECT == Toolbar.getToolId()) {
            display.select(null);
            return null;
        }
        return command;
    } else if (command.equals("Restore Selection")) {
        if (ProjectToolbar.SELECT == Toolbar.getToolId()) {
            selection.restore();
            return null;
        }
        return command;
    } else // IMAGE - TYPE menu
    if (command.equals("8-bit")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("16-bit")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("32-bit")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("8-bit Color")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("RGB Color")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("RGB Stack") || command.equals("HSB Stack")) {
        Utils.showMessage("Can't convert to " + command);
        return null;
    } else // IMAGE - ADJUST menu
    if (command.equals("Brightness/Contrast...")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Window/Level...")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Color Balance...")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Threshold...")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Size...")) {
        if (null != active)
            selection.specify();
        return null;
    } else if (command.equals("Canvas Size...")) {
        display.resizeCanvas();
        return null;
    } else // IMAGE menu
    if (command.equals("Show Info...")) {
        // TODO perhaps it should show only for images ...
        if (null == active) {
            ptree.showInfo(project.getRootProjectThing());
        } else {
            ProjectThing pt = project.findProjectThing(active);
            if (null != pt)
                ptree.showInfo(pt);
        }
        return null;
    } else // IMAGE - COLOR menu
    if (in(command, new String[] { "RGB Split", "RGB Merge...", "Stack to RGB", "Make Composite" })) {
        notAvailable(command);
        return null;
    } else if (command.equals("Show LUT")) {
        return setTempCurrentImage(command, active);
    } else if (command.equals("Edit LUT...")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("Average Color")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("RGB to CIELAB")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else if (command.equals("RGB to Luminance")) {
        // TODO forward to the active image, if any
        niy(command);
        return null;
    } else // IMAGE STACK menu
    if (in(command, new String[] { "Add Slice", "Delete Slice" })) {
        Utils.showMessage("Go to the Layer Tree and right-click to add/delete a layer.");
        return null;
    } else if (command.equals("Next Slice [>]")) {
        display.nextLayer(IJ.shiftKeyDown() ? Event.SHIFT_MASK : 0);
        return null;
    } else if (command.equals("Previous Slice [<]")) {
        display.previousLayer(IJ.shiftKeyDown() ? Event.SHIFT_MASK : 0);
        return null;
    } else if (in(command, new String[] { "Set Slice", "Images to Stack", "Stack to Images", "Make Montage..." })) {
        notAvailable(command);
        return null;
    } else if (command.equals("Reslice [/]...")) {
        // TODO
        niy(command);
        return null;
    } else if (command.equals("Z Project...")) {
        // TODO
        niy(command);
        return null;
    } else if (command.equals("3D Project...")) {
        // TODO
        niy(command);
        return null;
    } else if (command.equals("Plot Z-axis Profile")) {
        // TODO
        niy(command);
        return null;
    } else if (command.equals("Start Animation [\\]")) {
        // TODO
        niy(command);
        return null;
    } else if (command.equals("Stop Animation")) {
        // TODO
        niy(command);
        return null;
    } else // IMAGE menu again
    if (command.equals("Crop")) {
        notAvailable(command);
        return null;
    } else if (in(command, new String[] { "Translate...", "Scale..." })) {
        if (null != active)
            selection.specify();
        return null;
    } else if (command.equals("Duplicate...")) {
        if (null != active && active.getClass().equals(Patch.class)) {
            // TODO stacks?
            // 2.5 security factor: for awt in non-1.6.0 machines
            project.getLoader().releaseToFit((long) (project.getLoader().estimateImageFileSize((Patch) active, 0) * 2.5));
            new ImagePlus(active.getTitle(), ((Patch) active).getImageProcessor().duplicate()).show();
        }
        return null;
    } else if (command.equals("Rename...")) {
        if (null != active) {
            active.adjustProperties();
            Display.updateSelection();
        }
        return null;
    } else // IMAGE ROTATE menu
    if (command.equals("Flip Horizontally")) {
        selection.apply(2, new double[] { -1, 1 });
        return null;
    } else if (command.equals("Flip Vertically")) {
        selection.apply(2, new double[] { 1, -1 });
        return null;
    } else if (command.equals("Rotate 90 Degrees Right")) {
        selection.apply(1, new double[] { 90 });
        return null;
    } else if (command.equals("Rotate 90 Degrees Left")) {
