Merge pull request #1398 from virtualcell/jobindex-with-trial

redefine simulation JobIndex in terms of ScanIndex and TrialIndex
virtualcell · Dec 12, 2024 · 55ef45b · 55ef45b
2 parents 746eb9a + c0bba26
commit 55ef45b
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Showing 38 changed files with 702 additions and 502 deletions.
diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/NonspatialResultsConverter.java b/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/NonspatialResultsConverter.java
@@ -2,6 +2,7 @@
 
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.solver.MathOverrides;
 import cbit.vcell.solver.Simulation;
 import cbit.vcell.solver.TempSimulation;
 import org.apache.logging.log4j.LogManager;
@@ -168,7 +169,7 @@ public static Map<Report, List<Hdf5SedmlResults>> convertNonspatialResultsToSedm
                     String nameKey = dataSourceNonspatial.scanParameterNames[nameIndex];
                     scanValues[nameIndex] = new double[dataSourceNonspatial.scanBounds[nameIndex] + 1];
                     for (int scanIndex = 0; scanIndex < dataSourceNonspatial.scanBounds[nameIndex] + 1; scanIndex++){
-                        Expression overrideExp = dataSetValuesSource.vcSimulation.getMathOverrides().getActualExpression(nameKey, scanIndex);
+                        Expression overrideExp = dataSetValuesSource.vcSimulation.getMathOverrides().getActualExpression(nameKey, new MathOverrides.ScanIndex(scanIndex));
                         try { scanValues[nameIndex][scanIndex] = overrideExp.evaluateConstant(); }
                         catch (ExpressionException e){ throw new RuntimeException(e); }
                     }

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/SpatialResultsConverter.java b/vcell-cli/src/main/java/org/vcell/cli/run/hdf5/SpatialResultsConverter.java
@@ -3,6 +3,7 @@
 
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.solver.MathOverrides;
 import cbit.vcell.solver.TempSimulation;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -135,7 +136,7 @@ private static boolean processDataGenerator(SedML sedml, Report report, DataGene
                         String nameKey = convertedData.scanParameterNames[nameIndex];
                         scanValues[nameIndex] = new double[eachBound[nameIndex] + 1];
                         for (int scanIndex = 0; scanIndex < eachBound[nameIndex] + 1; scanIndex++){
-                            Expression overrideExp = vcellSimulation.getMathOverrides().getActualExpression(nameKey, scanIndex);
+                            Expression overrideExp = vcellSimulation.getMathOverrides().getActualExpression(nameKey, new MathOverrides.ScanIndex(scanIndex));
                             try { scanValues[nameIndex][scanIndex] = overrideExp.evaluateConstant(); }
                             catch (ExpressionException e){ throw new RuntimeException(e); }
                         }

diff --git a/vcell-client/src/main/java/cbit/vcell/client/TestingFrameworkWindowManager.java b/vcell-client/src/main/java/cbit/vcell/client/TestingFrameworkWindowManager.java
@@ -30,6 +30,7 @@
 import javax.swing.ListSelectionModel;
 import javax.swing.table.DefaultTableCellRenderer;
 
+import cbit.vcell.solver.*;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.client.logicalwindow.LWNamespace;
@@ -130,16 +131,7 @@
 import cbit.vcell.simdata.OutputContext;
 import cbit.vcell.simdata.PDEDataContext;
 import cbit.vcell.simdata.PDEDataManager;
-import cbit.vcell.solver.AnnotatedFunction;
 import cbit.vcell.solver.AnnotatedFunction.FunctionCategory;
-import cbit.vcell.solver.DefaultOutputTimeSpec;
-import cbit.vcell.solver.NonspatialStochSimOptions;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.SimulationInfo;
-import cbit.vcell.solver.SimulationSymbolTable;
-import cbit.vcell.solver.SolverDescription;
-import cbit.vcell.solver.SolverTaskDescription;
-import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.ode.ODESolverResultSet;
 import cbit.vcell.solver.ode.SensVariable;
 import cbit.vcell.solver.test.MathTestingUtilities;
@@ -1189,7 +1181,7 @@ private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew
         if (testSim.getScanCount() != 1) {
             throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
         }
-        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, 0);
+        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(testSim, MathOverrides.ScanIndex.ZERO);
 
