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/************************************************************
This example shows how to read and write array datatypes
to an attribute. The program first writes integers arrays
of dimension ADIM0xADIM1 to an attribute with a dataspace
of DIM0, then closes the file. Next, it reopens the
file, reads back the data, and outputs it to the screen.
This file is intended for use with HDF5 Library verion 1.6
************************************************************/
package examples.datatypes;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.object.Attribute;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.h5.H5Datatype;
import ncsa.hdf.object.h5.H5File;
import ncsa.hdf.object.h5.H5ScalarDS;
public class H5ObjectEx_T_ArrayAttribute {
private static String FILENAME = "H5ObjectEx_T_ArrayAttribute.h5";
private static String DATASETNAME = "DS1";
private static String ATTRIBUTENAME = "A1";
private static final int DIM0 = 4;
private static final int ADIM0 = 3;
private static final int ADIM1 = 5;
private static final int NDIMS = 2;
private static void CreateDataset() {
H5File file = null;
H5ScalarDS dset = null;
int filetype_id = -1;
int memtype_id = -1;
int dataset_id = -1;
int attribute_id = -1;
long[] dims = { DIM0 };
long[] adims = { ADIM0, ADIM1 };
int[][][] dset_data = new int[DIM0][ADIM0][ADIM1];
final H5Datatype typeIntArray = new H5Datatype(Datatype.CLASS_ARRAY, 8, Datatype.ORDER_LE, -1);
final H5Datatype typeInt = new H5Datatype(Datatype.CLASS_INTEGER, 4, Datatype.ORDER_LE, -1);
// Initialize data. indx is the element in the dataspace, jndx and kndx the
// elements within the array datatype.
for (int indx = 0; indx < DIM0; indx++)
for (int jndx = 0; jndx < ADIM0; jndx++)
for (int kndx = 0; kndx < ADIM1; kndx++)
dset_data[indx][jndx][kndx] = indx * jndx - jndx * kndx + indx * kndx;
// Create a new file using default properties.
try {
file = new H5File(FILENAME, FileFormat.CREATE);
file.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Create array datatypes for file.
try {
filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, NDIMS, adims);
typeIntArray.fromNative(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Create array datatypes for memory.
try {
memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, NDIMS, adims);
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataset with a scalar dataspace.
try {
dset = (H5ScalarDS) file.createScalarDS(DATASETNAME, null, typeInt, dims, null, null, 0, null);
dataset_id = dset.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute and write the array data to it.
try {
Attribute dataArray = new Attribute(ATTRIBUTENAME, typeIntArray, dims);
dset.writeMetadata(dataArray);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
if (dataset_id >= 0)
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
if ((attribute_id >= 0) && (memtype_id >= 0))
H5.H5Awrite(attribute_id, memtype_id, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
dset.close(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the file type.
try {
if (filetype_id >= 0)
H5.H5Tclose(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset() {
H5File file = null;
H5ScalarDS dset = null;
int filetype_id = -1;
int memtype_id = -1;
int dataset_id = -1;
int attribute_id = -1;
long[] dims = { DIM0 };
long[] adims = { ADIM0, ADIM1 };
int[][][] dset_data;
// Open an existing file.
try {
file = new H5File(FILENAME, FileFormat.READ);
file.open();
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
dset = (H5ScalarDS) file.get(DATASETNAME);
dataset_id = dset.open();
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get the datatype.
try {
if (attribute_id >= 0)
filetype_id = H5.H5Aget_type(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Get the datatype's dimensions.
try {
if (filetype_id >= 0)
H5.H5Tget_array_dims(filetype_id, adims);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
dset_data = new int[(int) dims[0]][(int) (adims[0])][(int) (adims[1])];
// Create array datatypes for memory.
try {
memtype_id = H5.H5Tarray_create(HDF5Constants.H5T_NATIVE_INT, 2, adims);
}
catch (Exception e) {
e.printStackTrace();
}
// Read data.
try {
if ((attribute_id >= 0) && (memtype_id >= 0))
H5.H5Aread(attribute_id, memtype_id, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(ATTRIBUTENAME + " [" + indx + "]:");
for (int jndx = 0; jndx < adims[0]; jndx++) {
System.out.print(" [");
for (int kndx = 0; kndx < adims[1]; kndx++)
System.out.print(dset_data[indx][jndx][kndx] + " ");
System.out.println("]");
}
System.out.println();
}
System.out.println();
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
dset.close(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the file type.
try {
if (filetype_id >= 0)
H5.H5Tclose(filetype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the mem type.
try {
if (memtype_id >= 0)
H5.H5Tclose(memtype_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
file.close();
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
H5ObjectEx_T_ArrayAttribute.CreateDataset();
// Now we begin the read section of this example. Here we assume
// the dataset and array have the same name and rank, but can have
// any size. Therefore we must allocate a new array to read in
// data using malloc().
H5ObjectEx_T_ArrayAttribute.ReadDataset();
}
}
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