code: /*******************************************************************************
   * Copyright (c) 2016 Attila Kovacs <attila[AT]sigmyne.com>.
   * All rights reserved. 
   * 
   * This file is part of crush.
   * 
   *     crush is free software: you can redistribute it and/or modify
   *     it under the terms of the GNU General Public License as published by
   *     the Free Software Foundation, either version 3 of the License, or
   *     (at your option) any later version.
   * 
   *     crush is distributed in the hope that it will be useful,
   *     but WITHOUT ANY WARRANTY; without even the implied warranty of
   *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   *     GNU General Public License for more details.
   * 
   *     You should have received a copy of the GNU General Public License
   *     along with crush.  If not, see <http://www.gnu.org/licenses/>.
   * 
   * Contributors:
   *     Attila Kovacs <attila[AT]sigmyne.com> - initial API and implementation
   ******************************************************************************/
  
  package crush.instrument.hawcplus;
  
  
  import crush.Channel;
  import crush.telescope.sofia.SofiaChannel;
  import jnum.Unit;
  import jnum.Util;
  import jnum.math.Vector2D;
  import jnum.text.SmartTokenizer;
  
  public class HawcPixel extends SofiaChannel {
  	/**
  	 * 
  	 */
  	private static final long serialVersionUID = 5898856651596856837L;
  	
  	public int pol = -1, sub = -1, subrow = -1, col = -1, mux = -1, row = -1, biasLine = -1, seriesArray = -1;
  	public double subGain = 1.0, muxGain = 1.0, pinGain = 1.0, biasGain = 1.0, seriesGain = 1.0;
  	
  	int fitsIndex, fitsRow, fitsCol;
  	
  	float jumpLevel = 0.0F;
  	boolean hasJumps = false;
  	
  	HawcPixel(Hawc array, int zeroIndex) {
  		super(array, zeroIndex);
  		
  		col = zeroIndex % Hawc.subarrayCols;
  		row = zeroIndex / Hawc.subarrayCols;
  		sub = zeroIndex / Hawc.subarrayPixels;
  		pol = (sub>>1);
  		
  		fitsRow = subrow = row % Hawc.rows;
  		biasLine = row >>> 1;
  		
  		fitsCol = mux = sub * Hawc.subarrayCols + col;
  		seriesArray = mux >>> 2;
  		
  		fitsIndex = fitsRow * HawcFrame.FITS_COLS + fitsCol;
  		
  		// Flag the dark squids as such...
  		if(subrow == Hawc.DARK_SQUID_ROW) flag(FLAG_BLIND);
  	}
  	
  	@Override
      public Hawc getInstrument() { return (Hawc) super.getInstrument(); }
  	
  	void calcSIBSPosition() {
  	    if(isFlagged(FLAG_BLIND)) getPixel().setPosition(null);
  	    getPixel().setPosition(getInstrument().getLayout().getSIBSPosition(sub, subrow, col));
  	}
  		
  	@Override
  	public int getCriticalFlags() {
  		return FLAG_DEAD;
  	}
  	
  	@Override
  	public void uniformGains() {
  		super.uniformGains();
  		muxGain = 1.0;
  	}
  	
  	@Override
  	public String toString() {
  		return super.toString() 
  		        + "\t" + Util.f3.format(coupling) 
  		        + "\t" + Util.f3.format(getInstrument().subarrayGainRenorm[sub])
  		        + "\t" + Util.f3.format(muxGain) 
  		        + "\t" + getFixedIndex() 
  		        + "\t" + sub 
  		        + "\t" + subrow 
  		        + "\t" + col;
  	}
  	
  	@Override
  	public void parseValues(SmartTokenizer tokens, int criticalFlags) {	
  		super.parseValues(tokens, criticalFlags);
  		
  		if(tokens.hasMoreTokens()) coupling = tokens.nextDouble();
  		if(tokens.hasMoreTokens()) tokens.nextToken();
  		if(tokens.hasMoreTokens()) muxGain = tokens.nextDouble();
  		
  		if(coupling < 0.3) flag(Channel.FLAG_DEAD);
  		else if(coupling > 3.0) flag(Channel.FLAG_DEAD);
  		else if(coupling == 1.0) flag(Channel.FLAG_DEAD);
  		
  		if(gain < 0.3) flag(Channel.FLAG_DEAD);
          else if(gain > 3.0) flag(Channel.FLAG_DEAD);
  			
  		if(isFlagged(Channel.FLAG_DEAD)) coupling = 0.0;
  	}
  	
  	@Override
      public String getID() {
  	    return Hawc.polID[pol] + (sub & 1) + "[" + subrow + "," + col + "]";
  	}
  	
  	public static final Vector2D physicalSize = new Vector2D(1.132 * Unit.mm, 1.132 * Unit.mm);
  	
  	//public final static int FLAG_POL = softwareFlags.next('p', "Bad polarray gain").value();
  	public final static int FLAG_SUB = softwareFlags.next('@', "Bad subarray gain").value();
  	public final static int FLAG_BIAS = softwareFlags.next('b', "Bad TES bias gain").value();
  	public final static int FLAG_MUX = softwareFlags.next('m', "Bad MUX gain").value();
  	public final static int FLAG_ROW = softwareFlags.next('R', "Bad detector row gain").value();
  	public final static int FLAG_SERIES_ARRAY = softwareFlags.next('M', "Bad series array gain").value();
  	public final static int FLAG_FLICKER = softwareFlags.next('T', "Flicker noise").value();
  
  
  }
  