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

Example 21 with Display

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

the class Loader method getJobsPopup.

public JPopupMenu getJobsPopup(final Display display) {
    synchronized (jobs) {
        this.popup_jobs = new JPopupMenu("Cancel jobs:");
        int i = 1;
        for (final Bureaucrat burro : jobs) {
            final JMenuItem item = new JMenuItem("Job " + i + ": " + burro.getTaskName());
            item.addActionListener(display);
            popup_jobs.add(item);
            i++;
        }
    }
    return popup_jobs;
}

Example 22 with Display

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

the class Loader method importGrid.

/**
 * Import a grid of images and put them in the layer. If the directory (@param dir) is null, it'll be asked for.
 */
public Bureaucrat importGrid(final Layer layer, String dir) {
    try {
        String file = null;
        if (null == dir) {
            final String[] dn = Utils.selectFile("Select first image");
            if (null == dn)
                return null;
            dir = dn[0];
            file = dn[1];
        }
        // char digit digit
        String convention = "cdd";
        boolean chars_are_columns = true;
        // examine file name
        /*
		if (file.matches("\\A[a-zA-Z]\\d\\d.*")) { // one letter, 2 numbers
			//means:
			//	\A		- beggining of input
			//	[a-zA-Z]	- any letter upper or lower case
			//	\d\d		- two consecutive digits
			//	.*		- any row of chars
			ini_grid_convention = true;
		}
		*/
        // ask for chars->rows, numbers->columns or viceversa
        final GenericDialog gd = new GenericDialog("Conventions");
        gd.addStringField("file_name_contains:", "");
        gd.addNumericField("base_x: ", 0, 3);
        gd.addNumericField("base_y: ", 0, 3);
        gd.addMessage("Use: x(any), c(haracter), d(igit)");
        gd.addStringField("convention: ", convention);
        final String[] cr = new String[] { "columns", "rows" };
        gd.addChoice("characters are: ", cr, cr[0]);
        gd.addMessage("[File extension ignored]");
        // as asked by Joachim Walter
        gd.addNumericField("bottom-top overlap: ", 0, 3);
        gd.addNumericField("left-right overlap: ", 0, 3);
        gd.addCheckbox("link_images", false);
        gd.addCheckbox("montage with phase correlation", false);
        gd.addCheckbox("homogenize_contrast", true);
        final Component[] c = { (Component) gd.getSliders().get(gd.getSliders().size() - 2), (Component) gd.getNumericFields().get(gd.getNumericFields().size() - 2), (Component) gd.getSliders().get(gd.getSliders().size() - 1), (Component) gd.getNumericFields().get(gd.getNumericFields().size() - 1), (Component) gd.getChoices().get(gd.getChoices().size() - 1) };
        // enable the checkbox to control the slider and its associated numeric field:
        Utils.addEnablerListener((Checkbox) gd.getCheckboxes().get(gd.getCheckboxes().size() - 1), c, null);
        // gd.addCheckbox("Apply non-linear deformation", false);
        gd.showDialog();
        if (gd.wasCanceled()) {
            return null;
        }
        // collect data
        // filter away files not containing this tag
        final String regex = gd.getNextString();
        // the base x,y of the whole grid
        final double bx = gd.getNextNumber();
        final double by = gd.getNextNumber();
        // if (!ini_grid_convention) {
        convention = gd.getNextString().toLowerCase();
        // }
        if (/*!ini_grid_convention && */
        (null == convention || convention.equals("") || -1 == convention.indexOf('c') || -1 == convention.indexOf('d'))) {
            // TODO check that the convention has only 'cdx' chars and also that there is an island of 'c's and of 'd's only.
            Utils.showMessage("Convention '" + convention + "' needs both c(haracters) and d(igits), optionally 'x', and nothing else!");
            return null;
        }
        chars_are_columns = (0 == gd.getNextChoiceIndex());
        final double bt_overlap = gd.getNextNumber();
        final double lr_overlap = gd.getNextNumber();
        final boolean link_images = gd.getNextBoolean();
        final boolean stitch_tiles = gd.getNextBoolean();
        final boolean homogenize_contrast = gd.getNextBoolean();
        // start magic
        // get ImageJ-openable files that comply with the convention
        final File images_dir = new File(dir);
        if (!(images_dir.exists() && images_dir.isDirectory())) {
            Utils.showMessage("Something went wrong:\n\tCan't find directory " + dir);
            return null;
        }
        final String[] file_names = images_dir.list(new ImageFileFilter(regex, convention));
        if (null == file && file_names.length > 0) {
            // the 'selected' file
            file = file_names[0];
        }
        Utils.showStatus("Adding " + file_names.length + " patches.", false);
        if (0 == file_names.length) {
            Utils.log("Zero files match the convention '" + convention + "'");
            return null;
        }
        // How to: select all files, and order their names in a double array as they should be placed in the Display. Then place them, displacing by offset, and resizing if necessary.
        // gather image files:
        final Montage montage = new Montage(convention, chars_are_columns);
        montage.addAll(file_names);
        // an array of Object[] arrays, of unequal length maybe, each containing a column of image file names
        final ArrayList<String[]> cols = montage.getCols();
        // !@#$%^&*
        final String dir_ = dir;
        final double bt_overlap_ = bt_overlap;
        final double lr_overlap_ = lr_overlap;
        final String file_ = file;
        return Bureaucrat.createAndStart(new Worker.Task("Insert grid", true) {

