Examples with ProjectThing ini.trakem2.tree.ProjectThing used on opensource projects

Example 26 with ProjectThing

use of ini.trakem2.tree.ProjectThing in project TrakEM2 by trakem2.

the class ProjectTree method selectInDisplay.

public void selectInDisplay(final ProjectThing thing, final boolean shift_down) {
    Object obd = thing.getObject();
    if (obd instanceof Displayable) {
        Displayable d = (Displayable) obd;
        if (!d.isVisible())
            d.setVisible(true);
        Display display = Display.getFront(d.getProject());
        if (null == display)
            return;
        display.select(d, shift_down);
    } else {
        // select all basic types under this leaf
        final List<Displayable> ds = thing.findChildrenOfType(Displayable.class);
        Display display = null;
        for (final Iterator<Displayable> it = ds.iterator(); it.hasNext(); ) {
            final Displayable d = it.next();
            if (null == display) {
                display = Display.getFront(d.getProject());
                if (null == display)
                    return;
            }
            if (!d.isVisible()) {
                Utils.log("Skipping non-visible object " + d);
                it.remove();
            }
        }
        if (null == display)
            return;
        if (!shift_down)
            display.getSelection().clear();
        display.getSelection().selectAll(ds);
    }
}

Example 27 with ProjectThing

use of ini.trakem2.tree.ProjectThing 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 28 with ProjectThing

use of ini.trakem2.tree.ProjectThing 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 29 with ProjectThing

use of ini.trakem2.tree.ProjectThing in project TrakEM2 by trakem2.

the class Compare method appendAndFork.

/**
 * Recursive.
 */
private static void appendAndFork(final ProjectThing parent, Chain chain, HashSet<ProjectThing> hs_c_done, final ArrayList<Chain> chains, final LayerSet ls, final Pattern exclude) throws Exception {
    if (null != exclude && exclude.matcher(parent.getTitle()).matches()) {
        Utils.logAll("Excluding node " + parent + " with title " + parent.getTitle() + ", and all its children nodes.");
        return;
    }
    final ArrayList<ProjectThing> children = parent.getChildren();
    if (null == children)
        return;
    if (null == hs_c_done)
        hs_c_done = new HashSet<ProjectThing>();
    for (final ProjectThing child : children) {
        if (hs_c_done.contains(child))
            continue;
        if (null != exclude && exclude.matcher(child.getTitle()).matches()) {
            Utils.log2("Excluding child " + child + " with title " + child.getTitle());
            continue;
        }
        hs_c_done.add(child);
        if (child.getObject() instanceof Line3D) {
            final Line3D pipe = (Line3D) child.getObject();
            // not from the same LayerSet, maybe from a nested one.
            if (!pipe.getLayerSet().equals(ls) || pipe.length() < 2)
                continue;
            if (null == chain) {
                chain = new Chain(pipe);
                chains.add(chain);
            } else {
                chain.append(pipe);
            }
            // find other children in the parent who contain children with child pipes
            boolean first = true;
            final Chain base = chain.duplicate();
            for (final ProjectThing c : children) {
                // already visited
                if (hs_c_done.contains(c))
                    continue;
                // c is at the same tree level as child (which contains a pipe directly)
                final ArrayList<Line3D> child_pipes = c.findChildrenOfType(Line3D.class);
                if (child_pipes.size() > 0) {
                    Chain ca;
                    if (first) {
                        // just append
                        ca = chain;
                        first = false;
                    } else {
                        // otherwise make a copy to branch out
                        // can't duplicate from chain itself, because it would have the previous child added to it.
                        ca = base.duplicate();
                        chains.add(ca);
                    }
                    appendAndFork(c, ca, hs_c_done, chains, ls, exclude);
                }
            }
            // pipe wrapping ProjectThing objects cannot have any children
            continue;
        }
        // if it does not have direct pipe children, cut chain - but keep inspecting
        if (0 == child.findChildrenOfType(Line3D.class).size()) {
            chain = null;
        }
        // inspect others down the unvisited tree nodes
        appendAndFork(child, chain, hs_c_done, chains, ls, exclude);
    }
}

Example 30 with ProjectThing

use of ini.trakem2.tree.ProjectThing in project TrakEM2 by trakem2.

the class Compare method gatherChains.

