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

Example 51 with Displayable

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

the class TemplateTree method renameType.

/**
 * Rename a TemplateThing type from @param old_name to @param new_name.
 *  If such a new_name already exists, the renaming will not occur and returns false.
 */
public boolean renameType(final String old_name, String new_name) {
    // to lower case!
    new_name = new_name.toLowerCase();
    Project project = root.getProject();
    if (new_name.equals(old_name)) {
        return true;
    } else if (project.typeExists(new_name)) {
        Utils.logAll("Type '" + new_name + "' exists already!");
        return false;
    }
    // process name change in all TemplateThing instances that have it
    ArrayList<TemplateThing> al = root.collectAllChildren(new ArrayList<TemplateThing>());
    al.add(root);
    for (final TemplateThing tet : al) {
        // Utils.log("\tchecking " + tet.getType() + " " + tet.getId());
        if (tet.getType().equals(old_name))
            tet.rename(new_name);
    }
    // and update the ProjectThing objects in the tree and its dependant Displayable objects in the open Displays
    project.getRootProjectThing().updateType(new_name, old_name);
    // tell the project about it
    project.updateTypeName(old_name, new_name);
    // repaint both trees (will update the type names)
    updateUILater();
    project.getProjectTree().updateUILater();
    return true;
}

Example 52 with Displayable

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

the class Search method createCoordinate.

private Coordinate<Displayable> createCoordinate(final Displayable d) {
    Rectangle r = d.getBoundingBox();
    Layer la = d instanceof ZDisplayable ? ((ZDisplayable) d).getFirstLayer() : d.getLayer();
    if (null == la) {
        Display display = Display.getFront(d.getProject());
        if (null == display)
            la = d.getProject().getRootLayerSet().getLayer(0);
        else
            la = display.getLayer();
    }
    return new Coordinate<Displayable>(r.x + r.width / 2, r.y + r.height / 2, la, d);
}

Example 53 with Displayable

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

the class Project method getParentTitle.

/**
 * Returns the title of the enclosing abstract node in the ProjectTree.
 */
public String getParentTitle(final Displayable d) {
    try {
        ProjectThing thing = findProjectThing(d);
        ProjectThing parent = (ProjectThing) thing.getParent();
        if (d instanceof Profile) {
            // skip the profile_list
            parent = (ProjectThing) parent.getParent();
        }
        if (null == parent)
            Utils.log2("null parent for " + d);
        if (null != parent && null == parent.getObject()) {
            Utils.log2("null ob for parent " + parent + " of " + d);
        }
        // the abstract thing should be enclosing a String object
        return parent.getObject().toString();
    } catch (Exception e) {
        IJError.print(e);
        return null;
    }
}

Example 54 with Displayable

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

the class AreaList method exportAsLabels.

