importClass(Packages.icy.roi.ROIUtil)
importClass(Packages.icy.roi.ROIDescriptor)
importClass(Packages.icy.gui.dialog.MessageDialog)
importClass(Packages.icy.sequence.Sequence)
importClass(Packages.java.util.ArrayList)
importClass(Packages.plugins.fab.spotDetector.detector.UDWTWavelet)
importClass(Packages.plugins.kernel.roi.roi2d.ROI2DRectangle)
importClass(java.awt.geom.Point2D)

// this is the parameters you asked for: considering the center of mass,
// the algo will look in a box of side boxSize*2+1 where the center of mass is the center of this box
//
// for boxSize = 2
//
// *****
// *****
// **X**
// *****
// *****
//
// with * : pixel considered for Rectangle ROI
// X: location of center of mass

boxSize = 1
removePreviousRois = false

// get the current sequence focused by the user
sequence = getSequence()

// check if the sequence exists
if ( sequence == null )
{
    MessageDialog.showDialog("Please open an image first", MessageDialog.INFORMATION_MESSAGE);
    throw "no sequence"; // stops the script and say why
}

w = sequence.getSizeX()
h = sequence.getSizeY()

// get all rois
rois = sequence.getROIs()
// get the number of rois
roiCount = rois.size()
println("Number of rois: " + roiCount)

// remove all existing ROI if requested
if (removePreviousRois)
    sequence.removeAllROI()

// cycle over all rois
for (i = 0; i < roiCount; i++)
{
    roi = rois.get(i) // get the spot

    x = ROIUtil.computeDescriptor("MassCenterX", roi, sequence).doubleValue()
    y = ROIUtil.computeDescriptor("MassCenterY", roi, sequence).doubleValue()
    
    surface = ROIUtil.computeDescriptor("Interior", roi, sequence).doubleValue()
    meanIntensity = ROIUtil.computeDescriptor("MeanIntensity", roi.getSubROI(-1, -1, 0), sequence).doubleValue()
    
    keepSpot = true

    // filtering
//    if (surface < 10) keepSpot = false // remove too small spots
//    if (surface > 60) keepSpot = false // remove too big spots
//    if (meanIntensity < 100) keepSpot = false // remove too big spots

    xmin = x - boxSize
    ymin = y - boxSize
    xmax = x + boxSize + 1
    ymax = y + boxSize + 1
    
    // remove spot if mass center too close from borders
    if (xmin < 0) keepSpot = false
    if (ymin < 0) keepSpot = false
    if (xmax > w) keepSpot = false
    if (ymax > h) keepSpot = false

    if (!keepSpot) continue

    // create the Rectangle ROI
    newRoi = new ROI2DRectangle(xmin, ymin, xmax, ymax)

    println(x)
    println(y)
    println(xmin)
    println(ymin)
    println(xmax)
    println(ymax)
    println(newRoi.getBounds2D())

    // preserve some settings from original ROI
    pos = roi.getPosition5D()
    newRoi.setName(roi.getName() + " - fixed")
    newRoi.setColor(roi.getColor())
    newRoi.setZ(pos.getZ())
    newRoi.setT(pos.getT())
    newRoi.setC(pos.getC())

    // add the ROI to the sequence
    sequence.addROI(newRoi)
}