loci.formats.services

Interface NetCDFService

All Superinterfaces:

loci.common.services.Service

All Known Implementing Classes:

NetCDFServiceImpl

public interface NetCDFService
extends loci.common.services.Service

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

Method Summary

Modifier and Type	Method and Description
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 path) Retrieves the length of a dimension.
java.lang.String	getFile() Retrieves the current initialized file path.
java.util.Hashtable<java.lang.String,java.lang.Object>	getVariableAttributes(java.lang.String path) 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 path) Retrieves a variable's value.
void	setFile(java.lang.String file) Initializes the service on a given file path.

Method Detail

setFile

void setFile(java.lang.String file)
      throws java.io.IOException

Initializes the service on a given file path.

Parameters:

file - Path to initialize the service with.

Throws:

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

getFile

java.lang.String getFile()

Retrieves the current initialized file path.

Returns:

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

getAttributeList

java.util.Vector<java.lang.String> getAttributeList()

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

Returns:

Collection of attribute paths.

getVariableList

java.util.Vector<java.lang.String> getVariableList()

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

Returns:

Collection of variable paths.

getAttributeValue

java.lang.String getAttributeValue(java.lang.String path)

Retrieves an attribute's value.

Parameters:

path - HDF path to the attribute.

Returns:

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

getVariableValue

java.lang.Object getVariableValue(java.lang.String path)
                           throws loci.common.services.ServiceException

Retrieves a variable's value.

Parameters:

path - 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

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

Retrieves an HDF path's values.

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

java.util.Hashtable<java.lang.String,java.lang.Object> getVariableAttributes(java.lang.String path)

Retrieves all of a variable's attributes.

Parameters:

path - 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

int getDimension(java.lang.String path)

Retrieves the length of a dimension.

Parameters:

path - HDF path to the dimension.

Returns:

Length of the dimension.

close

void close()
    throws java.io.IOException

Closes and resets the service.

Throws:

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