support image-based field data from pyvcell

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.9"
+version = "0.0.10"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <[email protected]>", "Ezequiel Valencia <[email protected]>"]
 repository = "https://github.com/virtualcell/libvcell"

vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java

@@ -12,6 +12,7 @@
 import cbit.vcell.messaging.server.SimulationTask;
 import cbit.vcell.mongodb.VCMongoMessage;
 import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.simdata.SimulationData;
 import cbit.vcell.solver.*;
 import cbit.vcell.xml.XMLSource;
 import cbit.vcell.xml.XmlHelper;
@@ -30,6 +31,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
+import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -49,24 +51,57 @@ public static void vcmlToFiniteVolumeInput(String vcml_content, String simulatio
         if (sim == null) {
             throw new IllegalArgumentException("Simulation not found: " + simulation_name);
         }
-        FieldDataIdentifierSpec[] fdiSpecs = getFieldDataIdentifierSpecs(sim, parentDir);
+        FieldDataIdentifierSpec[] fdiSpecs = getFieldDataIdentifierSpecs(sim, outputDir, parentDir);
 
         TempSimulation tempSimulation = new TempSimulation(sim, false);
         tempSimulation.setSimulationOwner(sim.getSimulationOwner());
         SimulationJob tempSimulationJob = new SimulationJob(tempSimulation, 0, fdiSpecs);
+
+        renameExistingFieldDataFiles(tempSimulation.getKey(), tempSimulationJob.getJobIndex(), outputDir);
+
         SimulationTask simTask = new SimulationTask(tempSimulationJob, 0);
         LocalFVSolverStandalone solver = new LocalFVSolverStandalone(simTask, outputDir);
         solver.initialize();
     }
 
-    private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation sim, File parentDir) throws MathException, ExpressionException {
+    private static void renameExistingFieldDataFiles(KeyValue tempSimKey, int jobId, File outputDir) {
+        File[] files = outputDir.listFiles();
+        if (files != null) {
+            for (File file : files) {
+                if (file.getName().startsWith("SimID_SIMULATIONKEY_JOBINDEX_")) {
+                    String newName = file.getName().replace("SIMULATIONKEY",tempSimKey.toString()).replace("JOBINDEX",String.valueOf(jobId));
+                    File newFile = new File(outputDir, newName);
+                    if (!file.renameTo(newFile)){
+                        throw new RuntimeException("Could not rename " + file.getName() + " to " + newFile.getAbsolutePath());
+                    }
+                }
+            }
+        }
+    }
+
+    private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation sim, File outputDir, File parentDir) throws MathException, ExpressionException {
         FieldDataIdentifierSpec[] fdiSpecs = null;
         FieldFunctionArguments[] fieldFuncArgs =  FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
         if (fieldFuncArgs != null) {
             List<FieldDataIdentifierSpec> fdiSpecList = new ArrayList<>();
             for (FieldFunctionArguments fieldFuncArg : fieldFuncArgs) {
                 if (fieldFuncArg != null) {
                     String name = fieldFuncArg.getFieldName();
+                    //
+                    // First, check if the resampled field data files are already present (e.g. if pyvcell wrote the files directly from image data)
+                    //
+                    ExternalDataIdentifier fakeExtDataId = new ExternalDataIdentifier(sim.getKey(), User.tempUser, name);
+                    String fieldDataFileName = SimulationData.createCanonicalResampleFileName(fakeExtDataId, fieldFuncArg);
+                    fieldDataFileName = fieldDataFileName.replace("SimID_" + sim.getKey().toString() + "_0_", "SimID_SIMULATIONKEY_JOBINDEX_");
+                    File preexistingFieldDataFile = new File(outputDir, fieldDataFileName);
+                    if (preexistingFieldDataFile.exists()) {
+                        fdiSpecList.add(new FieldDataIdentifierSpec(fieldFuncArg, fakeExtDataId));
+                        continue;
+                    }
+
+                    //
+                    // If not, check if the field data directory exists as a subdirectory of the parentDir - holding simulation results.
+                    //
                     File fieldDataDir = new File(parentDir, name);
                     if (!fieldDataDir.exists()) {
                         throw new IllegalArgumentException("Field data directory does not exist: " + fieldDataDir.getAbsolutePath());

vcell-native/src/main/java/org/vcell/libvcell/solvers/LocalFVSolverStandalone.java

