Examples with VectorString3D ini.trakem2.vector.VectorString3D used on opensource projects

Example 1 with VectorString3D

use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.

the class Pipe method measure.

/*
	// debug ---------------
	static private void showShape(final Shape shape) {
		Area area = new Area(shape);
		Rectangle b = area.getBounds();
		AffineTransform trans = new AffineTransform();
		trans.translate(-b.x, -b.y);
		area = area.createTransformedArea(trans);
		ij.process.ByteProcessor bp = new ij.process.ByteProcessor(b.width, b.height);
		ij.gui.ShapeRoi sr = new ij.gui.ShapeRoi(area);
		ij.ImagePlus imp = new ij.ImagePlus("pipe area", bp);
		imp.setRoi(sr);
		bp.setValue(255);
		sr.drawPixels(bp);
		imp.show();
	}
	*/
@Override
public ResultsTable measure(ResultsTable rt) {
    // reload
    if (-1 == n_points)
        setupForDisplay();
    if (0 == n_points)
        return rt;
    if (null == rt)
        rt = Utils.createResultsTable("Pipe results", new String[] { "id", "length", "name-id" });
    // measure length
    double len = 0;
    final Calibration cal = layer_set.getCalibration();
    if (n_points > 1) {
        final VectorString3D vs = asVectorString3D();
        vs.calibrate(cal);
        // no resampling
        len = vs.computeLength();
    }
    rt.incrementCounter();
    rt.addLabel("units", cal.getUnit());
    rt.addValue(0, this.id);
    rt.addValue(1, len);
    rt.addValue(2, getNameId());
    return rt;
}

Example 2 with VectorString3D

use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.

the class Pipe method asVectorString3D.

/**
 * Returns a non-calibrated VectorString3D.
 */
@Override
public synchronized VectorString3D asVectorString3D() {
    // local pointers, since they may be transformed
    int n_points = this.n_points;
    double[][] p = this.p;
    // double[][] p_r = this.p_r;
    // double[][] p_l = this.p_l;
    double[][] p_i = this.p_i;
    // double[] p_width = this.p_width;
    double[] p_width_i = this.p_width_i;
    if (!this.at.isIdentity()) {
        final Object[] ob = getTransformedData();
        p = (double[][]) ob[0];
        n_points = p[0].length;
        // p_l = (double[][])ob[1];
        // p_r = (double[][])ob[2];
        p_i = (double[][]) ob[3];
        // p_width = (double[])ob[4];
        p_width_i = (double[]) ob[5];
    }
    final int n = p_i[0].length;
    final int mm = n_points;
    final double[] z_values = new double[n];
    final int interval_points = n / (mm - 1);
    double z_val = 0;
    double z_val_next = 0;
    double z_diff = 0;
    int c = 0;
    double delta = 0;
    for (int j = 0; j < mm - 1; j++) {
        z_val = layer_set.getLayer(p_layer[j]).getZ();
        z_val_next = layer_set.getLayer(p_layer[j + 1]).getZ();
        z_diff = z_val_next - z_val;
        delta = z_diff / interval_points;
        z_values[c] = (0 == j ? z_val : z_values[c - 1]) + delta;
        for (int k = 1; k < interval_points; k++) {
            c++;
            z_values[c] = z_values[c - 1] + delta;
        }
        c++;
    }
    // setting last point
    z_values[n - 1] = layer_set.getLayer(p_layer[mm - 1]).getZ();
    final double[] px = p_i[0];
    final double[] py = p_i[1];
    final double[] pz = z_values;
    VectorString3D vs = null;
    try {
        vs = new VectorString3D(px, py, pz, false);
        vs.addDependent(p_width_i);
    } catch (final Exception e) {
        IJError.print(e);
    }
    return vs;
}

Example 3 with VectorString3D

use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.

the class Polyline method asVectorString3D.

/**
 * Returns a non-calibrated VectorString3D.
 */
@Override
public synchronized VectorString3D asVectorString3D() {
    // local pointers, since they may be transformed
    int n_points = this.n_points;
    double[][] p = this.p;
    if (!this.at.isIdentity()) {
        final Object[] ob = getTransformedData();
        p = (double[][]) ob[0];
        n_points = p[0].length;
    }
    final double[] z_values = new double[n_points];
    for (int i = 0; i < n_points; i++) {
        z_values[i] = layer_set.getLayer(p_layer[i]).getZ();
    }
    final double[] px = p[0];
    final double[] py = p[1];
    final double[] pz = z_values;
    VectorString3D vs = null;
    try {
        vs = new VectorString3D(px, py, pz, false);
    } catch (final Exception e) {
        IJError.print(e);
    }
    return vs;
}

Example 4 with VectorString3D

use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.

the class Compare method variabilityAnalysis.