        selection.apply(1, new double[] { -90 });
        return null;
    } else if (command.equals("Arbitrarily...")) {
        if (null != active)
            selection.specify();
        return null;
    } else // IMAGE ZOOM menu
    if (command.equals("To Selection")) {
        Roi roi = fimp.getRoi();
        if (null != roi) {
            Rectangle b = roi.getBounds();
            b.x -= b.width / 2;
            b.y -= b.height / 2;
            b.width *= 2;
            b.height *= 2;
            display.getCanvas().showCentered(b);
        }
        return null;
    } else if (command.equals("View 100%")) {
        // TODO
        niy(command);
        return null;
    } else // ANALYZE menu
    if (command.equals("Measure")) {
        // Minimal measurement: area of closed ROIs, length of unclosed ROIs, calibrated.
        Roi roi = fimp.getRoi();
        if (null != roi) {
            Calibration cal = fimp.getCalibration();
            AffineTransform caff = new AffineTransform();
            caff.scale(cal.pixelWidth, cal.pixelHeight);
            if (M.isAreaROI(roi)) {
                Area area = M.getArea(roi);
                area = area.createTransformedArea(caff);
                ResultsTable rt = Utils.createResultsTable("ROI area", new String[] { "area", "perimeter" });
                rt.incrementCounter();
                rt.addLabel("units", cal.getUnit());
                rt.addValue(0, Math.abs(AreaCalculations.area(area.getPathIterator(null))));
                rt.addValue(1, roi.getLength());
                rt.show("ROI area");
            } else {
                ResultsTable rt = Utils.createResultsTable("ROI length", new String[] { "length" });
                rt.incrementCounter();
                rt.addLabel("units", cal.getUnit());
                rt.addValue(0, roi.getLength());
                rt.show("ROI length");
            }
            return null;
        } else if (null != active) {
            // Measure the active displayable
            if (active.getClass() == Patch.class) {
                // measure like 'm' would in ImageJ for an image
                ImagePlus imp = ((Patch) active).getImagePlus();
                imp.setCalibration(active.getLayer().getParent().getCalibrationCopy());
                IJ.run(imp, "Measure", "");
            } else {
                // Call measure like ProjectThing does
                ProjectThing pt = active.getProject().findProjectThing(active);
                if (active instanceof Profile)
                    ((ProjectThing) pt.getParent()).measure();
                else
                    pt.measure();
            }
            return null;
        }
        Utils.log("Draw a ROI or select an object!");
        return null;
    } else if (in(command, new String[] { "Analyze Particles...", "Histogram", "Plot Profile", "Surface Plot...", "Color Inspector 3D", "3D Surface Plot", "Color Histogram" })) {
        return setTempCurrentImage(command, active);
    } else if (command.equals("Label")) {
        notAvailable(command);
        return null;
    } else // PLUGINS menu
    if (command.equals("Volume Viewer")) {
        return runOnVirtualLayerSet(command, layer_set, display);
    } else if (command.equals("3D Viewer")) {
        // it's virtual and non-caching, will appear as a regular ImageJ stack
        layer_set.createLayerStack(Displayable.class, ImagePlus.COLOR_RGB, display.getDisplayChannelAlphas()).getImagePlus().show();
        return command;
    } else // PROCESS menu and submenus
    if (in(command, new String[] { "FFT", "Fast FFT (2D/3D)" })) {
        return setTempCurrentImage(command, active);
    } else if (in(command, new String[] { "Bandpass Filter...", "Custom Filter...", "FD Math...", "Swap Quadrants", "Convolve...", "Gaussian Blur...", "Median...", "Mean...", "Minimum...", "Maximum...", "Unsharp Mask...", "Variance...", "Show Circular Masks...", "Subtract Background..." })) {
        return duplicate(command, active);
    } else if (in(command, new String[] { "Smooth", "Sharpen", "Find Edges", "Enhance Contrast", "Add Noise", "Add Specified Noise...", "Salt and Pepper", "Despeckle", "Remove Outliers...", "North", "Northeast", "East", "Southeast", "South", "Southwest", "West", "Northwest", "Make Binary", "Convert to Mask", "Find Maxima...", "Erode", "Dilate", "Open ", "Close-", "Outline", "Fill Holes", "Skeletonize", "Distance Map", "Ultimate Points", "Watershed", "Add...", "Subtract...", "Multiply...", "Divide...", "AND...", "OR...", "XOR...", "Min...", "Max...", "Gamma...", "Log", "Exp", "Square", "Square Root", "Reciprocal", "NaN Background", "Abs" })) {
        return duplicate(command, active);
    }
    /*else {
			// continue happily
			//Utils.log2("Skipping " + command);
		}*/
    // If it's part of "Save As", ignore it
    Menu menu = Menus.getSaveAsMenu();
    for (int i = menu.getItemCount() - 1; i > -1; i--) {
        if (command.equals(menu.getItem(i).getActionCommand())) {
            notAvailable(command);
            return null;
        }
    }
    // Give it back to ImageJ
    return command;
}

