Example usage for org.apache.commons.math3.geometry.partitioning Region getBoundarySize

Introduction

In this page you can find the example usage for org.apache.commons.math3.geometry.partitioning Region getBoundarySize.

Prototype

double getBoundarySize();

Source Link

Document

Get the size of the boundary.

Usage

From source file:org.micromanager.plugins.magellan.surfacesandregions.SurfaceInterpolator.java

private void fitXYPositionsToConvexHull(double overlap) throws InterruptedException {
    int fullTileWidth = JavaLayerImageConstructor.getInstance().getImageWidth();
    int fullTileHeight = JavaLayerImageConstructor.getInstance().getImageHeight();
    int overlapX = (int) (JavaLayerImageConstructor.getInstance().getImageWidth() * overlap / 100);
    int overlapY = (int) (JavaLayerImageConstructor.getInstance().getImageHeight() * overlap / 100);
    int tileWidthMinusOverlap = fullTileWidth - overlapX;
    int tileHeightMinusOverlap = fullTileHeight - overlapY;
    int pixelPadding = (int) (xyPadding_um_ / Magellan.getCore().getPixelSizeUm());
    numRows_ = (int) Math
            .ceil((boundYPixelMax_ - boundYPixelMin_ + pixelPadding) / (double) tileHeightMinusOverlap);
    numCols_ = (int) Math
            .ceil((boundXPixelMax_ - boundXPixelMin_ + pixelPadding) / (double) tileWidthMinusOverlap);

    //take center of bounding box and create grid
    int pixelCenterX = boundXPixelMin_ + (boundXPixelMax_ - boundXPixelMin_) / 2;
    int pixelCenterY = boundYPixelMin_ + (boundYPixelMax_ - boundYPixelMin_) / 2;

    AffineTransform transform = AffineUtils.getAffineTransform(getCurrentPixelSizeConfig(), 0, 0);
    ArrayList<XYStagePosition> positions = new ArrayList<XYStagePosition>();
    Point2D.Double gridCenterStageCoords = new Point2D.Double();
    transform.transform(new Point2D.Double(pixelCenterX, pixelCenterY), gridCenterStageCoords);
    gridCenterStageCoords.x += convexHullVertices_[0].getX();
    gridCenterStageCoords.y += convexHullVertices_[0].getY();
    //set affine transform translation relative to grid center
    double[] transformMaxtrix = new double[6];
    transform.getMatrix(transformMaxtrix);
    transformMaxtrix[4] = gridCenterStageCoords.x;
    transformMaxtrix[5] = gridCenterStageCoords.y;
    //create new transform with translation applied
    transform = new AffineTransform(transformMaxtrix);
    //add all positions of rectangle around convex hull
    for (int col = 0; col < numCols_; col++) {
        double xPixelOffset = (col - (numCols_ - 1) / 2.0) * (tileWidthMinusOverlap);
        for (int row = 0; row < numRows_; row++) {
            if (Thread.interrupted()) {
                throw new InterruptedException();
            }/*from ww  w .  j  av a 2  s .co  m*/
            double yPixelOffset = (row - (numRows_ - 1) / 2.0) * (tileHeightMinusOverlap);
            Point2D.Double pixelPos = new Point2D.Double(xPixelOffset, yPixelOffset);
            Point2D.Double stagePos = new Point2D.Double();
            transform.transform(pixelPos, stagePos);
            AffineTransform posTransform = AffineUtils.getAffineTransform(getCurrentPixelSizeConfig(),
                    stagePos.x, stagePos.y);
            positions.add(new XYStagePosition(stagePos, tileWidthMinusOverlap, tileHeightMinusOverlap,
                    fullTileWidth, fullTileHeight, row, col, posTransform));
        }
    }
    //delete positions squares (+padding) that do not overlap convex hull
    for (int i = positions.size() - 1; i >= 0; i--) {
        if (Thread.interrupted()) {
            throw new InterruptedException();
        }
        XYStagePosition pos = positions.get(i);
        //create square region correpsonding to stage pos
        Region<Euclidean2D> square = getStagePositionRegion(pos);
        //if convex hull and position have no intersection, delete
        Region<Euclidean2D> intersection = regionFacotry_.intersection(square, convexHullRegion_);
        if (intersection.isEmpty()) {
            positions.remove(i);
        }
        square.getBoundarySize();
    }
    if (Thread.interrupted()) {
        throw new InterruptedException();
    }
    synchronized (xyPositionLock_) {
        xyPositions_ = positions;
        xyPositionLock_.notifyAll();
    }

    //let manger know new parmas caluclated
    manager_.updateSurfaceTableAndCombos();
}

---