NPtGainAlgorithm.cpp

#include "NPtGainAlgorithm.h"
#include "AnalysisAlgorithmMap.h"
#include "AnalysisService.h"
#include "Sct/SctParameters.h"
#include "SctData/NPtGainTestResult.h"
#include "SctData/FitScanResult.h"
#include "SctData/FitObject.h"
#include "SctData/ResponseCurve.h"
#include "SctData/StandardDefects.h"
#include "SctData/ModuleConfiguration.h"
#include "SctData/ChipConfiguration.h"
#include <boost/shared_ptr.hpp>

using namespace Sct;
using namespace SctData;
using namespace boost;

using std::auto_ptr;

namespace SctAnalysis {
    

shared_ptr<AnalysisAlgorithm> NPtGainAlgorithm::clone(const TestData& testData, const string& moduleName) const throw() {
    return shared_ptr<AnalysisAlgorithm>(new NPtGainAlgorithm(testData, moduleName, *this));
}
    
shared_ptr<ResponseCurve> NPtGainAlgorithm::getResponseCurve(unsigned int nPts) throw(LogicError){
    if (nPts <= 3) {
    return shared_ptr<ResponseCurve> (new LinearResponseCurve());
    } else {
    return shared_ptr<ResponseCurve> (new ExponentialResponseCurve());
    }   
}
    
void NPtGainAlgorithm::setResponseCurve(auto_ptr<ResponseCurve> rc) throw() {
    static shared_ptr<ResponseCurve> s_responseCurve=shared_ptr<ResponseCurve>(rc.release());
}

bool NPtGainAlgorithm::inMap = AnalysisAlgorithmMap::instance().setAlgorithm("NPtGainTest", auto_ptr<AnalysisAlgorithm>(new NPtGainAlgorithm()));

shared_ptr<SctData::TestResult> NPtGainAlgorithm::createTestResult() const {
    shared_ptr<NPtGainTestResult> result (new NPtGainTestResult());
    result->setChipDataSize(nChipModule);
    result->setChannelDataSize(nChannelModule);
    
    return result;
}

void NPtGainAlgorithm::loadData() {
    loadAllFits();
}

bool NPtGainAlgorithm::canAnalyze() const {
    return hasAllFits();
}

void NPtGainAlgorithm::analyze() {
    shared_ptr<NPtGainTestResult> result = dynamic_pointer_cast<NPtGainTestResult> ( getTestResult() );
    result->setScanVariable(getFit(0)->getHeader().getVariable());  
    try{
    result->setSpecialScanPointValue(2.0);
    } catch (Sct::Throwable& e){
    e.sendToMrs(MRS_ERROR);
    }
    
    const ModuleConfiguration& config = getFit(0)->getConfiguration();
    //Reset counters
    nOnePointTrimmed = 0;
    nTwoPointTrimmed = 0;
    
    //Do chips
    for (unsigned int i=0; i<nChipModule; ++i) {
        setupGraph(i, ModuleElement::Chip(i), &FitScanResult::getChipFit, *result, result->getChipData(i), true);
        doFit(i, &FitScanResult::getChipFit, *result, result->getChipData(i));
    }

    //Do channels
    for (unsigned int i=0; i<nChannelModule; ++i) {
    ModuleElement element = ModuleElement::Channel(i);
        setupGraph(i, element, &FitScanResult::getChannelFit, *result, result->getChannelData(i), true);
    //Note - make sure we do this after we have setup the graph - that way we don't cause any problems with missing data
    //And we can check later if necessary
    if (config.channelIsMasked(i)) continue;
        doFit(i, &FitScanResult::getChannelFit, *result, result->getChannelData(i));
        doDefect(element, result->getDefects(), 
         result->getChannelData(i), result->getChipData(i/nChannelChip));
    }
    
    //mergeDefects();
    
    //Check for defects - fail if more than 15 defective channels or more than 7 consecutive defective channels
    const DefectList::DefectCollection& defects = result->getDefects().getAllDefects();
    bool passed = true;
    unsigned int totalChannels = 0;
    for (DefectList::DefectCollection::const_iterator i=defects.begin(); i!=defects.end(); ++i) {
    totalChannels += i->getModuleElement().getNChannels();
    if (i->getModuleElement().getNChannels()>7) {
        passed = false;
        break;
    }
    }
    if (totalChannels > 15) passed = false;
    
    //Add comment about number of channels trimmed
    if (nOnePointTrimmed != 0) {
    ostringstream oss;
    oss << nOnePointTrimmed << " channels had 1 point trimmed from fit";
    result->addComment(oss.str());
    }
    if (nTwoPointTrimmed != 0) {
    ostringstream oss;
    oss << nTwoPointTrimmed << " channels had 2 (or more) points trimmed from fit";
    result->addComment(oss.str());
    }
    
    result->setPassed(passed);
}
 
//Setup the graphs - also prune points
void NPtGainAlgorithm::setupGraph(unsigned int id, const ModuleElement& element, getFitFunction fitFunc, NPtGainTestResult& test, NPtGainTestResultData& testData, bool trimPoints) throw(LogicError) {
    
