Package | Description |
---|---|
org.anchoranalysis.annotation.io.assignment.generator |
Generates output images to illustrate a
Assignment between annotations. |
org.anchoranalysis.annotation.io.bean.comparer |
What to compare an annotation (ground truth) against?
|
org.anchoranalysis.feature.energy |
A particular stack used in feature-calculations called a
EnergyStack together with related classes. |
org.anchoranalysis.image.bean.displayer | |
org.anchoranalysis.image.bean.nonbean.init |
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
|
org.anchoranalysis.image.bean.nonbean.spatial.arrange |
Non-beans to specify how to form a single-image by spatially combining other images.
|
org.anchoranalysis.image.bean.provider |
Base classes for providers of different core data entities related to images.
|
org.anchoranalysis.image.bean.provider.stack |
A provider of
Stack s. |
org.anchoranalysis.image.core.bufferedimage |
Conversions and operations involving Java AWT's
BufferedImage . |
org.anchoranalysis.image.core.channel.convert |
Converts a channel to other data-types.
|
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.core.stack.named |
A collection of
Stack s, each with a unique identifier
as a name. |
org.anchoranalysis.image.feature.bean.evaluator |
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
|
org.anchoranalysis.image.inference.bean.segment.instance |
Instance-segmentation of a
Stack . |
org.anchoranalysis.image.inference.segment |
Non-beans pertaining to segmentation of images via model inference.
|
org.anchoranalysis.image.io.bean.stack.combine |
Beans to combine multiple stacks into a single stack before outputting.
|
org.anchoranalysis.image.io.bean.stack.reader |
Bean classes for reading raster-files from the filesystem.
|
org.anchoranalysis.image.io.bean.stack.writer |
Bean classes for writing raster-files to the filesystem.
|
org.anchoranalysis.image.io.channel.map |
Non-bean classes for a mapping of names to
Channel s. |
org.anchoranalysis.image.io.channel.output |
Non-bean classes for writing a
Channel to the
filesystem. |
org.anchoranalysis.image.io.object.output.grayscale |
Writing an
ObjectCollection to the filesystem as a
single-channeled stack. |
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 |
Writing an
ObjectCollection to the filesystem as
RGB raster-images. |
org.anchoranalysis.image.io.stack |
Non-bean classes for reading / writing a
Stack from
and to the filesystem. |
org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from the
filesystem. |
org.anchoranalysis.image.io.stack.output |
Non-bean classes for writing a
Stack to the
filesystem. |
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 |
Base classes for generators that ultimately write a
Stack to the filesystem. |
org.anchoranalysis.image.io.stack.time |
A time-sequence of
Stack s. |
org.anchoranalysis.io.bioformats.bean.writer |
Writing stacks to the file system using the Bioformats library.
|
org.anchoranalysis.io.imagej.bean.stack.writer |
Raster-writers that use ImageJ to write images to the filesystem.
|
org.anchoranalysis.io.imagej.convert |
Converts to and from ImageJ data-structures for images.
|
org.anchoranalysis.mpp.io.marks.generator | |
org.anchoranalysis.mpp.io.output |
Non-beans for writing data structures related to marked point processes from the file system.
|
org.anchoranalysis.plugin.image.bean.stack.provider |
Implementations of
StackProvider . |
org.anchoranalysis.plugin.image.bean.stack.provider.color |
Implementations of
StackProvider that color
portions of an image. |
org.anchoranalysis.plugin.image.bean.thumbnail.object |
Implementations of
ThumbnailFromObjects . |
org.anchoranalysis.plugin.image.bean.thumbnail.stack |
Implementations of
ThumbnailFromStack . |
org.anchoranalysis.plugin.image.task.bean.format |
Tasks for converting image-formats.
|
org.anchoranalysis.plugin.image.task.bean.scale |
Tasks to scale an image.
|
org.anchoranalysis.plugin.image.task.grouped |
Non-bean classes about grouping channels or other inputs.
|
org.anchoranalysis.plugin.imagej.bean.stack.provider |
Implementations of
StackProvider that call
ImageJ. |
org.anchoranalysis.plugin.io.bean.stack.writer |
Implementations of
StackWriter . |
org.anchoranalysis.plugin.io.multifile |
Non-bean classes to help use multiple files to represent a single
Stack . |
org.anchoranalysis.plugin.io.multifile.buffer |
Buffers used in
org.anchoranalysis.plugin.io.multifile . |
org.anchoranalysis.plugin.onnx.bean.object.segment.stack |
Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection . |
org.anchoranalysis.plugin.opencv.bean.color |
Operations involving color-spaces and OpenCV.
|
org.anchoranalysis.plugin.opencv.bean.object.segment.stack |
Segmentation of a
Stack using OpenCV. |
org.anchoranalysis.plugin.opencv.bean.stack | |
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
org.anchoranalysis.test.image |
Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
|
org.anchoranalysis.test.image.io |
Utilities for testing-related reading and writing to the filesystem.
|
org.anchoranalysis.test.image.load |
Load test image data.
|
org.anchoranalysis.test.image.segment |
Fixtures or other helper classes for testing image segmentation algorithms.
|
Modifier and Type | Method and Description |
---|---|
Stack |
DrawColoredObjects.createObjectsImage(Assignment<ObjectMask> assignment,
boolean left,
AssignmentColorPool colorPool)
Creates an image with the objects colored, as indicated in the class description.
|
Stack |
AssignmentGenerator.transform(Assignment<ObjectMask> element) |
Modifier and Type | Method and Description |
---|---|
List<NameValue<Stack>> |
MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation,
DisplayStack background,
Path annotationPath,
ColorScheme colorScheme,
Path modelDirectory,
OperationContext context,
boolean debugMode)
|
Modifier and Type | Method and Description |
---|---|
Stack |
EnergyStackWithoutParameters.asStack()
Derive a
Stack representation containing the identical channels to the current
instance. |
Stack |
EnergyStack.asStack()
Derive a
Stack representation containing the identical channels to the current
instance. |
Constructor and Description |
---|
EnergyStack(Stack stack)
Create from a
EnergyStack without any additional parameters. |
EnergyStack(Stack stack,
Dictionary dictionary)
Create from a
Stack with associated parameters in a Dictionary . |
EnergyStackWithoutParameters(Stack stack)
Create a energy-stack comprised of all channels from a stack
|
Modifier and Type | Method and Description |
---|---|
DisplayStack |
StackDisplayer.deriveFrom(Stack stack)
Derives a
DisplayStack from a RGBStack . |
Modifier and Type | Method and Description |
---|---|
NamedProvider<Stack> |
ImageInitialization.combinedStacks()
Exposes several entities that have natural
Stack representations as a unified NamedProvider . |
NamedProviderStore<Stack> |
ImageInitialization.stacks()
A collection of
Stack s, indexed by name. |
Modifier and Type | Method and Description |
---|---|
void |
ImageInitialization.addStack(String identifier,
Stack toAdd)
Adds a
Stack to the corresponding named-collection of stacks. |
Modifier and Type | Method and Description |
---|---|
void |
ImageInitialization.addStacksFrom(NamedProvider<Stack> source)
Adds all the
Stack s available in a NamedProvider using the corresponding
identifiers. |
Modifier and Type | Method and Description |
---|---|
static void |
StackCopierAtBox.copyImageInto(Stack source,
Stack destination,
BoundingBox box)
|
Modifier and Type | Method and Description |
---|---|
Stack |
MaskProvider.getAsStack() |
Stack |
ChannelProvider.getAsStack() |
Modifier and Type | Method and Description |
---|---|
protected abstract Stack |
StackProviderUnary.createFromStack(Stack stack)
Creates a
Stack given the entity provided by the delegate. |
Stack |
StackProviderUnary.get() |
Stack |
Arrange.get() |
Stack |
StackProvider.getAsStack() |
Modifier and Type | Method and Description |
---|---|
List<Provider<Stack>> |
Arrange.getList()
The stacks that are passed in respect order into
arrange . |
Provider<Stack> |
StackProviderUnary.getStack()
The delegate
Provider<Stack> that is called. |
Modifier and Type | Method and Description |
---|---|
protected abstract Stack |
StackProviderUnary.createFromStack(Stack stack)
Creates a
Stack given the entity provided by the delegate. |
Modifier and Type | Method and Description |
---|---|
void |
Arrange.addStack(Provider<Stack> provider)
Adds a stack to the existing list of stack-providers.
