| Package | Description |
|---|---|
| org.anchoranalysis.annotation.io |
Reading and writing annotations to the filesystem.
|
| org.anchoranalysis.annotation.io.assignment.generator |
Generates output images to illustrate a
Assignment between annotations. |
| org.anchoranalysis.annotation.io.bean |
Beans related to reading / writing / specifying annotations.
|
| org.anchoranalysis.bean.shared.color.scheme |
Beans that create lists or indices of colors according to particular schemes.
|
| org.anchoranalysis.core.collection |
Collection-related classes with general applicability that don't belong elsewhere.
|
| org.anchoranalysis.core.format |
File formats and associated extensions.
|
| org.anchoranalysis.core.graph |
Data-structures for directed and undirected graphs, with or without an edge payload.
|
| org.anchoranalysis.core.identifier.provider |
A collection of named-elements, a
NamedProvider and related operations. |
| org.anchoranalysis.core.identifier.provider.store |
Data structures like
NamedProvider with
supporting for adding new elements. |
| org.anchoranalysis.core.index |
Classes to support getting / setting / specifying unique-integers (indices) for elements.
|
| org.anchoranalysis.core.index.range |
A range of indices from minimum to maximum.
|
| org.anchoranalysis.core.value |
Encapsulating values or sets of named-values.
|
| org.anchoranalysis.experiment.bean.io |
Generic experiments that handle input and output in structured ways.
|
| org.anchoranalysis.experiment.bean.processor |
How a task is executed on multiple inputs.
|
| org.anchoranalysis.experiment.io |
Interfaces for replacing attributes of an experiment: input, output, task etc.
|
| org.anchoranalysis.experiment.log |
Helpful classes for logging.
|
| org.anchoranalysis.feature.energy |
A particular stack used in feature-calculations called a
EnergyStack together with related classes. |
| org.anchoranalysis.feature.initialization |
Initialization parameters used for beans in
org.anchoranalysis.feature.bean. |
| org.anchoranalysis.feature.session.cache.finder |
Strategies to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
|
| org.anchoranalysis.feature.session.replace |
Strategies on whether to reuse or invalidate a feature-input's cache.
|
| org.anchoranalysis.image.bean.channel |
Base classes for performing operations on
Channels. |
| org.anchoranalysis.image.bean.nonbean |
Classes that are used elsewhere in this package but which aren't themselves AnchorBeans.
|
| org.anchoranalysis.image.bean.nonbean.init |
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
|
| org.anchoranalysis.image.bean.object |
Beans pertaining to
ObjectMask and their
collections. |
| org.anchoranalysis.image.bean.spatial |
Beans to define entities or operate that consider Euclidian space.
|
| org.anchoranalysis.image.bean.spatial.arrange.align |
Aligning a
BoundingBox to fit inside another BoundingBox. |
| org.anchoranalysis.image.bean.threshold |
Base classes for thresholding and calculating levels for thresholding.
|
| org.anchoranalysis.image.bean.unitvalue.distance |
Converting quantities of distance between units.
|
| org.anchoranalysis.image.core.bufferedimage |
Conversions and operations involving Java AWT's
BufferedImage. |
| org.anchoranalysis.image.core.channel.convert.attached |
Converts a channel to another data-type based upon another object to which it is attached.
|
| org.anchoranalysis.image.core.channel.convert.attached.histogram |
Converts a channel to another data-type based upon a
Histogram to which it is attached. |
| org.anchoranalysis.image.core.dimensions.size.suggestion |
Suggestions on a size for an image.
|
| org.anchoranalysis.image.core.merge |
Merges two or more entities.
|
| org.anchoranalysis.image.core.object.scale |
Scaling object-collections, or lists of elements with object-representations.
|
| org.anchoranalysis.image.core.object.scale.method |
Scaling elements with an associated
ObjectMask
either collectively or independently. |
| org.anchoranalysis.image.core.points |
Operations that extract points from image data entities or vice versa.
|
| org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack, and related
classes. |
| org.anchoranalysis.image.core.stack.named |
A collection of
Stacks, 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 |
Inference of machine learning models on images.
|
| org.anchoranalysis.image.inference.bean.reduce |
Beans to reduce the number of results that are returned from inference, by removing overlaping
entities etc.
|
| org.anchoranalysis.image.inference.bean.segment.instance |
Instance-segmentation of a
Stack. |
| org.anchoranalysis.image.inference.bean.segment.reduce |
Non-bean classes to reduce the number of results that are returned from inference, by removing
overlapping entities etc.
|
| org.anchoranalysis.image.inference.segment |
Non-beans pertaining to segmentation of images via model inference.
|
| org.anchoranalysis.image.io.bean.object.draw |
How to represent an object-mask in a raster that is being drawn.
|
| org.anchoranalysis.image.io.channel.input |
Non-bean classes for reading a
Channel from the
filesystem. |
| org.anchoranalysis.image.io.channel.map |
Non-bean classes for a mapping of names to
Channels. |
| org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from 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
Stacks. |
| org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
| org.anchoranalysis.image.voxel.convert |
Converting
Voxels to different data-types. |
| org.anchoranalysis.image.voxel.iterator.neighbor.kernel |
Routines for moving a
KernelPointCursor around the
neighboring voxels of the point. |
| org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
| org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
| org.anchoranalysis.image.voxel.object.morphological.predicate |
Predicates to match certain voxels as used in
org.anchoranalysis.image.voxel.object.morphological. |
| org.anchoranalysis.image.voxel.projection |
Classes for calculating differnet kind of projections of voxel values across multiple buffers.
|
| org.anchoranalysis.image.voxel.projection.extrema |
Classes for performing both a Maximum Intensity
Projection and a minimum projection.
|
| org.anchoranalysis.image.voxel.statistics |
Statistics about aggregated voxel intensities.
|
| org.anchoranalysis.image.voxel.thresholder |
Thresholding operations on voxels.
|
| org.anchoranalysis.inference |
High-level classes for performing machine learning model inference.
|
| org.anchoranalysis.io.generator |
Base-classes and utilities for generators, which write different types of objects to the file
system.
|
| org.anchoranalysis.io.input |
Classes relating to creating inputs for an experiment / task.
|
| org.anchoranalysis.io.input.csv |
Classes for reading comma-separated-values (CSV) files.
|
| org.anchoranalysis.io.output.bean |
Beans for the framework around writing files to the file-system.
|
| org.anchoranalysis.math.equation |
Solving or manipulating equations.
|
| org.anchoranalysis.math.histogram |
The
Histogram data class and related operations. |
| org.anchoranalysis.mpp.bean.points |
Operations based on sets of points.
|
| org.anchoranalysis.mpp.bean.proposer |
Proposing
Marks or other data-structures with particular
attributes. |
| org.anchoranalysis.mpp.feature.bean.mark |
Features calculated on a
Mark. |
| org.anchoranalysis.mpp.init |
Parameters used to initialize certain types of beans.
|
| org.anchoranalysis.mpp.io.bean.report.feature |
Beans for communicating feature-values from data-structures in human-readable manner.
|
| org.anchoranalysis.mpp.io.input |
Non-beans for reading data structures related to marked point processes from the file system.
|
| org.anchoranalysis.mpp.io.marks.generator | |
| org.anchoranalysis.mpp.segment.bean.define |
DefineOutputter and its sub-classes. |
| org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
| org.anchoranalysis.mpp.segment.optimization.feedback.period |
Collecting optimization feedback periodically.
|
| org.anchoranalysis.mpp.segment.optimization.step |
Describes an individual step in the optimization.
|
| org.anchoranalysis.mpp.segment.transformer |
Mapping one type of optimization state to another.
|
| org.anchoranalysis.overlay.bean |
Beans relating to drawing an
Overlay on an image. |
| org.anchoranalysis.overlay.writer |
Drawing an overlay on an image.
|
| org.anchoranalysis.plugin.annotation.bean.strategy |
Strategies for how to annotate an image, such label per image etc.
|
| org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction |
Morphological grayscale-reconstruction algorithm.
|
| org.anchoranalysis.plugin.fiji.bean.threshold |
Implementations of
Thresholder that use FIJI. |
| org.anchoranalysis.plugin.image.bean.blur |
Filters that perform blurring.
|
| org.anchoranalysis.plugin.image.bean.channel.aggregator |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram. |
| org.anchoranalysis.plugin.image.bean.histogram.threshold |
Thresholding of intensity values represented in at
Histogram. |
| org.anchoranalysis.plugin.image.bean.object.filter |
Implementations of
ObjectFilter. |
| org.anchoranalysis.plugin.image.bean.object.filter.collective |
Implementations of
ObjectFilter that assess each
element in a collection collectively. |
| org.anchoranalysis.plugin.image.bean.object.filter.combine |
Implementations of
ObjectFilter that combine two or
more other ObjectFilters. |
| org.anchoranalysis.plugin.image.bean.object.filter.independent |
Implementations of
ObjectFilter that
independently assess each element in a collection. |
| org.anchoranalysis.plugin.image.bean.object.match |
Implementations of
ObjectMatcher. |
| org.anchoranalysis.plugin.image.bean.object.provider.merge |
Implementations of
ObjectCollectionProvider
involving merging objects together. |
| org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima |
Minima imposition for a Watershed transformation.
|
| org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction |
Grayscale reconstruction to support the Watershed transformation.
|
| org.anchoranalysis.plugin.image.bean.object.segment.reduce |
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
|
| org.anchoranalysis.plugin.image.bean.scale |
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions. |
| org.anchoranalysis.plugin.image.bean.thumbnail.object |
Implementations of
ThumbnailFromObjects. |
| org.anchoranalysis.plugin.image.feature.bean.score |
Implementations of
VoxelScore. |
| org.anchoranalysis.plugin.image.feature.object.calculation.single |
Implementations of
CalculationPart that that
process a single ObjectMask. |
| org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological |
Implementations of
CalculationPart that that
process a single ObjectMask - with morphological operations. |
| org.anchoranalysis.plugin.image.intensity |
Non-bean for operations or calculations relating to intensity.