         String simReportStatus = null;
         String simReportStatusMessage = null;
@@ -1321,7 +1313,7 @@ private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew
                             if (refSim.getScanCount() != 1) {
                                 throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                             }
-                            SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
+                            SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, MathOverrides.ScanIndex.ZERO);
 
                             String varsToCompare[] = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
                             SimulationComparisonSummary simCompSummary =
@@ -1418,7 +1410,7 @@ private String generateTestCriteriaReport(TestCaseNew testCase, TestCriteriaNew
                             if (refSim.getScanCount() != 1) {
                                 throw new RuntimeException("paramater scan is not supported in Math Testing Framework");
                             }
-                            SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, 0);
+                            SimulationSymbolTable refSimSymbolTable = new SimulationSymbolTable(refSim, MathOverrides.ScanIndex.ZERO);
 
                             String varsToTest[] = getVariableNamesToCompare(simSymbolTable, refSimSymbolTable);
 

diff --git a/vcell-client/src/main/java/cbit/vcell/client/data/ODETimePlotMultipleScansPanel.java b/vcell-client/src/main/java/cbit/vcell/client/data/ODETimePlotMultipleScansPanel.java
@@ -24,6 +24,7 @@
 import javax.swing.SwingConstants;
 import javax.swing.table.TableColumn;
 
+import cbit.vcell.solver.*;
 import org.vcell.util.document.VCDataIdentifier;
 
 import cbit.plot.Plot2D;
@@ -39,10 +40,6 @@
 import cbit.vcell.parser.SymbolTableEntry;
 import cbit.vcell.simdata.DataManager;
 import cbit.vcell.simdata.ODEDataManager;
-import cbit.vcell.solver.DefaultOutputTimeSpec;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.VCSimulationDataIdentifier;
-import cbit.vcell.solver.VCSimulationIdentifier;
 import cbit.vcell.solver.ode.ODESolverResultSet;
 import cbit.vcell.solver.ode.gui.ODESolverPlotSpecificationPanel;
 /**
@@ -88,6 +85,7 @@ private void initialize()  {
 
 	setLayout(new BorderLayout());
 	int scanCount = simulation.getScanCount();
+	int trialCount = simulation.getNumTrials();
 
 	plotPane = new PlotPane();
 	plotPane.getPlot2DDataPanel1().setXVarName(xVarColumnName);
@@ -129,7 +127,7 @@ public int getColumnCount() {
 
 		public Object getValueAt(int row, int col) { 
 			if (col == 0) {
-				return new Integer(row);
+				return row;
 			}
 			return rowData[row][col - 1]; 
 		}
@@ -145,12 +143,11 @@ public Class<?> getColumnClass(int columnIndex) {
 
 	values = new Double[scanCount][scanParams.length];
 	for (int i = 0; i < scanCount; i ++) {
+		MathOverrides.ScanIndex scanIndex = new MathOverrides.ScanIndex(i);
 		for (int j = 0; j < scanParams.length; j ++){
-		Expression scanConstantExp = simulation.getMathOverrides().getActualExpression(scanParams[j], i);
+		Expression scanConstantExp = simulation.getMathOverrides().getActualExpression(scanParams[j], scanIndex);
 			try {
 				values[i][j] = scanConstantExp.evaluateConstantWithSubstitution();
-			} catch (DivideByZeroException e1) {
-				e1.printStackTrace();
 			} catch (ExpressionException e1) {
 				e1.printStackTrace();
 			}

diff --git a/vcell-client/src/main/java/cbit/vcell/client/data/PDEExportDataPanel.java b/vcell-client/src/main/java/cbit/vcell/client/data/PDEExportDataPanel.java
@@ -656,7 +656,9 @@ private ExportSpecs getExportSpecs() {
 	if (vcDataIdentifier instanceof VCSimulationDataIdentifier){
         for (String filteredConstant : filteredConstants) {
 			String defaultValue = mathOverrides.getDefaultExpression(filteredConstant).infix();
-			String setValue = mathOverrides.getActualExpression(filteredConstant, ((VCSimulationDataIdentifier) vcDataIdentifier).getJobIndex()).infix();
+			int jobIndex = ((VCSimulationDataIdentifier) vcDataIdentifier).getJobIndex();
+			MathOverrides.ScanIndex scanIndex = simulation.getScanIndex(jobIndex);
+			String setValue = mathOverrides.getActualExpression(filteredConstant, scanIndex).infix();
 			if(!defaultValue.equals(setValue)){
 				differentParameterValues.add(filteredConstant + ":" +defaultValue + ":" + setValue);
 			}

