loci.formats.out

Class CellH5Writer

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.CellH5Writer

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatWriter, IMetadataConfigurable

public class CellH5Writer
extends FormatWriter

CellH5Writer is the file format writer for CellH5 format.

Field Summary

Fields

Modifier and Type	Field and Description
private long	bpp
private JHDFService	jhdf
private String	outputPath

Fields inherited from class loci.formats.FormatWriter

cm, compression, compressionTypes, fps, initialized, interleaved, metadataRetrieve, options, out, sequential, series, validBits

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Constructor Summary

Constructors

Constructor and Description
CellH5Writer()
CellH5Writer(String format, String[] exts)

Method Summary

Modifier and Type	Method and Description
boolean	canDoStacks() Reports whether the writer can save multiple images to a single file.
void	close()
int[]	getPixelTypes(String codec) Gets the supported pixel types for the given codec.
int	getPlaneCount() Retrieve the total number of planes in the current series.
void	saveBytes(int no, byte[] buf) Saves the given image to the specified (possibly already open) file.
void	saveBytes(int no, byte[] buf, int x, int y, int w, int h) Saves the given image tile to the current series in the current file.
void	setId(String id) Initializes a writer from the input file name.

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, createOutputStream, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, getSamplesPerPixel, getSamplesPerPixel, getSeries, getTileSizeX, getTileSizeY, isFullPlane, isInterleaved, isSupportedType, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setSeries, setTileSizeX, setTileSizeY, setValidBitsPerPixel, setWriteSequentially

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, isThisType, setMetadataOptions

Methods inherited from class java.lang.Object

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

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes, isThisType

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

jhdf

private transient JHDFService jhdf

bpp

private long bpp

outputPath

private String outputPath

Constructor Detail

CellH5Writer

public CellH5Writer()

CellH5Writer

public CellH5Writer(String format,
                    String[] exts)

Method Detail

setId

public void setId(String id)
           throws FormatException,
                  IOException

Description copied from class: FormatWriter

Initializes a writer from the input file name. Initializes a RandomAccessOutputStream for the output file and initializes the metadata for all the series using FormatWriter.setSeries(int).

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class FormatWriter

Parameters:

id - a String specifying the path to the file

Throws:

FormatException

IOException

saveBytes

public void saveBytes(int no,
                      byte[] buf)
               throws IOException,
                      FormatException

Saves the given image to the specified (possibly already open) file.

Specified by:

saveBytes in interface IFormatWriter

Overrides:

saveBytes in class FormatWriter

Parameters:

no - the image index within the current file, starting from 0.

buf - the byte array that represents the image.

Throws:

IOException - if there was a problem writing to the file.

FormatException - if one of the parameters is invalid.

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class FormatWriter

Throws:

IOException

getPlaneCount

public int getPlaneCount()

Description copied from class: FormatWriter

Retrieve the total number of planes in the current series.

Overrides:

getPlaneCount in class FormatWriter

saveBytes

public void saveBytes(int no,
                      byte[] buf,
                      int x,
                      int y,
                      int w,
                      int h)
               throws FormatException,
                      IOException

Description copied from interface: IFormatWriter

Saves the given image tile to the current series in the current file.

Parameters:

no - the image index within the current file, starting from 0.

buf - the byte array that represents the image tile.

x - the X coordinate of the upper-left corner of the image tile.

y - the Y coordinate of the upper-left corner of the image tile.

w - the width (in pixels) of the image tile.

h - the height (in pixels) of the image tile.

Throws:

FormatException - if one of the parameters is invalid.

IOException - if there was a problem writing to the file.

See Also:

IFormatWriter.saveBytes(int, byte[], int, int, int, int)

canDoStacks

public boolean canDoStacks()

Description copied from interface: IFormatWriter

Reports whether the writer can save multiple images to a single file.

Specified by:

canDoStacks in interface IFormatWriter

Overrides:

canDoStacks in class FormatWriter

getPixelTypes

public int[] getPixelTypes(String codec)

Description copied from interface: IFormatWriter

Gets the supported pixel types for the given codec.

Specified by:

getPixelTypes in interface IFormatWriter

Overrides:

getPixelTypes in class FormatWriter