|
| org.anchoranalysis.plugin.image.object |
Non-beans pertaining to
ObjectMasks. |
| org.anchoranalysis.plugin.image.object.merge |
Merging
ObjectMasks. |
| org.anchoranalysis.plugin.image.object.merge.condition |
Conditions for merging
ObjectMasks. |
| org.anchoranalysis.plugin.image.object.merge.priority |
Assigning priority when merging
ObjectMasks. |
| org.anchoranalysis.plugin.image.task.bean.combine |
Combining multiple images together into a single image.
|
| org.anchoranalysis.plugin.image.task.bean.feature.source |
Source of rows in feature-tables with
FeatureSource and derived classes. |
| org.anchoranalysis.plugin.image.task.bean.format.convertstyle |
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
|
| org.anchoranalysis.plugin.image.task.bean.grouped |
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
|
| org.anchoranalysis.plugin.image.task.bean.grouped.histogram |
Task(s) to export histograms of intensity values.
|
| org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels |
Selecting a subset of a set of channels.
|
| org.anchoranalysis.plugin.image.task.bean.labeller |
Associating labels with images.
|
| org.anchoranalysis.plugin.image.task.bean.scale |
Tasks to scale an image.
|
| org.anchoranalysis.plugin.image.task.channel.aggregator | |
| org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Features as used in tasks. |
| org.anchoranalysis.plugin.image.task.feature.calculator |
Non-beans for calculating
Features. |
| org.anchoranalysis.plugin.image.task.grouped |
Non-bean classes about grouping channels or other inputs.
|
| org.anchoranalysis.plugin.image.task.labeller |
Non-bean classes about labelling images.
|
| org.anchoranalysis.plugin.image.task.slice |
Non-bean classes pertaining to combining stacks into a single stack.
|
| org.anchoranalysis.plugin.image.task.stack |
Non-bean classes pertaining to stacks and channels as used in tasks.
|
| org.anchoranalysis.plugin.imagej.bean.threshold |
Implementations of
Thresholder that call ImageJ. |
| org.anchoranalysis.plugin.imagej.channel.provider |
Implementations of
ChannelProvider that call ImageJ. |
| org.anchoranalysis.plugin.imagej.mask |
Non-bean classes involving
ObjectMask that call ImageJ. |
| org.anchoranalysis.plugin.io.bean.file.copy.naming |
Rules for preserving or changing the naming of files when copying on the file-system.
|
| org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster |
Implementations of
CopyFilesNaming
that perform clustering of files. |
| org.anchoranalysis.plugin.io.bean.input.stack |
Implementations of
InputManager that process Stacks. |
| org.anchoranalysis.plugin.io.bean.summarizer |
Summarizing a set of elements into a descriptive-string.
|
| org.anchoranalysis.plugin.io.bean.summarizer.image |
Implementations of
Summarizer that summarize
images. |
| org.anchoranalysis.plugin.io.bean.summarizer.input |
Implementations of
Summarizer that summarize
generically InputFromManagers. |
| org.anchoranalysis.plugin.io.bean.summarizer.path |
Implementations of
Summarizer that summarize
generically Paths. |
| org.anchoranalysis.plugin.io.file.copy |
Non-bean classes to help tasks in
org.anchoranalysis.plugin.io.bean.file.copy. |
| org.anchoranalysis.plugin.io.input.path |
Non-bean classes to help in processing paths.
|
| org.anchoranalysis.plugin.io.shared |
Objects used in shared-state in
Tasks in this
plugin. |
| org.anchoranalysis.plugin.mpp.bean.check |
Implementations of
CheckMark. |
| org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler |
The
VisitScheduler and related
classes, as used in TraverseOuterContourOnImage. |
| org.anchoranalysis.plugin.mpp.bean.define | |
| org.anchoranalysis.plugin.mpp.bean.proposer.points.contour |
Finding a point on the external outer contour of an
ObjectMask. |
| org.anchoranalysis.plugin.mpp.bean.proposer.scalar |
Implementations of
ScalarProposer involving Mark or related classes. |
| org.anchoranalysis.plugin.mpp.contour |
Performs a walk on every voxel on the contour of an object-mask.
|
| org.anchoranalysis.plugin.mpp.contour.path.merge |
Merging multiple
ContiguousVoxelPath together. |
| org.anchoranalysis.plugin.mpp.experiment.bean.convert |
Converting from
NamedChannelsInput to the
input-type expected by a Task. |
| org.anchoranalysis.plugin.mpp.experiment.bean.feature.source |
Implementations of
FeatureSource. |
| org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition |
Defining columns used in
ExportObjectsFromCSV. |
| org.anchoranalysis.plugin.mpp.experiment.objects |
Non-bean classes used in
org.anchoranalysis.plugin.mpp.experiment.bean.objects. |
| org.anchoranalysis.plugin.mpp.experiment.objects.csv |
Reading rows from a CSV file.
|
| org.anchoranalysis.plugin.mpp.segment.bean.marks |
Beans to perform segmentation involving
Marks and related
classes. |
| org.anchoranalysis.plugin.mpp.segment.bean.marks.dual |
Implementations of
StateTransformerBean
involving DualVoxelizedMarks. |
| org.anchoranalysis.plugin.mpp.segment.bean.marks.partition |
Implementations of
StateTransformerBean
involving MarksFromPartition. |
| org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized |
Implementations of
StateTransformerBean
involving VoxelizedMarksWithEnergy. |
| org.anchoranalysis.plugin.mpp.segment.bean.optimization |
Beans related to performing optimization with marked-point-processes.
|
| org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn |
Decodes the outputted tensors from a Mask
R-CNN implementation.
|
| org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text |
Decodes the outputted tensors from text-segmentation models.
|
| org.anchoranalysis.plugin.onnx.bean.object.segment.stack |
Segmenting a
Stack using the ONNX Runtime to produce
an ObjectCollection. |
| org.anchoranalysis.plugin.onnx.model |
Non-bean classes for running an inference model with the ONNX
Runtime.
|
| org.anchoranalysis.plugin.opencv |
Plugins that call OpenCV.
|
| org.anchoranalysis.plugin.opencv.bean.object.segment.stack |
Segmentation of a
Stack using OpenCV. |
| org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
| org.anchoranalysis.plugin.opencv.segment |
Non-bean classes pertaining to segmentation.
|
| org.anchoranalysis.plugin.points.bean.fitter |
Fitting geometric structures to points.
|
| org.anchoranalysis.plugin.points.convexhull |
Non-bean convex hull operations.
|
| org.anchoranalysis.plugin.quick.bean.experiment |
Quickly defining experiments via several assumptions, including particular file-paths.
|
| org.anchoranalysis.plugin.quick.bean.structure |
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
|
| org.anchoranalysis.spatial.box |
Axis-aligned bounding-boxes and related operations.
|
| org.anchoranalysis.spatial.orientation |
Various methods to specify the orientation (general direction) of an entity.
|
| org.anchoranalysis.test.experiment.task |
Helper classes to execute
Tasks in tests. |
| org.anchoranalysis.test.feature.plugins.mockfeature |
A mocked feature internally using a feature-calculation.
|
| Modifier and Type | Method and Description |
|---|---|
Optional<String> |
AnnotationWithStrategy.label(OperationContext context)
A human-friendly textual description of the annotation, or
Optional.empty() if no
label is available. |
| Constructor and Description |
|---|
AnnotationWithStrategy(ProvidesStackInput input,
T strategy)
Creates for a particular input and associated annotation strategy.
|
| Modifier and Type | Method and Description |
|---|---|
ColorList |
AssignmentColorPool.createColors(int numberUnpaired)
Creates a list of colors to describe the assignment.
|
| Modifier and Type | Method and Description |
|---|---|
abstract Optional<String> |
AnnotatorStrategy.annotationLabelFor(ProvidesStackInput input,
OperationContext context)
A human-friendly textual description of the annotation, or
Optional.empty() if no
label is available. |
abstract Path |
AnnotatorStrategy.pathFor(ProvidesStackInput input)
The path to where an annotation file for a particular input would be located.
|
| Modifier and Type | Method and Description |
|---|---|
ColorIndex |
ColorScheme.colorForEachIndex(int numberColors)
Assigns a color to each index value from a list of size
numberColors. |
ColorList |
ColorSchemeUnary.createList(int size) |
ColorList |
FromList.createList(int size) |
abstract ColorList |
ColorScheme.createList(int size)
Creates a sequence of related colors.
|
ColorList |
FromSingle.createList(int size) |
| Modifier and Type | Method and Description |
|---|---|
void |
MapCreateCountdown.processElement(K key,
CheckedConsumer<V,OperationFailedException> operation)
Runs an operation on the element, creating if necessary, without decrementing the
count.
|
void |
MapCreateCountdown.processElementDecrement(K key,
CheckedConsumer<V,OperationFailedException> operation)
Runs an operation on the element, creating if necessary, and decrementing the count.
|
| Modifier and Type | Method and Description |
|---|---|
void |
MapCreateCountdown.cleanUpRemaining()
Applies the clean-up function on any keys remaining in the map.
|
void |
MapCreateCountdown.processElement(K key,
CheckedConsumer<V,OperationFailedException> operation)
Runs an operation on the element, creating if necessary, without decrementing the
count.
|
void |
MapCreateCountdown.processElementDecrement(K key,
CheckedConsumer<V,OperationFailedException> operation)
Runs an operation on the element, creating if necessary, and decrementing the count.
|
| Constructor and Description |
|---|
MapCreateCountdown(java.util.function.Supplier<V> createNewElement,
CheckedBiConsumer<K,V,OperationFailedException> cleanUpElement)
Creates without a comparator, using a
HashMap internally. |
| Modifier and Type | Method and Description |
|---|---|
static Path |
FormatExtensions.changeExtension(Path path,
NonImageFileFormat formatToChangeFrom,
FileFormat formatToAssign)
Change the extension in a path.
|
| Modifier and Type | Method and Description |
|---|---|
void |
GraphWithPayload.removeVertex(V vertex)
Removes a vertex and any edges connected to it.
