Index (anchor-image-io 0.2.1 API)

A B C D E F G H I K M N O P R S T V W
All Classes All Packages

A

add(String, StoreSupplier<TimeSeries>) - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore
add(IndexedChannel) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Adds a IndexedChannel into the map.
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Adds each Channel as a separate TimeSeries in a NamedProviderStore.
addAsSeparateChannels(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
addAsSeparateChannels(NamedStacks, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
addAsSeparateChannels(NamedStacks, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Adds each Channel as a separate Stack in a NamedStacks.
addAsSeparateChannels(NamedStacks, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds the current object to a named-store of stacks (using the default series).
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds any stacks exposed by the current element to a named-store of stacks - inferring the names of the Stacks.
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Adds any stacks exposed by the current element to a named-store of stacks - with a particular name.
allChannelsAsStack(int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
allChannelsAsStack(int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Combines all channels as a single Stack at a particular time-frame.
allChannelsAsStack(int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
allChannelsEightBit() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Whether all Channels in all frames in the times-series have a particular voxel-data type?
always2D() - Static method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: The stacks that are outputted are guaranteed to be two-dimensional.
always2D(boolean) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Derives a StackWriteAttributes that will always be 2D, but is otherwise unchanged.
and(StackWriteAttributes) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical and on each field.
asSet(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Exposes the input as a set of named stacks (inferring the names).
asStack(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: Exposes the input as a single Stack throw an error if more than one exists.

B

binaryChannel(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always a binary-channel, and depending on a flag, may be guaranteed to be 2D.
bitDepth(Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Bit-depth of image.
bitDepth(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The bit-depth of the image voxels e.g.

C

calculateOrientationChange(Logger) - Method in interface org.anchoranalysis.image.io.stack.CalculateOrientationChange: Calculates any needed orientation change.
CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack: Calculates any needed orientation change.
ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output: Writes a single channel to a file.
ChannelGenerator() - Constructor for class org.anchoranalysis.image.io.channel.output.ChannelGenerator
ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input: Retrieves a Channel by name from a particular time-point.
ChannelMap - Class in org.anchoranalysis.image.io.channel.input: A mapping of assigned channel-names to particular indices.
ChannelMap() - Constructor for class org.anchoranalysis.image.io.channel.input.ChannelMap
ChannelMapCreator - Class in org.anchoranalysis.image.io.bean.channel: Creates a ChannelMap for a particular OpenedImageFile.
ChannelMapCreator() - Constructor for class org.anchoranalysis.image.io.bean.channel.ChannelMapCreator
channelNames() - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
channelNames() - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: All channel-names.
channelNames() - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
channelNames(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The names of each channel, if they are known.
close() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Closes the opened image-file, removing any intermediate data-structures.
convert(DisplayStack, boolean) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts all of a DisplayStack to a RGBStack.
convert(Stack, StackDisplayer, boolean) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts all of a DisplayStack to a RGBStack.
convertBeforeAssign(DisplayStack) - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
convertBeforeAssign(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
convertBeforeAssign(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
convertBeforeAssign(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: Converts an element before setting it on the delegate.
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
convertBeforeTransform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: Converts an element before calling RasterGeneratorDelegateToRaster.transform(T) on the delegate.
convertCropped(DisplayStack, BoundingBox) - Static method in class org.anchoranalysis.image.io.stack.ConvertStackToRGB: Converts a bounding-box region in DisplayStack to a RGBStack.
ConvertStackToRGB - Class in org.anchoranalysis.image.io.stack: Converts a Stack or DisplayStack to a RGBStack.
create() - Static method in class org.anchoranalysis.image.io.object.output.mask.RasterDirectoryObjectsGenerator: Creates the Generator to write each object as a binary Mask in a directory.
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.image.io.bean.channel.ChannelMapCreator: Creates the ChannelMap.
create(InputOutputContext) - Static method in class org.anchoranalysis.image.io.ImageInitializationFactory: Create from an InputOutputContext - without any suggested size.
create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class org.anchoranalysis.image.io.ImageInitializationFactory: Create from an InputOutputContext - with a suggested size.
createChannelsForSeries(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Creates a NamedChannelsMap representing the channels for a particular series in this input.
createEmptyStackFor(Dimensions) - Static method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates an empty RGBStack.
createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates an extracted-object generator that draws an outline - with default color green and flattened in Z.
createFromPath(Path, OperationContext) - Static method in class org.anchoranalysis.image.io.object.input.ObjectCollectionReader: Reads an object-collection from a path (or path prefix) trying different methods to read the objects.
createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with maybe a stack as the background, or else an empty background - and with default color green and flattened in Z.
createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with a stack as the background - and with default color green and flattened across the Z-dimension.
createStackSequenceForSeries(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.StackSequenceInput: Creates a supplier of a TimeSeries of stacks for a particular series number.
createWithEmptyBackground(int, ColorIndex) - Static method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator: Creates the generator with an empty background - and with default color green and flattened in Z-dimension.

