Examples with Dataset ncsa.hdf.object.Dataset used on opensource projects

Example 1 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class DataSet method readHdf5SolutionMetaData.

private void readHdf5SolutionMetaData(InputStream is) throws Exception {
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = createTempHdf5File(is);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) solFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group solGroup = (Group) rootGroup.getMemberList().get(0);
        List<HObject> memberList = solGroup.getMemberList();
        for (HObject member : memberList) {
            if (!(member instanceof Dataset)) {
                continue;
            }
            Dataset dataset = (Dataset) member;
            String dsname = dataset.getName();
            int vt = -1;
            String domain = null;
            List<Attribute> solAttrList = dataset.getMetadata();
            for (Attribute attr : solAttrList) {
                String attrName = attr.getName();
                if (attrName.equals("variable type")) {
                    Object obj = attr.getValue();
                    vt = ((int[]) obj)[0];
                } else if (attrName.equals("domain")) {
                    Object obj = attr.getValue();
                    domain = ((String[]) obj)[0];
                }
            }
            long[] dims = dataset.getDims();
            String varName = domain == null ? dsname : domain + Variable.COMBINED_IDENTIFIER_SEPARATOR + dsname;
            dataBlockList.addElement(DataBlock.createDataBlock(varName, vt, (int) dims[0], 0));
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile);
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
}

Example 2 with Dataset

use of ncsa.hdf.object.Dataset 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 3 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class DataSet method readHdf5VariableSolution.

static double[] readHdf5VariableSolution(File zipfile, String fileName, String varName) throws Exception {
    File tempFile = null;
    FileFormat solFile = null;
    try {
        tempFile = createTempHdf5File(zipfile, fileName);
        FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
        solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
        solFile.open();
        if (varName != null) {
            String varPath = Hdf5Utils.getVarSolutionPath(varName);
            HObject solObj = FileFormat.findObject(solFile, varPath);
            if (solObj instanceof Dataset) {
                Dataset dataset = (Dataset) solObj;
                return (double[]) dataset.read();
            }
        }
    } finally {
        try {
            if (solFile != null) {
                solFile.close();
            }
            if (tempFile != null) {
                if (!tempFile.delete()) {
                    System.err.println("couldn't delete temp file " + tempFile.getAbsolutePath());
                }
            }
        } catch (Exception e) {
        // ignore
        }
    }
    return null;
}

Example 4 with Dataset

use of ncsa.hdf.object.Dataset 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 5 with Dataset

use of ncsa.hdf.object.Dataset in project vcell by virtualcell.

the class DataSet method readChomboExtrapolatedValues.

static double[] readChomboExtrapolatedValues(String varName, FileFormat solFile) throws Exception {
    double[] data = null;
    if (varName != null) {
        String varPath = Hdf5Utils.getVolVarExtrapolatedValuesPath(varName);
        HObject solObj = FileFormat.findObject(solFile, varPath);
        if (solObj == null) {
            throw new IOException("Extrapolated values for variable '" + varName + "' does not exist in the results.");
        }
        if (solObj instanceof Dataset) {
            Dataset dataset = (Dataset) solObj;
            return (double[]) dataset.read();
        }
    }
    return data;
}