ncsa.hdf.object.nc2.NC2File Maven / Gradle / Ivy
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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 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.nc2;
import java.io.*;
import java.util.*;
import javax.swing.tree.*;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ncsa.hdf.object.Dataset;
import ncsa.hdf.object.Datatype;
import ncsa.hdf.object.FileFormat;
import ncsa.hdf.object.Group;
import ncsa.hdf.object.HObject;
/**
* This class provides file level APIs. File access APIs include retrieving the
* file hierarchy, opening and closing file, and writing file content to disk.
*
* @version 2.4 9/4/2007
* @author Peter X. Cao
*/
public class NC2File extends FileFormat
{
public static final long serialVersionUID = HObject.serialVersionUID;
/**
* file identifier for the open file.
*/
private int fid;
/**
* the file access flag.
*/
private int flag;
/**
* The root node of the file hierearchy.
*/
private MutableTreeNode rootNode;
/** the netcdf file */
private NetcdfFile ncFile;
private static boolean isFileOpen;
/**
* Constructs an empty NC2File with read-only access.
*/
public NC2File() {
this("");
}
/**
* Constructs an NC2File object of given file name with read-only access.
*/
public NC2File(String pathname) {
super(pathname);
isReadOnly = true;
isFileOpen = false;
this.fid = -1;
try { ncFile = new NetcdfFile(fullFileName); }
catch (Exception ex) {}
}
/**
* Checks if the given file format is a NetCDF file.
*
* @param fileformat the fileformat to be checked.
* @return true if the given file is an NetCDF file; otherwise returns false.
*/
public boolean isThisType(FileFormat fileformat) {
return (fileformat instanceof NC2File);
}
/**
* Checks if a given file is a NetCDF file.
*
* @param filename the file to be checked.
* @return true if the given file is an NetCDF file; otherwise returns false.
*/
public boolean isThisType(String filename)
{
boolean is_netcdf = false;
RandomAccessFile raf = null;
try { raf = new RandomAccessFile(filename, "r"); }
catch (Exception ex) { raf = null; }
if (raf == null) {
try { raf.close();} catch (Exception ex) {}
return false;
}
byte[] header = new byte[4];
try { raf.read(header); }
catch (Exception ex) { header = null; }
if (header != null)
{
if (
// netCDF
((header[0]==67) &&
(header[1]==68) &&
(header[2]==70) &&
(header[3]<4)) ) {
is_netcdf = true;
} else {
is_netcdf = false;
}
}
try { raf.close();} catch (Exception ex) {}
return is_netcdf;
}
/**
* Creates an NC2File instance with specified file name and READ access.
*
* Regardless of specified access, the NC2File implementation uses
* READ.
*
* @see ncsa.hdf.object.FileFormat#createInstance(java.lang.String, int)
*/
public FileFormat createInstance(String filename, int access)
throws Exception
{
return new NC2File(filename);
}
// Implementing FileFormat
public int open() throws Exception {
if (!isFileOpen) {
isFileOpen = true;
rootNode = loadTree();
}
return 0;
}
private MutableTreeNode loadTree() {
long[] oid = {0};
NC2Group rootGroup = new NC2Group(
this,
getName(), // set the node name to the file name
null, // root node does not have a parent path
null, // root node does not have a parent node
oid);
DefaultMutableTreeNode root = new DefaultMutableTreeNode(rootGroup) {
public static final long serialVersionUID = HObject.serialVersionUID;
public boolean isLeaf() { return false; }
};
if (ncFile == null) {
return root;
}
Iterator it = ncFile.getVariables().iterator();
Variable ncDataset = null;
DefaultMutableTreeNode node = null;
NC2Dataset d = null;
while (it.hasNext()) {
ncDataset = (Variable)it.next();
oid[0] = ncDataset.hashCode();
d = new NC2Dataset(this, ncDataset, oid);
node = new DefaultMutableTreeNode(d);
root.add( node );
rootGroup.addToMemberList(d);
}
return root;
}
// Implementing FileFormat
public void close() throws IOException {
if (ncFile != null) {
ncFile.close();
}
}
// Implementing FileFormat
public TreeNode getRootNode() {
return rootNode;
}
public NetcdfFile getNetcdfFile() {
return ncFile;
}
// implementing FileFormat
public Group createGroup(String name, Group pgroup) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
// implementing FileFormat
public Datatype createDatatype(
int tclass,
int tsize,
int torder,
int tsign) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
public Datatype createDatatype(
int tclass,
int tsize,
int torder,
int tsign,
String name) throws Exception
{
throw new UnsupportedOperationException("Unsupported operation.");
}
// implementing FileFormat
public HObject createLink(Group parentGroup, String name, HObject currentObj) throws Exception
{
throw new UnsupportedOperationException("createLink() is not supported");
}
// implementing FileFormat
public Dataset createScalarDS(
String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
Object data) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
// implementing FileFormat
public Dataset createImage(
String name,
Group pgroup,
Datatype type,
long[] dims,
long[] maxdims,
long[] chunks,
int gzip,
int ncomp,
int intelace,
Object data) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
// implementing FileFormat
public void delete(HObject obj) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
// implementing FileFormat
public TreeNode copy(HObject srcObj, Group dstGroup, String dstName) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
/** copy a dataset into another group.
* @param srcDataset the dataset to be copied.
* @param pgroup teh group where the dataset is copied to.
* @return the treeNode containing the new copy of the dataset.
*/
private TreeNode copyDataset(Dataset srcDataset, NC2Group pgroup)
throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
private TreeNode copyGroup(NC2Group srcGroup, NC2Group pgroup)
throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
/**
* Copy attributes of the source object to the destination object.
*/
public void copyAttributes(HObject src, HObject dst) {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
/**
* Copy attributes of the source object to the destination object.
*/
public void copyAttributes(int src_id, int dst_id) {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
/**
* Creates a new attribute and attached to the object if attribute does
* not exist. Otherwise, just update the value of the attribute.
*
*
* @param obj the object which the attribute is to be attached to.
* @param attr the atribute to attach.
* @param attrExisted The indicator if the given attribute exists.
* @return true if successful and false otherwise.
*/
public void writeAttribute(HObject obj, ncsa.hdf.object.Attribute attr,
boolean attrExisted) throws Exception {
// not supported
throw new UnsupportedOperationException("Unsupported operation.");
}
/** converts a ucar.nc2.Attribute into an ncsa.hdf.object.Attribute */
public static ncsa.hdf.object.Attribute convertAttribute(ucar.nc2.Attribute netcdfAttr) {
ncsa.hdf.object.Attribute ncsaAttr = null;
if (netcdfAttr == null) {
return null;
}
String attrName = netcdfAttr.getName();
long[] attrDims = {netcdfAttr.getLength()};
Datatype attrType = new NC2Datatype(netcdfAttr.getDataType());
ncsaAttr = new ncsa.hdf.object.Attribute(attrName, attrType, attrDims);
ncsaAttr.setValue(netcdfAttr.getValues());
return ncsaAttr;
}
/**
* Returns the version of the library.
*/
public String getLibversion()
{
String ver = "NetCDF Java (version 2.4)";
return ver;
}
// implementing FileFormat
public HObject get(String path) throws Exception
{
throw new UnsupportedOperationException("get() is not supported");
}
}