Examples with VariableType cbit.vcell.math.VariableType used on opensource projects

Example 41 with VariableType

use of cbit.vcell.math.VariableType in project vcell by virtualcell.

the class OutputFunctionsPanel method getSubdomainComboBox.

private JComboBox getSubdomainComboBox() {
    if (subdomainComboBox == null) {
        try {
            subdomainComboBox = new JComboBox();
            subdomainComboBox.setRenderer(new DefaultListCellRenderer() {

                @Override
                public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                    super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                    if (value instanceof GeometryClass) {
                        setText(((GeometryClass) value).getName());
                    } else if (value instanceof VariableType) {
                        setText(((VariableType) value).getTypeName());
                    }
                    return this;
                }
            });
        } catch (java.lang.Throwable e) {
            e.printStackTrace(System.out);
        }
    }
    return subdomainComboBox;
}

Example 42 with VariableType

use of cbit.vcell.math.VariableType 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 43 with VariableType

use of cbit.vcell.math.VariableType in project vcell by virtualcell.

the class DataSet method readMBSDataMetadata.

private void readMBSDataMetadata() throws Exception {
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = null;
    try {
        solFile = fileFormat.createInstance(fileName, FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group solutionGroup = null;
        for (Object member : rootGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group) {
                MBSDataGroup group = MBSDataGroup.valueOf(memberName);
                if (group == MBSDataGroup.Solution) {
                    solutionGroup = (Group) member;
                    break;
                }
            }
        }
        if (solutionGroup == null) {
            throw new Exception("Group " + MBSDataGroup.Solution + " not found");
        }
        // find any timeGroup
        Group timeGroup = null;
        for (Object member : solutionGroup.getMemberList()) {
            String memberName = ((HObject) member).getName();
            if (member instanceof Group && memberName.startsWith("time")) {
                timeGroup = (Group) member;
                break;
            }
        }
        if (timeGroup == null) {
            throw new Exception("No time group found");
        }
        // find all the datasets in that time group
        for (Object member : timeGroup.getMemberList()) {
            if (member instanceof Dataset) {
                List<Attribute> solAttrList = ((Dataset) member).getMetadata();
                int size = 0;
                String varName = null;
                VariableType varType = null;
                for (Attribute attr : solAttrList) {
                    String attrName = attr.getName();
                    Object attrValue = attr.getValue();
                    if (attrName.equals(MSBDataAttribute.name.name())) {
                        varName = ((String[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.size.name())) {
                        size = ((int[]) attrValue)[0];
                    } else if (attrName.equals(MSBDataAttribute.type.name())) {
                        String vt = ((String[]) attrValue)[0];
                        if (vt.equals(MSBDataAttributeValue.Point.name())) {
                            varType = VariableType.POINT_VARIABLE;
                        } else if (vt.equals(MSBDataAttributeValue.Volume.name())) {
                            varType = VariableType.VOLUME;
                        } else if (vt.equals(MSBDataAttributeValue.PointSubDomain.name())) {
                        // Position for PointSubdomain
                        }
                    }
                }
                if (varType == VariableType.VOLUME) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
                if (varType == VariableType.POINT_VARIABLE) {
                    // only display volume
                    dataBlockList.addElement(DataBlock.createDataBlock(varName, varType.getType(), size, 0));
                }
            }
        }
    } finally {
        if (solFile != null) {
            try {
                solFile.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}

Example 44 with VariableType

use of cbit.vcell.math.VariableType in project vcell by virtualcell.

the class DataSetControllerImpl method findFunctionIndexes.