|
void |
Arrange.setList(List<Provider<Stack>> list)
The stacks that are passed in respect order into
arrange . |
void |
StackProviderUnary.setStack(Provider<Stack> stack)
The delegate
Provider<Stack> that is called. |
Modifier and Type | Method and Description |
---|---|
static Stack |
CreateStackFromBufferedImage.createFrom(BufferedImage bufferedImage)
Create a
Stack by converting a BufferedImage . |
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
BufferedImageFromStack.create(Stack stack)
Creates a
BufferedImage from a Stack . |
Modifier and Type | Method and Description |
---|---|
Stack |
ChannelConverter.convert(Stack stack,
ConversionPolicy changeExisting)
Like
ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack . |
Modifier and Type | Method and Description |
---|---|
Stack |
ChannelConverter.convert(Stack stack,
ConversionPolicy changeExisting)
Like
ChannelConverter.convert(Channel, ConversionPolicy) but converts every channel in a Stack . |
Modifier and Type | Method and Description |
---|---|
Stack |
RGBStack.asStack()
Exposes the underlying stack, storing the three RGB channels in respective order.
|
Stack |
DisplayStack.deriveStack(boolean alwaysNew)
Derives a
Stack from the display-stack that will be converted to 8-bit if necessary. |
Stack |
Stack.duplicateDeep()
Performs a deep copy of the stack, so that all channels are duplicated.
|
Stack |
Stack.duplicateShallow()
Performs a shallow copy of the stack, so that all channels are reused.
|
Stack |
Stack.extractSlice(int z)
Extract a particular z-slice from the
Stack as a new stack. |
Stack |
Stack.extractUpToThreeChannels()
|
Stack |
ProviderAsStack.getAsStack()
Retrieves or creates a
Stack representation of an entity. |
Stack |
DisplayStack.getStack()
The underlying stack that will be displayed, possibly after conversion.
|
Stack |
Stack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)
Produces a new stack with a particular mapping applied to each channel.
|
Stack |
Stack.mapChannelWithIndex(CheckedBiFunction<Channel,Integer,Channel,OperationFailedException> mapping)
Produces a new stack with a particular mapping applied to each channel (with an index of the
channel also available).
|
Stack |
Stack.projectMax()
Creates a Maximum
Intensity Projection of each channel.
|
Modifier and Type | Method and Description |
---|---|
void |
Stack.addChannelsFrom(Stack stack)
Add the channels from another instance into this instance.
|
boolean |
Stack.equalsDeep(Stack other,
boolean compareResolution)
Are the two stack equal using a deep voxel by voxel comparison of each channel?
|
Constructor and Description |
---|
DisplayStack(Stack stack)
Create for a particular
Stack where all channels are already guaranteed to be
unsigned-bit. |
DisplayStack(Stack stack,
boolean eventuallyThree,
java.util.function.Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)
Create for a particular
Stack that may needed to be converted. |
RGBStack(Stack stack)
Creates from an existing stack (which must have 1 or 3 channels).
