#include "predatorpreyprinter.h"
#include "predatorpreyaggregator.h"
#include "areatime.h"
#include "readword.h"
#include "readaggregation.h"
#include "errorhandler.h"
#include "predator.h"
#include "stockprey.h"
#include "gadget.h"
#include "runid.h"
#include "global.h"
PredatorPreyPrinter::PredatorPreyPrinter(CommentStream& infile, const TimeClass* const TimeInfo)
: Printer(PREDATORPREYPRINTER), aggregator(0), alptr(0), dptr(0) {
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
//read in the predator names
int i = 0;
infile >> text >> ws;
if (strcasecmp(text, "predatornames") != 0)
handle.logFileUnexpected(LOGFAIL, "predatornames", text);
infile >> text >> ws;
while (!infile.eof() && (strcasecmp(text, "preynames") != 0)) {
predatornames.resize(new char[strlen(text) + 1]);
strcpy(predatornames[i++], text);
infile >> text >> ws;
}
if (predatornames.Size() == 0)
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to read predators");
handle.logMessage(LOGMESSAGE, "Read predator data - number of predators", predatornames.Size());
//read in the prey names
i = 0;
infile >> text >> ws;
while (!infile.eof() && (strcasecmp(text, "areaaggfile") != 0)) {
preynames.resize(new char[strlen(text) + 1]);
strcpy(preynames[i++], text);
infile >> text >> ws;
}
if (preynames.Size() == 0)
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to read preys");
handle.logMessage(LOGMESSAGE, "Read prey data - number of preys", preynames.Size());
//read in area aggregation from file
filename = new char[MaxStrLength];
strncpy(filename, "", MaxStrLength);
ifstream datafile;
CommentStream subdata(datafile);
infile >> filename >> ws;
datafile.open(filename, ios::in);
handle.checkIfFailure(datafile, filename);
handle.Open(filename);
i = readAggregation(subdata, areas, areaindex);
handle.Close();
datafile.close();
datafile.clear();
//read in age aggregation from file
readWordAndValue(infile, "ageaggfile", filename);
datafile.open(filename, ios::in);
handle.checkIfFailure(datafile, filename);
handle.Open(filename);
i = readAggregation(subdata, ages, ageindex);
handle.Close();
datafile.close();
datafile.clear();
//read in length aggregation from file
DoubleVector lengths;
readWordAndValue(infile, "lenaggfile", filename);
datafile.open(filename, ios::in);
handle.checkIfFailure(datafile, filename);
handle.Open(filename);
i = readLengthAggregation(subdata, lengths, lenindex);
handle.Close();
datafile.close();
datafile.clear();
LgrpDiv = new LengthGroupDivision(lengths);
if (LgrpDiv->Error())
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - failed to create length group");
//open the printfile
readWordAndValue(infile, "printfile", filename);
outfile.open(filename, ios::out);
handle.checkIfFailure(outfile, filename);
infile >> text >> ws;
if (strcasecmp(text, "precision") == 0) {
infile >> precision >> ws >> text >> ws;
width = precision + 4;
} else {
// use default values
precision = largeprecision;
width = largewidth;
}
if (precision < 0)
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - invalid value of precision");
if (strcasecmp(text, "printatstart") == 0)
infile >> printtimeid >> ws >> text >> ws;
else
printtimeid = 0;
if (printtimeid != 0 && printtimeid != 1)
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - invalid value of printatstart");
if (strcasecmp(text, "yearsandsteps") != 0)
handle.logFileUnexpected(LOGFAIL, "yearsandsteps", text);
if (!AAT.readFromFile(infile, TimeInfo))
handle.logFileMessage(LOGFAIL, "\nError in predatorpreyprinter - wrong format for yearsandsteps");
//prepare for next printfile component
infile >> ws;
if (!infile.eof()) {
infile >> text >> ws;
if (strcasecmp(text, "[component]") != 0)
handle.logFileUnexpected(LOGFAIL, "[component]", text);
}
//finished initializing. Now print first lines
outfile << "; ";
RUNID.Print(outfile);
outfile << "; Predation output file for the following predators";
for (i = 0; i < predatornames.Size(); i++)
outfile << sep << predatornames[i];
outfile << "\n; Consuming the following preys";
for (i = 0; i < preynames.Size(); i++)
outfile << sep << preynames[i];
if (printtimeid == 0)
outfile << "\n; Printing the following information at the end of each timestep";
else
outfile << "\n; Printing the following information at the start of each timestep";
outfile << "\n; year-step-area-age-length-number consumed-biomass consumed-mortality\n";
outfile.flush();
}
void PredatorPreyPrinter::setPredAndPrey(PredatorPtrVector& predatorvec,
PreyPtrVector& preyvec, const AreaClass* const Area) {
PredatorPtrVector predators;
PreyPtrVector preys;
int i, j, k, found, minage, maxage;
delete aggregator;
for (i = 0; i < predatorvec.Size(); i++)
for (j = 0; j < predatornames.Size(); j++)
if (strcasecmp(predatorvec[i]->getName(), predatornames[j]) == 0)
predators.resize(predatorvec[i]);
if (predators.Size() != predatornames.Size()) {
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - failed to match predators");
for (i = 0; i < predatorvec.Size(); i++)
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - found predator", predatorvec[i]->getName());
for (i = 0; i < predatornames.Size(); i++)
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - looking for predator", predatornames[i]);
handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
}
for (i = 0; i < predators.Size(); i++)
for (j = 0; j < predators.Size(); j++)
if ((strcasecmp(predators[i]->getName(), predators[j]->getName()) == 0) && (i != j))
handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - repeated predator", predators[i]->getName());
for (i = 0; i < preyvec.Size(); i++)
for (j = 0; j < preynames.Size(); j++)
if (strcasecmp(preyvec[i]->getName(), preynames[j]) == 0)
preys.resize(preyvec[i]);
if (preys.Size() != preynames.Size()) {
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - failed to match preys");
for (i = 0; i < preyvec.Size(); i++)
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - found prey", preyvec[i]->getName());
for (i = 0; i < preynames.Size(); i++)
handle.logMessage(LOGWARN, "Error in predatorpreyprinter - looking for prey", preynames[i]);
handle.logMessage(LOGFAIL, ""); //JMB this will exit gadget
}
for (i = 0; i < preys.Size(); i++)
for (j = 0; j < preys.Size(); j++)
if ((strcasecmp(preys[i]->getName(), preys[j]->getName()) == 0) && (i != j))
handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - repeated prey", preys[i]->getName());
//check that the preys are stocks and not otherfood
for (i = 0; i < preys.Size(); i++)
if (preys[i]->getType() == LENGTHPREY)
handle.logMessage(LOGFAIL, "Error in predatorpreyprinter - cannot print prey", preys[i]->getName());
//change from outer areas to inner areas.
