loci.formats.out

Class ICSWriter

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatWriter

loci.formats.out.ICSWriter

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileWriter, IFormatHandler, IFormatWriter, IMetadataConfigurable, IPyramidHandler

public class ICSWriter
extends FormatWriter

ICSWriter is the file format writer for ICS files. It writes ICS version 1 and 2 files.

Field Summary

Fields

Modifier and Type	Field and Description
private int	dimensionLength
private long	dimensionOffset
private int	lastPlane
private java.lang.String	outputOrder
private long	pixelOffset
private loci.common.RandomAccessOutputStream	pixels
private java.util.List<java.lang.String>	uniqueFiles

Fields inherited from class loci.formats.FormatWriter

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

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Constructor Summary

Constructors

Constructor and Description
ICSWriter()

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(java.lang.String codec) Gets the supported pixel types for the given codec.
private int[]	overwriteDimensions(MetadataRetrieve meta)
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(java.lang.String id) Initializes a writer from the input file name.
void	setOutputOrder(java.lang.String outputOrder) Set the order in which dimensions should be written to the file.

Methods inherited from class loci.formats.FormatWriter

changeOutputFile, checkParams, createOutputStream, getCodecOptions, getColorModel, getCompression, getCompressionTypes, getFramesPerSecond, getMetadataRetrieve, getPixelTypes, getPlaneCount, getPlaneCount, getResolution, getResolutionCount, getResolutions, getSamplesPerPixel, getSamplesPerPixel, getSeries, getSizeX, getSizeY, getTileSizeX, getTileSizeY, hasResolutions, isFullPlane, isInterleaved, isSupportedType, saveBytes, saveBytes, savePlane, savePlane, savePlane, seekToPlaneOffset, setCodecOptions, setColorModel, setCompression, setFramesPerSecond, setInterleaved, setMetadataRetrieve, setResolution, setResolutions, 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

Methods inherited from interface loci.formats.ICompressedTileWriter

getCodec, saveCompressedBytes

Field Detail

dimensionOffset

private long dimensionOffset

dimensionLength

private int dimensionLength

pixelOffset

private long pixelOffset

lastPlane

private int lastPlane

pixels

private loci.common.RandomAccessOutputStream pixels

uniqueFiles

private java.util.List<java.lang.String> uniqueFiles

outputOrder

private java.lang.String outputOrder

Constructor Detail

ICSWriter

public ICSWriter()

Method Detail

setOutputOrder

public void setOutputOrder(java.lang.String outputOrder)

Set the order in which dimensions should be written to the file. Valid values are specified in the documentation for IFormatReader.getDimensionOrder() By default, the ordering is "XYZTC".

saveBytes

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

Description copied from interface: IFormatWriter

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

Parameters:

no - the plane index within the series.

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.

java.io.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(java.lang.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

setId

public void setId(java.lang.String id)
           throws FormatException,
                  java.io.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

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class FormatWriter

Throws:

java.io.IOException

overwriteDimensions

private int[] overwriteDimensions(MetadataRetrieve meta)
                           throws java.io.IOException

Throws:

java.io.IOException