|
Modifier and Type | Method and Description |
---|---|
NamedProvider<Stack> |
NamedStacksSupplier.get()
Gets the
NamedProvider of Stack s. |
Optional<Stack> |
NamedStacks.getOptional(String identifier) |
Modifier and Type | Method and Description |
---|---|
void |
NamedStacks.add(String identifier,
Stack stack)
Add a stack.
|
void |
NamedStacksUniformSize.add(String identifier,
Stack stack)
Adds an element to the store.
|
Modifier and Type | Method and Description |
---|---|
void |
NamedStacks.add(String identifier,
StoreSupplier<Stack> supplier) |
void |
NamedStacks.addFrom(NamedProvider<Stack> source)
Adds a
Stack from a NamedProvider . |
void |
NamedStacks.addFromWithPrefix(NamedProvider<Stack> source,
String prefix)
Like
NamedStacks.addFrom(NamedProvider) but additionally adds a prefix to the name when adding. |
NamedStacks |
NamedStacks.applyOperation(java.util.function.UnaryOperator<Stack> operation,
Optional<Dimensions> dimensions)
Applies an operation on each
Stack in the collection and returns a new derived
collection. |
<E extends Exception> |
NamedStacks.forEach(CheckedBiConsumer<String,StoreSupplier<Stack>,E> consumer)
Iterates over each entry in the map.
|
Modifier and Type | Method and Description |
---|---|
Provider<Stack> |
FeatureEvaluator.getStackEnergy()
Optionally specifies an energy-stack to be associated with every calculation input.
|
Modifier and Type | Method and Description |
---|---|
void |
FeatureEvaluator.setStackEnergy(Provider<Stack> stackEnergy)
Optionally specifies an energy-stack to be associated with every calculation input.
|
Modifier and Type | Method and Description |
---|---|
protected abstract T |
SegmentStackIntoObjectsScaleDecode.deriveInput(Stack stack,
Optional<double[]> subtractMeans)
Derives the input tensor from an image.
|
SegmentedObjects |
SegmentStackIntoObjectsScaleDecode.segment(Stack stack,
ConcurrentModelPool<S> modelPool,
ExecutionTimeRecorder executionTimeRecorder) |
abstract SegmentedObjects |
SegmentStackIntoObjectsPooled.segment(Stack stack,
ConcurrentModelPool<T> modelPool,
ExecutionTimeRecorder executionTimeRecorder)
Segments a stack to produce an object-collection.
|
SegmentedObjects |
SuppressNonMaximum.segment(Stack stack,
ConcurrentModelPool<T> modelPool,
ExecutionTimeRecorder executionTimeRecorder) |
SegmentedObjects |
SegmentStackIntoObjectsPooled.segment(Stack stack,
ExecutionTimeRecorder executionTimeRecorder)
Segments individually using a pool of size 1 just for one stack.
|
Modifier and Type | Method and Description |
---|---|
Stack |
SegmentedBackground.atInputScale()
The background scaled to match the size of the input-image.
|
Stack |
SegmentedBackground.atModelScale()
The background scaled to match the size of the input for model inference.
|
Stack |
SegmentedObjectsAtScale.background()
The background image associated with this particular scale.
|
Modifier and Type | Method and Description |
---|---|
DualScale<Stack> |
SegmentedBackground.getBackground()
The background image to use for segmentation, when visualizing segmentations.
|
Constructor and Description |
---|
SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source,
java.util.function.Function<MultiScaleObject,ObjectMask> extractObject,
Stack background,
StackDisplayer displayer,
ExecutionTimeRecorder executionTimeRecorder,
String executionTimeSuffix) |
Constructor and Description |
---|
SegmentedBackground(DualScale<Stack> background,
StackDisplayer displayer) |
Modifier and Type | Method and Description |
---|---|
Stack |
TileWithLabels.get() |
Stack |
WriteText.get() |
Modifier and Type | Method and Description |
---|---|
Provider<Stack> |
WriteText.getRepeatZProvider()
Repeats the generated (2D) string in z, so it's the same z-size as
intensityProvider |
Provider<Stack> |
StackProviderWithLabel.getStack()
Provides the stack.
