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

Example 1 with Group

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

the class VH5Path method walk.

/**
 * find next object in sequence
 * @param hobj previous element in sequence
 * @param steps name of each step
 * @param index current step
 * @return next object path, if present
 * @throws HDF5Exception
 */
private static Object walk(Object hobj, String[] steps, int index) throws Exception {
    final boolean isLastIndex = lastIndex(index, steps);
    final String finding = steps[index];
    Group g = BeanUtils.downcast(Group.class, hobj);
    if (g != null) {
        List<HObject> ml = g.getMemberList();
        for (HObject sub : ml) {
            // String full = sub.getFullName();
            if (finding.equals(sub.getName())) {
                if (isLastIndex) {
                    return sub;
                }
                return walk(sub, steps, index + 1);
            }
        }
    }
    H5CompoundDS cds = BeanUtils.downcast(H5CompoundDS.class, hobj);
    if (cds != null) {
        cds.read();
        String[] mn = cds.getMemberNames();
        for (int i = 0; i < mn.length; i++) {
            if (finding.equals(mn[i])) {
                Object c = cds.read();
                Vector<?> vec = BeanUtils.downcast(Vector.class, c);
                if (vec != null) {
                    VCAssert.assertTrue(i < vec.size(), "Disconnect between H5CompoundDS.getMemberNames( )  and returned Vector");
                    Object child = vec.get(i);
                    if (isLastIndex) {
                        return child;
                    }
                } else {
                    throw new UnsupportedOperationException("Unsupported H5CompoundDS subtype " + className(c));
                }
            }
        }
    }
    if (isLastIndex) {
        DataFormat df = BeanUtils.downcast(DataFormat.class, hobj);
        if (df != null && df.hasAttribute()) {
            try {
                @SuppressWarnings("unchecked") List<Object> meta = df.getMetadata();
                for (Object o : meta) {
                    Attribute a = BeanUtils.downcast(Attribute.class, o);
                    if (a != null) {
                        if (finding.equals(a.getName())) {
                            return a.getValue();
                        }
                    } else {
                        lg.warn(concat(steps, finding) + " fetching metadata unexpected type " + className(o));
                    }
                }
            } catch (Exception e) {
                throw new RuntimeException(concat(steps, finding) + " fetching metadata", e);
            }
        }
    }
    return null;
}

Example 2 with Group

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

use of ncsa.hdf.object.Group 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 4 with Group

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

the class DataSetControllerImpl method getDataProcessingOutput.