            @Override
            public void exec() {
                StitchingTEM.PhaseCorrelationParam pc_param = null;
                if (stitch_tiles) {
                    pc_param = new StitchingTEM.PhaseCorrelationParam();
                    pc_param.setup(layer);
                }
                insertGrid(layer, dir_, file_, file_names.length, cols, bx, by, bt_overlap_, lr_overlap_, link_images, stitch_tiles, homogenize_contrast, pc_param, this);
            }
        }, layer.getProject());
    } catch (final Exception e) {
        IJError.print(e);
    }
    return null;
}

Example 23 with Display

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

the class ProjectTiler method createRetiledSibling.

/**
 * Take a {@link Project}, a size for the image tiles, and a target directory,
 * and create a new copy of the current project in that folder but with the underlying
 * images converted to tiles with a translation-only transform (saved as zipped TIFFs,
 * with extension ".tif.zip").
 * The new, returned {@link Project} represents the given project but with much
 * simpler transformations (just translation) for the images and a defined size for
 * the latter, which helps a lot regarding storage space of the XML (and parsing and
 * saving time) and performance when browsing layers (keep in mind that, for a 32k x 32k image,
 * at 100% zoom one would have to load a 32k x 32k image and render just a tiny bit
 * of it). The copied Project preserves the ID of the {@link Layer}s of the original
 * {@link Project}, as well as the dimensions; this means the copy is a sibling of
 * the original, and it is possible to send segmentations from one to the other "as is"
 * (directly, without having to transform along with the images which would not be possible).
 *
 * Image files are stored as
 *
 * The non-image objects of the given project are copied into the new project as well.
 *
 * @param srcProject The project to create a sibling of.
 * @param targetDirectory The directory in which to create all the necessary data and mipmap folders for the new Project.
 * @param tileWidth The width of the tiles to create for the data of the new project.
 * @param tileHeight The height of the tiles.
 * @param exportImageType Any of {@link ImagePlus#GRAY8}, {@link ImagePlus#GRAY16} or {@link ImagePlus#COLOR_RGB}, otherwise an {@link IllegalArgumentException} is thrown.
 * @param onlyVisibleImages Whether to consider visible images only.
 * @param nExportThreads Number of layers to export in parallel. Use a small number when original images are huge (such as larger than 4096 x 4096 pixels).
 * @param createMipMaps Whether to generate the mipmaps when done or not.
 *
 * @throws Exception IllegalArgumentException When {@code exportImageType} is not {@link ImagePlus#GRAY16} or {@link ImagePlus#COLOR_RGB}, or when the directory exists and cannot be written to.
 */
public static final Project createRetiledSibling(final Project srcProject, final String targetDirectory, final int tileWidth, final int tileHeight, final int exportImageType, final boolean onlyVisibleImages, final int nExportThreads, final boolean createMipMaps) throws Exception {
    // Validate exportImageType
    switch(exportImageType) {
        case ImagePlus.GRAY8:
        case ImagePlus.GRAY16:
        case ImagePlus.COLOR_RGB:
            break;
        default:
            throw new IllegalArgumentException("Can only accept GRAY8, GRAY16 or COLOR_RGB as values for 'exportImageType'!");
    }
    // Validate targetDirectory
    final File fdir = new File(targetDirectory);
    if (fdir.exists()) {
        if (!fdir.isDirectory() || !fdir.canWrite())
            throw new IllegalArgumentException("Invalid directory: not a directory or cannot write to: " + targetDirectory);
    } else {
        if (!fdir.mkdirs()) {