/**
 * Insert the method's description here.
 * Creation date: (10/13/00 9:13:52 AM)
 * @return cbit.vcell.simdata.SimDataBlock
 * @param user cbit.vcell.server.User
 * @param simResults cbit.vcell.simdata.SimResults
 * @param function cbit.vcell.math.Function
 * @param time double
 */
private FunctionIndexes[] findFunctionIndexes(VCDataIdentifier vcdID, AnnotatedFunction function, int[] dataIndexes, OutputContext outputContext) throws ExpressionException, DataAccessException, IOException, MathException {
    if (function.getFunctionType().equals(VariableType.POSTPROCESSING)) {
        FunctionIndexes[] fiArr = new FunctionIndexes[dataIndexes.length];
        Vector<DataSetIdentifier> dependencyList = identifyDataDependencies(function);
        SimulationData simData = (SimulationData) getVCData(vcdID);
        String[] varNames = new String[dependencyList.size()];
        String[] simFileVarNames = new String[dependencyList.size()];
        for (int i = 0; i < varNames.length; i++) {
            varNames[i] = dependencyList.get(i).getName();
            simFileVarNames[i] = dependencyList.get(i).getName();
        }
        CartesianMesh mesh = simData.getPostProcessingMesh(function.getName(), outputContext);
        int[][] varIndexes = new int[dataIndexes.length][varNames.length];
        for (int i = 0; i < dataIndexes.length; i += 1) {
            for (int j = 0; j < varNames.length; j++) {
                varIndexes[i][j] = dataIndexes[i];
            }
        }
        // VolumeIndexNearFar[][] outside_near_far_indexes = null;//new VolumeIndexNearFar[dataIndexes.length][/*varNames.length*/];
        for (int i = 0; i < dataIndexes.length; i += 1) {
            fiArr[i] = new FunctionIndexes(function, mesh.getCoordinateFromVolumeIndex(dataIndexes[i]), varNames, simFileVarNames, varIndexes[i], null, null);
        }
        return fiArr;
    }
    VariableType variableType = function.getFunctionType();
    Vector<DataSetIdentifier> dependencyList = identifyDataDependencies(function);
    int varIndex = TXYZ_OFFSET + dependencyList.size();
    // 
    // get Indexes and simFileNames
    // 
    Coordinate initCoord = new Coordinate(0, 0, 0);
    Coordinate[] coords = new Coordinate[dataIndexes.length];
    for (int i = 0; i < coords.length; i += 1) {
        coords[i] = initCoord;
    }
    String[] varNames = new String[varIndex - TXYZ_OFFSET];
    String[] simFileVarNames = new String[varNames.length];
    int[][] varIndexes = new int[dataIndexes.length][varNames.length];
    // New data needed for INSIDE-OUTSIDE interpolation
    VolumeIndexNearFar[][] inside_near_far_indexes = new VolumeIndexNearFar[dataIndexes.length][varNames.length];
    VolumeIndexNearFar[][] outside_near_far_indexes = new VolumeIndexNearFar[dataIndexes.length][varNames.length];
    CartesianMesh mesh = getMesh(vcdID);
    // 
    for (int i = 0; i < dataIndexes.length; i += 1) {
        coords[i] = mesh.getCoordinateFromVolumeIndex(dataIndexes[i]);
        if (variableType.equals(VariableType.VOLUME)) {
            // coord = mesh.getCoordinateFromVolumeIndex(dataIndex);
            coords[i] = mesh.getCoordinateFromVolumeIndex(dataIndexes[i]);
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                if (dsi.getVariableType().equals(VariableType.VOLUME)) {
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = dataIndexes[i];
                } else if (dsi.getVariableType().equals(VariableType.VOLUME_REGION)) {
                    int volumeIndex = mesh.getVolumeRegionIndex(dataIndexes[i]);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = volumeIndex;
                }
            }
        } else if (variableType.equals(VariableType.VOLUME_REGION)) {
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                if (dsi.getVariableType().equals(VariableType.VOLUME_REGION)) {
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = dataIndexes[i];
                }
            }
        } else if (variableType.equals(VariableType.MEMBRANE)) {
            // coord = mesh.getCoordinateFromMembraneIndex(dataIndex);
            coords[i] = mesh.getCoordinateFromMembraneIndex(dataIndexes[i]);
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                if (dsi.getVariableType().equals(VariableType.VOLUME)) {
                    if (mesh.isChomboMesh()) {
                        // don't do any varname modifications here,
                        // because chombo needs this info to decide
                        // which data set to read, extrapolate values or solution.
                        // if varname doesn't have _INSIDE or _OUTSIDE
                        // add _INSIDE to varname to indicate it needs to read extrapolated values
                        String varName = dsi.getName();
                        if (!varName.endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX) && !varName.endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                            varName += InsideVariable.INSIDE_VARIABLE_SUFFIX;
                            // add this new varname to the list if it's not already there
                            getVCData(vcdID).getEntry(varName);
                        }
                        simFileVarNames[j] = varName;
                        varIndexes[i][j] = dataIndexes[i];
                    } else {
                        if (dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                            int volInsideIndex = mesh.getMembraneElements()[dataIndexes[i]].getInsideVolumeIndex();
                            varNames[j] = dsi.getName();
                            simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                            varIndexes[i][j] = volInsideIndex;
                            inside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], true, false);
