Micro-Manager continous acquisition on crops

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• Version 1 • Released on: 2018-03-19 19:15:15
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  Description:

  initial version

  importClass(Packages.icy.sequence.Sequence)
  importClass(Packages.icy.image.IcyBufferedImage)
  importClass(Packages.icy.image.IcyBufferedImageUtil)
  importClass(Packages.plugins.tprovoost.Microscopy.MicroManager.MicroManager)
  
  // get acquired image containing ROIs
  acquiredSeq = getSequence()
  // get image type
  dataType = acquiredSeq.getDataType_()
  // get rois
  rois = acquiredSeq.getROIs()
  
  cropImages = []
  
  // create result image
  for(r = 0; r < rois.size(); r++)
  {
  	roi = rois.get(r)
  	bnd = roi.getBounds5D()
  	img = new IcyBufferedImage(bnd.getSizeX(), bnd.getSizeY(), 1, dataType)
  
  	// store image
  	cropImages[r] = img
  
  	// create sequence
  	s = new Sequence(img)
  	// change sequence name
  	s.setName("image" + r + " - " + roi.getName())
  	// show it
  	gui.addSequence(s)
  }
  
  
  while(true)
  {
  	// snap image
  	newImage = MicroManager.snapImage()
  
  	for(r = 0; r < rois.size(); r++)
  	{
  		roi = rois.get(r)
  		bnd = roi.getBounds5D().toRectangle2D().getBounds()
  		
  		img = cropImages[r]
  		img.copyData(newImage, bnd, null)
  	}
  
  	// do processig here on cropped images
  }