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

Author:

caron

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/win_netcdf/"

Field Summary

Fields inherited from class ucar.nc2.iosp.AbstractIOServiceProvider

raf

Constructor Summary

Constructors

Constructor and Description
Nc4Iosp(NetcdfFileWriter.Version version)

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Close the file.
void	create(String filename, NetcdfFile ncfile, int extra, long preallocateSize, boolean largeFile) Create new file, populate it from the objects in ncfile.
void	flush() Flush all data buffers to disk.
String	getFileTypeDescription() Get a human-readable description for this file type.
String	getFileTypeId() Get a unique id for this file type.
static boolean	isClibraryPresent() Test if the netcdf C library is present and loaded
boolean	isValidFile(RandomAccessFile raf) Check if this is a valid file for this IOServiceProvider.
static void	main(String[] args)
void	open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) Open existing file, and populate ncfile with it.
NetcdfFile	open(String location)
Array	readData(Variable v2, Section section) Read data from a top level Variable and return a memory resident Array.
boolean	rewriteHeader(boolean largeFile)
void	setChunker(Nc4Chunking chunker)
void	setFill(boolean fill) Set the fill flag.
static void	setLibraryAndPath(String jna_path, String libname) set the path and name of the netcdf c library.
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, getStructureIterator, readSection, readToByteChannel, readToOutputStream, sendIospMessage, streamToByteChannel, sync, 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, readSection, readToByteChannel, readToOutputStream, sendIospMessage, streamToByteChannel, sync, syncExtend, toStringDebug

Constructor Detail

Nc4Iosp

public Nc4Iosp(NetcdfFileWriter.Version version)

Method Detail

isClibraryPresent

public static boolean isClibraryPresent()

Test if the netcdf C library is present and loaded

Returns:

true if present

setLibraryAndPath

public static void setLibraryAndPath(String jna_path,
                     String libname)

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

Parameters:

jna_path - path

libname - library name

setChunker

public void setChunker(Nc4Chunking chunker)

isValidFile

public boolean isValidFile(RandomAccessFile raf)
                    throws IOException

Description copied from interface: IOServiceProvider

Check if this is a valid file for this IOServiceProvider. You must make this method thread safe, ie dont keep any state.

Specified by:

isValidFile in interface IOServiceProvider

Parameters:

raf - RandomAccessFile

Returns:

true if valid.

Throws:

IOException - if read error

getFileTypeId

public 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:

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

getFileTypeDescription

public 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:

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

close

public void close()
           throws 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:

IOException - if read error

open

public void open(RandomAccessFile raf,
        NetcdfFile ncfile,
        CancelTask cancelTask)
          throws 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:

IOException - if read error

readData

public Array readData(Variable v2,
             Section section)
               throws 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:

IOException - if read error

InvalidRangeException - if invalid section

See Also:

Range

create

public void create(String filename,
          NetcdfFile ncfile,
          int extra,
          long preallocateSize,
          boolean largeFile)
            throws 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:

IOException - if I/O error

writeData

public void writeData(Variable v2,
             Section section,
             Array values)
               throws 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:

IOException - if I/O error

InvalidRangeException - if invalid section

flush

public void flush()
           throws IOException

Description copied from interface: IOServiceProviderWriter

Flush all data buffers to disk.

Specified by:

flush in interface IOServiceProviderWriter

Throws:

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. Leave 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 IOException

Specified by:

rewriteHeader in interface IOServiceProviderWriter

Throws:

IOException

updateAttribute

public void updateAttribute(Variable v2,
                   Attribute att)
                     throws 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:

IOException - if I/O error

open

public NetcdfFile open(String location)
                throws Exception

Throws:

Exception

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception