Examples with FieldDataIdentifierSpec cbit.vcell.field.FieldDataIdentifierSpec used on opensource projects

Example 16 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class XmlHelper method simTaskToXML.

public static String simTaskToXML(SimulationTask simTask) throws XmlParseException {
    String simTaskString = null;
    if (simTask == null) {
        throw new XmlParseException("Invalid input for SimulationTask: " + simTask);
    }
    Xmlproducer xmlProducer = new Xmlproducer(true);
    SimulationJob simJob = simTask.getSimulationJob();
    Simulation sim = simJob.getSimulation();
    Element container = new Element(SimulationTask_tag);
    int taskId = simTask.getTaskID();
    container.setAttribute(TaskId_attr, "" + taskId);
    int jobIndex = simJob.getJobIndex();
    container.setAttribute(JobIndex_attr, "" + jobIndex);
    String computeResource = simTask.getComputeResource();
    if (computeResource != null) {
        Element computeResourceElement = new Element(ComputeResource_tag);
        Text text = new Text(computeResource);
        computeResourceElement.addContent(text);
        container.addContent(computeResourceElement);
    }
    FieldDataIdentifierSpec[] fdisSpecs = simJob.getFieldDataIdentifierSpecs();
    if (fdisSpecs != null) {
        for (FieldDataIdentifierSpec fdisSpec : fdisSpecs) {
            Element fdisElement = new Element(FieldFunctionIdentifierSpec_tag);
            fdisElement.setText(fdisSpec.toCSVString());
            container.addContent(fdisElement);
        }
    }
    MathDescription md = sim.getMathDescription();
    Element mathElement = xmlProducer.getXML(md);
    container.addContent(mathElement);
    Element simElement = xmlProducer.getXML(sim);
    container.addContent(simElement);
    Geometry geom = md.getGeometry();
    if (geom != null) {
        Element geomElement = xmlProducer.getXML(geom);
        container.addContent(geomElement);
    } else {
        System.err.println("No corresponding geometry for the simulation: " + sim.getName());
    }
    container = XmlUtil.setDefaultNamespace(container, Namespace.getNamespace(XMLTags.VCML_NS));
    simTaskString = XmlUtil.xmlToString(container);
    return simTaskString;
}

Example 17 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class FRAPStudy method runFVSolverStandalone_ref.

public static void runFVSolverStandalone_ref(File simulationDataDir, Simulation sim, ExternalDataIdentifier imageDataExtDataID, ExternalDataIdentifier roiExtDataID, ExternalDataIdentifier psfExtDataID, ClientTaskStatusSupport progressListener, boolean bCheckSteadyState) throws Exception {
    FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
    for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
        if (fieldFunctionArgs[i].getFieldName().equals(imageDataExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], imageDataExtDataID);
        } else if (fieldFunctionArgs[i].getFieldName().equals(roiExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], roiExtDataID);
        } else if (fieldFunctionArgs[i].getFieldName().equals(psfExtDataID.getName())) {
            fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], psfExtDataID);
        } else {
            throw new RuntimeException("failed to resolve field named " + fieldFunctionArgs[i].getFieldName());
        }
    }
    int jobIndex = 0;
    SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs), 0);
    SolverUtilities.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
    // if we need to check steady state, do the following two lines
    if (bCheckSteadyState) {
        simTask.getSimulation().getSolverTaskDescription().setStopAtSpatiallyUniformErrorTolerance(ErrorTolerance.getDefaultSpatiallyUniformErrorTolerance());
    // simJob.getSimulation().getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-6, 1e-2));
    }
    FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simulationDataDir, false);
    fvSolver.startSolver();
    SolverStatus status = fvSolver.getSolverStatus();
    while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
        if (progressListener != null) {
            progressListener.setProgress((int) (fvSolver.getProgress() * 100));
            if (progressListener.isInterrupted()) {
                fvSolver.stopSolver();
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
        try {
            Thread.sleep(1000);
        } catch (InterruptedException ex) {
            ex.printStackTrace(System.out);
        // catch interrupted exception and ignore it, otherwise it will popup a dialog in user interface saying"sleep interrupted"
        }
        status = fvSolver.getSolverStatus();
    }
    if (status.getStatus() != SolverStatus.SOLVER_FINISHED) {
        throw new Exception("Sover did not finish normally." + status);
    }
}

Example 18 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class FRAPStudy method getPSFFieldData.

