Multiplicative ART

MART_simple.js

// MART: Multiplicative ART
// Jean-Christophe Taveau
// 5 nov 2012
// http://crazybiocomputing.blogspot.com

// ART Parameters
var nbCycles=5;
var relax=0.33;

// 1- Get sinogram information
var imp = IJ.getImage();
var w=imp.getWidth();
var nbProj=imp.getHeight();
var step=180/nbProj;

// Create output and temporary images/stack
var rec = IJ.createImage("Rec2D", "32-bit Black", w, w, 1);
var recStack = IJ.createImage("Rec2D_Cycles", "32-bit Black", w, w, nbCycles);
var a = IJ.createImage("tmp", "32-bit Black", w, 1, 1);

var ic = new ImageCalculator();

var stats = imp.getStatistics();
var avg=stats.mean;
rec.getProcessor().setValue(avg);
rec.getProcessor().fill();

// M  a  i  n     l  o  o  p

// Comment out the following lines to see the ART in action
// rec.show();
// recStack.show();

for (var i=0;i<nbCycles;i++)
{
  for (var j=0;j<nbProj;j++)
  {
    // 2- Compute projection from temporary 2D-rec
    calcProj(rec,step*j);
    // 3- Extract a 1D-projection (one row of sinogram)
    imp.setRoi(0,j,imp.getWidth(), 1);
    var proj = imp.duplicate();
    // 4- Compute the error between sinogram and calculated projections
    ic.run("Divide",proj,a);  
    IJ.run(proj, "Macro...", "code=[v=pow(v,"+relax+");]");
    // 5- Create the backprojected ray from this err pixel and add it to rec;
    IJ.run(proj, "Size...", "width="+w+" height="+w+" average interpolation=None");
    IJ.run(proj, "Rotate... ", "angle="+(-j * step)+" grid=1 interpolation=Bilinear fill");

    ic.run("Multiply",rec,proj);  
  }

  recStack.setSlice(i+1);
  recStack.setProcessor(rec.getProcessor().duplicate());
}
rec.show();
recStack.show();

// F U N C T I O N S

function calcProj(img, rotangle)
{
  var tmp = img.duplicate();
  tmp.getProcessor().setBackgroundValue(0.0);
  tmp.getProcessor().rotate(rotangle);
  tmp.setRoi(0,0,tmp.getWidth(), tmp.getHeight());
  var plot = new ProfilePlot(tmp);
  var data = plot.getProfile();
  for (var x in data)
    a.getProcessor().putPixelValue(x,0,data[x]);

  tmp.close();
}