ucar.nc2.jni.netcdf

Class Nc4Iosp

java.lang.Object

ucar.nc2.iosp.AbstractIOServiceProvider

ucar.nc2.jni.netcdf.Nc4Iosp

All Implemented Interfaces:

IOServiceProvider, IOServiceProviderWriter

public class Nc4Iosp
extends AbstractIOServiceProvider
implements IOServiceProviderWriter

IOSP for reading netcdf files through jni interface to netcdf4 library

Since:

Oct 30, 2008

See Also:

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

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	DEBUG
protected static java.lang.String	DEFAULTNETCDF4LIBNAME
static java.lang.String	JNA_PATH
static java.lang.String	JNA_PATH_ENV

Fields inherited from class ucar.nc2.iosp.AbstractIOServiceProvider

location, ncfile, raf, rafOrder

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
int	appendStructureData(Structure s, StructureData sdata) Append a structureData along the unlimited dimension
void	close() Close the file.
void	create(java.lang.String filename, NetcdfFile ncfile, int extra, long preallocateSize, boolean largeFile) Create new file, populate it from the objects in ncfile.
static void	dumpbytes(byte[] bytes, int start, int len, java.lang.String tag)
void	flush() Flush all data buffers to disk.
java.lang.String	getFileTypeDescription() Get a human-readable description for this file type.
java.lang.String	getFileTypeId() Get a unique id for this file type.
static long	getNativeAddr(int pos, java.nio.ByteBuffer buf)
static boolean	isClibraryPresent() Test if the netcdf C library is present and loaded
boolean	isValidFile(RandomAccessFile raf) Checks whether raf is a valid file NetCDF-4 file.
protected static java.lang.String	nullify(java.lang.String s) Convert a zero-length string to null
void	open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) Open existing file, and populate ncfile with it.
void	openForWriting(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) Open existing file and allow writing.
Array	readData(Variable v2, Section section) Read data from a top level Variable and return a memory resident Array.
boolean	rewriteHeader(boolean largeFile) if theres room before data, rewrite header without moving the data.
void	setChunker(Nc4Chunking chunker)
static void	setDebugFlags(DebugFlags flags)
void	setFill(boolean fill) Set the fill flag.
static void	setLibraryAndPath(java.lang.String jna_path, java.lang.String lib_name) set the path and name of the netcdf c library.
static java.lang.String	show(SizeT[] inta)
void	updateAttribute(Variable v2, Attribute att) Update the value of an existing attribute.
void	writeData(Variable v2, Section section, Array values) Write data into a variable.

Methods inherited from class ucar.nc2.iosp.AbstractIOServiceProvider

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

Field Detail

DEBUG

public static final boolean DEBUG

See Also:

Constant Field Values

JNA_PATH

public static final java.lang.String JNA_PATH

See Also:

Constant Field Values

JNA_PATH_ENV

public static final java.lang.String JNA_PATH_ENV

See Also:

Constant Field Values

DEFAULTNETCDF4LIBNAME

protected static java.lang.String DEFAULTNETCDF4LIBNAME

Constructor Detail

Nc4Iosp

public Nc4Iosp()

Nc4Iosp

public Nc4Iosp(NetcdfFileWriter.Version version)

Method Detail

setLibraryAndPath

public static void setLibraryAndPath(java.lang.String jna_path,
                                     java.lang.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

nullify

protected static java.lang.String nullify(java.lang.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

setDebugFlags

public static void setDebugFlags(DebugFlags flags)

setChunker

public void setChunker(Nc4Chunking chunker)

isValidFile

public boolean isValidFile(RandomAccessFile raf)
                    throws java.io.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 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:

java.io.IOException - if an I/O error occurs.

getFileTypeDescription

public java.lang.String getFileTypeDescription()

Description copied from interface: IOServiceProvider

Get a human-readable description for this file type.

Specified by:

getFileTypeDescription in interface IOServiceProvider

Returns:

description of the file type

See Also:

"https://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"

getFileTypeId

public java.lang.String getFileTypeId()

Description copied from interface: IOServiceProvider

Get a unique id for this file type.

Specified by:

getFileTypeId in interface IOServiceProvider

Returns:

registered id of the file type

See Also:

"https://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"

close

public void close()
           throws java.io.IOException

Description copied from interface: IOServiceProvider

Close the file. It is the IOServiceProvider's job to close the file (even though it didnt open it), and to free any other resources it has used.

Specified by:

close in interface IOServiceProvider

Overrides:

close in class AbstractIOServiceProvider

Throws:

java.io.IOException - if read error

open

public void open(RandomAccessFile raf,
                 NetcdfFile ncfile,
                 CancelTask cancelTask)
          throws java.io.IOException

Description copied from interface: IOServiceProvider

Open existing file, and populate ncfile with it. This method is only called by the NetcdfFile constructor on itself. The provided NetcdfFile object will be empty except for the location String and the IOServiceProvider associated with this NetcdfFile object.