D

dimensions() - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator: The dimensions associated with the objects (assumed to be constant across any change in element).
dimensions(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Dimensions of a particular series.
dimensions(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
dimensions(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The dimensions of each Channel.
dimensions(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
dimensionsForSeries(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The Dimensions associated with a particular series.
DisplayStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Writes a display-stack to the filesystem.
DisplayStackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator: Creates the generator.
DrawCroppedObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Similar to DrawObjectsGenerator, but with the background stack cropped to focus only on the region containing objects.
DrawCroppedObjectsGenerator(DrawObject, DisplayStack, Padding, ColorIndex) - Constructor for class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator: Create with a particular background and method for drawing-objects.
DrawObjectOnStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: Creates images of object(s) drawn on a background only in a local region around their bounding box.
DrawObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: Generates stacks of RGB images using a DrawObject to draw objects on a background.
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Filled
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse
drawSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline
drawText(String, BufferedImage, Extent) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Draws text on a BufferedImage.

E

ENERGY_STACK - Static variable in class org.anchoranalysis.image.io.stack.StackIdentifiers: The channels selected as inputs to an optimization routine or for feature calculation.
equals(Object) - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
EXTENT_X - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for x dimension of the extent.
EXTENT_Y - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for y dimension of the extent.
EXTENT_Z - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Attribute for z dimension of the extent.
ExtractBoundingBoxAreaFromStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box: An iterable-generator that outputs the portion of a stack corresponding to a bounding-box
ExtractBoundingBoxAreaFromStackGenerator(ScaleableBackground) - Constructor for class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
ExtractFrameStore - Class in org.anchoranalysis.image.io.stack.time: Exposes a NamedProviderStore<TimeSeries> as a NamedProviderStore<Stack> by extracting a frame from each series.
ExtractFrameStore(NamedProviderStore<Stack>) - Constructor for class org.anchoranalysis.image.io.stack.time.ExtractFrameStore: Creates to extract at time-index 0.
ExtractFrameStore(NamedProviderStore<Stack>, int) - Constructor for class org.anchoranalysis.image.io.stack.time.ExtractFrameStore: Creates to extract at time-index timeIndex.
ExtractMidpoint - Class in org.anchoranalysis.image.io.object: Extracts a Point3i representing the mid-point of an ObjectWithProperties.
extractRegionFromStack(BoundingBox) - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box

F

fileExtensionWriter(OutputWriteSettings, StackWriteOptions, Optional<Logger>) - Static method in class org.anchoranalysis.image.io.stack.output.generator.GeneratorOutputter: The file extension to use for the default StackWriter, as returned by GeneratorOutputter.writer(OutputWriteSettings).
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: The file format that will be written by the generator.
fileFormatWarnUnexpected(StackWriteOptions, Optional<Logger>) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: The file format that will be written by the generator, warning with a log message if different to suggestion.
Filled - Class in org.anchoranalysis.image.io.bean.object.draw: Draws a filled-in shape for each object.
Filled() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Filled
Flatten - Class in org.anchoranalysis.image.io.bean.object.draw: Performs a flattening (maximum intensity projection in each channel) of the output of another writer
Flatten() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Flatten
Flatten(DrawObject) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Flatten
FlattenStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Like a StackGenerator but first applies a maximum-intensity-projection.
FlattenStackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator: Creates with possible padding.
from(Stack) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: The options that narrowly describe a stack as possible.
FromStackReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader: Uses a StackReader to read the image-metadata.
FromStackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader
FromStackReader(StackReader) - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: Create from a StackReader.

