Detect spot and change parameter along time

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• Version 1 • Released on: 2013-03-27 16:24:43
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  Description:

  initial version

  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.icy.roi.ROI2DRectangle)
  importClass(java.awt.geom.Point2D)
   
  // creates a detector
  detector = new UDWTWavelet()
   
  // get the current sequence focused by the user
  sequence = getSequence()
  sequence.removeAllROI()
  // check if the sequence exists
  if ( sequence == null )
  {
          MessageDialog.showDialog("Please open a sequence first", MessageDialog.INFORMATION_MESSAGE );
          throw "no sequence"; // stops the script and say why
  }
  
  // loop over the image of a t sequence
  for ( frameNumber = 0 ; frameNumber < sequence.getSizeT() ; frameNumber++ )
  {
  	image = sequence.getImage( frameNumber , 0 ) // get image at t=0 and z=0
  	// create a temp sequence to perform the detection on it.
  
  	// This varies the threshold along time. In this example, at each frame the detector will become more and more sensitive
  	
  	parameterForScale2 = 100+frameNumber * 0.4
  	scaleParameters = [0, parameterForScale2] 
  
  	println("Time t=" + frameNumber );
  	println("Scale 2 parameter=" + parameterForScale2 );
  
  	tmpSequence = new Sequence();
  	tmpSequence.addImage( 0 , image );	
  	detector.detect(tmpSequence, false, false, scaleParameters)	
  	detectionResult = detector.getDetectionResult();
  
  	// get the number of detection
  	detectionSize = detectionResult.size();
  	println("Number of detection : " + detectionSize);
  
  	// display detection in original sequence as ROI
  
  	for (i = 0; i < detectionSize; i++) { // cycle over all the detections.
          	spot = detectionResult.get(i) // get the spot
  
   		// get mass center.
          	massCenter = spot.getMassCenter()
          	x = massCenter.x;
          	y = massCenter.y;
  
  		boxSize = 2;
          	roi = new ROI2DRectangle(
                  new Point2D.Double( x-boxSize , y-boxSize ),
                  new Point2D.Double( x+boxSize+1 , y+boxSize+1 ),
                  false ); // false: say to the system that the ROI is not in creation mode. 
            roi.setT(frameNumber)      
         	sequence.addROI(roi);
  	}
  
  
  }