Example 47 with Patch

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

the class ImageJCommandListener method duplicate.

/**
 * Duplicate the active image (if any) and set it as active, so the command is run on it.
 */
private String duplicate(final String command, final Displayable active) {
    if (!isPatch(command, active))
        return null;
    Patch pa = (Patch) active;
    Project project = pa.getProject();
    project.getLoader().releaseToFit((long) (project.getLoader().estimateImageFileSize(pa, 0) * 5));
    // don't show it yet
    ImagePlus imp = new ImagePlus("Copy of " + pa.getTitle(), pa.getImageProcessor().duplicate());
    WindowManager.setTempCurrentImage(imp);
    imp.show();
    // now execute command
    return command;
}

Example 48 with Patch

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

the class ImageJCommandListener method setTempCurrentImage.

/**
 * Set as current image the Patch ImagePlus only for half a second, for a plugin to see it and grab a pointer.
 * YES this is a tremendous hack that may not work in all situations, but will be reasonably ok for PlugInFilter operations.
 * This action is intended for commands that don't alter the original image.
 */
private String setTempCurrentImage(final String command, final Displayable active) {
    if (!isPatch(command, active))
        return null;
    final Patch pa = (Patch) active;
    final Project project = pa.getProject();
    WindowManager.setTempCurrentImage(pa.getImagePlus());
    project.getLoader().releaseToFit((long) (project.getLoader().estimateImageFileSize(pa, 0) * 5));
    return command;
}

Example 49 with Patch

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

the class Loader method addNewImage.

/**
 * Mipmaps for this image are generated asynchronously.
 */
public Patch addNewImage(final ImagePlus imp, final double x, final double y) {
    String filename = imp.getTitle();
    if (!filename.toLowerCase().endsWith(".tif"))
        filename += ".tif";
    final String path = getStorageFolder() + "/" + filename;
    new FileSaver(imp).saveAsTiff(path);
    final Patch pa = new Patch(Project.findProject(this), imp.getTitle(), x, y, imp);
    addedPatchFrom(path, pa);
    if (isMipMapsRegenerationEnabled())
        regenerateMipMaps(pa);
    return pa;
}

Example 50 with Patch

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

the class Loader method insertGrid.

