public void integrateStackDone(IntegrateExp integrator) {
// Store background if this integrator is responsible for calculating it
if (updateBG) {
double stableMedianOutside = calcStableMedian(0.4, 0.6, curBgOutside);
double stableMedianInside = calcStableMedian(0.4, 0.6, curBgInside);
/*
int medianOutside=EvListUtil.findPercentileInt(curBgOutside.elements(), 0.5, curBgOutside.size());
int medianInside=EvListUtil.findPercentileInt(curBgInside.elements(), 0.5, curBgInside.size());
double avg=(double)curBgInt/curBgVol;
double thisBG=EvMathUtil.minAll(medianOutside,medianInside,avg);
*/
double thisBG = Math.min(stableMedianOutside, stableMedianInside);
// int thisBG=EvMathUtil.minAll(medianOutside,medianInside); //average decreased value in a
// bad value for one recording!!! I think
bg.put(integrator.frame, thisBG);
// bg.put(integrator.frame, (double)median/curBg.size());
// bg.put(integrator.frame, curBgInt/curBgVol);
}
// Store pattern in lineage
for (int i = 0; i < numSubDiv; i++) {
// double avg = (double) sliceExp[i]/(double) sliceVol[i];
double avg = (double) sliceExp[i] / (double) sliceVol[i] - bg.get(integrator.frame);
// avg /= integrator.expTime;
Lineage.Particle nuc = lin.getCreateParticle("_slice" + i);
LineageExp exp = nuc.getCreateExp(integrator.expName);
exp.level.put(integrator.frame, avg);
if (Double.isInfinite(avg) || Double.isNaN(avg))
System.out.println(
"Slice inf or nan, frame: "
+ integrator.frame
+ " "
+ getClass().getSimpleName()
+ " vol: "
+ sliceVol[i]
+ " bg: "
+ bg.get(integrator.frame)
+ " slice: "
+ i);
// System.out.println(" "+avg);
}
// System.out.println();
}
public Lineage done(
IntegrateExp integrator, TreeMap<EvDecimal, Tuple<Double, Double>> correctedExposure) {
// Set override start and end times
for (int i = 0; i < numSubDiv; i++) {
Lineage.Particle nuc = lin.getCreateParticle("_slice" + i);
nuc.overrideStart = integrator.ch.getFirstFrame();
nuc.overrideEnd = integrator.ch.getLastFrame();
}
// For AP: calculate how to correct exposure
if (correctedExposure == null)
correctedExposure =
ExpUtil.calculateCorrectExposureChange20100709(
integrator.imset,
integrator.ch,
lin,
integrator.expName,
new TreeSet<EvDecimal>(integrator.ch.getFrames()),
bg);
this.correctedExposure = correctedExposure;
// Correct for exposure changes
ExpUtil.correctExposureChange(this.correctedExposure, lin, integrator.expName);
/*
System.out.println();
System.out.println("After exp correct: "+lin.getCreateNuc("_slice0").exp.get(integrator.expName).level);
*/
// This is only for the eye
double sigMax = ExpUtil.getSignalMax(lin, integrator.expName);
double sigMin = ExpUtil.getSignalMin(lin, integrator.expName);
// System.out.println("-----------old signal min: "+numSubDiv+" "+ExpUtil.getSignalMin(lin,
// integrator.expName));
ExpUtil.normalizeSignal(lin, integrator.expName, sigMax, sigMin, 1);
// System.out.println("-----------new signal min: "+numSubDiv+" "+ExpUtil.getSignalMin(lin,
// integrator.expName));
/*
System.out.println();
System.out.println("final exp: "+lin.getCreateNuc("_slice0").exp.get(integrator.expName).level.values());
*/
return lin;
}