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agomez |
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#include "sibylengthonstep.h" |
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#include "stock.h" |
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#include "areatime.h" |
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#include "errorhandler.h" |
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#include "mathfunc.h" |
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#include "gadget.h" |
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#include "global.h" |
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SIByLengthOnStep::SIByLengthOnStep(CommentStream& infile, const IntMatrix& areas,
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const DoubleVector& lengths, const CharPtrVector& areaindex,
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const CharPtrVector& lenindex, const TimeClass* const TimeInfo,
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const char* datafilename, const char* givenname, int bio)
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: SIOnStep(infile, datafilename, areaindex, TimeInfo, areas, lenindex, givenname, bio, SILENGTH) {
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LgrpDiv = new LengthGroupDivision(lengths);
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if (LgrpDiv->Error())
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handle.logMessage(LOGFAIL, "Error in surveyindex - failed to create length group");
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}
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SIByLengthOnStep::~SIByLengthOnStep() {
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if (aggregator != 0)
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delete aggregator;
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}
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void SIByLengthOnStep::setFleetsAndStocks(FleetPtrVector& Fleets, StockPtrVector& Stocks) {
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int i, found, minage, maxage;
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if (Stocks.Size() == 0)
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handle.logMessage(LOGFAIL, "Error in surveyindex - failed to initialise stock data");
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minage = Stocks[0]->minAge();
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maxage = Stocks[0]->maxAge();
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if (Stocks.Size() > 1) {
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for (i = 1; i < Stocks.Size(); i++) {
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minage = min(Stocks[i]->minAge(), minage);
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maxage = max(Stocks[i]->maxAge(), maxage);
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}
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}
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Ages.AddRows(1, maxage - minage + 1, 0);
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for (i = 0; i < Ages.Ncol(); i++)
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Ages[0][i] = i + minage;
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//check stock lengths
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if (handle.getLogLevel() >= LOGWARN) {
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found = 0;
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for (i = 0; i < Stocks.Size(); i++)
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if (LgrpDiv->maxLength(0) > Stocks[i]->getLengthGroupDiv()->minLength())
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in surveyindex - minimum length group less than stock length");
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found = 0;
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for (i = 0; i < Stocks.Size(); i++)
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if (LgrpDiv->minLength(LgrpDiv->numLengthGroups()) < Stocks[i]->getLengthGroupDiv()->maxLength())
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found++;
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if (found == 0)
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handle.logMessage(LOGWARN, "Warning in surveyindex - maximum length group greater than stock length");
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}
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aggregator = new StockAggregator(Stocks, LgrpDiv, Areas, Ages);
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}
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void SIByLengthOnStep::Sum(const TimeClass* const TimeInfo) {
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if (!AAT.atCurrentTime(TimeInfo))
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return;
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int a, i;
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timeindex = -1;
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for (i = 0; i < Years.Size(); i++)
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if ((Years[i] == TimeInfo->getYear()) && (Steps[i] == TimeInfo->getStep()))
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timeindex = i;
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if (timeindex == -1)
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handle.logMessage(LOGFAIL, "Error in surveyindex - invalid timestep");
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if (handle.getLogLevel() >= LOGMESSAGE)
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handle.logMessage(LOGMESSAGE, "Calculating index for surveyindex component", this->getName());
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aggregator->Sum();
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alptr = &aggregator->getSum();
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//alptr will only have one age group
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for (a = 0; a < Areas.Nrow(); a++)
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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(*modelIndex[timeindex])[a][i] = (*alptr)[a][0][i].N;
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if (biomass) //JMB experimental survey index based on the biomass
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for (a = 0; a < Areas.Nrow(); a++)
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for (i = 0; i < LgrpDiv->numLengthGroups(); i++)
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(*modelIndex[timeindex])[a][i] *= (*alptr)[a][0][i].W;
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}
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