Examples with MBSDataGroup cbit.vcell.solvers.CartesianMeshMovingBoundary.MBSDataGroup used on opensource projects

Example 1 with MBSDataGroup

use of cbit.vcell.solvers.CartesianMeshMovingBoundary.MBSDataGroup in project vcell by virtualcell.

the class DataSet method readMBSData.

private double[] readMBSData(String varName, Double time) throws Exception {
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    FileFormat solFile = null;
    double[] data = 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");
        }
        int varIndex = -1;
        int size = 0;
        for (int i = 0; i < dataBlockList.size(); ++i) {
            DataBlock dataBlock = dataBlockList.get(i);
            if (dataBlock.getVarName().equals(varName)) {
                varIndex = i;
                size = dataBlock.getSize();
                break;
            }
        }
        if (varIndex == -1) {
            throw new Exception("Variable " + varName + " not found");
        }
        // find time group for that time
        Group timeGroup = null;
        for (Object member : solutionGroup.getMemberList()) {
            if (member instanceof Group) {
                Group group = (Group) member;
                List<Attribute> dsAttrList = group.getMetadata();
                Attribute timeAttribute = null;
                for (Attribute attr : dsAttrList) {
                    if (attr.getName().equals(MSBDataAttribute.time.name())) {
                        timeAttribute = attr;
                        break;
                    }
                }
                if (timeAttribute != null) {
                    double t = ((double[]) timeAttribute.getValue())[0];
                    if (Math.abs(t - time) < 1e-8) {
                        timeGroup = group;
                        break;
                    }
                }
            }
        }
        if (timeGroup == null) {
            throw new Exception("No time group found for time=" + time);
        }
        // find variable dataset
        Dataset varDataset = null;
        for (Object member : timeGroup.getMemberList()) {
            if (member instanceof Dataset) {
                List<Attribute> dsAttrList = ((Dataset) member).getMetadata();
                String var = null;
                for (Attribute attr : dsAttrList) {
                    if (attr.getName().equals(MSBDataAttribute.name.name())) {
                        var = ((String[]) attr.getValue())[0];
                        break;
                    }
                }
                if (var != null && var.equals(varName)) {
                    varDataset = (Dataset) member;
                    break;
                }
            }
        }
        if (varDataset == null) {
            throw new Exception("Data for Variable " + varName + " at time " + time + " not found");
        }
        data = new double[size];
        System.arraycopy((double[]) varDataset.getData(), 0, data, 0, size);
        return data;
    } finally {
        if (solFile != null) {
            try {
                solFile.close();
            } catch (Exception e) {
            // ignore
            }
        }
    }
}

Example 2 with MBSDataGroup

use of cbit.vcell.solvers.CartesianMeshMovingBoundary.MBSDataGroup 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
            }
        }
    }
}