visad.data.bio

Class LociForm

java.lang.Object

visad.data.FormNode

visad.data.Form

visad.data.bio.LociForm

All Implemented Interfaces:

FormBlockReader, FormFileInformer, FormProgressInformer, MetadataReader

Direct Known Subclasses:

AVIForm, BioRadForm, DeltavisionForm, FluoviewTiffForm, GatanForm, ICSForm, ImageProSeqForm, IPLabForm, IPWForm, LegacyZVIForm, LeicaForm, MetamorphForm, OpenlabForm, PerkinElmerForm, PictForm, QTForm, TiffForm, ZeissForm, ZVIForm

public class LociForm
extends Form
implements FormBlockReader, FormFileInformer, FormProgressInformer, MetadataReader

LociForm is the VisAD data adapter for images handled by the Bio-Formats package (loci.formats). It works by wrapping a loci.formats.IFormatReader and/or loci.formats.IFormatWriter object.

Field Summary

Fields

Modifier and Type	Field and Description
protected double	percent Percent complete for current operation.
protected IFormatReader	reader Reader to use for open-related functions.
protected FileFilter[]	rFilters File filters for reader formats.
protected FileFilter[]	wFilters File filters for writer formats.
protected IFormatWriter	writer Writer to use for save-related functions.

Fields inherited from class visad.data.Form

mathType

Constructor Summary

Constructors

Constructor and Description
LociForm() Constructs a new LociForm that handles anything from loci.formats.
LociForm(IFormatReader reader) Constructs a new LociForm that handles the given reader.
LociForm(IFormatReader reader, IFormatWriter writer) Constructs a new LociForm that handles the given reader/writer pair.
LociForm(IFormatWriter writer) Constructs a new LociForm that handles the given writer.

Method Summary

Modifier and Type	Method and Description
void	add(String id, Data data, boolean replace) Adds data to an existing image file.
void	close() Closes any open files.
int	getBlockCount(String id) Determines the number of images in the given image file.
String[]	getDefaultSuffixes() Returns the default file suffixes for this file format.
FormNode	getForms(Data data) Returns the data forms that are compatible with a data object.
Hashtable	getMetadata(String id) Obtains the hashtable containing the metadata field/value pairs from the given image file.
Object	getMetadataValue(String id, String field) Obtains the specified metadata field's value for the given file.
double	getPercentComplete() Gets the percentage complete of the form's current operation.
IFormatReader	getReader() Gets the IFormatReader backing this form's reading capabilities.
FileFilter[]	getReaderFilters() Gets file filters for use with formats supported for reading.
IFormatWriter	getWriter() Gets the IFormatWriter backing this form's writing capabilities.
FileFilter[]	getWriterFilters() Gets file filters for use with formats supported for writing.
void	initHandler(IFormatHandler h, String id)
boolean	isThisType(byte[] block) Checks if the given block is a valid header for an image file.
boolean	isThisType(String name) Checks if the given string is a valid filename for an image file.
static void	main(String[] args)
DataImpl	open(String id) Opens an existing image file from the given filename.
DataImpl	open(String id, int block_number) Obtains the specified image from the given image file.
DataImpl	open(URL url) Opens an existing image file from the given URL.
void	save(String id, Data data, boolean replace) Saves a VisAD Data object at the given location.
void	setFrameRate(int fps) Sets the frames per second to use when writing files.
void	testRead(String[] args) A utility method for test reading a file from the command line, and displaying the results in a simple display.

Methods inherited from class visad.data.Form

getMathType

Methods inherited from class visad.data.FormNode

getName

Methods inherited from class java.lang.Object

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

Field Detail

reader

protected IFormatReader reader

Reader to use for open-related functions.

writer

protected IFormatWriter writer

Writer to use for save-related functions.

percent

protected double percent

Percent complete for current operation.

rFilters

protected FileFilter[] rFilters

File filters for reader formats.

wFilters

protected FileFilter[] wFilters

File filters for writer formats.

Constructor Detail

LociForm

public LociForm()

Constructs a new LociForm that handles anything from loci.formats.

LociForm

public LociForm(IFormatReader reader)

Constructs a new LociForm that handles the given reader.

LociForm

public LociForm(IFormatWriter writer)

Constructs a new LociForm that handles the given writer.

LociForm

public LociForm(IFormatReader reader,
                IFormatWriter writer)

Constructs a new LociForm that handles the given reader/writer pair.

