Package | Description |
---|---|
org.anchoranalysis.annotation.io |
Reading and writing annotations to the filesystem.
|
org.anchoranalysis.annotation.io.bean |
Beans related to reading / writing / specifying annotations.
|
org.anchoranalysis.annotation.io.bean.comparer |
What to compare an annotation (ground truth) against?
|
org.anchoranalysis.annotation.io.image |
Reading and writing whole-image label annotations.
|
org.anchoranalysis.annotation.io.mark |
Reading and writing
Mark -related annotations from/to the
file-system. |
org.anchoranalysis.core.serialize |
Utilities for serializing and deserializing objects.
|
org.anchoranalysis.image.bean.spatial.arrange |
Beans to specify how to form a single-image by spatially combining other images.
|
org.anchoranalysis.image.bean.spatial.arrange.fill |
Montages images together to completely fill the available space, while preserving aspect ratio.
|
org.anchoranalysis.image.bean.spatial.arrange.overlay |
Combining other images through overlaying.
|
org.anchoranalysis.image.bean.spatial.arrange.tile |
Combining other images through tiling.
|
org.anchoranalysis.image.io.bean.stack.metadata.reader |
Bean classes for reading
ImageMetadata from the
file-system. |
org.anchoranalysis.image.io.bean.stack.reader |
Bean classes for reading raster-files from the filesystem.
|
org.anchoranalysis.image.io.object.input |
Non-bean classes for reading an
ObjectCollection
from the filesystem. |
org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from the
filesystem. |
org.anchoranalysis.io.input.bean |
Beans related to collecting inputs from the file-system for an experiment.
|
org.anchoranalysis.io.output.bean |
Beans for the framework around writing files to the file-system.
|
org.anchoranalysis.io.output.outputter |
Classes for outputting to particular directories.
|
org.anchoranalysis.mpp.io.bean.report.feature |
Beans for communicating feature-values from data-structures in human-readable manner.
|
org.anchoranalysis.mpp.io.marks |
Non-beans to help write visualization of
Mark s to the
filesystem. |
org.anchoranalysis.mpp.proposer |
Non-bean classes for proposing
Mark s or other data-structures
with particular attributes. |
org.anchoranalysis.mpp.segment.optimization.kernel |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization.kernel |
org.anchoranalysis.plugin.annotation.bean.comparer |
Comparing the similarity of annotations from two images to each other.
|
org.anchoranalysis.plugin.annotation.bean.strategy |
Strategies for how to annotate an image, such label per image etc.
|
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.task.bean.combine |
Combining multiple images together into a single image.
|
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.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.stack |
Non-bean classes pertaining to stacks and channels as used in tasks.
|
org.anchoranalysis.plugin.io.bean.metadata.reader |
Implementations of
ImageMetadataReader . |
org.anchoranalysis.test |
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
|
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. |
Optional<T> |
AnnotationReader.read(Path path,
OperationContext context)
Reads an annotation, if possible, from the file-system.
|
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. |
Modifier and Type | Method and Description |
---|---|
List<NameValue<Stack>> |
MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation,
DisplayStack background,
Path annotationPath,
ColorScheme colorScheme,
Path modelDirectory,
OperationContext context,
boolean debugMode)
|
abstract Findable<ObjectCollection> |
ComparableSource.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context)
Loads the source of elements from the file-system and converts to a
ObjectCollection . |
Modifier and Type | Method and Description |
---|---|
Optional<ImageLabelAnnotation> |
ImageLabelAnnotationReader.read(Path path,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
Optional<DualMarksAnnotation<T>> |
DualMarksAnnotationReader.read(Path path,
OperationContext context) |
MarkCollection |
DualMarksAnnotationReader.readDefaultMarks(Path path,
OperationContext context)
Reads the annotations as a
MarkCollection from the file-system. |
Modifier and Type | Method and Description |
---|---|
T |
Deserializer.deserialize(Path filePath,
OperationContext context)
Deserializes a representation of an object stored on the filesystem.
|
T |
XStreamDeserializer.deserialize(Path filePath,
OperationContext context) |
T |
ObjectInputStreamDeserializer.deserialize(Path filePath,
OperationContext context) |
T |
DictionaryDeserializer.deserialize(Path filePath,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Single.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
abstract StackArrangement |
StackArranger.arrangeStacks(Iterator<Extent> extents,
OperationContext context)
Arranges stacks to that they fit together in a single raster.