Specified by:

open in interface IOServiceProvider

Overrides:

open in class AbstractIOServiceProvider

Parameters:

raf - the file to work on, it has already passed the isValidFile() test.

ncfile - add objects to this empty NetcdfFile

cancelTask - used to monitor user cancellation; may be null.

Throws:

java.io.IOException - if read error

openForWriting

public void openForWriting(RandomAccessFile raf,
                           NetcdfFile ncfile,
                           CancelTask cancelTask)
                    throws java.io.IOException

Description copied from interface: IOServiceProviderWriter

Open existing file and allow writing.

Specified by:

openForWriting in interface IOServiceProviderWriter

Parameters:

raf - the file to work on.

ncfile - add objects to this empty NetcdfFile

cancelTask - used to monitor user cancellation; may be null.

Throws:

java.io.IOException - if I/O error

dumpbytes

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

readData

public Array readData(Variable v2,
                      Section section)
               throws java.io.IOException,
                      InvalidRangeException

Description copied from interface: IOServiceProvider

Read data from a top level Variable and return a memory resident Array. This Array has the same element type as the Variable, and the requested shape.

Specified by:

readData in interface IOServiceProvider

Parameters:

v2 - a top-level Variable

section - the section of data to read. There must be a Range for each Dimension in the variable, in order. Note: no nulls allowed. IOSP may not modify.

Returns:

the requested data in a memory-resident Array

Throws:

java.io.IOException - if read error

InvalidRangeException - if invalid section

See Also:

Range

show

public static java.lang.String show(SizeT[] inta)

create

public void create(java.lang.String filename,
                   NetcdfFile ncfile,
                   int extra,
                   long preallocateSize,
                   boolean largeFile)
            throws java.io.IOException

Description copied from interface: IOServiceProviderWriter

Create new file, populate it from the objects in ncfile.

Specified by:

create in interface IOServiceProviderWriter

Parameters:

filename - name of file to create.

ncfile - get everything but data from here

extra - if > 0, pad header with extra bytes

preallocateSize - if > 0, set length of file to this upon creation - this (usually) pre-allocates contiguous storage.

largeFile - if want large file format

Throws:

java.io.IOException - if I/O error

writeData

public void writeData(Variable v2,
                      Section section,
                      Array values)
               throws java.io.IOException,
                      InvalidRangeException

Description copied from interface: IOServiceProviderWriter

Write data into a variable.

Specified by:

writeData in interface IOServiceProviderWriter

Parameters:

v2 - variable to write; must already exist.

section - the section of data to write. There must be a Range for each Dimension in the variable, in order. The shape must match the shape of values. The origin and stride indicate where the data is placed into the stored Variable array.

values - data to write. The shape must match section.getShape().

Throws:

java.io.IOException - if I/O error

InvalidRangeException - if invalid section

appendStructureData

public int appendStructureData(Structure s,
                               StructureData sdata)
                        throws java.io.IOException,
                               InvalidRangeException

Description copied from interface: IOServiceProviderWriter

Append a structureData along the unlimited dimension

Specified by:

appendStructureData in interface IOServiceProviderWriter

Parameters:

s - belongs to this structure

sdata - the stuctureData to append

Returns:

the recnum where it was written

Throws:

java.io.IOException

InvalidRangeException

flush

public void flush()
           throws java.io.IOException

Description copied from interface: IOServiceProviderWriter

Flush all data buffers to disk.

Specified by:

flush in interface IOServiceProviderWriter

Throws:

java.io.IOException - if I/O error

setFill

public void setFill(boolean fill)

Description copied from interface: IOServiceProviderWriter

Set the fill flag. For new files, set in the create() method. This method is to set fill for existing files that you want to write. If true, the data is first written with fill values. Set to false if you expect to write all data values, set to true if you want to be sure that unwritten data values have the fill value in it.

Specified by:

setFill in interface IOServiceProviderWriter

Parameters:

fill - set fill mode true or false

rewriteHeader

public boolean rewriteHeader(boolean largeFile)
                      throws java.io.IOException

Description copied from interface: IOServiceProviderWriter

if theres room before data, rewrite header without moving the data. netcdf3 only

Specified by:

rewriteHeader in interface IOServiceProviderWriter

Returns:

true if it worked

Throws:

java.io.IOException

updateAttribute

public void updateAttribute(Variable v2,
                            Attribute att)
                     throws java.io.IOException

Description copied from interface: IOServiceProviderWriter

Update the value of an existing attribute. Attribute is found by name, which must match exactly. You cannot make an attribute longer, or change the number of values. For strings: truncate if longer, zero fill if shorter. Strings are padded to 4 byte boundaries, ok to use padding if it exists. For numerics: must have same number of values.

Specified by:

updateAttribute in interface IOServiceProviderWriter

Parameters:

v2 - variable, or null for global attribute

att - replace with this value

Throws:

java.io.IOException - if I/O error

getNativeAddr

public static long getNativeAddr(int pos,
                                 java.nio.ByteBuffer buf)