Examples with DataSetControllerImpl cbit.vcell.simdata.DataSetControllerImpl used on opensource projects

Example 6 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class FVSolverStandalone method writeVCGAndResampleFieldData.

protected void writeVCGAndResampleFieldData() throws SolverException {
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_PROC_GEOM);
    try {
        // write subdomains file
        SubdomainInfo.write(new File(getSaveDirectory(), baseName + SimDataConstants.SUBDOMAINS_FILE_SUFFIX), simTask.getSimulation().getMathDescription());
        PrintWriter pw = new PrintWriter(new FileWriter(new File(getSaveDirectory(), baseName + SimDataConstants.VCG_FILE_EXTENSION)));
        GeometryFileWriter.write(pw, getResampledGeometry());
        pw.close();
        FieldDataIdentifierSpec[] argFieldDataIDSpecs = simTask.getSimulationJob().getFieldDataIdentifierSpecs();
        if (argFieldDataIDSpecs != null && argFieldDataIDSpecs.length > 0) {
            fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_RESAMPLE_FD);
            FieldFunctionArguments psfFieldFunc = null;
            Variable var = simTask.getSimulationJob().getSimulationSymbolTable().getVariable(Simulation.PSF_FUNCTION_NAME);
            if (var != null) {
                FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(var.getExpression());
                if (ffas == null || ffas.length == 0) {
                    throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
                } else {
                    Expression newexp;
                    try {
                        newexp = new Expression(ffas[0].infix());
                        if (!var.getExpression().compareEqual(newexp)) {
                            throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
                        }
                        psfFieldFunc = ffas[0];
                    } catch (ExpressionException e) {
                        e.printStackTrace();
                        throw new DataAccessException(e.getMessage());
                    }
                }
            }
            boolean[] bResample = new boolean[argFieldDataIDSpecs.length];
            Arrays.fill(bResample, true);
            for (int i = 0; i < argFieldDataIDSpecs.length; i++) {
                argFieldDataIDSpecs[i].getFieldFuncArgs().getTime().bindExpression(simTask.getSimulationJob().getSimulationSymbolTable());
                if (argFieldDataIDSpecs[i].getFieldFuncArgs().equals(psfFieldFunc)) {
                    bResample[i] = false;
                }
            }
            int numMembraneElements = getResampledGeometry().getGeometrySurfaceDescription().getSurfaceCollection().getTotalPolygonCount();
            CartesianMesh simpleMesh = CartesianMesh.createSimpleCartesianMesh(getResampledGeometry().getOrigin(), getResampledGeometry().getExtent(), simTask.getSimulation().getMeshSpecification().getSamplingSize(), getResampledGeometry().getGeometrySurfaceDescription().getRegionImage());
            String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
            DataSetControllerImpl dsci = new DataSetControllerImpl(null, getSaveDirectory().getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
            dsci.writeFieldFunctionData(null, argFieldDataIDSpecs, bResample, simpleMesh, simResampleInfoProvider, numMembraneElements, HESM_OVERWRITE_AND_CONTINUE);
        }
    } catch (Exception e) {
        throw new SolverException(e.getMessage());
    }
}

Example 7 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeFieldData.

