XLS export of ROIs mean intensity over time

Short Description

Export the mean intensity of the all ROIs of active sequence over time in an excel file.

Versions

• Version 3 • Released on: 2022-04-25 12:00:00
  Download
  Description:

  Rewrote to handle all ROIs from the sequence, multi page sheet to allow more than 256 rois, and only exporting mean intensity.

  importClass(Packages.plugins.tprovoost.scripteditor.uitools.filedialogs.FileDialog)
  importClass(Packages.icy.file.FileUtil)
  importClass(Packages.icy.util.XLSUtil)
  importClass(Packages.icy.roi.ROIUtil)
  
  outFile = FileDialog.save();
  sequence = getSequence()
  
  if (sequence != null)
  {	
  	// create new excel file
  	xls = XLSUtil.createWorkbook(outFile)
  
  	// get ROIs
  	rois = sequence.getROIs()
  
  	// sheet index
  	for(p = 0; p < (rois.size() + 255) / 256; p++)
  	{
  		rstart = p * 256;
  		rend = (p * 256) + 256
  		if (rend > rois.size()) rend = rois.size()
  		
  		// create a new page
  		xlsPage = XLSUtil.createNewPage(xls, "Spots " + rstart + " - " + (rend - 1))
  		
  		for(r = rstart; r < rend; r++)
  		{
  			roi = rois.get(r)
  			rpage = r - (p * 256)
  			
  			// write header (roi name)
  			XLSUtil.setCellString(xlsPage, rpage, 0, roi.getName())
  	
  			// iterate over frames
  			for(t = 0; t < sequence.getSizeT(); t++)
  			{
  				// compute mean intensity for this frame
  				mean = ROIUtil.getMeanIntensity(sequence, roi, -1, t, -1)
  				XLSUtil.setCellNumber(xlsPage, rpage, t+1, mean)
  			}
  	
  			println("processing roi #" + r + " - " + roi.getName())
  		}
  	}
  	
  	println("done !")
  	
  	// save excel file
  	XLSUtil.saveAndClose(xls)
  }
  

• Version 2 • Released on: 2014-08-07 15:54:30
  Download
  Description:

  Added min / max intensity information.

  importClass(Packages.icy.file.FileUtil)
  importClass(Packages.icy.util.XLSUtil)
  importClass(Packages.icy.roi.ROIUtil)
  
  sequence = getSequence()
  
  if (sequence != null)
  {
  	roi = sequence.getSelectedROI()
  
  	if (roi != null)
  	{
  		// create new excel file
  		xls = XLSUtil.createWorkbook(FileUtil.setExtension(sequence.getFilename(), ".xls"))
  		// create a new page
  		xlsPage = XLSUtil.createNewPage(xls, roi.getName())
  
  		// write header
  		XLSUtil.setCellString(xlsPage, 0, 0, "T position")
  		XLSUtil.setCellString(xlsPage, 2, 0, "Min intensity")
  		XLSUtil.setCellString(xlsPage, 3, 0, "Mean intensity")
  		XLSUtil.setCellString(xlsPage, 4, 0, "Max intensity")
  		
  		for(t = 0; t < sequence.getSizeT(); t++)
  		{
  			// compute intensities for this frame
  			min = ROIUtil.getMinIntensity(sequence, roi, -1, t, -1)
  			mean = ROIUtil.getMeanIntensity(sequence, roi, -1, t, -1)
  			max = ROIUtil.getMaxIntensity(sequence, roi, -1, t, -1)
  			
  			// write value
  			XLSUtil.setCellNumber(xlsPage, 0, t + 2, t)
  			XLSUtil.setCellNumber(xlsPage, 2, t + 2, min)
  			XLSUtil.setCellNumber(xlsPage, 3, t + 2, mean)
  			XLSUtil.setCellNumber(xlsPage, 4, t + 2, max)
  		}
  
  		// save excel file
  		XLSUtil.saveAndClose(xls)
  	}
  }
  

• Version 1 • Released on: 2014-08-07 15:50:45
  Download
  Description:

  initial version

  importClass(Packages.icy.file.FileUtil)
  importClass(Packages.icy.util.XLSUtil)
  importClass(Packages.icy.roi.ROIUtil)
  
  sequence = getSequence()
  
  if (sequence != null)
  {
  	roi = sequence.getSelectedROI()
  
  	if (roi != null)
  	{
  		// create new excel file
  		xls = XLSUtil.createWorkbook(FileUtil.setExtension(sequence.getFilename(), ".xls"))
  		// create a new page
  		xlsPage = XLSUtil.createNewPage(xls, roi.getName())
  
  		// write header
  		XLSUtil.setCellString(xlsPage, 0, 0, "T position")
  		XLSUtil.setCellString(xlsPage, 1, 0, "Mean intensity")
  		
  		for(t = 0; t < sequence.getSizeT(); t++)
  		{
  			// compute mean intensity for this frame
  			d = ROIUtil.getMeanIntensity(sequence, roi, -1, t, -1)
  			
  			// write value
  			XLSUtil.setCellNumber(xlsPage, 0, t + 2, t)
  			XLSUtil.setCellNumber(xlsPage, 1, t + 2, d)
  		}
  
  		// save excel file
  		XLSUtil.saveAndClose(xls)
  	}
  }