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Mods for 1.3.3
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@rklasky
rklasky committed Sep 23, 2022
1 parent b2478e9 commit e59b633
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Showing 4 changed files with 57 additions and 66 deletions.
8 changes: 7 additions & 1 deletion MSSPM_GuiDiagnostic/nmfDiagnosticTab02.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -241,6 +241,12 @@ nmfDiagnostic_Tab2::isAMohnsRhoRunForSingleRun()
return m_isMohnsRhoRunForSingleRun;
}

bool
nmfDiagnostic_Tab2::isPageVisible()
{
return m_Diagnostic_Tab2_RunPB->isVisible();
}

void
nmfDiagnostic_Tab2::setMohnsRhoForSingleRun(bool state)
{
Expand Down Expand Up @@ -349,7 +355,7 @@ std::cout << "range: " << StartYear << ", " << EndYear-i << std::endl;
// } else {
m_isMohnsRhoRunForMultiRun = false;
m_isMohnsRhoRunForSingleRun = true;
emit RunDiagnosticEstimation(ranges);
emit RunRetrospectiveAnalysis(ranges);
// }
}

Expand Down
7 changes: 6 additions & 1 deletion MSSPM_GuiDiagnostic/nmfDiagnosticTab02.h
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,11 @@ class nmfDiagnostic_Tab2: public QObject
* @return Boolean signifying if the user just started a Mohns Rho run using the last Multi Run
*/
bool isAMohnsRhoRunForMultiRun();
/**
* @brief Notifies the user if the page is visible
* @return true if visible, false otherwise
*/
bool isPageVisible();
/**
* @brief Loads the GUI widgets without any peels. It calls the overloaded loadWidgets with a -1.
*/
Expand Down Expand Up @@ -178,7 +183,7 @@ class nmfDiagnostic_Tab2: public QObject
* @brief Signals to the main routine to run the Mohn's Rho anaylsis with the passed year ranges
* @param YearRanges : year ranges to run for Mohn's Rho analysis
*/
void RunDiagnosticEstimation(std::vector<std::pair<int,int> > YearRanges);
void RunRetrospectiveAnalysis(std::vector<std::pair<int,int> > YearRanges);
/**
* @brief Signals to the main routine to run the Mohn's Rho anaylsis on a Multi Run with the passed year ranges
* @param YearRanges : year ranges to run for Mohn's Rho analysis on a Multi Run
Expand Down
95 changes: 41 additions & 54 deletions MSSPM_Main/nmfMainWindow.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1749,6 +1749,7 @@ nmfMainWindow::menu_toggleManagerMode()
QString msg = "\nAt least one forecast must be created prior to using REMORA.\n";
QMessageBox::warning(this, "Warning", msg, QMessageBox::Ok);
m_UI->actionToggleManagerMode->setChecked(false);
menu_layoutDefault();
return;
}

Expand Down Expand Up @@ -1792,6 +1793,8 @@ nmfMainWindow::setVisibilityToolbarButtons(bool isVisible)
m_UI->actionNLoptTB->setEnabled(isVisible);
m_UI->actionScreenShotAll->setEnabled(isVisible);
m_UI->actionMultiShot->setEnabled(isVisible);
m_UI->actionRunTB->setEnabled(isVisible);
m_UI->actionToggleSignificantDigits->setEnabled(isVisible);
}

bool
Expand Down Expand Up @@ -2069,7 +2072,7 @@ void
nmfMainWindow::menu_about()
{
QString name = "Multi-Species Surplus Production Model";
QString version = "MSSPM v1.3.2 ";
QString version = "MSSPM v1.3.3 ";
QString specialAcknowledgement = "";
QString cppVersion = "C++??";
QString mysqlVersion = "?";
Expand Down Expand Up @@ -2193,20 +2196,12 @@ nmfMainWindow::menu_troubleshooting()
QString eol;
QString msg;
QStringList groups;
QStringList importTopics,guiTopics,estimationTopics,helpTopics;
QStringList importSolutions,guiSolutions,estimationSolutions,helpSolutions;
QStringList importTopics,guiTopics,estimationTopics,helpTopics,mysqlTopics;
QStringList importSolutions,guiSolutions,estimationSolutions,helpSolutions,mysqlSolutions;
QMessageBox mbox;
std::vector<QStringList> topics;
std::vector<QStringList> solutions;

// List troubleshooting topics here
// topics << "Import doesn't work";
// topics << "No Models available after an Import";
// topics << "Accidentally closed a sub-panel";
// topics << "How to revert back to default GUI layout";
// topics << "Poor fit when estimating parameters";
// topics << "How to get help";

