Mods for 1.7.5

nmfs-fish-tools · Oct 3, 2023 · 1c08089 · 1c08089
1 parent b8ae775
commit 1c08089
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Showing 13 changed files with 483 additions and 275 deletions.
diff --git a/MSSPM_GuiEstimation/nmfEstimationTab01.cpp b/MSSPM_GuiEstimation/nmfEstimationTab01.cpp
@@ -471,17 +471,20 @@ nmfEstimation_Tab1::importSpeciesData(const QString& tableName,
     if (loadOK && updateSetup) {
         // Load signal with data to send to Species Setup tab
         QList<QString> SpeciesNames;
+        QList<QString> SpeciesMinimumBiomass;
         QList<QString> SpeciesInitBiomass;
         QList<QString> SpeciesGrowthRate;
         QList<QString> SpeciesK;
         for (int row=0; row<m_SpeciesModel->rowCount(); ++row) {
             SpeciesNames.push_back(      m_SpeciesModel->item(row,m_ColumnMap["SpeName"])->text());
+            SpeciesMinimumBiomass.push_back(m_SpeciesModel->item(row,m_ColumnMap["MinimumBiomass"])->text().remove(","));
             SpeciesInitBiomass.push_back(m_SpeciesModel->item(row,m_ColumnMap["InitBiomass"])->text().remove(","));
             SpeciesGrowthRate.push_back( m_SpeciesModel->item(row,m_ColumnMap["GrowthRate"])->text());
             SpeciesK.push_back(          m_SpeciesModel->item(row,m_ColumnMap["SpeciesK"])->text().remove(","));
         }
 
-        emit UpdateSpeciesSetupData(SpeciesNames,SpeciesGuilds,SpeciesInitBiomass,
+        emit UpdateSpeciesSetupData(SpeciesNames,SpeciesGuilds,
+                                    SpeciesMinimumBiomass,SpeciesInitBiomass,
                                     SpeciesGrowthRate,SpeciesK);
         QMessageBox::information(Estimation_Tabs, "Data Updated",
                                  "\nSpecies/Guild table has been successfully updated.\n",
@@ -600,6 +603,7 @@ nmfEstimation_Tab1::checkSpeciesDataPrimary(bool showPopup)
 {
     double WeightVal = 0;
     QString SpeName;
+    QString MinimumBiomass;
     QString InitBiomass;
     QString GrowthRate;
     QString SpeciesK;
@@ -613,13 +617,15 @@ nmfEstimation_Tab1::checkSpeciesDataPrimary(bool showPopup)
         WeightVal = Weight.toDouble();
         index = m_SpeciesModel->index(i,m_ColumnMap["SpeName"]);
         SpeName = index.data().toString().remove(",");
+        index = m_SpeciesModel->index(i,m_ColumnMap["MinimumBiomass"]);
+        MinimumBiomass = index.data().toString().remove(",");
         index = m_SpeciesModel->index(i,m_ColumnMap["InitBiomass"]);
         InitBiomass = index.data().toString().remove(",");
         index = m_SpeciesModel->index(i,m_ColumnMap["GrowthRate"]);
         GrowthRate = index.data().toString().remove(",");
         index = m_SpeciesModel->index(i,m_ColumnMap["SpeciesK"]);
         SpeciesK = index.data().toString().remove(",");
-        if (nmfUtilsQt::emptyField({Weight,SpeName,InitBiomass,GrowthRate,SpeciesK})) {
+        if (nmfUtilsQt::emptyField({Weight,SpeName,MinimumBiomass,InitBiomass,GrowthRate,SpeciesK})) {
             checkAndShowEmptyFieldError(showPopup,"checkSpeciesDataPrimary");
             return false;
         }
@@ -701,6 +707,7 @@ nmfEstimation_Tab1::showAllColumns(QTableView* tv)
         tv->setColumnHidden( i,false);
     }
     showCovariateColumns(tv,false); // Hide them for now as covariates are entered in their own tab (Tab 6)
+    showMinimumBiomassColumn(tv,false);
 }
 
 void
@@ -720,6 +727,19 @@ nmfEstimation_Tab1::showCovariateColumns(QTableView* tv, const bool& show)
     }
 }
 
