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

Example 81 with Displayable

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

the class Render method accumulate.

/**
 * Recursive; returns the last added profile.
 */
private Profile accumulate(final HashSet<Profile> hs_done, final ArrayList<Profile> al, final Profile step, int z_trend) {
    final HashSet<Displayable> hs_linked = step.getLinked(Profile.class);
    if (al.size() > 1 && hs_linked.size() > 2) {
        // base found
        return step;
    }
    double step_z = step.getLayer().getZ();
    Profile next_step = null;
    boolean started = false;
    for (final Displayable ob : hs_linked) {
        // loop only one cycle, to move only in one direction
        if (al.contains(ob) || started || hs_done.contains(ob))
            continue;
        started = true;
        next_step = (Profile) ob;
        double next_z = next_step.getLayer().getZ();
        if (0 == z_trend) {
            // define trend
            if (next_z > step_z) {
                z_trend = 1;
            } else {
                z_trend = -1;
            }
            // add!
            al.add(next_step);
        } else {
            // if the z trend is broken, finish
            if ((next_z > step_z && 1 == z_trend) || (next_z < step_z && -1 == z_trend)) {
                // z trend continues
                al.add(next_step);
            } else {
                // z trend broken
                next_step = null;
            }
        }
    }
    Profile last = step;
    // Utils.log2("next_step is " + next_step);
    if (null != next_step) {
        hs_done.add(next_step);
        last = accumulate(hs_done, al, next_step, z_trend);
    }
    // Utils.log2("returning last " + last);
    return last;
}

Example 82 with Displayable

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

the class Search method executeSearch.

private void executeSearch() {
    final Project project = Project.getProjects().get(projects.getSelectedIndex());
    if (null == project) {
        // Should not happen
        return;
    }
    Bureaucrat.createAndStart(new Worker.Task("Searching") {

