Examples with ChomboMembraneVarData org.vcell.vis.chombo.ChomboMembraneVarData used on opensource projects

Example 1 with ChomboMembraneVarData

use of org.vcell.vis.chombo.ChomboMembraneVarData in project vcell by virtualcell.

the class ChomboFileReader method readMembraneVarData.

// 
// Membrane data are stored as a UCHC (or vcell) extension to the normal Chombo Data.
// ChomboMembraneVarData was formally called VCellSolution by Fei.
// 
private static void readMembraneVarData(ChomboMeshData chomboMeshData, Group rootGroup) {
    // I added solution and extrapolated_volumes group to hold all the solutions from vcell
    String[] groups = new String[] { "solution" /*, "extrapolated_volumes"*/
    };
    for (String group : groups) {
        try {
            Group vcellGroup = Hdf5Reader.getChildGroup(rootGroup, group);
            if (vcellGroup != null) {
                List<HObject> children = vcellGroup.getMemberList();
                for (HObject c : children) {
                    if (c instanceof Dataset) {
                        Dataset dataset = (Dataset) c;
                        String name = dataset.getName();
                        List<Attribute> solAttrList = dataset.getMetadata();
                        String domain = null;
                        for (Attribute attr : solAttrList) {
                            String attrName = attr.getName();
                            if (attrName.equals("domain")) {
                                Object obj = attr.getValue();
                                domain = ((String[]) obj)[0];
                                break;
                            }
                        }
                        ChomboMembraneVarData vcellSolution = new ChomboMembraneVarData(name, domain, (double[]) dataset.read());
                        chomboMeshData.addMembraneVarData(vcellSolution);
                    }
                }
            }
        } catch (Exception ex) {
        // it is ok if there is no vcell group
        }
    }
}

Example 2 with ChomboMembraneVarData

use of org.vcell.vis.chombo.ChomboMembraneVarData in project vcell by virtualcell.

the class ChomboVtkFileWriter method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(ChomboFiles chomboFiles, OutputContext outputContext, VCData vcData) throws DataAccessException, IOException {
    // 
    // read the time=0 chombo dataset into memory to get the var names (probably a more efficient way of doing this).
    // 
    ChomboDataset chomboDataset;
    try {
        int timeIndex = 0;
        chomboDataset = ChomboFileReader.readDataset(chomboFiles, chomboFiles.getTimeIndices().get(timeIndex));
    } catch (Exception e) {
        throw new DataAccessException("failed to read chombo dataset: " + e.getMessage(), e);
    }
    DataIdentifier[] dataIdentifiers = vcData.getVarAndFunctionDataIdentifiers(outputContext);
    for (DataIdentifier di : dataIdentifiers) {
        System.out.println(((di.getDomain() != null) ? di.getDomain().getName() : "none") + "::" + di.getName() + "-" + di.getVariableType());
    }
    // 
    // for each ChomboDomain get list of built-in (mesh) variables, component (regular) volume variables, and Membrane Variables (still tied to the volume).
    // 
    ArrayList<VtuVarInfo> varInfos = new ArrayList<VtuVarInfo>();
    for (ChomboCombinedVolumeMembraneDomain chomboCombinedVolumeMembraneDomain : chomboDataset.getCombinedVolumeMembraneDomains()) {
        ChomboMeshData chomboMeshData = chomboCombinedVolumeMembraneDomain.getChomboMeshData();
        // 
        // process Volume variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String volumeDomainName = chomboCombinedVolumeMembraneDomain.getVolumeDomainName();
            VariableDomain volVariableDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
            for (String builtinVarName : chomboMeshData.getVolumeBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String componentVarName : chomboMeshData.getVisibleVolumeDataNames()) {
                String varName = componentVarName;
                String displayName = "(" + volumeDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_VOLUME && (dataID.getDomain() == null || dataID.getDomain().getName().equals(volumeDomainName))) {
                    String displayName = "(" + volumeDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, volumeDomainName, volVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
        // 
        // process membrane variables for this combined domain (chombo stores membrane data with volume)
        // 
        {
            String memDomainName = chomboCombinedVolumeMembraneDomain.getMembraneDomainName();
            VariableDomain memVariableDomain = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
            for (ChomboMembraneVarData membraneVarData : chomboMeshData.getMembraneVarData()) {
                String varName = membraneVarData.getName();
                String displayName = "(" + membraneVarData.getDomainName() + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = false;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (String builtinVarName : chomboMeshData.getMembraneBuiltinNames()) {
                String varName = builtinVarName;
                String displayName = "(" + memDomainName + ")  " + varName;
                String expressionString = null;
                boolean bMeshVariable = true;
                varInfos.add(new VtuVarInfo(varName, displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVariable));
            }
            for (DataIdentifier dataID : dataIdentifiers) {
                if (dataID.isVisible() && dataID.getVariableType().getVariableDomain() == VariableDomain.VARIABLEDOMAIN_MEMBRANE && (dataID.getDomain() == null || dataID.getDomain().getName().equals(memDomainName))) {
                    String displayName = "(" + memDomainName + ")  " + dataID.getDisplayName();
                    String expressionString = null;
                    AnnotatedFunction f = vcData.getFunction(outputContext, dataID.getName());
                    if (f != null) {
                        expressionString = f.getExpression().infix();
                    }
                    boolean bMeshVar = false;
                    varInfos.add(new VtuVarInfo(dataID.getName(), displayName, memDomainName, memVariableDomain, expressionString, DataType.CellData, bMeshVar));
                }
            }
        }
    }
    return varInfos.toArray(new VtuVarInfo[0]);
}