Example usage for org.apache.commons.collections.primitives ArrayFloatList ArrayFloatList

Introduction

In this page you can find the example usage for org.apache.commons.collections.primitives ArrayFloatList ArrayFloatList.

Prototype

public ArrayFloatList(float[] array) 

Source Link

Document

Constructs a list by copying the specified array.

Usage

From source file:pipeline.plugins.cell_manipulation.CellBallQuantify.java

IProjector getProjector(ClickedPoint p, IPluginIOList<ClickedPoint> allInputPoints, IPluginIOStack input) {

    IProjector projector = getProjector();

    double radius = diameter / 2;
    double radiusSq = radius * radius;
    if (useEmbeddedDiameter) {
        if (!p.hasQuantifiedProperty("localDiameter")) {
            throw new IllegalArgumentException("localDiameter field is missing");
        }//from   w  ww  . j a  v  a  2 s .  c om
        radius = p.getQuantifiedProperty("localDiameter") * 0.5;
        radiusSq = radius * radius;
    }

    final int width = input.getWidth();
    final int height = input.getHeight();
    final int depth = input.getDepth();

    double xCenter = p.x;
    double yCenter = p.y;
    double zCenter = p.z;

    int xCenterInt = (int) xCenter;
    int yCenterInt = (int) yCenter;
    int zCenterInt = (int) zCenter;

    double xyCalib = diameterInPixels || p.xyCalibration == 0 ? 1 : p.xyCalibration;
    double zCalib = diameterInPixels || p.zCalibration == 0 ? 1 : p.zCalibration;

    boolean noPixels = false;

    final FloatCollection pixelValues;
    if (computeOverallPercentiles) {
        pixelValues = new ArrayFloatList(500);
    } else {
        pixelValues = null;
    }

    if (!useSegmentation) {
        int x0, x1, y0, y1, z0, z1;

        z0 = (int) (diskOnly ? 0 : Math.min(zCenter, radius / xyCalib));
        z1 = (int) (diskOnly ? 0 : Math.min(depth - 1 - zCenter, radius / xyCalib));

        y0 = (int) Math.min(yCenter, radius / xyCalib);
        y1 = (int) Math.min(height - 1 - (yCenter), radius / xyCalib);

        x0 = (int) Math.min(xCenter, radius / zCalib);
        x1 = (int) Math.min(width - 1 - xCenter, radius / zCalib);

        for (int k = -z0; k <= z1; k++) {
            double kSq = k * k * zCalib * zCalib;
            for (int j = -y0; j <= y1; j++) {
                double jSq = j * j * xyCalib;
                for (int i = -x0; i <= x1; i++) {
                    double iSq = i * i * xyCalib;
                    if ((!useRectangularShape) && kSq + jSq + iSq > radiusSq)
                        continue;
                    float f = input.getFloat(xCenterInt + i, yCenterInt + j, zCenterInt + k);
                    if (ignoreZero && f == 0)
                        continue;
                    projector.add(f);
                    if (pixelValues != null) {
                        pixelValues.add(f);
                    }
                }
            }
        }
    } else { // use segmentation
        int[] xCoord = usePerimSeg ? p.imagePerimsegCoordsX : p.imageFullSegCoordsX;
        int[] yCoord = usePerimSeg ? p.imagePerimsegCoordsY : p.imageFullSegCoordsY;
        int[] zCoord = usePerimSeg ? p.imagePerimsegCoordsZ : p.imageFullSegCoordsZ;

        if (xCoord == null)
            throw new IllegalArgumentException("Missing segmentation");

        if (xCoord.length == 0) {
            noPixels = true;
        }
        float f;

        for (int i = 0; i < xCoord.length; i++) {
            if (applyRadiusToSegmentation && !useRectangularShape) {
                double distanceSq = Math.pow((xCoord[i] - xCenter) * xyCalib, 2)
                        + Math.pow((yCoord[i] - yCenter) * xyCalib, 2)
                        + Math.pow((zCoord[i] - zCenter) * zCalib, 2);
                if (distanceSq > radiusSq)
                    continue;
            }
            if (diskOnly && zCoord[i] != zCenter)
                continue;
            f = input.getFloat(xCoord[i], yCoord[i], zCoord[i]);
            if (ignoreZero && f == 0)
                continue;
            projector.add(f);
            if (pixelValues != null) {
                pixelValues.add(f);
            }
        }
    }

    if (computeOverallPercentiles) {
        synchronized (allPixelValues) {
            allPixelValues.addAll(pixelValues);
        }
    }

    if (noPixels)
        return null;
    else
        return projector;
}

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