        public void exec() {
            String pattern = search_field.getText();
            if (null == pattern || 0 == pattern.length()) {
                return;
            }
            // fix pattern
            final String typed_pattern = pattern;
            // I hate java
            final StringBuilder sb = new StringBuilder();
            if (!pattern.startsWith("^"))
                sb.append("^.*");
            for (int i = 0; i < pattern.length(); i++) {
                sb.append(pattern.charAt(i));
            }
            if (!pattern.endsWith("$"))
                sb.append(".*$");
            pattern = sb.toString();
            final Pattern pat = Pattern.compile(pattern, Pattern.CASE_INSENSITIVE | Pattern.MULTILINE | Pattern.DOTALL);
            // Utils.log2("pattern after: " + pattern);
            final ArrayList<DBObject> al = new ArrayList<DBObject>();
            // Utils.log("types[pulldown] = " +
            // types[pulldown.getSelectedIndex()]);
            find(project.getRootLayerSet(), al, types[pulldown.getSelectedIndex()]);
            // Utils.log2("found labels: " + al.size());
            if (0 == al.size())
                return;
            final Vector<DBObject> v_obs = new Vector<DBObject>();
            final Vector<String> v_txt = new Vector<String>();
            final Vector<Coordinate<?>> v_co = new Vector<Coordinate<?>>();
            Coordinate<?> co = null;
            for (final DBObject dbo : al) {
                if (Thread.currentThread().isInterrupted()) {
                    return;
                }
                boolean matched = false;
                // Search in its title
                Displayable d = null;
                if (dbo instanceof Displayable) {
                    d = (Displayable) dbo;
                }
                String txt;
                String meaningful_title = null;
                if (null == d || Patch.class == d.getClass())
                    txt = dbo.getTitle();
                else {
                    txt = meaningful_title = dbo.getProject().getMeaningfulTitle(d);
                }
                if (null == txt || 0 == txt.trim().length())
                    continue;
                matched = pat.matcher(txt).matches();
                if (!matched && null != d) {
                    // Search also in its annotation
                    txt = d.getAnnotation();
                    if (null != txt)
                        matched = pat.matcher(txt).matches();
                }
                if (!matched) {
                    // Search also in its toString()
                    txt = dbo.toString();
                    matched = pat.matcher(txt).matches();
                }
                if (!matched) {
                    // Search also in its id
                    txt = Long.toString(dbo.getId());
                    matched = pat.matcher(txt).matches();
                    if (matched)
                        txt = "id: #" + txt;
                }
                if (!matched && null != d) {
                    // Search also in its properties
                    Map<String, String> props = d.getProperties();
                    if (null != props) {
                        for (final Map.Entry<String, String> e : props.entrySet()) {
                            if (pat.matcher(e.getKey()).matches() || pat.matcher(e.getValue()).matches()) {
                                matched = true;
                                txt = e.getKey() + " => " + e.getValue() + " [property]";
                                break;
                            }
                        }
                    }
                    if (!matched) {
                        Map<Displayable, Map<String, String>> linked_props = ((Displayable) dbo).getLinkedProperties();
                        if (null != linked_props) {
                            for (final Map.Entry<Displayable, Map<String, String>> e : linked_props.entrySet()) {
                                for (final Map.Entry<String, String> ee : e.getValue().entrySet()) {
                                    if (pat.matcher(ee.getKey()).matches() || pat.matcher(ee.getValue()).matches()) {
                                        matched = true;
                                        txt = ee.getKey() + " => " + e.getValue() + " [linked property]";
                                        break;
                                    }
                                }
                            }
                        }
                    }
                }
                if (!matched && dbo instanceof Tree<?>) {
                    // search Node tags
                    Node<?> root = ((Tree<?>) dbo).getRoot();
                    if (null == root)
                        continue;
                    for (final Node<?> nd : root.getSubtreeNodes()) {
                        Set<Tag> tags = nd.getTags();
                        if (null == tags)
                            continue;
                        for (final Tag tag : tags) {
                            if (pat.matcher(tag.toString()).matches()) {
                                v_obs.add(dbo);
                                v_txt.add(new StringBuilder(tag.toString()).append(" (").append(null == meaningful_title ? dbo.toString() : meaningful_title).append(')').toString());
                                v_co.add(createCoordinate((Tree<?>) dbo, nd));
                            }
                        }
                    }
                    // all added if any
                    continue;
                }
                if (!matched)
                    continue;
                // txt = txt.length() > 30 ? txt.substring(0, 27) + "..." :
                // txt;
                v_obs.add(dbo);
                v_txt.add(txt);
                v_co.add(co);
            }
            if (0 == v_obs.size()) {
                Utils.showMessage("Nothing found.");
                return;
            }
            final JPanel result = new JPanel();
            GridBagLayout gb = new GridBagLayout();
            result.setLayout(gb);
            GridBagConstraints c = new GridBagConstraints();
            c.anchor = GridBagConstraints.NORTHWEST;
            c.fill = GridBagConstraints.HORIZONTAL;
            c.insets = new Insets(5, 10, 5, 10);
            String xml = "";
            if (project.getLoader() instanceof FSLoader) {
                String path = ((FSLoader) project.getLoader()).getProjectXMLPath();
                if (null != path) {
                    xml = " [" + new File(path).getName() + "]";
                }
            }
            JLabel projectTitle = new JLabel(project.getTitle() + xml);
            gb.setConstraints(projectTitle, c);
            result.add(projectTitle);
            c.insets = new Insets(0, 0, 0, 0);
            JPanel padding = new JPanel();
            c.weightx = 1;
            gb.setConstraints(padding, c);
            result.add(padding);
            c.gridy = 1;
            c.gridwidth = 2;
            c.fill = GridBagConstraints.BOTH;
            c.weighty = 1;
            JScrollPane jsp = makeTable(new DisplayableTableModel(v_obs, v_txt, v_co), project);
            gb.setConstraints(jsp, c);
            result.add(jsp);
            search_tabs.addTab(typed_pattern, result);
            search_tabs.setSelectedComponent(result);
            synchronized (tabMap) {
                List<JPanel> cs = tabMap.get(project);
                if (null == cs) {
                    cs = new ArrayList<JPanel>();
                    tabMap.put(project, cs);
                }
                cs.add(result);
            }
        }
    }, project);
}