|
void |
GraphWithoutPayload.removeVertex(V vertex)
Removes a vertex and any edges connected to it.
|
| Modifier and Type | Method and Description |
|---|---|
default T |
NamedProvider.getArbitraryElement()
Gets one element of the provider (arbitrarily).
|
| Modifier and Type | Method and Description |
|---|---|
static <T> CachedSupplier<T,OperationFailedException> |
StoreSupplier.cacheResettable(StoreSupplier<T> supplier)
Memoizes (caches) the supplied object, and returning it with a
CachedSupplier
interface |
| Modifier and Type | Method and Description |
|---|---|
void |
LazyEvaluationStore.add(String identifier,
StoreSupplier<T> supplier) |
void |
NamedProviderStore.add(String identifier,
StoreSupplier<T> supplier)
Adds an element to the store.
|
void |
EagerEvaluationStore.add(String identifier,
StoreSupplier<T> supplier) |
T |
StoreSupplier.get()
Gets the object being supplied to the store.
|
| Modifier and Type | Method and Description |
|---|---|
OperationFailedException |
GetOperationFailedException.asOperationFailedException()
Converts to a
OperationFailedException using an identical message. |
| Modifier and Type | Method and Description |
|---|---|
int |
IndexRangeNegative.correctedEndIndex(int size)
The end-index, maybe corrected so that it is no longer negative.
|
int |
IndexRangeNegative.correctedStartIndex(int size)
The start-index, maybe corrected so that it is no longer negative.
|
<T> List<T> |
IndexRangeNegative.extract(int numberElements,
java.util.function.IntFunction<T> extractIndex)
Extracts a subset of elements from a collection according to the specified index/range.
|
<T> List<T> |
IndexRangeNegative.extract(List<T> list)
Extracts a subset of elements from a list according to the specified index/range.
|
static IndexRangeNegative |
IndexRangeNegativeFactory.parse(String str)
Parses a string to convert it into an
IndexRangeNegative. |
| Constructor and Description |
|---|
IndexRangeNegative(int startIndex,
int endIndex)
Create with a start and end index.
|
| Modifier and Type | Method and Description |
|---|---|
void |
Dictionary.putCheck(Dictionary dictionary)
Inserts all key/value pairs from another dictionary, checking that no key already exists.
|
void |
Dictionary.putCheck(String key,
double value)
Inserts a key/value pair, checking that the key doesn't already exist.
|
void |
Dictionary.putCheck(String key,
String value)
Inserts a key/value pair, checking that the key doesn't already exist.
|
| Modifier and Type | Method and Description |
|---|---|
void |
InputOutputExperiment.replaceInputManager(InputManager<T> inputManager) |
void |
InputOutputExperiment.replaceOutputManager(OutputManager output) |
void |
InputOutputExperiment.replaceTask(Task<T,S> taskToReplace) |
| Modifier and Type | Method and Description |
|---|---|
void |
JobProcessor.replaceTask(Task<T,S> taskToReplace) |
| Modifier and Type | Method and Description |
|---|---|
void |
ReplaceInputManager.replaceInputManager(InputManager<T> inputManager)
Replace the existing @{link InputManager} associated with this class.
|
void |
ReplaceOutputManager.replaceOutputManager(OutputManager output)
Replace the currently-assigned
OutputManager with another. |
void |
ReplaceTask.replaceTask(Task<T,S> taskToReplace)
Replace the currently-assigned
Task with another. |
| Modifier and Type | Method and Description |
|---|---|
void |
MultipleLoggers.start() |
void |
StatefulMessageLogger.start()
Starts logging.
|
void |
TextFileMessageLogger.start() |
| Modifier and Type | Method and Description |
|---|---|
EnergyStackWithoutParameters |
EnergyStackWithoutParameters.extractSlice(int z)
Extract a particular z-slice from the
EnergyStackWithoutParameters as a new stack. |
EnergyStack |
EnergyStack.extractSlice(int z)
Extract a particular z-slice from the
EnergyStack as a new stack. |
| Modifier and Type | Method and Description |
|---|---|
void |
FeatureRelatedInitialization.populate(List<NamedBean<FeatureListProvider<FeatureInput>>> namedProviders,
Logger logger)
Adds features into the shared-feature storage from a list of named-beans.
|
| Modifier and Type | Method and Description |
|---|---|
Optional<FeatureCalculationInput<T>> |
CacheTransferSource.getInputIfPresent(T input)
Gets corresponding
FeatureCalculationInput for an input, if present, but
doesn't create any new entry if it's absent. |
| Constructor and Description |
|---|
CacheTransferSource(CacheSupplier<T,OperationFailedException> cacheToSearch,
Set<ChildCacheName> specificChildren) |
| Modifier and Type | Method and Description |
|---|---|
FeatureCalculationInput<T> |
ReuseSingletonStrategy.createOrReuse(T input) |
FeatureCalculationInput<T> |
CacheAndReuseStrategy.createOrReuse(T input) |
FeatureCalculationInput<T> |
ReplaceStrategy.createOrReuse(T input)
Find or create a
FeatureCalculationInput to associate with input. |
| Modifier and Type | Method and Description |
|---|---|
void |
ChannelAggregator.addChannel(Channel channel,
Logger logger)
Adds a
Channel to the aggregation. |
protected abstract void |
ChannelAggregator.addChannelAfterCheck(Channel channel)
Adds a
Channel to the aggregation - after checking channel has acceptable
dimensions. |
Channel |
ChannelAggregator.aggregatedChannel()
Retrieve or create a
Channel with containing the aggregated values. |
| Modifier and Type | Method and Description |
|---|---|
void |
ConsistentChannelChecker.checkChannelType(Channel channel)
Checks that a channel has the same type (max value) as the others.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ImageInitialization.addDictionary(String identifier,
Dictionary toAdd)
Adds a
Dictionary to the corresponding named-collection of dictionaries. |
void |
ImageInitialization.addObjectsFrom(NamedProvider<ObjectCollection> source)
Adds all the
ObjectCollections available in a NamedProvider using the
corresponding identifiers. |
void |
ImageInitialization.addSharedObjectsDictionary(Optional<SharedObjects> sharedObjects,
Optional<Dictionary> dictionary)
Adds stacks and object-collections from a
SharedObjects using the respective
identifiers, and also adds a Dictionary. |
void |
ImageInitialization.addStack(String identifier,
Stack toAdd)
Adds a
Stack to the corresponding named-collection of stacks. |
void |
ImageInitialization.addStacksFrom(NamedProvider<Stack> source)
Adds all the
Stacks available in a NamedProvider using the corresponding
identifiers. |
<S extends InitializableBean<S,V>> |
PopulateStoreFromDefine.copyInitialize(Class<?> defineClass,
NamedProviderStore<S> destination)
Copies objects of a particular class from the define and initializes.
|
<S extends InitializableBean<?,V> & Provider<T>,T> |
PopulateStoreFromDefine.copyProviderInitialize(Class<?> defineClass,
NamedProviderStore<T> destination)
Copies objects of a particular class (which must be a
Provider) from define
and initializes each. |
<S extends AnchorBean<S>> |
PopulateStoreFromDefine.copyWithoutInitialize(Class<?> defineClass,
NamedProviderStore<S> destination)
Copies objects of a particular class from the define without performing any
initialization.
|
void |
ImageInitialization.populate(BeanInitializer<?> propertyInitializer,
Define define,
Logger logger)
Adds diverse entities from a
Define into the corresponding name-collections. |
| Modifier and Type | Method and Description |
|---|---|
abstract ObjectCollection |
ObjectFilter.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dimensions)
Filters an
ObjectCollection to remove objects. |
abstract List<MatchedObject> |
ObjectMatcher.findMatch(ObjectCollection sourceObjects)
Finds matches for objects.
|
| Modifier and Type | Method and Description |
|---|---|
abstract ScaleFactor |
ScaleCalculator.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize)
Calculates a scaling-factor for a source image/entity of particular dimensions.
|
| Modifier and Type | Method and Description |
|---|---|
abstract int |
CalculateLevel.calculateLevel(Histogram histogram)
Determines a voxel intensity that can be used for thresholding.
|
protected int |
CalculateLevelUnary.calculateLevelFromDelegate(Histogram histogram)
Determines a voxel intensity that can be used for thresholding from the delegate
calculateLevel. |
BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels)
Like
Thresholder.threshold(VoxelsUntyped) but using default binary-values. |
BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues)
Like
Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the
thresholding to the entire set of voxels. |
BinaryVoxels<UnsignedByteBuffer> |
ThresholderGlobal.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
abstract BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask)
Thresholds voxels (across a range of values) so that they have only binary range (i.e.
|
| Modifier and Type | Method and Description |
|---|---|
abstract double |
UnitValueDistance.resolve(Optional<UnitConverter> unitConverter,
DirectionVector direction)
Resolves the distance using a
DirectionVector. |
double |
DistancePhysical.resolve(Optional<UnitConverter> unitConverter,
DirectionVector direction) |
double |
UnitValueDistance.resolve(Optional<UnitConverter> unitConverter,
Point3d point1,
Point3d point2)
Resolves the distance using the direction between two points of type
Point3d. |
double |
UnitValueDistance.resolve(Optional<UnitConverter> unitConverter,
Point3i point1,
Point3i point2)
Resolves the distance using the direction between two points of type
Point3i. |
double |
UnitValueDistance.resolveForAxis(Optional<UnitConverter> unitConverter,
Axis axis)
Resolves the distance in a direction aligned to a particular axis.
|
| 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 |
|---|---|
void |
ChannelConverterAttached.attachObject(S object)
Associate the convert with a particular object.
|
| Modifier and Type | Method and Description |
|---|---|
void |
QuantileIntensityFromHistogram.attachObject(Histogram object) |
void |
MaxIntensityFromHistogram.attachObject(Histogram histogram) |
void |
UpperLowerQuantileIntensityFromHistogram.attachObject(Histogram histogram) |
| Modifier and Type | Method and Description |
|---|---|
ScaleFactor |
ImageSizeSuggestion.calculateScaleFactor(Optional<Extent> extentToBeScaled)
Calculates the scaling factor.
