loci.formats.services

Class NetCDFServiceImpl

java.lang.Object

loci.common.services.AbstractService

loci.formats.services.NetCDFServiceImpl

All Implemented Interfaces:

com.esotericsoftware.kryo.KryoSerializable, loci.common.services.Service, NetCDFService

public class NetCDFServiceImpl
extends loci.common.services.AbstractService
implements NetCDFService, com.esotericsoftware.kryo.KryoSerializable

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

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.Vector<java.lang.String>	attributeList
private java.lang.String	currentFile
private ucar.nc2.NetcdfFile	netCDFFile NetCDF file instance.
static java.lang.String	NO_NETCDF_MSG
private ucar.nc2.Group	root Root of the NetCDF file.
private java.util.Vector<java.lang.String>	variableList

Constructor Summary

Constructors

Constructor and Description
NetCDFServiceImpl() Default constructor.

Method Summary

Modifier and Type	Method and Description
private java.lang.String	arrayToString(ucar.ma2.Array values)
void	close() Closes and resets the service.
java.lang.Object	getArray(java.lang.String path, int[] origin, int[] shape) Retrieves an HDF path's values.
java.util.Vector<java.lang.String>	getAttributeList() Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.
java.lang.String	getAttributeValue(java.lang.String path) Retrieves an attribute's value.
int	getDimension(java.lang.String name) Retrieves the length of a dimension.
private java.lang.String	getDirectory(java.lang.String path)
java.lang.String	getFile() Retrieves the current initialized file path.
private ucar.nc2.Group	getGroup(java.lang.String path) Retrieves a group based on its fully qualified path.
private java.lang.String	getName(java.lang.String path)
java.util.Hashtable<java.lang.String,java.lang.Object>	getVariableAttributes(java.lang.String name) Retrieves all of a variable's attributes.
java.util.Vector<java.lang.String>	getVariableList() Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.
java.lang.Object	getVariableValue(java.lang.String name) Retrieves a variable's value.
private void	init()
private void	parseAttributesAndVariables(java.util.List<ucar.nc2.Group> groups) Recursively parses attribute and variable paths, filling attributeList and variableList.
void	read(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Input in)
void	setFile(java.lang.String file) Initializes the service on a given file path.
void	write(com.esotericsoftware.kryo.Kryo kryo, com.esotericsoftware.kryo.io.Output out)

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 java.lang.String NO_NETCDF_MSG

currentFile

private java.lang.String currentFile

attributeList

private java.util.Vector<java.lang.String> attributeList

variableList

private java.util.Vector<java.lang.String> variableList

netCDFFile

private ucar.nc2.NetcdfFile netCDFFile

NetCDF file instance.

root

private ucar.nc2.Group root

Root of the NetCDF file.

Constructor Detail

NetCDFServiceImpl

public NetCDFServiceImpl()

Default constructor.

Method Detail

setFile

public void setFile(java.lang.String file)
             throws java.io.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:

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

getFile

public java.lang.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 java.util.Vector<java.lang.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 java.util.Vector<java.lang.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 java.lang.String getAttributeValue(java.lang.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 java.lang.Object getVariableValue(java.lang.String name)
                                  throws loci.common.services.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:

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

See Also:

Array.copyTo1DJavaArray()

getArray

public java.lang.Object getArray(java.lang.String path,
                                 int[] origin,
                                 int[] shape)
                          throws loci.common.services.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:

loci.common.services.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 java.util.Hashtable<java.lang.String,java.lang.Object> getVariableAttributes(java.lang.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(java.lang.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 java.io.IOException

Description copied from interface: NetCDFService

Closes and resets the service.

Specified by:

close in interface NetCDFService

Throws:

java.io.IOException - If there is an error closing the file.

parseAttributesAndVariables

private void parseAttributesAndVariables(java.util.List<ucar.nc2.Group> groups)

Recursively parses attribute and variable paths, filling attributeList and variableList.

Parameters:

groups - List of groups to recursively parse.

getGroup

private ucar.nc2.Group getGroup(java.lang.String path)

Retrieves a group based on its fully qualified path.

Parameters:

path - Fully qualified path to the group.

Returns:

Group or root if the group cannot be found.

getDirectory

private java.lang.String getDirectory(java.lang.String path)

getName

private java.lang.String getName(java.lang.String path)

arrayToString

private java.lang.String arrayToString(ucar.ma2.Array values)

init

private void init()
           throws java.io.IOException

Throws:

java.io.IOException

read

public void read(com.esotericsoftware.kryo.Kryo kryo,
                 com.esotericsoftware.kryo.io.Input in)

Specified by:

read in interface com.esotericsoftware.kryo.KryoSerializable

write

public void write(com.esotericsoftware.kryo.Kryo kryo,
                  com.esotericsoftware.kryo.io.Output out)

Specified by:

write in interface com.esotericsoftware.kryo.KryoSerializable