accommodate existing field data files written by pyvcell

Author: jcschaff

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

@@ -7,8 +7,10 @@
 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;
@@ -66,15 +68,7 @@ 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 +98,34 @@ 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();
+            File existingFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName(fieldDataIDSpec.getExternalDataIdentifier(), 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());
+        }
+    }
+
 }