G

generalWriteException(Class<T>, Path, Exception) - Static method in class org.anchoranalysis.image.io.bean.stack.writer.WriterErrorMessageHelper: Creates a ImageIOException with an error message that image-writing failed.
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator
generateBackgroundRegion(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates a RGBStack containing the background, without objects being drawn upon it.
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawCroppedObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator
generateMasks(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: Creates a ObjectCollectionWithProperties indicative of the masks that will be imposed on top of the background-region.
generator() - Static method in class org.anchoranalysis.image.io.object.output.hdf5.ObjectCollectionWriter: A Generator which writes an ObjectCollection to the file-system.
GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator: Settings and methods for writing to the filesystem from a generator.
get() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels
get() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
get(String) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Gets the index corresponding to a particular channel-name.
getAcqusitionTime() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes: A timestamp, if available, of when the image was first physically created by the camera/device.
getAttributes() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes: Timestamps and other metadata associated with an image file-path, but not with the file's contents.
getAttributes() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteOptions: The attributes of the particular stack to write.
getBackground() - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
getChannel(String, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.input.ChannelGetter: Retrieve the Channel corresponding to channelName at a particular time-frame.
getChannel(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
getChannel(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
getChannelOptional(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
getChannelOptional(String, int, Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Gets a channel if it exists, returning empty if it doesn't.
getChannelOptional(String, int, Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
getDelegate() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster: The delegate.
getException(String) - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: Like ChannelMap.get(java.lang.String) but throws an exception if a particular channel-name does not exist in the map.
getExtension() - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Which extension to use to write the image (without any leading period).
getFeature() - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: A list of features to calculate in an evaluation context.
getFontColor() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-color of drawn text
getFontName() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-name of drawn text
getFontSize() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-size of drawn text
getFrame(int) - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Gets a frame in the time-series.
getIndex() - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The index (starting at zero) of this Channel relative to others.
getLabel() - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: The label associated with stack.
getList() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: The list of StackProviderWithLabels that are tiled.
getName() - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The name of the Channel this entry represents.
getNumberChannels() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Number of channels in the background.
getNumColumns() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: How many columns when tiling, so long as there are sufficient StackProviderWithLabels.
getObjects() - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The objects for which features are calculated.
getOptional(String) - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore
getOutlineWidth() - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: The size of the outline, in terms of the number of voxels.
getRepeatZProvider() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
getRgb() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether it's an RGB or RGBA image when it has three/four channels respectively.
getSeriesIndex() - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The series to open to the read the metadata (zero-indexed).
getSize() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Explicit size of the image the string is draw on.
getStack() - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Provides the stack.
getStackReader() - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The StackReader to use to read the image metadata.
getStackReader() - Method in class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader: How to read an image from the file-system.
getStyle() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
getSuggestedFormatToWrite() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteOptions: A suggestion on what file-format to write.
getText() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Text to draw on an image.
getWhenFalse() - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==false.
getWhenTrue() - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==true.
getWriter() - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.channel.output.ChannelGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.DisplayStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.FlattenStackGenerator
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Guarantees on the attributes of all images created by the generator.
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster
guaranteedImageAttributes() - Method in class org.anchoranalysis.image.io.stack.output.generator.StackGenerator

H

hasChannel(String) - Method in interface org.anchoranalysis.image.io.channel.input.ChannelGetter: Does a particular channel-name exist?
hasChannel(String) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
hasChannel(String) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
hashCode() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
hasHdf5Extension(Path) - Static method in class org.anchoranalysis.image.io.object.input.ObjectCollectionReader: Whether a path has a suitable extension to be considered a HDF5 file?
HDF5ObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.hdf5: A generator that writes a ObjectCollection to a HDF5 file.
HDF5ObjectsGenerator() - Constructor for class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator: Creates with compression activated.
HDF5ObjectsGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator
HDF5PathHelper - Class in org.anchoranalysis.image.io.object: Paths to identify objects in the HDF5 for object-masks.
HistogramCSVGenerator - Class in org.anchoranalysis.image.io.histogram.output: Writes a histogram to a CSV file.
HistogramCSVGenerator() - Constructor for class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator
HistogramCSVReader - Class in org.anchoranalysis.image.io.histogram.input: Reads a CSV file from the file-system that describes a histogram of voxel values.

