#include "renewal.h"
#include "errorhandler.h"
#include "readfunc.h"
#include "keeper.h"
#include "readword.h"
#include "gadget.h"
#include "global.h"
RenewalData::RenewalData(CommentStream& infile, const IntVector& Areas,
const AreaClass* const Area, const TimeClass* const TimeInfo, Keeper* const keeper,
const char* refWeightFile, const char* givenname, int minage, int maxage, double DL)
: HasName(givenname), LivesOnAreas(Areas), CI(0), LgrpDiv(0) {
keeper->addString("renewaldata");
ifstream subfile;
CommentStream subcomment(subfile);
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
index = 0;
int i, j;
double minlength, maxlength, dl;
readWordAndVariable(infile, "minlength", minlength);
readWordAndVariable(infile, "maxlength", maxlength);
//JMB - changed to make the reading of dl optional
//if it isnt specifed here, it will default to the dl value of the stock
infile >> ws;
char c = infile.peek();
if ((c == 'd') || (c == 'D'))
readWordAndVariable(infile, "dl", dl);
else
dl = DL;
LgrpDiv = new LengthGroupDivision(minlength, maxlength, dl);
if (LgrpDiv->Error())
handle.logMessage(LOGFAIL, "Error in renewal - failed to create length group");
infile >> text >> ws;
if ((strcasecmp(text, "normalcondfile") == 0)) {
//read renewal data in mean length format, using the reference weight file
readoption = 0;
infile >> text >> ws;
subfile.open(text, ios::in);
handle.checkIfFailure(subfile, text);
handle.Open(text);
this->readNormalConditionData(subcomment, keeper, TimeInfo, Area, minage, maxage);
handle.Close();
subfile.close();
subfile.clear();
//read information on reference weights.
DoubleMatrix tmpRefW;
keeper->addString("referenceweights");
subfile.open(refWeightFile, ios::in);
handle.checkIfFailure(subfile, refWeightFile);
handle.Open(refWeightFile);
readRefWeights(subcomment, tmpRefW);
handle.Close();
subfile.close();
subfile.clear();
//Interpolate the reference weights. First there are some error checks.
if (LgrpDiv->meanLength(0) < tmpRefW[0][0] ||
LgrpDiv->meanLength(LgrpDiv->numLengthGroups() - 1) > tmpRefW[tmpRefW.Nrow() - 1][0])
handle.logFileMessage(LOGFAIL, "lengths for reference weights must span the range of initial condition lengths");
//Aggregate the reference weight data to be the same format
double ratio, tmplen;
refWeight.resize(LgrpDiv->numLengthGroups(), 0.0);
int pos = 0;
for (j = 0; j < LgrpDiv->numLengthGroups(); j++) {
tmplen = LgrpDiv->meanLength(j);
for (i = pos; i < tmpRefW.Nrow() - 1; i++) {
if (((tmplen > tmpRefW[i][0]) || (isEqual(tmplen, tmpRefW[i][0]))) &&
((tmplen < tmpRefW[i + 1][0]) || (isEqual(tmplen, tmpRefW[i + 1][0])))) {
ratio = (tmplen - tmpRefW[i][0]) / (tmpRefW[i + 1][0] - tmpRefW[i][0]);
refWeight[j] = tmpRefW[i][1] + ratio * (tmpRefW[i + 1][1] - tmpRefW[i][1]);
pos = i;
}
}
}
keeper->clearLast();
} else if ((strcasecmp(text, "renewaldatafile") == 0) || (strcasecmp(text, "normalparamfile") == 0)) {
//read renewal data in mean length format, using a length weight relationship
readoption = 1;
infile >> text >> ws;
subfile.open(text, ios::in);
handle.checkIfFailure(subfile, text);
handle.Open(text);
this->readNormalParameterData(subcomment, keeper, TimeInfo, Area, minage, maxage);
handle.Close();
subfile.close();
subfile.clear();
} else if ((strcasecmp(text, "numberfile") == 0)) {
//read renewal data in number format
readoption = 2;
infile >> text >> ws;
subfile.open(text, ios::in);
handle.checkIfFailure(subfile, text);
handle.Open(text);
this->readNumberData(subcomment, keeper, TimeInfo, Area, minage, maxage);
handle.Close();
subfile.close();
subfile.clear();
} else
handle.logFileMessage(LOGFAIL, "unrecognised renewal data format", text);
keeper->clearLast();
}
void RenewalData::readNormalParameterData(CommentStream& infile, Keeper* const keeper,