|
| Modifier and Type | Method and Description |
|---|---|
static ObjectMask |
ObjectMaskMerger.merge(ObjectCollection objects)
Merges all the objects together that are found in a collection.
|
static BoundingBox |
ObjectMaskMerger.mergeBoundingBoxes(ObjectCollection objects)
Merges all the bounding boxes of a collection of objects.
|
| Modifier and Type | Method and Description |
|---|---|
static <T> ScaledElements<T> |
Scaler.scaleElements(List<T> elements,
ScaleFactor factor,
boolean overlappingObjects,
Extent clipTo,
AccessObjectMask<T> access)
Scales every element in a list collectively, ensuring the results remain inside a particular
region.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor)
Scales every object-mask in a collection collectively.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Extent clipTo)
Scales every object-mask in a collection collectively, ensuring the results remain
inside a particular region.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Optional<java.util.function.UnaryOperator<ObjectMask>> preOperation,
Optional<java.util.function.UnaryOperator<ObjectMask>> postOperation)
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
|
| Modifier and Type | Method and Description |
|---|---|
default <T> Map<T,T> |
ObjectScalingMethod.scaleElements(List<T> elements,
ScaleFactor scaleFactor,
AccessObjectMask<T> access)
Applies a scaling factor to elements, where each element is associated with a unique
ObjectMask. |
<T> Map<T,T> |
ObjectScalingMethod.scaleElements(List<T> elements,
ScaleFactor scaleFactor,
Optional<java.util.function.UnaryOperator<T>> preOperation,
Optional<java.util.function.UnaryOperator<T>> postOperation,
AccessObjectMask<T> access)
Applies a scaling factor to elements, where each element is associated with a unique
ObjectMask. |
| Modifier and Type | Method and Description |
|---|---|
static BoundingBox |
BoundingBoxFromPoints.fromStream(java.util.stream.Stream<Point3i> points)
Create from a stream of
Point3is. |
| Modifier and Type | Method and Description |
|---|---|
RGBStack |
RGBStack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)
Produces a new stack with a particular mapping applied to each channel.
|
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).
|
| Modifier and Type | Method and Description |
|---|---|
void |
Stack.addBlankChannel()
Adds a new empty
Channel in the final-most position in the list. |
RGBStack |
RGBStack.mapChannel(CheckedUnaryOperator<Channel,OperationFailedException> mapping)
Produces a new stack with a particular mapping applied to each channel.
|
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).
|
Optional<ObjectMask> |
RGBStack.objectWithColor(RGBColor color)
Extracts an
ObjectMask from a Channel of all voxels that have a particular
color. |
| Modifier and Type | Method and Description |
|---|---|
void |
NamedStacksUniformSize.add(String identifier,
Stack stack)
Adds an element to the store.
|
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. |
NamedProvider<Stack> |
NamedStacksSupplier.get()
Gets the
NamedProvider of Stacks. |
| Modifier and Type | Method and Description |
|---|---|
FeatureCalculatorSingle<T> |
FeatureEvaluator.createFeatureSession()
Creates session for evaluating
feature optionally adding an energy-stack. |
NamedFeatureCalculatorMulti<T> |
FeatureListEvaluator.createFeatureSession(java.util.function.UnaryOperator<FeatureList<T>> addFeatures,
SharedObjects sharedObjects)
Creates session for evaluating
features. |
Optional<EnergyStack> |
FeatureEvaluator.energyStack()
The specified energy stack.
|
| Modifier and Type | Method and Description |
|---|---|
<S> S |
ImageInferenceModel.performInference(T input,
String inputName,
List<String> outputIdentifiers,
CheckedFunction<List<T>,S,OperationFailedException> convertOutput)
Performs inference on a single-input, to create an output.
|
| Modifier and Type | Method and Description |
|---|---|
<S> S |
ImageInferenceModel.performInference(T input,
String inputName,
List<String> outputIdentifiers,
CheckedFunction<List<T>,S,OperationFailedException> convertOutput)
Performs inference on a single-input, to create an output.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ReduceObjectsGraph.removeVertex(ObjectForReduction vertex)
Removes a vertex and any edges connected to it.
|
| Modifier and Type | Method and Description |
|---|---|
abstract List<LabelledWithConfidence<MultiScaleObject>> |
DecodeInstanceSegmentation.decode(List<T> inferenceOutput,
ImageInferenceContext context)
Decodes the output tensors from inference into
ObjectMasks with confidence and
labels. |
protected abstract T |
SegmentStackIntoObjectsScaleDecode.deriveInput(Stack stack,
Optional<double[]> subtractMeans)
Derives the input tensor from an image.
|
| Modifier and Type | Method and Description |
|---|---|
abstract ReductionOutcome<LabelledWithConfidence<T>> |
ReduceElements.reduce(List<LabelledWithConfidence<T>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder)
Reduce a list of elements (each with a confidence score and a label) to a
smaller-list.
|
| Modifier and Type | Method and Description |
|---|---|
SegmentedObjects |
SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce,
boolean separateEachLabel,
ExecutionTimeRecorder executionTimeRecorder)
Reduces the segmented-objects, applying a reduction algorithm separately to each
object-class.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IfElse.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Outline.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Flatten.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
void |
Filled.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo) |
| Modifier and Type | Method and Description |
|---|---|
void |
NamedChannelsInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
void |
NamedChannelsInput.addToStoreWithName(String name,
NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
void |
OpenedNamedChannels.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination,
int timeIndex,
Logger logger) |
void |
NamedChannelsConcatenate.addAsSeparateChannels(NamedProviderStore<TimeSeries> stackCollection,
int timeIndex,
Logger logger) |
void |
NamedChannelsMap.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination,
int timeIndex,
Logger logger)
|
void |
OpenedNamedChannels.addAsSeparateChannels(NamedStacks destination,
int timeIndex,
Logger logger) |
void |
NamedChannelsConcatenate.addAsSeparateChannels(NamedStacks stackCollection,
int t,
Logger logger) |
void |
NamedChannelsMap.addAsSeparateChannels(NamedStacks destination,
int timeIndex,
Logger logger)
|
| 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).
|
void |
ProvidesStackInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger)
Adds any stacks exposed by the current element to a named-store of stacks - inferring the
names of the
Stacks. |
void |
ProvidesStackInput.addToStoreWithName(String name,
NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger)
Adds any stacks exposed by the current element to a named-store of stacks - with a particular
name.
|
default NamedStacks |
ProvidesStackInput.asSet(Logger logger)
Exposes the input as a set of named stacks (inferring the names).
|
default Stack |
ProvidesStackInput.asStack(Logger logger)
Exposes the input as a single
Stack throw an error if more than one exists. |
int |
ProvidesStackInput.numberFrames()
The number of time-frames in the underlying input image.
|
| 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
|
| Modifier and Type | Method and Description |
|---|---|
protected Stack |
DisplayStackGenerator.convertBeforeAssign(DisplayStack element) |
protected Stack |
FlattenStackGenerator.convertBeforeAssign(Stack element) |
protected abstract S |
RasterGeneratorDelegateToRaster.convertBeforeAssign(T element)
Converts an element before setting it on the
delegate. |
protected V |
RasterGeneratorBridge.convertBeforeAssign(T element) |
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. |
| Modifier and Type | Method and Description |
|---|---|
void |
ExtractFrameStore.add(String identifier,
StoreSupplier<TimeSeries> supplier) |
| Modifier and Type | Method and Description |
|---|---|
BoundedVoxels<T> |
BoundedVoxels.growBuffer(Point3i growthNegative,
Point3i growthPositive,
Optional<Extent> clipRegion,
VoxelsFactoryTypeBound<T> factory)
Grows the voxel buffer in the positive and negative directions by a certain amount.
|
BoundedVoxels<T> |
BoundedVoxels.growToZ(int sizeZ,
VoxelsFactoryTypeBound<T> factory)
Grows a single z-sliced
BoundedVoxels by duplicating the slice across the z-dimension
sizeZ number of times. |
| Modifier and Type | Method and Description |
|---|---|
void |
VoxelsConverter.copyFrom(VoxelsUntyped from,
Voxels<T> to)
Copies voxels from a source (of any type) to voxels of type
T. |
void |
VoxelsConverter.copyFromFloat(Voxels<FloatBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link FloatBuffer} to voxels of type
T. |
void |
VoxelsConverter.copyFromUnsignedByte(Voxels<UnsignedByteBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type
T. |
void |
VoxelsConverter.copyFromUnsignedInt(Voxels<UnsignedIntBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type
T. |
void |
VoxelsConverter.copyFromUnsignedShort(Voxels<UnsignedShortBuffer> from,
Voxels<T> to)
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type
T. |
| Modifier and Type | Method and Description |
|---|---|
static void |
IterateKernelHelper.overBox(Kernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
ProcessKernelPointCursor processor)
Iterates over only voxels contained within a bounding-box.
|
static boolean |
IterateKernelHelper.overBoxUntil(Kernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters,
PredicateKernelPointCursor predicate)
Iterates over only voxels contained within a bounding-box until a predicate is matched
on a voxel.
|
| Modifier and Type | Method and Description |
|---|---|
static int |
ApplyKernel.applyForCount(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters)
Applies the kernel to voxels and sums the returned value.
|
static boolean |
ApplyKernel.applyUntilPositive(CountKernel kernel,
BinaryVoxels<UnsignedByteBuffer> voxels,
BoundingBox box,
KernelApplicationParameters parameters)
Applies the kernel to voxels until a positive value is returned, then exits with true.
|
| Modifier and Type | Method and Description |
|---|---|
ObjectMask |
ObjectMask.growBuffer(Point3i growthNegative,
Point3i growthPositive,
Optional<Extent> clipRegion)
Grows the object-mask's voxel buffers in the positive and negative directions by a certain
amount.