                        } else if (dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                            int volOutsideIndex = mesh.getMembraneElements()[dataIndexes[i]].getOutsideVolumeIndex();
                            varNames[j] = dsi.getName();
                            simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                            varIndexes[i][j] = volOutsideIndex;
                            outside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], false, false);
                        } else {
                            varNames[j] = dsi.getName();
                            simFileVarNames[j] = dsi.getName();
                            if (isDomainInside(mesh, dsi.getDomain(), dataIndexes[i])) {
                                inside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dsi.getDomain(), dataIndexes[i], false);
                                varIndexes[i][j] = inside_near_far_indexes[i][j].volIndexNear;
                            } else {
                                outside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dsi.getDomain(), dataIndexes[i], false);
                                varIndexes[i][j] = outside_near_far_indexes[i][j].volIndexNear;
                            }
                        }
                    }
                } else if (dsi.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    int insideVolumeIndex = mesh.getMembraneElements()[dataIndexes[i]].getInsideVolumeIndex();
                    int volRegionIndex = mesh.getVolumeRegionIndex(insideVolumeIndex);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                    varIndexes[i][j] = volRegionIndex;
                    inside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], true, true);
                } else if (dsi.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    int outsideVolumeIndex = mesh.getMembraneElements()[dataIndexes[i]].getOutsideVolumeIndex();
                    int volRegionIndex = mesh.getVolumeRegionIndex(outsideVolumeIndex);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                    varIndexes[i][j] = volRegionIndex;
                    outside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], false, true);
                } else if (dsi.getVariableType().equals(VariableType.MEMBRANE)) {
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = dataIndexes[i];
                } else if (dsi.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                    int memRegionIndex = mesh.getMembraneRegionIndex(dataIndexes[i]);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = memRegionIndex;
                }
            }
        } else if (variableType.equals(VariableType.MEMBRANE_REGION)) {
            for (int j = 0; j < varIndex - TXYZ_OFFSET; j++) {
                DataSetIdentifier dsi = (DataSetIdentifier) dependencyList.elementAt(j);
                if (dsi.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX)) {
                    // 
                    // find "inside" volume element index for first membrane element in MembraneRegion 'i'.
                    // 
                    int insideVolumeIndex = -1;
                    for (int k = 0; k < mesh.getMembraneElements().length; k++) {
                        if (mesh.getMembraneRegionIndex(k) == dataIndexes[i]) {
                            insideVolumeIndex = mesh.getMembraneElements()[k].getInsideVolumeIndex();
                            break;
                        }
                    }
                    int volRegionIndex = mesh.getVolumeRegionIndex(insideVolumeIndex);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                    varIndexes[i][j] = volRegionIndex;
                    inside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], true, true);
                    ;
                } else if (dsi.getVariableType().equals(VariableType.VOLUME_REGION) && dsi.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    // 
                    // find "outside" volume element index for first membrane element in MembraneRegion 'i'.
                    // 
                    int outsideVolumeIndex = -1;
                    for (int k = 0; k < mesh.getMembraneElements().length; k++) {
                        if (mesh.getMembraneRegionIndex(k) == dataIndexes[i]) {
                            outsideVolumeIndex = mesh.getMembraneElements()[k].getOutsideVolumeIndex();
                            break;
                        }
                    }
                    int volRegionIndex = mesh.getVolumeRegionIndex(outsideVolumeIndex);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName().substring(0, dsi.getName().lastIndexOf("_"));
                    varIndexes[i][j] = volRegionIndex;
                    outside_near_far_indexes[i][j] = interpolateFindNearFarIndex(mesh, dataIndexes[i], false, true);
                } else if (dsi.getVariableType().equals(VariableType.MEMBRANE)) {
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = dataIndexes[i];
                } else if (dsi.getVariableType().equals(VariableType.MEMBRANE_REGION)) {
                    int memRegionIndex = mesh.getMembraneRegionIndex(dataIndexes[i]);
                    varNames[j] = dsi.getName();
                    simFileVarNames[j] = dsi.getName();
                    varIndexes[i][j] = memRegionIndex;
                }
            }
        }
    }
    FunctionIndexes[] fiArr = new FunctionIndexes[dataIndexes.length];
    for (int i = 0; i < dataIndexes.length; i += 1) {
        fiArr[i] = new FunctionIndexes(function, coords[i], varNames, simFileVarNames, varIndexes[i], inside_near_far_indexes[i], outside_near_far_indexes[i]);
    }
    return fiArr;
// 
}

Example 45 with VariableType

use of cbit.vcell.math.VariableType 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;
}