+void
+nmfEstimation_Tab1::showMinimumBiomassColumn(QTableView* tv, const bool& show)
+{
+    QString colName;
+    QStringList SpeciesSupp = {"MinimumBiomass"};
+
+    for (int i = 0; i < tv->model()->columnCount(); ++i) {
+        colName = tv->model()->headerData(i, Qt::Horizontal).toString();
+        if (SpeciesSupp.contains(colName)) {
+            tv->setColumnHidden(i,!show);
+        }
+    }
+}
 
 void
 nmfEstimation_Tab1::showPrimaryColumns(QTableView* tv)
@@ -1561,7 +1581,8 @@ nmfEstimation_Tab1::callback_ExportPB()
     QList<QString> GuildGrowthRate;
     QList<QString> GuildK;
     QList<QString> SpeciesName;
-//    QList<QString> SpeciesGuild;
+//  QList<QString> SpeciesGuild;
+    QList<QString> SpeciesMinimumBiomass;
     QList<QString> SpeciesInitialBiomass;
     QList<QString> SpeciesGrowthRate;
     QList<QString> SpeciesK;
@@ -1572,8 +1593,10 @@ nmfEstimation_Tab1::callback_ExportPB()
             saveGuildsCSVFile(tableNameStr,GuildName,GuildGrowthRate,GuildK);
         } else {
             emit LoadSpeciesGuild();
-            callback_SaveSpeciesCSVFile(tableNameStr,SpeciesName,m_SpeciesGuild,
-                               SpeciesInitialBiomass,SpeciesGrowthRate,SpeciesK);
+            callback_SaveSpeciesCSVFile(
+                        tableNameStr,SpeciesName,m_SpeciesGuild,
+                        SpeciesMinimumBiomass,SpeciesInitialBiomass,
+                        SpeciesGrowthRate,SpeciesK);
         }
     }
 }
@@ -1590,6 +1613,7 @@ nmfEstimation_Tab1::callback_QueryAndSaveSpeciesCSVFile(
         QString tableNameStr,
         QList<QString> SpeciesName,
         QList<QString> SpeciesGuild,
+        QList<QString> SpeciesMinimumBiomass,
         QList<QString> SpeciesInitialBiomass,
         QList<QString> SpeciesGrowthRate,
         QList<QString> SpeciesK)
@@ -1600,6 +1624,7 @@ nmfEstimation_Tab1::callback_QueryAndSaveSpeciesCSVFile(
                 tableNameStr,
                 SpeciesName,
                 SpeciesGuild,
+                SpeciesMinimumBiomass,
                 SpeciesInitialBiomass,
                 SpeciesGrowthRate,
                 SpeciesK);
@@ -1611,6 +1636,7 @@ nmfEstimation_Tab1::callback_SaveSpeciesCSVFile(
         QString tableName,
         QList<QString> SpeciesName,
         QList<QString> SpeciesGuild,
+        QList<QString> SpeciesMinimumBiomass,
         QList<QString> SpeciesInitialBiomass,
         QList<QString> SpeciesGrowthRate,
         QList<QString> SpeciesK)
@@ -1626,7 +1652,8 @@ nmfEstimation_Tab1::callback_SaveSpeciesCSVFile(
                                               smodel,
                                               m_ColumnMap,
                                               inputDataPath,tableNameStr,
-                                              SpeciesName,SpeciesGuild,SpeciesInitialBiomass,
+                                              SpeciesName,SpeciesGuild,
+                                              SpeciesMinimumBiomass,SpeciesInitialBiomass,
                                               SpeciesGrowthRate,SpeciesK);
 
     QFileInfo fileInfo(tableNameStr);
@@ -1969,13 +1996,13 @@ nmfEstimation_Tab1::loadSpecies()
     m_Logger->logMsg(nmfConstants::Normal,"nmfEstimation_Tab1::loadSpecies()");
 
     // Load Population tableview
-    fields = {"Weight","SpeName","InitBiomass","InitBiomassMin","InitBiomassMax",
+    fields = {"Weight","SpeName","MinimumBiomass","InitBiomass","InitBiomassMin","InitBiomassMax",
               "GrowthRate","GrowthRateMin","GrowthRateMax",
               "GrowthRateShape","GrowthRateShapeMin","GrowthRateShapeMax",
               "SpeciesK","SpeciesKMin","SpeciesKMax",
               "SurveyQ","SurveyQMin","SurveyQMax","Catchability",
               "CatchabilityMin","CatchabilityMax"};
-    queryStr   = "SELECT Weight,SpeName,InitBiomass,InitBiomassMin,InitBiomassMax,";
+    queryStr   = "SELECT Weight,SpeName,MinimumBiomass,InitBiomass,InitBiomassMin,InitBiomassMax,";
     queryStr  += "GrowthRate,GrowthRateMin,GrowthRateMax,";
     queryStr  += "GrowthRateShape,GrowthRateShapeMin,GrowthRateShapeMax,";
     queryStr  += "SpeciesK,SpeciesKMin,SpeciesKMax,";