const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
char c;
int year, step, area, age, keepdata, count, reject;
PopInfoIndexVector poptmp(LgrpDiv->numLengthGroups(), 0);
//We now expect to find the renewal data in the following format
//year, step, area, age, number, mean, sdev, alpha, beta
infile >> ws;
if (countColumns(infile) != 9)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 9");
year = step = area = age = count = reject = 0;
while (!infile.eof()) {
//crude check to see if something has gone wrong and avoid infinite loops
if (!(isdigit(infile.peek())))
handle.logFileMessage(LOGFAIL, "failed to read data from file");
keepdata = 1;
infile >> year >> step >> area >> age >> ws;
if (!(TimeInfo->isWithinPeriod(year, step)))
keepdata = 0;
if (!(this->isInArea(Area->getInnerArea(area))))
keepdata = 0;
if ((age < minage) || (age > maxage))
keepdata = 0;
if (keepdata == 1) {
//renewal data is required, so store it
renewalTime.resize(1, TimeInfo->calcSteps(year, step));
renewalArea.resize(1, Area->getInnerArea(area));
renewalAge.resize(1, age);
renewalMult.resize(1, keeper);
meanLength.resize(1, keeper);
sdevLength.resize(1, keeper);
alpha.resize(1, keeper);
beta.resize(1, keeper);
renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
infile >> renewalMult[count] >> ws;
infile >> meanLength[count] >> ws;
infile >> sdevLength[count] >> ws;
infile >> alpha[count] >> ws;
infile >> beta[count] >> ws;
renewalMult[count].Inform(keeper);
meanLength[count].Inform(keeper);
sdevLength[count].Inform(keeper);
alpha[count].Inform(keeper);
beta[count].Inform(keeper);
count++;
} else { //renewal data not required - skip rest of line
reject++;
infile.get(c);
while (c != '\n' && !infile.eof())
infile.get(c);
infile >> ws;
}
}
if (count == 0)
handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
}
void RenewalData::readNormalConditionData(CommentStream& infile, Keeper* const keeper,
const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
char c;
int year, step, area, age, keepdata, count, reject;
PopInfoIndexVector poptmp(LgrpDiv->numLengthGroups(), 0);
//We now expect to find the renewal data in the following format
//year, step, area, age, number, mean, sdev, cond
infile >> ws;
if (countColumns(infile) != 8)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 8");
year = step = area = age = count = reject = 0;
while (!infile.eof()) {
//crude check to see if something has gone wrong and avoid infinite loops
if (!(isdigit(infile.peek())))
handle.logFileMessage(LOGFAIL, "failed to read data from file");
keepdata = 1;
infile >> year >> step >> area >> age >> ws;
if (!(TimeInfo->isWithinPeriod(year, step)))
keepdata = 0;
if (!(this->isInArea(Area->getInnerArea(area))))
keepdata = 0;
if ((age < minage) || (age > maxage))
keepdata = 0;
if (keepdata == 1) {
//renewal data is required, so store it
renewalTime.resize(1, TimeInfo->calcSteps(year, step));
renewalArea.resize(1, Area->getInnerArea(area));
renewalAge.resize(1, age);
renewalMult.resize(1, keeper);
meanLength.resize(1, keeper);
sdevLength.resize(1, keeper);
relCond.resize(1, keeper);
renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
infile >> renewalMult[count] >> ws;
infile >> meanLength[count] >> ws;
infile >> sdevLength[count] >> ws;
infile >> relCond[count] >> ws;
renewalMult[count].Inform(keeper);
meanLength[count].Inform(keeper);
sdevLength[count].Inform(keeper);
relCond[count].Inform(keeper);
count++;
} else { //renewal data not required - skip rest of line
reject++;
infile.get(c);
while (c != '\n' && !infile.eof())
infile.get(c);
infile >> ws;
}
}
if (count == 0)
handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
}
void RenewalData::readNumberData(CommentStream& infile, Keeper* const keeper,
