#include "initialcond.h"
#include "errorhandler.h"
#include "readfunc.h"
#include "readword.h"
#include "mathfunc.h"
#include "gadget.h"
#include "global.h"
void InitialCond::readNormalConditionData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area) {
int noareas = areas.Size();
int i, age, area, ageid, areaid, tmparea, keepdata, count, reject;
char c;
//Resize the matrices to hold the data
areaFactor.AddRows(noareas, numage, 0.0);
ageFactor.AddRows(noareas, numage, 0.0);
meanLength.AddRows(noareas, numage, 0.0);
sdevLength.AddRows(noareas, numage, 0.0);
relCond.AddRows(noareas, numage, 0.0);
//Find the start of the data in the following format
//age - area - agedist - areadist - meanlen - standdev - relcond
infile >> ws;
if (countColumns(infile) != 7)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 7");
area = age = ageid = count = reject = 0;
keeper->addString("meandata");
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 >> age >> area >> ws;
//crude age data check - perhaps there should be a better check?
if ((age < minage) || (age >= (numage + minage)))
keepdata = 0;
else
ageid = age - minage;
//crude area data check
areaid = -1;
tmparea = Area->getInnerArea(area);
for (i = 0; i < noareas; i++)
if (areas[i] == tmparea)
areaid = i;
if (areaid == -1)
keepdata = 0;
if (keepdata == 1) {
//initial data is required, so store it
count++;
infile >> ageFactor[areaid][ageid] >> ws;
infile >> areaFactor[areaid][ageid] >> ws;
infile >> meanLength[areaid][ageid] >> ws;
infile >> sdevLength[areaid][ageid] >> ws;
infile >> relCond[areaid][ageid] >> ws;
} else { //initial 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 initial conditions - found no data in the data file");
else if (count < (noareas * numage))
handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
else if (count > (noareas * numage))
handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
areaFactor.Inform(keeper);
ageFactor.Inform(keeper);
meanLength.Inform(keeper);
sdevLength.Inform(keeper);
relCond.Inform(keeper);
keeper->clearLast();
}
void InitialCond::readNormalParameterData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area) {
int noareas = areas.Size();
int i, age, area, ageid, areaid, tmparea, keepdata, count, reject;
char c;
//Resize the matrices to hold the data
areaFactor.AddRows(noareas, numage, 0.0);
ageFactor.AddRows(noareas, numage, 0.0);
meanLength.AddRows(noareas, numage, 0.0);
sdevLength.AddRows(noareas, numage, 0.0);
alpha.AddRows(noareas, numage, 0.0);
beta.AddRows(noareas, numage, 0.0);
//Find the start of the data in the following format
//age - area - agedist - areadist - meanlen - standdev - alpha - beta
infile >> ws;
if (countColumns(infile) != 8)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 8");
area = age = ageid = count = reject = 0;
keeper->addString("meandata");
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 >> age >> area >> ws;
//crude age data check - perhaps there should be a better check?
if ((age < minage) || (age >= (numage + minage)))
keepdata = 0;
else
ageid = age - minage;
//crude area data check
areaid = -1;
tmparea = Area->getInnerArea(area);
for (i = 0; i < noareas; i++)
if (areas[i] == tmparea)
areaid = i;
if (areaid == -1)
keepdata = 0;
if (keepdata == 1) {
//initial data is required, so store it
count++;
infile >> ageFactor[areaid][ageid] >> ws;
infile >> areaFactor[areaid][ageid] >> ws;
infile >> meanLength[areaid][ageid] >> ws;
infile >> sdevLength[areaid][ageid] >> ws;
infile >> alpha[areaid][ageid] >> ws;
infile >> beta[areaid][ageid] >> ws;
} else { //initial 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 initial conditions - found no data in the data file");
else if (count < (noareas * numage))
handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
else if (count > (noareas * numage))
handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
areaFactor.Inform(keeper);
ageFactor.Inform(keeper);
meanLength.Inform(keeper);
sdevLength.Inform(keeper);
alpha.Inform(keeper);
beta.Inform(keeper);
keeper->clearLast();
}
void InitialCond::readNumberData(CommentStream& infile, Keeper* const keeper,
int numage, int minage, const AreaClass* const Area) {
int i, age, area, tmparea, count, reject;
int keepdata, areaid, lengthid;
double length;
char c;
int noareas = areas.Size();
int numlen = LgrpDiv->numLengthGroups();
//initialise things
for (areaid = 0; areaid < noareas; areaid++) {
initialNumber.resize(new FormulaMatrix(numage, numlen, 0.0));
initialPop[areaid].setToZero();
}
//Find the start of the data in the following format
//area - age - meanlength - number - weight
infile >> ws;
if (countColumns(infile) != 5)
handle.logFileMessage(LOGFAIL, "wrong number of columns in inputfile - should be 5");
area = age = count = reject = 0;
keeper->addString("numberdata");
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 >> area >> age >> length >> ws;
//crude area data check
areaid = -1;
tmparea = Area->getInnerArea(area);
for (i = 0; i < noareas; i++)
if (areas[i] == tmparea)
areaid = i;
if (areaid == -1)
keepdata = 0;
//crude age data check - perhaps there should be a better check?
