ucar.nc2.jni.netcdf

Class Nc4Iosp

java.lang.Object

ucar.nc2.iosp.AbstractIOServiceProvider

ucar.nc2.jni.netcdf.Nc4Iosp

All Implemented Interfaces:

ucar.nc2.iosp.IOServiceProvider, ucar.nc2.iosp.IOServiceProviderWriter

public class Nc4Iosp
extends ucar.nc2.iosp.AbstractIOServiceProvider
implements ucar.nc2.iosp.IOServiceProviderWriter

IOSP for reading netcdf files through jni interface to netcdf4 library

Since:

Oct 30, 2008

See Also:

"http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-c.html", "http://earthdata.nasa.gov/sites/default/files/field/document/ESDS-RFC-022v1.pdf", "http://www.unidata.ucar.edu/software/netcdf/docs/faq.html#How-can-I-convert-HDF5-files-into-netCDF-4-files" hdf5 features not supported, "http://www.unidata.ucar.edu/software/netcdf/win_netcdf/"

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	DEBUG
protected static String	DEFAULTNETCDF4LIBNAME
static String	JNA_LOG_LEVEL
static String	JNA_PATH
static String	JNA_PATH_ENV
static int	NC_TURN_OFF_LOGGING
static String	TRANSLATE_NC4
static String	TRANSLATE_NONE
static String	TRANSLATECONTROL
static String	UCARTAGOPAQUE
static String	UCARTAGORIGTYPE
static String	UCARTAGVLEN

Fields inherited from class ucar.nc2.iosp.AbstractIOServiceProvider

location, ncfile, raf, rafOrder

Constructor Summary

Constructors

Constructor and Description
Nc4Iosp()
Nc4Iosp(ucar.nc2.NetcdfFileWriter.Version version)

Method Summary

Modifier and Type	Method and Description
int	appendStructureData(ucar.nc2.Structure s, ucar.ma2.StructureData sdata)
void	close()
void	create(String filename, ucar.nc2.NetcdfFile ncfile, int extra, long preallocateSize, boolean largeFile)
static void	dumpbytes(byte[] bytes, int start, int len, String tag)
void	flush()
static Nc4prototypes	getCLibrary()
String	getFileTypeDescription()
String	getFileTypeId()
static long	getNativeAddr(int pos, ByteBuffer buf)
static boolean	isClibraryPresent() Test if the netcdf C library is present and loaded
boolean	isValidFile(ucar.unidata.io.RandomAccessFile raf) Checks whether raf is a valid file NetCDF-4 file.
protected static String	nullify(String s) Convert a zero-length string to null
void	open(ucar.unidata.io.RandomAccessFile raf, ucar.nc2.NetcdfFile ncfile, ucar.nc2.util.CancelTask cancelTask)
void	openForWriting(ucar.unidata.io.RandomAccessFile raf, ucar.nc2.NetcdfFile ncfile, ucar.nc2.util.CancelTask cancelTask)
ucar.ma2.Array	readData(ucar.nc2.Variable v2, ucar.ma2.Section section)
boolean	rewriteHeader(boolean largeFile)
Object	sendIospMessage(Object message)
Nc4Iosp	setAddReserved(boolean tf)
void	setChunker(ucar.nc2.write.Nc4Chunking chunker)
static void	setDebugFlags(ucar.nc2.util.DebugFlags flags)
void	setFill(boolean fill)
static void	setLibraryAndPath(String jna_path, String lib_name) set the path and name of the netcdf c library.
static int	setLogLevel(int level) Set the log level for loaded library.
static String	show(SizeT[] inta)
void	updateAttribute(ucar.nc2.Variable v2, ucar.nc2.Attribute att)
static void	useHdfEos(boolean val)
void	writeData(ucar.nc2.Variable v2, ucar.ma2.Section section, ucar.ma2.Array values)

Methods inherited from class ucar.nc2.iosp.AbstractIOServiceProvider

getDetailInfo, getFileTypeVersion, getLastModified, getStructureIterator, reacquire, readSection, readToByteChannel, readToOutputStream, release, streamToByteChannel, syncExtend, toStringDebug

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ucar.nc2.iosp.IOServiceProvider

getDetailInfo, getFileTypeVersion, getStructureIterator, reacquire, readSection, readToByteChannel, readToOutputStream, release, streamToByteChannel, syncExtend, toStringDebug

Field Detail

DEBUG

public static final boolean DEBUG

See Also:

Constant Field Values

NC_TURN_OFF_LOGGING

public static int NC_TURN_OFF_LOGGING

JNA_PATH

public static final String JNA_PATH

See Also:

Constant Field Values

JNA_PATH_ENV

public static final String JNA_PATH_ENV

See Also:

Constant Field Values

JNA_LOG_LEVEL

public static final String JNA_LOG_LEVEL

See Also:

Constant Field Values

TRANSLATECONTROL

public static final String TRANSLATECONTROL

See Also:

Constant Field Values

TRANSLATE_NONE

public static final String TRANSLATE_NONE

See Also:

Constant Field Values

TRANSLATE_NC4

public static final String TRANSLATE_NC4

See Also:

Constant Field Values

UCARTAGOPAQUE

public static final String UCARTAGOPAQUE

See Also:

Constant Field Values

UCARTAGVLEN

public static final String UCARTAGVLEN

See Also:

Constant Field Values

UCARTAGORIGTYPE

public static final String UCARTAGORIGTYPE

See Also:

Constant Field Values

DEFAULTNETCDF4LIBNAME

protected static String DEFAULTNETCDF4LIBNAME

Constructor Detail

Nc4Iosp

public Nc4Iosp()

Nc4Iosp

public Nc4Iosp(ucar.nc2.NetcdfFileWriter.Version version)

Method Detail

setLibraryAndPath

public static void setLibraryAndPath(String jna_path,
                                     String lib_name)

set the path and name of the netcdf c library. must be called before load() is called.