/**
 * Export all given AreaLists as one per pixel value, what is called a "labels" file; a file dialog is offered to save the image as a tiff stack.
 */
public static void exportAsLabels(final List<Displayable> listToPaint, final ij.gui.Roi roi, final float scale, int first_layer, int last_layer, final boolean visible_only, final boolean to_file, final boolean as_amira_labels) {
    // survive everything:
    if (null == listToPaint || 0 == listToPaint.size()) {
        Utils.log("Null or empty list.");
        return;
    }
    if (scale < 0 || scale > 1) {
        Utils.log("Improper scale value. Must be 0 < scale <= 1");
        return;
    }
    // Select the subset to paint
    final ArrayList<AreaList> list = new ArrayList<AreaList>();
    for (final Displayable d : listToPaint) {
        if (visible_only && !d.isVisible())
            continue;
        if (d instanceof AreaList)
            list.add((AreaList) d);
    }
    Utils.log2("exportAsLabels: list.size() is " + list.size());
    // Current AmiraMeshEncoder supports ByteProcessor only: 256 labels max, including background at zero.
    if (as_amira_labels && list.size() > 255) {
        Utils.log("Saving ONLY first 255 AreaLists!\nDiscarded:");
        final StringBuilder sb = new StringBuilder();
        for (final Displayable d : list.subList(255, list.size())) {
            sb.append("    ").append(d.getProject().getShortMeaningfulTitle(d)).append('\n');
        }
        Utils.log(sb.toString());
        final ArrayList<AreaList> li = new ArrayList<AreaList>(list);
        list.clear();
        list.addAll(li.subList(0, 255));
    }
    String path = null;
    if (to_file) {
        final String ext = as_amira_labels ? ".am" : ".tif";
        final File f = Utils.chooseFile("labels", ext);
        if (null == f)
            return;
        path = f.getAbsolutePath().replace('\\', '/');
    }
    final LayerSet layer_set = list.get(0).getLayerSet();
    if (first_layer > last_layer) {
        final int tmp = first_layer;
        first_layer = last_layer;
        last_layer = tmp;
        if (first_layer < 0)
            first_layer = 0;
        if (last_layer >= layer_set.size())
            last_layer = layer_set.size() - 1;
    }
    // Create image according to roi and scale
    final int width, height;
    final Rectangle broi;
    if (null == roi) {
        broi = null;
        width = (int) (layer_set.getLayerWidth() * scale);
        height = (int) (layer_set.getLayerHeight() * scale);
    } else {
        broi = roi.getBounds();
        width = (int) (broi.width * scale);
        height = (int) (broi.height * scale);
    }
    // Compute highest label value, which affects of course the stack image type
    final TreeSet<Integer> label_values = new TreeSet<Integer>();
    for (final Displayable d : list) {
        final String label = d.getProperty("label");
        if (null != label)
            label_values.add(Integer.parseInt(label));
    }
    int lowest = 0, highest = 0;
    if (label_values.size() > 0) {
        lowest = label_values.first();
        highest = label_values.last();
    }
    final int n_non_labeled = list.size() - label_values.size();
    final int max_label_value = highest + n_non_labeled;
    int type_ = ImagePlus.GRAY8;
    if (max_label_value > 255) {
        type_ = ImagePlus.GRAY16;
        if (max_label_value > 65535) {
            type_ = ImagePlus.GRAY32;
        }
    }
    final int type = type_;
    final ImageStack stack = new ImageStack(width, height);
    final Calibration cal = layer_set.getCalibration();
    String amira_params = null;
    if (as_amira_labels) {
        final StringBuilder sb = new StringBuilder("CoordType \"uniform\"\nMaterials {\nExterior {\n Id 0,\nColor 0 0 0\n}\n");
        final float[] c = new float[3];
        int value = 0;
        for (final Displayable d : list) {
            // 0 is background
            value++;
            d.getColor().getRGBColorComponents(c);
            String s = d.getProject().getShortMeaningfulTitle(d);
            s = s.replace('-', '_').replaceAll(" #", " id");
            sb.append(Utils.makeValidIdentifier(s)).append(" {\n").append("Id ").append(value).append(",\n").append("Color ").append(c[0]).append(' ').append(c[1]).append(' ').append(c[2]).append("\n}\n");
        }
        sb.append("}\n");
        amira_params = sb.toString();
    }
    final float len = last_layer - first_layer + 1;
    // Assign labels
    final HashMap<AreaList, Integer> labels = new HashMap<AreaList, Integer>();
    for (final AreaList d : list) {
        final String slabel = d.getProperty("label");
        int label;
        if (null != slabel) {
            label = Integer.parseInt(slabel);
        } else {
            // 0 is background
            label = (++highest);
        }
        labels.put(d, label);
    }
    final ExecutorService exec = Utils.newFixedThreadPool("labels");
    final Map<Integer, ImageProcessor> slices = Collections.synchronizedMap(new TreeMap<Integer, ImageProcessor>());
    final List<Future<?>> fus = new ArrayList<Future<?>>();
    final List<Layer> layers = layer_set.getLayers().subList(first_layer, last_layer + 1);
    for (int k = 0; k < layers.size(); k++) {
        final Layer la = layers.get(k);
        final int slice = k;
        fus.add(exec.submit(new Runnable() {