public static DataOperationResults getDataProcessingOutput(DataOperation dataOperation, File dataProcessingOutputFileHDF5) throws Exception {
    DataOperationResults dataProcessingOutputResults = null;
    FileFormat hdf5FileFormat = null;
    try {
        if (dataProcessingOutputFileHDF5.exists()) {
            // retrieve an instance of H5File
            FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
            if (fileFormat == null) {
                throw new Exception("Cannot find HDF5 FileFormat.");
            }
            // open the file with read-only access
            hdf5FileFormat = fileFormat.open(dataProcessingOutputFileHDF5.getAbsolutePath(), FileFormat.READ);
            hdf5FileFormat.setMaxMembers(Simulation.MAX_LIMIT_SPATIAL_TIMEPOINTS);
            // open the file and retrieve the file structure
            hdf5FileFormat.open();
            Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) hdf5FileFormat.getRootNode()).getUserObject();
            if (dataOperation instanceof DataProcessingOutputInfoOP) {
                DataProcessingHelper dataProcessingHelper = new DataProcessingHelper();
                iterateHDF5(root, "", dataProcessingHelper);
                dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputInfo(dataOperation.getVCDataIdentifier(), dataProcessingHelper.getVarNames(), dataProcessingHelper.getVarISizes(), dataProcessingHelper.times, dataProcessingHelper.getVarUnits(), dataProcessingHelper.getPostProcessDataTypes(), dataProcessingHelper.getVarOrigins(), dataProcessingHelper.getVarExtents(), dataProcessingHelper.getVarStatValues());
                // map function names to PostProcess state variable name
                ArrayList<String> postProcessImageVarNames = new ArrayList<String>();
                for (int i = 0; i < ((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getVariableNames().length; i++) {
                    String variableName = ((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getVariableNames()[i];
                    if (((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults).getPostProcessDataType(variableName).equals(DataOperationResults.DataProcessingOutputInfo.PostProcessDataType.image)) {
                        postProcessImageVarNames.add(variableName);
                    }
                }
                HashMap<String, String> mapFunctionNameToStateVarName = null;
                if (((DataProcessingOutputInfoOP) dataOperation).getOutputContext() != null) {
                    mapFunctionNameToStateVarName = new HashMap<String, String>();
                    for (int i = 0; i < ((DataProcessingOutputInfoOP) dataOperation).getOutputContext().getOutputFunctions().length; i++) {
                        AnnotatedFunction annotatedFunction = ((DataProcessingOutputInfoOP) dataOperation).getOutputContext().getOutputFunctions()[i];
                        if (annotatedFunction.getFunctionType().equals(VariableType.POSTPROCESSING)) {
                            String[] symbols = annotatedFunction.getExpression().flatten().getSymbols();
                            // Find any PostProcess state var that matches a symbol in the function
                            for (int j = 0; j < symbols.length; j++) {
                                if (postProcessImageVarNames.contains(symbols[j])) {
                                    mapFunctionNameToStateVarName.put(annotatedFunction.getName(), symbols[j]);
                                    break;
                                }
                            }
                        }
                    }
                }
                if (mapFunctionNameToStateVarName != null && mapFunctionNameToStateVarName.size() > 0) {
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputInfo(((DataOperationResults.DataProcessingOutputInfo) dataProcessingOutputResults), mapFunctionNameToStateVarName);
                }
            } else {
                OutputContext outputContext = dataOperation.getOutputContext();
                String[] variableNames = null;
                DataIndexHelper dataIndexHelper = null;
                TimePointHelper timePointHelper = null;
                if (dataOperation instanceof DataOperation.DataProcessingOutputDataValuesOP) {
                    variableNames = new String[] { ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getVariableName() };
                    dataIndexHelper = ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getDataIndexHelper();
                    timePointHelper = ((DataOperation.DataProcessingOutputDataValuesOP) dataOperation).getTimePointHelper();
                } else if (dataOperation instanceof DataOperation.DataProcessingOutputTimeSeriesOP) {
                    variableNames = ((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getTimeSeriesJobSpec().getVariableNames();
                    TimeSeriesJobSpec timeSeriesJobSpec = ((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getTimeSeriesJobSpec();
                    double[] specificTimepoints = extractTimeRange(((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getAllDatasetTimes(), timeSeriesJobSpec.getStartTime(), timeSeriesJobSpec.getEndTime());
                    timePointHelper = TimePointHelper.createSpecificTimePointHelper(specificTimepoints);
                    timeSeriesJobSpec.initIndices();
                    dataIndexHelper = DataIndexHelper.createSpecificDataIndexHelper(timeSeriesJobSpec.getIndices()[0]);
                } else {