|
Modifier and Type | Method and Description |
---|---|
void |
WriteText.setRepeatZProvider(Provider<Stack> repeatZProvider)
Repeats the generated (2D) string in z, so it's the same z-size as
intensityProvider |
void |
StackProviderWithLabel.setStack(Provider<Stack> stack)
Provides the stack.
|
Constructor and Description |
---|
StackProviderWithLabel(Stack stack,
String label)
Create for a particular
Stack and label. |
Modifier and Type | Method and Description |
---|---|
Stack |
StackReader.readStack(Path path,
OperationContext context)
Opens a file at
path that should contain only a single-stack. |
Modifier and Type | Method and Description |
---|---|
void |
OneOrThreeChannelsWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
abstract void |
StackWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options)
Writes a stack to the filesystem at a particular path.
|
protected abstract void |
OneOrThreeChannelsWriter.writeStackAfterCheck(Stack stack,
Path filePath)
Writes the
Stack to the file-system, after a check has already occurred that the
correct number of channels exist. |
Path |
StackWriter.writeStackWithExtension(Stack stack,
Path filePath,
StackWriteOptions options)
Writes a stack to the filesystem at a particular path with an extension appended to the path.
|
Modifier and Type | Method and Description |
---|---|
StoreSupplier<Stack> |
OpenedNamedChannels.allChannelsAsStack(int t,
Logger logger) |
StoreSupplier<Stack> |
NamedChannelsConcatenate.allChannelsAsStack(int t,
Logger logger) |
StoreSupplier<Stack> |
NamedChannelsMap.allChannelsAsStack(int timeIndex,
Logger logger)
Combines all channels as a single
Stack at a particular time-frame. |
Modifier and Type | Method and Description |
---|---|
Stack |
ChannelGenerator.transform(Channel element) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectsMergedAsMaskGenerator.transform(ObjectCollection element) |
Stack |
ObjectsAsUniqueValueGenerator.transform(ObjectCollection element) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectAsMaskGenerator.transform(ObjectMask element) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectsAsRGBGenerator.transform(ObjectCollectionWithProperties element) |
Modifier and Type | Method and Description |
---|---|
static RGBStack |
ConvertStackToRGB.convert(Stack stack,
StackDisplayer displayer,
boolean alwaysNew)
Converts all of a
DisplayStack to a RGBStack . |
Modifier and Type | Method and Description |
---|---|
default Stack |
ProvidesStackInput.asStack(Logger logger)
Exposes the input as a single
Stack throw an error if more than one exists. |
Modifier and Type | Method and Description |
---|---|
default void |
ProvidesStackInput.addToStoreInferNames(NamedProviderStore<Stack> store,
Logger logger)
Adds the current object to a named-store of stacks (using the default series).
|
Modifier and Type | Method and Description |
---|---|
OutputSequenceIncrementing<Stack> |
OutputSequenceStackFactory.incrementingByOne(String subdirectoryName,
OutputterChecked outputter)
Creates an sequence of stacks in a subdirectory with a number in the outputted file name that
increments each time by one.
|
OutputSequenceIndexed<Stack,String> |
OutputSequenceStackFactory.withoutOrderCurrentDirectory(String outputName,
OutputterChecked outputter)
Creates a sequence of stacks in the current context's directory that has no pattern.
|
Modifier and Type | Method and Description |
---|---|
static StackWriteAttributes |
StackWriteAttributesFactory.from(Stack stack)
The options that narrowly describe a stack as possible.
|
boolean |
StackWriteAttributes.writeAsRGB(Stack stack)
Whether to write a stack in RGB mode?
|
Modifier and Type | Method and Description |
---|---|
static void |
NamedStacksOutputter.output(NamedProvider<Stack> stacks,
String outputName,
boolean suppressSubdirectory,
OutputterChecked outputter)
Writes all or a subset from a set of named-stacks to a directory as a raster.
