ncsa.hdf.object.h5.H5Group Maven / Gradle / Ivy
/*****************************************************************************
* Copyright by The HDF Group. *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of the HDF Java Products distribution. *
* The full 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. *
* Or, see http://hdfgroup.org/products/hdf-java/doc/Copyright.html. *
* If you do not have access to either file, you may request a copy from *
* [email protected]. *
****************************************************************************/
package ncsa.hdf.object.h5;
import java.util.List;
import java.util.Vector;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.hdf5lib.HDFNativeData;
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
import ncsa.hdf.hdf5lib.structs.H5G_info_t;
import ncsa.hdf.hdf5lib.structs.H5O_info_t;
import ncsa.hdf.object.Attribute;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.Group;
import ncsa.hdf.object.HObject;
/**
* An H5Group object represents an existing HDF5 group in file.
*
* In HDF5, every object has at least one name. An HDF5 group is used to store a
* set of the names together in one place, i.e. a group. The general structure
* of a group is similar to that of the UNIX file system in that the group may
* contain references to other groups or data objects just as the UNIX directory
* may contain sub-directories or files.
*
* For more information on HDF5 Groups,
*
* @see HDF5 User's Guide
*
* @version 1.1 9/4/2007
* @author Peter X. Cao
*/
public class H5Group extends Group {
/**
*
*/
private static final long serialVersionUID = -951164512330444150L;
/**
* The list of attributes of this data object. Members of the list are
* instance of Attribute.
*/
protected List attributeList;
private int nAttributes = -1;
private H5O_info_t obj_info;
/**
* Constructs an HDF5 group with specific name, path, and parent.
*
*
* @param theFile
* the file which containing the group.
* @param name
* the name of this group, e.g. "grp01".
* @param path
* the full path of this group, e.g. "/groups/".
* @param parent
* the parent of this group.
*/
public H5Group(FileFormat theFile, String name, String path, Group parent) {
this(theFile, name, path, parent, null);
}
/**
* @deprecated Not for public use in the future.
* Using {@link #H5Group(FileFormat, String, String, Group)}
*/
@Deprecated
public H5Group(FileFormat theFile, String name, String path, Group parent, long[] oid) {
super(theFile, name, path, parent, oid);
nMembersInFile = -1;
obj_info = new H5O_info_t(-1L, -1L, 0, 0, -1L, 0L, 0L, 0L, 0L, null, null, null);
if ((oid == null) && (theFile != null)) {
// retrieve the object ID
try {
byte[] ref_buf = H5.H5Rcreate(theFile.getFID(), this.getFullName(), HDF5Constants.H5R_OBJECT, -1);
this.oid = new long[1];
this.oid[0] = HDFNativeData.byteToLong(ref_buf, 0);
}
catch (Exception ex) {
this.oid = new long[1];
this.oid[0] = 0;
}
}
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.DataFormat#hasAttribute()
*/
public boolean hasAttribute() {
obj_info.num_attrs = nAttributes;
if (obj_info.num_attrs < 0) {
int gid = open();
if (gid > 0) {
try {
obj_info = H5.H5Oget_info(gid);
}
catch (Exception ex) {
obj_info.num_attrs = 0;
}
close(gid);
}
}
return (obj_info.num_attrs > 0);
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.Group#getNumberOfMembersInFile()
*/
@Override
public int getNumberOfMembersInFile() {
if (nMembersInFile < 0) {
int gid = open();
if (gid > 0) {
try {
H5G_info_t group_info = null;
group_info = H5.H5Gget_info(gid);
nMembersInFile = (int) group_info.nlinks;
}
catch (Exception ex) {
nMembersInFile = 0;
}
close(gid);
}
}
return nMembersInFile;
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.Group#clear()
*/
@Override
public void clear() {
super.clear();
if (attributeList != null) {
((Vector) attributeList).setSize(0);
}
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.DataFormat#getMetadata()
*/
public List getMetadata() throws HDF5Exception {
return this.getMetadata(fileFormat.getIndexType(null), fileFormat.getIndexOrder(null));
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.DataFormat#getMetadata(int...)
*/
public List getMetadata(int... attrPropList) throws HDF5Exception {
if (attributeList == null) {
int gid = open();
int indxType = fileFormat.getIndexType(null);
int order = fileFormat.getIndexOrder(null);
if (attrPropList.length > 0) {
indxType = attrPropList[0];
if (attrPropList.length > 1) {
order = attrPropList[1];
}
}
try {
attributeList = H5File.getAttribute(gid, indxType, order);
}
finally {
close(gid);
}
}
try {
this.linkTargetObjName = H5File.getLinkTargetName(this);
}
catch (Exception ex) {
}
return attributeList;
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.DataFormat#writeMetadata(java.lang.Object)
*/
public void writeMetadata(Object info) throws Exception {
// only attribute metadata is supported.