I

IfElse - Class in org.anchoranalysis.image.io.bean.object.draw: Branches to two different DrawObject depending on a predicate.
IfElse() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.IfElse
IfElse(IfElse.Predicate, DrawObject, DrawObject) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.IfElse: Creates for a particular condition.
IfElse.Predicate - Interface in org.anchoranalysis.image.io.bean.object.draw: Interface for the condition that is tested, to determine which DrawObject to use.
ImageInitializationFactory - Class in org.anchoranalysis.image.io: Creates instances of ImageInitialization based upon an InputOutputContext.
ImageIOException - Exception in org.anchoranalysis.image.io: When an error occurs reading or writing an image to/from the file-system.
ImageIOException(String) - Constructor for exception org.anchoranalysis.image.io.ImageIOException: Create with a message only.
ImageIOException(String, Throwable) - Constructor for exception org.anchoranalysis.image.io.ImageIOException: Create with a message and cause.
ImageIOException(Throwable) - Constructor for exception org.anchoranalysis.image.io.ImageIOException: Create with a cause only.
ImageMetadataInput - Class in org.anchoranalysis.image.io.stack.input: An input that provides a ImageMetadata but only lazily when first called.
ImageMetadataInput(NamedFile, CheckedSupplier<ImageMetadata, ImageIOException>) - Constructor for class org.anchoranalysis.image.io.stack.input.ImageMetadataInput: Create for a particular file and metadata.
ImageMetadataReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader: Reads an ImageMetadata from the file-system.
ImageMetadataReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.metadata.reader.ImageMetadataReader
ImageTimestampsAttributes - Class in org.anchoranalysis.image.io.stack.input: This combines ImageFileAttributes plus a timestamp for image-acqusition.
ImageTimestampsAttributes(ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
incrementingByOne(String, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Creates an sequence of stacks in a subdirectory with a number in the outputted file name that increments each time by one.
IndexedChannel - Class in org.anchoranalysis.image.io.bean.channel: A particular Channel to be read from a file, identified by its position (index) in the file.
IndexedChannel(String, int) - Constructor for class org.anchoranalysis.image.io.bean.channel.IndexedChannel
INPUT_IMAGE - Static variable in class org.anchoranalysis.image.io.stack.StackIdentifiers: The image used as the primary input for a task.
InputManagerWithStackReader<T extends InputFromManager> - Class in org.anchoranalysis.image.io.bean.stack.reader: Extends an InputManager to add a StackReader bean property.
InputManagerWithStackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader
isAlways2D() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether the output is guaranteed to only ever 2D i.e.
isBinary() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether all channels represent a binary image.
isBold() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Whether to bold the drawn text
isCreateShort() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the voxel-data-type of the created image is unsigned short, otherwise unsigned byte.
isCreateShort() - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: When true, text is drawn across all z-slices in the stack.
isEightBitChannels() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether each channel is 8 bits.
isEmpty() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: Whether the series contains no frames?
isExpandLabelZ() - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the label is repeated across all z-slices in the stack.
isIgnoreZeros() - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator: Iff true bins in the histogram with a zero count are not written
isIncludeZ() - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary
isRGB() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Does the display-stack contain an RGB image?
isRGB(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
isRGB(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: Whether the channels describe an RGB image.
isRGB(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
isRGB(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Whether the image-file has RGB encoded voxels.
isSingleChannel() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: The number of channels is guaranteed to be 1 in the output.
isThreeChannels() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: The number of channels is guaranteed to be 3 in the output.
iterator() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries

K

keys() - Method in class org.anchoranalysis.image.io.stack.time.ExtractFrameStore

M

MaskReader - Class in org.anchoranalysis.image.io.stack.input: Utility functions for reading a Mask from the file-system.
max(StackRGBState) - Method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Finds the maximum of this value and another, according to an ordering.
maybeAlways2D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which, depending on a flag, may be guaranteed to be 2D.
maybeRGB(boolean, boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which depending on a flags, may be RGB/RGBA or not, may be guaranteed to be 2D or not.
maybeRGBWithoutAlpha(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which depending on a flags, may be RGB or not.
metadata() - Method in class org.anchoranalysis.image.io.stack.input.ImageMetadataInput: The associated image metadata.
metadata(int, Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: The image-metadata associated with a particular series.
metadata(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Extracts metadata about the image.
midpoint(ObjectWithProperties, boolean) - Static method in class org.anchoranalysis.image.io.object.ExtractMidpoint: Calculates the midpoint of object.
min(StackRGBState) - Method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Finds the minimum of this value and another, according to an ordering.
multiplex(boolean, boolean) - Static method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Returns one of the three RGB_ states based upon two boolean flags.
multiplexAlpha(boolean) - Static method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Returns one of the two RGB_ states based upon a boolean flag.

N

NamedChannelsConcatenate - Class in org.anchoranalysis.image.io.channel.map: Exposes one or more instances of a NamedChannelsMap as a single aggregated NamedChannelsMap.
NamedChannelsConcatenate(NamedChannelsMap...) - Constructor for class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate: Create with arguments to concatenate.
NamedChannelsInput - Class in org.anchoranalysis.image.io.channel.input: Provides a set of channels as an input, with each channel having a name.
NamedChannelsInput() - Constructor for class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
NamedChannelsInputPart - Class in org.anchoranalysis.image.io.channel.input: One part of a NamedChannelsInput that can be combined with others.
NamedChannelsInputPart() - Constructor for class org.anchoranalysis.image.io.channel.input.NamedChannelsInputPart
NamedChannelsMap - Interface in org.anchoranalysis.image.io.channel.map: A collection of Channels, each identified by a unique name and a time-index.
NamedStacksOutputter - Class in org.anchoranalysis.image.io.stack.output: Outputs a named-set of stacks, performing appropriate checks on what is enabled or not.
names() - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: The names of the Channels in the map.
NO_RESTRICTIONS - Static variable in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: A factory with no restrictions on what kind of stacks can be outputted.
noScaling(DisplayStack) - Static method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Creates a background from a stack without any scaling.
NOT_RGB - org.anchoranalysis.image.io.stack.output.StackRGBState: Not a RGB image.
NUMBER_OBJECTS_ATTRIBUTE_NAME - Static variable in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator: Name of the attribute in the root of the HDF5 that stores the number of objects.
numberChannels() - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
numberChannels() - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The number of channels that exist for the series.
numberChannels() - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
numberChannels(Logger) - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Number of channels.
numberChannels(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of channels in the image-file e.g.
numberFrames() - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput
numberFrames() - Method in interface org.anchoranalysis.image.io.stack.input.ProvidesStackInput: The number of time-frames in the underlying input image.
numberFrames(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of frames in the image-file i.e.
numberSeries() - Method in class org.anchoranalysis.image.io.channel.input.NamedChannelsInput: Number of series that exist.
numberSeries() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The number of series (distinct sets of images) in the image-file.

