Examples with ArrayUtil mcib3d.utils.ArrayUtil used on opensource projects

Example 26 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class ManualSpot method initInterface.

private void initInterface() {
    // adjust slider threshold
    jSliderConstant.setMaximum((int) spot3DImage.getMax());
    jSliderConstant.setMinimum(0);
    ArrayUtil hist = new ArrayUtil(spot3DImage.getHistogram(new BlankMask(spot3DImage)));
    int pcHigh = hist.indexOfSumPercent(0.999);
    jSliderConstant.setValue(pcHigh);
    // set tool point and open RoiManager
    IJ.setTool(Toolbar.POINT);
    RoiManager manager = RoiManager.getInstance();
    if (manager == null) {
        manager = new RoiManager();
    }
}

Example 27 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class AllRegionsAssociation method computeAllRegionsAssociationPairs.

public void computeAllRegionsAssociationPairs(ImageHandler img, int BorderValue) {
    list = new ArrayList<AssociationRegion>();
    for (int z = 1; z < img.sizeZ - 1; z++) {
        IJ.showStatus("Analysing " + z);
        for (int x = 1; x < img.sizeX - 1; x++) {
            for (int y = 1; y < img.sizeY - 1; y++) {
                if (((BorderValue >= 0) && (img.getPixel(x, y, z) == BorderValue)) || (BorderValue < 0)) {
                    ArrayUtil tab = img.getNeighborhoodCross3D(x, y, z);
                    int val = (int) img.getPixel(x, y, z);
                    tab = tab.distinctValues();
                    for (int i = 0; i < tab.getSize(); i++) {
                        int val2 = tab.getValueInt(i);
                        if (val2 != val) {
                            AssociationRegion asso = new AssociationRegion();
                            asso.addRegion(val);
                            asso.addRegion(val2);
                            this.addAssoRegion(asso);
                        }
                    }
                }
            }
        }
    }
}

Example 28 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class AllRegionsAssociation method getNbClusters.

public int getNbClusters() {
    if (clusters == null) {
        computeClusters();
    }
    ArrayUtil tab = new ArrayUtil(clusters);
    tab = tab.distinctValues();
    if (tab.getMinimum() == 0) {
        return tab.getSize() - 1;
    } else {
        return tab.getSize();
    }
}

Example 29 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class AllRegionsAssociation method getClusters.

public ArrayList<Cluster> getClusters() {
    if (clusters == null) {
        computeClusters();
    }
    ArrayUtil tab = new ArrayUtil(clusters);
    int nbClusters = (int) tab.getMaximum() + 1;
    ArrayList<Cluster> clus = new ArrayList<Cluster>(nbClusters);
    for (int i = 0; i < nbClusters; i++) {
        clus.add(new Cluster());
    }
    for (AssociationRegion asso : list) {
        int c = clusters[asso.getFirst()];
        if (c != 0) {
            clus.get(c).addAssoRegion(asso);
        }
    }
    return clus;
}

Example 30 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class RegionGrowing method mergeLabels.

public int mergeLabels(int[] oldLabels, ArrayList<Voxel3D> borders) {
    // get borders between these labels
    // ArrayList<Voxel3D> borders = this.getBordersMerge(oldLabels, outsideBorders);
    watershedImage.resetStats(null);
    int newLabel = (int) watershedImage.getMax() + 1;
    for (Voxel3D V : borders) {
        watershedImage.setPixel(V, newLabel);
    }
    // update image
    watershedImage.replacePixelsValue(oldLabels, newLabel);
    // update associations
    if (computeAssociation) {
        ArrayList<String> toRemove = new ArrayList();
        ArrayList<String> toAdd = new ArrayList();
        for (String S : associations) {
            boolean reprep = false;
            String[] asso = S.split("_");
            ArrayUtil assoTab = new ArrayUtil(asso.length);
            for (int i = 0; i < assoTab.getSize(); i++) {
                int val = Integer.parseInt(asso[i]);
                boolean rep = false;
                for (int old : oldLabels) {
                    if (val == old) {
                        rep = true;
                        reprep = true;
                        break;
                    }
                }
                if (rep) {
                    assoTab.putValue(i, newLabel);
                } else {
                    assoTab.putValue(i, val);
                }
            }
            if (reprep) {
                assoTab = assoTab.distinctValues();
                // array from max to min with unique values
                assoTab.reverse();
                if (assoTab.getSize() == 1) {
                    toRemove.add(S);
                } else {
                    String assoRep = "" + (int) assoTab.getValue(0);
                    for (int i = 1; i < assoTab.getSize(); i++) {
                        assoRep = assoRep.concat("_" + (int) assoTab.getValue(i));
                    }
                    toRemove.add(S);
                    toAdd.add(assoRep);
                }
            }
        }
        if (!toRemove.isEmpty()) {
            associations.removeAll(toRemove);
        }
        if (!toAdd.isEmpty()) {
            for (String A : toAdd) {
                // test if association exists already
                boolean ok = true;
                for (String S : associations) {
                    if ((S.compareTo(A)) == 0) {
                        ok = false;
                        break;
                    }
                }
                if (ok) {
                    associations.add(A);
                }
            }
        }
        // With allRegions
        assoRegions.replaceRegion(oldLabels, newLabel);
    }
    // ??
    if (computeUpdatedLabels) {
    }
    // update volumes
    if (computeVolumes) {
        double newVol = 0;
        for (int i : oldLabels) {
            newVol += volumeLabels.get(i);
            // volumeLabels.get(i)[1] = 0;
            volumeLabels.set(i, 0.0);
        }
        newVol += borders.size();
        volumeLabels.add(newVol);
    }
    return newLabel;
}