/**
 * Gather chains for all projects considering the cp.regex, and transforms all relative to the reference Project p[0].
 *  Will ignore any for which a match exists in @param ignore.
 */
public static final Object[] gatherChains(final Project[] p, final CATAParameters cp, final String[] ignore) throws Exception {
    String regex_exclude = null;
    if (null != ignore) {
        final StringBuilder sb = new StringBuilder();
        for (final String ig : ignore) {
            sb.append("(.*").append(ig).append(".*)|");
        }
        sb.setLength(sb.length() - 1);
        regex_exclude = sb.toString();
    }
    Utils.logAll("Compare/gatherChains: using ignore string: " + regex_exclude);
    Utils.logAll("Compare/gatherChains: using regex: " + cp.regex);
    // gather all chains
    // to keep track of each project's chains
    final ArrayList[] p_chains = new ArrayList[p.length];
    final ArrayList<Chain> chains = new ArrayList<Chain>();
    for (int i = 0; i < p.length; i++) {
        // for each project:
        if (null == cp.regex) {
            p_chains[i] = createPipeChains(p[i].getRootProjectThing(), p[i].getRootLayerSet(), regex_exclude);
        } else {
            // Search (shallow) for cp.regex matches
            for (final ProjectThing pt : p[i].getRootProjectThing().findChildren(cp.regex, regex_exclude, true)) {
                final ArrayList<Chain> ac = createPipeChains(pt, p[i].getRootLayerSet(), regex_exclude);
                if (null == p_chains[i])
                    p_chains[i] = ac;
                else
                    p_chains[i].addAll(ac);
            }
            // empty
            if (null == p_chains[i])
                p_chains[i] = new ArrayList<Chain>();
        }
        chains.addAll(p_chains[i]);
        // calibrate
        final Calibration cal = p[i].getRootLayerSet().getCalibrationCopy();
        for (final Chain chain : (ArrayList<Chain>) p_chains[i]) chain.vs.calibrate(cal);
    }
    final int n_chains = chains.size();
    // register all, or relative
    if (4 == cp.transform_type) {
        // compute global average delta
        if (0 == cp.delta) {
            for (final Chain chain : chains) {
                cp.delta += (chain.vs.getAverageDelta() / n_chains);
            }
        }
        Utils.log2("Using delta: " + cp.delta);
        for (final Chain chain : chains) {
            // BEFORE making it relative
            chain.vs.resample(cp.delta, cp.with_source);
            chain.vs.relative();
        }
    } else {
        if (3 == cp.transform_type) {
            // '3' means moving least squares computed from 3D landmarks
            Utils.log2("Moving Least Squares Registration based on common fiducial points");
            // Find fiducial points, if any
            final HashMap<Project, Map<String, Tuple3d>> fiducials = new HashMap<Project, Map<String, Tuple3d>>();
            for (final Project pr : p) {
                final Set<ProjectThing> fids = pr.getRootProjectThing().findChildrenOfTypeR("fiducial_points");
                if (null == fids || 0 == fids.size()) {
                    Utils.log("No fiducial points found in project: " + pr);
                } else {
                    // the first fiducial group
                    fiducials.put(pr, Compare.extractPoints(fids.iterator().next()));
                }
            }
            if (!fiducials.isEmpty()) {
                // Register all VectorString3D relative to the first project:
                final List<VectorString3D> lvs = new ArrayList<VectorString3D>();
                final Calibration cal2 = p[0].getRootLayerSet().getCalibrationCopy();
                for (final Chain chain : chains) {
                    final Project pr = chain.pipes.get(0).getProject();
                    // first project is reference, no need to transform.
                    if (pr == p[0])
                        continue;
                    lvs.clear();
                    lvs.add(chain.vs);
                    chain.vs = transferVectorStrings(lvs, fiducials.get(pr), fiducials.get(p[0])).get(0);
                    // Set (but do not apply!) the calibration of the reference project
                    chain.vs.setCalibration(cal2);
                }
            }
        } else if (cp.transform_type < 3) {
            // '0', '1' and '2' involve a 3D affine computed from the 3 axes
            // no need //VectorString3D[][] vs_axes = new VectorString3D[p.length][];
            Vector3d[][] o = new Vector3d[p.length][];
            for (int i = 0; i < p.length; i++) {
                // 1 - find pipes to work as axes for each project
                final ArrayList<ZDisplayable> pipes = p[i].getRootLayerSet().getZDisplayables(Line3D.class, true);
                final String[] pipe_names = new String[pipes.size()];
                for (int k = 0; k < pipes.size(); k++) {
                    pipe_names[k] = p[i].getMeaningfulTitle(pipes.get(k));
                }
                final int[] s = findFirstXYZAxes(cp.preset, pipes, pipe_names);
                // if axes are -1, forget it: not found
                if (-1 == s[0] || -1 == s[1] || -1 == s[2]) {
                    Utils.log("Can't find axes for project " + p[i]);
                    o = null;
                    return null;
                }
                // obtain axes and origin
                final Object[] pack = obtainOrigin(new Line3D[] { (Line3D) pipes.get(s[0]), (Line3D) pipes.get(s[1]), (Line3D) pipes.get(s[2]) }, cp.transform_type, // will be null for the first, which will then be non-null and act as the reference for the others.
                o[0]);
                // no need //vs_axes[i] = (VectorString3D[])pack[0];
                o[i] = (Vector3d[]) pack[1];
            }
            /* // OLD WAY
				// match the scales to make the largest be 1.0
				final double scaling_factor = VectorString3D.matchOrigins(o, transform_type);
				Utils.log2("matchOrigins scaling factor: " + scaling_factor + " for transform_type " + transform_type);
				*/
            // transform all except the first (which acts as reference)
            final Transform3D M_ref = Compare.createTransform(o[0]);
            for (int i = 1; i < p.length; i++) {
                final Vector3d trans = new Vector3d(-o[i][3].x, -o[i][3].y, -o[i][3].z);
                final Transform3D M_query = Compare.createTransform(o[i]);
                // The transfer T transform: from query space to reference space.
                final Transform3D T = new Transform3D(M_ref);
                T.mulInverse(M_query);
                for (final Chain chain : (ArrayList<Chain>) p_chains[i]) {
                    // in place
                    chain.vs.transform(T);
                }
            }
        }
        // compute global average delta, after correcting calibration and transformation
        if (0 == cp.delta) {
            for (final Chain chain : chains) {
                cp.delta += (chain.vs.getAverageDelta() / n_chains);
            }
        }
        Utils.log2("Using delta: " + cp.delta);
        // After calibration and transformation, resample all to the same delta
        for (final Chain chain : chains) chain.vs.resample(cp.delta, cp.with_source);
    }
    return new Object[] { chains, p_chains };
}