            throw new IllegalArgumentException("Cannot create directory at: " + targetDirectory);
        }
    }
    final String targetDir = Utils.fixDir(targetDirectory);
    // Create "data" directory
    final String dataDir = new StringBuilder(targetDir).append("data/").toString();
    final File fDataDir = new File(dataDir);
    if (fDataDir.exists() && (!fDataDir.isDirectory() || !fDataDir.canWrite())) {
        throw new IllegalArgumentException("Cannot create or write to 'data' directory in the targetDirectory at: " + targetDir);
    } else {
        fDataDir.mkdir();
    }
    // Create new Project, plain, without any automatic creation of a Layer or a Display
    final Project newProject = Project.newFSProject("blank", null, targetDir, false);
    final LayerSet newLayerSet = newProject.getRootLayerSet();
    newLayerSet.setCalibration(srcProject.getRootLayerSet().getCalibrationCopy());
    if (!createMipMaps) {
        Utils.log("MipMaps are DISABLED:\n --> When done, right-click and choose 'Display - Properties...' and enable mipmaps,\n     and then run 'Project - Regenerate all mipmaps'\n");
        newProject.getLoader().setMipMapsRegeneration(false);
        Utils.log("mipmaps enabled? " + newProject.getLoader().isMipMapsRegenerationEnabled());
    }
    // Copy the Template Tree of types
    newProject.resetRootTemplateThing(srcProject.getRootTemplateThing().clone(newProject, true), null);
    for (final TemplateThing tt : newProject.getRootTemplateThing().getUniqueTypes(new HashMap<String, TemplateThing>()).values()) {
        newProject.addUniqueType(tt);
    }
    // Clone layers with the exact same IDs, so that the two projects are siblings at the layer-level:
    // (Being siblings allows for treelines, arealists, etc. to be transferred from one to another "as is").
    final List<Layer> srcLayers = srcProject.getRootLayerSet().getLayers();
    final List<Layer> newLayers = new ArrayList<Layer>();
    for (final Layer srcLayer : srcLayers) {
        final Layer newLayer = new Layer(newProject, srcLayer.getId(), srcLayer.getZ(), srcLayer.getThickness());
        // to update the ID generator in FSLoader
        newLayer.addToDatabase();
        newLayerSet.add(newLayer);
        newLayers.add(newLayer);
        newProject.getRootLayerThing().addChild(new LayerThing(newProject.getRootLayerThing().getChildTemplate("layer"), newProject, newLayer));
    }
    newProject.getLayerTree().rebuild();
    // Update the LayerSet
    newLayerSet.setDimensions(srcProject.getRootLayerSet().getLayerWidth(), srcProject.getRootLayerSet().getLayerHeight(), LayerSet.NORTHWEST);
    Display.updateLayerScroller(newLayerSet);
    Display.update(newLayerSet);
    // Copy template from the src Project
    // (It's done after creating layers so the IDs will not collide with those of the Layers)
    newProject.resetRootTemplateThing(srcProject.getRootTemplateThing().clone(newProject, false), null);
    // Export tiles as new Patch instances, creating new image files in disk
    final int numThreads = Math.max(1, Math.min(nExportThreads, Runtime.getRuntime().availableProcessors()));
    int i = 0;
    for (final Layer srcLayer : srcLayers) {
        Utils.log("Processing layer " + (i + 1) + "/" + srcLayers.size() + " -- " + new Date());
        final int layerIndex = i++;
        // Create subDirectory
        final String dir = dataDir + "/" + layerIndex + "/";
        new File(dir).mkdir();
        // Create a new Layer with the same Z and thickness
        final Layer newLayer = newLayers.get(layerIndex);
        // Export layer tiles
        final ArrayList<Patch> patches = new ArrayList<Patch>();
        if (ImagePlus.GRAY16 == exportImageType) {
            Process.progressive(ExportUnsignedShort.exportTiles(srcLayer, tileWidth, tileHeight, onlyVisibleImages), new CountingTaskFactory<Callable<ExportedTile>, Patch>() {

