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

Example 11 with Group

use of ncsa.hdf.object.Group 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 12 with Group

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

the class DataSetControllerImpl method iterateHDF5.

private static void iterateHDF5(HObject hObject, String indent, DataProcessingHelper dataProcessingHelper) throws Exception {
    if (hObject instanceof Group) {
        Group group = ((Group) hObject);
        printInfo(group, indent);
        if (group.getName().equals("/") || group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_POSTPROCESSING)) {
            List<HObject> postProcessMembers = ((Group) hObject).getMemberList();
            for (HObject nextHObject : postProcessMembers) {
                iterateHDF5(nextHObject, indent + " ", dataProcessingHelper);
            }
        } else if (group.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_VARIABLESTATISTICS) && dataProcessingHelper.isInfoOnly()) {
            populateStatNamesAndUnits(hObject, dataProcessingHelper);
            List<HObject> statDataAtEachTime = group.getMemberList();
            dataProcessingHelper.statValues = new double[dataProcessingHelper.statVarNames.length][statDataAtEachTime.size()];
            for (HObject nextStatData : statDataAtEachTime) {
                printInfo(nextStatData, indent + " ");
                // always get stats data when ask for info
                processDims(nextStatData, dataProcessingHelper, false);
                double[] stats = (double[]) dataProcessingHelper.tempData;
                int timeIndex = Integer.parseInt(nextStatData.getName().substring("time".length()));
                for (int j = 0; j < stats.length; j++) {
                    dataProcessingHelper.statValues[j][timeIndex] = stats[j];
                }
            }
        } else {
            // must be image data
            if (dataProcessingHelper.isInfoOnly()) {
                dataProcessingHelper.imageNames = new ArrayList<String>();
                dataProcessingHelper.imageISize = new ArrayList<ISize>();
                dataProcessingHelper.imageOrigin = new ArrayList<Origin>();
                dataProcessingHelper.imageExtent = new ArrayList<Extent>();
                Origin imgDataOrigin;
                Extent imgDataExtent;
                HashMap<String, String> attrHashMap = getHDF5Attributes(group);
                if (attrHashMap.size() == 2) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), 0, 0);
                    // this is 1D, however the extentY, Z cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), 1, 1);
                } else if (attrHashMap.size() == 4) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), 0);
                    // this is 2D, however the extentZ cannot take 0
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), 1);
                } else if (attrHashMap.size() == 6) {
                    imgDataOrigin = new Origin(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_ORIGINZ)));
                    imgDataExtent = new Extent(Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTX)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTY)), Double.valueOf(attrHashMap.get(DATA_PROCESSING_OUTPUT_EXTENTZ)));
                } else {
                    throw new Exception("Unexpected number of origin/extent values");
                }
                dataProcessingHelper.imageNames.add(hObject.getName());
                dataProcessingHelper.imageOrigin.add(imgDataOrigin);
                dataProcessingHelper.imageExtent.add(imgDataExtent);
                // get ISize
                processDims((H5ScalarDS) (((Group) hObject).getMemberList()).get(0), dataProcessingHelper, true);
                long[] dims = dataProcessingHelper.tempDims;
                ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                dataProcessingHelper.imageISize.add(isize);
            } else {
                int currentVarNameIndex = -1;
                for (int i = 0; i < dataProcessingHelper.specificVarNames.length; i++) {
                    if (group.getName().equals(dataProcessingHelper.specificVarNames[i])) {
                        currentVarNameIndex = i;
                        break;
                    }
                }
                if (currentVarNameIndex == -1) {
                    // skip this group
                    return;
                }
                dataProcessingHelper.specificDataValues[currentVarNameIndex] = new double[(dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? dataProcessingHelper.times.length : dataProcessingHelper.specificTimePointHelper.getTimePoints().length)][];
                List<HObject> imageDataAtEachTime = ((Group) hObject).getMemberList();
                int foundTimePointIndex = 0;
                for (HObject nextImageData : imageDataAtEachTime) {
                    // if(dataProcessingHelper.isInfoOnly()){
                    // printInfo(nextImageData,indent+" ");
                    // processDims(nextImageData, dataProcessingHelper,true);
                    // long[] dims = dataProcessingHelper.tempDims;
                    // ISize isize = new ISize((int)dims[0], (int)(dims.length>1?dims[1]:1), (int)(dims.length>2?dims[2]:1));
                    // dataProcessingHelper.imageISize.add(isize);
                    // break;//only need 1st one for info
                    // }else{
                    int hdf5GroupTimeIndex = Integer.parseInt(nextImageData.getName().substring(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMEPREFIX.length()));
                    if (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() || dataProcessingHelper.specificTimePointHelper.getTimePoints()[foundTimePointIndex] == dataProcessingHelper.times[hdf5GroupTimeIndex]) {
                        int timeIndex = (dataProcessingHelper.specificTimePointHelper.isAllTimePoints() ? hdf5GroupTimeIndex : foundTimePointIndex);
                        processDims(nextImageData, dataProcessingHelper, false);
                        long[] dims = dataProcessingHelper.tempDims;
                        ISize isize = new ISize((int) dims[0], (int) (dims.length > 1 ? dims[1] : 1), (int) (dims.length > 2 ? dims[2] : 1));
                        if (dataProcessingHelper.specificDataIndexHelper.isAllDataIndexes()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = (double[]) dataProcessingHelper.tempData;
                        } else if (dataProcessingHelper.specificDataIndexHelper.isSingleSlice()) {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[isize.getX() * isize.getY()];
                            System.arraycopy((double[]) dataProcessingHelper.tempData, dataProcessingHelper.specificDataIndexHelper.getSliceIndex() * (isize.getX() * isize.getY()), dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex], 0, isize.getX() * isize.getY());
                        } else {
                            dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex] = new double[dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length];
                            for (int i = 0; i < dataProcessingHelper.specificDataIndexHelper.getDataIndexes().length; i++) {
                                dataProcessingHelper.specificDataValues[currentVarNameIndex][timeIndex][i] = ((double[]) dataProcessingHelper.tempData)[dataProcessingHelper.specificDataIndexHelper.getDataIndexes()[i]];
                            }
                        }
                        foundTimePointIndex++;
                        if (!dataProcessingHelper.specificTimePointHelper.isAllTimePoints() && foundTimePointIndex == dataProcessingHelper.specificTimePointHelper.getTimePoints().length) {
                            // break out after we get our data
                            break;
                        }
                    }
                // }
                }
            }
        }
    } else if (hObject instanceof Dataset) {
        Dataset dataset = (Dataset) hObject;
        printInfo(dataset, indent);
        if (dataset.getName().equals(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_TIMES)) {
            processDims(hObject, dataProcessingHelper, false);
            dataProcessingHelper.times = (double[]) dataProcessingHelper.tempData;
        }
    } else if (hObject instanceof Datatype) {
        printInfo(hObject, indent);
    } else {
        printInfo(hObject, indent);
    }
}

