Detection script using WAT for each ROI

Short Description

Versions

• Version 1 • Released on: 2013-04-23 16:01:16
  Download
  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)
  
  // get the current sequence focused by the user
  sequence = getSequence()
  
  // 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
  }
  
  image = sequence.getImage( 0 , 0 ) // get image at t=0 and z=0
  
  // store the list of ROI
  
  roiList = sequence.getROIs();
  
  try // this keyword is use to prevent problems during exectution of the script. (See finally keyword at the end of the script)
  {
  
  	// loop over all the ROIs
  	for ( i = 0 ; i < roiList.size() ; i++ )
  	{
  		currentROI = roiList.get( i );
  	
  		// remove all ROIs in the sequence, and add the currentROI.
  		sequence.removeAllROI();
  		sequence.addROI( currentROI );
  	
  		// perform detection
  	
  		// creates a detector
  		
  		detector = new UDWTWavelet()
  	
  		// enable scale 2 with a coefficient of 100. (scale 1 is disabled here as the parameter is 0)
  		scaleParameters = [0, 100]
  	
  		// performs the detection
  		detector.detect( sequence, // sequence to perform detection
  					false, // false: detect bright spot over dark background.
  					true,  // true: use WAT computed in the union of ROIs present in sequence.
  					scaleParameters)
  	
  		detectionResult = detector.getDetectionResult();
  	
  		// the detection is global to the image,
  		// so we now need to find the detections within the ROI
  		// we store them in filteredDetectionList
  	 	
  	 	var filteredDetectionList = new Array();
  		
  		detectionSize = detectionResult.size();
  		for ( detectionIndex = 0; detectionIndex < detectionSize; detectionIndex++) { // cycle over all the detections.
  	        spot = detectionResult.get( detectionIndex );
  	        if ( currentROI.contains( spot.getMassCenter().x , spot.getMassCenter().y , spot.getMassCenter().z , 0 , 0 ) ) // the last 2 zero are for t and channel
  			{
  				filteredDetectionList.push( spot );
  			}
  		}
  		
  		// get the number of detection in ROI.
  		detectionSize = filteredDetectionList.length;
  		println("ROI Name: " + currentROI.getName() );
  		println("Number of detection : " + detectionSize);
  		
  	}
  }
  finally 			
  {
  	// if anything goes wrong while running the part of script in the try section,
  	// the execution will jump to this 'finally' statement.
  	// And if everything worked fine, this section will be executed anyway to restore the ROIs.	
  
  	// restore all ROIs.
  	sequence.removeAllROI();
  	for ( i = 0 ; i < roiList.size() ; i++ )
  	{
  		currentROI = roiList.get( i );
  		sequence.addROI( currentROI );
  	}	
  }
  
  // end of script.
  
  // ( if you need specific output or display please check others scripts available on the website )