Fix AHDC pulse indexing and estimate the pedestal of the AHDC waveform using the first five samples (#480)

* Recover more data from AHDC pulse

* caotjava for mon12/ahdc (fix merging conflicts)

* Don't change HipoExtractor but Override ModeAHDC

* Declare `protected` some methods of HipoExtractor

* Estimate the pedestal using the first five samples

* Fix AHDC pulse indexing

---------

Co-authored-by: Felix Touchte Codjo <touchte@ifarm2402.jlab.org>
Co-authored-by: Felix Touchte Codjo <touchte@ifarm2401.jlab.org>

Author: 3 people

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/ModeAHDC.java

@@ -58,7 +58,7 @@ public List<Pulse> extract(NamedEntry pars, int id, short... samples){
 		float leadingEdgeTime = 0; // moment when the signal reaches a Constant Fraction of its Amplitude uphill (fitted)
 		float trailingEdgeTime = 0; // moment when the signal reaches a Constant Fraction of its Amplitude downhill (fitted)
 		float timeOverThreshold = 0; // is equal to (timeFallCFA - timeRiseCFA)
-		float constantFractionTime ; // time extracted using the Constant Fraction Discriminator (CFD) algorithm (fitted)
+		float constantFractionTime = 0; // time extracted using the Constant Fraction Discriminator (CFD) algorithm (fitted)
 		/// /////////////////////////
 		// Begin waveform correction
 		/// ////////////////////////
@@ -75,11 +75,14 @@ public List<Pulse> extract(NamedEntry pars, int id, short... samples){
 		//private void waveformCorrection(short[] samples, short adcOffset, float samplingTime, int sparseSample, int binMax, int adcMax, int integral, short samplesCorr[], int binOffset, int timeMax){
 			binNumber = samples.length;
 			binMax = 0;
+			if (binNumber >= 5) {
+				adcOffset = (short) ((samples[0] + samples[1] + samples[2] + samples[3] + samples[4])/5); // try to estimate the baseline (pedestal) using the first five samples
+			}
 			adcMax = (short) (samples[0] - adcOffset);
 			integral = 0;
 			samplesCorr = new short[binNumber];
 			for (int bin = 0; bin < binNumber; bin++){
-				samplesCorr[bin] = (short) (samples[bin] - adcOffset);
+				samplesCorr[bin] = (short) Math.max(samples[bin] - adcOffset, 0);
 				if (adcMax < samplesCorr[bin]){
 					adcMax = samplesCorr[bin];
 					binMax = bin;
@@ -239,6 +242,7 @@ public List<Pulse> extract(NamedEntry pars, int id, short... samples){
 		//}
 		// output
 		Pulse pulse = new Pulse();
+		pulse.id = id;
 		pulse.adcMax = adcMax;
 		pulse.time = timeMax;
 		pulse.timestamp = timestamp;