Uses of Class
org.anchoranalysis.core.log.Logger

Packages that use Logger

Package	Description
org.anchoranalysis.annotation.io	Reading and writing annotations to the filesystem.
org.anchoranalysis.annotation.io.image.findable	The outcome of searching for annotations or images on the file-system.
org.anchoranalysis.bean	Defining, loading, initializing Anchor Beans.
org.anchoranalysis.bean.initializable	Initializing beans with particular parameters, including recursively.
org.anchoranalysis.bean.initializable.property	Initializating a bean with parameters.
org.anchoranalysis.core.log	Interfaces to log messages, both information and error messages.
org.anchoranalysis.core.time	Recording the execution-time of operations for profiling.
org.anchoranalysis.experiment.io	Interfaces for replacing attributes of an experiment: input, output, task etc.
org.anchoranalysis.experiment.task	Non-bean classes related to a Task.
org.anchoranalysis.feature.bean.list	A feature-list (custom list type for features) and associated providers.
org.anchoranalysis.feature.calculate.cache	Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
org.anchoranalysis.feature.initialization	Initialization parameters used for beans in org.anchoranalysis.feature.bean.
org.anchoranalysis.feature.session	A defined context in which one or more features are provided inputs and produce results.
org.anchoranalysis.feature.session.cache	Creates a FeatureCalculationCache to use during feature-calculations.
org.anchoranalysis.feature.session.replace	Strategies on whether to reuse or invalidate a feature-input's cache.
org.anchoranalysis.feature.shared	Features shared for referencing among calculations.
org.anchoranalysis.image.bean.channel	Base classes for performing operations on Channels.
org.anchoranalysis.image.bean.nonbean.init	Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
org.anchoranalysis.image.feature.calculator	Implementations of FeatureCalculatorMulti related to images, especially to create tables of feature-calculations.
org.anchoranalysis.image.feature.calculator.merged	A particular implementation of FeatureCalculatorMulti for feature-calculations based upon pairs of image-objects.
org.anchoranalysis.image.inference	Inference of machine learning models on images.
org.anchoranalysis.image.inference.bean.segment.instance	Instance-segmentation of a Stack.
org.anchoranalysis.image.io.bean.channel	Beans pertaining to reading Channels as input.
org.anchoranalysis.image.io.bean.stack.writer	Bean classes for writing raster-files to the filesystem.
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.object.output.hdf5	Writing an ObjectCollection to the filesystem in HDF5 format.
org.anchoranalysis.image.io.stack	Non-bean classes for reading / writing a Stack from and to the filesystem.
org.anchoranalysis.image.io.stack.input	Non-bean classes for reading a Stack from the filesystem.
org.anchoranalysis.image.io.stack.output.generator	Base classes for generators that ultimately write a Stack to the filesystem.
org.anchoranalysis.inference.concurrency	Specifying how many CPUs and GPUs can be allocated for some purpose.
org.anchoranalysis.io.generator	Base-classes and utilities for generators, which write different types of objects to the file system.
org.anchoranalysis.io.generator.serialized	Generators for writing serialized objects.
org.anchoranalysis.io.generator.tabular	Generators for writing tabular data, including CSV.
org.anchoranalysis.io.generator.text	Generators for writing textual data, including strings.
org.anchoranalysis.io.generator.xml	Generators for writing XML data.
org.anchoranalysis.io.input.bean	Beans related to collecting inputs from the file-system for an experiment.
org.anchoranalysis.io.input.file	Non-bean classes that relate to using files during inputting.
org.anchoranalysis.io.output.outputter	Classes for outputting to particular directories.
org.anchoranalysis.io.output.writer	Allows a generators to write element(s) to the filesystem.
org.anchoranalysis.launcher	Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.executor	Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.run	Parses command-line arguments and runs an experiment.
org.anchoranalysis.mpp.feature.addcriteria	Criteria for adding edges during optimization of marked-point-processes.
org.anchoranalysis.mpp.feature.energy.saved	Saved snapshots of energy-calculations.
org.anchoranalysis.mpp.feature.energy.scheme	Factorized form of storing the energy during an energy-minimization optimization scheme.
org.anchoranalysis.mpp.init	Parameters used to initialize certain types of beans.
org.anchoranalysis.mpp.io.input	Non-beans for reading data structures related to marked point processes from the file system.
org.anchoranalysis.mpp.mark	Non-bean classes related to Marks.
org.anchoranalysis.plugin.image.feature.bean.object.combine	Features from combinations of 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.format.convertstyle	Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
org.anchoranalysis.plugin.image.task.feature	Non-bean classes pertaining to Features 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.channel.map	Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.input.stack	Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.multifile	Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.onnx.bean.object.segment.stack	Segmenting a Stack using the ONNX Runtime to produce an ObjectCollection.
org.anchoranalysis.plugin.opencv.bean.object.segment.stack	Segmentation of a Stack using OpenCV.
org.anchoranalysis.plugin.points.bean	Beans that fit or otherwise manipulate sets of points.
org.anchoranalysis.test	Testing utilities and fixtures with no greater downstream dependency than anchor-core.
org.anchoranalysis.test.experiment	Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
org.anchoranalysis.test.image	Testing utilities and fixtures with no greater downstream dependency than anchor-image-io or anchor-io-bioformats or anchor-imagej.