|
ObjectMask |
ObjectMask.growToZ(int sizeZ)
Grows a single z-sliced
ObjectMask by duplicating the slice across the z-dimension
sizeZ number of times. |
| Modifier and Type | Method and Description |
|---|---|
boolean |
AcceptIterationPredicate.accept(BinaryVoxels<UnsignedByteBuffer> voxels)
Whether a particular
voxels fulfills the condition or not. |
boolean |
AcceptIterationList.accept(BinaryVoxels<UnsignedByteBuffer> voxels) |
| Modifier and Type | Method and Description |
|---|---|
static <T> ProjectableBuffer<T> |
MeanIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
StandardDeviationIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a standard-deviation projection for unsigned byte voxels.
|
| Modifier and Type | Method and Description |
|---|---|
static <T> ProjectableBuffer<T> |
MaxIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a maximum-intensity projection for unsigned byte voxels.
|
static <T> ProjectableBuffer<T> |
MinIntensityProjection.create(VoxelDataType dataType,
Extent extent)
Creates a buffer for a minimum-intensity projection for unsigned byte voxels.
|
| Modifier and Type | Method and Description |
|---|---|
Histogram |
VoxelStatistics.histogram()
A
Histogram of all voxel values. |
Histogram |
VoxelStatisticsCombined.histogram() |
double |
VoxelStatistics.quantile(double quantile)
The voxel value corresponding to a particular quantile.
|
double |
VoxelStatisticsFromHistogram.quantile(double quantile) |
| Modifier and Type | Method and Description |
|---|---|
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.threshold(VoxelsUntyped voxels,
float level,
BinaryValuesByte binaryValues,
Optional<ObjectMask> objectMask,
boolean alwaysDuplicate)
Applies thresholding to
VoxelsUntyped. |
| Modifier and Type | Method and Description |
|---|---|
void |
InferenceModel.close()
Indicates that the model will no longer be used, and does appropriate tidying up and freeing
of resources.
|
| Modifier and Type | Method and Description |
|---|---|
String |
SingleFileTypeGeneratorBridge.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
abstract String |
SingleFileTypeGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger)
Selects the file/extension to be used for outputting the file.
|
| Modifier and Type | Method and Description |
|---|---|
Collection<NamedFile> |
InputsWithDirectory.findAllNonInputFiles()
Find all files in the input directory are not used as inputs.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ProcessCSVLine.processLine(String[] line,
boolean firstLine)
Called when a single line is read by a CSV-reader to determine how the entry is further
processed.
|
| Modifier and Type | Method and Description |
|---|---|
ColorIndex |
OutputWriteSettings.defaultColorIndexFor(int numberColors) |
abstract String |
ReportFeature.featureDescription(T param,
OperationContext context) |
| Modifier and Type | Method and Description |
|---|---|
static QuadraticEquationSolver.QuadraticRoots |
QuadraticEquationSolver.solveQuadraticEquation(double a,
double b,
double c)
Solves a quadratic equation in form
x^2 + b^x + c = 0. |
| Modifier and Type | Method and Description |
|---|---|
void |
Histogram.addHistogram(Histogram other)
Adds the counts from another histogram to the current object.
|
int |
Histogram.calculateMaximum()
Calculates the maximum value with non zero-count among the histogram values.
|
int |
Histogram.calculateMinimum()
Calculates the minimum value with non zero-count among the histogram values.
|
int |
Histogram.calculateMode()
Calculates the mode of the histogram values.
|
static double |
HistogramStatistics.coefficientOfVariation(Histogram histogram)
Calculates the coefficient-of-variation of a distribution of values, represented by
their histogram.
|
static double |
HistogramStatistics.kurtosis(Histogram histogram)
Calculates the kurtosis of a distribution of values, represented by their histogram.
|
double |
Histogram.mean()
Calculates the mean of the histogram values, considering their frequency.
|
double |
Histogram.mean(double power)
Calculates the mean of the values in the distribution, if each value is raised to a power.
|
double |
Histogram.mean(double power,
double subtractValue)
Like
Histogram.mean(double) but a value may be subtracted before raising to a power. |
int |
Histogram.quantile(double quantile)
Calculates the corresponding value for a particular quantile in the distribution of
values in the histogram.
|
static double |
HistogramStatistics.skewness(Histogram histogram)
Calculates the skewness of a distribution of values, represented by their histogram.
|
double |
Histogram.standardDeviation()
Calculates the standard-deviation of the distribution represented by the histogram.
|
double |
Histogram.variance()
Calculates the variance of the distribution represented by the histogram.
|
| Modifier and Type | Method and Description |
|---|---|
Optional<Mark> |
CreateMarkFromPoints.fitMarkToPointsFromMarks(MarkCollection marks,
Dimensions dimensions)
Extract points from a marks, creates a new mark from markProvider and then fits this mark the
extracted points
|
| Modifier and Type | Method and Description |
|---|---|
abstract double |
ScalarProposer.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
| Modifier and Type | Method and Description |
|---|---|
abstract double |
PxlListOperationFromMark.doOperation(VoxelizedMarkMemo pxlMarkMemo,
Dimensions dimensions) |
void |
CheckMark.start(EnergyStack energyStack)
|
| Modifier and Type | Method and Description |
|---|---|
void |
MarksInitialization.populate(BeanInitializer<?> initializer,
Define define,
Logger logger) |
void |
PointsInitialization.populate(BeanInitializer<?> initializer,
Define define,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
protected FeatureCalculatorSingle<T> |
ReportFeatureEvaluator.createAndStartSession() |
String |
ReportFeatureOnMarks.featureDescription(MarksInitialization param,
OperationContext context) |
String |
ReportFeatureOnMark.featureDescription(MarksInitialization param,
OperationContext context) |
String |
ReportFeatureOnObjectsBase.featureDescription(MarksInitialization initialization,
OperationContext context) |
String |
ReportFeatureWrapError.featureDescription(MarksInitialization param,
OperationContext context) |
| Modifier and Type | Method and Description |
|---|---|
void |
OperationMap.addToStore(NamedProviderStore<T> namedStore,
Logger logger) |
void |
MultiInputSubMap.addToStore(NamedProviderStore<T> namedStore,
Logger logger)
Copies all the existing entries into a
NamedProviderStore. |
void |
StackWithMap.addToStore(NamedProviderStore<TimeSeries> stackCollection,
int seriesNum,
Logger logger) |
void |
StackWithMap.addToStore(NamedProviderStore<TimeSeries> stackCollection,
Logger logger) |
void |
MultiInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
void |
MultiInput.addToStoreWithName(String name,
NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
void |
MultiInput.copyTo(SharedObjects target,
Logger logger) |
void |
ExportSharedObjects.copyTo(SharedObjects target,
Logger logger)
Adds any exported shared-objects to
sharedObjects. |
StoreSupplier<T> |
OperationMap.get(String name) |
StoreSupplier<T> |
MultiInputSubMap.get(String name)
Returns null if non-existent
|
StoreSupplier<TimeSeries> |
StackWithMap.get(String name) |
int |
MultiInput.numberFrames() |
int |
StackWithMap.numFrames() |
| Modifier and Type | Method and Description |
|---|---|
protected abstract DisplayStack |
MarksGeneratorBase.background(DisplayStack stack) |
protected DisplayStack |
MarksFlattenedGenerator.background(DisplayStack stack) |
| Modifier and Type | Method and Description |
|---|---|
<S> void |
DefineOutputter.process(InputBound<MultiInput,S> input,
DefineOutputter.Processor<ImageInitialization> operation) |
void |
DefineOutputter.Processor.process(T initialization) |
| Modifier and Type | Method and Description |
|---|---|
T |
DualState.releaseKeepBest() |
<S> DualState<S> |
DualState.transform(StateTransformer<T,S> func,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
void |
PeriodTriggerBank.incr(Reporting<S> reporting) |
| Modifier and Type | Method and Description |
|---|---|
T |
OptimizationStep.releaseKeepBest() |
<U> Reporting<U> |
OptimizationStep.reporting(int iter,
StateReporter<T,U> stateReporter,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
T |
Compose.transform(S in,
TransformationContext context) |
X |
StateTransformer.transform(W item,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
void |
DrawObject.drawCollection(ObjectCollectionWithProperties objects,
RGBStack stack,
ObjectDrawAttributes attributes)
Writes object-masks onto of a
RGBStack - across all of the stack. |
void |
DrawObject.drawCollection(ObjectCollectionWithProperties objects,
RGBStack stack,
ObjectDrawAttributes attributes,
BoundingBox boxContainer)
Writes object-masks onto of a
RGBStack - within a bounding box only. |
abstract void |
DrawObject.drawSingle(ObjectWithProperties object,
RGBStack stack,
ObjectDrawAttributes attributes,
int iteration,
BoundingBox restrictTo)
Draws a single-object on top of a RGB-stack.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DrawOverlay.drawOverlays(ColoredOverlayCollection overlays,
RGBStack stack,
IdentifierGetter<Overlay> idGetter)
Draw a collection of colored-overlays on top of a
RGBStack. |
| Modifier and Type | Method and Description |
|---|---|
Optional<String> |
ImageLabelStrategy.annotationLabelFor(ProvidesStackInput item,
OperationContext context) |
Path |
SinglePathStrategy.pathFor(ProvidesStackInput input) |
| Modifier and Type | Method and Description |
|---|---|
VoxelsUntyped |
GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
| Modifier and Type | Method and Description |
|---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
| Modifier and Type | Method and Description |
|---|---|
abstract void |
BlurStrategy.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussian3D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussianEachSlice2D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
protected double |
BlurStrategy.calculateSigma(Dimensions dimensions,
MessageLogger logger) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
ProjectableBufferAggregator.addChannelAfterCheck(Channel channel) |
protected abstract ProjectableBuffer<T> |
ProjectableBufferAggregator.create(VoxelDataType dataType,