if ((age < minage) || (age >= (numage + minage)))
keepdata = 0;
//crude length data check
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) {
//initial data is required, so store it
infile >> (*initialNumber[areaid])[age - minage][lengthid] >> ws;
infile >> initialPop[areaid][age][lengthid].W >> ws;
count++;
} else { //initial 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 < initialNumber.Size(); i++)
(*initialNumber[i]).Inform(keeper);
if (count == 0)
handle.logMessage(LOGWARN, "Warning in initial conditions - found no data in the data file");
else if (count < (noareas * numage * numlen))
handle.logMessage(LOGWARN, "Warning in initial conditions - missing entries from data file");
else if (count > (noareas * numage * numlen))
handle.logMessage(LOGWARN, "Warning in initial conditions - repeated entries in data file");
if (reject != 0)
handle.logMessage(LOGMESSAGE, "Discarded invalid initial conditions data - number of invalid entries", reject);
handle.logMessage(LOGMESSAGE, "Read initial conditions data file - number of entries", count);
keeper->clearLast();
}
InitialCond::InitialCond(CommentStream& infile, const IntVector& Areas,
Keeper* const keeper, const char* refWeightFile,
const char* givenname, const AreaClass* const Area, double DL)
: HasName(givenname), LivesOnAreas(Areas), LgrpDiv(0), CI(0) {
ifstream subfile;
CommentStream subcomment(subfile);
char text[MaxStrLength];
strncpy(text, "", MaxStrLength);
int i, j, k;
int minage, maxage;
char c;
double minlength, maxlength, dl;
keeper->addString("initialcond");
infile >> ws;
c = infile.peek();
if ((c == 'n') || (c == 'N'))
infile >> text >> ws; //read in the word 'numbers' if it exists
readWordAndVariable(infile, "minage", minage);
readWordAndVariable(infile, "maxage", maxage);
readWordAndVariable(infile, "minlength", minlength);
readWordAndVariable(infile, "maxlength", maxlength);
int numage = maxage - minage + 1;
//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;
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 initial conditions - failed to create length group");
//read the standard deviation multiplier - default to 1.0
keeper->addString("sdevmultiplier");
infile >> ws;
c = infile.peek();
if ((c == 's') || (c == 'S'))
readWordAndVariable(infile, "sdev", sdevMult);
else
sdevMult.setValue(1.0);
sdevMult.Inform(keeper);
keeper->clearLast();
//create the initialPop object of the correct size
PopInfo tmppop;
tmppop.N = 1.0;
PopInfoMatrix popmatrix(numage, LgrpDiv->numLengthGroups(), tmppop);
initialPop.resize(areas.Size(), minage, 0, popmatrix);
infile >> text >> ws;
if ((strcasecmp(text, "initstockfile") == 0) || (strcasecmp(text, "normalcondfile") == 0)) {
//read initial 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, numage, minage, Area);
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, "normalparamfile") == 0)) {
//read initial 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, numage, minage, Area);
handle.Close();
subfile.close();
subfile.clear();
} else if ((strcasecmp(text, "numberfile") == 0)) {
//read initial 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, numage, minage, Area);
handle.Close();
subfile.close();
subfile.clear();
} else
handle.logFileMessage(LOGFAIL, "unrecognised initial conditions format", text);
keeper->clearLast();
}
InitialCond::~InitialCond() {
int i;
delete LgrpDiv;
delete CI;
for (i = 0; i < initialNumber.Size(); i++)
delete initialNumber[i];
}
void InitialCond::setCI(const LengthGroupDivision* const GivenLDiv) {
if (!checkLengthGroupStructure(GivenLDiv, LgrpDiv))