const TimeClass* const TimeInfo, const AreaClass* const Area, int minage, int maxage) {
char c;
double length;
int i, year, step, area, age, keepdata, count, id, lengthid, reject;
int numlen = LgrpDiv->numLengthGroups();
PopInfoIndexVector poptmp(numlen, 0);
//We now expect to find the renewal data in the following format
//year, step, area, age, length, number, mean weight
infile >> ws;
if (countColumns(infile) != 7)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
year = step = area = age = count = reject = 0;
while (!infile.eof()) {
//crude check to see if something has gone wrong and avoid infinite loops
if (!(isdigit(infile.peek())))
handle.logFileMessage(LOGFAIL, "failed to read data from file");
keepdata = 1;
infile >> year >> step >> area >> age >> length >> ws;
if (!(TimeInfo->isWithinPeriod(year, step)))
keepdata = 0;
if (!(this->isInArea(Area->getInnerArea(area))))
keepdata = 0;
if ((age < minage) || (age > maxage))
keepdata = 0;
lengthid = -1;
for (i = 0; i < numlen; i++)
if (isEqual(length, LgrpDiv->minLength(i)))
lengthid = i;
//OK the length doesnt match a minimum length so find the length group it is in
if ((lengthid == -1) && (length > LgrpDiv->minLength()) && (length < LgrpDiv->maxLength())) {
for (i = 1; i < numlen; i++) {
if (length < LgrpDiv->minLength(i)) {
lengthid = i - 1;
break;
}
}
if (lengthid == -1)
lengthid = numlen - 1; //then this must be the last length group
}
if (lengthid == -1)
keepdata = 0;
if (keepdata == 1) {
//renewal data is required, so store it
id = -1;
for (i = 0; i < renewalTime.Size(); i++)
if ((renewalTime[i] == TimeInfo->calcSteps(year, step))
&& (renewalArea[i] == Area->getInnerArea(area))
&& (renewalAge[i] == age))
id = i;
if (id == -1) {
//this is a new timestep/area combination
renewalTime.resize(1, TimeInfo->calcSteps(year, step));
renewalArea.resize(1, Area->getInnerArea(area));
renewalAge.resize(1, age);
id = renewalTime.Size() - 1;
renewalDistribution.resize(1, new AgeBandMatrix(age, poptmp));
renewalNumber.resize(new FormulaMatrix(maxage - minage + 1, numlen, 0.0));
}
renewalDistribution[id][age][lengthid].N = 0.0;
infile >> (*renewalNumber[id])[age - minage][lengthid] >> ws;
infile >> renewalDistribution[id][age][lengthid].W >> ws;
count++;
} else { //renewal data not required - skip rest of line
reject++;
infile.get(c);
while (c != '\n' && !infile.eof())
infile.get(c);
infile >> ws;
}
}
for (i = 0; i < renewalNumber.Size(); i++)
(*renewalNumber[i]).Inform(keeper);
if (count == 0)
handle.logMessage(LOGWARN, "Warning in renewal - found no data in the data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid renewal data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read renewal data file - number of entries", count);
}
RenewalData::~RenewalData() {
int i;
delete LgrpDiv;
delete CI;
for (i = 0; i < renewalNumber.Size(); i++)
delete renewalNumber[i];
}
void RenewalData::setCI(const LengthGroupDivision* const GivenLDiv) {
if (!checkLengthGroupStructure(GivenLDiv, LgrpDiv))
handle.logMessage(LOGFAIL, "Error in renewal - invalid length group structure for stock", this->getName());
//check minimum and maximum lengths
if (LgrpDiv->minLength() < GivenLDiv->minLength())
handle.logMessage(LOGWARN, "Warning in renewal - minimum length less than stock length for stock", this->getName());
if (LgrpDiv->maxLength() > GivenLDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in renewal - maximum length greater than stock length for stock", this->getName());
CI = new ConversionIndex(LgrpDiv, GivenLDiv);
if (CI->Error())
handle.logMessage(LOGFAIL, "Error in renewal - error when checking length structure");
}
void RenewalData::Print(ofstream& outfile) const {
int i;
outfile << "\nRenewal data\n\t";
LgrpDiv->Print(outfile);
//need to find all areas and ages for current index value ...