Extent extent)
Creates the
ProjectableBuffer used for aggregation. |
protected ProjectableBuffer<T> |
MeanProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MinProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
MaxProjection.create(VoxelDataType dataType,
Extent extent) |
protected ProjectableBuffer<T> |
StandardDeviationProjection.create(VoxelDataType dataType,
Extent extent) |
| Modifier and Type | Method and Description |
|---|---|
int |
Minimum.calculateLevel(Histogram h) |
int |
EmptyHistogramConstant.calculateLevel(Histogram histogram) |
int |
OtsuWeighted.calculateLevel(Histogram histogram) |
int |
Quantile.calculateLevel(Histogram histogram) |
int |
Maximum.calculateLevel(Histogram h) |
int |
Otsu.calculateLevel(Histogram histogram) |
int |
CalculateLevelRelativeToThreshold.calculateLevel(Histogram histogram) |
int |
ClampHistogramMax.calculateLevel(Histogram histogram) |
| Modifier and Type | Method and Description |
|---|---|
protected abstract void |
ObjectFilterPredicate.end() |
protected void |
ObjectFilterRelation.end() |
ObjectCollection |
ObjectFilterPredicate.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dimensions) |
protected abstract boolean |
ObjectFilterPredicate.match(ObjectMask object,
Optional<Dimensions> dimensions)
A predicate condition for an object to be kept in the collection
|
protected boolean |
ObjectFilterRelation.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected abstract boolean |
ObjectFilterRelation.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
protected void |
ObjectFilterPredicate.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
ObjectFilterRelation.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
DiscardOutliers.end() |
protected void |
RelationWithMatches.end() |
protected boolean |
DiscardOutliers.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
RelationWithMatches.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
protected void |
DiscardOutliers.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
RelationWithMatches.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
| Modifier and Type | Method and Description |
|---|---|
ObjectCollection |
And.filter(ObjectCollection objects,
Optional<Dimensions> dim) |
ObjectCollection |
Or.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dim) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
ThresholdedFeature.end() |
protected void |
NotTouchingSceneBorder.end() |
protected void |
GreaterIntersectionWith.end() |
protected void |
IntersectsWith.end() |
protected void |
IntensityGreaterEqualThan.end() |
protected boolean |
NotTouchingSceneBorder.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
GreaterIntersectionWith.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
IntersectsWith.match(ObjectMask objectToIntersectWith,
Optional<Dimensions> dimensions) |
protected boolean |
IntensityGreaterEqualThan.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
ThresholdedFeature.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
protected void |
ThresholdedVolume.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
ThresholdedFeature.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
GreaterIntersectionWith.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
IntersectsWith.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
IntensityGreaterEqualThan.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
| Modifier and Type | Method and Description |
|---|---|
List<MatchedObject> |
Bridge.findMatch(ObjectCollection sourceObjects) |
List<MatchedObject> |
Always.findMatch(ObjectCollection sourceObjects) |
List<MatchedObject> |
Intersection.findMatch(ObjectCollection sourceObjects) |
| Modifier and Type | Method and Description |
|---|---|
protected PayloadCalculator |
MergeToIncreaseObjectFeature.createPayloadCalculator() |
protected abstract PayloadCalculator |
MergeWithFeature.createPayloadCalculator()
Determines the payload for any given or potential vertex
|
protected AssignPriority |
MergeToIncreaseObjectFeature.createPrioritizer() |
protected abstract AssignPriority |
MergeWithFeature.createPrioritizer()
Determines the priority (and selection criteria) used to allow merges between neighbors
|
protected AssignPriority |
MergePairs.createPrioritizer() |
protected ObjectCollection |
MergeBase.mergeMultiplex(ObjectCollection objects,
MergeBase.MergeObjects mergeFunc)
Merges either in a container, or altogether
|
ObjectCollection |
MergeBase.MergeObjects.mergeObjects(ObjectCollection objects) |
protected Resolution |
MergeBase.resolutionRequired() |
protected Optional<UnitConverter> |
MergeBase.unitConvertOptional() |
| Modifier and Type | Method and Description |
|---|---|
abstract Channel |
MinimaImposition.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Channel |
MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
| Modifier and Type | Method and Description |
|---|---|
abstract VoxelsUntyped |
GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
| Modifier and Type | Method and Description |
|---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
| Modifier and Type | Method and Description |
|---|---|
ScaleFactor |
FitTo.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ToDimensions.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ConstantScaleFactor.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ToSuggested.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
Invert.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
MinimumXYResolution.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
| 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 |
|---|---|
protected abstract void |
CalculateLevelBase.beforeCalcSetup(Histogram histogram,
int level) |
protected void |
DifferenceCalculateLevelStandardDeviation.beforeCalcSetup(Histogram histogram,
int level) |
| Modifier and Type | Method and Description |
|---|---|
protected abstract ObjectMask |
CalculateIncrementalOperationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
| Modifier and Type | Method and Description |
|---|---|
protected ObjectMask |
CalculateErosionMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
protected ObjectMask |
CalculateDilationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
| Modifier and Type | Method and Description |
|---|---|
static Histogram |
HistogramThresholder.withCalculateLevel(Histogram histogram,
CalculateLevel calculateLevel)
Retains the portion of the histogram greater or equal to the calculated-level.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ColoredObjectCollection.addObjectsWithColor(ObjectCollectionProvider provider,
RGBColor color)
Adds objects from a
ObjectCollectionProvider all with one specific color |
static ObjectCollection |
ObjectIntersectionRemover.removeIntersectingVoxels(ObjectCollection objects,
Dimensions dimensions,
boolean errorDisconnectedObjects) |
| Modifier and Type | Method and Description |
|---|---|
List<ObjectVertex> |
MergeGraph.addObjectsToGraph(ObjectCollection objects) |
ObjectVertex |
MergeGraph.merge(TypedEdge<ObjectVertex,PrioritisedVertex> bestImprovement) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
AndCondition.accept(ObjectMask destination) |
boolean |
WrapAsUpdatable.accept(ObjectMask destination) |
boolean |
UpdatableBeforeCondition.accept(ObjectMask destination) |
boolean |
AfterCondition.accept(ObjectMask source,
ObjectMask destination,
ObjectMask merged) |
boolean |
IncreaseFeatureCondition.accept(ObjectMask source,
ObjectMask destination,
ObjectMask merged) |
boolean |
DistanceCondition.accept(ObjectMask source,
ObjectMask destination,
Optional<UnitConverter> unitConverter) |
boolean |
BeforeCondition.accept(ObjectMask source,
ObjectMask destination,
Optional<UnitConverter> unitConverter) |
void |
AndCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
WrapAsUpdatable.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
UpdatableBeforeCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
NeighborhoodCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
| Modifier and Type | Method and Description |
|---|---|
PrioritisedVertex |
AssignPriority.assignPriority(ObjectVertex source,
ObjectVertex destination,
GraphLogger logger)
Assigns a priority to a potential merge
|
protected abstract PrioritisedVertex |
AssignPriority.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merge,
ErrorReporter errorReporter) |
PrioritisedVertex |
AssignPriorityFromImprovement.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merged,
ErrorReporter errorReporter) |
PrioritisedVertex |
AssignPriorityFromPair.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merged,
ErrorReporter errorReporter) |
PrioritisedVertex |
Prioritizer.createPriority(ObjectVertex source,
ObjectVertex destination,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
AggregateChannelTask.processIndividual(String name,
Channel individual,
boolean partOfGroup,
CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
InputOutputContext context) |
| Modifier and Type | Method and Description |
|---|---|
protected CheckedFunction<Channel,Channel,CreateException> |
AggregateChannelTask.createChannelDeriver(ChannelSource source) |
protected void |
AggregateChannelTask.processIndividual(String name,
Channel individual,
boolean partOfGroup,
CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
InputOutputContext context) |
| Modifier and Type | Method and Description |
|---|---|
protected Optional<String[]> |
FromImageMetadata.additionalLabelsFor(ImageMetadataInput input) |
protected abstract Optional<String[]> |
SingleRowPerInput.additionalLabelsFor(T input)
Additional labels for an input to include (after the identifier, and before any group
labels).
|
void |
SingleRowPerInput.calculateAndOutput(T input,
FeatureCalculationContext<FeatureList<S>> context) |
abstract void |
FeatureSource.calculateAndOutput(T input,
FeatureCalculationContext<S> context)
Processes one input to calculate feature-results and output them to the file-system.
|
| Modifier and Type | Method and Description |
|---|---|
NamedStacks |
IndependentChannels.convert(Set<String> channelNames,
ChannelGetterForTimepoint channelGetter,
Logger logger) |
abstract NamedStacks |
ChannelConvertStyle.convert(Set<String> channelNames,
ChannelGetterForTimepoint channelGetter,
Logger logger)
Converts a particular set of channels.