diff --git a/vcell-client/src/main/java/cbit/vcell/client/data/SimResultsViewer.java b/vcell-client/src/main/java/cbit/vcell/client/data/SimResultsViewer.java
@@ -21,11 +21,12 @@
 import cbit.vcell.math.Constant;
 import cbit.vcell.mathmodel.MathModel;
 import cbit.vcell.simdata.*;
+import cbit.vcell.solver.MathOverrides;
 import cbit.vcell.solver.Simulation;
+import cbit.vcell.solver.SolverTaskDescription;
 import cbit.vcell.solver.VCSimulationDataIdentifier;
 import cbit.vcell.solver.ode.ODESolverResultSet;
 import org.vcell.util.ArrayUtils;
-import org.vcell.util.BeanUtils;
 import org.vcell.util.DataAccessException;
 import org.vcell.util.UserCancelException;
 import org.vcell.util.document.VCDataIdentifier;
@@ -37,6 +38,9 @@
 import java.awt.event.ActionListener;
 import java.util.Arrays;
 import java.util.Hashtable;
+
+import static cbit.vcell.solver.MathOverrides.parameterScanCoordinateToScanIndex;
+
 /**
  * Insert the type's description here.
  * Creation date: (10/17/2005 11:22:58 PM)
@@ -387,7 +391,12 @@ private int getSelectedParamScanJobIndex(){
 	}
 	int selectedJobIndex = -1;
 	try {
-		selectedJobIndex = BeanUtils.parameterScanCoordinateToJobIndex(indices, bounds);
+		MathOverrides.ScanIndex scanIndex = MathOverrides.parameterScanCoordinateToScanIndex(indices, bounds);
+		SolverTaskDescription.TrialIndex trialIndex = SolverTaskDescription.TrialIndex.ZERO;
+		if (getSimulation().getNumTrials() > 1) {
+			System.err.println("SimResultsViewer.getSelectedParamScanJobIndex: multiple trials not supported yet");
+		}
+		selectedJobIndex = getSimulation().getJobIndex(scanIndex, trialIndex);
 	} catch (RuntimeException exc) {
 		exc.printStackTrace();
 	}

diff --git a/vcell-client/src/main/java/cbit/vcell/client/desktop/simulation/SimulationWorkspace.java b/vcell-client/src/main/java/cbit/vcell/client/desktop/simulation/SimulationWorkspace.java
@@ -134,7 +134,7 @@ public static String checkCompatibility(SimulationOwner simOwner, Simulation sim
  * @param simulation cbit.vcell.solver.Simulation
  */
 private static boolean checkSimulationParameters(Simulation simulation, Component parent,boolean bCheckLimits) {
-	SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, 0);
+	SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, MathOverrides.ScanIndex.ZERO);
 
 	String errorMessage = null;
 	long maxTimepoints = Simulation.MAX_LIMIT_NON_SPATIAL_TIMEPOINTS;

diff --git a/vcell-client/src/main/java/cbit/vcell/client/task/RunSims.java b/vcell-client/src/main/java/cbit/vcell/client/task/RunSims.java
@@ -13,6 +13,7 @@
 import java.util.Hashtable;
 import java.util.Vector;
 
+import cbit.vcell.solver.*;
 import org.vcell.util.*;
 import org.vcell.util.document.VCDocument;
 import org.vcell.util.gui.DialogUtils;
@@ -34,13 +35,7 @@
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.server.SimulationStatus;
-import cbit.vcell.solver.DataProcessingInstructions;
-import cbit.vcell.solver.MeshSpecification;
-import cbit.vcell.solver.Simulation;
-import cbit.vcell.solver.SimulationInfo;
-import cbit.vcell.solver.SimulationJob;
-import cbit.vcell.solver.SimulationSymbolTable;
-import cbit.vcell.solver.SolverDescription;
+
 /**
  * Insert the type's description here.
  * Creation date: (5/31/2004 6:03:16 PM)
@@ -71,8 +66,9 @@ public RunSims() {
 	}
 
