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

Example 36 with VCSimulationDataIdentifier

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

the class HybridSolverTester method runHybridTest.

public void runHybridTest(String site) {
    try {
        double[] timePoints = null;
        File mathModelFile = new File(mathModelVCMLFileName);
        XMLSource vcmlSource = new XMLSource(mathModelFile);
        MathModel mathModel = XmlHelper.XMLToMathModel(vcmlSource);
        File simDataDir = mathModelFile.getParentFile();
        Simulation sim = mathModel.getSimulations()[0];
        // run multiple trials and each run will have a simID = origSimID + i
        for (int i = 0; i < numRuns; i++) {
            System.out.println("--------------Trial No: " + (startTrialNo + i) + "----------------");
            // replace random seed
            sim.getSolverTaskDescription().getSmoldynSimulationOptions().setRandomSeed(new Integer(startTrialNo + i));
            // create sim job
            int jobIndex = startTrialNo + i;
            SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
            /*
				 * When you want to run the multiple trials on local uncomment the line below.
				 */
            // ResourceUtil.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
            /*
				 * When you want to run the multiple trials on server (without VCell user interface), use the next line of code 
				 * Corresponding changes should be made in the shell script runhybridtest for the location of executable on server
				 */
            FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simDataDir, false);
            fvSolver.startSolver();
            SolverStatus status = fvSolver.getSolverStatus();
            while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
                System.out.println("progress: " + (int) (fvSolver.getProgress() * 100) + "%");
                // ask status every 2 seconds
                Thread.sleep(2000);
                status = fvSolver.getSolverStatus();
            }
            if (status.getStatus() == SolverStatus.SOLVER_FINISHED) {
                // get data
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getVersion().getVersionKey(), sim.getVersion().getOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
                File hdf5File = new File(simDataDir, vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
                DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimDataID, false, null), hdf5File);
                if (i == 0) {
                    // do only one time
                    timePoints = dataProcessingOutputInfo.getVariableTimePoints();
                    for (int j = 0; j < varNames.length; j++) {
                        // row: numTimePoints, col:first col time + numRuns
                        double[][] data = new double[numRuns + 1][timePoints.length];
                        data[0] = timePoints;
                        results.add(data);
                    }
                }
                // write into results after each run
                for (int j = 0; j < varNames.length; j++) {
                    results.get(j)[i + 1] = dataProcessingOutputInfo.getVariableStatValues().get(varNames[j]);
                }
                // delete the file generated for this run
                deleteSimFiles(simDataDir, vcSimDataID);
            } else {
                throw new Exception("Sover did not finish normally." + status);
            }
        }
        // write to output file, tab delimited
        if (results != null && results.size() > 0) {
            for (int j = 0; j < varNames.length; j++) {
                File file = new File(simDataDir, "SimID_" + sim.getVersion().getVersionKey().toString() + "_" + varNames[j] + "_" + startTrialNo + ".txt");
                PrintWriter pw = new PrintWriter(file);
                double[][] data = results.get(j);
                if (data != null) {
                    for (int k = 0; k < data.length; k++) {
                        if (!bPrintTime && k == 0) {
                            continue;
                        }
                        String rowStr = (k == 0) ? "Time\t" : ("trialNo_" + (startTrialNo + k - 1) + "\t");
                        double[] rowData = data[k];
                        for (int q = 0; q < rowData.length; q++) {
                            rowStr += rowData[q] + "\t";
                        }
                        pw.println(rowStr);
                    }
                }
                pw.close();
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 37 with VCSimulationDataIdentifier

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

the class RestDatabaseService method getDataSetTimeSeries.

public DataSetTimeSeries getDataSetTimeSeries(SimDataValuesServerResource resource, User vcellUser) throws DataAccessException, ObjectNotFoundException, SQLException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String jobIndexString = resource.getAttribute(VCellApiApplication.JOBINDEX);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    int jobIndex = Integer.parseInt(jobIndexString);
    // TODO: pass in variables names from the query parameters.
    String[] variableNames = null;
    User owner = simRep.getOwner();
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetTimeSeries dataSetTimeSeries = rpcDataServerProxy.getDataSetTimeSeries(vcdID, variableNames);
        return dataSetTimeSeries;
    } finally {
        rpcSession.close();
    }
}

Example 38 with VCSimulationDataIdentifier

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

the class BioModelWindowManager method simStatusChanged.