O

ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes an object-mask as a mask (i.e.
ObjectAsMaskGenerator() - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator: Creates using a default image-resolution.
ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input: Reads an ObjectCollection from the filesystem
ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5: Centralized point to access a Generator which writes an ObjectCollection to the file-system.
OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class org.anchoranalysis.image.io.object.HDF5PathHelper: Hardcoded string that identifies in the HDF5 file for where the object-collection is stored.
ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Base class for generators that accept a set of objects as input.
ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsGrayscaleGenerator
ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb: A base class for generators that draw an ObjectCollection upon a RGBStack.
ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator
ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects as an image with an incrementing unique integer id value for each object.
ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsUniqueValueGenerator: Create with a particular dimensions.
ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale: Writes objects merged together as a mask.
ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class org.anchoranalysis.image.io.object.output.grayscale.ObjectsMergedAsMaskGenerator: Create with particular size for the mask image.
ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Like ObjectAsMaskGenerator but additionally outputs a serialized bounding box.
ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.io.object.output.mask.ObjectWithBoundingBoxGenerator: Create with a resolution, if it is known.
OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: A base-class for a StackWriter that writes an image that has either one or three channels.
OneOrThreeChannelsWriter() - Constructor for class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
open(int, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Open when we don't have a specific-type.
open(Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Open the first series when we don't have a specific-type.
openCheckType(int, VoxelDataType, Logger) - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Opens a time-series, and checks that it is a particular type.
OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input: An image file that has been opened for reading containing one or more series of image-Stacks.
OpenedNamedChannels - Class in org.anchoranalysis.image.io.channel.map: A set of named Channels available from an OpenedImageFile.
OpenedNamedChannels(OpenedImageFile, ChannelMap, int) - Constructor for class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReader: Opens a file containing one or more images.
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.ImageMetadataReader: Opens a file containing one or more images but does not read an image.
openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReaderOrientationCorrection: Opens a file containing one or more images but does not read an image.
openMask(StackReader, Path, BinaryValuesInt, OperationContext) - Static method in class org.anchoranalysis.image.io.stack.input.MaskReader: Utility functions for opening a single-channeled stack as a Mask.
or(StackWriteAttributes) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Combines with another StackWriteAttributes by performing a logical or on each field.
org.anchoranalysis.image.io - package org.anchoranalysis.image.io: Reading and writing of image-related data objects to and from the filesystem.
org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel: Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw: How to represent an object-mask in a raster that is being drawn.
org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature: Beans to specify the outputting of features into CSV from a ObjectCollection.
org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine: Beans to combine multiple stacks into a single stack before outputting.
org.anchoranalysis.image.io.bean.stack.metadata.reader - package org.anchoranalysis.image.io.bean.stack.metadata.reader: Bean classes for reading ImageMetadata from the file-system.
org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader: Bean classes for reading raster-files from the filesystem.
org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer: Bean classes for writing raster-files to the filesystem.
org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input: Non-bean classes for reading a Channel from the filesystem.
org.anchoranalysis.image.io.channel.map - package org.anchoranalysis.image.io.channel.map: Non-bean classes for a mapping of names to Channels.
org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output: Non-bean classes for writing a Channel to the filesystem.
org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input: Non-bean classes for reading a Histogram from the filesystem.
org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output: Non-bean classes for writing a Histogram to the filesystem.
org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object: Non-bean classes for reading / writing an ObjectCollection from and to the filesystem.
org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input: Non-bean classes for reading an ObjectCollection from the filesystem.
org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale: Writing an ObjectCollection to the filesystem as a single-channeled stack.
org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5: Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask: Writing an ObjectCollection to the filesystem as multiple binary singled-channeled images.
org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb: Writing an ObjectCollection to the filesystem as RGB raster-images.
org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack: Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input: Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output: Non-bean classes for writing a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box: Base classes for generators that ultimately write only a bounding-box portion of a Stack to the filesystem.
org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator: Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.image.io.stack.time - package org.anchoranalysis.image.io.stack.time: A time-sequence of Stacks.
Outline - Class in org.anchoranalysis.image.io.bean.object.draw: Draws the outline of each object-mask.
Outline() - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline: Creates with an outline-width of 1 voxel.
Outline(int) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline: Create with a particular outline-width.
Outline(int, boolean) - Constructor for class org.anchoranalysis.image.io.bean.object.draw.Outline
outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using a single color for all objects.
outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using varied colors for the objects.
outlineVariedColors(int, int, DisplayStack) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects on a background using varied colors for the objects.
outlineWithColorIndex(int, ColorIndex) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an outline around objects using a particular ColorIndex.
output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class org.anchoranalysis.image.io.stack.output.NamedStacksOutputter: Writes all or a subset from a set of named-stacks to a directory as a raster.
output(InputOutputContext) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: Outputs the feature-table.
OUTPUT_FEATURE_TABLE - Static variable in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The output-name for a CSV table of feature-values.
OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature: Specifies a table of feature-calculations on objects.
OutputFeatureTable() - Constructor for class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable
OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output: Creates output-sequences of different kinds for writing stacks to a directory.