                    throw new Exception("Unknown Dataoperation " + dataOperation.getClass().getName());
                }
                if (variableNames.length != 1) {
                    throw new Exception("Only 1 variable request at a time");
                }
                AnnotatedFunction[] annotatedFunctions = (outputContext == null ? null : outputContext.getOutputFunctions());
                AnnotatedFunction foundFunction = null;
                if (annotatedFunctions != null) {
                    for (int i = 0; i < annotatedFunctions.length; i++) {
                        if (annotatedFunctions[i].getName().equals(variableNames[0])) {
                            foundFunction = annotatedFunctions[i];
                            break;
                        }
                    }
                }
                double[] alltimes = null;
                if (foundFunction != null) {
                    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(dataOperation.getVCDataIdentifier(), false, dataOperation.getOutputContext()), dataProcessingOutputFileHDF5);
                    alltimes = dataProcessingOutputInfo.getVariableTimePoints();
                    FunctionHelper functionHelper = getPostProcessStateVariables(foundFunction, dataProcessingOutputInfo);
                    DataProcessingHelper dataProcessingHelper = new DataProcessingHelper(functionHelper.postProcessStateVars, timePointHelper, dataIndexHelper);
                    iterateHDF5(root, "", dataProcessingHelper);
                    dataProcessingOutputResults = evaluatePostProcessFunction(dataProcessingOutputInfo, functionHelper.postProcessStateVars, dataProcessingHelper.specificDataValues, dataIndexHelper, timePointHelper, functionHelper.flattenedBoundExpression, variableNames[0]);
                } else {
                    DataProcessingHelper dataProcessingHelper = new DataProcessingHelper(new String[] { variableNames[0] }, timePointHelper, dataIndexHelper);
                    iterateHDF5(root, "", dataProcessingHelper);
                    alltimes = dataProcessingHelper.times;
                    if (dataProcessingHelper.specificDataValues == null) {
                        throw new Exception("Couldn't find postprocess data as specified for var=" + variableNames[0]);
                    }
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputDataValues(dataOperation.getVCDataIdentifier(), variableNames[0], timePointHelper, dataIndexHelper, dataProcessingHelper.specificDataValues[0]);
                }
                if (dataOperation instanceof DataOperation.DataProcessingOutputTimeSeriesOP) {
                    TimeSeriesJobResults timeSeriesJobResults = null;
                    DataProcessingOutputTimeSeriesOP dataProcessingOutputTimeSeriesOP = (DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation;
                    // [time][data]
                    double[][] dataValues = ((DataOperationResults.DataProcessingOutputDataValues) dataProcessingOutputResults).getDataValues();
                    double[] desiredTimes = (timePointHelper.isAllTimePoints() ? alltimes : timePointHelper.getTimePoints());
                    double[][][] timeSeriesFormatedValuesArr = new double[variableNames.length][dataIndexHelper.getDataIndexes().length + 1][desiredTimes.length];
                    for (int i = 0; i < timeSeriesFormatedValuesArr.length; i++) {
                        // var
                        for (int j = 0; j < timeSeriesFormatedValuesArr[i].length; j++) {
                            // index
                            if (j == 0) {
                                timeSeriesFormatedValuesArr[i][j] = desiredTimes;
                                continue;
                            }
                            for (int k = 0; k < timeSeriesFormatedValuesArr[i][j].length; k++) {
                                // time
                                // assume 1 variable for now
                                timeSeriesFormatedValuesArr[i][j][k] = dataValues[k][j - 1];
                            }
                        }
                    }
                    if (dataProcessingOutputTimeSeriesOP.getTimeSeriesJobSpec().isCalcSpaceStats()) {
                        SpatialStatsInfo spatialStatsInfo = new SpatialStatsInfo();
                        spatialStatsInfo.bWeightsValid = false;
                        timeSeriesJobResults = calculateStatisticsFromWhole(dataProcessingOutputTimeSeriesOP.getTimeSeriesJobSpec(), timeSeriesFormatedValuesArr, timePointHelper.getTimePoints(), spatialStatsInfo);
                    } else {
                        timeSeriesJobResults = new TSJobResultsNoStats(variableNames, new int[][] { dataIndexHelper.getDataIndexes() }, timePointHelper.getTimePoints(), timeSeriesFormatedValuesArr);
                    }
                    dataProcessingOutputResults = new DataOperationResults.DataProcessingOutputTimeSeriesValues(dataOperation.getVCDataIdentifier(), timeSeriesJobResults);
                }
            }
        } else {
            throw new FileNotFoundException("Data Processing Output file '" + dataProcessingOutputFileHDF5.getPath() + "' not found");
        }
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (hdf5FileFormat != null) {
            try {
                hdf5FileFormat.close();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return dataProcessingOutputResults;
}

Example 5 with Group

use of ncsa.hdf.object.Group 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
            }
        }
    }
}