// Step 1. Add topic in appropriate group, creating a group if need be
estimationTopics << "Estimation doesn't run";
estimationTopics << "Poor fit when estimating parameters";
Expand All @@ -2217,9 +2212,10 @@ nmfMainWindow::menu_troubleshooting()
helpTopics << "No Log file found";
importTopics << "Import doesn't work";
importTopics << "No Models available after an Import";
mysqlTopics << "Can't connect to MySQL";

// Step 2. Add the group name to the groups list
groups << "Estimation" << "GUI" << "Help" << "Import";
groups << "Estimation" << "GUI" << "Help" << "Import" << "MySQL";

// Step 3. Add the topic solutions here
estimationSolutions << "If estimation doesn't produce any plots it could be a permission issue. If on Windows, exit the application and re-run as Administrator.";
Expand All @@ -2239,17 +2235,13 @@ nmfMainWindow::menu_troubleshooting()
helpSolutions << "If no Log files found on disk after clicking the Refresh button in the Log panel it could mean a permission problem. Exit the application and re-run as Administrator.";
importSolutions << "The import feature uses the mysql exe found on disk. Please make sure the executable is found when you type it at the command prompt. On Windows, must add mysql.exe path to Path system environment variable";
importSolutions << "The project name of an imported database must be the same as the current project name.";
mysqlSolutions << "This will happen if the user enters the incorrect MySQL password when starting the application or if the MySQL server needs to be restarted.";

// Display the troubleshooting topics as links
int i=1;
msg = "<h3 id=\"top\"><center><b><br>Topics</b></center></h3>";

// Original lines...no grouping
// for (QString topic : topics) {
// msg += QString::number(i) + ". " + "<a href=\"#Topic" + QString::number(i) + "\">" + topic + "</a><br><br>";
// ++i;
// }
topics = {estimationTopics,guiTopics,helpTopics,importTopics};
topics = {estimationTopics,guiTopics,helpTopics,importTopics,mysqlTopics};
int groupNum = 0;
for (QString group : groups) {
msg += "<br><b>" + group + "</b><br>";
Expand All @@ -2263,7 +2255,7 @@ nmfMainWindow::menu_troubleshooting()
i = 1;
groupNum = 0;
QStringList aSolution;
solutions = {estimationSolutions,guiSolutions,helpSolutions,importSolutions};
solutions = {estimationSolutions,guiSolutions,helpSolutions,importSolutions,mysqlSolutions};
msg += "<h3 id=\"solutions\"><center><b>Solutions</b></center></h3>";
for (QString group : groups) {
int j=0;
Expand Down Expand Up @@ -3580,7 +3572,7 @@ nmfMainWindow::initConnections()
Output_Controls_ptr, SLOT(callback_ResetOutputWidgetsForAggProd()));
connect(Diagnostic_Tab1_ptr, SIGNAL(SetChartType(std::string,std::string)),
this, SLOT(callback_SetChartType(std::string,std::string)));
connect(Diagnostic_Tab2_ptr, SIGNAL(RunDiagnosticEstimation(std::vector<std::pair<int,int> >)),
connect(Diagnostic_Tab2_ptr, SIGNAL(RunRetrospectiveAnalysis(std::vector<std::pair<int,int> >)),
this, SLOT(callback_RunRetrospectiveAnalysisEstimation(std::vector<std::pair<int,int> >)));
// connect(Diagnostic_Tab2_ptr, SIGNAL(RunDiagnosticEstimationMultiRun(std::vector<std::pair<int,int> >)),
// this, SLOT(callback_RunRetrospectiveAnalysisEstimationMultiRun(std::vector<std::pair<int,int> >)));
Expand Down Expand Up @@ -4120,6 +4112,7 @@ nmfMainWindow::menu_saveCurrentRun()
int NumSpecies;
int StartYear=0;
int NumGuilds;
int NumYears;
int RunLength;
int RunNum=0;
int InitialYear=0;
Expand Down Expand Up @@ -4177,6 +4170,7 @@ nmfMainWindow::menu_saveCurrentRun()
RunLength,InitialYear,isBiomassAbsolute)) {
return;
}
NumYears = RunLength + 1;

//std::cout << "#######: StartYear: " << StartYear << std::endl;
//std::cout << "#######: RunLength: " << RunLength << std::endl;
Expand Down Expand Up @@ -5809,7 +5803,7 @@ nmfMainWindow::updateOutputBiomassTable(std::string& ForecastName,

// Load the appropriate Harvest tables
if (HarvestFormName == nmfConstantsMSSPM::HarvestCatch.toStdString()) {
std::cout << "isMonteCarlo,ForecastName: " << isMonteCarlo << "," << ForecastName << std::endl;
//std::cout << "isMonteCarlo,ForecastName: " << isMonteCarlo << "," << ForecastName << std::endl;
if (! loadHarvestCatchTables(isAggProd,isMonteCarlo,ForecastName,HarvestFormName,
harvestFormPtr,HarvestRandomValues,HarvestUncertainty,
previousUnits,NumSpeciesOrGuilds,RunLength,Catch)) {
Expand Down Expand Up @@ -5837,19 +5831,21 @@ std::cout << "isMonteCarlo,ForecastName: " << isMonteCarlo << "," << ForecastNam
}