/**
 * @param reference_project If null, then the first one found in the Project.getProjects() lists is used.
 * @param regex A String (can be null) to filter objects by, to limit what gets processed.
 *              If regex is not null, then only ProjectThing nodes with the matching regex are analyzed (shallow: none of their children are questioned, but pipes will be built from them all).
 * @param generate_plots Whether to generate the variability plots at all.
 * @param show_plots If generate_plots, whether to show the plots in a stack image window or to save them.
 * @param show_3D Whether to show any 3D data.
 * @param show_condensed_3D If show_3D, whether to show the condensed vector strings, i.e. the "average" pipes.
 * @param show_sources_3D If show_3D, whether to show the source pipes from which the condensed vector string was generated.
 * @param sources_color_table Which colors to give to the pipes of which Project.
 * @param show_envelope_3D If show_3D, whether to generate the variability envelope.
 * @param envelope_alpha If show_envelope_3D, the envelope takes an alpha value between 0 (total transparency) and 1 (total opacity)
 * @param delta_envelope The delta to resample the envelope to. When smaller than or equal to 1, no envelope resampling occurs.
 * @param show_axes_3D If show_3D, whether to display the reference axes as well.
 * @param heat_map If show_3D, whether to color the variability with a Fire LUT.
 *                 If not show_condensed_3D, then the variability is shown in color-coded 3D spheres placed at the entry point to the neuropile.
 * @param map_condensed If not null, all VectorString3D are put into this map.
 * @param projects The projects to use.
 */
public static Bureaucrat variabilityAnalysis(final Project reference_project, final String regex, final String[] ignore, final boolean show_cata_dialog, final boolean generate_plots, final boolean show_plots, final String plot_dir_, final boolean show_3D, final boolean show_condensed_3D, final boolean show_sources_3D, final Map<Project, Color> sources_color_table, final boolean show_envelope_3D, final float envelope_alpha, final double delta_envelope, final int envelope_type, final boolean show_axes_3D, final boolean heat_map, final Map<String, VectorString3D> map_condensed, final Project[] projects) {
    // gather all open projects
    final Project[] p = null == projects ? Project.getProjects().toArray(new Project[0]) : projects;
    // make the reference_project be the first in the array
    if (null != reference_project && reference_project != p[0]) {
        for (int i = 0; i < p.length; i++) {
            if (reference_project == p[i]) {
                p[i] = p[0];
                p[0] = reference_project;
                break;
            }
        }
    }
    final Worker worker = new Worker("Comparing all to all") {

