Examples with H5ScalarDS ncsa.hdf.object.h5.H5ScalarDS used on opensource projects

Example 1 with H5ScalarDS

use of ncsa.hdf.object.h5.H5ScalarDS in project vcell by virtualcell.

the class VH5Dataset method info.

public static void info(H5ScalarDS ds) throws Exception {
    Datatype dt = ds.getDatatype();
    System.out.println(dt.getFullName());
    System.out.println(dt.getDatatypeDescription());
    int n = dt.toNative();
    Datatype nt = new H5Datatype(n);
    // dt = dt.getBasetype();
    System.out.println(nt.getFullName());
    System.out.println(nt.getDatatypeDescription());
    System.out.println(H5Client.parseMeta(dt));
// ds.init();
// int did = ds.open();
// ds.read();
// 
// int cdt = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND,128);
// int vtype = H5.H5Tvlen_create(cdt);
// int ndims = ds.getRank();
// long dims[] = new long[ndims];
// long maxdims[] = new long[ndims];
// int space = H5.H5Dget_space(did);
// H5.H5Sget_simple_extent_dims(space, dims,maxdims);
// System.out.println(StringUtils.join(dims));
// long bsize = H5.H5Dvlen_get_buf_size_long(did,vtype,space);
// 
// double bdata[][] = new double[2][(int)dims[0]];
// int status = H5.H5Dread(did,vtype,HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL,HDF5Constants.H5P_DEFAULT,bdata);
// System.out.println(status);
}

Example 2 with H5ScalarDS

use of ncsa.hdf.object.h5.H5ScalarDS 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 3 with H5ScalarDS

use of ncsa.hdf.object.h5.H5ScalarDS 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 4 with H5ScalarDS

use of ncsa.hdf.object.h5.H5ScalarDS in project vcell by virtualcell.

the class DataSetControllerImpl method processDims.

private static void processDims(HObject hObject, DataProcessingHelper dataProcessingHelper, boolean bInfoOnly) throws Exception {
    H5ScalarDS h5ScalarDS = (H5ScalarDS) hObject;
    h5ScalarDS.init();
    dataProcessingHelper.tempDims = h5ScalarDS.getDims();
    // make sure all dimensions are selected for loading if 3D
    // note: for 3D, only 1st slice selected by default
    long[] selectedDims = h5ScalarDS.getSelectedDims();
    if (selectedDims != null && selectedDims.length > 2) {
        // changes internal class variable used during read
        selectedDims[2] = dataProcessingHelper.tempDims[2];
    }
    if (!bInfoOnly) {
        // load all data
        dataProcessingHelper.tempData = h5ScalarDS.read();
    }
    if (dataProcessingHelper.tempDims != null) {
        if (dataProcessingHelper.tempDims.length > 1) {
            // For HDF5View (x stored in index 1) and (y stored in index 0) so must switch back to normal assumption
            long dimsY = dataProcessingHelper.tempDims[0];
            dataProcessingHelper.tempDims[0] = dataProcessingHelper.tempDims[1];
            dataProcessingHelper.tempDims[1] = dimsY;
        }
    // //uncomment for Debug
    // System.out.print(" dims=(");
    // for (int j = 0; j < dataProcessingHelper.tempDims.length; j++) {
    // System.out.print((j>0?"x":"")+dataProcessingHelper.tempDims[j]);
    // }
    // System.out.print(")");
    }
}

Example 5 with H5ScalarDS

use of ncsa.hdf.object.h5.H5ScalarDS in project vcell by virtualcell.

the class MovingBoundaryReader method getBoundaryIndexes.

public int[] getBoundaryIndexes(int timeIndex) {
    try {
        VCAssert.assertTrue(timeIndex >= 0, "negative time index");
        validateTimeIndex(timeIndex);
        VH5TypedPath<H5ScalarDS> path = new VH5TypedPath<>(root, H5ScalarDS.class, "boundaries");
        H5ScalarDS hsd = path.get();
        hsd.init();
        long[] start = hsd.getStartDims();
        long[] stride = hsd.getStride();
        long[] sdims = hsd.getSelectedDims();
        stride[0] = 1;
        start[0] = timeIndex;
        sdims[0] = 1;
        String[] data = (String[]) hsd.read();
        String blob = data[0];
        return getPointIndexes(blob, 0);
    } catch (Exception e) {
        throw new RuntimeException("Exception building outer boundary indexes", e);
    }
}