diff --git a/MSSPM_GuiEstimation/nmfEstimationTab01.h b/MSSPM_GuiEstimation/nmfEstimationTab01.h
@@ -139,6 +139,7 @@ class nmfEstimation_Tab1: public QObject
     void setupHelpSpecies();
     void setupHelpGuilds();
     void showCovariateColumns(QTableView* tv, const bool& show);
+    void showMinimumBiomassColumn(QTableView* tv, const bool& show);
     void showNoColumns(QTableView* tv);
     void showAllColumns(QTableView* tv);
     void showPrimaryColumns(QTableView* tv);
@@ -212,13 +213,15 @@ class nmfEstimation_Tab1: public QObject
      * @brief Signal sent so the Species Setup tab will be updated with the appropriate Species fields
      * @param SpeciesNames : list of species names
      * @param SpeciesGuilds : list of guilds that each species is in
+     * @param SpeciesMinimumBiomass : list of species minimum biomass values
      * @param SpeciesInitBiomass : list of species initial biomass values
      * @param SpeciesGrowthRate : list of species growth rates
      * @param SpeciesK : list of species carrying capacities
      */
     void UpdateSpeciesSetupData(
             QList<QString> SpeciesNames,
             QList<QString> SpeciesGuilds,
+            QList<QString> SpeciesMinimumBiomass,
             QList<QString> SpeciesInitBiomass,
             QList<QString> SpeciesGrowthRate,
             QList<QString> SpeciesK);
@@ -342,6 +345,7 @@ public Q_SLOTS:
      * @param TableName: name of table to save data from
      * @param SpeciesName : list of species names
      * @param SpeciesGuild : list of guilds that each species is a member of
+     * @param SpeciesMinimumBiomass : list of minimum biomass per species
      * @param SpeciesInitialBiomass : list of initial biomass per species
      * @param SpeciesGrowthRate : list of growth rate per species
      * @param SpeciesK : list of carrying capacities per species
@@ -350,6 +354,7 @@ public Q_SLOTS:
             QString TableName,
             QList<QString> SpeciesName,
             QList<QString> SpeciesGuild,
+            QList<QString> SpeciesMinimumBiomass,
             QList<QString> SpeciesInitialBiomass,
             QList<QString> SpeciesGrowthRate,
             QList<QString> SpeciesK);
@@ -378,6 +383,7 @@ public Q_SLOTS:
      * @param TableName: name of table to save data from
      * @param SpeciesName : list of species names
      * @param SpeciesGuild : list of guilds that each species is a member of
+     * @param SpeciesMinimumBiomass : list of minimum biomass per species
      * @param SpeciesInitialBiomass : list of initial biomass per species
      * @param SpeciesGrowthRate : list of growth rate per species
      * @param SpeciesK : list of carrying capacities per species
@@ -386,6 +392,7 @@ public Q_SLOTS:
             QString TableName,
             QList<QString> SpeciesName,
             QList<QString> SpeciesGuild,
+            QList<QString> SpeciesMinimumBiomass,
             QList<QString> SpeciesInitialBiomass,
             QList<QString> SpeciesGrowthRate,
             QList<QString> SpeciesK);

