216bff5778
* OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace
377 lines
12 KiB
Java
377 lines
12 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
|
|
* 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 create and extend an unlimited
|
|
dataset. The program first writes integers to a dataset
|
|
with dataspace dimensions of DIM_XxDIM_Y, then closes the
|
|
file. Next, it reopens the file, reads back the data,
|
|
outputs it to the screen, extends the dataset, and writes
|
|
new data to the entire extended dataset. Finally it
|
|
reopens the file again, reads back the data, and utputs it
|
|
to the screen.
|
|
************************************************************/
|
|
package examples.datasets;
|
|
|
|
import hdf.hdf5lib.H5;
|
|
import hdf.hdf5lib.HDF5Constants;
|
|
|
|
public class H5Ex_D_UnlimitedMod {
|
|
private static String FILENAME = "H5Ex_D_UnlimitedMod.h5";
|
|
private static String DATASETNAME = "DS1";
|
|
private static final int DIM_X = 4;
|
|
private static final int DIM_Y = 7;
|
|
private static final int EDIM_X = 6;
|
|
private static final int EDIM_Y = 10;
|
|
private static final int CHUNK_X = 4;
|
|
private static final int CHUNK_Y = 4;
|
|
private static final int RANK = 2;
|
|
private static final int NDIMS = 2;
|
|
|
|
private static void writeUnlimited() {
|
|
long file_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dcpl_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataset_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = { DIM_X, DIM_Y };
|
|
long[] chunk_dims = { CHUNK_X, CHUNK_Y };
|
|
long[] maxdims = { HDF5Constants.H5S_UNLIMITED, HDF5Constants.H5S_UNLIMITED };
|
|
int[][] dset_data = new int[DIM_X][DIM_Y];
|
|
|
|
// Initialize the dataset.
|
|
for (int indx = 0; indx < DIM_X; indx++)
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
dset_data[indx][jndx] = indx * jndx - jndx;
|
|
|
|
// 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 dataspace with unlimited dimensions.
|
|
try {
|
|
dataspace_id = H5.H5Screate_simple(RANK, dims, maxdims);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Create the dataset creation property list.
|
|
try {
|
|
dcpl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Set the chunk size.
|
|
try {
|
|
if (dcpl_id >= 0)
|
|
H5.H5Pset_chunk(dcpl_id, NDIMS, chunk_dims);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Create the unlimited dataset.
|
|
try {
|
|
if ((file_id >= 0) && (dataspace_id >= 0) && (dcpl_id >= 0))
|
|
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
|
|
HDF5Constants.H5P_DEFAULT, dcpl_id, HDF5Constants.H5P_DEFAULT);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Write the data to the dataset.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// End access to the dataset and release resources used by it.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dclose(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sclose(dataspace_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dcpl_id >= 0)
|
|
H5.H5Pclose(dcpl_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 extendUnlimited() {
|
|
long file_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataset_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = { DIM_X, DIM_Y };
|
|
long[] extdims = { EDIM_X, EDIM_Y };
|
|
int[][] dset_data;
|
|
int[][] extend_dset_data = new int[EDIM_X][EDIM_Y];
|
|
|
|
// Open an existing file.
|
|
try {
|
|
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDWR, 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();
|
|
}
|
|
|
|
// Get dataspace and allocate memory for read buffer. This is a
|
|
// two dimensional dataset so the dynamic allocation must be done
|
|
// in steps.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
dataspace_id = H5.H5Dget_space(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Allocate array of pointers to rows.
|
|
dset_data = new int[(int) dims[0]][(int) dims[1]];
|
|
|
|
// Read the data using the default properties.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Output the data to the screen.
|
|
System.out.println("Dataset before extension:");
|
|
for (int indx = 0; indx < DIM_X; indx++) {
|
|
System.out.print(" [ ");
|
|
for (int jndx = 0; jndx < DIM_Y; jndx++)
|
|
System.out.print(dset_data[indx][jndx] + " ");
|
|
System.out.println("]");
|
|
}
|
|
System.out.println();
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sclose(dataspace_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Extend the dataset.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dset_extent(dataset_id, extdims);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Retrieve the dataspace for the newly extended dataset.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
dataspace_id = H5.H5Dget_space(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Initialize data for writing to the extended dataset.
|
|
for (int indx = 0; indx < EDIM_X; indx++)
|
|
for (int jndx = 0; jndx < EDIM_Y; jndx++)
|
|
extend_dset_data[indx][jndx] = jndx;
|
|
|
|
// Write the data tto the extended dataset.
|
|
try {
|
|
if ((dataspace_id >= 0) && (dataset_id >= 0))
|
|
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, dataspace_id,
|
|
HDF5Constants.H5P_DEFAULT, extend_dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// End access to the dataset and release resources used by it.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dclose(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sclose(dataspace_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 readUnlimited() {
|
|
long file_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataspace_id = HDF5Constants.H5I_INVALID_HID;
|
|
long dataset_id = HDF5Constants.H5I_INVALID_HID;
|
|
long[] dims = { DIM_X, DIM_Y };
|
|
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();
|
|
}
|
|
|
|
// Get dataspace and allocate memory for the read buffer as before.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
dataspace_id = H5.H5Dget_space(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
// Allocate array of pointers to rows.
|
|
dset_data = new int[(int) dims[0]][(int) dims[1]];
|
|
|
|
// Read the data using the default properties.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
|
|
HDF5Constants.H5P_DEFAULT, dset_data);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
// Output the data to the screen.
|
|
System.out.println("Dataset after extension:");
|
|
for (int indx = 0; indx < dims[0]; indx++) {
|
|
System.out.print(" [ ");
|
|
for (int jndx = 0; jndx < dims[1]; jndx++)
|
|
System.out.print(dset_data[indx][jndx] + " ");
|
|
System.out.println("]");
|
|
}
|
|
System.out.println();
|
|
|
|
// End access to the dataset and release resources used by it.
|
|
try {
|
|
if (dataset_id >= 0)
|
|
H5.H5Dclose(dataset_id);
|
|
}
|
|
catch (Exception e) {
|
|
e.printStackTrace();
|
|
}
|
|
|
|
try {
|
|
if (dataspace_id >= 0)
|
|
H5.H5Sclose(dataspace_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_D_UnlimitedMod.writeUnlimited();
|
|
H5Ex_D_UnlimitedMod.extendUnlimited();
|
|
H5Ex_D_UnlimitedMod.readUnlimited();
|
|
}
|
|
|
|
}
|