diff -u -r1.5 -r1.6
--- HPSAPV25.java	11 Apr 2012 23:57:12 -0000	1.5
+++ HPSAPV25.java	21 Apr 2012 07:39:18 -0000	1.6
@@ -15,7 +15,7 @@

 /**
  *
  * @author Omar Moreno <[log in to unmask]>

- * @version $Id: HPSAPV25.java,v 1.5 2012/04/11 23:57:12 meeg Exp $

+ * @version $Id: HPSAPV25.java,v 1.6 2012/04/21 07:39:18 omoreno Exp $

  */
 public class HPSAPV25 {
 

@@ -27,21 +27,27 @@

 	private static final double APV25_NOISE_INTERCEPT_DECON = 396;  //e- RMS
 	private static final double APV25_NOISE_SLOPE_PEAK = 36;       // e- rms/pF
 	private static final double APV25_NOISE_SLOPE_DECON = 59.4;       // e- rms/pF

+	

 	// Number of electron-hole pairs created by a min. ionizing particle 
 	// in 300 micrometers of Si
 	private static final int MIP = 25000;  // electron-hole pairs

+	

 	// Total number of channels per APV25 chip
 	private static final int APV25_CHANNELS = 128;

+	

 	// APV25 trigger bit
 	public static boolean triggerBit = false;

+	

 	// 
 	private int apv25ShapingTime = 35; // [ns] 
 	private int apv25SamplingTime = 24; // [ns]
 	private double analogDCLevel = 0;  // [mA] (Pedestal)
 	public int apv25ClockCycle = 0;
 	private String apv25Mode = "multi-peak";

+	

 	// APV25 Channel
 	private APV25Channel channel;

+	

 	// Histograms
 	protected AIDA aida = AIDA.defaultInstance();
 

@@ -110,9 +116,8 @@

 	 * @param charge   : Total charge being injected
 	 * @param pipeline : Analog pipeline associated with a channel
 	 */

-	public void injectCharge(double charge,
-			double noiseRMS,
-			APV25AnalogPipeline pipeline) {

+	public void injectCharge(double charge, double noiseRMS, APV25AnalogPipeline pipeline) {
+		

 		// Shape the injected charge
 		getChannel().shapeSignal(charge);
 

@@ -126,14 +131,12 @@

 	 * 
 	 * @param analogPipelineMap : 
 	 */

-	public void incrementAllPointerPositions(
-			Map<Integer, APV25AnalogPipeline> analogPipelineMap) {

+	public void incrementAllPointerPositions(Map<Integer, APV25AnalogPipeline> analogPipelineMap) {

 		// Loop through all of the channels and increment the position of
 		// all the trigger and writer pointers
 		for (Map.Entry<Integer, APV25AnalogPipeline> entry : analogPipelineMap.entrySet()) {
 			entry.getValue().step();
 		}

-

 	}
 
 	/**

@@ -164,21 +167,15 @@

 		double[] output;
 
 		// Create the data streams

-		for (int chipIndex = 0;
-				chipIndex < Math.ceil((double) pipelineMap.size() / APV25_CHANNELS);
-				chipIndex++) {
-

+		for (int chipIndex = 0; chipIndex < Math.ceil((double) pipelineMap.size() / APV25_CHANNELS); chipIndex++) {

 			apv25Map.put(chipIndex, createOutputArray(apv25Address, -4));
 		}
 
 		// Loop over all channels and readout the cells which the
 		// trigger pointer points to
 		for (int channelN = 0; channelN < pipelineMap.size(); channelN++) {

-

 			output = apv25Map.get((int) Math.floor(channelN / APV25_CHANNELS));

-

 			output[channelN % 128 + 12] += (pipelineMap.get(channelN).readOut() / APV25_FRONT_END_GAIN) * APV25_MULTIPLEXER_GAIN + analogDCLevel;

-

 		}
 		return apv25Map;
 	}

@@ -239,14 +236,9 @@

 		 * @return noise in electrons
 		 */
 		public double computeNoise(double capacitance) {

-			if (apv25Mode.equals("peak")
-					|| apv25Mode.equals("multi-peak")) {
-				return APV25_NOISE_INTERCEPT_PEAK
-						+ APV25_NOISE_SLOPE_PEAK * capacitance;
-			} else {
-				return APV25_NOISE_INTERCEPT_DECON
-						+ APV25_NOISE_SLOPE_DECON * capacitance;
-			}

+			if (apv25Mode.equals("peak") || apv25Mode.equals("multi-peak"))
+				return APV25_NOISE_INTERCEPT_PEAK + APV25_NOISE_SLOPE_PEAK * capacitance;
+			else return APV25_NOISE_INTERCEPT_DECON + APV25_NOISE_SLOPE_DECON * capacitance;

 		}
 
 		/**

@@ -272,19 +264,12 @@

 				// Sample the shaper signal
 				double sample = shaperSignal.getAmplitudeAtTime(sample_time);
 

-				// Only add the value into the buffer if it is greater than
-				// the noise threshold. Note that this isn't done within
-				// the apv25, however, it will clean up the signal a bit
-				// for simulation purposes
-				// This should be done by the data processing module
-				//if( sample > 0.0001 /*(1*noiseRMS/MIP)*APV25_FRONT_END_GAIN)*/) {

 				pipeline.addToCell(cell, sample);

-				//}

 			}
 		}
 
 		//-----------------------------------//

-		//--- APV25 Shaper Signal ---//

+		//---     APV25 Shaper Signal     ---//

 		//-----------------------------------//
 		/**
 		 * 

@@ -315,9 +300,7 @@

 			 *               sampled
 			 */
 			private double getAmplitudeAtTime(double time) {

-
-				return maxAmp * (Math.max(0, time) / apv25ShapingTime) * Math.exp(
-						1 - (time / apv25ShapingTime));

+				return maxAmp * (Math.max(0, time) / apv25ShapingTime) * Math.exp(1 - (time / apv25ShapingTime));

 			}
 		}
 

@@ -328,9 +311,7 @@

 		public class APV25AnalogPipeline extends RingBuffer {
 			private int _trigger_latency = (int) Math.floor(220 / apv25SamplingTime);
 

-			public APV25AnalogPipeline() {
-				super(ANALOG_PIPELINE_LENGTH);
-			}

+			public APV25AnalogPipeline() { super(ANALOG_PIPELINE_LENGTH); }

 
 			/**
 			 * Set the trigger latency