handle.logMessage(LOGFAIL, "Error in initial conditions - invalid length group structure for stock", this->getName());
//check minimum and maximum lengths
if (LgrpDiv->minLength() < GivenLDiv->minLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - minimum length less than stock length for stock", this->getName());
if (LgrpDiv->maxLength() > GivenLDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - maximum length greater than stock length for stock"), this->getName();
CI = new ConversionIndex(LgrpDiv, GivenLDiv);
if (CI->Error())
handle.logMessage(LOGFAIL, "Error in initial conditions - error when checking length structure for stock", this->getName());
}
void InitialCond::Print(ofstream& outfile) const {
int i, j;
outfile << "\nInitial conditions\n";
for (i = 0; i < areas.Size(); i++) {
outfile << "\tInternal area " << areas[i] << endl;
initialPop[i].printNumbers(outfile);
}
if ((readoption == 0) || (readoption == 1)) {
//JMB print the multipliers that are used to scale the population
outfile << "\tArea multipliers used to scale the population\n";
for (i = 0; i < areaFactor.Nrow(); i++) {
for (j = 0; j < areaFactor.Ncol(i); j++)
outfile << TAB << areaFactor[i][j];
outfile << endl;
}
outfile << "\tAge multipliers used to scale the population\n";
for (i = 0; i < ageFactor.Nrow(); i++) {
for (j = 0; j < ageFactor.Ncol(i); j++)
outfile << TAB << ageFactor[i][j];
outfile << endl;
}
}
outfile << endl;
outfile.flush();
}
void InitialCond::Initialise(AgeBandMatrixPtrVector& Alkeys) {
int area, age, l;
int minage, maxage;
double mult, scaler, dnorm;
if (readoption == 0) {
if (isZero(sdevMult)) //JMB this should never happen ...
handle.logMessage(LOGFAIL, "Error in initial conditions - multiplier for standard deviation is zero");
for (area = 0; area < areas.Size(); area++) {
minage = initialPop[area].minAge();
maxage = initialPop[area].maxAge();
for (age = minage; age <= maxage; age++) {
//JMB check that the length data is valid
if (isZero(meanLength[area][age - minage]) || sdevLength[area][age - minage] < 0.04) {
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
handle.logMessage(LOGWARN, "Warning in initial conditions - invalid length data for stock", this->getName());
//JMB set the population to zero
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
initialPop[area][age][l].setToZero();
} else {
//JMB check that the mean length is within the length group range
if (meanLength[area][age - minage] < LgrpDiv->minLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is less than minimum length for stock", this->getName());
if (meanLength[area][age - minage] > LgrpDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is greater than maximum length for stock", this->getName());
scaler = 0.0;
mult = 1.0 / (sdevLength[area][age - minage] * sdevMult);
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
dnorm = (LgrpDiv->meanLength(l) - meanLength[area][age - minage]) * mult;
initialPop[area][age][l].N = exp(-(dnorm * dnorm) * 0.5);
scaler += initialPop[area][age][l].N;
}
if (isZero(scaler)) {
handle.logMessage(LOGWARN, "Warning in initial population - calculated zero population");
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
initialPop[area][age][l].setToZero();
} else {
scaler = 10000.0 / scaler;
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
initialPop[area][age][l].N *= scaler;
initialPop[area][age][l].W = refWeight[l] * relCond[area][age - minage];
if ((handle.getLogLevel() >= LOGWARN) && (isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
}
}
}
}
}
} else if (readoption == 1) {
if (isZero(sdevMult)) //JMB this should never happen ...