 	private boolean isSmoldynTimeStepOK(Simulation sim) {
-		for (int jobIndex = 0; jobIndex < sim.getScanCount(); jobIndex ++) {
-			SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, jobIndex);
+		for (int scan = 0; scan < sim.getScanCount(); scan ++) {
+			MathOverrides.ScanIndex scanIndex = new MathOverrides.ScanIndex(scan);
+			SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, scanIndex);
 			double Dmax = 0;
 			MathDescription mathDesc = sim.getMathDescription();
 

diff --git a/vcell-client/src/main/java/cbit/vcell/desktop/VCellCopyPasteHelper.java b/vcell-client/src/main/java/cbit/vcell/desktop/VCellCopyPasteHelper.java
@@ -218,7 +218,7 @@ public static void chooseApplyPaste(Component requester,
 		Object newValue = newMathOverridesValuesV.elementAt(i);
 		if(newValue instanceof Expression){
 			bEnableDisplay[i] = !Compare.isEqualOrNull(
-					mathOverrides.getActualExpression(changingMathOverridesNames[i],0),
+					mathOverrides.getActualExpression(changingMathOverridesNames[i],MathOverrides.ScanIndex.ZERO),
 					((Expression)newValue));
 		}else if(newValue instanceof ConstantArraySpec){
 			bEnableDisplay[i] =	!Compare.isEqualOrNull(
@@ -282,7 +282,7 @@ public static void chooseApplyPaste_NOT_USED(Component requester,
 	boolean[] bEnableDisplay = new boolean[changingMathOverridesNames.length];
 	for(int i=0;i<changingMathOverridesNames.length;i+= 1){
 		//bEnableDisplay[i] = !changingParamters[i].getExpression().equals(newParameterExpression[i]);
-		bEnableDisplay[i] = !Compare.isEqualOrNull(mathOverrides.getActualExpression(changingMathOverridesNames[i],0),newMathOverridesValues[i].getExpression());
+		bEnableDisplay[i] = !Compare.isEqualOrNull(mathOverrides.getActualExpression(changingMathOverridesNames[i],MathOverrides.ScanIndex.ZERO),newMathOverridesValues[i].getExpression());
 		bAtLeatOneDifferent = bAtLeatOneDifferent || bEnableDisplay[i];
 	}
 

diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MathOverridesPanel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MathOverridesPanel.java
@@ -320,7 +320,7 @@ private synchronized void copyCells(String actionCommand) {
                 for (int row : rows) {
                     String rowName = (String) getJTableFixed().getValueAt(row, MathOverridesTableModel.COLUMN_PARAMETER);
                     primarySymbolTableEntriesV.add(getMathOverrides().getConstant(rowName));
-                    resolvedValuesV.add(getMathOverrides().getActualExpression(rowName, 0));
+                    resolvedValuesV.add(getMathOverrides().getActualExpression(rowName, MathOverrides.ScanIndex.ZERO));
 
                 }
                 VCellTransferable.ResolvedValuesSelection rvs =
@@ -761,8 +761,8 @@ private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEve
                                 String originalValueDescription = null;
                                 if (getMathOverrides().getConstantArraySpec(rowName) != null) {
                                     originalValueDescription = getMathOverrides().getConstantArraySpec(rowName).toString();
-                                } else if (getMathOverrides().getActualExpression(rowName, 0) != null) {
-                                    originalValueDescription = getMathOverrides().getActualExpression(rowName, 0).infix();
+                                } else if (getMathOverrides().getActualExpression(rowName, MathOverrides.ScanIndex.ZERO) != null) {
+                                    originalValueDescription = getMathOverrides().getActualExpression(rowName, MathOverrides.ScanIndex.ZERO).infix();
                                 } else {
                                     throw new Exception("MathOverridesPanel can't find value for '" + rowName + "'");
                                 }