public static FieldDataIdentifierSpec getPSFFieldData(LocalWorkspace localWorkspace) {
    // create ROI image
    short[] psfFieldData = null;
    psfFieldData = new short[9];
    psfFieldData[4] = (short) 1;
    // create field data
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psfFieldData;
    // get extental data id
    ExternalDataIdentifier newPsfExtDataID = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.PSF_DATA_NAME).getExternalDataIdentifier();
    CartesianMesh cartesianMesh;
    try {
        Origin origin = new Origin(0, 0, 0);
        Extent ext = new Extent(1, 1, 1);
        ISize isize = new ISize(3, 3, 1);
        cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
        FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
        fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
        fdos.cartesianMesh = cartesianMesh;
        fdos.shortSpecData = pixData;
        fdos.specEDI = newPsfExtDataID;
        fdos.varNames = new String[] { "psfVar" };
        fdos.owner = LocalWorkspace.getDefaultOwner();
        fdos.times = new double[] { 0.0 };
        fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
        fdos.origin = origin;
        fdos.extent = ext;
        fdos.isize = isize;
        localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        FieldFunctionArguments psfFieldFunc = new FieldFunctionArguments(PSF_DATA_NAME, "psfVar", new Expression(0.0), VariableType.VOLUME);
        FieldDataIdentifierSpec fdis = new FieldDataIdentifierSpec(psfFieldFunc, newPsfExtDataID);
        return fdis;
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return null;
    }
}

Example 19 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class ROIDataGenerator method getROIDataGeneratorDescription.

public String getROIDataGeneratorDescription(File userDirectory, SimulationJob simulationJob) throws Exception {
    // DataAccessException, FileNotFoundException, MathException, IOException, DivideByZeroException, ExpressionException
    Simulation simulation = simulationJob.getSimulation();
    StringBuffer sb = new StringBuffer();
    sb.append(ROI_GENERATOR_BEGIN + " " + name + "\n");
    sb.append("VolumePoints " + volumePoints.length + "\n");
    for (int i = 0; i < volumePoints.length; i++) {
        sb.append(volumePoints[i] + " ");
        if ((i + 1) % 20 == 0) {
            sb.append("\n");
        }
    }
    sb.append("\n");
    if (membranePoints != null && membranePoints.length > 0) {
        sb.append("MembranePoints " + membranePoints.length + "\n");
        for (int i = 0; i < membranePoints.length; i++) {
            sb.append(membranePoints[i] + " ");
            if ((i + 1) % 20 == 0) {
                sb.append("\n");
            }
        }
        sb.append("\n");
    }
    sb.append("SampleImage " + numImgRegions + " " + zSlice + " " + fieldDataKey + " " + fieldFuncArguments.infix() + "\n");
    sb.append("StoreEnabled " + bStoreEnabled + "\n");
    // sample image field data file
    FieldDataIdentifierSpec fdis = getSampleImageFieldData(simulation.getVersion().getOwner());
    if (fdis == null) {
        throw new DataAccessException("Can't find sample image in ROI data generator.");
    }
    String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
    DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
    CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
    SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
    VariableType varType = fdis.getFieldFuncArgs().getVariableType();
    VariableType dataVarType = simDataBlock.getVariableType();
    if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
        throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
    }
    double[] origData = simDataBlock.getData();
    String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simulationJob.getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
    File fdatFile = new File(userDirectory, filename);
    DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
    sb.append("SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile + "\n");
    sb.append(ROI_GENERATOR_END);
    return sb.toString();
}

Example 20 with FieldDataIdentifierSpec

use of cbit.vcell.field.FieldDataIdentifierSpec in project vcell by virtualcell.

the class DataSetControllerImpl method getVariableTypeForFieldFunction.

private VariableType getVariableTypeForFieldFunction(OutputContext outputContext, VCDataIdentifier vcdID, AnnotatedFunction function) throws DataAccessException {
    VariableType funcType = function.getFunctionType();
    if (funcType == null || funcType.equals(VariableType.UNKNOWN)) {
        FieldFunctionArguments[] ffas = FieldUtilities.getFieldFunctionArguments(function.getExpression());
        if (ffas == null || ffas.length == 0) {
            throw new DataAccessException("Unknown function type for function " + function.getName());
        }
        // use the type from the first field function
        FieldDataIdentifierSpec[] fdiss = getFieldDataIdentifierSpecs(ffas, vcdID.getOwner());
        SimDataBlock dataBlock = getSimDataBlock(outputContext, fdiss[0].getExternalDataIdentifier(), ffas[0].getVariableName(), 0.0);
        funcType = dataBlock.getVariableType();
    }
    return funcType;
}