handle.logMessage(LOGFAIL, "Error in initial conditions - multiplier for standard deviation is zero for stock", this->getName());
for (area = 0; area < areas.Size(); area++) {
minage = initialPop[area].minAge();
maxage = initialPop[area].maxAge();
for (age = minage; age <= maxage; age++) {
//JMB check that the length data is valid
if (isZero(meanLength[area][age - minage]) || sdevLength[area][age - minage] < 0.04) {
//JMB the limit has been set at 0.04 to keep the exponential calculation sane
handle.logMessage(LOGWARN, "Warning in initial conditions - invalid length data");
//JMB set the population to zero
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
initialPop[area][age][l].setToZero();
} else {
//JMB check that the mean length is within the length group range
if (meanLength[area][age - minage] < LgrpDiv->minLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is less than minimum length for stock", this->getName());
if (meanLength[area][age - minage] > LgrpDiv->maxLength())
handle.logMessage(LOGWARN, "Warning in initial conditions - mean length is greater than maximum length for stock", this->getName());
scaler = 0.0;
mult = 1.0 / (sdevLength[area][age - minage] * sdevMult);
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
dnorm = (LgrpDiv->meanLength(l) - meanLength[area][age - minage]) * mult;
initialPop[area][age][l].N = exp(-(dnorm * dnorm) * 0.5);
scaler += initialPop[area][age][l].N;
}
if (isZero(scaler)) {
handle.logMessage(LOGWARN, "Warning in initial population - calculated zero population for stock", this->getName());
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++)
initialPop[area][age][l].setToZero();
} else {
scaler = 10000.0 / scaler;
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
initialPop[area][age][l].N *= scaler;
initialPop[area][age][l].W = alpha[area][age - minage] * pow(LgrpDiv->meanLength(l), beta[area][age - minage]);
if ((handle.getLogLevel() >= LOGWARN) && (isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
}
}
}
}
}
} else if (readoption == 2) {
for (area = 0; area < areas.Size(); area++) {
minage = initialPop[area].minAge();
maxage = initialPop[area].maxAge();
for (age = minage; age <= maxage; age++) {
for (l = initialPop[area].minLength(age); l < initialPop[area].maxLength(age); l++) {
initialPop[area][age][l].N = (*initialNumber[area])[age - minage][l];
if (handle.getLogLevel() >= LOGWARN) {
if (initialPop[area][age][l].N < 0.0)
handle.logMessage(LOGWARN, "Warning in initial conditions - negative initial population for stock", this->getName());
if ((isZero(initialPop[area][age][l].W)) && (initialPop[area][age][l].N > 0.0))
handle.logMessage(LOGWARN, "Warning in initial conditions - zero mean weight for stock", this->getName());
}
}
}
}
} else
handle.logMessage(LOGFAIL, "Error in initial conditions - unrecognised data format");
mult = 1.0;
for (area = 0; area < areas.Size(); area++) {
Alkeys[area].setToZero();
//check minimum and maximum ages
if (handle.getLogLevel() >= LOGWARN) {
if (initialPop[area].minAge() < Alkeys[area].minAge())
handle.logMessage(LOGWARN, "Warning in initial conditions - minimum age less than stock age for stock", this->getName());
if (initialPop[area].maxAge() > Alkeys[area].maxAge())
handle.logMessage(LOGWARN, "Warning in initial conditions - maximum age greater than stock age for stock", this->getName());
}
minage = max(Alkeys[area].minAge(), initialPop[area].minAge());
maxage = min(Alkeys[area].maxAge(), initialPop[area].maxAge());
if (maxage < minage)
handle.logMessage(LOGFAIL, "Error in initial conditions - maximum age less than minimum age for stock", this->getName());
for (age = minage; age <= maxage; age++) {
if ((readoption == 0) || (readoption == 1))
mult = areaFactor[area][age - minage] * ageFactor[area][age - minage];
if (mult < 0.0) {
handle.logMessage(LOGWARN, "Warning in initial conditions - negative stock multiplier", mult);
mult = -mult;
}
Alkeys[area][age].Add(initialPop[area][age], *CI, mult);
}
}
if (handle.getLogLevel() >= LOGMESSAGE)
handle.logMessage(LOGMESSAGE, "Calculated initial condition data for stock", this->getName());
}
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