Examples with H5CompoundDS ncsa.hdf.object.h5.H5CompoundDS used on opensource projects

Example 1 with H5CompoundDS

use of ncsa.hdf.object.h5.H5CompoundDS 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 H5CompoundDS

use of ncsa.hdf.object.h5.H5CompoundDS in project vcell by virtualcell.

the class Hdf5Reader method getDataTable.

public static Hdf5Reader.DataColumn[] getDataTable(Group group, String name) throws Exception {
    List<HObject> memberList = group.getMemberList();
    for (HObject member : memberList) {
        if (member.getName().equals(name)) {
            if (member instanceof H5CompoundDS) {
                H5CompoundDS compoundDataSet = (H5CompoundDS) member;
                Vector columnValueArrays = (Vector) compoundDataSet.read();
                String[] columnNames = compoundDataSet.getMemberNames();
                ArrayList<Hdf5Reader.DataColumn> dataColumns = new ArrayList<Hdf5Reader.DataColumn>();
                for (int c = 0; c < columnNames.length; c++) {
                    Object column = columnValueArrays.get(c);
                    if (column instanceof int[]) {
                        dataColumns.add(new Hdf5Reader.IntColumn(columnNames[c], (int[]) columnValueArrays.get(c)));
                    } else if (column instanceof double[]) {
                        dataColumns.add(new Hdf5Reader.DoubleColumn(columnNames[c], (double[]) columnValueArrays.get(c)));
                    } else {
                        throw new RuntimeException("unexpected type '" + column.getClass().getName() + "' for group member '" + name + "'");
                    }
                }
                return dataColumns.toArray(new Hdf5Reader.DataColumn[0]);
            } else if (member instanceof H5ScalarDS) {
                H5ScalarDS compoundDataSet = (H5ScalarDS) member;
                Object column = compoundDataSet.read();
                if (column instanceof int[]) {
                    return new Hdf5Reader.DataColumn[] { new Hdf5Reader.IntColumn("col", (int[]) column) };
                } else if (column instanceof double[]) {
                    return new Hdf5Reader.DataColumn[] { new Hdf5Reader.DoubleColumn("col", (double[]) column) };
                } else if (column instanceof long[]) {
                    return new Hdf5Reader.DataColumn[] { new Hdf5Reader.LongColumn("col", (long[]) column) };
                } else {
                    throw new RuntimeException("unexpected type '" + column.getClass().getName() + "' for group member '" + name + "'");
                }
            } else {
                throw new RuntimeException("expecting type H5CompoundDS for group member '" + name + "', found type " + member.getClass().getName());
            }
        }
    }
    throw new RuntimeException("group member '" + name + "' not found");
}

Example 3 with H5CompoundDS

use of ncsa.hdf.object.h5.H5CompoundDS in project vcell by virtualcell.

the class VH5Dataset method info.

public void info() {
    try {
        System.out.println(dataset.getName());
        System.out.println(dataset.getFullName());
        H5ScalarDS sds = BeanUtils.downcast(H5ScalarDS.class, dataset);
        if (sds != null) {
            info(sds);
        }
        H5CompoundDS cds = BeanUtils.downcast(H5CompoundDS.class, dataset);
        int rank = dataset.getRank();
        long[] d = dataset.getDims();
        long[] s = dataset.getSelectedDims();
        for (int i = 0; i < rank; i++) {
            s[i] = d[i];
        }
        if (cds != null) {
            info(cds);
        } else {
            Object obj = dataset.read();
            analyze(obj);
        }
        String[] names = dataset.getDimNames();
        if (names == null) {
            names = new String[rank];
        }
        long[] dims = dataset.getMaxDims();
        for (int i = 0; i < rank; i++) {
            System.out.println("n " + StringUtils.defaultString(names[i]) + " has " + dims[i]);
        }
        System.out.println("current dims " + Arrays.toString(dataset.getDims()));
        System.out.println("chunk size " + Arrays.toString(dataset.getChunkSize()));
        System.out.println("selected " + Arrays.toString(dataset.getSelectedDims()));
        System.out.println("start " + Arrays.toString(dataset.getStartDims()));
        System.out.println("stride " + Arrays.toString(dataset.getStride()));
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 4 with H5CompoundDS

use of ncsa.hdf.object.h5.H5CompoundDS in project vcell by virtualcell.

