io.scif.formats

Class ICSFormat.Reader

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractGroupable

io.scif.AbstractReader<M,ByteArrayPlane>

io.scif.ByteArrayReader<ICSFormat.Metadata>

io.scif.formats.ICSFormat.Reader

All Implemented Interfaces:

Groupable, HasFormat, HasSource, Reader, SCIFIOPlugin, TypedReader<ICSFormat.Metadata,ByteArrayPlane>, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

Enclosing class:

ICSFormat

public static class ICSFormat.Reader
extends ByteArrayReader<ICSFormat.Metadata>

File format SCIFIO Reader for Image Cytometry Standard (ICS) images. Version 1 and 2 supported.

Constructor Summary

Constructors

Constructor and Description
Reader()

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
protected String[]	createDomainArray() Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.
String[]	getDomains() Returns the list of domains represented by the current file.
ByteArrayPlane	openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
void	setMetadata(ICSFormat.Metadata meta) Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).
void	setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, SCIFIOConfig config) As Reader.setSource(DataHandle) with configuration options.

Methods inherited from class io.scif.ByteArrayReader

createPlane, createPlane

Methods inherited from class io.scif.AbstractReader

castToTypedPlane, getCurrentLocation, getHandle, getImageCount, getMetadata, getOptimalTileHeight, getOptimalTileWidth, getPlaneClass, getPlaneCount, hasCompanionFiles, isNormalized, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, readPlane, readPlane, readPlane, readPlane, setMetadata, setNormalized, setSource, setSource, setSource

Methods inherited from class io.scif.AbstractGroupable

fileGroupOption, isSingleFile

Methods inherited from class io.scif.AbstractHasSource

close

Methods inherited from class io.scif.AbstractHasFormat

asBrowsableLocation, asBrowsableLocation, getFormat, getFormatName

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.HasFormat

getFormat, getFormatName

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface io.scif.HasSource

close

Methods inherited from interface io.scif.Groupable

fileGroupOption, isSingleFile

Constructor Detail

Reader

public Reader()

Method Detail

createDomainArray

protected String[] createDomainArray()

Description copied from class: AbstractReader

Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.

Specified by:

createDomainArray in class AbstractReader<ICSFormat.Metadata,ByteArrayPlane>

openPlane

public ByteArrayPlane openPlane(int imageIndex,
                                long planeIndex,
                                ByteArrayPlane plane,
                                net.imglib2.Interval bounds,
                                SCIFIOConfig config)
                         throws FormatException,
                                IOException

Throws:

FormatException

IOException

See Also:

TypedReader.openPlane(int, long, DataPlane, Interval)

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Overrides:

close in class AbstractReader<ICSFormat.Metadata,ByteArrayPlane>

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException

setMetadata

public void setMetadata(ICSFormat.Metadata meta)
                 throws IOException

Description copied from interface: TypedReader

Generic-parameterized setMetadata method, using TypedMetadata to avoid type erasure conflicts with Reader.setMetadata(Metadata).

Specified by:

setMetadata in interface TypedReader<ICSFormat.Metadata,ByteArrayPlane>

Overrides:

setMetadata in class AbstractReader<ICSFormat.Metadata,ByteArrayPlane>

Throws:

IOException

See Also:

Reader.setMetadata(Metadata)

setSource

public void setSource(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream,
                      SCIFIOConfig config)
               throws IOException

Description copied from interface: Reader

As Reader.setSource(DataHandle) with configuration options.

Specified by:

setSource in interface Reader

Overrides:

setSource in class AbstractReader<ICSFormat.Metadata,ByteArrayPlane>

Parameters:

stream - - The handle to read from

config - Configuration information to use for this read.

Throws:

IOException

getDomains

public String[] getDomains()

Description copied from interface: Reader

Returns the list of domains represented by the current file.

Specified by:

getDomains in interface Reader

Overrides:

getDomains in class AbstractReader<ICSFormat.Metadata,ByteArrayPlane>