Uses of Logger in org.anchoranalysis.annotation.io

Methods in org.anchoranalysis.annotation.io with parameters of type Logger

Modifier and Type	Method	Description
NamedStacksSupplier	AnnotationWithStrategy.stacks(Logger logger)	All stacks associated with the input, lazily evaluated.

Uses of Logger in org.anchoranalysis.annotation.io.image.findable

Methods in org.anchoranalysis.annotation.io.image.findable with parameters of type Logger

Modifier and Type	Method	Description
Optional<T>	Findable.getOrLog(String name, Logger logger)	Gets an object or otherwise logs a message describing what went wrong.
Optional<T>	Found.getOrLog(String name, Logger logger)
Optional<T>	NotFound.getOrLog(String name, Logger logger)

Uses of Logger in org.anchoranalysis.bean

Methods in org.anchoranalysis.bean with parameters of type Logger

Modifier and Type	Method	Description
void	NullParametersBean.initializeRecursive(Logger logger)	Initialize this bean and any suitable child beans.

Uses of Logger in org.anchoranalysis.bean.initializable

Methods in org.anchoranalysis.bean.initializable that return Logger

Modifier and Type	Method	Description
protected Logger	InitializableBean.getLogger()	The logger.

Methods in org.anchoranalysis.bean.initializable with parameters of type Logger

Modifier and Type	Method	Description
void	InitializableBean.initialize(P parameters, Logger logger)	Initializes the bean with the necessary parameters.
void	InitializableBean.initializeRecursive(P parameters, Logger logger)	Initializes this object, and all children objects, so long as they have P once a Bean doesn't have P, the children are not evaluated.
void	InitializableBean.initRecursiveWithInitializer(BeanInitializer<?> initializer, Logger logger)	Initializes the bean and recursively all contained beans (who have compatible initialization requirements)

Uses of Logger in org.anchoranalysis.bean.initializable.property

Methods in org.anchoranalysis.bean.initializable.property with parameters of type Logger

Modifier and Type	Method	Description
boolean	BeanInitializer.applyInitializationIfPossibleTo(Object bean, Object parent, Logger logger)	Applies the initialization to a bean if possible.
void	AssignerMatchClass.assignInitializationToProperties(Object bean, Object initialization, Object parent, Logger logger)
void	InitializationParameterAssigner.assignInitializationToProperties(Object bean, Object initialization, Object parent, Logger logger)	Assigns the parameter to the bean.

Uses of Logger in org.anchoranalysis.core.log

Methods in org.anchoranalysis.core.log that return Logger

Modifier and Type	Method	Description
Logger	CommonContext.getLogger()	The logger.

Constructors in org.anchoranalysis.core.log with parameters of type Logger

Modifier	Constructor	Description
	CommonContext(Logger logger, Path modelDirectory)	Creates a new CommonContext instance.

Uses of Logger in org.anchoranalysis.core.time

Methods in org.anchoranalysis.core.time that return Logger

Modifier and Type	Method	Description
Logger	OperationContext.getLogger()	Where to write informative messages to, and and any non-fatal errors (fatal errors are throw as exceptions).

