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

Example 6 with FileFormat

use of ncsa.hdf.object.FileFormat 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 7 with FileFormat

use of ncsa.hdf.object.FileFormat 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 8 with FileFormat

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

the class LocalVCellConnectionFactory method linkHDFLib.

/**
 * trigger loading of HDF library when running local
 */
private void linkHDFLib() {
    try {
        // lifted from hdf5group website
        Class<?> fileclass = Class.forName("ncsa.hdf.object.h5.H5File");
        FileFormat fileformat = (FileFormat) fileclass.newInstance();
        if (fileformat != null) {
            FileFormat.addFileFormat(FileFormat.FILE_TYPE_HDF5, fileformat);
        }
    } catch (Throwable t) {
        t.printStackTrace();
    }
}

Example 9 with FileFormat

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

the class CartesianMeshChombo method readMeshFile.

public static CartesianMeshChombo readMeshFile(File chomboMeshFile) throws Exception {
    CartesianMeshChombo chomboMesh = new CartesianMeshChombo();
    if (H5.H5open() < 0) {
        throw new Exception("H5.H5open() failed");
    }
    FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
    if (fileFormat == null) {
        throw new Exception("FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5) failed, returned null.");
    }
    FileFormat meshFile = null;
    try {
        meshFile = fileFormat.createInstance(chomboMeshFile.getAbsolutePath(), FileFormat.READ);
        meshFile.open();
        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) meshFile.getRootNode();
        Group rootGroup = (Group) rootNode.getUserObject();
        Group meshGroup = (Group) rootGroup.getMemberList().get(0);
        List<Attribute> meshAttrList = meshGroup.getMetadata();
        for (Attribute attr : meshAttrList) {
            String attrName = attr.getName();
            MeshAttribute mattr = null;
            try {
                mattr = MeshAttribute.valueOf(attrName);
            } catch (IllegalArgumentException ex) {
            }
            if (mattr == null) {
                // if not found, then we don't care about this attribute
                logger.debug("mesh attribute " + attrName + " is not defined in Java");
                continue;
            }
            Object value = attr.getValue();
            switch(mattr) {
                case dimension:
                    chomboMesh.dimension = ((int[]) value)[0];
                    break;
                case numLevels:
                    chomboMesh.numLevels = ((int[]) value)[0];
                    break;
                case viewLevel:
                    chomboMesh.viewLevel = ((int[]) value)[0];
                    break;
                case refineRatios:
                    chomboMesh.refineRatios = (int[]) value;
                    break;
                case Dx:
                case extent:
                case Nx:
                case origin:
                    // these 4 has format of {};
                    String[] valueStrArray = (String[]) value;
                    String value0 = valueStrArray[0];
                    StringTokenizer st = new StringTokenizer(value0, "{,} ");
                    int numTokens = st.countTokens();
                    // we need 3 for 3d
                    double[] values = new double[Math.max(3, numTokens)];
                    for (int i = 0; i < Math.min(3, numTokens); ++i) {
                        String token = st.nextToken();
                        values[i] = Double.parseDouble(token);
                    }
                    switch(mattr) {
                        case Dx:
                            chomboMesh.dx = new double[3];
                            System.arraycopy(values, 0, chomboMesh.dx, 0, values.length);
                            break;
                        case extent:
                            chomboMesh.extent = new Extent(values[0], values[1], values[2] == 0 ? 1 : values[2]);
                            break;
                        case Nx:
                            chomboMesh.size = new ISize((int) values[0], (int) values[1], values[2] == 0 ? 1 : (int) values[2]);
                            break;
                        case origin:
                            chomboMesh.origin = new Origin(values[0], values[1], values[2]);
                            break;
                    }
                    break;
            }
        }
        List<HObject> memberList = meshGroup.getMemberList();
        for (HObject member : memberList) {
            if (!(member instanceof Dataset)) {
                continue;
            }
            Dataset dataset = (Dataset) member;
            Vector vectValues = (Vector) dataset.read();
            String name = dataset.getName();
            MeshDataSet mdataset = null;
            try {
                mdataset = MeshDataSet.valueOfName(name);
            } catch (IllegalArgumentException ex) {
                logger.debug("mesh dataset " + name + " is not defined in Java");
            }
            if (mdataset == null) {
                // if not found, then we don't care about this dataset
                continue;
            }
            switch(mdataset) {
                case vertices:
                    collectVertices(chomboMesh, vectValues);
                    break;
                case segments:
                    collect2dSegments(chomboMesh, vectValues);
                    break;
                case structures:
                    collectStructures(chomboMesh, vectValues);
                    break;
                case featurephasevols:
                    collectFeaturePhaseVols(chomboMesh, vectValues);
                    break;
                case membraneids:
                    collectMembraneIds(chomboMesh, vectValues);
                    break;
                case membrane_elements:
                case membrane_elements_old:
                    collectMembraneElements(chomboMesh, vectValues);
                    break;
                case surface_triangles:
                    collect3dSurfaceTriangles(chomboMesh, vectValues);
                    break;
                case slice_view:
                    collect3dSliceView(chomboMesh, vectValues);
                    break;
            }
        }
    } finally {
        if (meshFile != null) {
            meshFile.close();
        }
    }
    // set neighbors to membrane elements
    if (chomboMesh.dimension == 2 && chomboMesh.membraneElements != null) {
        for (int i = 0; i < chomboMesh.membraneElements.length; ++i) {
            MembraneElement me = chomboMesh.membraneElements[i];
            me.setConnectivity(chomboMesh.segments[i].prevNeigbhor, chomboMesh.segments[i].nextNeigbhor, -1, -1);
        }
    }
    return chomboMesh;
}

Example 10 with FileFormat

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

the class DataSet method readChomboExtrapolatedValues.

static double[] readChomboExtrapolatedValues(String varName, File pdeFile, File zipFile) throws IOException {
    double[] data = null;
    if (zipFile != null && isChombo(zipFile)) {
        File tempFile = null;
        FileFormat solFile = null;
        try {
            tempFile = createTempHdf5File(zipFile, pdeFile.getName());
            FileFormat fileFormat = FileFormat.getFileFormat(FileFormat.FILE_TYPE_HDF5);
            solFile = fileFormat.createInstance(tempFile.getAbsolutePath(), FileFormat.READ);
            solFile.open();
            data = readChomboExtrapolatedValues(varName, solFile);
        } catch (Exception e) {
            throw new IOException(e.getMessage(), e);
        } 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 data;
}