io.scif.formats

Class MinimalTIFFFormat.Reader<M extends MinimalTIFFFormat.Metadata>

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<M>

io.scif.formats.MinimalTIFFFormat.Reader<M>

All Implemented Interfaces:

Groupable, HasFormat, HasSource, Reader, SCIFIOPlugin, TypedReader<M,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

Direct Known Subclasses:

TIFFFormat.Reader

Enclosing class:

MinimalTIFFFormat

public static class MinimalTIFFFormat.Reader<M extends MinimalTIFFFormat.Metadata>
extends ByteArrayReader<M>

Constructor Summary

Constructors

Constructor and Description
Reader()

Method Summary

Modifier and Type	Method and Description
protected String[]	createDomainArray() Helper method to lazily create the domain array for this reader instance, to avoid constantly re-creating the array.
long	getOptimalTileHeight(int imageIndex) Returns the optimal sub-image height for use with Reader.openPlane(int, long).
long	getOptimalTileWidth(int imageIndex) Returns the optimal sub-image width for use with Reader.openPlane(int, long).
ByteArrayPlane	openPlane(int imageIndex, long planeIndex, ByteArrayPlane plane, net.imglib2.Interval bounds, SCIFIOConfig config)
protected void	setResolutionLevel(IFD ifd) Sets the resolution level when we have JPEG 2000 compressed data.

Methods inherited from class io.scif.ByteArrayReader

createPlane, createPlane

Methods inherited from class io.scif.AbstractReader

castToTypedPlane, close, getCurrentLocation, getDomains, getHandle, getImageCount, getMetadata, getPlaneClass, getPlaneCount, hasCompanionFiles, isNormalized, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, openPlane, readPlane, readPlane, readPlane, readPlane, setMetadata, setMetadata, setNormalized, setSource, 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<M extends MinimalTIFFFormat.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)

getOptimalTileWidth

public long getOptimalTileWidth(int imageIndex)

Description copied from interface: Reader

Returns the optimal sub-image width for use with Reader.openPlane(int, long).

Specified by:

getOptimalTileWidth in interface Reader

Overrides:

getOptimalTileWidth in class AbstractReader<M extends MinimalTIFFFormat.Metadata,ByteArrayPlane>

getOptimalTileHeight

public long getOptimalTileHeight(int imageIndex)

Description copied from interface: Reader

Returns the optimal sub-image height for use with Reader.openPlane(int, long).

Specified by:

getOptimalTileHeight in interface Reader

Overrides:

getOptimalTileHeight in class AbstractReader<M extends MinimalTIFFFormat.Metadata,ByteArrayPlane>

setResolutionLevel

protected void setResolutionLevel(IFD ifd)

Sets the resolution level when we have JPEG 2000 compressed data.

Parameters:

ifd - The active IFD that is being used in our current openBytes() calling context. It will be the sub-resolution IFD if currentSeries > 0.