if (!(info instanceof Attribute)) {
return;
}
boolean attrExisted = false;
Attribute attr = (Attribute) info;
String name = attr.getName();
if (attributeList == null) {
this.getMetadata();
}
if (attributeList != null) attrExisted = attributeList.contains(attr);
getFileFormat().writeAttribute(this, attr, attrExisted);
// add the new attribute into attribute list
if (!attrExisted) {
attributeList.add(attr);
nAttributes = attributeList.size();
}
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.DataFormat#removeMetadata(java.lang.Object)
*/
public void removeMetadata(Object info) throws HDF5Exception {
// only attribute metadata is supported.
if (!(info instanceof Attribute)) {
return;
}
Attribute attr = (Attribute) info;
int gid = open();
try {
H5.H5Adelete(gid, attr.getName());
List attrList = getMetadata();
attrList.remove(attr);
nAttributes = attributeList.size();
}
finally {
close(gid);
}
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.HObject#open()
*/
@Override
public int open() {
int gid = -1;
try {
if (isRoot()) {
gid = H5.H5Gopen(getFID(), separator, HDF5Constants.H5P_DEFAULT);
}
else {
gid = H5.H5Gopen(getFID(), getPath() + getName(), HDF5Constants.H5P_DEFAULT);
}
}
catch (HDF5Exception ex) {
gid = -1;
}
return gid;
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.HObject#close(int)
*/
@Override
public void close(int gid) {
try {
H5.H5Gclose(gid);
}
catch (HDF5Exception ex) {}
}
/**
* Creates a new group with a name in a group and with the group creation
* properties specified in gplist.
*
* The gplist contains a sequence of group creation property list
* identifiers, lcpl, gcpl, gapl. It allows the user to create a group with
* group creation properties. It will close the group creation properties
* specified in gplist.
*
* @see ncsa.hdf.hdf5lib.H5#H5Gcreate(int, String, int, int, int) for the
* order of property list identifiers.
*
* @param name
* The name of a new group.
* @param pgroup
* The parent group object.
* @param gplist
* The group creation properties, in which the order of the
* properties conforms the HDF5 library API, H5Gcreate(), i.e.
* lcpl, gcpl and gapl, where
*
* - lcpl : Property list for link creation
- gcpl : Property
* list for group creation
- gapl : Property list for group
* access
*
*
* @return The new group if successful; otherwise returns null.
*/
public static H5Group create(String name, Group pgroup, int... gplist) throws Exception {
H5Group group = null;
String fullPath = null;
int lcpl = HDF5Constants.H5P_DEFAULT;
int gcpl = HDF5Constants.H5P_DEFAULT;
int gapl = HDF5Constants.H5P_DEFAULT;
if (gplist.length > 0) {
lcpl = gplist[0];
if (gplist.length > 1) {
gcpl = gplist[1];
if (gplist.length > 2) gapl = gplist[2];
}
}
if ((name == null) || (pgroup == null)) {
System.err.println("(name == null) || (pgroup == null)");
return null;
}
H5File file = (H5File) pgroup.getFileFormat();
if (file == null) {
System.err.println("Could not get file that contains object");
return null;
}
String path = HObject.separator;
if (!pgroup.isRoot()) {
path = pgroup.getPath() + pgroup.getName() + HObject.separator;
if (name.endsWith("/")) {
name = name.substring(0, name.length() - 1);
}
int idx = name.lastIndexOf("/");
if (idx >= 0) {
name = name.substring(idx + 1);
}
}
fullPath = path + name;
// create a new group and add it to the parent node
int gid = H5.H5Gcreate(file.open(), fullPath, lcpl, gcpl, gapl);
try {
H5.H5Gclose(gid);
}
catch (Exception ex) {
}
byte[] ref_buf = H5.H5Rcreate(file.open(), fullPath, HDF5Constants.H5R_OBJECT, -1);
long l = HDFNativeData.byteToLong(ref_buf, 0);
long[] oid = { l };
group = new H5Group(file, name, path, pgroup, oid);
if (group != null) {
pgroup.addToMemberList(group);
}
if (gcpl > 0) {
try {
H5.H5Pclose(gcpl);
}
catch (final Exception ex) {
}
}
return group;
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.HObject#setName(java.lang.String)
*/
@Override
public void setName(String newName) throws Exception {
H5File.renameObject(this, newName);
super.setName(newName);
}
/*
* (non-Javadoc)
*
* @see ncsa.hdf.object.HObject#setPath(java.lang.String)
*/
@Override
public void setPath(String newPath) throws Exception {
super.setPath(newPath);
List members = this.getMemberList();
if (members == null) {
return;
}
int n = members.size();
HObject obj = null;
for (int i = 0; i < n; i++) {
obj = (HObject) members.get(i);
obj.setPath(getPath() + getName() + HObject.separator);
}
}
}