Skip to content

Commit

Permalink
Mods for 1.3.5
Browse files Browse the repository at this point in the history
  • Loading branch information
@rklasky
rklasky committed Sep 30, 2022
1 parent 1b56da9 commit 11acb3a
Show file tree
Hide file tree
Showing 6 changed files with 430 additions and 245 deletions.
131 changes: 78 additions & 53 deletions MSSPM_GuiDiagnostic/nmfDiagnosticTab01.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -554,7 +554,7 @@ nmfDiagnostic_Tab1::callback_RunPB()
}

for (QString parameterName : vectorParameterNames) {
//qDebug() << "processing parameterName: " << parameterName;
//qDebug() << "\nprocessing parameterName: " << parameterName;
nmfUtilsQt::updateProgressDlg(m_Logger,progressDlg,"Processing parameter: "+parameterName.toStdString(),pInc);

EstParameter.clear();
Expand All @@ -571,7 +571,8 @@ nmfDiagnostic_Tab1::callback_RunPB()
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
return;
}

//qDebug() << "loaded name: " << parameterName;
//qDebug() << EstParameter;
if (parameterName == surfaceParameter1Name) {
surfaceParameter1 = EstParameter;
} else if (parameterName == surfaceParameter2Name) {
Expand All @@ -585,47 +586,59 @@ nmfDiagnostic_Tab1::callback_RunPB()
inc = (estParameter - startVal)/numPoints;
diagnosticParameterValue = startVal;

// Skip the current species if there's no estimated data for it. This cold be
// Skip the current species if there's no estimated data for it. This could be
// the case for the covariate coefficient parameters if non have been estimated
// for certain species.
if ((estParameter != 0) && (startVal != 0)) {
if (1) { // ((estParameter != 0) && (startVal != 0)) { // RSK revisit this logic
for (int j=0; j<=totalNumPoints; ++j) {
//if (i == 0) {
//qDebug() << "p1: " << j << parameterName << " " << diagnosticParameterValue << " " << estParameter << inc; // << fitness;
//if (i == 9 && parameterName == "SurveyQ") {
// qDebug() << "\nparameter name: " << parameterName << estParameter << startVal << inc << diagnosticParameterValue; // << fitness;
//}

if ((estParameter == 0) || (startVal == 0)) {
aDiagnosticTuple = std::make_tuple(SpeciesOrGuildNames[i],j,0,0);
DiagnosticTupleVector.push_back(aDiagnosticTuple);
} else {
try {
parameterItem = std::make_pair(parameterName,diagnosticParameterValue);
//if (i == 9 && parameterName == "SurveyQ") {
// qDebug() << "before calculateFitness call";
//}
fitness = calculateFitness(i,{parameterItem});
//if (i == 9 && parameterName == "SurveyQ") {
//qDebug() << "after calculateFitness call, fitness: " << fitness;
//}
try {
parameterItem = std::make_pair(parameterName,diagnosticParameterValue);
fitness = calculateFitness(i,{parameterItem});
} catch (...) {
msg = "Warning (2): Please run an Estimation prior to running this Diagnostic.";
m_Logger->logMsg(nmfConstants::Warning,msg.toStdString());
QMessageBox::warning(m_Diagnostic_Tabs,tr("Warning"),"\n"+msg,QMessageBox::Ok);
progressDlg->close();
emit EnableRunButtons(true);
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
return;
}

if (fitness == -1) {
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
progressDlg->close();
emit EnableRunButtons(true);
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
return;
}

aDiagnosticTuple = std::make_tuple(SpeciesOrGuildNames[i],
diagnosticParameterValue-estParameter,
diagnosticParameterValue,
fitness);

DiagnosticTupleVector.push_back(aDiagnosticTuple);
diagnosticParameterValue += inc;
} catch (...) {
msg = "Warning (2): Please run an Estimation prior to running this Diagnostic.";
m_Logger->logMsg(nmfConstants::Warning,msg.toStdString());
QMessageBox::warning(m_Diagnostic_Tabs,tr("Warning"),"\n"+msg,QMessageBox::Ok);
progressDlg->close();
emit EnableRunButtons(true);
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
return;
}

if (fitness == -1) {
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
progressDlg->close();
emit EnableRunButtons(true);
m_Diagnostic_Tabs->setCursor(Qt::ArrowCursor);
return;
}

aDiagnosticTuple = std::make_tuple(SpeciesOrGuildNames[i],
diagnosticParameterValue-estParameter,
diagnosticParameterValue,
fitness);