Example 13 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();
        List<HObject> solGroups = rootGroup.getMemberList();
        for (HObject memberGroup : solGroups) {
            if (memberGroup instanceof Group && memberGroup.getName().equals("solution")) {
                Group solGroup = (Group) memberGroup;
                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));
                }
                break;
            }
        }
    } 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 14 with Group

use of ncsa.hdf.object.Group 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 15 with Group

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

the class VH5PathTest method run.

@Test
public void run() {
    // create the file and add groups ans dataset into the file
    try {
        Group root = (Group) ((javax.swing.tree.DefaultMutableTreeNode) testFile.getRootNode()).getUserObject();
        VH5Path vpath = new VH5Path(root, "elements", "volume");
        System.out.println(vpath.foundType());
        VH5TypedPath<double[]> tpath = new VH5TypedPath<double[]>(root, double[].class, "elements", "volume");
        double[] e = tpath.get();
        System.out.println(e[0]);
        VH5Path bpPath = new VH5Path(root, "elements", "boundaryPosition");
        Object data = bpPath.getData();
        System.out.println(data.getClass().getSimpleName());
        VH5Path vpPath = new VH5Path(root, "elements", "volumePoints");
        data = vpPath.getData();
        System.out.println(data.getClass().getSimpleName());
        // VH5TypedPath<String[]> spath = new VH5TypedPath<String[]>(root, String[].class,"elements" ,"front description");
        VH5TypedPath<String> spath = new VH5TypedPath<String>(root, String.class, "elements", "front description");
        // String[] sdata = spath.get();
        // System.out.println(sdata[0]);
        System.out.println(spath.get());
        VH5Path xpath = new VH5Path(root, "elements", "front description");
        Object o = xpath.getData();
        System.out.println(o);
        dtype("elements", "endX");
        dtype("endTime");
        dtype("generationTimes");
        dtype("moveTimes");
        dtype("runTime");
        dtype("solverTimeStep");
        dtype("timeStep");
        dtype("timeStepTimes");
        VH5TypedPath<int[]> ipath = new VH5TypedPath<int[]>(root, int[].class, "lastTimeIndex");
        System.out.println(Arrays.toString(ipath.get()));
        VH5TypedPath<long[]> lpath = new VH5TypedPath<long[]>(root, long[].class, "elements", "numX");
        System.out.println(Arrays.toString(lpath.get()));
    // System.out.println("-------");
    // VH5TypedPath<H5ScalarDS> spath = new VH5TypedPath<H5ScalarDS>(root, H5ScalarDS.class,"endTime");
    // H5ScalarDS ds = spath.get( );
    // Object o = ds.read();
    // VH5Dataset vds = new VH5Dataset(ds);
    // vds.info();
    /*
    		Next to do; use lastTimeIndex as maximum index into elements and species data sets. Select one X-Y plane at a time and read.
    		*/
    // close file resource
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}