/**
 * Insert the method's description here.
 * Creation date: (6/9/2004 3:58:21 PM)
 * @param newJobStatus cbit.vcell.messaging.db.SimulationJobStatus
 * @param progress java.lang.Double
 * @param timePoint java.lang.Double
 */
public void simStatusChanged(SimStatusEvent simStatusEvent) {
    // ** events are only generated from server side job statuses **
    KeyValue simKey = simStatusEvent.getVCSimulationIdentifier().getSimulationKey();
    // do we have the sim?
    Simulation[] sims = getBioModel().getSimulations();
    if (sims == null) {
        // we don't have it
        return;
    }
    Simulation simulation = null;
    for (int i = 0; i < sims.length; i++) {
        if (sims[i].getSimulationInfo() != null && simKey.equals(sims[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier().getSimulationKey())) {
            simulation = sims[i];
            break;
        }
    }
    if (simulation == null) {
        // we don't have it
        return;
    }
    // we have it; get current server side status
    SimulationStatus simStatus = getRequestManager().getServerSimulationStatus(simulation.getSimulationInfo());
    // if failed, notify
    if (simStatusEvent.isNewFailureEvent()) {
        String qualifier = "";
        if (simulation.getScanCount() > 1) {
            qualifier += "One job from ";
        }
        PopupGenerator.showErrorDialog(this, qualifier + "Simulation '" + simulation.getName() + "' failed\n" + simStatus.getDetails());
    }
    // was the gui on it ever opened?
    SimulationContext simContext = null;
    simulation = null;
    Enumeration<SimulationContext> en = getApplicationsHash().keys();
    while (en.hasMoreElements()) {
        SimulationContext sc = (SimulationContext) en.nextElement();
        sims = sc.getSimulations();
        if (sims != null) {
        }
        for (int i = 0; i < sims.length; i++) {
            if (sims[i].getSimulationInfo() != null && simKey.equals(sims[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier().getSimulationKey())) {
                simulation = sims[i];
                break;
            }
        }
        if (simulation != null) {
            simContext = sc;
            break;
        }
    }
    if (simulation == null || simContext == null) {
        return;
    }
    // the gui was opened, update status display
    ApplicationComponents appComponents = (ApplicationComponents) getApplicationsHash().get(simContext);
    ClientSimManager simManager = appComponents.getSimulationWorkspace().getClientSimManager();
    simManager.updateStatusFromServer(simulation);
    // is there new data?
    if (simStatusEvent.isNewDataEvent()) {
        fireNewData(new DataEvent(this, new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), simStatusEvent.getJobIndex())));
    }
}

Example 39 with VCSimulationDataIdentifier

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

the class NonGUIFRAPTest method runSolver.

