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+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * 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 files COPYING and Copyright.html. COPYING can be found at the root *
+ * of the source code distribution tree; Copyright.html can be found at the *
+ * root level of an installed copy of the electronic HDF5 document set and *
+ * is linked from the top-level documents page. It can also be found at *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
+ * access to either file, you may request a copy from help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+import hdf.hdf5lib.H5;
+import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.structs.H5G_info_t;
+import hdf.hdf5lib.structs.H5O_token_t;
+
+/**
+ * <p>
+ * Title: HDF Native Package (Java) Example
+ * </p>
+ * <p>
+ * Description: this example shows how to retrieve HDF file structure using the
+ * "HDF Native Package (Java)". The example created the group structure and
+ * datasets, and print out the file structure:
+ *
+ * <pre>
+ * "/" (root)
+ * integer arrays
+ * 2D 32-bit integer 20x10
+ * 3D unsigned 8-bit integer 20x10x5
+ * float arrays
+ * 2D 64-bit double 20x10
+ * 3D 32-bit float 20x10x5
+ * </pre>
+ *
+ * </p>
+ */
+public class HDF5FileStructure {
+ private static String fname = "HDF5FileStructure.h5";
+
+ private static void FileStructure()
+ {
+ long file_id = HDF5Constants.H5I_INVALID_HID;
+ long group_id = HDF5Constants.H5I_INVALID_HID;
+
+ // create the file and add groups and dataset into the file
+ try {
+ createFile();
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Open file using the default properties.
+ try {
+ file_id = H5.H5Fopen(fname, HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Open the group, obtaining a new handle.
+ try {
+ if (file_id >= 0)
+ group_id = H5.H5Gopen(file_id, "/", HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ try {
+ printGroup(group_id, "/", "");
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the group.
+ try {
+ if (group_id >= 0)
+ H5.H5Gclose(group_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the file.
+ try {
+ if (file_id >= 0)
+ H5.H5Fclose(file_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Recursively print a group and its members.
+ *
+ * @throws Exception
+ */
+ private static void printGroup(long g_id, String gname, String indent) throws Exception
+ {
+ if (g_id < 0)
+ return;
+
+ H5G_info_t members = H5.H5Gget_info(g_id);
+ String objNames[] = new String[(int)members.nlinks];
+ int objTypes[] = new int[(int)members.nlinks];
+ int lnkTypes[] = new int[(int)members.nlinks];
+ H5O_token_t objTokens[] = new H5O_token_t[(int)members.nlinks];
+ int names_found = 0;
+ try {
+ names_found = H5.H5Gget_obj_info_all(g_id, null, objNames, objTypes, lnkTypes, objTokens,
+ HDF5Constants.H5_INDEX_NAME);
+ }
+ catch (Throwable err) {
+ err.printStackTrace();
+ }
+
+ indent += " ";
+ for (int i = 0; i < names_found; i++) {
+ System.out.println(indent + objNames[i]);
+ long group_id = HDF5Constants.H5I_INVALID_HID;
+ if (objTypes[i] == HDF5Constants.H5O_TYPE_GROUP) {
+ // Open the group, obtaining a new handle.
+ try {
+ if (g_id >= 0)
+ group_id = H5.H5Gopen(g_id, objNames[i], HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ if (group_id >= 0)
+ printGroup(group_id, objNames[i], indent);
+
+ // Close the group.
+ try {
+ if (group_id >= 0)
+ H5.H5Gclose(group_id);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * create the file and add groups ans dataset into the file, which is the
+ * same as javaExample.H5DatasetCreate
+ *
+ * @see javaExample.HDF5DatasetCreate
+ * @throws Exception
+ */
+ private static void createFile() throws Exception
+ {
+ long[] dims2D = {20, 10};
+ long[] dims3D = {20, 10, 5};
+ long file_id = HDF5Constants.H5I_INVALID_HID;
+ long dataset_id = HDF5Constants.H5I_INVALID_HID;
+ long dataspace_id1 = HDF5Constants.H5I_INVALID_HID;
+ long dataspace_id2 = HDF5Constants.H5I_INVALID_HID;
+ long group_id1 = HDF5Constants.H5I_INVALID_HID;
+ long group_id2 = HDF5Constants.H5I_INVALID_HID;
+
+ // Create a new file using default properties.