for (i = 0; i < areas.Nrow(); i++)
for (j = 0; j < areas.Ncol(i); j++)
areas[i][j] = Area->getInnerArea(areas[i][j]);
//check predator and prey areas, ages and length groups
if (handle.getLogLevel() >= LOGWARN) {
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (i = 0; i < predators.Size(); i++)
for (k = 0; k < areas.Ncol(j); k++)
if (predators[i]->isInArea(areas[j][k]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - predators not defined on all areas");
}
for (j = 0; j < areas.Nrow(); j++) {
found = 0;
for (i = 0; i < preys.Size(); i++)
for (k = 0; k < areas.Ncol(j); k++)
if (preys[i]->isInArea(areas[j][k]))
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - preys not defined on all areas");
}
minage = 9999;
maxage = -1;
for (i = 0; i < ages.Nrow(); i++) {
for (j = 0; j < ages.Ncol(i); j++) {
minage = min(ages[i][j], minage);
maxage = max(ages[i][j], maxage);
}
}
found = 0;
for (i = 0; i < preys.Size(); i++)
if (minage >= ((StockPrey*)preys[i])->minAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - minimum age less than prey age");
found = 0;
for (i = 0; i < preys.Size(); i++)
if (maxage <= ((StockPrey*)preys[i])->maxAge())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - maximum age greater than prey age");
found = 0;
for (i = 0; i < preys.Size(); i++)
if (LgrpDiv->maxLength(0) > preys[i]->getLengthGroupDiv()->minLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - minimum length group less than prey length");
found = 0;
for (i = 0; i < preys.Size(); i++)
if (LgrpDiv->minLength(LgrpDiv->numLengthGroups()) < preys[i]->getLengthGroupDiv()->maxLength())
found++;
if (found == 0)
handle.logMessage(LOGWARN, "Warning in predatorpreyprinter - maximum length group greater than prey length");
}
aggregator = new PredatorPreyAggregator(predators, preys, LgrpDiv, areas, ages);
}
void PredatorPreyPrinter::Print(const TimeClass* const TimeInfo, int printtime) {
if ((!AAT.atCurrentTime(TimeInfo)) || (printtime != printtimeid))
return;
int a, age, len;
aggregator->Sum(TimeInfo);
alptr = &aggregator->getConsumption();
for (a = 0; a < areas.Nrow(); a++) {
dptr = aggregator->getMortality()[a];
for (age = (*alptr)[a].minAge(); age <= (*alptr)[a].maxAge(); age++) {
for (len = (*alptr)[a].minLength(age); len < (*alptr)[a].maxLength(age); len++) {
outfile << setw(lowwidth) << TimeInfo->getYear() << sep
<< setw(lowwidth) << TimeInfo->getStep() << sep
<< setw(printwidth) << areaindex[a] << sep
<< setw(printwidth) << ageindex[age] << sep
<< setw(printwidth) << lenindex[len] << sep;
//JMB crude filter to remove the 'silly' values from the output
if (((*alptr)[a][age][len].N < rathersmall) || ((*alptr)[a][age][len].W < 0.0))
outfile << setw(width) << 0 << sep << setw(width) << 0 << sep << setw(width) << 0 << endl;
else
outfile << setprecision(precision) << setw(width) << (*alptr)[a][age][len].N
<< sep << setprecision(precision) << setw(width)
<< (*alptr)[a][age][len].N * (*alptr)[a][age][len].W
<< sep << setprecision(precision) << setw(width)
<< (*dptr)[age][len] << endl;
}
}
}
outfile.flush();
}
PredatorPreyPrinter::~PredatorPreyPrinter() {
outfile.close();
outfile.clear();
delete LgrpDiv;
delete aggregator;
int i;
for (i = 0; i < predatornames.Size(); i++)
delete[] predatornames[i];
for (i = 0; i < preynames.Size(); i++)
delete[] preynames[i];
for (i = 0; i < lenindex.Size(); i++)
delete[] lenindex[i];
for (i = 0; i < ageindex.Size(); i++)
delete[] ageindex[i];
for (i = 0; i < areaindex.Size(); i++)
delete[] areaindex[i];
}