Examples with Project ini.trakem2.Project used on opensource projects

Example 21 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class Util method serializeFeatures.

/**
 * Save a {@link Collection} of {@link Feature Features} to the TrakEM2
 * project folder.  The saved file contains a key {@link Object} which
 * may specify the properties of the {@link Feature} {@link Collection}.
 *
 * @param project
 * @param key
 * @param prefix
 * @param id
 * @param f
 * @return
 */
public static final boolean serializeFeatures(final Project project, final Object key, final String prefix, final long id, final Collection<Feature> f) {
    final ArrayList<Feature> list = new ArrayList<Feature>();
    list.addAll(f);
    final String name = prefix == null ? "features" : prefix + ".features";
    final Loader loader = project.getLoader();
    final Features fe = new Features(key, list);
    return loader.serialize(fe, new StringBuilder(loader.getUNUIdFolder()).append("features.ser/").append(FSLoader.createIdPath(Long.toString(id), name, ".ser")).toString());
}

Example 22 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class Util method serializePointMatches.

/**
 * Save a {@link Collection} of {@link PointMatch PointMatches} two-sided.
 * Creates two serialization files which is desperately required to clean
 * up properly invalid serializations on change of a {@link Patch}.
 *
 * @param project
 * @param key
 * @param prefix
 * @param id1
 * @param id2
 * @param m
 * @return
 */
public static final boolean serializePointMatches(final Project project, final Object key, final String prefix, final long id1, final long id2, final Collection<PointMatch> m) {
    final ArrayList<PointMatch> list = new ArrayList<PointMatch>();
    list.addAll(m);
    final ArrayList<PointMatch> tsil = new ArrayList<PointMatch>();
    PointMatch.flip(m, tsil);
    final String name = prefix == null ? "pointmatches" : prefix + ".pointmatches";
    final Loader loader = project.getLoader();
    return loader.serialize(new PointMatches(key, list), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(id1) + "_" + Long.toString(id2), name, ".ser")).toString()) && loader.serialize(new PointMatches(key, tsil), new StringBuilder(loader.getUNUIdFolder()).append("pointmatches.ser/").append(FSLoader.createIdPath(Long.toString(id2) + "_" + Long.toString(id1), name, ".ser")).toString());
}

Example 23 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class MatchIntensities method main.

public static final void main(final String... args) {
    new ImageJ();
    final Project project = Project.openFSProject("/home/saalfeld/tmp/intensity-corrected/elastic.xml", true);
    final MatchIntensities matcher = new MatchIntensities();
    matcher.invoke(project.getRootLayerSet());
}

Example 24 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class Render method main.

public static final void main(final String... args) {
    new ImageJ();
    final double scale = 0.05;
    // final double scale = 1;
    final int numCoefficients = 4;
    final Project project = Project.openFSProject("/home/saalfeld/tmp/bock-lens-correction/subproject.xml", false);
    final Layer layer = project.getRootLayerSet().getLayer(0);
    final ArrayList<Patch> patches = (ArrayList) layer.getDisplayables(Patch.class);
    final Patch patch1 = patches.get(0);
    final Patch patch2 = patches.get(2);
    final Rectangle box = patch1.getBoundingBox().intersection(patch2.getBoundingBox());
    // final Rectangle box = patch1.getBoundingBox();
    final int w = (int) (box.width * scale + 0.5);
    final int h = (int) (box.height * scale + 0.5);
    final FloatProcessor pixels1 = new FloatProcessor(w, h);
    final FloatProcessor weights1 = new FloatProcessor(w, h);
    final ColorProcessor coefficients1 = new ColorProcessor(w, h);
    final FloatProcessor pixels2 = new FloatProcessor(w, h);
    final FloatProcessor weights2 = new FloatProcessor(w, h);
    final ColorProcessor coefficients2 = new ColorProcessor(w, h);
    render(patch1, numCoefficients, numCoefficients, pixels1, weights1, coefficients1, box.x, box.y, scale);
    render(patch2, numCoefficients, numCoefficients, pixels2, weights2, coefficients2, box.x, box.y, scale);
    final ImageStack stack = new ImageStack(w, h);
    stack.addSlice(pixels1);
    stack.addSlice(pixels2);
    stack.addSlice(weights1);
    stack.addSlice(weights2);
    stack.addSlice(coefficients1.convertToFloatProcessor());
    stack.addSlice(coefficients2.convertToFloatProcessor());
    new ImagePlus("", stack).show();
}

Example 25 with Project

use of ini.trakem2.Project in project TrakEM2 by trakem2.

the class Display method findLandmarkNodes.

private static final Hashtable<String, ProjectThing> findLandmarkNodes(final Project p, final String landmarks_type) {
    final Set<ProjectThing> landmark_nodes = p.getRootProjectThing().findChildrenOfTypeR(landmarks_type);
    final Hashtable<String, ProjectThing> map = new Hashtable<String, ProjectThing>();
    for (final ProjectThing pt : landmark_nodes) {
        map.put(pt.toString() + "# " + pt.getId(), pt);
    }
    return map;
}