/**
 * Insert grid in layer (with optional stitching)
 *
 * @param layer The Layer to inser the grid into
 * @param dir The base dir of the images to open
 * @param first_image_name name of the first image in the list
 * @param cols The list of columns, containing each an array of String file names in each column.
 * @param bx The top-left X coordinate of the grid to insert
 * @param by The top-left Y coordinate of the grid to insert
 * @param bt_overlap bottom-top overlap of the images
 * @param lr_overlap left-right overlap of the images
 * @param link_images Link images to their neighbors
 * @param stitch_tiles montage option
 * @param cc_percent_overlap tiles overlap
 * @param cc_scale tiles scaling previous to stitching (1 = no scaling)
 * @param min_R regression threshold (minimum acceptable R)
 * @param homogenize_contrast contrast homogenization option
 * @param stitching_rule stitching rule (upper left corner or free)
 */
private void insertGrid(final Layer layer, final String dir_, final String first_image_name, final int n_images, final ArrayList<String[]> cols, final double bx, final double by, final double bt_overlap, final double lr_overlap, final boolean link_images, final boolean stitch_tiles, final boolean homogenize_contrast, final StitchingTEM.PhaseCorrelationParam pc_param, final Worker worker) {
    // create a Worker, then give it to the Bureaucrat
    try {
        String dir = dir_;
        final ArrayList<Patch> al = new ArrayList<Patch>();
        Utils.showProgress(0.0D);
        // less repaints on IJ status bar
        opener.setSilentMode(true);
        int x = 0;
        int y = 0;
        int largest_y = 0;
        ImagePlus img = null;
        // open the selected image, to use as reference for width and height
        // w1nd0wz safe
        dir = dir.replace('\\', '/');
        if (!dir.endsWith("/"))
            dir += "/";
        String path = dir + first_image_name;
        // TODO arbitrary x3 factor
        releaseToFit(new File(path).length() * 3);
        IJ.redirectErrorMessages();
        ImagePlus first_img = openImagePlus(path);
        if (null == first_img) {
            Utils.log("Selected image to open first is null.");
            return;
        }
        if (null == first_img)
            return;
        final int first_image_width = first_img.getWidth();
        final int first_image_height = first_img.getHeight();
        final int first_image_type = first_img.getType();
        // start
        final Patch[][] pall = new Patch[cols.size()][((String[]) cols.get(0)).length];
        int width, height;
        // counter
        int k = 0;
        boolean auto_fix_all = false;
        boolean ignore_all = false;
        boolean resize = false;
        if (!ControlWindow.isGUIEnabled()) {
            // headless mode: autofix all
            auto_fix_all = true;
            resize = true;
        }
        // Accumulate mipmap generation tasks
        final ArrayList<Future<?>> fus = new ArrayList<Future<?>>();
        startLargeUpdate();
        for (int i = 0; i < cols.size(); i++) {
            final String[] rows = (String[]) cols.get(i);
            if (i > 0) {
                x -= lr_overlap;
            }
            for (int j = 0; j < rows.length; j++) {
                if (Thread.currentThread().isInterrupted()) {
                    Display.repaint(layer);
                    rollback();
                    return;
                }
                if (j > 0) {
                    y -= bt_overlap;
                }
                // get file name
                final String file_name = (String) rows[j];
                path = dir + file_name;
                if (null != first_img && file_name.equals(first_image_name)) {
                    img = first_img;
                    // release pointer
                    first_img = null;
                } else {
                    // open image
                    releaseToFit(first_image_width, first_image_height, first_image_type, 1.5f);
                    try {
                        IJ.redirectErrorMessages();
                        img = openImagePlus(path);
                    } catch (final OutOfMemoryError oome) {
                        printMemState();
                        throw oome;
                    }
                }
                if (null == img) {
                    Utils.log("null image! skipping.");
                    pall[i][j] = null;
                    continue;
                }
                width = img.getWidth();
                height = img.getHeight();
                int rw = width;
                int rh = height;
                if (width != first_image_width || height != first_image_height) {
                    int new_width = first_image_width;
                    int new_height = first_image_height;
