content: /*
   * Copyright (C) 2010-2018 Mathias Unberath
   * CONRAD is developed as an Open Source project under the GNU General Public License (GPL).
  */
  package edu.stanford.rsl.conrad.angio.reconstruction.proximal.smoothFunctions;
  
  import ij.ImageJ;
  
  import java.util.ArrayList;
  
  import edu.stanford.rsl.conrad.data.numeric.Grid3D;
  import edu.stanford.rsl.conrad.data.numeric.MultiChannelGrid3D;
  import edu.stanford.rsl.conrad.data.numeric.NumericPointwiseOperators;
  import edu.stanford.rsl.conrad.geometry.Projection;
  import edu.stanford.rsl.conrad.angio.motion.respiratory.graphicalMoCo.tools.Container;
  import edu.stanford.rsl.conrad.angio.reconstruction.proximal.SmoothFunction;
  import edu.stanford.rsl.conrad.angio.reconstruction.proximal.util.BackProjCL;
  import edu.stanford.rsl.conrad.angio.reconstruction.proximal.util.ForwProjCL;
  import edu.stanford.rsl.conrad.angio.util.data.organization.Angiogram;
  
  public class SquaredResidual extends SmoothFunction{
  
  	private Angiogram ang;
  	
  	private int[] phaseAssignment;
  	private int[] imgsPerPhase;
  		
  	public SquaredResidual(Angiogram ang){
  		this.ang = ang;
  	}
  	
  	public void setPhaseInformation(int[] phaseAssignment, int[] imgsPerPhase){
  		this.phaseAssignment = phaseAssignment;
  		this.imgsPerPhase = imgsPerPhase;
  	}
  	
  	@Override
  	public float evaluate(ArrayList<MultiChannelGrid3D> x) {
  		// TODO Auto-generated method stub
  		return 0;
  	}
  
  	@Override
  	public void evaluateGradient(ArrayList<MultiChannelGrid3D> x,
  			ArrayList<MultiChannelGrid3D> xGrad) {
  		
  		if(imgsPerPhase == null){
  			imgsPerPhase = new int[]{ang.getNumProjections()};
  			phaseAssignment = new int[ang.getNumProjections()];
  		}
  		
  		int[] gSize = x.get(0).getSize();
  		double[] gSpace = x.get(0).getSpacing(); 
  		double[] gOrigin = x.get(0).getOrigin(); 
  		
  		for(int i = 0; i < x.size(); i++){
  			Container data = assembleDataAtPhase(i);
  			ForwProjCL fp = new ForwProjCL();
  			fp.configure(x.get(i).getChannel(0), 
  					data.img.getSize(), data.img.getSpacing(), data.pMats);
  			Grid3D sino = fp.project();
  			fp.unload();
  			Grid3D diff = (Grid3D)NumericPointwiseOperators.subtractedBy(sino, data.img);
  						
  			BackProjCL cb = new BackProjCL(gSize,gSpace,gOrigin,data.pMats);
  			Grid3D recon = cb.backprojectPixelDrivenCL(diff);
  			cb.unload();
  			MultiChannelGrid3D reconMult = xGrad.get(i);
  			reconMult.setChannel(0, recon);
  			xGrad.set(i, reconMult);
  		}	
  	}
  	
  	private Container assembleDataAtPhase(int i) {
  		Grid3D projs = new Grid3D(ang.getProjections().getSize()[0],ang.getProjections().getSize()[1],imgsPerPhase[i]);
  		projs.setSpacing(ang.getProjections().getSpacing());
  		projs.setOrigin(ang.getProjections().getOrigin());
  		Projection[] pms = new Projection[imgsPerPhase[i]];
  		int count = 0;
  		for(int k = 0; k < phaseAssignment.length; k++){
  			if(phaseAssignment[k] == i){
  				projs.setSubGrid(count, ang.getProjections().getSubGrid(k));
  				pms[count] = ang.getPMatrices()[k];
  				count++;
  			}
  		}
  		return new Container(projs,pms);
  	}
  	
  }
  