Parameters:

jna_path - path to shared libraries

lib_name - library name

isClibraryPresent

public static boolean isClibraryPresent()

Test if the netcdf C library is present and loaded

Returns:

true if present

getCLibrary

public static Nc4prototypes getCLibrary()

setLogLevel

public static int setLogLevel(int level)

Set the log level for loaded library. Do nothing if set_log_level is not available.

nullify

protected static String nullify(String s)

Convert a zero-length string to null

Parameters:

s - the string to check for length

Returns:

null if s.length() == 0, s otherwise

useHdfEos

public static void useHdfEos(boolean val)

setDebugFlags

public static void setDebugFlags(ucar.nc2.util.DebugFlags flags)

setChunker

public void setChunker(ucar.nc2.write.Nc4Chunking chunker)

isValidFile

public boolean isValidFile(ucar.unidata.io.RandomAccessFile raf)
                    throws IOException

Checks whether raf is a valid file NetCDF-4 file. Actually, it checks whether it is a valid HDF-5 file of any type. Furthermore, it checks whether the NetCDF C library is available on the system. If both conditions are satisfied, this method returns true; otherwise it returns false.

Specified by:

isValidFile in interface ucar.nc2.iosp.IOServiceProvider

Parameters:

raf - a file on disk.

Returns:

true if raf is a valid HDF-5 file and the NetCDF C library is available.

Throws:

IOException - if an I/O error occurs.

getFileTypeDescription

public String getFileTypeDescription()

Specified by:

getFileTypeDescription in interface ucar.nc2.iosp.IOServiceProvider

getFileTypeId

public String getFileTypeId()

Specified by:

getFileTypeId in interface ucar.nc2.iosp.IOServiceProvider

close

public void close()
           throws IOException

Specified by:

close in interface ucar.nc2.iosp.IOServiceProvider

Overrides:

close in class ucar.nc2.iosp.AbstractIOServiceProvider

Throws:

IOException

open

public void open(ucar.unidata.io.RandomAccessFile raf,
                 ucar.nc2.NetcdfFile ncfile,
                 ucar.nc2.util.CancelTask cancelTask)
          throws IOException

Specified by:

open in interface ucar.nc2.iosp.IOServiceProvider

Overrides:

open in class ucar.nc2.iosp.AbstractIOServiceProvider

Throws:

IOException

openForWriting

public void openForWriting(ucar.unidata.io.RandomAccessFile raf,
                           ucar.nc2.NetcdfFile ncfile,
                           ucar.nc2.util.CancelTask cancelTask)
                    throws IOException

Specified by:

openForWriting in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

dumpbytes

public static void dumpbytes(byte[] bytes,
                             int start,
                             int len,
                             String tag)

readData

public ucar.ma2.Array readData(ucar.nc2.Variable v2,
                               ucar.ma2.Section section)
                        throws IOException,
                               ucar.ma2.InvalidRangeException

Specified by:

readData in interface ucar.nc2.iosp.IOServiceProvider

Throws:

IOException

ucar.ma2.InvalidRangeException

show

public static String show(SizeT[] inta)

create

public void create(String filename,
                   ucar.nc2.NetcdfFile ncfile,
                   int extra,
                   long preallocateSize,
                   boolean largeFile)
            throws IOException

Specified by:

create in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

writeData

public void writeData(ucar.nc2.Variable v2,
                      ucar.ma2.Section section,
                      ucar.ma2.Array values)
               throws IOException,
                      ucar.ma2.InvalidRangeException

Specified by:

writeData in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

ucar.ma2.InvalidRangeException

appendStructureData

public int appendStructureData(ucar.nc2.Structure s,
                               ucar.ma2.StructureData sdata)
                        throws IOException,
                               ucar.ma2.InvalidRangeException

Specified by:

appendStructureData in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

ucar.ma2.InvalidRangeException

flush

public void flush()
           throws IOException

Specified by:

flush in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

setAddReserved

public Nc4Iosp setAddReserved(boolean tf)

setFill

public void setFill(boolean fill)

Specified by:

setFill in interface ucar.nc2.iosp.IOServiceProviderWriter

rewriteHeader

public boolean rewriteHeader(boolean largeFile)
                      throws IOException

Specified by:

rewriteHeader in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

updateAttribute

public void updateAttribute(ucar.nc2.Variable v2,
                            ucar.nc2.Attribute att)
                     throws IOException

Specified by:

updateAttribute in interface ucar.nc2.iosp.IOServiceProviderWriter

Throws:

IOException

getNativeAddr

public static long getNativeAddr(int pos,
                                 ByteBuffer buf)

sendIospMessage

public Object sendIospMessage(Object message)

Specified by:

sendIospMessage in interface ucar.nc2.iosp.IOServiceProvider

Overrides:

sendIospMessage in class ucar.nc2.iosp.AbstractIOServiceProvider