diff --git a/MSSPM_GuiEstimation/nmfEstimationTab06.cpp b/MSSPM_GuiEstimation/nmfEstimationTab06.cpp
@@ -667,6 +667,7 @@ nmfEstimation_Tab6::loadCovariateInitialValuesAndRangesTable()
         //                         QMessageBox::Ok);
         return false;
     }
+
     int NumParameters = NumRecords/NumSpecies;
     int m = -1;
     int modelCol = 0;
@@ -676,14 +677,14 @@ nmfEstimation_Tab6::loadCovariateInitialValuesAndRangesTable()
             ++m;
             modelCol += 3;
             coeffValue = dataMap["CoeffValue"][m];
-            if (! QString::fromStdString(coeffValue).trimmed().isEmpty()) {                
-                item = new QStandardItem(QString::fromStdString(coeffValue));
+            if (! QString::fromStdString(coeffValue).trimmed().isEmpty()) {
+                item = nmfUtilsQt::itemFixedOrScientific(std::stod(coeffValue));
                 item->setTextAlignment(Qt::AlignCenter);
                 smodelIR->setItem(species,modelCol+0,item);
-                item = new QStandardItem(QString::fromStdString(dataMap["CoeffMinValue"][m]));
+                item = nmfUtilsQt::itemFixedOrScientific(std::stod(dataMap["CoeffMinValue"][m]));
                 item->setTextAlignment(Qt::AlignCenter);
                 smodelIR->setItem(species,modelCol+1,item);
-                item = new QStandardItem(QString::fromStdString(dataMap["CoeffMaxValue"][m]));
+                item = nmfUtilsQt::itemFixedOrScientific(std::stod(dataMap["CoeffMaxValue"][m]));
                 item->setTextAlignment(Qt::AlignCenter);
                 smodelIR->setItem(species,modelCol+2,item);
             } else {
@@ -1520,13 +1521,15 @@ nmfEstimation_Tab6::callback_SpeciesRangeSB(int pct)
                     valueWithoutComma = initialIndex.data().toString().remove(",");
                     if ((rangeType == "min/max") || (rangeType == "min only")) {
                         newValue = valueWithoutComma.toDouble()*(1.0-pctVal);
-                        minItem = new QStandardItem(QString::number(newValue,'f',6));
+//                        minItem = new QStandardItem(QString::number(newValue,'f',6));
+                        minItem = nmfUtilsQt::itemFixedOrScientific(newValue);
                         minItem->setTextAlignment(Qt::AlignCenter);
                         m_smodelIR->setItem(row,col+1,minItem);
                     }
                     if ((rangeType == "min/max") || (rangeType == "max only")) {
                         newValue = valueWithoutComma.toDouble()*(1.0+pctVal);
-                        maxItem = new QStandardItem(QString::number(newValue,'f',6));
+//                        maxItem = new QStandardItem(QString::number(newValue,'f',6));
+                        maxItem = nmfUtilsQt::itemFixedOrScientific(newValue);
                         maxItem->setTextAlignment(Qt::AlignCenter);
                         m_smodelIR->setItem(row,col+2,maxItem);
                     }
@@ -1545,7 +1548,8 @@ nmfEstimation_Tab6::callback_SpeciesRangeSB(int pct)
                 valueWithoutComma = initialIndex.data().toString().remove(",");
                 if ((rangeType == "min/max") || (rangeType == "min only")) {
                     newValue = valueWithoutComma.toDouble()*(1.0-pctVal);
-                    minItem = new QStandardItem(QString::number(newValue,'f',6));
+//                    minItem = new QStandardItem(QString::number(newValue,'f',6));
+                    minItem = nmfUtilsQt::itemFixedOrScientific(newValue);
                     minItem->setTextAlignment(Qt::AlignCenter);
                     m_smodelIR->setItem(row,col,minItem);
                 }
@@ -1555,7 +1559,8 @@ nmfEstimation_Tab6::callback_SpeciesRangeSB(int pct)
                 valueWithoutComma = initialIndex.data().toString().remove(",");
                 if ((rangeType == "min/max") || (rangeType == "max only")) {
                     newValue = valueWithoutComma.toDouble()*(1.0+pctVal);
-                    maxItem = new QStandardItem(QString::number(newValue,'f',6));
+//                    maxItem = new QStandardItem(QString::number(newValue,'f',6));
+                    maxItem = nmfUtilsQt::itemFixedOrScientific(newValue);
                     maxItem->setTextAlignment(Qt::AlignCenter);
                     m_smodelIR->setItem(row,col,maxItem);
                 }

diff --git a/MSSPM_GuiOutput/nmfOutputControls.cpp b/MSSPM_GuiOutput/nmfOutputControls.cpp
@@ -930,6 +930,11 @@ nmfOutputControls::getGuilds(int&         NumGuilds,
     return true;
 }
 
+void
+nmfOutputControls::refreshBrightnessSlider()
+{
+    OutputLineBrightnessSL->setValue(OutputLineBrightnessSL->value());
+}
 
 void
 nmfOutputControls::callback_OutputLineBrightnessSL(int value)

diff --git a/MSSPM_GuiOutput/nmfOutputControls.h b/MSSPM_GuiOutput/nmfOutputControls.h
@@ -380,6 +380,10 @@ class nmfOutputControls: public QObject
      * @brief Resets the Output Type widget as well as reloading the Scenario widget
      */
     void refresh();
+    /**
+     * @brief Refreshes the current chart by resetting the brightness slider
+     */
+    void refreshBrightnessSlider();
     /**
      * @brief Refreshes the current chart by flipping to another chart type and back to the current
      */

diff --git a/MSSPM_GuiSetup/nmfSetupTab02.cpp b/MSSPM_GuiSetup/nmfSetupTab02.cpp
@@ -859,6 +859,7 @@ nmfSetup_Tab2::createTables(QString databaseName)
     cmd  = "CREATE TABLE IF NOT EXISTS " + fullTableName;
     cmd += "(SpeName              varchar(100) NOT NULL,";
     cmd += " GuildName            varchar(100) NULL,";
+    cmd += " MinimumBiomass       double NULL,";
     cmd += " InitBiomass          double NULL,";
     cmd += " SurveyQ              float  NULL,";
     cmd += " SpeciesK             double NULL,";