P

ProvidesStackInput - Interface in org.anchoranalysis.image.io.stack.input: Base class for inputs which somehow eventually send up providing stacks, with or without names.
pyramid() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: Metadata to describe an image-pyramid, if it exists for this opened-image.

R

RasterDirectoryObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.mask: Writes each object as a binary Mask in a directory.
RasterGenerator<T> - Class in org.anchoranalysis.image.io.stack.output.generator: Transforms an entity to a Stack and writes it to the file-system.
RasterGenerator() - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator
RasterGeneratorBridge<T,V> - Class in org.anchoranalysis.image.io.stack.output.generator: Allows us to call an RasterGenerator<S> as if it was an RasterGenerator<T> using an function to connect the two.
RasterGeneratorBridge(RasterGenerator<V>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge: Creates with a delegate and a function to bridge the exposed element-type to the delegate element-type.
RasterGeneratorDelegateToDisplayStack<T> - Class in org.anchoranalysis.image.io.stack.output.generator: Delegates a RasterGeneratorSelectFormat to a SingleFileTypeGenerator<T, DisplayStack>.
RasterGeneratorDelegateToDisplayStack(SingleFileTypeGenerator<T, DisplayStack>, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack
RasterGeneratorDelegateToRaster<S,T> - Class in org.anchoranalysis.image.io.stack.output.generator: Uses a delegate raster-generator and optionally applies a conversions before calling RasterGeneratorDelegateToRaster.transform(T).
RasterGeneratorDelegateToRaster(RasterGenerator<S>) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster
RasterGeneratorSelectFormat<T> - Class in org.anchoranalysis.image.io.stack.output.generator: A RasterGenerator that selects an appropriate output-format based upon each generated image.
RasterGeneratorSelectFormat() - Constructor for class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat
readHistogramFromFile(Path) - Static method in class org.anchoranalysis.image.io.histogram.input.HistogramCSVReader: Reads a CSV file from the file-system that describes a histogram of voxel values.
readStack(Path, OperationContext) - Method in class org.anchoranalysis.image.io.bean.stack.reader.StackReader: Opens a file at path that should contain only a single-stack.
rgb(boolean) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Derives a StackWriteAttributes that will be RGB or RGB-A, but is otherwise unchanged.
rgb(boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always RGB, and depending on a flag, may be guaranteed to be 2D.
RGB_WITH_ALPHA - org.anchoranalysis.image.io.stack.output.StackRGBState: RGB with a alpha channel.
RGB_WITHOUT_ALPHA - org.anchoranalysis.image.io.stack.output.StackRGBState: RGB without any alpha channel.
rgbMaybe3D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always RGB/RGBA, and is not guaranteed to be 2D.

