/* Method for reporting integrated intensity of traced cells.
    Tracings are stored in .zip files with same title as images.
    This particular version written for single image files, but could easily be adaptend to any filetype/organization.

    last tested on ImageJ 1.50i
*/

var tab = " \t ";
var bg = 28;        // or use rolling ball 50 and set to zero here


macro "open metadata" {
  openPath = getDirectory("Choose a Directory");
  fileList = getFileList(openPath);
  for (i=0; i<fileList.length; i++) {
    if ( (endsWith(fileList[i], ".lsm")) || (endsWith(fileList[i], ".LSM" )) ) {                
      run("Bio-Formats Importer", "open='" + openPath + fileList[i] + "' color_mode=Default display_metadata view=[Metadata only] stack_order=Default");
    } // if
  }  //  for each image
} // end macro

//====================================================================
macro "Save ROI Manager [F7]" {
  if ( getInfo("window.type") != "Image" )  exit("Make sure running macro from image window.");
  dir = getDirectory("image");                         // where to save results
//print(dir);
  if (lengthOf(dir) < 1) exit("Make sure the image was opened from disk.");
  title = getTitleStripExtension();    
//print(title);
  newName =dir + title + ".zip";
//print(newName);
  roiManager("Save", newName);
  roiManager("reset");
}


//=========================================
macro "measure entire directory with ROIs" {
  outputtitle = "results" + tab + "satcount" + tab + "inden180" + tab + "count180" + tab + "inden128" + tab + "count128" + tab + "inden64" + tab + "count64" + tab + "indenall" + tab + "countall";
  print(outputtitle);
  //wrap inside an open every file loop
  requires("1.50");
  run("Close All");
  openPath = getDirectory("Choose a Directory");
  fileList = getFileList(openPath);
  for (i=0; i<fileList.length; i++) {
    if ( (endsWith(fileList[i], ".lsm")) || (endsWith(fileList[i], ".LSM" )) ) {                
      run("Bio-Formats Importer", "open='" + openPath + fileList[i] + "' color_mode=Default view=[Hyperstack] stack_order=Default ");
      title = getTitleStripExtension(getTitle());
      roiManager("reset");
      open(openPath + title + ".zip");

      resultsOfOneImage();
  }  //  for each image

}

//=========================================
macro "measure current open image [q]" {
      resultsOfOneImage();

}



//=========================================
function resultsOfOneImage() {
  title = getTitle();
  run("Hyperstack to Stack");
  setSlice(2);                                          // This will change depending on the dataset
  run("Set Measurements...", "area mean limit display redirect=None decimal=2");
  resetThreshold();

  //run("Select All");       // or open matching ROI file from disk and use these
  for (r=  roiManager("count")
    getHistogram(values, counts, 256);
    sumcount = 0;
    intden = 0;

    outputstring = title + tab;
    for (i=255; i>bg; i--) {                                 // only works for 8 bit images
      sumcount = sumcount + counts[i];
      intden = intden + (counts[i] * (values[i]-bg));
      if (i==255) outputstring = outputstring + sumcount + tab;    // reports the number of saturated pixels
      if (i==180) outputstring = outputstring + intden + tab + sumcount + tab;          // reports integrated density at threshhold 180 not including bg subtraction      
      if (i==128) outputstring = outputstring + intden + tab + sumcount + tab;          // reports integrated density at threshhold 128 not including bg subtraction
      if (i== 64) outputstring = outputstring + intden + tab + sumcount + tab;          // reports integrated density at threshhold 64 not including bg subtraction
    } 
    outputstring = outputstring + intden + tab + sumcount; 
    close();
  
  print(outputstring);
  selectWindow("Log");
  // get results from this table and report them as area * mean


}




//====================================
// Use this function to strip any number of extensions
// off images.
// Returns the title without the extension.
// new version uses an array
//====================================
function getTitleStripExtension() {
  t = getTitle();
  t = replace(t, ".tif", "");        t = replace(t, ".TIF", "");  
  t = replace(t, ".tiff", "");       t = replace(t, ".TIFF", "");
  t = replace(t, ".lif", "");        t = replace(t, ".LIF", "");
  t = replace(t, ".lsm", "");     t = replace(t, ".LSM", "");
  t = replace(t, ".czi", "");      t = replace(t, ".CZI", "");
  t = replace(t, ".nd2", "");    t = replace(t, ".ND2", "");
  return t;
}