// Update the Forecast Monte Carlo Parameters table
if (! m_DatabasePtr->updateForecastMonteCarloParameters(
0,m_Logger,m_ProjectName,m_ModelName,
ForecastName,Algorithm,Minimizer,ObjectiveCriterion,Scaling,
SpeciesList,RunNum,
GrowthRateRandomValues,
CarryingCapacityRandomValues,CatchabilityRandomValues,
PredationExponentRandomValues,CompetitionAlphaRandomValues,
CompetitionBetaSpeciesRandomValues,CompetitionBetaGuildsRandomValues,
CompetitionBetaGuildsGuildsRandomValues,
PredationRhoRandomValues,PredationHandlingRandomValues,HarvestRandomValues,
GrowthRateCovCoeffRandomValues,CarryingCapacityCovCoeffRandomValues,
CatchabilityCovCoeffRandomValues,SurveyQCovCoeffRandomValues)) {
return false;
if (!ForecastName.empty()) {
if (! m_DatabasePtr->updateForecastMonteCarloParameters(
0,m_Logger,m_ProjectName,m_ModelName,
ForecastName,Algorithm,Minimizer,ObjectiveCriterion,Scaling,
SpeciesList,RunNum,
GrowthRateRandomValues,
CarryingCapacityRandomValues,CatchabilityRandomValues,
PredationExponentRandomValues,CompetitionAlphaRandomValues,
CompetitionBetaSpeciesRandomValues,CompetitionBetaGuildsRandomValues,
CompetitionBetaGuildsGuildsRandomValues,
PredationRhoRandomValues,PredationHandlingRandomValues,HarvestRandomValues,
GrowthRateCovCoeffRandomValues,CarryingCapacityCovCoeffRandomValues,
CatchabilityCovCoeffRandomValues,SurveyQCovCoeffRandomValues)) {
return false;
}
}

// If not running a forecast, initial biomass is the first observed biomass.
Expand Down Expand Up @@ -8046,10 +8042,10 @@ nmfMainWindow::calculateSummaryStatisticsStruct(

// Calculate the meanObserved from the observed
m = 0;
for (int i=0;i<NumSpeciesOrGuilds;++i) {
for (int species=0; species<NumSpeciesOrGuilds; ++species) {
meanVal = 0;
for (int j=0; j<=RunLength;++j) {
meanVal += ObservedBiomass(j,i);
for (int time=0; time<=RunLength; ++time) {
meanVal += ObservedBiomass(time,species);
}
meanVal /= (RunLength+1);
meanObserved.push_back(meanVal);
Expand Down Expand Up @@ -8349,17 +8345,8 @@ nmfMainWindow::loadSummaryStatisticsModel(
bool
nmfMainWindow::isAMohnsRhoMultiRun()
{
// return Diagnostic_Tab2_ptr->isAMohnsRhoRun() ||
// (Output_Controls_ptr->getOutputChartType() == "Diagnostics" &&
// Output_Controls_ptr->isSetToRetrospectiveAnalysis());

QString NavigatorStr = NavigatorTree->currentItem()->text(0);

return ( Diagnostic_Tab2_ptr->isAMohnsRhoRunForSingleRun() ||
(Output_Controls_ptr->getOutputChartType() == "Diagnostics" &&
Output_Controls_ptr->isSetToRetrospectiveAnalysis()));
// && (NavigatorStr.contains("Retrospective Analysis") ||
// NavigatorStr.contains("Parameter Profiles")) ));
Diagnostic_Tab2_ptr->isPageVisible());
}

bool
Expand Down Expand Up @@ -8880,6 +8867,7 @@ nmfMainWindow::getMonteCarloUncertaintyData(
std::string str;
std::string ForecastHarvestType;
std::string GrowthForm,HarvestForm,CompetitionForm,PredationForm;
std::string msg;