diff --git a/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MathOverridesTableModel.java b/vcell-client/src/main/java/cbit/vcell/solver/ode/gui/MathOverridesTableModel.java
@@ -233,7 +233,7 @@ public Object getValueAt(int row, int column) {
 				if (getMathOverrides().isScan(fieldKeys[row])) {
 					return getMathOverrides().getConstantArraySpec(fieldKeys[row]);
 				} else {
-					Expression actualExpression = getMathOverrides().getActualExpression(fieldKeys[row], 0);
+					Expression actualExpression = getMathOverrides().getActualExpression(fieldKeys[row], MathOverrides.ScanIndex.ZERO);
 					if(actualExpression == null) {
 						return null;
 					}
@@ -387,7 +387,7 @@ private void updateKeys(MathOverrides mathOverrides) {
 			fieldKeys = mathOverrides.getOverridenConstantNames();
 		}
 		Arrays.sort(fieldKeys);
-		simSymbolTable = new SimulationSymbolTable(getMathOverrides().getSimulation(), 0);
+		simSymbolTable = new SimulationSymbolTable(getMathOverrides().getSimulation(), MathOverrides.ScanIndex.ZERO);
 	}
 }
 

diff --git a/vcell-client/src/main/java/org/vcell/util/gui/exporter/SbmlExtensionFilter.java b/vcell-client/src/main/java/org/vcell/util/gui/exporter/SbmlExtensionFilter.java
@@ -9,6 +9,7 @@
 import javax.swing.JOptionPane;
 
 import cbit.vcell.biomodel.BioModelTransforms;
+import cbit.vcell.solver.MathOverrides;
 import cbit.vcell.xml.XMLSource;
 import org.apache.commons.io.FilenameUtils;
 import org.vcell.sbml.gui.ApplnSelectionAndStructureSizeInputPanel;
@@ -255,11 +256,12 @@ public void writeBioModel(DocumentManager documentManager, BioModel bioModel, Fi
 			clonedBM.refreshDependencies();
 			String originalExportFilename = exportFile.getPath();
 			Files.deleteIfExists(Paths.get(originalExportFilename));
-			for (int jobIndex = 0; jobIndex < selectedSimWOSBE.getScanCount(); jobIndex++) {
-				BioModelTransforms.applyMathOverrides(selectedSimWOSBE, jobIndex, clonedBM);
+			for (int scan = 0; scan < selectedSimWOSBE.getScanCount(); scan++) {
+				MathOverrides.ScanIndex scanIndex = new MathOverrides.ScanIndex(scan);
+				BioModelTransforms.applyMathOverrides(selectedSimWOSBE, scanIndex, clonedBM);
 				String resultString = XmlHelper.exportSBML(clonedBM, sbmlLevel, sbmlVersion, sbmlPkgVersion, isSpatial, selectedSimContext, bRoundTripValidation);
 				// Need to export each parameter scan into a separate file
-				String newExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf(".xml")) + "_" + jobIndex + ".xml";
+				String newExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf(".xml")) + "_" + scanIndex.index + ".xml";
 				Files.deleteIfExists(Paths.get(newExportFileName));
 				XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
 				exportFile.renameTo(new File(newExportFileName));

diff --git a/vcell-core/src/main/java/cbit/vcell/biomodel/BioModelTransforms.java b/vcell-core/src/main/java/cbit/vcell/biomodel/BioModelTransforms.java
@@ -413,7 +413,7 @@ public static void reconcileLegacyAbsRelSizes(BioModel bioModel) {
         }
     }
 
-    public static void applyMathOverrides(Simulation simulation, int jobIndex, BioModel bioModel) throws MappingException, ExpressionException {
+    public static void applyMathOverrides(Simulation simulation, MathOverrides.ScanIndex scanIndex, BioModel bioModel) throws MappingException, ExpressionException {
         if (simulation == null) {
             throw new RuntimeException("simulation was null");
         }
@@ -443,7 +443,7 @@ public static void applyMathOverrides(Simulation simulation, int jobIndex, BioMo
                 throw new RuntimeException("biological symbol table entry for variable '"+overriddenConstantName+"'");
             }
             Expression defaultExpression = mathOverrides.getDefaultExpression(overriddenConstantName);
-            SimulationSymbolTable simulationSymbolTable = new SimulationSymbolTable(simulation, jobIndex);
+            SimulationSymbolTable simulationSymbolTable = new SimulationSymbolTable(simulation, scanIndex);
             Expression actualExpression = simulationSymbolTable.getLocalConstant((Constant)var).getExpression().flatten();
             if (!actualExpression.isNumeric()){
                 throw new RuntimeException("applying non-numeric overrides to a biomodel not yet supported: "+overriddenConstantName+": default = "+defaultExpression.infix()+", actual = "+actualExpression.infix());