/**
 * @param args
 */
public static void runSolver(String[] args) throws Exception {
    String startingIndexForRecovery = args[0];
    String freeDiffusionRateStr = args[1];
    String freeMobileFractionStr = args[2];
    String complexDiffusionRateStr = args[3];
    String complexMobileFractionStr = args[4];
    String bleachWhileMonitoringRateString = args[5];
    String immobileFractionStr = args[6];
    String bindingSiteConcentrationStr = args[7];
    String reacOnRateStr = args[8];
    String reacOffRateStr = args[9];
    String workingDirectoryPath = args[10];
    String inputFRAPDataFileName = args[11];
    String inputCellROIFileName = args[12];
    String inputBleachROIFileName = args[13];
    String inputBackgroundROIFileName = args[14];
    String outputXMLFileName = args[15];
    String commaSepTimeStamps = args[16];
    String commaSepExtentXYZ = args[17];
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDirectoryPath));
    ExternalDataFileContents extDataFileContents = readExternalDataContents(inputFRAPDataFileName, inputCellROIFileName, inputBleachROIFileName, inputBackgroundROIFileName);
    ROI cellROI = new ROI(extDataFileContents.cellROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = new ROI(extDataFileContents.bleachROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = new ROI(extDataFileContents.backgroundROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // Insert Time information
    double[] timeStamps = new double[extDataFileContents.imageData.getAllImages().length];
    StringTokenizer commaStringTokenizer = new StringTokenizer(commaSepTimeStamps, ",");
    int timeCount = 0;
    while (commaStringTokenizer.hasMoreTokens()) {
        timeStamps[timeCount] = Double.parseDouble(commaStringTokenizer.nextToken());
        timeCount++;
    }
    ImageDataset frapDataImageDataSet = new ImageDataset(extDataFileContents.imageData.getAllImages(), timeStamps, 1);
    // Insert Extent information
    commaStringTokenizer = new StringTokenizer(commaSepExtentXYZ, ",");
    Extent extent = new Extent(Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()));
    frapDataImageDataSet.setExtent(extent);
    bleachROI.getRoiImages()[0].setExtent(extent);
    cellROI.getRoiImages()[0].setExtent(extent);
    backgroundROI.getRoiImages()[0].setExtent(extent);
    FRAPData frapData = FrapDataUtils.importFRAPDataFromImageDataSet(frapDataImageDataSet);
    frapData.addReplaceRoi(bleachROI);
    frapData.addReplaceRoi(cellROI);
    frapData.addReplaceRoi(backgroundROI);
    FRAPStudy frapStudy = new FRAPStudy();
    frapStudy.setFrapData(frapData);
    // old model parameters, need to rewrite
    // FRAPStudy.FRAPModelParameters frapModelParameters = new FRAPStudy.FRAPModelParameters(
    // new FRAPStudy.InitialModelParameters(freeDiffusionRateStr, freeMobileFractionStr, bleachWhileMonitoringRateString, startingIndexForRecovery),
    // null,
    // null);
    // frapStudy.setFrapModelParameters(frapModelParameters);
    frapStudy.refreshDependentROIs();
    ExternalDataInfo imageDatasetExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME);
    ExternalDataInfo roiExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME);
    frapStudy.setFrapDataExternalDataInfo(imageDatasetExternalDataInfo);
    frapStudy.setRoiExternalDataInfo(roiExternalDataInfo);
    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    // Double bleachWhileMonitoringRate =
    // (!bleachWhileMonitoringRateString.equals("-")
    // ?Double.parseDouble(bleachWhileMonitoringRateString)
    // :null);
    double fd, ff, bwmr, cd, cf, imf, bs, on, off;
    try {
        fd = Double.parseDouble(freeDiffusionRateStr);
        ff = Double.parseDouble(freeMobileFractionStr);
        bwmr = Double.parseDouble(bleachWhileMonitoringRateString);
        cd = Double.parseDouble(complexDiffusionRateStr);
        cf = Double.parseDouble(complexMobileFractionStr);
        imf = Double.parseDouble(immobileFractionStr);
        bs = Double.parseDouble(bindingSiteConcentrationStr);
        on = Double.parseDouble(reacOnRateStr);
        off = Double.parseDouble(reacOffRateStr);
    } catch (NumberFormatException e) {
        throw new Exception("Input parameters are not all valid. Check if they are empty or in illegal forms.");
    }
    BioModel bioModel = FRAPStudy.createNewSimBioModel(frapStudy, createParameterArray(fd, ff, bwmr, cd, cf, imf, bs, on, off), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), new Integer(frapStudy.getStartingIndexForRecovery()));
    frapStudy.setBioModel(bioModel);
    // no progress listener, need to change
    MicroscopyXmlproducer.writeXMLFile(frapStudy, new File(outputXMLFileName), true, null, false);
    FRAPStudy.runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), imageDatasetExternalDataInfo.getExternalDataIdentifier(), roiExternalDataInfo.getExternalDataIdentifier(), null);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(bioModel.getSimulations()[0].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
    PDEDataManager simulationDataManager = new PDEDataManager(null, localWorkspace.getVCDataManager(), vcSimulationDataIdentifier);
    double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
    VCDataManager testVCDataManager = localWorkspace.getVCDataManager();
    double[] prebleachAverage = testVCDataManager.getSimDataBlock(null, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), "prebleach_avg", 0).getData();
    // TODO: need to create parameters here.
    Parameter[] parameters = null;
    SpatialAnalysisResults spatialAnalysisResults = FRAPStudy.spatialAnalysis(simulationDataManager, new Integer(frapStudy.getStartingIndexForRecovery()), frapDataTimeStamps[new Integer(frapStudy.getStartingIndexForRecovery())], parameters, frapData, prebleachAverage);
    dumpSummaryReport(spatialAnalysisResults, frapDataTimeStamps, new Integer(startingIndexForRecovery).intValue(), new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
    dumpSpatialResults(spatialAnalysisResults, frapDataTimeStamps, new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
}

Example 40 with VCSimulationDataIdentifier

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

the class SimulationData method getVCellSimFiles.

@Override
public VCellSimFiles getVCellSimFiles() throws FileNotFoundException, DataAccessException {
    File cartesianMeshFile = getMeshFile();
    File meshMetricsFile = getMembraneMeshMetricsFile();
    File subdomainFile = getSubdomainFile();
    File logFile = getLogFile();
    File postprocessingFile = getDataProcessingOutputSourceFileHDF5();
    if (!(vcDataId instanceof VCSimulationDataIdentifier)) {
        throw new RuntimeException("cannot process vtk, vcDataId not " + VCSimulationDataIdentifier.class.getSimpleName());
    }
    VCSimulationDataIdentifier vcSimDataID = (VCSimulationDataIdentifier) vcDataId;
    VCellSimFiles vcellSimFiles = new VCellSimFiles(vcSimDataID.getSimulationKey(), vcSimDataID.getJobIndex(), cartesianMeshFile, meshMetricsFile, subdomainFile, logFile, postprocessingFile);
    refreshLogFile();
    double[] times = getDataTimes();
    for (int i = 0; i < times.length; i++) {
        File pdeDataFile = getPDEDataFile(times[i]);
        File zipFile = getPDEDataZipFile(times[i]);
        vcellSimFiles.addDataFileEntry(zipFile, pdeDataFile, times[i]);
    }
    return vcellSimFiles;
}