Uses of Class
org.anchoranalysis.io.bioformats.bean.options.ReadOptions

Packages that use ReadOptions

Package	Description
org.anchoranalysis.io.bioformats	Non-bean classes for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean	Beans for filesystem I/O using Bioformats.
org.anchoranalysis.io.bioformats.bean.options	User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
org.anchoranalysis.io.bioformats.copyconvert	Converts the byte stream opened by Bioformats into channels of particular data-type.

Uses of ReadOptions in org.anchoranalysis.io.bioformats

Methods in org.anchoranalysis.io.bioformats with parameters of type ReadOptions

Modifier and Type	Method	Description
Dimensions	DimensionsCreator.apply(loci.formats.IFormatReader reader, ReadOptions readOptions, int seriesIndex)	Infers the dimensions from an image file.

Uses of ReadOptions in org.anchoranalysis.io.bioformats.bean

Methods in org.anchoranalysis.io.bioformats.bean that return ReadOptions

Modifier and Type	Method	Description
ReadOptions	BioformatsReader.getOptions()	Options that influence how stack is read.

Methods in org.anchoranalysis.io.bioformats.bean with parameters of type ReadOptions

Modifier and Type	Method	Description
void	BioformatsReader.setOptions(ReadOptions options)	Options that influence how stack is read.

Constructors in org.anchoranalysis.io.bioformats.bean with parameters of type ReadOptions

Modifier	Constructor	Description
	BioformatsReader(ReadOptions options)	Create with particular options.

Uses of ReadOptions in org.anchoranalysis.io.bioformats.bean.options

Subclasses of ReadOptions in org.anchoranalysis.io.bioformats.bean.options

Modifier and Type	Class	Description
class	Default	A default set of ReadOptions without special behavior.
class	ForceBitsPerPixel	Forces the bits per pixel to be a specific-value, irrespective of what bioformats infers.
class	ForceNumberChannels	Forces the number of channels to be a specific-value, irrespective of what bioformats infers.
class	ForceNumberFrames	Forces the number of frames to be a specific-value, irrespective of what bioformats infers.
class	ForceTimeSeriesToStack	Treats a time-series as if it was a z-stack
class	ReadOptionsDelegate	Forces a particular settings, but otherwise uses settings from a delegate
class	SwitchChannelTime	Treats the channel index as if it's time, and vice versa

Methods in org.anchoranalysis.io.bioformats.bean.options that return ReadOptions

Modifier and Type	Method	Description
protected ReadOptions	ReadOptionsDelegate.delegate()	The ReadOptions that is used as a delegate by sub-classes.
ReadOptions	ReadOptionsDelegate.getOptions()	Options can be specified to alter how an image file is read.

Methods in org.anchoranalysis.io.bioformats.bean.options with parameters of type ReadOptions

Modifier and Type	Method	Description
void	ReadOptionsDelegate.setOptions(ReadOptions options)	Options can be specified to alter how an image file is read.

Uses of ReadOptions in org.anchoranalysis.io.bioformats.copyconvert

Methods in org.anchoranalysis.io.bioformats.copyconvert with parameters of type ReadOptions

Modifier and Type	Method	Description
static void	CopyConvert.copyAllFrames(loci.formats.IFormatReader reader, List<Channel> destination, ImageFileShape targetShape, ConvertTo<?> convertTo, ReadOptions readOptions, OrientationChange orientationCorrection)	Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way.