DiagnosticTupleVector.push_back(aDiagnosticTuple);
diagnosticParameterValue += inc;
} // end else
} // end for
} // end if

} // end for

//std::cout << "Upt: before updateParameterTable" << std::endl;
updateParameterTable(NumSpeciesOrGuilds, totalNumPoints,
Algorithm,Minimizer,ObjectiveCriterion,Scaling,
isAggProdStr,parameterName,DiagnosticTupleVector);
Expand Down Expand Up @@ -747,6 +760,7 @@ nmfDiagnostic_Tab1::calculateFitness(const int& SpeciesOrGuildNum,
int GrowthRateOffset,GrowthRateCovarOffset,CarryingCapacityOffset,CarryingCapacityCovarOffset;
int CatchabilityOffset,CatchabilityCovarOffset;
int SurveyQOffset,SurveyQCovarOffset;
int InitBiomassOffset = 0;
double unused2[] = {0};
double retv = 0;
std::string Algorithm;
Expand Down Expand Up @@ -784,12 +798,16 @@ nmfDiagnostic_Tab1::calculateFitness(const int& SpeciesOrGuildNum,
isAggProdStr = std::to_string(isAggProd);

// Load up parameters (covariates are included from within the following load methods)
int initBiomassOffset = 0;
loadOutputParameters(nmfConstantsMSSPM::TableOutputInitBiomass,NumSpeciesOrGuilds,
Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,initBiomassParameters);
offset = initBiomassParameters.size();
loadGrowthParameters(NumSpeciesOrGuilds,Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,growthParameters,
offset,GrowthRateOffset,GrowthRateCovarOffset,CarryingCapacityOffset,CarryingCapacityCovarOffset);
//std::cout << "GrowthRateOffset: " << GrowthRateOffset << std::endl;
//std::cout << "GrowthRateCovarOffset: " << GrowthRateCovarOffset << std::endl;
//std::cout << "CarryingCapacityOffset: " << CarryingCapacityOffset << std::endl;
//std::cout << "CarryingCapacityCovarOffset: " << CarryingCapacityCovarOffset << std::endl;

offset = CarryingCapacityCovarOffset;
loadHarvestParameters(NumSpeciesOrGuilds,Algorithm,Minimizer,ObjectiveCriterion,Scaling,
harvestParameters,offset,CatchabilityOffset,CatchabilityCovarOffset);
Expand All @@ -798,27 +816,34 @@ nmfDiagnostic_Tab1::calculateFitness(const int& SpeciesOrGuildNum,
offset += competitionParameters.size();
loadPredationParameters(NumSpeciesOrGuilds,Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,predationParameters);
offset += predationParameters.size();
SurveyQOffset = offset;
// SurveyQOffset = offset;
loadOutputParameters(nmfConstantsMSSPM::TableOutputSurveyQ,NumSpeciesOrGuilds,
Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,surveyQParameters);
SurveyQCovarOffset = offset + surveyQParameters.size();
// loadOutputParameters(nmfConstantsMSSPM::TableOutputSurveyQCovariateCoeffs,NumSpeciesOrGuilds,
// Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,surveyQCovCoeffParameters);
loadOutputParameters(nmfConstantsMSSPM::TableOutputSurveyQCovariateCoeffs,NumSpeciesOrGuilds,
Algorithm,Minimizer,ObjectiveCriterion,Scaling,isAggProdStr,surveyQCovCoeffParameters);
//qDebug() << "RSK - TBD implement surveyQCovCoeff logic";
//qDebug() << "SurveyQCovarOffset: " << SurveyQCovarOffset;

// Append all of the Estimated Parameters to: parameters
InitBiomassOffset = parameters.size();
nmfUtils::append(initBiomassParameters,parameters);
nmfUtils::append(growthParameters, parameters);
nmfUtils::append(harvestParameters, parameters);
nmfUtils::append(competitionParameters,parameters);
nmfUtils::append(predationParameters, parameters);
SurveyQOffset = parameters.size();
nmfUtils::append(surveyQParameters, parameters);
SurveyQCovarOffset = parameters.size();
nmfUtils::append(surveyQCovCoeffParameters, parameters);