|
NamedStacks |
RGBIfNamesMatch.convert(Set<String> channelNames,
ChannelGetterForTimepoint channelGetter,
Logger logger) |
NamedStacks |
ExtractToRGB.convert(Set<String> channelNames,
ChannelGetterForTimepoint channelGetter,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
protected abstract void |
GroupedStackBase.processIndividual(String name,
S individual,
boolean partOfGroup,
CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual,
InputOutputContext context)
Processes each derived individual element from a
Channel, calling consumeIndividual one or more times. |
| Modifier and Type | Method and Description |
|---|---|
protected abstract CheckedFunction<Channel,S,CreateException> |
GroupedStackBase.createChannelDeriver(ChannelSource source)
A function to derive the individual type used for aggregation from a
Channel. |
protected abstract void |
GroupedStackBase.processIndividual(String name,
S individual,
boolean partOfGroup,
CheckedBiConsumer<String,S,OperationFailedException> consumeIndividual,
InputOutputContext context)
Processes each derived individual element from a
Channel, calling consumeIndividual one or more times. |
| Modifier and Type | Method and Description |
|---|---|
protected void |
ExportImageHistograms.processIndividual(String name,
Histogram individual,
boolean partOfGroup,
CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual,
InputOutputContext context) |
| Modifier and Type | Method and Description |
|---|---|
protected CheckedFunction<Channel,Histogram,CreateException> |
ExportImageHistograms.createChannelDeriver(ChannelSource source) |
protected void |
ExportImageHistograms.processIndividual(String name,
Histogram individual,
boolean partOfGroup,
CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual,
InputOutputContext context) |
| Modifier and Type | Method and Description |
|---|---|
NamedChannels |
All.selectChannels(ChannelSource source,
boolean checkType) |
NamedChannels |
SpecificAndRename.selectChannels(ChannelSource source,
boolean checkType) |
abstract NamedChannels |
FromStacks.selectChannels(ChannelSource source,
boolean checkType)
Takes a stack-collection and extracts a set of references to particular channels (each with a
name)
|
NamedChannels |
One.selectChannels(ChannelSource source,
boolean checkType) |
| Modifier and Type | Method and Description |
|---|---|
String |
ImageCSVLabeller.labelFor(ImageCSVLabellerInitialization sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
ImageLabellerStringMap.labelFor(ImageLabellerStringMapInitialization<T> sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
DescriptiveNameContainsImageLabeller.labelFor(NoSharedState sharedState,
ProvidesStackInput input,
InputOutputContext context) |
String |
BinaryClassifierImageLabeller.labelFor(NoSharedState sharedState,
ProvidesStackInput input,
InputOutputContext context) |
abstract String |
ImageLabeller.labelFor(T sharedState,
ProvidesStackInput input,
InputOutputContext context)
Determines a particular group-identifier for an input
|
| 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 |
|---|---|
void |
NamedChannels.add(String name,
Channel channel)
Adds a
Channel with a name. |
| Constructor and Description |
|---|
NamedChannels(java.util.stream.Stream<NamedChannels> channelsToCombine)
Creates by combining multiple existing existing
NamedChannels. |
| Modifier and Type | Method and Description |
|---|---|
CheckedSupplier<ResultsVector,OperationFailedException> |
ResultsVectorWithThumbnail.getResultsVector() |
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> |
ResultsVectorWithThumbnail.getThumbnail() |
| Modifier and Type | Method and Description |
|---|---|
void |
FeatureResultsAndThumbnails.add(CheckedSupplier<LabelledResultsVector,OperationFailedException> resultToAdd,
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)
Adds results, together with a thumbnail.
|
void |
FeatureResultsAndThumbnails.add(CheckedSupplier<LabelledResultsVector,OperationFailedException> resultToAdd,
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)
Adds results, together with a thumbnail.
|
| Modifier and Type | Method and Description |
|---|---|
void |
FeatureResultsAndThumbnails.add(CheckedSupplier<LabelledResultsVector,OperationFailedException> resultToAdd,
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail)
Adds results, together with a thumbnail.
|
LabelledResultsVector |
LabelledResultsVectorWithThumbnail.withoutThumbnail()
Exposes as a
LabelledResultsVector without a thumbnail. |
| Constructor and Description |
|---|
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector,OperationFailedException> resultsVector) |
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector,OperationFailedException> resultsVector,
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail) |
ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector,OperationFailedException> resultsVector,
CheckedSupplier<Optional<DisplayStack>,OperationFailedException> thumbnail) |
| Modifier and Type | Method and Description |
|---|---|
void |
CalculateFeaturesForObjects.calculateForObjects(ObjectCollection objects,
EnergyStack energyStack,
LabelsForInput labelsForInput)
Calculates the feature-results for
objects, and stores the results. |
void |
CalculateFeaturesForObjects.calculateForObjects(ObjectCollectionProvider provider,
LabelsForInput labelsForInput) |
FeatureCalculatorSingle<T> |
FeatureCalculatorFromProvider.calculatorSingleFromProvider(FeatureListProvider<T> provider,
String providerName)
Calculates a single-feature that comes from a provider (but can reference the other features
from the store)
|
static EnergyStack |
FeatureCalculatorRepeated.extractStack(ProvidesStackInput input,
StackProvider stackEnergy,
InputOutputContext context) |
| Constructor and Description |
|---|
CalculateFeaturesForObjects(CombineObjectsForFeatures<T> table,
InitializationWithEnergyStack initialization,
boolean suppressErrors,
FeatureCalculationContext<FeatureTableCalculator<T>> context) |
FeatureCalculatorFromProvider(ProvidesStackInput stackInput,
Optional<StackProvider> stackEnergy,
InputOutputContext context) |
| Modifier and Type | Method and Description |
|---|---|
void |
GroupMapByName.add(Optional<String> groupIdentifier,
List<org.apache.commons.math3.util.Pair<String,S>> singleItemsToAdd)
Adds an item with a non-group identifier, and also optionally a group identifier.
|
void |
AddToAggregateItem.add(S individual,
T aggregate) |
void |
ConsistentChannelNamesChecker.checkChannelNames(Set<String> channelNames,
boolean rgb)
Checks that the channel-names are consistent.
|
Channel |
ChannelSource.extractChannel(Stack stack,
boolean checkType,
int index) |
Channel |
ChannelSource.extractChannel(String stackName,
boolean checkType)
|
Channel |
ChannelSource.extractChannel(String stackName,
boolean checkType,
int index) |
void |
GroupMapByName.outputAnyRemainingGroups()
Outputs any groups that have not already been outputted.
|
| Constructor and Description |
|---|
GroupMapByName(String nounT,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
java.util.function.Supplier<T> createAggregator,
CheckedBiConsumer<S,T,OperationFailedException> addSingleToAggregator)
Creates a group-map.
|
| Modifier and Type | Method and Description |
|---|---|
String |
SharedStateFilteredImageOutput.labelFor(ProvidesStackInput input,
InputOutputContext context)
Determines a particular group-identifier for an input
|
| Modifier and Type | Method and Description |
|---|---|
void |
MontageSharedState.drawAllLabels(double ratioHeightForLabel,
BoxAligner aligner)
Draw all labels that have been queued during calls to
MontageSharedState.copyStackInto(org.anchoranalysis.core.functional.checked.CheckedSupplier<org.anchoranalysis.image.core.stack.RGBStack, org.anchoranalysis.io.input.InputReadFailedException>, java.lang.String, java.nio.file.Path, java.util.Optional<java.lang.String>). |
| Modifier and Type | Method and Description |
|---|---|
static ImageInitialization |
InitializationFactory.createWithStacks(ProvidesStackInput input,
InitializationContext context) |
| Modifier and Type | Method and Description |
|---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
| Modifier and Type | Method and Description |
|---|---|
static Channel |
FilterHelper.applyRankFilter(Channel channel,
int radius,
int filterType)
Applies a 2D rank-filter to each slice independently.
|
| Modifier and Type | Method and Description |
|---|---|
static BinaryVoxels<UnsignedByteBuffer> |
ApplyImageJMorphologicalOperation.applyOperation(BinaryVoxels<UnsignedByteBuffer> voxels,
String command,
int iterations) |
static void |
ApplyImageJMorphologicalOperation.fill(BinaryVoxels<UnsignedByteBuffer> voxels) |
| Modifier and Type | Method and Description |
|---|---|
NoSharedState |
CopyFilesNamingWithoutSharedState.beforeCopying(Path destinationDirectory,
List<FileWithDirectoryInput> inputs) |
abstract T |
CopyFilesNaming.beforeCopying(Path destinationDirectory,
List<FileWithDirectoryInput> inputs)
To be called once before any calls to
CopyFilesNaming.destinationPath(File,
DirectoryWithPrefix, int, CopyContext). |
NoSharedState |
CopyFilesNamingOne.beforeCopying(Path destinationDirectory,
List<FileWithDirectoryInput> inputs) |
| Modifier and Type | Method and Description |
|---|---|
ClusterMembership |
ClusterByTimestamp.beforeCopying(Path destinationDirectory,
List<FileWithDirectoryInput> inputs) |
String |
ClusterIdentifier.name()
Derives a name for the cluster, based upon its contents.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ConvertNamedChannelsInputToStack.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
void |
ConvertNamedChannelsInputToStack.addToStoreWithName(String name,
NamedProviderStore<TimeSeries> stacks,
int seriesIndex,
Logger logger) |
int |
ConvertNamedChannelsInputToStack.numberFrames() |
| Modifier and Type | Method and Description |
|---|---|
void |
SummarizerListMultiline.add(T element) |
void |
SummarizerSplitMoreThan.add(T element) |
abstract void |
Summarizer.add(T element)
Adds a element to the summary.
|
void |
SummarizerAggregate.add(T element) |
void |
Summarizer.addAll(Collection<T> elements)
Adds the elements to the summary.
|
String |
SummarizerListMultiline.describe() |
String |
SummarizerSplitMoreThan.describe() |
abstract String |
Summarizer.describe()
A string summarizing this item.
|
String |
SummarizerAggregate.describe() |
boolean |
SummarizerSplitMoreThan.requiresImageMetadata() |
abstract boolean |
Summarizer.requiresImageMetadata()
Whether a
ImageMetadataInput is required as an input. |
boolean |
SummarizerAggregate.requiresImageMetadata() |
| Modifier and Type | Method and Description |
|---|---|
void |
ImageSize.add(ImageMetadataInput input) |
void |
SummarizerImageMetadataSimple.add(ImageMetadataInput element) |
String |
SummarizerImageMetadata.describe() |
| Modifier and Type | Method and Description |
|---|---|
void |
SummarizerInputFromManager.add(T element) |
String |
SummarizerInputFromManager.describe() |
| Modifier and Type | Method and Description |
|---|---|
void |
FilePathPattern.add(Path element) |
void |
FileSizeStatistics.add(Path filePath) |
String |
FilePathPattern.describe() |
String |
FileSizeStatistics.describe() |
| Constructor and Description |
|---|
FilePathPattern(String... paths)
Create with one or more paths.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ClusterMembership.associateFileWithCluster(File file,
long timestamp,
ClusterIdentifier clusterIdentifier)
Indicates a particular file is a member of a particular cluster.
|
| Modifier and Type | Method and Description |
|---|---|
void |
RootPathMap.addFromXmlFile(Path path)
Adds root-paths contained in a list of XML Beans in an xml file
|
| Modifier and Type | Method and Description |
|---|---|
void |
RecordingCounter.recordCopiedOutput(Path source,
Optional<Path> destination,
int index)
Records an copy operation in the log / CSV path mapping.
