Examples with Compound gdsc.smlm.ij.settings.Compound used on opensource projects

Example 1 with Compound

use of gdsc.smlm.ij.settings.Compound in project GDSC-SMLM by aherbert.

the class CreateData method logExampleCompounds.

private void logExampleCompounds() {
    comment(TITLE + " example compounds");
    IJ.log("");
    comment("Compounds are described using XML");
    comment("Multiple compounds can be combined using fractional ratios");
    comment("Coordinates are specified in nanometres");
    comment("Coordinates describe the relative positions of molecules in the compound. Compounds will have a randomly assigned XYZ position for their centre-of-mass. Rotation will be about the centre of mass");
    IJ.log("");
    Atom a1 = new Atom(10, 0, 0, 0);
    Atom a2 = new Atom(30, 0, 0, 0);
    Atom a3 = new Atom(20, 1000, 0, 0);
    Compound m1 = new Compound(1, 0, DiffusionType.RANDOM_WALK.toString(), a1);
    Compound m2 = new Compound(1, 1, DiffusionType.GRID_WALK.toString(), a2, a3);
    // Create a hexamer big enough to see with the default pixel pitch
    Atom b1 = new Atom(1, 0, 0, 0);
    Atom b2 = new Atom(1, 1000, 0, 0);
    Atom b3 = new Atom(1, 1500, 866, 0);
    Atom b4 = new Atom(1, 1000, 1732, 0);
    Atom b5 = new Atom(1, 0, 1732, 0);
    Atom b6 = new Atom(1, -500, 866, 0);
    Compound m3 = new Compound(1, 2, DiffusionType.RANDOM_WALK.toString(), b1, b2, b3, b4, b5, b6);
    comment("Single compounds");
    IJ.log("");
    comment("Monomer");
    demo(m1);
    comment("Dimer");
    demo(m2);
    comment("Hexamer");
    demo(m3);
    comment("Combined compounds");
    IJ.log("");
    comment("Two compounds with a ratio of 2:1");
    m1.fraction = 2;
    demo(m1, m2);
}

Example 2 with Compound

use of gdsc.smlm.ij.settings.Compound in project GDSC-SMLM by aherbert.

the class CreateData method demo.

private void demo(Compound... compounds) {
    List<Compound> list = new LinkedList<Compound>();
    for (Compound c : compounds) list.add(c);
    IJ.log(createXStream().toXML(list));
    IJ.log("");
}

Example 3 with Compound

use of gdsc.smlm.ij.settings.Compound in project GDSC-SMLM by aherbert.

the class CreateData method createCompoundMolecules.

@SuppressWarnings("unchecked")
private List<CompoundMoleculeModel> createCompoundMolecules() {
    // Diffusion rate is um^2/sec. Convert to pixels per simulation frame.
    final double diffusionFactor = (1000000.0 / (settings.pixelPitch * settings.pixelPitch)) / settings.stepsPerSecond;
    List<CompoundMoleculeModel> compounds;
    if (settings.compoundMolecules) {
        // Try and load the compounds from the XML specification
        try {
            Object fromXML = createXStream().fromXML(settings.compoundText);
            List<Compound> rawCompounds = (List<Compound>) fromXML;
            // Convert from the XML serialised objects to the compound model
            compounds = new ArrayList<CompoundMoleculeModel>(rawCompounds.size());
            int id = 1;
            for (Compound c : rawCompounds) {
                MoleculeModel[] molecules = new MoleculeModel[c.atoms.length];
                for (int i = 0; i < c.atoms.length; i++) {
                    Atom a = c.atoms[i];
                    molecules[i] = new MoleculeModel(a.mass, a.x, a.y, a.z);
                }
                CompoundMoleculeModel m = new CompoundMoleculeModel(id++, 0, 0, 0, Arrays.asList(molecules));
                m.setFraction(c.fraction);
                m.setDiffusionRate(c.D * diffusionFactor);
                m.setDiffusionType(DiffusionType.fromString(c.diffusionType));
                compounds.add(m);
            }
            // Convert coordinates from nm to pixels
            final double scaleFactor = 1.0 / settings.pixelPitch;
            for (CompoundMoleculeModel c : compounds) {
                c.scale(scaleFactor);
            }
        } catch (Exception e) {
            IJ.error(TITLE, "Unable to create compound molecules");
            return null;
        }
    } else {
        // Create a simple compound with one molecule at the origin
        compounds = new ArrayList<CompoundMoleculeModel>(1);
        CompoundMoleculeModel m = new CompoundMoleculeModel(1, 0, 0, 0, Arrays.asList(new MoleculeModel(0, 0, 0, 0)));
        m.setDiffusionRate(settings.diffusionRate * diffusionFactor);
        m.setDiffusionType(settings.getDiffusionType());
        compounds.add(m);
    }
    return compounds;
}