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

Example 6 with SimDataBlock

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

the class RasterExporter method makeVTKImageData.

public ExportOutput[] makeVTKImageData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
        exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "VTKIMG", (double) (j - timeSpecs.getBeginTimeIndex()) / (double) (timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1));
        StringBuffer sb = new StringBuffer();
        sb.append("# vtk DataFile Version 2.0" + "\n");
        sb.append("Simulation " + vcdID.toString() + "\n");
        sb.append("ASCII" + "\n");
        sb.append("DATASET STRUCTURED_POINTS" + "\n");
        sb.append("DIMENSIONS " + mesh.getSizeX() + " " + mesh.getSizeY() + " " + mesh.getSizeZ() + "\n");
        sb.append("SPACING " + mesh.getExtent().getX() + " " + mesh.getExtent().getY() + " " + mesh.getExtent().getZ() + "\n");
        sb.append("ORIGIN " + mesh.getOrigin().getX() + " " + mesh.getOrigin().getY() + " " + mesh.getOrigin().getZ() + "\n");
        sb.append("POINT_DATA " + mesh.getNumVolumeElements() + "\n");
        // write volume region ids
        sb.append("SCALARS " + "regionID" + " double 1" + "\n");
        sb.append("LOOKUP_TABLE default" + "\n");
        int yzSize = mesh.getSizeY() * mesh.getSizeZ();
        int index = 0;
        for (int yz = 0; yz < yzSize; yz++) {
            for (int x = 0; x < mesh.getSizeX(); x++) {
                sb.append((x != 0 ? " " : "") + mesh.getVolumeRegionIndex(index));
                index++;
            }
            sb.append("\n");
        }
        sb.append("\n");
        for (int k = 0; k < variableSpecs.getVariableNames().length; k++) {
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[k], timeSpecs.getAllTimes()[j]);
            if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                sb.append("SCALARS " + variableSpecs.getVariableNames()[k] + " double 1" + "\n");
                sb.append("LOOKUP_TABLE default" + "\n");
                double[] volumeData = simDataBlock.getData();
                index = 0;
                for (int yz = 0; yz < yzSize; yz++) {
                    for (int x = 0; x < mesh.getSizeX(); x++) {
                        sb.append((x != 0 ? " " : "") + volumeData[index]);
                        index++;
                    }
                    sb.append("\n");
                }
                ExportOutput exportOut = new ExportOutput(true, ".vtk", simID.toString(), "_vol_" + j, fileDataContainerManager);
                fileDataContainerManager.append(exportOut.getFileDataContainerID(), sb.toString());
                exportOutV.add(exportOut);
            } else {
                throw new RuntimeException("VTK Image format only for volume data");
            }
        }
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}