                    if (!auto_fix_all && !ignore_all) {
                        final GenericDialog gdr = new GenericDialog("Size mismatch!");
                        gdr.addMessage("The size of " + file_name + " is " + width + " x " + height);
                        gdr.addMessage("but the selected image was " + first_image_width + " x " + first_image_height);
                        gdr.addMessage("Adjust to selected image dimensions?");
                        gdr.addNumericField("width: ", (double) first_image_width, 0);
                        // should not be editable ... or at least, explain in some way that the dimensions can be edited just for this image --> done below
                        gdr.addNumericField("height: ", (double) first_image_height, 0);
                        gdr.addMessage("[If dimensions are changed they will apply only to this image]");
                        gdr.addMessage("");
                        final String[] au = new String[] { "fix all", "ignore all" };
                        gdr.addChoice("Automate:", au, au[1]);
                        gdr.addMessage("Cancel == NO    OK = YES");
                        gdr.showDialog();
                        if (gdr.wasCanceled()) {
                            resize = false;
                        // do nothing: don't fix/resize
                        }
                        resize = true;
                        // catch values
                        new_width = (int) gdr.getNextNumber();
                        new_height = (int) gdr.getNextNumber();
                        final int iau = gdr.getNextChoiceIndex();
                        if (new_width != first_image_width || new_height != first_image_height) {
                            auto_fix_all = false;
                        } else {
                            auto_fix_all = (0 == iau);
                        }
                        ignore_all = (1 == iau);
                        if (ignore_all)
                            resize = false;
                    }
                    if (resize) {
                        // resize Patch dimensions
                        rw = first_image_width;
                        rh = first_image_height;
                    }
                }
                // add new Patch at base bx,by plus the x,y of the grid
                // will call back and cache the image
                final Patch patch = new Patch(layer.getProject(), img.getTitle(), bx + x, by + y, img);
                if (width != rw || height != rh)
                    patch.setDimensions(rw, rh, false);
                addedPatchFrom(path, patch);
                if (// prevent it
                homogenize_contrast)
                    // prevent it
                    setMipMapsRegeneration(false);
                else
                    fus.add(regenerateMipMaps(patch));
                // 
                // after the above two lines! Otherwise it will paint fine, but throw exceptions on the way
                layer.add(patch, true);
                // otherwise when reopening it has to fetch all ImagePlus and scale and zip them all! This method though creates the awt and the snap, thus filling up memory and slowing down, but it's worth it.
                patch.updateInDatabase("tiff_snapshot");
                pall[i][j] = patch;
                al.add(patch);
                if (ControlWindow.isGUIEnabled()) {
                    // northwest to prevent screwing up Patch coordinates.
                    layer.getParent().enlargeToFit(patch, LayerSet.NORTHWEST);
                }
                y += img.getHeight();
                Utils.showProgress((double) k / n_images);
                k++;
            }
            x += img.getWidth();
            if (largest_y < y) {
                largest_y = y;
            }
            // resetting!
            y = 0;
        }
        // build list
        final Patch[] pa = new Patch[al.size()];
        int f = 0;
        // list in row-first order
        for (int j = 0; j < pall[0].length; j++) {
            // 'j' is row
            for (int i = 0; i < pall.length; i++) {
                // 'i' is column
                pa[f++] = pall[i][j];
            }
        }
        // optimize repaints: all to background image
        Display.clearSelection(layer);
        // make the first one be top, and the rest under it in left-right and top-bottom order
        for (int j = 0; j < pa.length; j++) {
            layer.moveBottom(pa[j]);
        }
        // make picture
        // getFlatImage(layer, layer.getMinimalBoundingBox(Patch.class), 0.25, 1, ImagePlus.GRAY8, Patch.class, null, false).show();
        // optimize repaints: all to background image
        Display.clearSelection(layer);