for (i = 0; i < renewalTime.Size(); i++) {
if (renewalTime[i] == renewalTime[index]) {
outfile << "\tInternal area " << renewalArea[i] << " age " << renewalAge[i];
if (readoption == 2)
outfile << "\n\tNumbers\n";
else
outfile << " multiplier " << renewalMult[i] << "\n\tNumbers\n";
renewalDistribution[i].printNumbers(outfile);
outfile << "\tMean weights\n";
renewalDistribution[i].printWeights(outfile);
}
}
outfile.flush();
}
void RenewalData::Reset() {
int i, age, l, minage;
double sum, mult, dnorm;
index = 0;
if (readoption == 0) {
for (i = 0; i < renewalTime.Size(); i++) {
age = renewalAge[i];
//JMB check that the length data is valid
if (isZero(meanLength[i]) || sdevLength[i] < 0.04) {
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
handle.logMessage(LOGWARN, "Warning in renewal - invalid length data");
//JMB set the population to zero
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
renewalDistribution[i][age][l].setToZero();
} else {
//JMB check that the mean length is within the length group range
if (meanLength[i] < LgrpDiv->minLength())
handle.logMessage(LOGWARN, "Warning in renewal - mean length is less than minimum length for stock", this->getName());
if (meanLength[i] > LgrpDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in renewal - mean length is greater than maximum length for stock", this->getName());
sum = 0.0;
mult = 1.0 / sdevLength[i];
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
dnorm = (LgrpDiv->meanLength(l) - meanLength[i]) * mult;
renewalDistribution[i][age][l].N = exp(-(dnorm * dnorm) * 0.5);
sum += renewalDistribution[i][age][l].N;
}
if (isZero(sum)) {
handle.logMessage(LOGWARN, "Warning in renewal - calculated zero recruits for stock", this->getName());
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
renewalDistribution[i][age][l].setToZero();
} else {
sum = 10000.0 / sum;
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
renewalDistribution[i][age][l].N *= sum;
renewalDistribution[i][age][l].W = refWeight[l] * relCond[i];
if ((handle.getLogLevel() >= LOGWARN) && (isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
}
}
}
}
} else if (readoption == 1) {
for (i = 0; i < renewalTime.Size(); i++) {
age = renewalAge[i];
//JMB check that the length data is valid
if (isZero(meanLength[i]) || sdevLength[i] < 0.04) {
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
handle.logMessage(LOGWARN, "Warning in renewal - invalid length data");
//JMB set the population to zero
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
renewalDistribution[i][age][l].setToZero();
} else {
//JMB check that the mean length is within the length group range
if (meanLength[i] < LgrpDiv->minLength())
handle.logMessage(LOGWARN, "Warning in renewal - mean length is less than minimum length for stock", this->getName());
if (meanLength[i] > LgrpDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in renewal - mean length is greater than maximum length for stock", this->getName());
sum = 0.0;
mult = 1.0 / sdevLength[i];
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
dnorm = (LgrpDiv->meanLength(l) - meanLength[i]) * mult;
renewalDistribution[i][age][l].N = exp(-(dnorm * dnorm) * 0.5);
sum += renewalDistribution[i][age][l].N;
}
if (isZero(sum)) {
handle.logMessage(LOGWARN, "Warning in renewal - calculated zero recruits for stock", this->getName());
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++)
renewalDistribution[i][age][l].setToZero();
} else {
sum = 10000.0 / sum;
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
renewalDistribution[i][age][l].N *= sum;
renewalDistribution[i][age][l].W = alpha[i] * pow(LgrpDiv->meanLength(l), beta[i]);
if ((handle.getLogLevel() >= LOGWARN) && (isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
}
}
}
}
} else if (readoption == 2) {
for (i = 0; i < renewalTime.Size(); i++) {
age = renewalAge[i];
minage = renewalDistribution[i].minAge();
for (l = renewalDistribution[i].minLength(age); l < renewalDistribution[i].maxLength(age); l++) {
renewalDistribution[i][age][l].N = (*renewalNumber[i])[age - minage][l];
if (handle.getLogLevel() >= LOGWARN) {
if (renewalDistribution[i][age][l].N < 0.0)
handle.logMessage(LOGWARN, "Warning in renewal - negative number of recruits", renewalDistribution[i][age][l].N);
if ((isZero(renewalDistribution[i][age][l].W)) && (renewalDistribution[i][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in renewal - zero mean weight for stock", this->getName());
}
}
}
} else
handle.logMessage(LOGFAIL, "Error in renewal - unrecognised data format");
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Reset renewal data for stock", this->getName());
}
int RenewalData::isRenewalStepArea(int area, const TimeClass* const TimeInfo) {
int i;
for (i = 0; i < renewalTime.Size(); i++)
if ((renewalTime[i] == TimeInfo->getTime()) && (renewalArea[i] == area))
return 1;
return 0;
}
void RenewalData::addRenewal(AgeBandMatrix& Alkeys, int area, const TimeClass* const TimeInfo) {
int i;
for (i = 0; i < renewalTime.Size(); i++) {
if ((renewalTime[i] == TimeInfo->getTime()) && (renewalArea[i] == area)) {
index = i;
if (readoption == 2)
Alkeys.Add(renewalDistribution[i], *CI);
else if (renewalMult[i] > verysmall)
Alkeys.Add(renewalDistribution[i], *CI, renewalMult[i]);
}
}
}