Example 83 with Displayable

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

the class Merger method makeGUI.

private static void makeGUI(final Project p1, final Project p2, HashSet<ZDisplayable> empty1, HashSet<ZDisplayable> empty2, HashMap<Displayable, List<Change>> matched, HashSet<ZDisplayable> unmatched1, HashSet<ZDisplayable> unmatched2) {
    final ArrayList<Row> rows = new ArrayList<Row>();
    for (Map.Entry<Displayable, List<Change>> e : matched.entrySet()) {
        for (Change c : e.getValue()) {
            rows.add(new Row(c));
        }
        if (e.getValue().size() > 1) {
            Utils.log("More than one assigned to " + e.getKey());
        }
    }
    JTabbedPane tabs = new JTabbedPane();
    final Table table = new Table();
    tabs.addTab("Matched", new JScrollPane(table));
    JTable tu1 = createTable(unmatched1, "Unmatched 1", p1, p2);
    JTable tu2 = createTable(unmatched2, "Unmatched 2", p1, p2);
    JTable tu3 = createTable(empty1, "Empty 1", p1, p2);
    JTable tu4 = createTable(empty2, "Empty 2", p1, p2);
    tabs.addTab("Unmatched 1", new JScrollPane(tu1));
    tabs.addTab("Unmatched 2", new JScrollPane(tu2));
    tabs.addTab("Empty 1", new JScrollPane(tu3));
    tabs.addTab("Empty 2", new JScrollPane(tu4));
    for (int i = 0; i < tabs.getTabCount(); i++) {
        if (null == tabs.getTabComponentAt(i)) {
            Utils.log2("null at " + i);
            continue;
        }
        tabs.getTabComponentAt(i).setPreferredSize(new Dimension(1024, 768));
    }
    String xml1 = new File(((FSLoader) p1.getLoader()).getProjectXMLPath()).getName();
    String xml2 = new File(((FSLoader) p2.getLoader()).getProjectXMLPath()).getName();
    JFrame frame = new JFrame("1: " + xml1 + "  ||  2: " + xml2);
    tabs.setPreferredSize(new Dimension(1024, 768));
    frame.getContentPane().add(tabs);
    frame.pack();
    frame.setVisible(true);
    // so the bullshit starts: any other way to set the model fails, because it tries to render it while setting it
    SwingUtilities.invokeLater(new Runnable() {

        public void run() {
            table.setModel(new Model(rows));
            CustomCellRenderer cc = new CustomCellRenderer();
            for (int i = 0; i < Row.COLUMNS; i++) {
                table.setDefaultRenderer(table.getColumnClass(i), cc);
            }
        }
    });
}

Example 84 with Displayable

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

the class AreaUtils method generateTriangles.