|
void |
OutputSequenceStackFactory.withoutOrderSubset(NamedProvider<Stack> stacks,
String outputName,
boolean suppressSubdirectory,
OutputterChecked outputter)
Writes all or a subset from a set of named-stacks to a directory.
|
Modifier and Type | Method and Description |
---|---|
Stack |
ScaleableBackground.extractRegionFromStack(BoundingBox box)
Extracts a portion of a stack (flattened and maybe scaled) corresponding to a bounding-box
|
Stack |
DrawObjectOnStackGenerator.transform(BoundedList<ObjectMask> element) |
Stack |
ExtractBoundingBoxAreaFromStackGenerator.transform(BoundingBox element) |
Modifier and Type | Method and Description |
---|---|
static DrawObjectOnStackGenerator |
DrawObjectOnStackGenerator.createFromGenerator(TransformingGenerator<BoundingBox,Stack> backgroundGenerator,
int outlineWidth,
ColorIndex colors)
Creates an extracted-object generator that draws an outline - with default color green and
flattened in Z.
|
Modifier and Type | Method and Description |
---|---|
protected Stack |
DisplayStackGenerator.convertBeforeAssign(DisplayStack element) |
protected Stack |
FlattenStackGenerator.convertBeforeAssign(Stack element) |
protected Stack |
FlattenStackGenerator.convertBeforeTransform(Stack stack) |
protected abstract Stack |
RasterGeneratorDelegateToRaster.convertBeforeTransform(Stack stack)
Converts an element before calling
RasterGeneratorDelegateToRaster.transform(T) on the delegate . |
protected Stack |
RasterGeneratorBridge.convertBeforeTransform(Stack stack) |
protected Stack |
DisplayStackGenerator.convertBeforeTransform(Stack stack) |
Stack |
StackGenerator.transform(Stack element) |
Stack |
RasterGeneratorDelegateToRaster.transform(T element) |
Stack |
RasterGeneratorBridge.transform(T element) |
Stack |
RasterGeneratorDelegateToDisplayStack.transform(T element) |
Modifier and Type | Method and Description |
---|---|
protected Stack |
FlattenStackGenerator.convertBeforeAssign(Stack element) |
protected Stack |
FlattenStackGenerator.convertBeforeTransform(Stack stack) |
protected abstract Stack |
RasterGeneratorDelegateToRaster.convertBeforeTransform(Stack stack)
Converts an element before calling
RasterGeneratorDelegateToRaster.transform(T) on the delegate . |
protected Stack |
RasterGeneratorBridge.convertBeforeTransform(Stack stack) |
protected Stack |
DisplayStackGenerator.convertBeforeTransform(Stack stack) |
protected abstract String |
RasterGenerator.selectFileExtension(Stack stack,
StackWriteOptions options,
OutputWriteSettings settings,
Optional<Logger> logger)
Selects the file-extension to use for a particular stack.
|
protected String |
RasterGeneratorSelectFormat.selectFileExtension(Stack stack,
StackWriteOptions options,
OutputWriteSettings settings,
Optional<Logger> logger)
Combines stack-write-options derived for a particular stack with the general write-options
associated with the
RasterGenerator . |
Stack |
StackGenerator.transform(Stack element) |
protected abstract void |
RasterGenerator.writeToFile(T untransformedElement,
Stack transformedElement,
StackWriteOptions options,
OutputWriteSettings settings,
Path filePath)
Writes a stack to the file-system.
|
protected void |
RasterGeneratorSelectFormat.writeToFile(T element,
Stack transformedElement,
StackWriteOptions options,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
Stack |
TimeSeries.getFrame(int index)
Gets a frame in the time-series.