Example 7 with SimDataBlock

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

the class MathTestingUtilities method comparePDEResultsWithExact.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResultsWithExact(SimulationSymbolTable simSymbolTable, PDEDataManager dataManager, String type, double absErrorThreshold, double relErrorThreshold) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    double[] timeArray = dataManager.getDataSetTimes();
    Variable[] vars = simSymbolTable.getVariables();
    CartesianMesh mesh = dataManager.getMesh();
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable
    int numVol = mesh.getSizeX() * mesh.getSizeY() * mesh.getSizeZ();
    CompartmentSubDomain[] volSubDomainLookup = new CompartmentSubDomain[numVol];
    for (int i = 0; i < numVol; i++) {
        int subVolumeIndex = mesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = mathDesc.getCompartmentSubDomain(subVolume.getName());
        volSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable
    int numMem = mesh.getMembraneElements().length;
    MembraneSubDomain[] memSubDomainLookup = new MembraneSubDomain[numMem];
    for (int i = 0; i < numMem; i++) {
        int insideVolIndex = mesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = mesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = mathDesc.getMembraneSubDomain(volSubDomainLookup[insideVolIndex], volSubDomainLookup[outsideVolIndex]);
        memSubDomainLookup[i] = memSubDomain;
    }
    double[] valueArray = new double[4];
    SimpleSymbolTable symbolTable = new SimpleSymbolTable(new String[] { "t", "x", "y", "z" });
    int tIndex = symbolTable.getEntry("t").getIndex();
    int xIndex = symbolTable.getEntry("x").getIndex();
    int yIndex = symbolTable.getEntry("y").getIndex();
    int zIndex = symbolTable.getEntry("z").getIndex();
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    long dataLength = 0;
    // for each var, do the following :
    for (int i = 0; i < vars.length; i++) {
        if (vars[i] instanceof VolVariable || vars[i] instanceof MemVariable || vars[i] instanceof FilamentVariable || vars[i] instanceof VolumeRegionVariable || vars[i] instanceof MembraneRegionVariable || vars[i] instanceof FilamentRegionVariable) {
            // for each time in timeArray,
            for (int j = 0; j < timeArray.length; j++) {
                if (type.equals(TestCaseNew.EXACT_STEADY)) {
                    if (j != (timeArray.length - 1)) {
                        continue;
                    }
                }
                // get data block from varName, data from datablock
                SimDataBlock simDataBlock = dataManager.getSimDataBlock(vars[i].getName(), timeArray[j]);
                double[] data = simDataBlock.getData();
                dataLength = data.length;
                SubDomain subDomain = null;
                Coordinate subDomainCoord = null;
                // for each point in data block ...
                for (int k = 0; k < dataLength; k++) {
                    // Get subdomain from mesh (from the lookupTable), get coordinates (x,y,z) from mesh, evaluate EXACT SOLN at that coord
                    if (vars[i] instanceof VolVariable) {
                        subDomain = volSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromVolumeIndex(k);
                    } else if (vars[i] instanceof MemVariable) {
                        subDomain = memSubDomainLookup[k];
                        subDomainCoord = mesh.getCoordinateFromMembraneIndex(k);
                    } else {
                        throw new RuntimeException("Var " + vars[i].getName() + " not supported yet!");
                    }
                    hashKey = vars[i].getName() + ":" + subDomain.getName();
                    DataErrorSummary tempVar = (DataErrorSummary) tempVarHash.get(hashKey);
                    if (tempVar == null) {
                        Expression exp = new Expression(subDomain.getEquation(vars[i]).getExactSolution());
                        exp.bindExpression(simSymbolTable);
                        exp = MathUtilities.substituteFunctions(exp, simSymbolTable);
                        exp = exp.flatten();
                        exp.bindExpression(symbolTable);
                        tempVar = new DataErrorSummary(exp);
                        tempVarHash.put(hashKey, tempVar);
                    }
                    // time
                    valueArray[tIndex] = timeArray[j];
                    // x
                    valueArray[xIndex] = subDomainCoord.getX();
                    // y
                    valueArray[yIndex] = subDomainCoord.getY();
                    // z
                    valueArray[zIndex] = subDomainCoord.getZ();
                    // EXACT soln at coord subDomainCoord
                    double value = tempVar.getExactExp().evaluateVector(valueArray);
                    tempVar.addDataValues(value, data[k], timeArray[j], k, absErrorThreshold, relErrorThreshold);
                }
            // end for (k)
            }
        // end for (j)
        }
    // end - if (var)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 8 with SimDataBlock

use of cbit.vcell.simdata.SimDataBlock 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 9 with SimDataBlock

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

the class RunSimulation2DOp method runRefSimulation.

public ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, String varName, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, varName, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 10 with SimDataBlock

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

the class RunRefSimulationOp method runRefSimulation.

private static ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, ROI cellROI, double timeStepVal, TimeBounds timeBounds, FloatImage initRefConc, double baseDiffusionRate, ClientTaskStatusSupport progressListener) throws Exception {
    String INITCONC_EXTDATA_NAME = "initConc";
    String INITCONC_EXTDATA_VARNAME = "conc";
    String VAR_NAME = "species";
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), baseDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), initialConcentrationExtData.getExternalDataIdentifier(), progressListener, true);
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, VAR_NAME, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}