                public Patch process(final Callable<ExportedTile> c, final int index) {
                    try {
                        // Create the tile
                        final ExportedTile t = c.call();
                        // Store the file
                        final String title = layerIndex + "-" + index;
                        final String path = dir + title + ".tif.zip";
                        final ImagePlus imp = new ImagePlus(title, t.sp);
                        if (!new FileSaver(imp).saveAsZip(path)) {
                            throw new Exception("Could not save tile: " + path);
                        }
                        // Create a Patch
                        final Patch patch = new Patch(newProject, title, t.x, t.y, imp);
                        patch.setLocked(true);
                        newProject.getLoader().addedPatchFrom(path, patch);
                        return patch;
                    } catch (Exception e) {
                        IJError.print(e);
                        return null;
                    }
                }
            }, patches, numThreads);
        } else {
            // GRAY8 or COLOR_RGB: created from mipmaps
            Process.progressive(tileSequence(srcLayer, tileWidth, tileHeight, onlyVisibleImages), new CountingTaskFactory<Rectangle, Patch>() {

                @Override
                public Patch process(final Rectangle bounds, final int index) {
                    try {
                        // Create the tile
                        final ImagePlus imp = srcLayer.getProject().getLoader().getFlatImage(srcLayer, bounds, 1.0, -1, exportImageType, Patch.class, null, false, Color.black);
                        final String title = layerIndex + "-" + index;
                        imp.setTitle(title);
                        final String path = dir + title + ".tif.zip";
                        if (!new FileSaver(imp).saveAsZip(path)) {
                            throw new Exception("Could not save tile: " + path);
                        }
                        // Create a Patch
                        final Patch patch = new Patch(newProject, title, bounds.x, bounds.y, imp);
                        patch.setLocked(true);
                        newProject.getLoader().addedPatchFrom(path, patch);
                        return patch;
                    } catch (Exception e) {
                        IJError.print(e);
                        return null;
                    }
                }
            }, patches, numThreads);
        }
        // Add all Patches to the new Layer
        for (final Patch p : patches) {
            newLayer.add(p);
        }
    }
    // Copy all segmentations "As is"
    final ProjectThing root = srcProject.getRootProjectThing();
    if (null != root.getChildren() && !root.getChildren().isEmpty()) {
        final ProjectThing source_pt = srcProject.getRootProjectThing().getChildren().get(0);
        // "As is"
        final int transfer_mode = 0;
        final ProjectThing landing_parent = newProject.getRootProjectThing();
        srcProject.getProjectTree().rawSendToSiblingProject(source_pt, transfer_mode, newProject, landing_parent);
    }
    // Copy all floating text labels
    i = 0;
    for (final Layer srcLayer : srcLayers) {
        for (final DLabel srcLabel : srcLayer.getAll(DLabel.class)) {
            newLayers.get(i++).add(srcLabel.clone(newProject, false));
        }
    }
    if (createMipMaps) {
        final LinkedList<Future<?>> fus = new LinkedList<Future<?>>();
        final int batch = Runtime.getRuntime().availableProcessors();
        for (final Layer newLayer : newLayers) {
            for (final Patch p : newLayer.getAll(Patch.class)) {
                fus.add(p.updateMipMaps());
                // Don't build-up too much
                if (fus.size() > batch * 3) {
                    while (fus.size() > batch) {
                        try {
                            fus.removeFirst().get();
                        } catch (Exception e) {
                            IJError.print(e);
                        }
                    }
                }
            }
        }
        Utils.wait(fus);
    }
    // Save:
    newProject.saveAs(targetDir + "exported.xml", false);
    return newProject;
}

