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

Example 16 with DataSetControllerImpl

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

the class SimulationServiceImpl method getData.

public List<Double> getData(SimulationInfo simInfo, VariableInfo varInfo, int timeIndex) throws ThriftDataAccessException, TException {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    if (simServiceContext == null) {
        throw new RuntimeException("simulation results not found");
    }
    DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
    try {
        double[] times = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        SimDataBlock simDataBlock = datasetController.getSimDataBlock(outputContext, simServiceContext.vcDataIdentifier, varInfo.getVariableVtuName(), times[timeIndex]);
        double[] dataArray = simDataBlock.getData();
        ArrayList<Double> dataList = new ArrayList<Double>();
        for (double d : dataArray) {
            dataList.add(d);
        }
        return dataList;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve data for variable " + varInfo.getVariableVtuName() + ": " + e.getMessage());
    }
}

Example 17 with DataSetControllerImpl

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

the class SimulationServiceImpl method mesh.

private CartesianMesh mesh(SimulationInfo simInfo) {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    try {
        DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
        CartesianMesh mesh = datasetController.getMesh(simServiceContext.vcDataIdentifier);
        return mesh;
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}

Example 18 with DataSetControllerImpl

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

the class SimulationServiceImpl method getVariableList.

public List<VariableInfo> getVariableList(SimulationInfo simInfo) throws ThriftDataAccessException, TException {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    if (simServiceContext == null) {
        throw new ThriftDataAccessException("simulation results not found");
    }
    try {
        DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final DataIdentifier[] dataIdentifiers;
        try {
            dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
        } catch (IOException | DataAccessException e) {
            e.printStackTrace();
            throw new RuntimeException("failed to retrieve variable information: " + e.getMessage(), e);
        }
        ArrayList<VariableInfo> varInfos = new ArrayList<VariableInfo>();
        for (DataIdentifier dataIdentifier : dataIdentifiers) {
            final DomainType domainType;
            if (dataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
                domainType = DomainType.VOLUME;
            } else if (dataIdentifier.getVariableType().equals(VariableType.MEMBRANE)) {
                domainType = DomainType.MEMBRANE;
            } else {
                continue;
            }
            String domainName = "";
            if (dataIdentifier.getDomain() != null) {
                domainName = dataIdentifier.getDomain().getName();
            }
            VariableInfo varInfo = new VariableInfo(dataIdentifier.getName(), dataIdentifier.getDisplayName(), domainName, domainType);
            varInfos.add(varInfo);
        }
        return varInfos;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve variable list: " + e.getMessage());
    }
}

Example 19 with DataSetControllerImpl

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

the class SimulationServiceImpl method getDataSetController.

private static DataSetControllerImpl getDataSetController(SimulationServiceContext simServiceContext) {
    try {
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        Cachetable cacheTable = new Cachetable(10000);
        DataSetControllerImpl datasetController = new DataSetControllerImpl(cacheTable, simServiceContext.localSimDataDir.getParentFile(), null);
        simServiceContext.times = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
        simServiceContext.dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
        return datasetController;
    } catch (IOException | DataAccessException e1) {
        e1.printStackTrace();
        throw new RuntimeException("failed to read dataset: " + e1.getMessage());
    }
}

Example 20 with DataSetControllerImpl

use of cbit.vcell.simdata.DataSetControllerImpl 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();
}