        if (homogenize_contrast) {
            if (null != worker)
                worker.setTaskName("Enhancing contrast");
            // 0 - check that all images are of the same type
            int tmp_type = pa[0].getType();
            for (int e = 1; e < pa.length; e++) {
                if (pa[e].getType() != tmp_type) {
                    // can't continue
                    tmp_type = Integer.MAX_VALUE;
                    Utils.log("Can't homogenize histograms: images are not all of the same type.\nFirst offending image is: " + al.get(e));
                    break;
                }
            }
            if (Integer.MAX_VALUE != tmp_type) {
                // checking on error flag
                // Set min and max for all images
                // 1 - fetch statistics for each image
                final ArrayList<ImageStatistics> al_st = new ArrayList<ImageStatistics>();
                // list of Patch ordered by stdDev ASC
                final ArrayList<Patch> al_p = new ArrayList<Patch>();
                int type = -1;
                for (int i = 0; i < pa.length; i++) {
                    if (Thread.currentThread().isInterrupted()) {
                        Display.repaint(layer);
                        rollback();
                        return;
                    }
                    ImagePlus imp = fetchImagePlus(pa[i]);
                    // speed-up trick: extract data from smaller image
                    if (imp.getWidth() > 1024) {
                        releaseToFit(1024, (int) ((imp.getHeight() * 1024) / imp.getWidth()), imp.getType(), 1.1f);
                        // cheap and fast nearest-point resizing
                        imp = new ImagePlus(imp.getTitle(), imp.getProcessor().resize(1024));
                    }
                    if (-1 == type)
                        type = imp.getType();
                    final ImageStatistics i_st = imp.getStatistics();
                    // order by stdDev, from small to big
                    int q = 0;
                    for (final ImageStatistics st : al_st) {
                        q++;
                        if (st.stdDev > i_st.stdDev)
                            break;
                    }
                    if (q == al.size()) {
                        // append at the end. WARNING if importing thousands of images, this is a potential source of out of memory errors. I could just recompute it when I needed it again below
                        al_st.add(i_st);
                        al_p.add(pa[i]);
                    } else {
                        al_st.add(q, i_st);
                        al_p.add(q, pa[i]);
                    }
                }
                // shallow copy of the ordered list
                final ArrayList<Patch> al_p2 = new ArrayList<Patch>(al_p);
                // 2 - discard the first and last 25% (TODO: a proper histogram clustering analysis and histogram examination should apply here)
                if (pa.length > 3) {
                    // under 4 images, use them all
                    int i = 0;
                    while (i <= pa.length * 0.25) {
                        al_p.remove(i);
                        i++;
                    }
                    final int count = i;
                    i = pa.length - 1 - count;
                    while (i > (pa.length * 0.75) - count) {
                        al_p.remove(i);
                        i--;
                    }
                }
                // 3 - compute common histogram for the middle 50% images
                final Patch[] p50 = new Patch[al_p.size()];
                al_p.toArray(p50);
                final StackStatistics stats = new StackStatistics(new PatchStack(p50, 1));
                // 4 - compute autoAdjust min and max values
                // extracting code from ij.plugin.frame.ContrastAdjuster, method autoAdjust
                int autoThreshold = 0;
                double min = 0;
                double max = 0;
                // once for 8-bit and color, twice for 16 and 32-bit (thus the 2501 autoThreshold value)
                final int limit = stats.pixelCount / 10;
                final int[] histogram = stats.histogram;
                // else autoThreshold /= 2;
                if (ImagePlus.GRAY16 == type || ImagePlus.GRAY32 == type)
                    autoThreshold = 2500;
                else
                    autoThreshold = 5000;
                final int threshold = stats.pixelCount / autoThreshold;
                int i = -1;
                boolean found = false;
                int count;
                do {
                    i++;
                    count = histogram[i];
                    if (count > limit)
                        count = 0;
                    found = count > threshold;