|
RGBStack |
StackArranger.combine(List<RGBStack> stacks,
VoxelsResizer resizer,
ChannelFactorySingleType factory,
OperationContext context)
|
RGBStack |
StackArranger.combine(List<RGBStack> stacks,
VoxelsResizer resizer,
OperationContext context)
|
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Fill.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Overlay.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
StackArrangement |
Tile.arrangeStacks(Iterator<Extent> extents,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
ImageMetadata |
FromStackReader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
abstract ImageMetadata |
ImageMetadataReader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context)
Opens a file containing one or more images but does not read an image.
|
Modifier and Type | Method and Description |
---|---|
Stack |
StackReader.readStack(Path path,
OperationContext context)
Opens a file at
path that should contain only a single-stack. |
Modifier and Type | Method and Description |
---|---|
static ObjectCollection |
ObjectCollectionReader.createFromPath(Path path,
OperationContext context)
Reads an object-collection from a path (or path prefix) trying different methods to read the
objects.
|
Modifier and Type | Method and Description |
---|---|
static Mask |
MaskReader.openMask(StackReader stackReader,
Path path,
BinaryValuesInt binaryValues,
OperationContext context)
Utility functions for opening a single-channeled stack as a
Mask . |
Modifier and Type | Method and Description |
---|---|
OperationContext |
InputManagerParameters.getOperationContext()
Allows for logging and recording the execution-time of particular operations.
|
Constructor and Description |
---|
InputManagerParameters(InputContextParameters inputContext,
OperationContext operationContext) |
InputManagerParameters(OperationContext operationContext)
Create with only a
OperationContext , and using sensible default values for the other
fields. |
Modifier and Type | Method and Description |
---|---|
abstract String |
ReportFeature.featureDescription(T param,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
default OperationContext |
InputOutputContext.operationContext() |
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
MarkCollection |
MarkCollectionDeserializer.deserialize(Path filePath,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
OperationContext |
ProposerContext.getOperationContext() |
Constructor and Description |
---|
ProposerContext(RandomNumberGenerator randomNumberGenerator,
EnergyStack energyStack,
RegionMap regionMap,
OperationContext operationContext,
ErrorNode errorNode) |
Modifier and Type | Method and Description |
---|---|
OperationContext |
MarkFactoryContext.getOperationContext()
Context for reading a stack from the file-system.
|
Constructor and Description |
---|
MarkFactoryContext(MarkWithIdentifierFactory markFactory,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
Findable<ObjectCollection> |
Objects.loadAsObjects(Path filePathSource,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
DualMarksAnnotationAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MarksAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MaskAsObject.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
Optional<String> |
MarkProposerStrategy.annotationLabelFor(ProvidesStackInput item,
OperationContext operationContext) |
Optional<String> |
ImageLabelStrategy.annotationLabelFor(ProvidesStackInput item,
OperationContext context) |
static Optional<ImageLabelAnnotation> |
ReadAnnotationFromFile.readAssumeExists(Path path,
OperationContext context) |
static Optional<ImageLabelAnnotation> |
ReadAnnotationFromFile.readCheckExists(Path path,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
ListWithThumbnails<T,ObjectCollection> |
CombineObjectsForFeatures.deriveInputsStartBatch(ObjectCollection objects,
EnergyStack energyStack,
boolean thumbnailsEnabled,
OperationContext context)
Derives a list of inputs (i.e.
|
Modifier and Type | Method and Description |
---|---|
protected GroupMapByName<Channel,ChannelAggregator> |
AggregateChannelTask.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
protected abstract GroupMapByName<S,T> |
GroupedStackBase.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext)
Creates a map for the storing an aggregate-data-object for each group.
|
Modifier and Type | Method and Description |
---|---|
protected GroupMapByName<Histogram,Histogram> |
ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
OperationContext |
FeatureCalculationContext.getOperationContext() |
Constructor and Description |
---|
ImageSizePrereader(ImageMetadataReader imageMetadataReader,
StackReader stackReader,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
ImageMetadata |
AlwaysReject.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
ImageMetadata |
InferFromHeader.openFile(Path path,
StackReader defaultStackReader,
OperationContext context) |
Modifier and Type | Method and Description |
---|---|
static OperationContext |
LoggerFixture.suppressedOperationContext()
An
OperationContext containing a logger that doesn't output anything. |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.