Examples with NameMap gov.sandia.n2a.backend.neuroml.PartMap.NameMap used on opensource projects

Example 1 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method ionChannel.

public void ionChannel(Node node) {
    String id = getAttribute(node, "id");
    String type = getAttribute(node, "type");
    String species = getAttribute(node, "species");
    String inherit;
    if (type.isEmpty())
        inherit = node.getNodeName();
    else
        inherit = type;
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    // Expect to always create this part rather than fetch an existing child.
    MNode part = models.childOrCreate(modelName, id);
    part.set("$inherit", "\"" + inherit + "\"");
    addDependency(part, inherit);
    if (!species.isEmpty())
        part.set("$metadata", "species", species);
    addAttributes(node, part, nameMap, "id", "type", "species");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() != Node.ELEMENT_NODE)
            continue;
        String name = child.getNodeName();
        if (name.startsWith("q10"))
            q10(child, part);
        else if (name.startsWith("gate"))
            gate(child, part);
        else
            genericPart(child, part);
    }
}

Example 2 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method transition.

public void transition(Node node, MNode container) {
    String id = getAttribute(node, "id");
    MNode part = container.set(id, "");
    NameMap nameMap = partMap.importMap(node.getNodeName());
    part.set("$inherit", "\"" + nameMap.internal + "\"");
    addAttributes(node, part, nameMap, "id");
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE)
            rate(child, part, true, false);
    }
}

Example 3 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method spikingSynapse.

/**
 *        Create a spike generator, which may be associated with its intended synapse.
 */
public void spikingSynapse(Node node) {
    String id = getAttribute(node, "id");
    String synapse = getAttribute(node, "synapse");
    // "spikeTarget" appears to be redundant with "synapse". Probably exists due to some oddity in LEMS.
    MNode part = models.childOrCreate(modelName, id);
    String inherit = node.getNodeName();
    NameMap nameMap = partMap.importMap(inherit);
    inherit = nameMap.internal;
    if (!inherit.isEmpty()) {
        part.set("$inherit", inherit);
        addDependency(part, inherit);
    }
    // "spikeArray" does not have an associated synapse.
    if (!synapse.isEmpty())
        part.set("$metadata", "backend.lems.synapse", synapse);
    addAttributes(node, part, nameMap, "id", "synapse", "spikeTarget");
    Map<Double, String> sorted = new TreeMap<Double, String>();
    for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
        if (child.getNodeType() == Node.ELEMENT_NODE && child.getNodeName().equals("spike")) {
            String time = biophysicalUnits(getAttribute(child, "time"));
            sorted.put(Scalar.convert(time), time);
        }
    }
    if (// generate spikeArray-like code
    sorted.size() > 0) {
        String times = "";
        for (String s : sorted.values()) times += ";" + s;
        // This shuts down spiking after last specified time.
        times += ";∞";
        times = "[" + times.substring(1) + "]";
        part.set("times", times);
    }
}

Example 4 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ImportJob method channel.

public void channel(Node node, MNode part, boolean doDependency) {
    String name = node.getNodeName();
    String number = part.get("number");
    String ionChannel = part.get("ionChannel");
    part.clear("ionChannel");
    // There is only one internal part for all ion-channel-related components in NeuroML. It includes both individual channels and populations/densities.
    NameMap nameMap = partMap.importMap("ionChannel");
    remap(part, nameMap);
    // multiple inheritance, combining the ion channel with the given mix-in
    String potential = "";
    if (name.contains("Nernst"))
        potential = "Potential Nernst";
    else if (name.contains("GHK2"))
        potential = "Potential GHK 2";
    else if (name.contains("GHK"))
        potential = "Potential GHK";
    if (potential.isEmpty()) {
        part.set("$inherit", "\"" + ionChannel + "\"");
    } else {
        // For now, assume that ion channel is already defined
        String species = "ca";
        if (name.contains("Ca2"))
            species = "ca2";
        species = models.getOrDefault(modelName, ionChannel, "$metadata", "species", species);
        // connect to species/concentration model, which the user is responsible to create
        part.set("c", species);
        part.set("$inherit", "\"" + potential + "\",\"" + ionChannel + "\"");
        if (doDependency)
            addDependency(part, potential);
    }
    if (doDependency)
        addDependency(part, ionChannel);
    if (!number.isEmpty()) {
        // The default is Gdensity*surfaceArea
        part.set("Gall", "G1*population");
    }
}

Example 5 with NameMap

use of gov.sandia.n2a.backend.neuroml.PartMap.NameMap in project n2a by frothga.

the class ExportJob method input.

public String input(MPart source, List<Element> parentElements, Synapse synapse) {
    String type = source.get("$metadata", "backend.lems.part");
    List<Element> inputElements = new ArrayList<Element>();
    List<String> skip = new ArrayList<String>();
    for (MNode c : source) {
        MPart p = (MPart) c;
        if (p.isPart()) {
            skip.add(p.key());
            input(p, inputElements, null);
        } else if (p.key().equals("times")) {
            skip.add("times");
            String[] pieces = p.get().split("\\[", 2)[1].split("]", 2)[0].split(";");
            for (int i = 0; i < pieces.length; i++) {
                if (Scalar.convert(pieces[i]) == Double.POSITIVE_INFINITY)
                    continue;
                Element spike = addElement("spike", inputElements);
                spike.setAttribute("id", String.valueOf(i));
                spike.setAttribute("time", biophysicalUnits(pieces[i]));
            }
        }
    }
    if (// decide between them
    type.contains("ramp") && type.contains("pulse")) {
        NameMap nameMap = partMap.importMap("rampGenerator");
        EquationSet sourceEquations = getEquations(source);
        Variable high1 = sourceEquations.find(new Variable(nameMap.importName("startAmplitude"), 0));
        Variable high2 = sourceEquations.find(new Variable(nameMap.importName("finishAmplitude"), 0));
        try {
            double value1 = ((Scalar) high1.eval(context)).value;
            double value2 = ((Scalar) high2.eval(context)).value;
            if (value1 == value2)
                type = "pulseGenerator";
            else
                type = "rampGenerator";
        } catch (// eval can fail if eqset contains fatal errors
        Exception e) {
            if (source.get("high2").equals("high1"))
                type = "pulseGenerator";
            else
                type = "rampGenerator";
        }
    } else if (// more action is needed
    type.contains(",")) {
        if (synapse != null) {
            String[] types = type.split(",");
            for (String t : types) {
                if (// prefix of both "Synapse" and "Synaptic"
                t.contains("Synap")) {
                    type = t;
                    break;
                }
            }
        }
        // remove any remaining ambiguity
        type = type.split(",")[0];
    }
    Element input = addElement(type, parentElements);
    String id;
    if (synapse == null) {
        id = source.get("$metadata", "backend.lems.id");
        if (id.isEmpty())
            id = source.key();
    } else {
        id = synapse.id;
        input.setAttribute("synapse", synapse.chainID);
        input.setAttribute("spikeTarget", "./" + synapse.chainID);
    }
    input.setAttribute("id", id);
    standalone(source, input, inputElements);
    genericPart(source, input, skip.toArray(new String[] {}));
    sequencer.append(input, inputElements);
    return id;
}