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.
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 path) Retrieves the length of a dimension.
String	getFile() Retrieves the current initialized file path.
Hashtable<String,Object>	getVariableAttributes(String path) 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 path) Retrieves a variable's value.
void	setFile(String file) Initializes the service on a given file path.

Method Detail

setFile

void setFile(String file)
      throws IOException

Initializes the service on a given file path.

Parameters:

file - Path to initialize the service with.

Throws:

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

getFile

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

Vector<String> getAttributeList()

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

Returns:

Collection of attribute paths.

getVariableList

Vector<String> getVariableList()

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

Returns:

Collection of variable paths.

getAttributeValue

String getAttributeValue(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

Object getVariableValue(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

Object getArray(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

Hashtable<String,Object> getVariableAttributes(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(String path)

Retrieves the length of a dimension.

Parameters:

path - HDF path to the dimension.

Returns:

Length of the dimension.

close

void close()
    throws IOException

Closes and resets the service.

Throws:

IOException - If there is an error closing the file.