/**
 * Expects areas in local coordinates to the Displayable @param d.
 *  @param d
 *  @param scale The scaling of the entire universe, to limit the overall box
 *  @param resample_ The optimization parameter for marching cubes (i.e. a value of 2 will scale down to half, then apply marching cubes, then scale up by 2 the vertices coordinates).
 *  @param areas
 *  @return The List of triangles involved, specified as three consecutive vertices. A list of Point3f vertices.
 */
public static List<Point3f> generateTriangles(final Displayable d, final double scale, final int resample_, final Map<Layer, Area> areas) {
    // in the LayerSet, layers are ordered by Z already.
    try {
        int n = areas.size();
        if (0 == n)
            return null;
        final int resample;
        if (resample_ <= 0) {
            resample = 1;
            Utils.log2("Fixing zero or negative resampling value to 1.");
        } else
            resample = resample_;
        final LayerSet layer_set = d.getLayerSet();
        final AffineTransform aff = d.getAffineTransformCopy();
        final Rectangle r = d.getBoundingBox(null);
        // remove translation from a copy of the Displayable's AffineTransform
        final AffineTransform at_translate = new AffineTransform();
        at_translate.translate(-r.x, -r.y);
        aff.preConcatenate(at_translate);
        // incorporate resampling scaling into the transform
        final AffineTransform atK = new AffineTransform();
        // Utils.log("resample: " + resample + "  scale: " + scale);
        // 'scale' is there to limit gigantic universes
        final double K = (1.0 / resample) * scale;
        atK.scale(K, K);
        aff.preConcatenate(atK);
        final Calibration cal = layer_set.getCalibrationCopy();
        // Find first layer, compute depth, and fill in the depth vs area map
        Layer first_layer = null, last_layer = null;
        final int w = (int) Math.ceil(r.width * K);
        final int h = (int) Math.ceil(r.height * K);
        int depth = 0;
        final Map<Integer, Area> ma = new HashMap<Integer, Area>();
        for (final Layer la : layer_set.getLayers()) {
            // layers sorted by Z ASC
            final Area area = areas.get(la);
            if (null != area) {
                ma.put(depth, area);
                if (null == first_layer) {
                    first_layer = la;
                }
                // Utils.log("area at depth " + depth + " for layer " + la);
                depth++;
                n--;
            } else if (0 != depth) {
                // Utils.log("Empty area at depth " + depth);
                // an empty layer
                depth++;
            }
            if (0 == n) {
                last_layer = la;
                // no more areas to paint
                break;
            }
        }
        if (0 == depth) {
            Utils.log("ERROR could not find any areas for " + d);
            return null;
        }
        if (0 != n) {
            Utils.log("WARNING could not find all areas for " + d);
        }
        // No zero-padding: Marching Cubes now can handle edges
        final ShapeList<ByteType> shapeList = new ShapeListCached<ByteType>(new int[] { w, h, depth }, new ByteType(), 32);
        final Image<ByteType> shapeListImage = new Image<ByteType>(shapeList, shapeList.getBackground(), "ShapeListContainer");
        // 255 or -1 don't work !? So, giving the highest value (127) that is both a byte and an int.
        final ByteType intensity = new ByteType((byte) 127);
        for (final Map.Entry<Integer, Area> e : ma.entrySet()) {
            Area a = e.getValue();
            if (!aff.isIdentity()) {
                a = M.areaInIntsByRounding(a.createTransformedArea(aff));
            }
            shapeList.addShape(a, intensity, new int[] { e.getKey() });
        }
        // debug:
        // ImagePlus imp = ImageJFunctions.displayAsVirtualStack(shapeListImage);
        // imp.getProcessor().setMinAndMax( 0, 255 );
        // imp.show();
        // Utils.log2("Using imglib Shape List Image Container");
        // Now marching cubes
        // origins at 0,0,0: uncalibrated
        final List<Point3f> list = new MCTriangulator().getTriangles(shapeListImage, 1, new float[3]);
        // The list of triangles has coordinates:
        // - in x,y: in pixels, scaled by K = (1 / resample) * scale,
        // translated by r.x, r.y (the top-left coordinate of this AreaList bounding box)
        // - in z: in stack slice indices
        // So all x,y,z must be corrected in x,y and z of the proper layer
        // final double offset = first_layer.getZ();
        final int i_first_layer = layer_set.indexOf(first_layer);