Example 24 with Display

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

the class LayerThing method getPopupItems.

public JMenuItem[] getPopupItems(ActionListener listener) {
    JMenuItem item;
    ArrayList<JMenuItem> al_items = new ArrayList<JMenuItem>();
    JMenu menu = new JMenu("Add...");
    ArrayList<TemplateThing> tc = template.getChildren();
    if (null != tc) {
        for (Iterator<TemplateThing> it = tc.iterator(); it.hasNext(); ) {
            // changing underscores for spaces, for the 'layer_set' type to read nice
            item = new JMenuItem("new " + it.next().getType().replace('_', ' '));
            item.addActionListener(listener);
            menu.add(item);
        }
        if (template.getType().replaceAll("_", " ").equals("layer set")) {
            item = new JMenuItem("many new layers...");
            item.addActionListener(listener);
            menu.add(item);
        }
    }
    if (0 != menu.getItemCount()) {
        al_items.add(menu);
    }
    // Add a "Show" for all except the root LayerSet
    if (null != parent) {
        item = new JMenuItem("Show");
        item.addActionListener(listener);
        al_items.add(item);
    }
    if (template.getType().equals("layer")) {
        // adjust z and thickness
        item = new JMenuItem("Adjust...");
        item.addActionListener(listener);
        al_items.add(item);
    }
    item = new JMenuItem("Rename...");
    item.addActionListener(listener);
    al_items.add(item);
    if (template.getType().replaceAll("_", " ").equals("layer set")) {
        if (null != parent) {
            item = new JMenuItem("Show centered in Display");
            item.addActionListener(listener);
            al_items.add(item);
        }
        item = new JMenuItem("Resize LayerSet...");
        item.addActionListener(listener);
        al_items.add(item);
        LayerSet layer_set = (LayerSet) object;
        final boolean empty = 0 == layer_set.getLayers().size();
        item = new JMenuItem("Autoresize LayerSet");
        item.addActionListener(listener);
        al_items.add(item);
        if (empty)
            item.setEnabled(false);
        item = new JMenuItem("Translate layers in Z...");
        item.addActionListener(listener);
        al_items.add(item);
        if (empty)
            item.setEnabled(false);
        item = new JMenuItem("Reverse layer Z coords...");
        item.addActionListener(listener);
        al_items.add(item);
        if (empty)
            item.setEnabled(false);
        item = new JMenuItem("Reset layer Z and thickness");
        item.addActionListener(listener);
        al_items.add(item);
        if (empty)
            item.setEnabled(false);
        item = new JMenuItem("Search...");
        item.addActionListener(listener);
        al_items.add(item);
        if (empty)
            item.setEnabled(false);
    }
    item = new JMenuItem("Import stack...");
    // contains layers already, wouldn't know where to put it!
    if (template.getType().replaceAll("_", " ").equals("layer set") && 0 != ((LayerSet) object).getLayers().size())
        item.setEnabled(false);
    item.addActionListener(listener);
    al_items.add(item);
    if (template.getType().equals("layer")) {
        item = new JMenuItem("Import grid...");
        item.addActionListener(listener);
        al_items.add(item);
        item = new JMenuItem("Import sequence as grid...");
        item.addActionListener(listener);
        al_items.add(item);
        item = new JMenuItem("Import from text file...");
        item.addActionListener(listener);
        al_items.add(item);
    }
    // add a delete to all except the root LayerSet
    if (null != parent) {
        al_items.add(new JMenuItem(""));
        item = new JMenuItem("Delete...");
        item.addActionListener(listener);
        al_items.add(item);
    }
    JMenuItem[] items = new JMenuItem[al_items.size()];
    al_items.toArray(items);
    return items;
}