        @Override
        public void run() {
            startedWorking();
            try {
                Utils.log2("Asking for CATAParameters...");
                final CATAParameters cp = new CATAParameters();
                cp.regex = regex;
                cp.delta_envelope = delta_envelope;
                cp.envelope_type = envelope_type;
                if (show_cata_dialog && !cp.setup(false, regex, true, true)) {
                    finishedWorking();
                    return;
                }
                // so source points are stored in VectorString3D for each resampled and interpolated point
                cp.with_source = true;
                // Store a series of results, depending on options
                final HashMap<String, Display3D> results = new HashMap<String, Display3D>();
                String plot_dir = plot_dir_;
                if (generate_plots && !show_plots) {
                    // Save plots
                    if (null == plot_dir) {
                        final DirectoryChooser dc = new DirectoryChooser("Choose plots directory");
                        plot_dir = dc.getDirectory();
                        if (null == plot_dir) {
                            finishedWorking();
                            return;
                        }
                    }
                    if (IJ.isWindows())
                        plot_dir = plot_dir.replace('\\', '/');
                    if (!plot_dir.endsWith("/"))
                        plot_dir += "/";
                }
                Utils.log2("Gathering chains...");
                // Gather chains that do not match the ignore regexes
                // will transform them as well to the reference found in the first project in the p array
                Object[] ob = gatherChains(p, cp, ignore);
                ArrayList<Chain> chains = (ArrayList<Chain>) ob[0];
                // to keep track of each project's chains
                final ArrayList[] p_chains = (ArrayList[]) ob[1];
                ob = null;
                if (null == chains) {
                    finishedWorking();
                    return;
                }
                Utils.log2("Collecting bundles...");
                final HashMap<Project, HashMap<String, VectorString3D>> axes = new HashMap<Project, HashMap<String, VectorString3D>>();
                // Sort out into groups by unique names of lineage bundles
                final HashMap<String, ArrayList<Chain>> bundles = new HashMap<String, ArrayList<Chain>>();
                for (final Chain chain : chains) {
                    String title = chain.getCellTitle();
                    final String t = title.toLowerCase();
                    // unnamed
                    if (0 == t.indexOf('[') || 0 == t.indexOf('#'))
                        continue;
                    Utils.log("Accepting " + title);
                    title = title.substring(0, title.indexOf(' '));
                    // lineage bundle instance chains
                    ArrayList<Chain> bc = bundles.get(title);
                    if (null == bc) {
                        bc = new ArrayList<Chain>();
                        bundles.put(title, bc);
                    }
                    bc.add(chain);
                }
                Utils.log2("Found " + bundles.size() + " bundles.");
                chains = null;
                if (null != cp.regex && show_axes_3D && axes.size() < 3) {
                    // Must find the Mushroom Body lobes separately
                    final String cp_regex = cp.regex;
                    cp.regex = "mb";
                    final Object[] o = gatherChains(p, cp, ignore);
                    final ArrayList<Chain> lobes = (ArrayList<Chain>) o[0];
                    Utils.logAll("Found " + lobes.size() + " chains for lobes");
                    for (final Chain chain : lobes) {
                        final String t = chain.getCellTitle().toLowerCase();
                        if (-1 != t.indexOf("peduncle") || -1 != t.indexOf("medial lobe") || -1 != t.indexOf("dorsal lobe")) {
                            Utils.logAll("adding " + t);
                            final Project pr = chain.pipes.get(0).getProject();
                            HashMap<String, VectorString3D> m = axes.get(pr);
                            if (null == m) {
                                m = new HashMap<String, VectorString3D>();
                                axes.put(pr, m);
                            }
                            m.put(t, chain.vs);
                            continue;
                        }
                    }
                    cp.regex = cp_regex;
                } else {
                    Utils.logAll("Not: cp.regex = " + cp.regex + "  show_axes_3D = " + show_axes_3D + "  axes.size() = " + axes.size());
                }
                final HashMap<String, VectorString3D> condensed = new HashMap<String, VectorString3D>();
                Utils.log2("Condensing each bundle...");
                // Condense each into a single VectorString3D
                for (final Map.Entry<String, ArrayList<Chain>> entry : bundles.entrySet()) {
                    final ArrayList<Chain> bc = entry.getValue();
                    if (bc.size() < 2) {
                        Utils.log2("Skipping single: " + entry.getKey());
                        continue;
                    }
                    final VectorString3D[] vs = new VectorString3D[bc.size()];
                    for (int i = 0; i < vs.length; i++) vs[i] = bc.get(i).vs;
                    final VectorString3D c = condense(cp, vs, this);
                    c.setCalibration(p[0].getRootLayerSet().getCalibrationCopy());
                    condensed.put(entry.getKey(), c);
                    if (this.hasQuitted())
                        return;
                }
                // Store:
                if (null != map_condensed) {
                    map_condensed.putAll(condensed);
                }
                if (generate_plots) {
                    Utils.log2("Plotting stdDev for each condensed bundle...");
                    // Y axis: the stdDev at each point, computed from the group of points that contribute to each
                    for (final Map.Entry<String, VectorString3D> e : condensed.entrySet()) {
                        final String name = e.getKey();
                        final VectorString3D c = e.getValue();
                        final Plot plot = makePlot(cp, name, c);
                        // FAILS//plot.addLabel(10, cp.plot_height-5, name); // must be added after setting size
                        if (show_plots)
                            plot.show();
                        else if (null != plot_dir)
                            new FileSaver(plot.getImagePlus()).saveAsPng(plot_dir + name.replace('/', '-') + ".png");
                    }
                }
                if (show_3D) {
                    final HashMap<String, Color> heat_table = new HashMap<String, Color>();
                    if (heat_map || show_envelope_3D) {
                        // Create a Fire LUT
                        final ImagePlus lutimp = new ImagePlus("lut", new ByteProcessor(4, 4));
                        IJ.run(lutimp, "Fire", "");
                        final IndexColorModel icm = (IndexColorModel) lutimp.getProcessor().getColorModel();