        // The x,y translation to correct each point by:
        final float dx = (float) (r.x * scale * cal.pixelWidth);
        final float dy = (float) (r.y * scale * cal.pixelHeight);
        // Correct x,y by resampling and calibration, but not scale
        // scale is already in the pixel coordinates
        final float rsw = (float) (resample * cal.pixelWidth);
        final float rsh = (float) (resample * cal.pixelHeight);
        // no resampling in Z. and Uses pixelWidth, not pixelDepth.
        final double sz = scale * cal.pixelWidth;
        // debug:
        /*
			// which p.z types exist?
			final TreeSet<Float> ts = new TreeSet<Float>();
			for (final Iterator it = list.iterator(); it.hasNext(); ) {
				ts.add(((Point3f)it.next()).z);
			}
			for (final Float pz : ts) Utils.log2("A z: " + pz);
			*/
        // debug: How many different Z?
        /*
			HashSet<Float> zs = new HashSet<Float>();
			for (Point3f p : list) {
				zs.add(p.z);
			}
			ArrayList<Float> a = new ArrayList<Float>(zs);
			java.util.Collections.sort(a);
			for (Float f : a) {
				Utils.log("f: " + f);
			}
			*/
        // Utils.log2("Number of slices: " + imp.getNSlices());
        // Fix all points:
        // Read from list, modify and put into verts
        // and don't modify it if the verts already has it (it's just coincident)
        final Point3f[] verts = new Point3f[list.size()];
        // Utils.log("number of verts: " + verts.length + " mod 3: " + (verts.length % 3));
        final TreeMap<Integer, Point3f> output = new TreeMap<Integer, Point3f>();
        // The first section generates vertices at -1 and 0
        // The last section generates them at last_section_index and last_section_index +1
        // Capture from -1 to 0
        fix3DPoints(list, output, verts, first_layer.getZ(), 0, -1, dx, dy, rsw, rsh, sz, 1);
        int slice_index = 0;
        for (final Layer la : layer_set.getLayers().subList(i_first_layer, i_first_layer + depth)) {
            // If layer is empty, continue
            /* // YEAH don't! At least the immediate next layer would have points, like the extra Z level after last layer, to account for the thickness of the layer!
				if (empty_layers.contains(la)) {
					slice_index++;
					continue;
				}
				*/
            fix3DPoints(list, output, verts, la.getZ(), la.getThickness(), slice_index, dx, dy, rsw, rsh, sz, 1);
            slice_index++;
        }
        // Do the last layer again. The last layer has two Z planes in which it has pixels:
        try {
            // Capture from last_section_index to last_section_index+1, inclusive
            fix3DPoints(list, output, verts, last_layer.getZ() + last_layer.getThickness(), 0, slice_index, dx, dy, rsw, rsh, sz, 2);
        } catch (final Exception ee) {
            IJError.print(ee);
        }
        // Handle potential errors:
        if (0 != list.size() - output.size()) {
            Utils.log2("Unprocessed/unused points: " + (list.size() - output.size()));
            for (int i = 0; i < verts.length; i++) {
                if (null == verts[i]) {
                    final Point3f p = (Point3f) list.get(i);
                    Utils.log2("verts[" + i + "] = " + p.x + ", " + p.y + ", " + p.z + "  p.z as int: " + ((int) (p.z + 0.05f)));
                }
            }
            return new ArrayList<Point3f>(output.values());
        } else {
            return java.util.Arrays.asList(verts);
        }
    } catch (final Exception e) {
        e.printStackTrace();
    }
    return null;
}

Example 85 with Displayable

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

the class StitchingTEM method montageWithPhaseCorrelation.

/**
 * @param layers
 * @param worker Optional, the {@link Worker} running this task.
 */
public static void montageWithPhaseCorrelation(final List<Layer> layers, final Worker worker) {
    final PhaseCorrelationParam param = new PhaseCorrelationParam();
    final Collection<Displayable> col = layers.get(0).getDisplayables(Patch.class);
    if (!param.setup(col.size() > 0 ? (Patch) col.iterator().next() : null)) {
        return;
    }
    final int i = 1;
    for (final Layer la : layers) {
        if (Thread.currentThread().isInterrupted() || (null != worker && worker.hasQuitted()))
            return;
        if (null != worker)
            worker.setTaskName("Montage layer " + i + "/" + layers.size());
        final Collection<Patch> patches = (Collection<Patch>) (Collection) la.getDisplayables(Patch.class);
        AlignTask.transformPatchesAndVectorData(patches, new Runnable() {

            @Override
            public void run() {
                montageWithPhaseCorrelation(patches, param);
            }
        });
    }
}