if (! m_DatabasePtr->getForecastInfo(
m_ProjectName,m_ModelName,ForecastName,RunLength,StartYearForecast,
Expand All @@ -8906,7 +8894,11 @@ nmfMainWindow::getMonteCarloUncertaintyData(
dataMap = m_DatabasePtr->nmfQueryDatabase(queryStr, fields);
NumRecords = dataMap["SpeName"].size();
if (NumRecords < NumRuns) {
m_Logger->logMsg(nmfConstants::Error,"Couldn't find sufficient uncertainty records in ForecastMonteCarloParameters");
msg = "Couldn't find sufficient uncertainty records in ForecastMonteCarloParameters ";
msg += "Found " + std::to_string(NumRecords) + " table records, but there are " +
std::to_string(NumRuns) + " runs.";
m_Logger->logMsg(nmfConstants::Error,msg);
m_Logger->logMsg(nmfConstants::Error,queryStr);
for (int i=0; i<NumRuns; ++i) {
formattedUncertaintyData << "";
}
Expand Down Expand Up @@ -11316,15 +11308,11 @@ nmfMainWindow::runNLoptAlgorithm(bool showDiagnosticChart,
this, SLOT(callback_AllSubRunsCompleted()));
connect(m_Estimator_NLopt, SIGNAL(AMohnsRhoMultiRunCompleted()),
this, SLOT(callback_AMohnsRhoMultiRunCompleted()));

connect(m_Estimator_NLopt, SIGNAL(NLoptFailureStopRunsAndReset()),
m_ProgressWidget, SLOT(callback_stopPB()));


connect(m_ProgressWidget, SIGNAL(StopAllRuns()),
this, SLOT(callback_StopAllRuns()));


updateProgressChartAnnotation(0,(double)m_DataStruct.NLoptStopAfterIter,5.0);

// Run the optimizer
Expand Down Expand Up @@ -11596,7 +11584,6 @@ nmfMainWindow::calculateSubRunBiomass(std::vector<double>& EstInitBiomass,
nmfUtilsQt::convertMatrix(Catch, previousUnits[tableHarvestCatch], "mt", nmfConstantsMSSPM::ConvertAll);
}

double EstCarryingCapacityValue = 0;
for (int time = 1; time <= RunLength; time++) {
timeMinus1 = time-1;
for (int species=0; species<NumSpeciesOrGuilds; ++species)
Expand All @@ -11620,7 +11607,7 @@ nmfMainWindow::calculateSubRunBiomass(std::vector<double>& EstInitBiomass,
EstGrowthRateCovariateCoeffs[species],
GrowthRateCovariate(timeMinus1,species),
EstCarryingCapacities[species],
EstCarryingCapacityValue,
EstCarryingCapacityCovariateCoeffs[species],
CarryingCapacityCovariate(timeMinus1,species));
HarvestTerm = harvestForm->evaluate(CovariateAlgorithmType,
timeMinus1,species,EstBiomassVal,
Expand Down
13 changes: 3 additions & 10 deletions MSSPM_ParameterEstimationNLoptAlgorithm/NLopt_Estimator.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -861,7 +861,6 @@ NLopt_Estimator::estimateParameters(nmfStructsQt::ModelDataStruct &NLoptStruct,
std::vector<QString>& MultiRunLines,
int& TotalIndividualRuns)
{

bool isAMultiRun = bools.first;
bool isSetToDeterministic = bools.second;
bool foundOneNLoptRun = false;
Expand Down Expand Up @@ -896,7 +895,7 @@ NLopt_Estimator::estimateParameters(nmfStructsQt::ModelDataStruct &NLoptStruct,
NumEstParameters = ParameterRanges.size();
std::cout << "*** NumEstParam: " << NumEstParameters << std::endl;
//for (int i=0; i< NumEstParameters; ++i) {
// std::cout << " " << ParameterRanges[i].first << ", " << ParameterRanges[i].second << std::endl;
// std::cout << " (1) " << ParameterRanges[i].first << ", " << ParameterRanges[i].second << std::endl;
//}

if (isAMultiRun) {
Expand Down Expand Up @@ -930,16 +929,12 @@ std::cout << "*** NumEstParam: " << NumEstParameters << std::endl;
}
m_Seed = 0;
foundOneNLoptRun = true;

for (int run=0; run<NumSubRuns; ++run) {
m_Quit = false;

if (NLoptStruct.isMohnsRho) {
m_MohnsRhoOffset = run;
}
m_MohnsRhoOffset = (NLoptStruct.isMohnsRho) ? run : m_MohnsRhoOffset;

// Initialize the optimizer with the appropriate algorithm
//std::cout << "LOADING: " << NLoptStruct.MinimizerAlgorithm
// << " with " << m_MinimizerToEnum[NLoptStruct.MinimizerAlgorithm] << std::endl;
m_Optimizer = nlopt::opt(m_MinimizerToEnum[NLoptStruct.MinimizerAlgorithm],NumEstParameters);
setAdditionalParameters(NLoptStruct);

Expand Down Expand Up @@ -1056,7 +1051,6 @@ NLopt_Estimator::stoppedByUser()
return retv;
}


void
NLopt_Estimator::callback_StopAllRuns()
{
Expand All @@ -1065,7 +1059,6 @@ std::cout << "Stopping all runs" << std::endl;
nlopt::forced_stop();
}


void
NLopt_Estimator::callback_StopTheOptimizer()
{
Expand Down

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