Problem with Create Fix size ROI from barycenter script

Hi,

Since last version of Icy, you don’t need to pass anymore by a script to do that, you can use the new ‘to Circle’ and ‘to Square’ ROI operations :

But just in case, here’s the fixed script (i tried to update it on the website but i couldn’t do it for now) :

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("Mass center X", roi, sequence).doubleValue()
y = ROIUtil.computeDescriptor("Mass center Y", roi, sequence).doubleValue()

keepSpot = true

// filtering

surface = ROIUtil.computeDescriptor("Interior", roi, sequence).doubleValue()
meanIntensity = ROIUtil.computeDescriptor("Mean intensity", roi.getSubROI(-1, -1, 0), sequence).doubleValue()
//
// 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)

// preserve some settings from original ROI
ROIUtil.copyROIProperties(roi, newRoi, false)
newRoi.setName(roi.getName() + " - fixed")

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

About inserting image from the forum, you can do it using the toolbar :

Note that sometime you need to refresh the page to get the toolbar to display (we are working on fixing that).

Best,

Hello,

I noticed the script changed slightly when I launched it. Just to be clear, I can now use the ‘to Circle’ and ‘to Square’ ROI operations, choosing the box size, and it will do the same as the previous script (based on the barycenter of the spot) – is that correct?

Best