            @Override
            public void run() {
                Utils.showProgress(slice / len);
                final ImageProcessor ip;
                if (ImagePlus.GRAY8 == type) {
                    final BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_GRAY);
                    final Graphics2D g = bi.createGraphics();
                    for (final AreaList ali : list) {
                        final Area area = ali.getArea(la);
                        if (null == area || area.isEmpty())
                            continue;
                        // Transform: the scale and the roi
                        final AffineTransform aff = new AffineTransform();
                        /* 3 - To scale: */
                        if (1 != scale)
                            aff.scale(scale, scale);
                        /* 2 - To roi coordinates: */
                        if (null != broi)
                            aff.translate(-broi.x, -broi.y);
                        /* 1 - To world coordinates: */
                        aff.concatenate(ali.at);
                        g.setTransform(aff);
                        final int label = labels.get(ali);
                        g.setColor(new Color(label, label, label));
                        g.fill(area);
                    }
                    g.dispose();
                    ip = new ByteProcessor(bi);
                    bi.flush();
                } else if (ImagePlus.GRAY16 == type) {
                    final USHORTPaint paint = new USHORTPaint((short) 0);
                    final BufferedImage bi = new BufferedImage(paint.getComponentColorModel(), paint.getComponentColorModel().createCompatibleWritableRaster(width, height), false, null);
                    final Graphics2D g = bi.createGraphics();
                    // final ColorSpace ugray = ColorSpace.getInstance(ColorSpace.CS_GRAY);
                    int painted = 0;
                    for (final AreaList ali : list) {
                        final Area area = ali.getArea(la);
                        if (null == area || area.isEmpty())
                            continue;
                        // Transform: the scale and the roi
                        final AffineTransform aff = new AffineTransform();
                        /* 3 - To scale: */
                        if (1 != scale)
                            aff.scale(scale, scale);
                        /* 2 - To roi coordinates: */
                        if (null != broi)
                            aff.translate(-broi.x, -broi.y);
                        /* 1 - To world coordinates: */
                        aff.concatenate(ali.at);
                        // Fill
                        g.setTransform(aff);
                        // The color doesn't work: paints in a stretched 8-bit mode
                        // g.setColor(new Color(ugray, new float[]{((float)labels.get(d)) / range}, 1));
                        Utils.log2("value: " + labels.get(ali).shortValue());
                        paint.setValue(labels.get(ali).shortValue());
                        g.setPaint(paint);
                        // .createTransformedArea(aff));
                        g.fill(area);
                        painted += 1;
                    }
                    g.dispose();
                    ip = new ShortProcessor(bi);
                    bi.flush();
                    Utils.log2("painted: " + painted);
                } else {
                    // Option 1: could use the same as above, but shifted by 65536, so that 65537 is 1, 65538 is 2, etc.
                    // and keep doing it until no more need to be shifted.
                    // The PROBLEM: cannot keep the order without complicated gymnastics to remember
                    // which label in which image has to be merged to the final image, which prevent
                    // a simple one-pass blitter.
                    // 
                    // Option 2: paint each arealist, extract the image, use it as a mask for filling:
                    final FloatProcessor fp = new FloatProcessor(width, height);
                    final float[] fpix = (float[]) fp.getPixels();
                    ip = fp;
                    final BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_BYTE_GRAY);
                    final Graphics2D gbi = bi.createGraphics();
                    for (final AreaList ali : list) {
                        final Area area = ali.getArea(la);
                        if (null == area || area.isEmpty()) {
                            continue;
                        }
                        // Transform: the scale and the roi
                        // reverse order of transformations:
                        final AffineTransform aff = new AffineTransform();
                        /* 3 - To scale: */
                        if (1 != scale)
                            aff.scale(scale, scale);
                        /* 2 - To ROI coordinates: */
                        if (null != broi)
                            aff.translate(-broi.x, -broi.y);
                        /* 1 - To world coordinates: */
                        aff.concatenate(ali.at);
                        final Area s = area.createTransformedArea(aff);
                        final Rectangle sBounds = s.getBounds();
                        // Need to paint at all?
                        if (0 == sBounds.width || 0 == sBounds.height || !sBounds.intersects(0, 0, width, height))
                            continue;
                        // Paint shape
                        gbi.setColor(Color.white);
                        gbi.fill(s);
                        // Read out painted region
                        final int x0 = Math.max(0, sBounds.x);
                        final int y0 = Math.max(0, sBounds.y);
                        final int xN = Math.min(width, sBounds.x + sBounds.width);
                        final int yN = Math.min(height, sBounds.y + sBounds.height);
                        // Get the array
                        final byte[] bpix = ((DataBufferByte) bi.getRaster().getDataBuffer()).getData();
                        final float value = labels.get(ali);
                        // For every non-black pixel, set a 'value' pixel in the FloatProcessor
                        for (int y = y0; y < yN; ++y) {
                            for (int x = x0; x < xN; ++x) {
                                final int pos = y * width + x;
                                // black
                                if (0 == bpix[pos])
                                    continue;
                                fpix[pos] = value;
                            }
                        }
                        // Clear image region
                        gbi.setColor(Color.black);
                        gbi.fill(s);
                    }
                    gbi.dispose();
                    bi.flush();
                }
                slices.put(slice, ip);
            }
        }));
    }
    Utils.wait(fus);
    exec.shutdownNow();
    for (final Map.Entry<Integer, ImageProcessor> e : slices.entrySet()) {
        final Layer la = layers.get(e.getKey());
        stack.addSlice(la.getZ() * cal.pixelWidth + "", e.getValue());
        if (ImagePlus.GRAY8 != type) {
            e.getValue().setMinAndMax(lowest, highest);
        }
    }
    Utils.showProgress(1);
    // Save via file dialog:
    final ImagePlus imp = new ImagePlus("Labels", stack);
    if (as_amira_labels)
        imp.setProperty("Info", amira_params);
    imp.setCalibration(layer_set.getCalibrationCopy());
    if (to_file) {
        if (as_amira_labels) {
            final AmiraMeshEncoder ame = new AmiraMeshEncoder(path);
            if (!ame.open()) {
                Utils.log("Could not write to file " + path);
                return;
            }
            if (!ame.write(imp)) {
                Utils.log("Error in writing Amira file!");
                return;
            }
        } else {
            new FileSaver(imp).saveAsTiff(path);
        }
    } else
        imp.show();
}

