Examples with OutputFunctionContext cbit.vcell.solver.OutputFunctionContext used on opensource projects

Example 6 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class SimulationContextDbDriver method getSimulationContextSQL.

/**
 * getModel method comment.
 */
private SimulationContext getSimulationContextSQL(QueryHashtable dbc, Connection con, User user, KeyValue simContextKey) throws /*, ReactStepDbDriver reactStepDB*/
SQLException, DataAccessException, IllegalMappingException, PropertyVetoException {
    SimulationContext simContext = null;
    String sql;
    Field[] f = { new cbit.sql.StarField(simContextTable), userTable.userid };
    Table[] t = { simContextTable, userTable };
    String condition = simContextTable.id.getQualifiedColName() + " = " + simContextKey + " AND " + simContextTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            simContext = simContextTable.getSimContext(dbc, con, user, rset, geomDB, modelDB, mathDescDB);
        } else {
            throw new ObjectNotFoundException("SimulationContext id=" + simContextKey + " not found for user '" + user + "'");
        }
    } finally {
        stmt.close();
    }
    DataSymbolTable.table.populateDataSymbols(con, simContextKey, simContext.getDataContext(), user, simContext.getModel().getUnitSystem());
    ArrayList<AnnotatedFunction> outputFunctionList = ApplicationMathTable.table.getOutputFunctionsSimcontext(con, simContextKey, dbSyntax);
    if (outputFunctionList != null) {
        OutputFunctionContext outputFnContext = simContext.getOutputFunctionContext();
        outputFnContext.setOutputFunctions(outputFunctionList);
    }
    SimContextTable.table.readAppComponents(con, simContext, dbSyntax);
    assignStimuliSQL(con, simContextKey, simContext);
    assignStructureMappingsSQL(dbc, con, simContextKey, simContext);
    assignSpeciesContextSpecsSQL(con, simContextKey, simContext);
    assignReactionSpecsSQL(con, simContextKey, simContext);
    for (GeometryClass gc : simContext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(simContext, gc);
        } catch (Exception e) {
            lg.error("failed to updateUnitStructureSizes", e);
        }
    }
    simContext.getGeometryContext().enforceHierarchicalBoundaryConditions(simContext.getModel().getStructureTopology());
    simContext.getModel().refreshDependencies();
    assignAnalysisTasksSQL(con, simContextKey, simContext);
    // really needed to calculate MembraneMapping parameters that are not stored (inside/outside flux correction factors).
    simContext.refreshDependencies();
    return simContext;
}

Example 7 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class CLIUtils method exportPDE2HDF5.

public static void exportPDE2HDF5(cbit.vcell.solver.Simulation sim, File userDir, File hdf5OutputFile) throws DataAccessException, IOException {
    SimulationContext sc = (SimulationContext) sim.getSimulationOwner();
    BioModel bm = sc.getBioModel();
    // VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getKey(), sim.getSimulationInfo().getVersion().getOwner());
    User user = new User(userDir.getName(), null);
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getKey(), user);
    if (sim.getScanCount() > 1) {
        throw new IllegalArgumentException("Parameter scans to be implemented");
    }
    VCSimulationDataIdentifier vcId = new VCSimulationDataIdentifier(vcSimID, 0);
    Species[] species = bm.getModel().getSpecies();
    String[] variableNames = new String[species.length];
    for (int i = 0; i < species.length; i++) {
        variableNames[i] = species[i].getCommonName();
    }
    VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
    DataSetControllerImpl dsControllerImpl = new DataSetControllerImpl(null, userDir.getParentFile(), null);
    double[] dataSetTimes = dsControllerImpl.getDataSetTimes(vcId);
    TimeSpecs timeSpecs = new TimeSpecs(0, dataSetTimes.length - 1, dataSetTimes, ExportConstants.TIME_RANGE);
    timeSpecs = new TimeSpecs(0, 0, dataSetTimes, ExportConstants.TIME_RANGE);
    int geoMode = ExportConstants.GEOMETRY_FULL;
    SpatialSelection[] selections = new SpatialSelection[0];
    selections = null;
    int axis = 2;
    int sliceNumber = 0;
    GeometrySpecs geometrySpecs = new GeometrySpecs(selections, axis, sliceNumber, geoMode);
    ExportConstants.DataType dataType = ExportConstants.DataType.PDE_VARIABLE_DATA;
    boolean switchRowsColumns = false;
    // String simulationName,VCSimulationIdentifier vcSimulationIdentifier,ExportParamScanInfo exportParamScanInfo
    ExportSpecs.SimNameSimDataID snsdi = new ExportSpecs.SimNameSimDataID(sim.getName(), vcSimID, null);
    ExportSpecs.SimNameSimDataID[] simNameSimDataIDs = { snsdi };
    int[] exportMultipleParamScans = null;
    boolean isHDF5 = true;
    FormatSpecificSpecs formatSpecificSpecs = new ASCIISpecs(ExportFormat.CSV, dataType, switchRowsColumns, simNameSimDataIDs, exportMultipleParamScans, csvRoiLayout.var_time_val, isHDF5);
    OutputFunctionContext ofc = sc.getOutputFunctionContext();
    ArrayList<AnnotatedFunction> outputFunctionsList = ofc.getOutputFunctionsList();
    AnnotatedFunction[] af = outputFunctionsList.toArray(new AnnotatedFunction[0]);
    OutputContext outputContext = new OutputContext(af);
    ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
    ASCIIExporter ae = new ASCIIExporter(exportServiceImpl);
    String contextName = bm.getName() + ":" + sc.getName();
    ExportSpecs exportSpecs = new ExportSpecs(vcId, ExportFormat.HDF5, variableSpecs, timeSpecs, geometrySpecs, formatSpecificSpecs, sim.getName(), contextName);
    DataServerImpl dataServerImpl = new DataServerImpl(dsControllerImpl, exportServiceImpl);
    FileDataContainerManager fileDataContainerManager = new FileDataContainerManager();
    JobRequest jobRequest = JobRequest.createExportJobRequest(vcId.getOwner());
    Collection<ExportOutput> eo = ae.makeASCIIData(outputContext, jobRequest, vcId.getOwner(), dataServerImpl, exportSpecs, fileDataContainerManager);
    Iterator<ExportOutput> iterator = eo.iterator();
    ExportOutput aaa = iterator.next();
    if (((ASCIISpecs) exportSpecs.getFormatSpecificSpecs()).isHDF5()) {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        // Get location of temp HDF5 file
        aaa.writeDataToOutputStream(baos, fileDataContainerManager);
        File tempHDF5File = new File(baos.toString());
        Files.copy(tempHDF5File, hdf5OutputFile);
        tempHDF5File.delete();
    }
}

Example 8 with OutputFunctionContext

use of cbit.vcell.solver.OutputFunctionContext in project vcell by virtualcell.

the class OutputFunctionsListTableModel method setOutputFunctionContext.

public void setOutputFunctionContext(OutputFunctionContext newValue) {
    OutputFunctionContext oldValue = this.outputFunctionContext;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        oldValue.getSimulationOwner().removePropertyChangeListener(this);
    }
    this.outputFunctionContext = newValue;
    if (this.outputFunctionContext != null) {
        this.outputFunctionContext.addPropertyChangeListener(this);
        newValue.getSimulationOwner().addPropertyChangeListener(this);
    }
    if (newValue == null) {
        setData(null);
    } else {
        fireTableStructureChanged();
        setData(newValue.getOutputFunctionsList());
    }
}