/**
 * # Field Data
 * FIELD_DATA_BEGIN
 * #id, name, varname, time filename
 * 0 _VCell_FieldData_0 FRAP_binding_ALPHA rfB 0.1 \\users\\fgao\\SimID_22489731_0_FRAP_binding_ALPHA_rfB_0_1.fdat
 * FIELD_DATA_END
 * @throws FileNotFoundException
 * @throws ExpressionException
 * @throws DataAccessException
 */
private void writeFieldData() throws FileNotFoundException, ExpressionException, DataAccessException {
    FieldDataIdentifierSpec[] fieldDataIDSpecs = simTask.getSimulationJob().getFieldDataIdentifierSpecs();
    if (fieldDataIDSpecs == null || fieldDataIDSpecs.length == 0) {
        return;
    }
    String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
    DataSetControllerImpl dsci = new DataSetControllerImpl(null, workingDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
    printWriter.println("# Field Data");
    printWriter.println("FIELD_DATA_BEGIN");
    printWriter.println("#id, type, new name, name, varname, time, filename");
    FieldFunctionArguments psfFieldFunc = null;
    Variable var = simTask.getSimulationJob().getSimulationSymbolTable().getVariable(Simulation.PSF_FUNCTION_NAME);
    if (var != null) {
        FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(var.getExpression());
        if (ffas == null || ffas.length == 0) {
            throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
        } else {
            Expression newexp = new Expression(ffas[0].infix());
            if (!var.getExpression().compareEqual(newexp)) {
                throw new DataAccessException("Point Spread Function " + Simulation.PSF_FUNCTION_NAME + " can only be a single field function.");
            }
            psfFieldFunc = ffas[0];
        }
    }
    int index = 0;
    HashSet<FieldDataIdentifierSpec> uniqueFieldDataIDSpecs = new HashSet<FieldDataIdentifierSpec>();
    uniqueFieldDataNSet = new HashSet<FieldDataNumerics>();
    for (int i = 0; i < fieldDataIDSpecs.length; i++) {
        if (!uniqueFieldDataIDSpecs.contains(fieldDataIDSpecs[i])) {
            FieldFunctionArguments ffa = fieldDataIDSpecs[i].getFieldFuncArgs();
            File newResampledFieldDataFile = new File(workingDirectory, SimulationData.createCanonicalResampleFileName((VCSimulationDataIdentifier) simTask.getSimulationJob().getVCDataIdentifier(), fieldDataIDSpecs[i].getFieldFuncArgs()));
            uniqueFieldDataIDSpecs.add(fieldDataIDSpecs[i]);
            VariableType varType = fieldDataIDSpecs[i].getFieldFuncArgs().getVariableType();
            SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fieldDataIDSpecs[i].getExternalDataIdentifier(), fieldDataIDSpecs[i].getFieldFuncArgs().getVariableName(), fieldDataIDSpecs[i].getFieldFuncArgs().getTime().evaluateConstant());
            VariableType dataVarType = simDataBlock.getVariableType();
            if (varType.equals(VariableType.UNKNOWN)) {
                varType = dataVarType;
            } else if (!varType.equals(dataVarType)) {
                throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
            }
            if (psfFieldFunc != null && psfFieldFunc.equals(ffa)) {
                psfFieldIndex = index;
            }
            String fieldDataID = "_VCell_FieldData_" + index;
            printWriter.println(index + " " + varType.getTypeName() + " " + fieldDataID + " " + ffa.getFieldName() + " " + ffa.getVariableName() + " " + ffa.getTime().infix() + " " + newResampledFieldDataFile);
            uniqueFieldDataNSet.add(new FieldDataNumerics(SimulationData.createCanonicalFieldFunctionSyntax(ffa.getFieldName(), ffa.getVariableName(), ffa.getTime().evaluateConstant(), ffa.getVariableType().getTypeName()), fieldDataID));
            index++;
        }
    }
    if (psfFieldIndex >= 0) {
        printWriter.println("PSF_FIELD_DATA_INDEX " + psfFieldIndex);
    }
    printWriter.println("FIELD_DATA_END");
    printWriter.println();
}

Example 8 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getVtkManager.

@Override
public VtkManager getVtkManager(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException, DataAccessException {
    VCSimulationDataIdentifier vcSimulationDataIdentifier = getVCSimulationDataIdentifier(simulationDataSetRef);
    VtkManager vtkManager = null;
    if (!simulationDataSetRef.isLocal) {
        vtkManager = vcellClient.getRequestManager().getVtkManager(null, vcSimulationDataIdentifier);
    } else {
        // ---- preliminary : construct the localDatasetControllerProvider
        File primaryDir = ResourceUtil.getLocalRootDir();
        User usr = User.tempUser;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
        ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
        LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
        VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
        vtkManager = new VtkManager(null, vcDataManager, vcSimulationDataIdentifier);
    }
    return vtkManager;
}