Example 55 with Displayable

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

the class Graph method extractAndShowGraph.

/**
 * Shows a dialog to pick which classes is one interested in.
 */
public static final void extractAndShowGraph(final LayerSet ls) {
    GenericDialog gd = new GenericDialog("Graph elements");
    Class<Displayable>[] c = new Class[] { AreaList.class, AreaTree.class, Ball.class, Connector.class, Patch.class, Pipe.class, Polyline.class, Profile.class, DLabel.class, Treeline.class };
    String[] types = new String[] { "AreaList", "AreaTree", "Ball", "Connector", "Image", "Pipe", "Polyline", "Profile", "Text", "Treeline" };
    boolean[] states = new boolean[] { true, true, false, false, false, false, true, true, false, true };
    assert (c.length == types.length && types.length == states.length);
    for (int i = 0; i < c.length; i++) {
        if (ZDisplayable.class.isAssignableFrom(c[i])) {
            if (!ls.contains(c[i]))
                states[i] = false;
        } else if (!ls.containsDisplayable(c[i]))
            states[i] = false;
    }
    gd.addCheckboxGroup(types.length, 1, types, states, new String[] { "Include only:" });
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    HashSet<Class<Displayable>> only = new HashSet<Class<Displayable>>();
    for (int i = 0; i < types.length; i++) {
        if (gd.getNextBoolean())
            only.add(c[i]);
    }
    Graph.extractAndShowGraph(ls, only);
}