loci.formats.services

Class NetCDFServiceImpl

java.lang.Object

loci.common.services.AbstractService

loci.formats.services.NetCDFServiceImpl

All Implemented Interfaces:

Service, NetCDFService

public class NetCDFServiceImpl
extends AbstractService
implements NetCDFService

Utility class for working with NetCDF/HDF files. Uses reflection to call the NetCDF Java library.

Source code:

Trac, Gitweb

Field Summary

Fields

Modifier and Type	Field and Description
static String	NO_NETCDF_MSG

Constructor Summary

Constructors

Constructor and Description
NetCDFServiceImpl() Default constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes and resets the service.
Object	getArray(String path, int[] origin, int[] shape) Retrieves an HDF path's values.
Vector<String>	getAttributeList() Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.
String	getAttributeValue(String path) Retrieves an attribute's value.
int	getDimension(String name) Retrieves the length of a dimension.
String	getFile() Retrieves the current initialized file path.
Hashtable<String,Object>	getVariableAttributes(String name) Retrieves all of a variable's attributes.
Vector<String>	getVariableList() Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.
Object	getVariableValue(String name) Retrieves a variable's value.
void	setFile(String file) Initializes the service on a given file path.

Methods inherited from class loci.common.services.AbstractService

checkClassDependency

Methods inherited from class java.lang.Object

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

Field Detail

NO_NETCDF_MSG

public static final String NO_NETCDF_MSG

See Also:

Constant Field Values

Constructor Detail

NetCDFServiceImpl

public NetCDFServiceImpl()

Default constructor.

Method Detail

setFile

public void setFile(String file)
             throws IOException

Description copied from interface: NetCDFService

Initializes the service on a given file path.

Specified by:

setFile in interface NetCDFService

Parameters:

file - Path to initialize the service with.

Throws:

IOException - If there is an error initializing the service with file.

getFile

public String getFile()

Description copied from interface: NetCDFService

Retrieves the current initialized file path.

Specified by:

getFile in interface NetCDFService

Returns:

Current initialized file path or null if the service has yet to be initialized or is closed.

getAttributeList

public Vector<String> getAttributeList()

Description copied from interface: NetCDFService

Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.

Specified by:

getAttributeList in interface NetCDFService

Returns:

Collection of attribute paths.

getVariableList

public Vector<String> getVariableList()

Description copied from interface: NetCDFService

Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.

Specified by:

getVariableList in interface NetCDFService

Returns:

Collection of variable paths.

getAttributeValue

public String getAttributeValue(String path)

Description copied from interface: NetCDFService

Retrieves an attribute's value.

Specified by:

getAttributeValue in interface NetCDFService

Parameters:

path - HDF path to the attribute.

Returns:

String value or null if the attribute is not a string.

getVariableValue

public Object getVariableValue(String name)
                        throws ServiceException

Description copied from interface: NetCDFService

Retrieves a variable's value.

Specified by:

getVariableValue in interface NetCDFService

Parameters:

name - HDF path to the variable.

Returns:

The Java one-dimensional array representation of the variable's values.

Throws:

ServiceException - If there is an error with the range of values or reading from the file.

See Also:

Array.copyTo1DJavaArray()

getArray

public Object getArray(String path,
              int[] origin,
              int[] shape)
                throws ServiceException

Description copied from interface: NetCDFService

Retrieves an HDF path's values.

Specified by:

getArray in interface NetCDFService

Parameters:

path - HDF path to the values.

origin - Array specifying the starting index. If null, assume all zeroes.

shape - Array specifying the extents in each dimension. This becomes the shape of the returned Array.

Returns:

The Java n-dimensional array representation of the path's values.

Throws:

ServiceException - If there is an error with the range of values or reading from the file.

See Also:

Variable.read(int[], int[]), Array.copyToNDJavaArray()

getVariableAttributes

public Hashtable<String,Object> getVariableAttributes(String name)

Description copied from interface: NetCDFService

Retrieves all of a variable's attributes.

Specified by:

getVariableAttributes in interface NetCDFService

Parameters:

name - HDF path to the variable.

Returns:

Hash table of attributes to Java one-dimensional array representations of the attribute's values.

See Also:

Array.copyTo1DJavaArray()

getDimension

public int getDimension(String name)

Description copied from interface: NetCDFService

Retrieves the length of a dimension.

Specified by:

getDimension in interface NetCDFService

Parameters:

name - HDF path to the dimension.

Returns:

Length of the dimension.

close

public void close()
           throws IOException

Description copied from interface: NetCDFService

Closes and resets the service.

Specified by:

close in interface NetCDFService

Throws:

IOException - If there is an error closing the file.