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/*
Ray
Copyright (C) 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program 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, version 3 of the License.
This program 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 have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "LibraryPeakFinder.h"
#include <RayPlatform/core/statistics.h>
#include <math.h>
#include <iostream>
#include <stdint.h>
#include <assert.h>
using namespace std;
#define CONFIG_SOFT_SIGNAL_THRESHOLD 32
#define CONFIG_PEAK_MINIMUM_SIGNAL 2
/** find multiple peaks in the distribution of inserts for a library */
void LibraryPeakFinder::findPeaks(vector<int>*x,vector<int>*y,vector<int>*peakAverages,vector<int>*peakStandardDeviation){
/* the special case of simulated data
* with a standard deviation of 0 */
uint64_t total=0;
for(int i=0;i<(int)y->size();i++){
total+=y->at(i);
}
for(int i=0;i<(int)y->size();i++){
if(total==0){
break;
}
double ratio=y->at(i)/(total+0.0);
if(y->size()<=16 && ratio>=0.90){
peakAverages->push_back(x->at(i));
peakStandardDeviation->push_back(i);
cout<<"[LibraryPeakFinder] too few points"<<endl;
return;
}
}
// Now we begin the real analysis
vector<int> backgroundData;
for(int i=0;i<(int)y->size();i++){
int verticalValue=y->at(i);
if(verticalValue < CONFIG_PEAK_MINIMUM_SIGNAL){
continue;
}
if(verticalValue < CONFIG_SOFT_SIGNAL_THRESHOLD){
backgroundData.push_back(y->at(i));
}
}
int signalAverage=(int)getAverage(&backgroundData);
#define VERBOSE
#ifdef VERBOSE
int signalMode=getMode(&backgroundData);
cout<<"Mode= "<<signalMode<<" signalAverage= "<<signalAverage<<endl;
#endif
#undef VERBOSE
int signalThreshold=signalAverage;
int minimumAccumulatedNoiseSignals=8;
int minimumAccumulatedWorthySignals=16;
int accumulatedNoiseSignals=0;
int accumulatedWorthySignals=0;
vector<int> bestHits;
bool hasHit=false;
int bestHit=-1;
for(int i=0;i<(int)x->size();i++){
int x1=x->at(i);
int y1=y->at(i);
/* skip the noise */
if(y1 < signalThreshold){
accumulatedNoiseSignals++;
if(hasHit
&& accumulatedNoiseSignals >= minimumAccumulatedNoiseSignals
){
cout<<"CURRENT IS NOISE, "<<x1<<endl;
bestHits.push_back(bestHit);
hasHit=false;
cout<<"GOT HIT "<<x->at(bestHit)<<endl;
}
accumulatedWorthySignals=0;
//cout<<"DATA "<<x1<<" "<<y1<<" NOISE"<<endl;
continue;
}
//cout<<"DATA "<<x1<<" "<<y1<<" WORTHY"<<endl;
/* if we don't have a hit, take this one */
if(!hasHit && accumulatedWorthySignals >= minimumAccumulatedWorthySignals){
accumulatedWorthySignals=0;
hasHit=true;
bestHit=i;
}
accumulatedWorthySignals++;
accumulatedNoiseSignals=0;
/* this is better than the old stuff, take it */
if(hasHit && y1 > y->at(bestHit) && accumulatedWorthySignals >= minimumAccumulatedWorthySignals){
bestHit=i;
}
}
/* harvest crops */
for(int i=0;i<(int)bestHits.size();i++){
int index=bestHits[i];
int left=index-1;
int accumulated=0;
while(left>=0 && accumulated<minimumAccumulatedNoiseSignals){
if(y->at(left) < signalThreshold){
accumulated++;
}
left--;
}
accumulated=0;
int right=index+1;
while(right<(int)y->size() && accumulated < minimumAccumulatedNoiseSignals){
if(y->at(right) < signalThreshold){
accumulated++;
}
right++;
}
vector<int> data;
vector<int> frequencies;
if(left<0)
left=0;
if(right>=(int)y->size())
right=y->size()-1;
for(int j=left;j<=right;j++){
data.push_back(x->at(j));
frequencies.push_back(y->at(j));
}
int average=getAverageFromFrequencies(&data,&frequencies);
int standardDeviation=getDeviationFromFrequencies(&data,&frequencies);
peakAverages->push_back(average);
peakStandardDeviation->push_back(standardDeviation);
}
}
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