|
| Constructor and Description |
|---|
RecordingCounter(Counter counter,
Outputter outputter,
T namingSharedState) |
| Modifier and Type | Method and Description |
|---|---|
void |
AndList.start(EnergyStack energyStack) |
void |
FeatureValueCheckMark.start(EnergyStack energyStack) |
| Modifier and Type | Method and Description |
|---|---|
abstract Optional<Tuple3i> |
VisitScheduler.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerUniformSample.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
Optional<Tuple3i> |
VisitSchedulerAnd.maxDistanceFromRootPoint(Optional<Resolution> resolution) |
| Modifier and Type | Method and Description |
|---|---|
S |
DefineOutputterWithEnergy.ProcessWithEnergyStack.process(T initialization,
EnergyStack energyStack) |
<S> void |
DefineOutputterWithEnergy.processInput(ExportSharedObjects input,
InitializationContext context,
DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization,S> operation) |
<S> S |
DefineOutputterWithEnergy.processInput(InitializationContext context,
SharedObjects sharedObjects,
Optional<Dictionary> dictionary,
DefineOutputterWithEnergy.ProcessWithEnergyStack<ImageInitialization,S> operation) |
| Modifier and Type | Method and Description |
|---|---|
Optional<Point3i> |
FindPointOnContourWalk.pointOnContour(Point3d centerPoint,
Orientation orientation) |
abstract Optional<Point3i> |
FindPointOnContour.pointOnContour(Point3d centerPoint,
Orientation orientation) |
| Modifier and Type | Method and Description |
|---|---|
double |
Constant.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
GaussianSampler.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
Scale.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
FromUnitValueDistance.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
double |
MaxWithConstant.propose(RandomNumberGenerator randomNumberGenerator,
Optional<Resolution> resolution) |
| Modifier and Type | Method and Description |
|---|---|
void |
ContourTraverser.traverseGlobal(Point3i root,
java.util.function.Consumer<Point3i> pointConsumer)
Traverse
contourToTraverse using global-coordinates. |
| Modifier and Type | Method and Description |
|---|---|
static ContiguousVoxelPath |
CombineToOnePath.combineToOnePath(List<ContiguousVoxelPath> paths)
Combines all the contiguous paths to a single-path.
|
| Modifier and Type | Method and Description |
|---|---|
void |
ConvertNamedChannels.replaceTask(Task<U,S> taskToReplace) |
| Modifier and Type | Method and Description |
|---|---|
void |
FromObjects.calculateAndOutput(MultiInput input,
FeatureCalculationContext<FeatureTableCalculator<T>> context) |
| Modifier and Type | Method and Description |
|---|---|
ObjectCollectionWithProperties |
Pairwise.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
abstract ObjectCollectionWithProperties |
ColumnDefinition.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
ObjectCollectionWithProperties |
Single.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
| Modifier and Type | Method and Description |
|---|---|
void |
FromCSVInput.copyTo(SharedObjects target,
Logger logger) |
| Modifier and Type | Method and Description |
|---|---|
ObjectCollectionWithProperties |
CSVRow.findObjectsMatchingRow(IntersectingObjects<ObjectMask> allObjects) |
| Modifier and Type | Method and Description |
|---|---|
VoxelizedMarksWithEnergy |
PointsFitter.transform(MarkCollection in,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
VoxelizedMarksWithEnergy |
RetrieveDestinationFromDual.transform(DualVoxelizedMarks in,
TransformationContext context) |
VoxelizedMarksWithEnergy |
RetrieveSourceFromDual.transform(DualVoxelizedMarks in,
TransformationContext context) |
DualVoxelizedMarks |
AddDualTransformer.transform(VoxelizedMarksWithEnergy in,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
MarkCollection |
RemovePartition.transform(MarksFromPartition marks,
TransformationContext context) |
T |
RemovePartitionAndThen.transform(MarksFromPartition marks,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
VoxelizedMarksWithEnergy |
AddEnergy.transform(MarkCollection in,
TransformationContext context) |
T |
RetrieveSourceFromVoxelized.transform(ToVoxelized<T> in,
TransformationContext context) |
VoxelizedMarksWithEnergy |
RetrieveDestinationFromVoxelized.transform(ToVoxelized<T> in,
TransformationContext context) |
ToVoxelized<T> |
VoxelizeWithTransform.transform(T in,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
Optional<X> |
TransformMapOptional.transform(Optional<W> item,
TransformationContext context) |
| Modifier and Type | Method and Description |
|---|---|
List<LabelledWithConfidence<MultiScaleObject>> |
DecodeMaskRCNN.decode(List<ai.onnxruntime.OnnxTensor> inferenceOutput,
ImageInferenceContext context) |
| Modifier and Type | Method and Description |
|---|---|
List<LabelledWithConfidence<MultiScaleObject>> |
DecodeEAST.decode(List<ai.onnxruntime.OnnxTensor> inferenceOutput,
ImageInferenceContext context) |
| Modifier and Type | Method and Description |
|---|---|
protected ai.onnxruntime.OnnxTensor |
SegmentObjectsFromONNXModel.deriveInput(Stack stack,
Optional<double[]> subtractMeans) |
| Modifier and Type | Method and Description |
|---|---|
<S> S |
OnnxModel.performInference(ai.onnxruntime.OnnxTensor input,
String inputName,
List<String> outputNames,
CheckedFunction<List<ai.onnxruntime.OnnxTensor>,S,OperationFailedException> convertFunction) |
| Modifier and Type | Method and Description |
|---|---|
void |
OnnxModel.close() |
<S> S |
OnnxModel.performInference(ai.onnxruntime.OnnxTensor input,
String inputName,
List<String> outputNames,
CheckedFunction<List<ai.onnxruntime.OnnxTensor>,S,OperationFailedException> convertFunction) |
| Modifier and Type | Method and Description |
|---|---|
static List<Contour> |
CVFindContours.contoursForObject(ObjectMask object)
Calculates the extreme outer contours from an
ObjectMask as OpenCV defines contours. |
| Modifier and Type | Method and Description |
|---|---|
protected org.opencv.core.Mat |
SegmentObjectsFromTensorFlowModel.deriveInput(Stack stack,
Optional<double[]> subtractMeans) |
| Modifier and Type | Method and Description |
|---|---|
static Stack |
ConvertFromMat.toStack(org.opencv.core.Mat mat)
Convert from an OpenCV
Mat to a Stack. |
static VoxelBuffer<?> |
VoxelBufferFromMat.toVoxelBuffer(org.opencv.core.Mat mat,
Extent extent)
Converts a
Mat to a VoxelBuffer. |
| Modifier and Type | Method and Description |
|---|---|
<S> S |
OpenCVModel.performInference(org.opencv.core.Mat input,
String inputName,
List<String> outputNames,
CheckedFunction<List<org.opencv.core.Mat>,S,OperationFailedException> convertFunction) |
| Modifier and Type | Method and Description |
|---|---|
<S> S |
OpenCVModel.performInference(org.opencv.core.Mat input,
String inputName,
List<String> outputNames,
CheckedFunction<List<org.opencv.core.Mat>,S,OperationFailedException> convertFunction) |
| Modifier and Type | Method and Description |
|---|---|
void |
PointsFitterToMark.fitPointsToMark(List<Point3f> pointsForFitter,
Mark mark,
Dimensions dim) |
| Modifier and Type | Method and Description |
|---|---|
static List<Point2i> |
ConvexHullUtilities.convexHull2D(List<Point2i> points)
Like
ConvexHullUtilities.convexHull2D(List, int) but uses a default minimum number of points. |
static List<Point2i> |
ConvexHullUtilities.convexHull2D(List<Point2i> points,
int minNumberPoints)
Apply a convex-hull algorithm to filter a set of points.
|
| Modifier and Type | Method and Description |
|---|---|
void |
QuickMultiDatasetExperiment.replaceInputManager(InputManager<T> inputManager) |
void |
QuickMultiDatasetExperiment.replaceOutputManager(OutputManager output) |
| Modifier and Type | Method and Description |
|---|---|
void |
QuickMultiDatasetStructuredExperiment.replaceInputManager(InputManager<T> inputManager) |
void |
QuickMultiDatasetStructuredExperiment.replaceOutputManager(OutputManager output) |
| Modifier and Type | Method and Description |
|---|---|
BoundingBox |
PointRange.toBoundingBox()
Creates a
BoundingBox to just cover the range of points that have been added. |
| Modifier and Type | Method and Description |
|---|---|
Point3d |
RotationMatrix.column(int columnIndex)
Extracts a column from the rotation-matrix as a point.
|
| Modifier and Type | Method and Description |
|---|---|
<T extends InputFromManager,S,V extends Task<T,S>> |
ExecuteTaskHelper.assertExpectedTaskOutputs(List<T> inputs,
V task,
Path pathDirectoryOutput,
String pathDirectorySaved,
Iterable<String> pathsFileToCompare)
Executes a task on a multiple inputs and asserts expected outputs - with task arguments.
|
<T extends InputFromManager,S,V extends Task<T,S>> |
ExecuteTaskHelper.assertExpectedTaskOutputs(T input,
V task,
Path pathDirectoryOutput,
String pathDirectorySaved,
Iterable<String> pathsFileToCompare)
Executes a task on a single-input.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
MockFeatureWithCalculationFixture.executeAndAssertCount(int expectedCountCalc,
int expectedCountExecute,
CheckedRunnable<OperationFailedException> operation)
Executes an operation, and afterwards asserts an expected number of times certain internal
methods are called on a mock-calculation.
|
| Modifier and Type | Method and Description |
|---|---|
static void |
MockFeatureWithCalculationFixture.executeAndAssertCount(int expectedCountCalc,
int expectedCountExecute,
CheckedRunnable<OperationFailedException> operation)
Executes an operation, and afterwards asserts an expected number of times certain internal
methods are called on a mock-calculation.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.