Constructors in org.anchoranalysis.core.time with parameters of type Logger

Modifier	Constructor	Description
	OperationContext(Logger logger)	Creates with a Logger ignoring execution-times.
	OperationContext(ExecutionTimeRecorder executionTimeRecorder, Logger logger)	Creates a new OperationContext instance.

Uses of Logger in org.anchoranalysis.experiment.io

Methods in org.anchoranalysis.experiment.io that return Logger

Modifier and Type	Method	Description
Logger	InitializationContext.getLogger()	The associated logger.

Uses of Logger in org.anchoranalysis.experiment.task

Methods in org.anchoranalysis.experiment.task that return Logger

Modifier and Type	Method	Description
Logger	InputBound.getLogger()	The Logger associated with this input, as it is being processed as a job.
Logger	InputOutputContextStateful.getLogger()

Uses of Logger in org.anchoranalysis.feature.bean.list

Methods in org.anchoranalysis.feature.bean.list with parameters of type Logger

Modifier and Type	Method	Description
void	FeatureList.initializeRecursive(FeatureInitialization initialization, Logger logger)	Initializes all features in the list, and recursively any features they contain.

Uses of Logger in org.anchoranalysis.feature.calculate.cache

Methods in org.anchoranalysis.feature.calculate.cache with parameters of type Logger

Modifier and Type	Method	Description
void	FeatureCalculationCache.initialize(FeatureInitialization initialization, Logger logger)	Initializes the cache.

Uses of Logger in org.anchoranalysis.feature.initialization

Methods in org.anchoranalysis.feature.initialization with parameters of type Logger

Modifier and Type	Method	Description
static FeatureRelatedInitialization	FeatureRelatedInitialization.create(Logger logger, Path modelDirectory)	Creates a log and a model-directory, and otherwise empty initialization.
void	FeatureRelatedInitialization.populate(List<NamedBean<FeatureListProvider<FeatureInput>>> namedProviders, Logger logger)	Adds features into the shared-feature storage from a list of named-beans.

Uses of Logger in org.anchoranalysis.feature.session

Methods in org.anchoranalysis.feature.session with parameters of type Logger

Modifier and Type	Method	Description
static <T extends FeatureInput> double	FeatureSession.calculateWith(Feature<T> feature, T input, Logger logger)	Starts a feature-session for a single feature - and performs a calculation.
void	SequentialSession.start(FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts the session.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, Logger logger)	Starts a feature-session for a single feature.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a single feature, with specific initialization.
static <T extends FeatureInput> FeatureCalculatorSingle<T>	FeatureSession.with(Feature<T> feature, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a single feature, with default initialization.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, Logger logger)	Starts a feature-session for a list of features, with default initialization.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, FeatureInitialization initialization, Optional<SharedFeatures> sharedFeatures, Logger logger, BoundReplaceStrategy<T,? extends ReplaceStrategy<T>> replaceStrategy)	Starts a feature-session for a list of features, with particular initialization, and a replaceStrategy.
static <T extends FeatureInput> FeatureCalculatorMulti<T>	FeatureSession.with(FeatureList<T> features, FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Starts a feature-session for a list of features, with particular initialization.

Uses of Logger in org.anchoranalysis.feature.session.cache

Constructors in org.anchoranalysis.feature.session.cache with parameters of type Logger

Modifier	Constructor	Description
	HorizontalCacheCreator(FeatureList<? extends FeatureInput> namedFeatures, SharedFeatures sharedFeatures, FeatureInitialization initialization, Logger logger)	Creates a new HorizontalCacheCreator instance.

Uses of Logger in org.anchoranalysis.feature.session.replace

Methods in org.anchoranalysis.feature.session.replace with parameters of type Logger

Modifier and Type	Method	Description
ReplaceStrategy<T>	BoundReplaceStrategy.createOrReuse(FeatureList<T> features, FeatureInitialization initialization, SharedFeatures sharedFeatures, Logger logger)	Creates a ReplaceStrategy for a particular CacheCreator, or reuses any previously-created ReplaceStrategy if it exists.