@@ -167,7 +167,6 @@ public void writeFieldFunctionData(OutputContext outputContext, FieldDataIdentif
         HashMap<FieldDataIdentifierSpec, Boolean> bFieldDataResample = new HashMap<>();
         int i=0;
         for (FieldDataIdentifierSpec fdiSpec: argFieldDataIDSpecs) {
-            File ext_dataDir = new File(this.parentDir, fdiSpec.getFieldFuncArgs().getFieldName());
             if (!uniqueFieldDataIDSpecAndFileH.containsKey(fdiSpec)){
                 File newResampledFieldDataFile = new File(dataDir, SimulationData.createCanonicalResampleFileName(getSimulationJob().getVCDataIdentifier(), fdiSpec.getFieldFuncArgs()));
                 uniqueFieldDataIDSpecAndFileH.put(fdiSpec,newResampledFieldDataFile);
@@ -179,6 +178,9 @@ public void writeFieldFunctionData(OutputContext outputContext, FieldDataIdentif
             Set<Map.Entry<FieldDataIdentifierSpec, File>> resampleSet = uniqueFieldDataIDSpecAndFileH.entrySet();
             for (Map.Entry<FieldDataIdentifierSpec, File> resampleEntry : resampleSet) {
                 if (resampleEntry.getValue().exists()) {
+                    // field data file has already been written
+                    // 1. in a previous loop iteration
+                    // 2. from pyvcell writing the field data file directly into this directory for an image-based field data
                     continue;
                 }
                 FieldDataIdentifierSpec fieldDataIdSpec = resampleEntry.getKey();

vcell-native/src/main/java/org/vcell/libvcell/solvers/LocalFiniteVolumeFileWriter.java

@@ -7,14 +7,18 @@
 import cbit.vcell.math.Variable;
 import cbit.vcell.math.VariableType;
 import cbit.vcell.messaging.server.SimulationTask;
+import cbit.vcell.parser.DivideByZeroException;
 import cbit.vcell.parser.Expression;
 import cbit.vcell.parser.ExpressionException;
+import cbit.vcell.simdata.DataSet;
 import cbit.vcell.simdata.SimDataBlock;
 import cbit.vcell.simdata.SimulationData;
 import cbit.vcell.simdata.VCData;
 import cbit.vcell.solver.Simulation;
 import cbit.vcell.solvers.FiniteVolumeFileWriter;
 import org.vcell.util.DataAccessException;
+import org.vcell.util.document.ExternalDataIdentifier;
+import org.vcell.util.document.User;
 
 import java.io.File;
 import java.io.IOException;
@@ -66,15 +70,7 @@ protected void writeFieldData() throws ExpressionException, DataAccessException
                 );
                 uniqueFieldDataIDSpecs.add(fieldDataIDSpec);
                 VariableType varType = fieldDataIDSpec.getFieldFuncArgs().getVariableType();
-                final VariableType dataVarType;
-                try {
-                    File ext_data_dir = new File(workingDirectory.getParentFile(), ffa.getFieldName());
-                    VCData vcData = new SimulationData(fieldDataIDSpec.getExternalDataIdentifier(), ext_data_dir, ext_data_dir, null);
-                    SimDataBlock simDataBlock = vcData.getSimDataBlock(null, ffa.getVariableName(), ffa.getTime().evaluateConstant());
-                    dataVarType = simDataBlock.getVariableType();
-                } catch (IOException e) {
-                    throw new DataAccessException("Error reading field data file: " + e.getMessage());
-                }
+                final VariableType dataVarType = getVariableTypeFromFieldDataFiles(fieldDataIDSpec, ffa);
                 if (varType.equals(VariableType.UNKNOWN)) {
                     varType = dataVarType;
                 } else if (!varType.equals(dataVarType)) {
@@ -104,4 +100,35 @@ protected void writeFieldData() throws ExpressionException, DataAccessException
         printWriter.println();
     }
 