    unsigned int lastPoint = test.getNScans()-1;
    //Filter out points above 5fC if they are broad and we have more than 5 points
    if (trimPoints && test.getNScans() > 5) {
    double sigmaCut = 0;
    for (unsigned int i=0; i<test.getNScans(); ++i) {
        sigmaCut+= (getFit(i).get()->*fitFunc)(id).getParameter("Sigma");
    }
    sigmaCut *= 1.5/test.getNScans();   //We want 1.5*mean sigma
    //cout << "Sigma Cut set to: " << sigmaCut << endl;
    for (unsigned int i=test.getNScans() - 1; i>4; --i) {
        //cout << "Point: " << i << " sigma: " << (getFit(i).get()->*fitFunc)(id).getParameter("Sigma") << " TestPoint: " << test.getTestPointAt(i) << endl;
        const DefectList& defects = getFit(i)->getDefects();
        if (test.getTestPointAt(i) > 5 && ((getFit(i).get()->*fitFunc)(id).getParameter("Sigma") > sigmaCut || 
                           defects.defectSeverityAffectingElement(element) >= SERIOUS)) {
        lastPoint = i-1;
        }
    }
    
    //Note we should only record trimed points for chips... 
    if (lastPoint != test.getNScans() - 1) {
        if (element.isChip()) {
        ostringstream oss;
        oss << "Points trimed from response curve for chip: " << id << ". Last point " << lastPoint << " with charge " << test.getTestPointAt(lastPoint);
        test.addComment(oss.str());
        } else {    //Element is a channel
        if (lastPoint+1-test.getNScans() == 1) ++nOnePointTrimmed;
        else ++nTwoPointTrimmed;
        }
    }
    }
    
    mergeDefects(test, element, lastPoint);

    shared_ptr<TGraph> g (new TGraph(lastPoint+1));
    if (!g)
        throw InvariantViolatedError("NPtGainTestResult::setupGraph couldn't make TGraph", __FILE__, __LINE__);
    
    
    for (unsigned int j = 0; j <= lastPoint; ++j) {
        g->SetPoint(j, test.getTestPointAt(j), (getFit(j).get()->*fitFunc)(id).getParameter("Mean"));
    }
    testData.graph = g;

    shared_ptr<ResponseCurve> r=getResponseCurve(test.getNScans());
    testData.rc = r;    
}

void NPtGainAlgorithm::mergeDefects(NPtGainTestResult& test, const ModuleElement& element, unsigned int lastPoint) {
    for (unsigned int i=0; i<lastPoint; ++i) {
    auto_ptr<DefectList> defects = getFit(i)->getDefects().getDefectsEncompassingElement(element);
    const DefectList::DefectCollection& allDefects = defects->getAllDefects();
    for (DefectList::DefectCollection::const_iterator it=allDefects.begin(); it!=allDefects.end(); ++it) {
        test.getDefects().addDefect(Defect(it->getPrototype(), element));
    }
    }
}

void NPtGainAlgorithm::doFit(unsigned int id, getFitFunction fitFunc, NPtGainTestResult& test,
                              NPtGainTestResultData& testData) throw(LogicError) {
    //testData.graph->Fit(&testData.rc->getFunction(), "NQ", "", 0, 10);
    // replaced below with generalised fitting, 17/7/03 Alan Barr

    testData.rc->getFunction()->SetRange(0,10);
    AnalysisService::instance().getFitStrategy().fitTGraph(*testData.graph, *testData.rc->getFunction() );
    
    testData.gain = testData.rc->getGain(test.getSpecialScanPointValue());

    shared_ptr<const FitScanResult> specialFit = getFit(test.getSpecialScanIndex());
    //6250 is a magic number that converts noise to ENC
    if (testData.gain != 0) testData.noise = 6250 * (specialFit.get()->*fitFunc)(id).getParameter("Sigma") / testData.gain;
    else  testData.noise = 0;
    testData.offset= testData.rc->getFunction()->Eval(0.);
}

void NPtGainAlgorithm::doDefect(const ModuleElement& element, DefectList& defects, 
                const NPtGainTestResultData& data,
                const NPtGainTestResultData& comparisonData) throw(LogicError) {
    
    if (data.gain < StandardDefects::VLO_GAIN.getParameter() * comparisonData.gain)
        defects.addDefect(Defect(StandardDefects::VLO_GAIN, element));
    
    if (data.gain < StandardDefects::LO_GAIN.getParameter() * comparisonData.gain)
        defects.addDefect(Defect(StandardDefects::LO_GAIN, element));
    else if (data.gain > StandardDefects::HI_GAIN.getParameter() * comparisonData.gain)
        defects.addDefect(Defect(StandardDefects::HI_GAIN, element));

    if (data.offset < StandardDefects::LO_OFFSET.getParameter())
        defects.addDefect(Defect(StandardDefects::LO_OFFSET, element));
    else if (data.offset > StandardDefects::HI_OFFSET.getParameter())
        defects.addDefect(Defect(StandardDefects::HI_OFFSET, element));

    if (data.noise < StandardDefects::UNBONDED.getParameter())
        defects.addDefect(Defect(StandardDefects::UNBONDED, element));
    else if (data.noise < StandardDefects::PARTBONDED.getParameter())
        defects.addDefect(Defect(StandardDefects::PARTBONDED, element));
    else if (data.noise > StandardDefects::NOISY.getParameter() * comparisonData.noise)
        defects.addDefect(Defect(StandardDefects::NOISY, element));
    
    if (data.noise > StandardDefects::V_NOISY.getParameter() * comparisonData.noise)
        defects.addDefect(Defect(StandardDefects::V_NOISY, element));
}
}

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