Uses of Logger in org.anchoranalysis.feature.shared

Methods in org.anchoranalysis.feature.shared with parameters of type Logger

Modifier and Type	Method	Description
void	SharedFeaturesSubset.initializeRecursive(FeatureInitialization initialization, Logger logger)	Initialize all features in this instance, recursively also initializating any child-features.

Uses of Logger in org.anchoranalysis.image.bean.channel

Methods in org.anchoranalysis.image.bean.channel with parameters of type Logger

Modifier and Type	Method	Description
void	ChannelAggregator.addChannel(Channel channel, Logger logger)	Adds a Channel to the aggregation.

Uses of Logger in org.anchoranalysis.image.bean.nonbean.init

Methods in org.anchoranalysis.image.bean.nonbean.init with parameters of type Logger

Modifier and Type	Method	Description
void	ImageInitialization.populate(BeanInitializer<?> propertyInitializer, Define define, Logger logger)	Adds diverse entities from a Define into the corresponding name-collections.

Constructors in org.anchoranalysis.image.bean.nonbean.init with parameters of type Logger

Modifier	Constructor	Description
	PopulateStoreFromDefine(Define define, BeanInitializer<?> propertyInitializer, Logger logger)	Creates a new PopulateStoreFromDefine instance.

Uses of Logger in org.anchoranalysis.image.feature.calculator

Methods in org.anchoranalysis.image.feature.calculator with parameters of type Logger

Modifier and Type	Method	Description
void	FeatureTableCalculator.start(ImageInitialization initialization, Optional<EnergyStack> energyStack, Logger logger)	Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object.
void	SingleTableCalculator.start(ImageInitialization initialization, Optional<EnergyStack> energyStack, Logger logger)

Uses of Logger in org.anchoranalysis.image.feature.calculator.merged

Methods in org.anchoranalysis.image.feature.calculator.merged with parameters of type Logger

Modifier and Type	Method	Description
void	PairsTableCalculator.start(ImageInitialization initializtion, Optional<EnergyStack> energyStack, Logger logger)

Uses of Logger in org.anchoranalysis.image.inference

Methods in org.anchoranalysis.image.inference that return Logger

Modifier and Type	Method	Description
Logger	ImageInferenceContext.getLogger()	Where to log information messages during inference.

Constructors in org.anchoranalysis.image.inference with parameters of type Logger

Modifier	Constructor	Description
	ImageInferenceContext(DualScale<Dimensions> dimensions, ScaleFactor scaleFactor, Optional<List<String>> classLabels, VoxelsResizer resizer, ExecutionTimeRecorder executionTimeRecorder, Logger logger)	Creates a new ImageInferenceContext instance.

Uses of Logger in org.anchoranalysis.image.inference.bean.segment.instance

Methods in org.anchoranalysis.image.inference.bean.segment.instance with parameters of type Logger

Modifier and Type	Method	Description
abstract ConcurrentModelPool<T>	SegmentStackIntoObjectsPooled.createModelPool(ConcurrencyPlan plan, Logger logger)	Creates the model pool (to be used by multiple threads).
ConcurrentModelPool<T>	SuppressNonMaximum.createModelPool(ConcurrencyPlan plan, Logger logger)

Uses of Logger in org.anchoranalysis.image.io.bean.channel

Methods in org.anchoranalysis.image.io.bean.channel with parameters of type Logger

Modifier and Type	Method	Description
abstract ChannelMap	ChannelMapCreator.create(OpenedImageFile openedFile, Logger logger)	Creates the ChannelMap.

Uses of Logger in org.anchoranalysis.image.io.bean.stack.writer

Method parameters in org.anchoranalysis.image.io.bean.stack.writer with type arguments of type Logger

Modifier and Type	Method	Description
ImageFileFormat	StackWriter.fileFormatWarnUnexpected(StackWriteOptions writeOptions, Optional<Logger> logger)	The file format that will be written by the generator, warning with a log message if different to suggestion.