Example 9 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class VCellServices method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    OperatingSystemInfo.getInstance();
    if (args.length != 3 && args.length != 0) {
        System.out.println("Missing arguments: " + VCellServices.class.getName() + " [sshHost sshUser sshKeyFile] ");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties(REQUIRED_SERVICE_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        new LibraryLoaderThread(false).start();
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.VTK, PythonPackage.THRIFT });
        CommandService commandService = null;
        if (args.length == 3) {
            String sshHost = args[0];
            String sshUser = args[1];
            File sshKeyFile = new File(args[2]);
            try {
                commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile);
                commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                lg.trace("SSH Connection test passed with installed keyfile, running ls as user " + sshUser + " on " + sshHost);
            } catch (Exception e) {
                e.printStackTrace();
                try {
                    commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile, new File("/root"));
                    commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                    lg.trace("SSH Connection test passed after installing keyfile, running ls as user " + sshUser + " on " + sshHost);
                } catch (Exception e2) {
                    e.printStackTrace();
                    throw new RuntimeException("failed to establish an ssh command connection to " + sshHost + " as user '" + sshUser + "' using key '" + sshKeyFile + "'", e);
                }
            }
            // can't make user directories, they are remote.
            AbstractSolver.bMakeUserDirs = false;
        } else {
            commandService = new CommandServiceLocal();
        }
        BatchSystemType batchSystemType = BatchSystemType.SLURM;
        HtcProxy htcProxy = null;
        switch(batchSystemType) {
            case SLURM:
                {
                    htcProxy = new SlurmProxy(commandService, PropertyLoader.getRequiredProperty(PropertyLoader.htcUser));
                    break;
                }
            default:
                {
                    throw new RuntimeException("unrecognized batch scheduling option :" + batchSystemType);
                }
        }
        int serviceOrdinal = 0;
        VCMongoMessage.serviceStartup(ServiceName.dispatch, new Integer(serviceOrdinal), args);
        // //
        // // JMX registration
        // //
        // MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        // mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        ServiceInstanceStatus serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.MASTER, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        SimulationDatabase simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, true);
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty))));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        // add dataJobListener
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        VCellServices vcellServices = new VCellServices(htcProxy, vcMessagingService, serviceInstanceStatus, databaseServerImpl, dataServerImpl, simulationDatabase);
        dataSetControllerImpl.addDataJobListener(vcellServices);
        exportServiceImpl.addExportListener(vcellServices);
        vcellServices.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}

Example 10 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl in project vcell by virtualcell.

the class SimDataServer method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    if (args.length < 1) {
        System.out.println("Missing arguments: " + SimDataServer.class.getName() + " serviceOrdinal [EXPORTONLY] [logdir]");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties();
        int serviceOrdinal = Integer.parseInt(args[0]);
        String logdir = null;
        boolean bExportOnly = false;
        if (args.length > 1) {
            if (args[1].equalsIgnoreCase("EXPORTONLY")) {
                bExportOnly = true;
                VCMongoMessage.serviceStartup(ServiceName.export, new Integer(serviceOrdinal), args);
                if (args.length > 2) {
                    logdir = args[2];
                }
            } else {
                VCMongoMessage.serviceStartup(ServiceName.simData, new Integer(serviceOrdinal), args);
                logdir = args[1];
            }
        }
        ServiceInstanceStatus serviceInstanceStatus = null;
        ServiceName serviceName = null;
        if (bExportOnly) {
            serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATAEXPORT, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
            serviceName = ServiceName.export;
        } else {
            serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATA, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
            serviceName = ServiceName.simData;
        }
        VCMongoMessage.serviceStartup(serviceName, new Integer(serviceOrdinal), args);
        // 
        // JMX registration
        // 
        MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        SimDataServer simDataServer = new SimDataServer(serviceInstanceStatus, dataServerImpl, vcMessagingService, false);
        // add dataJobListener
        dataSetControllerImpl.addDataJobListener(simDataServer);
        // add export listener
        exportServiceImpl.addExportListener(simDataServer);
        simDataServer.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}