//std::cout << "ParameterData size: " << ParameterData.size() << std::endl;
// Modify the estimated parameter data with the diagnostic "tweaks" to the estimated parameters
for (std::pair<QString,double> ParameterItem : ParameterData) {
offset = 0;
//std::cout << "parameter first: " << ParameterItem.first.toStdString() << std::endl;
offset = 0; // RSK bug is here I think...
if (ParameterItem.first == "Initial Biomass (B₀)") {
offset = initBiomassOffset;
offset = InitBiomassOffset;
} else if (ParameterItem.first == "Growth Rate (r)") { // RSK revisit this...make all the constants more consistent
offset = GrowthRateOffset;
} else if (ParameterItem.first == "Carrying Capacity (K)") {
Expand All @@ -827,32 +852,30 @@ nmfDiagnostic_Tab1::calculateFitness(const int& SpeciesOrGuildNum,
offset = CatchabilityOffset+NumSpeciesOrGuilds;
} else if (ParameterItem.first == nmfConstantsMSSPM::ParameterNameSurveyQ) {
offset = SurveyQOffset;
//std::cout << "SurveyQ offset: " << offset << std::endl;
} else if (ParameterItem.first == nmfConstantsMSSPM::ParameterNameGrowthRateCovCoeff) {
offset = GrowthRateCovarOffset;
} else if (ParameterItem.first == nmfConstantsMSSPM::ParameterNameCarryingCapacityCovCoeff) {
offset = CarryingCapacityCovarOffset;
} else if (ParameterItem.first == nmfConstantsMSSPM::ParameterNameCatchabilityCovCoeff) {
offset = CatchabilityCovarOffset;
} else if (ParameterItem.first == nmfConstantsMSSPM::ParameterNameSurveyQCovCoeff) {
//qDebug() << "found SQCovCoeff";
offset = SurveyQCovarOffset;
} else {
msg = "Error: Invalid parameter name: " + ParameterItem.first.toStdString();
m_Logger->logMsg(nmfConstants::Error,msg);
return -1;
}
parameters[offset+SpeciesOrGuildNum] = ParameterItem.second;
//if (SpeciesOrGuildNum == 0 && ParameterItem.first == nmfConstantsMSSPM::ParameterNameGrowthRateCovCoeff) {
//std::cout << "Assigning: parameters[" << offset+SpeciesOrGuildNum << "]: " << ParameterItem.second << std::endl;
//}
}
// InitBiomass, r, r cov coeff, ...
//if (SpeciesOrGuildNum == 0) {
// std::cout << "rcv: ";
//for (int i=20; i<30; ++i) {
// std::cout << parameters[i] << ", ";
//}
//std::cout << std::endl;

//for (int i=150;i<160;++i) {
//std::cout << " parameters[159]: " << parameters[159] << std::endl;
//}



m_DatabasePtr->getAlgorithmIdentifiers(
m_Diagnostic_Tabs,m_Logger,m_ProjectName,m_ModelName,
Algorithm,Minimizer,ObjectiveCriterion,
Expand Down Expand Up @@ -1247,6 +1270,7 @@ nmfDiagnostic_Tab1::updateParameterTable(const int& NumSpeciesOrGuilds,
m_Logger->logMsg(nmfConstants::Error,"nmfDiagnostic_Tab1::updateParameterTable: DiagnosticTupleVector is empty");
return;
}
//std::cout << "Upt: " << TableName << std::endl;

cmd = "DELETE FROM " + TableName +
" WHERE ProjectName = '" + m_ProjectName +
Expand Down Expand Up @@ -1282,8 +1306,9 @@ nmfDiagnostic_Tab1::updateParameterTable(const int& NumSpeciesOrGuilds,
cmd = cmd.substr(0,cmd.size()-1);
errorMsg = m_DatabasePtr->nmfUpdateDatabase(cmd);
if (nmfUtilsQt::isAnError(errorMsg)) {
m_Logger->logMsg(nmfConstants::Error,"[Error 2] UpdateParameterTable: Write table error: " + errorMsg);
m_Logger->logMsg(nmfConstants::Error,"cmd: " + cmd);
m_Logger->logMsg(nmfConstants::Warning,"[Warning 2] UpdateParameterTable: Write table error: " + errorMsg);
m_Logger->logMsg(nmfConstants::Warning,"This may be due to no covariate diagnostic data available.");
m_Logger->logMsg(nmfConstants::Warning,"cmd: " + cmd);
return;
}

Expand Down
Loading

0 comments on commit 11acb3a

Please sign in to comment.