Uses of Logger in org.anchoranalysis.image.io.channel.input

Methods in org.anchoranalysis.image.io.channel.input with parameters of type Logger

Modifier and Type	Method	Description
void	NamedChannelsInput.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	NamedChannelsInput.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
abstract int	NamedChannelsInput.bitDepth(Logger logger)	Bit-depth of image.
abstract NamedChannelsMap	NamedChannelsInput.createChannelsForSeries(int seriesIndex, Logger logger)	Creates a NamedChannelsMap representing the channels for a particular series in this input.
abstract Dimensions	NamedChannelsInput.dimensions(int seriesIndex, Logger logger)	Dimensions of a particular series.
Channel	ChannelGetter.getChannel(String channelName, int timeIndex, Logger logger)	Retrieve the Channel corresponding to channelName at a particular time-frame.
abstract ImageMetadata	NamedChannelsInput.metadata(int seriesIndex, Logger logger)	The image-metadata associated with a particular series.
abstract int	NamedChannelsInput.numberChannels(Logger logger)	Number of channels.

Uses of Logger in org.anchoranalysis.image.io.channel.map

Methods in org.anchoranalysis.image.io.channel.map with parameters of type Logger

Modifier and Type	Method	Description
void	NamedChannelsConcatenate.addAsSeparateChannels(NamedProviderStore<TimeSeries> stackCollection, int timeIndex, Logger logger)
void	NamedChannelsConcatenate.addAsSeparateChannels(NamedStacks stackCollection, int t, Logger logger)
void	NamedChannelsMap.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination, int timeIndex, Logger logger)	Adds each Channel as a separate TimeSeries in a NamedProviderStore.
void	NamedChannelsMap.addAsSeparateChannels(NamedStacks destination, int timeIndex, Logger logger)	Adds each Channel as a separate Stack in a NamedStacks.
void	OpenedNamedChannels.addAsSeparateChannels(NamedProviderStore<TimeSeries> destination, int timeIndex, Logger logger)
void	OpenedNamedChannels.addAsSeparateChannels(NamedStacks destination, int timeIndex, Logger logger)
StoreSupplier<Stack>	NamedChannelsConcatenate.allChannelsAsStack(int t, Logger logger)
StoreSupplier<Stack>	NamedChannelsMap.allChannelsAsStack(int timeIndex, Logger logger)	Combines all channels as a single Stack at a particular time-frame.
StoreSupplier<Stack>	OpenedNamedChannels.allChannelsAsStack(int t, Logger logger)
Dimensions	NamedChannelsConcatenate.dimensions(Logger logger)
Dimensions	NamedChannelsMap.dimensions(Logger logger)	The dimensions of each Channel.
Dimensions	OpenedNamedChannels.dimensions(Logger logger)
Channel	NamedChannelsConcatenate.getChannel(String channelName, int timeIndex, Logger logger)
Channel	OpenedNamedChannels.getChannel(String channelName, int timeIndex, Logger logger)
Optional<Channel>	NamedChannelsConcatenate.getChannelOptional(String channelName, int timeIndex, Logger logger)
Optional<Channel>	NamedChannelsMap.getChannelOptional(String channelName, int timeIndex, Logger logger)	Gets a channel if it exists, returning empty if it doesn't.
Optional<Channel>	OpenedNamedChannels.getChannelOptional(String channelName, int timeIndex, Logger logger)
boolean	NamedChannelsConcatenate.isRGB(Logger logger)
boolean	NamedChannelsMap.isRGB(Logger logger)	Whether the channels describe an RGB image.
boolean	OpenedNamedChannels.isRGB(Logger logger)
int	NamedChannelsConcatenate.sizeT(Logger logger)
int	NamedChannelsMap.sizeT(Logger logger)	The number of frames along the time-axis.
int	OpenedNamedChannels.sizeT(Logger logger)

Uses of Logger in org.anchoranalysis.image.io.object.output.hdf5

Method parameters in org.anchoranalysis.image.io.object.output.hdf5 with type arguments of type Logger

Modifier and Type	Method	Description
String	HDF5ObjectsGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.image.io.stack

Methods in org.anchoranalysis.image.io.stack with parameters of type Logger

Modifier and Type	Method	Description
OrientationChange	CalculateOrientationChange.calculateOrientationChange(Logger logger)	Calculates any needed orientation change.