the class VH5Dataset method info.

public void info(H5CompoundDS ds) throws Exception {
    Datatype dt = ds.getDatatype();
    String[] mn = ds.getMemberNames();
    System.out.println(ArrayUtils.toString(mn));
    System.out.println(dt.getFullName());
    System.out.println(dt.getDatatypeDescription());
    Object obj = ds.read();
    Collection<?> coll = BeanUtils.downcast(Collection.class, obj);
    VCAssert.assertTrue(coll.size() == mn.length, "collection matches names");
    int i = 0;
    for (Object o : coll) {
        System.out.println(mn[i++] + " ");
        analyze(o);
    }
}

Example 5 with H5CompoundDS

use of ncsa.hdf.object.h5.H5CompoundDS in project vcell by virtualcell.

the class SimulationDataSpatialHdf5 method readMeshFile.

public static ChomboMesh readMeshFile(File chomboMeshFile) throws Exception {
    // if (chomboMesh != null)
    // {
    // return;
    // }
    ChomboMesh chomboMesh = new ChomboMesh();
    // File mfile = new File(userDirectory, getMeshFileName());
    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 = 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();
        Object value = attr.getValue();
        if (attrName.equals(MESH_ATTR_DIMENSION)) {
            chomboMesh.dimension = ((int[]) value)[0];
        } else {
            String[] valueStrArray = (String[]) value;
            String value0 = valueStrArray[0];
            StringTokenizer st = new StringTokenizer(value0, "{,} ");
            List<Double> valueList = new ArrayList<Double>();
            while (st.hasMoreTokens()) {
                String token = st.nextToken();
                valueList.add(Double.parseDouble(token));
            }
            if (attrName.equals(MESH_ATTR_DX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.dx[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_EXTENT)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.extent[i] = valueList.get(i);
                }
            } else if (attrName.equals(MESH_ATTR_NX)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.nx[i] = valueList.get(i).intValue();
                }
            } else if (attrName.equals(MESH_ATTR_ORIGIN)) {
                for (int i = 0; i < valueList.size(); ++i) {
                    chomboMesh.origin[i] = valueList.get(i);
                }
            }
        }
    }
    List<HObject> memberList = meshGroup.getMemberList();
    for (HObject member : memberList) {
        if (member instanceof Dataset) {
            Dataset dataset = (Dataset) member;
            Vector vectValues = (Vector) dataset.read();
            String name = dataset.getName();
            if (name.equals(BOXES_DATASET)) {
            // not needed right now
            } else if (name.equals(METRICS_DATASET)) {
                H5CompoundDS compoundDataSet = (H5CompoundDS) dataset;
                chomboMesh.metricsColumnNames = compoundDataSet.getMemberNames();
                int c = -1;
                int[] index = (int[]) vectValues.get(++c);
                int[] i = (int[]) vectValues.get(++c);
                int[] j = (int[]) vectValues.get(++c);
                int[] k = null;
                if (chomboMesh.dimension == 3) {
                    k = (int[]) vectValues.get(++c);
                }
                double[] x = (double[]) vectValues.get(++c);
                double[] y = (double[]) vectValues.get(++c);
                double[] z = null;
                if (chomboMesh.dimension == 3) {
                    z = (double[]) vectValues.get(++c);
                }
                double[] normalx = (double[]) vectValues.get(++c);
                double[] normaly = (double[]) vectValues.get(++c);
                double[] normalz = null;
                if (chomboMesh.dimension == 3) {
                    normalz = (double[]) vectValues.get(++c);
                }
                double[] volFrac = (double[]) vectValues.get(++c);
                double[] areaFrac = (double[]) vectValues.get(++c);
                for (int n = 0; n < index.length; ++n) {
                    ChomboMeshMetricsEntry entry = new ChomboMeshMetricsEntry(index[n], i[n], j[n], k == null ? 0 : k[n], x[n], y[n], z == null ? 0 : z[n], normalx[n], normaly[n], normalz == null ? 0 : normalz[n], volFrac[n], areaFrac[n]);
                    chomboMesh.metrics.add(entry);
                }
            } else if (name.equals(SURFACE_DATASET)) {
            // not needed right now
            } else if (name.equals(SLICE_VIEW_DATASET)) {
            // not needed right now
            }
        }
    }
    return chomboMesh;
}