                        final byte[] reds = new byte[256];
                        final byte[] greens = new byte[256];
                        final byte[] blues = new byte[256];
                        icm.getReds(reds);
                        icm.getGreens(greens);
                        icm.getBlues(blues);
                        final List<String> names = new ArrayList<String>(bundles.keySet());
                        Collections.sort(names);
                        // find max stdDev
                        double max = 0;
                        final HashMap<String, Double> heats = new HashMap<String, Double>();
                        for (final String name : names) {
                            final VectorString3D vs_merged = condensed.get(name);
                            if (null == vs_merged) {
                                Utils.logAll("WARNING could not find a condensed pipe for " + name);
                                continue;
                            }
                            final double[] stdDev = vs_merged.getStdDevAtEachPoint();
                            // double avg = 0;
                            // for (int i=0; i<stdDev.length; i++) avg += stdDev[i];
                            // avg = avg/stdDev.length;
                            Arrays.sort(stdDev);
                            // median is more representative than average
                            final double median = stdDev[stdDev.length / 2];
                            if (max < median)
                                max = median;
                            heats.put(name, median);
                        }
                        for (final Map.Entry<String, Double> e : heats.entrySet()) {
                            final String name = e.getKey();
                            final double median = e.getValue();
                            // scale between 0 and max to get a Fire LUT color:
                            int index = (int) ((median / max) * 255);
                            if (index > 255)
                                index = 255;
                            final Color color = new Color(0xff & reds[index], 0xff & greens[index], 0xff & blues[index]);
                            Utils.log2(new StringBuilder(name).append('\t').append(median).append('\t').append(reds[index]).append('\t').append(greens[index]).append('\t').append(blues[index]).toString());
                            heat_table.put(name, color);
                        }
                    }
                    final LayerSet common_ls = new LayerSet(p[0], -1, "Common", 10, 10, 0, 0, 0, 512, 512, false, 2, new AffineTransform());
                    final Display3D d3d = Display3D.get(common_ls);
                    float env_alpha = envelope_alpha;
                    if (env_alpha < 0) {
                        Utils.log2("WARNING envelope_alpha is invalid: " + envelope_alpha + "\n    Using 0.4f instead");
                        env_alpha = 0.4f;
                    } else if (env_alpha > 1)
                        env_alpha = 1.0f;
                    for (final String name : bundles.keySet()) {
                        final ArrayList<Chain> bc = bundles.get(name);
                        final VectorString3D vs_merged = condensed.get(name);
                        if (null == vs_merged) {
                            Utils.logAll("WARNING: could not find a condensed vs for " + name);
                            continue;
                        }
                        if (show_sources_3D) {
                            if (null != sources_color_table) {
                                final HashSet<String> titles = new HashSet<String>();
                                for (final Chain chain : bc) {
                                    final Color c = sources_color_table.get(chain.getRoot().getProject());
                                    final String title = chain.getCellTitle();
                                    String t = title;
                                    int i = 2;
                                    while (titles.contains(t)) {
                                        t = title + "-" + i;
                                        i += 1;
                                    }
                                    titles.add(t);
                                    Display3D.addMesh(common_ls, chain.vs, t, null != c ? c : Color.gray);
                                }
                            } else {
                                for (final Chain chain : bc) Display3D.addMesh(common_ls, chain.vs, chain.getCellTitle(), Color.gray);
                            }
                        }
                        if (show_condensed_3D) {
                            Display3D.addMesh(common_ls, vs_merged, name + "-condensed", heat_map ? heat_table.get(name) : Color.red);
                        }
                        if (show_envelope_3D) {
                            double[] widths = makeEnvelope(cp, vs_merged);
                            if (cp.delta_envelope > 1) {
                                vs_merged.addDependent(widths);
                                vs_merged.resample(cp.delta_envelope);
                                widths = vs_merged.getDependent(0);
                            }
                            Display3D.addMesh(common_ls, vs_merged, name + "-envelope", heat_map ? heat_table.get(name) : Color.red, widths, env_alpha);
                        } else if (heat_map) {
                            // Show spheres in place of envelopes, at the starting tip (neuropile entry point)
                            final double x = vs_merged.getPoints(0)[0];
                            final double y = vs_merged.getPoints(1)[0];
                            final double z = vs_merged.getPoints(2)[0];
                            final double r = 10;
                            final Color color = heat_table.get(name);
                            if (null == color) {
                                Utils.logAll("WARNING: heat table does not have a color for " + name);
                                continue;
                            }
                            final Content sphere = d3d.getUniverse().addMesh(ij3d.Mesh_Maker.createSphere(x, y, z, r), new Color3f(heat_table.get(name)), name + "-sphere", 1);
                        }
                    }
                    if (show_axes_3D) {
                        for (int i = 0; i < p.length; i++) {
                            final Map<String, VectorString3D> m = axes.get(p[i]);
                            if (null == m) {
                                Utils.log2("No axes found for project " + p[i]);
                                continue;
                            }
                            for (final Map.Entry<String, VectorString3D> e : m.entrySet()) {
                                Display3D.addMesh(common_ls, e.getValue(), e.getKey() + "-" + i, Color.gray);
                            }
                        }
                    }
                    results.put("d3d", Display3D.get(common_ls));
                }
                this.result = results;
                Utils.log2("Done.");
            } catch (final Exception e) {
                IJError.print(e);
            } finally {
                finishedWorking();
            }
        }
    };
    return Bureaucrat.createAndStart(worker, p[0]);
}