Method Detail

getReader

public IFormatReader getReader()

Gets the IFormatReader backing this form's reading capabilities.

getWriter

public IFormatWriter getWriter()

Gets the IFormatWriter backing this form's writing capabilities.

setFrameRate

public void setFrameRate(int fps)

Sets the frames per second to use when writing files.

testRead

public void testRead(String[] args)
              throws VisADException,
                     IOException

A utility method for test reading a file from the command line, and displaying the results in a simple display.

Throws:

VisADException

IOException

getReaderFilters

public FileFilter[] getReaderFilters()

Gets file filters for use with formats supported for reading.

getWriterFilters

public FileFilter[] getWriterFilters()

Gets file filters for use with formats supported for writing.

open

public DataImpl open(String id)
              throws BadFormException,
                     IOException,
                     VisADException

Opens an existing image file from the given filename.

Specified by:

open in class FormNode

Returns:

VisAD Data object containing image data

Throws:

BadFormException

IOException

VisADException

save

public void save(String id,
                 Data data,
                 boolean replace)
          throws BadFormException,
                 IOException,
                 RemoteException,
                 VisADException

Saves a VisAD Data object at the given location.

Specified by:

save in class FormNode

Throws:

BadFormException

IOException

RemoteException

VisADException

add

public void add(String id,
                Data data,
                boolean replace)
         throws BadFormException

Adds data to an existing image file.

Specified by:

add in class FormNode

Throws:

BadFormException - Always thrown (this method not implemented).

open

public DataImpl open(URL url)
              throws BadFormException,
                     IOException,
                     VisADException

Opens an existing image file from the given URL.

Specified by:

open in class FormNode

Returns:

VisAD data object containing image data

Throws:

UnimplementedException - Always thrown (this method not implemented).

BadFormException

IOException

VisADException

getForms

public FormNode getForms(Data data)

Returns the data forms that are compatible with a data object.

Specified by:

getForms in class FormNode

open

public DataImpl open(String id,
                     int block_number)
              throws BadFormException,
                     IOException,
                     VisADException

Obtains the specified image from the given image file.

Specified by:

open in interface FormBlockReader

Parameters:

id - The file from which to load data blocks.

block_number - The block number of the block to load.

Throws:

VisADException - If the block number is invalid.

BadFormException

IOException

getBlockCount

public int getBlockCount(String id)
                  throws BadFormException,
                         IOException,
                         VisADException

Determines the number of images in the given image file.

Specified by:

getBlockCount in interface FormBlockReader

Parameters:

id - The file for which to get a block count.

Throws:

BadFormException

IOException

VisADException

close

public void close()
           throws BadFormException,
                  IOException,
                  VisADException

Closes any open files.

Specified by:

close in interface FormBlockReader

Throws:

BadFormException

IOException

VisADException

isThisType

public boolean isThisType(String name)

Checks if the given string is a valid filename for an image file.

Specified by:

isThisType in interface FormFileInformer

Parameters:

name - name of the file

Returns:

true if the name is right for this type of form

isThisType

public boolean isThisType(byte[] block)

Checks if the given block is a valid header for an image file.

Specified by:

isThisType in interface FormFileInformer

Parameters:

block - block of bytes from file

Returns:

true if the magic number is right

getDefaultSuffixes

public String[] getDefaultSuffixes()

Returns the default file suffixes for this file format.

Specified by:

getDefaultSuffixes in interface FormFileInformer

Returns:

array of suffixes

getPercentComplete

public double getPercentComplete()

Gets the percentage complete of the form's current operation.

Specified by:

getPercentComplete in interface FormProgressInformer

Returns:

The percentage complete (0.0 - 100.0), or Double.NaN if no operation is currently taking place.

getMetadataValue

public Object getMetadataValue(String id,
                               String field)
                        throws BadFormException,
                               IOException,
                               VisADException

Obtains the specified metadata field's value for the given file.

Specified by:

getMetadataValue in interface MetadataReader

Parameters:

field - the name associated with the metadata field

Returns:

the value, or null if the field doesn't exist

Throws:

BadFormException

IOException

VisADException

getMetadata

public Hashtable getMetadata(String id)
                      throws BadFormException,
                             IOException,
                             VisADException

Obtains the hashtable containing the metadata field/value pairs from the given image file.

Specified by:

getMetadata in interface MetadataReader

Parameters:

id - the filename

Returns:

the hashtable containing all metadata from the file

Throws:

BadFormException

IOException

VisADException

main

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

Throws:

Exception

initHandler

public void initHandler(IFormatHandler h,
                        String id)
                 throws BadFormException,
                        IOException

Throws:

BadFormException

IOException