Example 25 with Display

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

the class LayerTree method mousePressed.

public void mousePressed(MouseEvent me) {
    Object source = me.getSource();
    if (!source.equals(this) || !project.isInputEnabled()) {
        return;
    }
    // ignore if doing multiple selection
    if (!Utils.isPopupTrigger(me) && (me.isShiftDown() || (!ij.IJ.isMacOSX() && me.isControlDown()))) {
        return;
    }
    int x = me.getX();
    int y = me.getY();
    // check if there is a multiple selection
    TreePath[] paths = this.getSelectionPaths();
    if (null != paths && paths.length > 1) {
        if (Utils.isPopupTrigger(me)) {
            // check that all items are of the same type
            String type_first = ((LayerThing) ((DefaultMutableTreeNode) paths[0].getLastPathComponent()).getUserObject()).getType();
            for (int i = 1; i < paths.length; i++) {
                String type = ((LayerThing) ((DefaultMutableTreeNode) paths[i].getLastPathComponent()).getUserObject()).getType();
                if (!type.equals(type_first)) {
                    Utils.showMessage("All selected items must be of the same type for operations on multiple items.");
                    return;
                }
            }
            // prepare popup menu
            JPopupMenu popup = new JPopupMenu();
            JMenuItem item = null;
            if (type_first.equals("layer")) {
                item = new JMenuItem("Reverse layer Z coords");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Translate layers in Z...");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Scale Z and thickness...");
                item.addActionListener(this);
                popup.add(item);
                item = new JMenuItem("Delete...");
                item.addActionListener(this);
                popup.add(item);
            }
            if (popup.getSubElements().length > 0) {
                popup.show(this, x, y);
            }
        }
        // disable commands depending upon a single node being selected
        selected_node = null;
        return;
    }
    // find the node and set it selected
    TreePath path = getPathForLocation(x, y);
    if (null == path) {
        return;
    }
    setSelectionPath(path);
    selected_node = (DefaultMutableTreeNode) path.getLastPathComponent();
    if (2 == me.getClickCount() && !Utils.isPopupTrigger(me) && MouseEvent.BUTTON1 == me.getButton()) {
        // create a new Display
        LayerThing thing = (LayerThing) selected_node.getUserObject();
        DBObject ob = (DBObject) thing.getObject();
        if (thing.getType().toLowerCase().replace('_', ' ').equals("layer set") && null == ((LayerSet) ob).getParent()) {
            // the top level LayerSet
            return;
        }
        // new Display(ob.getProject(), thing.getType().toLowerCase().equals("layer") ? (Layer)ob : ((LayerSet)ob).getParent());
        Display.createDisplay(ob.getProject(), thing.getType().toLowerCase().equals("layer") ? (Layer) ob : ((LayerSet) ob).getParent());
        return;
    } else if (Utils.isPopupTrigger(me)) {
        JPopupMenu popup = getPopupMenu(selected_node);
        if (null == popup)
            return;
        popup.show(this, x, y);
        return;
    }
}