S

ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box: A stack that can be used as a background (and maybe scaled).
scaleBy(DisplayStack, ScaleFactor, VoxelsResizer) - Static method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: Creates a background from a stack with scaling.
selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Selects the file-extension to use for a particular stack.
selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat: Combines stack-write-options derived for a particular stack with the general write-options associated with the RasterGenerator.
selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator
setBackground(Either<Dimensions, DisplayStack>) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator: A background image or dimensions to define an empty background.
setBold(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Whether to bold the drawn text
setCreateShort(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the voxel-data-type of the created image is unsigned short, otherwise unsigned byte.
setCreateShort(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: When true, text is drawn across all z-slices in the stack.
setExpandLabelZ(boolean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: When true, the label is repeated across all z-slices in the stack.
setExtension(String) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Which extension to use to write the image (without any leading period).
setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: A list of features to calculate in an evaluation context.
setFontColor(RGBColorBean) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-color of drawn text
setFontName(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-name of drawn text
setFontSize(int) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TextStyle: Font-size of drawn text
setIgnoreZeros(boolean) - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator: Iff true bins in the histogram with a zero count are not written
setIncludeZ(boolean) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: If true the outline is also applied in the z-dimension, otherwise this is ignored as possible boundary
setIndex(int) - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The index (starting at zero) of this Channel relative to others.
setLabel(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: The label associated with stack.
setList(List<StackProviderWithLabel>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: The list of StackProviderWithLabels that are tiled.
setName(String) - Method in class org.anchoranalysis.image.io.bean.channel.IndexedChannel: The name of the Channel this entry represents.
setNumColumns(int) - Method in class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels: How many columns when tiling, so long as there are sufficient StackProviderWithLabels.
setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.image.io.bean.object.feature.OutputFeatureTable: The objects for which features are calculated.
setOutlineWidth(int) - Method in class org.anchoranalysis.image.io.bean.object.draw.Outline: The size of the outline, in terms of the number of voxels.
setRepeatZProvider(Provider<Stack>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Repeats the generated (2D) string in z, so it's the same z-size as intensityProvider
setSeriesIndex(int) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The series to open to the read the metadata (zero-indexed).
setSize(SizeXY) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Explicit size of the image the string is draw on.
setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Provides the stack.
setStackReader(StackReader) - Method in class org.anchoranalysis.image.io.bean.stack.metadata.reader.FromStackReader: The StackReader to use to read the image metadata.
setStackReader(StackReader) - Method in class org.anchoranalysis.image.io.bean.stack.reader.InputManagerWithStackReader: How to read an image from the file-system.
setStyle(TextStyle) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText
setText(String) - Method in class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Text to draw on an image.
setWhenFalse(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==false.
setWhenTrue(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.IfElse: The DrawObject that is used when condition==true.
setWriter(DrawObject) - Method in class org.anchoranalysis.image.io.bean.object.draw.Flatten
singleChannelMaybe3D(boolean) - Static method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributesFactory: A StackWriteAttributes which is always a single-channel, and depending on a flag, may be guaranteed to be 2D.
size() - Method in class org.anchoranalysis.image.io.stack.time.TimeSeries: The number of frames in the time-series.
sizeAfterAnyScaling() - Method in class org.anchoranalysis.image.io.stack.output.box.ScaleableBackground: The size of the background after any scaling has occurred.
sizeT(Logger) - Method in class org.anchoranalysis.image.io.channel.map.NamedChannelsConcatenate
sizeT(Logger) - Method in interface org.anchoranalysis.image.io.channel.map.NamedChannelsMap: The number of frames along the time-axis.
sizeT(Logger) - Method in class org.anchoranalysis.image.io.channel.map.OpenedNamedChannels
StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator: Writes a stack to the filesystem.
StackGenerator(boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator: Creates a generator that performs no padding.
StackGenerator(boolean, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator: Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's dimensions.
StackGenerator(boolean, StackWriteAttributes) - Constructor for class org.anchoranalysis.image.io.stack.output.generator.StackGenerator
StackIdentifiers - Class in org.anchoranalysis.image.io.stack: Common identifiers used for storing particular types of images.
StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine: Combines a Provider<Stack> with a label.
StackProviderWithLabel() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel
StackProviderWithLabel(Stack, String) - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.StackProviderWithLabel: Create for a particular Stack and label.
StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader: Reads an image-Stack from the file-system.
StackReader() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.StackReader
StackReaderOrientationCorrection - Class in org.anchoranalysis.image.io.bean.stack.reader: A StackReader that supports the correction of orientation as images are read from the file-system.
StackReaderOrientationCorrection() - Constructor for class org.anchoranalysis.image.io.bean.stack.reader.StackReaderOrientationCorrection
StackRGBState - Enum in org.anchoranalysis.image.io.stack.output: Whether a stack is RGB or RGBA or neither.
StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input: Provides a single stack (or a time series of such stacks) as an input
StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output: Attributes describing stack which may determine which writer is used.
StackWriteAttributes(boolean, boolean, boolean, StackRGBState, boolean) - Constructor for class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Alternative constructor that assumes each channel is 8-bits.
StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output: Creates StackWriteAttributes to describe certain attributes.
StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output: A combination of attributions describing how to write a particular stack and any suggestions from the user.
StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class org.anchoranalysis.image.io.stack.output.StackWriteOptions
StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer: Writes a stack (i.e.
StackWriter() - Constructor for class org.anchoranalysis.image.io.bean.stack.writer.StackWriter