                } while (!found && i < 255);
                final int hmin = i;
                i = 256;
                do {
                    i--;
                    count = histogram[i];
                    if (count > limit)
                        count = 0;
                    found = count > threshold;
                } while (!found && i > 0);
                final int hmax = i;
                if (hmax >= hmin) {
                    min = stats.histMin + hmin * stats.binSize;
                    max = stats.histMin + hmax * stats.binSize;
                    if (min == max) {
                        min = stats.min;
                        max = stats.max;
                    }
                }
                // 5 - compute common mean within min,max range
                final double target_mean = getMeanOfRange(stats, min, max);
                Utils.log2("Loader min,max: " + min + ", " + max + ",   target mean: " + target_mean);
                // 6 - apply to all
                for (i = al_p2.size() - 1; i > -1; i--) {
                    // the order is different, thus getting it from the proper list
                    final Patch p = (Patch) al_p2.get(i);
                    final double dm = target_mean - getMeanOfRange((ImageStatistics) al_st.get(i), min, max);
                    // displacing in the opposite direction, makes sense, so that the range is drifted upwards and thus the target 256 range for an awt.Image will be closer to the ideal target_mean
                    p.setMinAndMax(min - dm, max - dm);
                // OBSOLETE and wrong //p.putMinAndMax(fetchImagePlus(p));
                }
                setMipMapsRegeneration(true);
                if (isMipMapsRegenerationEnabled()) {
                    // recreate files
                    for (final Patch p : al) fus.add(regenerateMipMaps(p));
                }
                Display.repaint(layer, new Rectangle(0, 0, (int) layer.getParent().getLayerWidth(), (int) layer.getParent().getLayerHeight()), 0);
            // make picture
            // getFlatImage(layer, layer.getMinimalBoundingBox(Patch.class), 0.25, 1, ImagePlus.GRAY8, Patch.class, null, false).show();
            }
        }
        if (stitch_tiles) {
            // Wait until all mipmaps for the new images have been generated before attempting to register
            Utils.wait(fus);
            // create undo
            layer.getParent().addTransformStep(new HashSet<Displayable>(layer.getDisplayables(Patch.class)));
            // wait until repainting operations have finished (otherwise, calling crop on an ImageProcessor fails with out of bounds exception sometimes)
            if (null != Display.getFront())
                Display.getFront().getCanvas().waitForRepaint();
            if (null != worker)
                worker.setTaskName("Stitching");
            StitchingTEM.stitch(pa, cols.size(), bt_overlap, lr_overlap, true, pc_param).run();
        }
        // link with images on top, bottom, left and right.
        if (link_images) {
            if (null != worker)
                worker.setTaskName("Linking");
            for (int i = 0; i < pall.length; i++) {
                // 'i' is column
                for (int j = 0; j < pall[0].length; j++) {
                    // 'j' is row
                    final Patch p = pall[i][j];
                    // can happen if a slot is empty
                    if (null == p)
                        continue;
                    if (i > 0 && null != pall[i - 1][j])
                        p.link(pall[i - 1][j]);
                    if (i < pall.length - 1 && null != pall[i + 1][j])
                        p.link(pall[i + 1][j]);
                    if (j > 0 && null != pall[i][j - 1])
                        p.link(pall[i][j - 1]);
                    if (j < pall[0].length - 1 && null != pall[i][j + 1])
                        p.link(pall[i][j + 1]);
                }
            }
        }
        commitLargeUpdate();
        // resize LayerSet
        // int new_width = x;
        // int new_height = largest_y;
        // Math.abs(bx) + new_width, Math.abs(by) + new_height);
        layer.getParent().setMinimumDimensions();
        // update indexes
        // so its done once only
        layer.updateInDatabase("stack_index");
        // create panels in all Displays showing this layer
        /* // not needed anymore
Iterator it = al.iterator();
while (it.hasNext()) {
	Display.add(layer, (Displayable)it.next(), false); // don't set it active, don't want to reload the ImagePlus!
}
			 */
        // update Displays
        Display.update(layer);
        layer.recreateBuckets();
    // debug:
    } catch (final Throwable t) {
        IJError.print(t);
        rollback();
        setMipMapsRegeneration(true);
    }
}