|
Modifier and Type | Method and Description |
---|---|
Iterator<Stack> |
TimeSeries.iterator() |
Constructor and Description |
---|
TimeSeries(Stack frame)
Creates a
TimeSeries containing a single frame only. |
Constructor and Description |
---|
ExtractFrameStore(NamedProviderStore<Stack> stacks)
Creates to extract at time-index 0.
|
ExtractFrameStore(NamedProviderStore<Stack> stacks,
int timeIndex)
Creates to extract at time-index
timeIndex . |
TimeSeries(java.util.stream.Stream<Stack> frames)
Creates a
TimeSeries from a stream of frames. |
Modifier and Type | Method and Description |
---|---|
void |
BioformatsWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
void |
Tiff.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
Modifier and Type | Method and Description |
---|---|
void |
ImageJRasterWriter.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
protected void |
ImageJRasterWriter.writeStackTime(Stack stack,
Path path,
boolean makeRGB)
Writes a stack as a time-sequence (many images together in a single file.).
|
Modifier and Type | Method and Description |
---|---|
static ij.ImagePlus |
ConvertToImagePlus.from(Stack stack,
boolean makeRGB)
Creates an
ImagePlus from a Stack . |
Modifier and Type | Method and Description |
---|---|
Stack |
MarksGeneratorBase.transform(ColoredMarksWithDisplayStack element) |
Stack |
MarksAsUniqueValueGenerator.transform(MarkCollection element) |
Modifier and Type | Method and Description |
---|---|
static DisplayStack |
BackgroundCreator.createBackground(NamedProviderStore<Stack> stackCollection,
String backgroundStackName,
StackDisplayer displayer) |
Modifier and Type | Method and Description |
---|---|
Stack |
Reference.get() |
Stack |
FromInput.get() |
Stack |
FromChannelOrMask.get() |
Stack |
Concatenate.get() |
Modifier and Type | Method and Description |
---|---|
static Stack |
ThreeChannels.createRGBStack(Channel channelRed,
Channel channelGreen,
Channel channelBlue,
VoxelDataType outputType) |
Stack |
ThreeChannels.get() |
Stack |
ColoredBase.get() |
Modifier and Type | Method and Description |
---|---|
abstract ThumbnailBatch<ObjectCollection> |
ThumbnailFromObjects.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> background,
ExecutionTimeRecorder executionTimeRecorder)
Initializes a batch to create thumbnails.
|
ThumbnailBatch<ObjectCollection> |
OutlinePreserveRelativeSize.start(ObjectCollection objects,
StreamableCollection<BoundingBox> boundingBoxes,
Optional<Stack> backgroundSource,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
abstract DisplayStack |
ThumbnailFromStack.thumbnailFor(Stack stack)
Creates a thumbnail for a stack
|
DisplayStack |
ScaleToSize.thumbnailFor(Stack stack) |
Modifier and Type | Method and Description |
---|---|
protected OutputSequenceIndexed<Stack,String> |
ConvertImageFormat.createSharedStateJob(InputOutputContext context)
Sets a new output-sequence for the series.