T

test(ObjectWithProperties, RGBStack, int) - Method in interface org.anchoranalysis.image.io.bean.object.draw.IfElse.Predicate: Evaluates whether the condition is true or not.
TextStyle - Class in org.anchoranalysis.image.io.bean.stack.combine: The size and style of text as it should appear in an image.
TextStyle() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.TextStyle
tile(List<StackProviderWithLabel>, int, boolean, boolean) - Static method in class org.anchoranalysis.image.io.stack.input.TileStackProviders: Creates a StackProvider that provides a tiled-representation of providers.
TileStackProviders - Class in org.anchoranalysis.image.io.stack.input: Tile multiple StackProviders into a single StackProvider.
TileWithLabels - Class in org.anchoranalysis.image.io.bean.stack.combine: Tiles a number of StackProviderWithLabels as a single StackProvider.
TileWithLabels() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.TileWithLabels
TimeSeries - Class in org.anchoranalysis.image.io.stack.time: An ordered collection of Stacks, each representing a frame in a time-series.
TimeSeries(Stream<Stack>) - Constructor for class org.anchoranalysis.image.io.stack.time.TimeSeries: Creates a TimeSeries from a stream of frames.
TimeSeries(Stack) - Constructor for class org.anchoranalysis.image.io.stack.time.TimeSeries: Creates a TimeSeries containing a single frame only.
timestamps() - Method in interface org.anchoranalysis.image.io.stack.input.OpenedImageFile: The timestamps and file-attributes associated with the image.
toString() - Method in class org.anchoranalysis.image.io.stack.input.ImageTimestampsAttributes
toString() - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: A user-friendly description of the stack-type to include in error and warning messages.
transform(Channel) - Method in class org.anchoranalysis.image.io.channel.output.ChannelGenerator
transform(ObjectCollectionWithProperties) - Method in class org.anchoranalysis.image.io.object.output.rgb.ObjectsAsRGBGenerator
transform(Stack) - Method in class org.anchoranalysis.image.io.stack.output.generator.StackGenerator
transform(ObjectCollection) - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsAsUniqueValueGenerator
transform(ObjectCollection) - Method in class org.anchoranalysis.image.io.object.output.grayscale.ObjectsMergedAsMaskGenerator
transform(ObjectMask) - Method in class org.anchoranalysis.image.io.object.output.mask.ObjectAsMaskGenerator
transform(BoundedList<ObjectMask>) - Method in class org.anchoranalysis.image.io.stack.output.box.DrawObjectOnStackGenerator
transform(BoundingBox) - Method in class org.anchoranalysis.image.io.stack.output.box.ExtractBoundingBoxAreaFromStackGenerator
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorBridge
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToDisplayStack
transform(T) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorDelegateToRaster

V

valueOf(String) - Static method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Returns the enum constant of this type with the specified name.
values() - Method in class org.anchoranalysis.image.io.channel.input.ChannelMap: All IndexedChannels that exist in the map.
values() - Static method in enum org.anchoranalysis.image.io.stack.output.StackRGBState: Returns an array containing the constants of this enum type, in the order they are declared.

W

withBackgroundAndColors(DrawObject, DisplayStack, ColorIndex) - Static method in class org.anchoranalysis.image.io.object.output.rgb.DrawObjectsGenerator: Creates a generator that draws an object in a particular way with particular colors and background.
withoutOrderCurrentDirectory(String, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Creates a sequence of stacks in the current context's directory that has no pattern.
withoutOrderSubset(NamedProvider<Stack>, String, boolean, OutputterChecked) - Method in class org.anchoranalysis.image.io.stack.output.OutputSequenceStackFactory: Writes all or a subset from a set of named-stacks to a directory.
write(T, OutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator
writeAsRGB(Stack) - Method in class org.anchoranalysis.image.io.stack.output.StackWriteAttributes: Whether to write a stack in RGB mode?
writer(OutputWriteSettings) - Static method in class org.anchoranalysis.image.io.stack.output.generator.GeneratorOutputter: Gets the default StackWriter.
WriterErrorMessageHelper - Class in org.anchoranalysis.image.io.bean.stack.writer: Helps create similar error messages among StackWriters.
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: Writes a stack to the filesystem at a particular path.
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.image.io.bean.stack.writer.OneOrThreeChannelsWriter: Writes the Stack to the file-system, after a check has already occurred that the correct number of channels exist.
writeStackWithExtension(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.image.io.bean.stack.writer.StackWriter: Writes a stack to the filesystem at a particular path with an extension appended to the path.
WriteText - Class in org.anchoranalysis.image.io.bean.stack.combine: Creates an image that contains text only.
WriteText() - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.WriteText
WriteText(String) - Constructor for class org.anchoranalysis.image.io.bean.stack.combine.WriteText: Creates the bean to write particular text, otherwise using default settings.
writeToFile(ObjectCollection, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.object.output.hdf5.HDF5ObjectsGenerator
writeToFile(Histogram, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.histogram.output.HistogramCSVGenerator
writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: Writes a stack to the file-system.
writeToFile(T, Stack, StackWriteOptions, OutputWriteSettings, Path) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGeneratorSelectFormat
writeWithIndex(T, String, IndexableOutputNameStyle, ElementOutputter) - Method in class org.anchoranalysis.image.io.stack.output.generator.RasterGenerator: As only a single-file is involved, this methods delegates to a simpler virtual method.

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