+    private VariableType getVariableTypeFromFieldDataFiles(FieldDataIdentifierSpec fieldDataIDSpec, FieldFunctionArguments ffa) throws DataAccessException {
+
+        try {
+            final VariableType dataVarType;
+            //
+            // First, look to see if the processed field data file already exists, if so, use it to determine the variable type
+            //
+            DataSet dataSet = new DataSet();
+            ExternalDataIdentifier existingFieldDataID = new ExternalDataIdentifier(this.simTask.getSimKey(), User.tempUser, ffa.getFieldName());
+            File existingFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName(existingFieldDataID, ffa));
+            if (existingFieldDataFile.exists()) {
+                // field data file may already exist
+                // 1. from pyvcell writing the field data file directly into this directory for an image-based field data
+                dataSet.read(existingFieldDataFile, null);
+                int varTypeInteger = dataSet.getVariableTypeInteger(fieldDataIDSpec.getFieldFuncArgs().getVariableName());
+                dataVarType = VariableType.getVariableTypeFromInteger(varTypeInteger);
+            }else {
+                //
+                // Else, read the unprocessed simulation results referenced in the FieldDataIdentifierSpec and extract the VariableType
+                //
+                File ext_data_dir = new File(workingDirectory.getParentFile(), ffa.getFieldName());
+                VCData vcData = new SimulationData(fieldDataIDSpec.getExternalDataIdentifier(), ext_data_dir, ext_data_dir, null);
+                SimDataBlock simDataBlock = vcData.getSimDataBlock(null, ffa.getVariableName(), ffa.getTime().evaluateConstant());
+                dataVarType = simDataBlock.getVariableType();
+            }
+            return dataVarType;
+        } catch (IOException | ExpressionException | DataAccessException e) {
+            throw new DataAccessException("Error reading field data file: " + e.getMessage());
+        }
+    }
+
 }

vcell-native/src/test/java/org/vcell/libvcell/ModelEntrypointsTest.java

@@ -0,0 +1,47 @@
+package org.vcell.libvcell;
+
+import cbit.util.xml.VCLoggerException;
+import cbit.vcell.mapping.MappingException;
+import cbit.vcell.xml.XmlParseException;
+import org.junit.jupiter.api.Test;
+import org.vcell.sbml.SbmlException;
+
+import javax.xml.stream.XMLStreamException;
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+
+import static org.vcell.libvcell.ModelUtils.*;
+import static org.vcell.libvcell.TestUtils.getFileContentsAsString;
+
+public class ModelEntrypointsTest {
+
+    @Test
+    public void test_sbml_to_vcml() throws MappingException, IOException, XmlParseException, VCLoggerException {
+        String sbmlContent = getFileContentsAsString("/TinySpatialProject_Application0.xml");
+        File parent_dir = Files.createTempDirectory("sbmlToVcml").toFile();
+        File vcml_temp_file = new File(parent_dir, "temp.vcml");
+        sbml_to_vcml(sbmlContent, vcml_temp_file.toPath());
+        assert(vcml_temp_file.exists());
+    }
+
+    @Test
+    public void test_vcml_to_sbml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
+        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToSbml").toFile();
+        File sbml_temp_file = new File(parent_dir, "temp.sbml");
+        String applicationName = "unnamed_spatialGeom";
+        vcml_to_sbml(vcmlContent, applicationName, sbml_temp_file.toPath());
+        assert(sbml_temp_file.exists());
+    }
+
+    @Test
+    public void test_vcml_to_vcml() throws MappingException, IOException, XmlParseException, XMLStreamException, SbmlException {
+        String vcmlContent = getFileContentsAsString("/TinySpatialProject_Application0.vcml");
+        File parent_dir = Files.createTempDirectory("vcmlToVcml").toFile();
+        File vcml_temp_file = new File(parent_dir, "temp.vcml");
+        vcml_to_vcml(vcmlContent, vcml_temp_file.toPath());
+        assert(vcml_temp_file.exists());
+    }
+
+}