|
Modifier and Type | Method and Description |
---|---|
void |
ConvertImageFormat.doStack(InputBound<NamedChannelsInput,NoSharedState> input,
OutputSequenceIndexed<Stack,String> sharedStateJob,
int seriesIndex,
int numberSeries,
InputOutputContext context) |
void |
ConvertImageFormat.endSeries(NoSharedState sharedStateTask,
OutputSequenceIndexed<Stack,String> sharedStateJob,
InputOutputContext context) |
void |
ConvertImageFormat.startSeries(NoSharedState sharedStateTask,
OutputSequenceIndexed<Stack,String> sharedStateJob,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected Stack |
ScaleImageCommonSize.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
CommonSize sharedState) |
protected Stack |
ScaleImageIndependently.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
NoSharedState sharedState) |
protected abstract Stack |
ScaleImage.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
S sharedState)
Produce a scaled version of a
Stack , mapping each channel to a scaled version of
itself. |
Modifier and Type | Method and Description |
---|---|
protected Stack |
ScaleImageCommonSize.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
CommonSize sharedState) |
protected Stack |
ScaleImageIndependently.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
NoSharedState sharedState) |
protected abstract Stack |
ScaleImage.scaleStack(Stack stack,
Optional<ImageSizeSuggestion> suggestedSize,
VoxelsResizer voxelsResizer,
S sharedState)
Produce a scaled version of a
Stack , mapping each channel to a scaled version of
itself. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelSource.extractChannel(Stack stack,
boolean checkType,
int index) |
Modifier and Type | Method and Description |
---|---|
Stack |
MontageSlices.createFromStack(Stack stack) |
Modifier and Type | Method and Description |
---|---|
Stack |
MontageSlices.createFromStack(Stack stack) |
Modifier and Type | Method and Description |
---|---|
void |
StackWriterDelegateBase.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
void |
WriteResolutionXml.writeStack(Stack stack,
Path filePath,
StackWriteOptions options) |
protected void |
ImageIOWriter.writeStackAfterCheck(Stack stack,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
void |
SizeExtents.populateMissingFromArbitrarySlice(Stack stackArbitrarySlice) |
Modifier and Type | Method and Description |
---|---|
void |
MultiBufferSized.populateFrom(Stack stackForFile,
Optional<Integer> channelNum,
Optional<Integer> sliceNum,
Optional<Integer> timeIndex) |
Constructor and Description |
---|
MultiBufferSized(Stack stack,
SizeExtents size) |
Modifier and Type | Method and Description |
---|---|
protected ai.onnxruntime.OnnxTensor |
SegmentObjectsFromONNXModel.deriveInput(Stack stack,
Optional<double[]> subtractMeans) |
Modifier and Type | Method and Description |
---|---|
Stack |
ColorConverterBase.createFromStack(Stack stackRGB) |
Modifier and Type | Method and Description |
---|---|
Stack |
ColorConverterBase.createFromStack(Stack stackRGB) |
Modifier and Type | Method and Description |
---|---|
protected org.opencv.core.Mat |
SegmentObjectsFromTensorFlowModel.deriveInput(Stack stack,
Optional<double[]> subtractMeans) |
Modifier and Type | Method and Description |
---|---|
protected void |
OpenCVWriter.writeStackAfterCheck(Stack stack,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
static Stack |
ConvertFromMat.toStack(org.opencv.core.Mat mat)
Convert from an OpenCV
Mat to a Stack . |
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromStack(Stack stack)
Converts a
Stack to a Mat . |
static org.opencv.core.Mat |
ConvertToMat.makeRGBStack(Stack stack,
boolean swapRedBlueChannels)
Derives a
Mat representing an RGB stack. |
Modifier and Type | Method and Description |
---|---|
Stack |
StackFixture.create(ChannelSpecification channelSpecification,
Extent extent)
Creates a stack with a particular number of the channels of particular size.
|
Modifier and Type | Method and Description |
---|---|
void |
WriteIntoDirectory.writeObjects(String outputName,
ObjectCollection objects,
Stack background)
Writes the outline of objects on a background.
|
Modifier and Type | Method and Description |
---|---|
Stack |
TestLoaderImage.openStackFromFilePath(Path filePath) |
Stack |
TestLoaderImage.openStackFromTestPath(String testPath) |
Modifier and Type | Method and Description |
---|---|
Stack |
CarImageLoader.carGrayscale16Bit() |
Stack |
CarImageLoader.carGrayscale8Bit() |
Stack |
CarImageLoader.carRGB() |
Modifier and Type | Method and Description |
---|---|
protected Stack |
InstanceSegmentationTestBase.stackGrayscale()
The grayscale stack that is tested.
|
protected Stack |
InstanceSegmentationTestBase.stackRGB()
The RGB stack that is tested.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.