+ try {
+ file_id = H5.H5Fcreate(fname, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Create groups in the file.
+ try {
+ if (file_id >= 0) {
+ group_id1 = H5.H5Gcreate(file_id,
+ "/"
+ + "integer arrays",
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT);
+ group_id1 = H5.H5Gcreate(file_id,
+ "/"
+ + "float arrays",
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT);
+ }
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Create the data space for the datasets.
+ try {
+ dataspace_id1 = H5.H5Screate_simple(2, dims2D, null);
+ dataspace_id2 = H5.H5Screate_simple(3, dims3D, null);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // create 2D 32-bit (4 bytes) integer dataset of 20 by 10
+ try {
+ if ((file_id >= 0) && (dataspace_id1 >= 0))
+ dataset_id =
+ H5.H5Dcreate(file_id,
+ "/"
+ + "integer arrays"
+ + "/"
+ + "2D 32-bit integer 20x10",
+ HDF5Constants.H5T_STD_I32LE, dataspace_id1, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the dataset.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ dataset_id = HDF5Constants.H5I_INVALID_HID;
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // create 3D 8-bit (1 byte) unsigned integer dataset of 20 by 10 by 5
+ try {
+ if ((file_id >= 0) && (dataspace_id2 >= 0))
+ dataset_id =
+ H5.H5Dcreate(file_id,
+ "/"
+ + "integer arrays"
+ + "/"
+ + "3D 8-bit unsigned integer 20x10x5",
+ HDF5Constants.H5T_STD_I64LE, dataspace_id2, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the dataset.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ dataset_id = HDF5Constants.H5I_INVALID_HID;
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // create 2D 64-bit (8 bytes) double dataset of 20 by 10
+ try {
+ if ((file_id >= 0) && (dataspace_id1 >= 0))
+ dataset_id =
+ H5.H5Dcreate(file_id,
+ "/"
+ + "float arrays"
+ + "/"
+ + "2D 64-bit double 20x10",
+ HDF5Constants.H5T_NATIVE_DOUBLE, dataspace_id1, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the dataset.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ dataset_id = HDF5Constants.H5I_INVALID_HID;
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // create 3D 32-bit (4 bytes) float dataset of 20 by 10 by 5
+ try {
+ if ((file_id >= 0) && (dataspace_id2 >= 0))
+ dataset_id =
+ H5.H5Dcreate(file_id,
+ "/"
+ + "float arrays"
+ + "/"
+ + "3D 32-bit float 20x10x5",
+ HDF5Constants.H5T_NATIVE_FLOAT, dataspace_id2, HDF5Constants.H5P_DEFAULT,
+ HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the dataset.
+ try {
+ if (dataset_id >= 0)
+ H5.H5Dclose(dataset_id);
+ dataset_id = HDF5Constants.H5I_INVALID_HID;
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the data space.
+ try {
+ if (dataspace_id1 >= 0)
+ H5.H5Sclose(dataspace_id1);
+ dataspace_id1 = HDF5Constants.H5I_INVALID_HID;
+ if (dataspace_id2 >= 0)
+ H5.H5Sclose(dataspace_id2);
+ dataspace_id2 = HDF5Constants.H5I_INVALID_HID;
+ }
+ catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ // Close the groups.
+ try {
+ if (group_id1 >= 0)
+ H5.H5Gclose(group_id1);
+ if (group_id2 >= 0)
+ H5.H5Gclose(group_id2);
+ }
+ 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) { HDF5FileStructure.FileStructure(); }
+}
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