Examples with FixedParameterTreeNode edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.fixedparameterclustering.FixedParameterTreeNode used on opensource projects

Example 1 with FixedParameterTreeNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.fixedparameterclustering.FixedParameterTreeNode in project clusterMaker2 by RBVI.

the class ConnectedComponent method reduceCC.

private boolean reduceCC(ConnectedComponent cc, float clusteringScore2) {
    FixedParameterTreeNode fptn = initFirstTreeNode(cc, clusteringScore2);
    if (fptn.size == cc.getNodeNumber())
        return false;
    ICCEdges ccedges = TaskConfig.ccEdgesEnum.createCCEdges(fptn.size);
    for (int i = 0; i < fptn.size; i++) {
        for (int j = i + 1; j < fptn.size; j++) {
            ccedges.setEdgeCost(i, j, fptn.edgeCosts[i][j]);
        }
    }
    String[] objectIds = new String[fptn.size];
    for (int i = 0; i < objectIds.length; i++) {
        String id = "";
        for (int j = 0; j < fptn.clusters[i].length; j++) {
            if (fptn.clusters[i][j]) {
                id += cc.getObjectID(j) + ";";
            }
        }
        objectIds[i] = id;
    }
    cc.setNodeNumber(fptn.size);
    cc.setCCEdges(ccedges);
    cc.setObjectIDs(objectIds);
    cc.setClusters(new int[fptn.size]);
    cc.setReductionCost(fptn.costs);
    return true;
}

Example 2 with FixedParameterTreeNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.fixedparameterclustering.FixedParameterTreeNode in project clusterMaker2 by RBVI.

the class ConnectedComponent method initFirstTreeNode.

public static FixedParameterTreeNode initFirstTreeNode(ConnectedComponent cc, double maxK) {
    FixedParameterTreeNode fptn = new FixedParameterTreeNode(cc.getNodeNumber(), 0, cc.getNodeNumber());
    for (int i = 0; i < fptn.size; i++) {
        fptn.clusters[i][i] = true;
        for (int j = i + 1; j < fptn.size; j++) {
            fptn.edgeCosts[i][j] = fptn.edgeCosts[j][i] = cc.getCCEdges().getEdgeCost(i, j);
        }
    }
    fptn = reductionicf(fptn, maxK, cc);
    return fptn;
}

Example 3 with FixedParameterTreeNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.fixedparameterclustering.FixedParameterTreeNode in project clusterMaker2 by RBVI.

the class ConnectedComponent method mergeNodes.

public static FixedParameterTreeNode mergeNodes(FixedParameterTreeNode fptn, int node_i, int node_j, float costsForMerging, ConnectedComponent cc) {
    FixedParameterTreeNode fptnNew = new FixedParameterTreeNode(fptn.size - 1, fptn.costs, cc.getNodeNumber());
    fptnNew.costs = (fptn.costs + costsForMerging);
    int[] mappingOld2New = new int[fptn.size];
    for (int i = 0, j = 0; i < fptn.size; i++) {
        if (i == node_i || i == node_j)
            continue;
        mappingOld2New[i] = j;
        fptnNew.clusters[j] = fptn.clusters[i];
        j++;
    }
    for (int i = 0; i < mappingOld2New.length; i++) {
        if (i == node_i || i == node_j)
            continue;
        for (int j = i + 1; j < mappingOld2New.length; j++) {
            if (j == node_i || j == node_j)
                continue;
            fptnNew.edgeCosts[mappingOld2New[i]][mappingOld2New[j]] = fptnNew.edgeCosts[mappingOld2New[j]][mappingOld2New[i]] = fptn.edgeCosts[i][j];
        }
    }
    for (int i = 0; i < cc.getNodeNumber(); i++) {
        fptnNew.clusters[fptnNew.size - 1][i] = (fptn.clusters[node_i][i] || fptn.clusters[node_j][i]);
    }
    for (int i = 0; i < fptn.size; i++) {
        if (i == node_i || i == node_j)
            continue;
        fptnNew.edgeCosts[mappingOld2New[i]][fptnNew.size - 1] = fptnNew.edgeCosts[fptnNew.size - 1][mappingOld2New[i]] = fptn.edgeCosts[i][node_i] + fptn.edgeCosts[i][node_j];
    }
    return fptnNew;
}

Example 4 with FixedParameterTreeNode

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.de.layclust.fixedparameterclustering.FixedParameterTreeNode in project clusterMaker2 by RBVI.

the class ConnectedComponent method reductionicf.

public static FixedParameterTreeNode reductionicf(FixedParameterTreeNode fptnNew, double maxK, ConnectedComponent cc) {
    for (int i = 0; i < fptnNew.size; i++) {
        for (int j = i + 1; j < fptnNew.size; j++) {
            float sumIcf = calculateCostsForSetForbidden(fptnNew, i, j);
            if (sumIcf + fptnNew.costs > maxK) {
                float costsForMerging = calculateCostsForMerging(fptnNew, i, j);
                FixedParameterTreeNode fptnNew2 = mergeNodes(fptnNew, i, j, costsForMerging, cc);
                fptnNew2 = reductionicf(fptnNew2, maxK, cc);
                return fptnNew2;
            }
        }
    }
    return fptnNew;
}