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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/************************************************************
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.
************************************************************/
import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
public class H5Ex_T_ArrayAttribute {
private static String FILENAME = "H5Ex_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 RANK = 1;
private static final int NDIMS = 2;
private static void CreateDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long filetype_id = HDF5Constants.H5I_INVALID_HID;
long memtype_id = HDF5Constants.H5I_INVALID_HID;
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM0};
long[] adims = {ADIM0, ADIM1};
int[][][] dset_data = new int[DIM0][ADIM0][ADIM1];
// 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_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Create array datatypes for file.
try {
filetype_id = H5.H5Tarray_create(HDF5Constants.H5T_STD_I64LE, NDIMS, adims);
}
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 {
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
if (dataspace_id >= 0) {
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
H5.H5Sclose(dataspace_id);
dataspace_id = HDF5Constants.H5I_INVALID_HID;
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute and write the array data to it.
try {
if ((dataset_id >= 0) && (dataspace_id >= 0) && (filetype_id >= 0))
attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, filetype_id, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
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)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_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 {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset()
{
long file_id = HDF5Constants.H5I_INVALID_HID;
long filetype_id = HDF5Constants.H5I_INVALID_HID;
long memtype_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = {DIM0};
long[] adims = {ADIM0, ADIM1};
int[][][] dset_data;
// Open an existing file.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
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)
H5.H5Dclose(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 {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args)
{
H5Ex_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().
H5Ex_T_ArrayAttribute.ReadDataset();
}
}
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