Example 5 with VectorString3D

use of ini.trakem2.vector.VectorString3D in project TrakEM2 by trakem2.

the class Compare method transferVectorStrings.

/**
 * Transform all points of all VectorString3D in vs using a Moving Least Squares Transform defined by the pairing of points in source to those in target.
 *  In short, bring source into target.
 */
public static List<VectorString3D> transferVectorStrings(final List<VectorString3D> vs, final List<Tuple3d> source, final List<Tuple3d> target, final Class<AffineModel3D> model_class) throws Exception {
    if (source.size() != target.size()) {
        Utils.log2("Could not generate a MovingLeastSquaresTransform: different number of source and target points.");
        return null;
    }
    if (source.size() < 1 || target.size() < 1) {
        Utils.log2("Cannot transform with less than one point correspondence!");
        return null;
    }
    // 1 - Create the MovingLeastSquaresTransform from the point matches
    final ArrayList<PointMatch> pm = new ArrayList<PointMatch>();
    for (final Iterator<Tuple3d> si = source.iterator(), ti = target.iterator(); si.hasNext(); ) {
        final Tuple3d sp = si.next();
        final Tuple3d tp = ti.next();
        pm.add(new PointMatch(new mpicbg.models.Point(new double[] { sp.x, sp.y, sp.z }), new mpicbg.models.Point(new double[] { tp.x, tp.y, tp.z }), 1));
    }
    final MovingLeastSquaresTransform mls = new MovingLeastSquaresTransform();
    mls.setModel(model_class);
    mls.setMatches(pm);
    final double[] point = new double[3];
    // 1.1 - Test: transfer source points
    /*
		for (final Iterator<Tuple3d> si = source.iterator(), ti = target.iterator(); si.hasNext(); ) {
			Tuple3d sp = si.next();
			point[0] = (double) sp.x;
			point[1] = (double) sp.y;
			point[2] = (double) sp.z;
			mls.applyInPlace(point);

			Tuple3d tp = ti.next();
			Utils.log2("== target: " + (double)tp.x + ", " + (double)tp.y + ", " + (double)tp.z +
				   "\n o source: " + (double)sp.x + ", " + (double)sp.y + ", " + (double)sp.z +

				   "\n   source: " + point[0] + ", " + point[1] + ", " + point[2]);
		}
		*/
    // 2 - Transfer each VectorString3D in vs with mls
    final List<VectorString3D> vt = new ArrayList<VectorString3D>();
    for (final VectorString3D vi : vs) {
        // The points of the VectorString3D:
        final double[] x = vi.getPoints(0);
        final double[] y = vi.getPoints(1);
        final double[] z = vi.getPoints(2);
        // Empty arrays to fill with the points to transfer:
        final double[] tx = new double[x.length];
        final double[] ty = new double[x.length];
        final double[] tz = new double[x.length];
        // Transfer point by point:
        for (int i = 0; i < x.length; i++) {
            point[0] = x[i];
            point[1] = y[i];
            point[2] = z[i];
            mls.applyInPlace(point);
            tx[i] = point[0];
            ty[i] = point[1];
            tz[i] = point[2];
        }
        try {
            vt.add(new VectorString3D(tx, ty, tz, vi.isClosed()));
        } catch (final Exception e) {
        }
    }
    return vt;
}