Uses of Logger in org.anchoranalysis.image.io.stack.input

Methods in org.anchoranalysis.image.io.stack.input with parameters of type Logger

Modifier and Type	Method	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	OpenedImageFile.bitDepth(Logger logger)	The bit-depth of the image voxels e.g. 8 for 8-bit, 16 for 16-bit etc.
Optional<List<String>>	OpenedImageFile.channelNames(Logger logger)	The names of each channel, if they are known.
TimeSeries	StackSequenceInput.createStackSequenceForSeries(int seriesIndex, Logger logger)	Creates a supplier of a TimeSeries of stacks for a particular series number.
Dimensions	OpenedImageFile.dimensionsForSeries(int seriesIndex, Logger logger)	The Dimensions associated with a particular series.
boolean	OpenedImageFile.isRGB(Logger logger)	Whether the image-file has RGB encoded voxels.
default ImageMetadata	OpenedImageFile.metadata(int seriesIndex, Logger logger)	Extracts metadata about the image.
int	OpenedImageFile.numberChannels(Logger logger)	The number of channels in the image-file e.g. 1 for grayscale, 3 for RGB.
int	OpenedImageFile.numberFrames(Logger logger)	The number of frames in the image-file i.e. distinct images for a particular time-point.
TimeSeries	OpenedImageFile.open(int seriesIndex, Logger logger)	Open when we don't have a specific-type.
default TimeSeries	OpenedImageFile.open(Logger logger)	Open the first series when we don't have a specific-type.
default TimeSeries	OpenedImageFile.openCheckType(int seriesIndex, VoxelDataType channelDataType, Logger logger)	Opens a time-series, and checks that it is a particular type.

Uses of Logger in org.anchoranalysis.image.io.stack.output.generator

Method parameters in org.anchoranalysis.image.io.stack.output.generator with type arguments of type Logger

Modifier and Type	Method	Description
static String	GeneratorOutputter.fileExtensionWriter(OutputWriteSettings settings, StackWriteOptions writeOptions, Optional<Logger> logger)	The file extension to use for the default StackWriter, as returned by GeneratorOutputter.writer(OutputWriteSettings).
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.

Uses of Logger in org.anchoranalysis.inference.concurrency

Constructors in org.anchoranalysis.inference.concurrency with parameters of type Logger

Modifier	Constructor	Description
	ConcurrentModelPool(ConcurrencyPlan plan, CreateModelForPool<T> createModel, Logger logger)	Creates with a particular plan and function to create models.

Uses of Logger in org.anchoranalysis.io.generator

Method parameters in org.anchoranalysis.io.generator with type arguments of type Logger

Modifier and Type	Method	Description
abstract String	SingleFileTypeGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)	Selects the file/extension to be used for outputting the file.
String	SingleFileTypeGeneratorBridge.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.io.generator.serialized

Method parameters in org.anchoranalysis.io.generator.serialized with type arguments of type Logger

Modifier and Type	Method	Description
String	DictionaryGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)
String	SerializedGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.io.generator.tabular

Method parameters in org.anchoranalysis.io.generator.tabular with type arguments of type Logger

Modifier and Type	Method	Description
String	CSVGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.io.generator.text

Method parameters in org.anchoranalysis.io.generator.text with type arguments of type Logger

Modifier and Type	Method	Description
String	StringGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.io.generator.xml

Method parameters in org.anchoranalysis.io.generator.xml with type arguments of type Logger

Modifier and Type	Method	Description
String	XMLGenerator.selectFileExtension(OutputWriteSettings settings, Optional<Logger> logger)

Uses of Logger in org.anchoranalysis.io.input.bean

Methods in org.anchoranalysis.io.input.bean that return Logger

Modifier and Type	Method	Description
Logger	InputManagerParameters.getLogger()	Where to write informative messages to, and and any non-fatal errors (fatal errors are throw as exceptions).

Constructors in org.anchoranalysis.io.input.bean with parameters of type Logger

Modifier	Constructor	Description
	InputManagerParameters(Logger logger)	Create with only a logger, and using sensible default values for the other fields.

Uses of Logger in org.anchoranalysis.io.input.file

Methods in org.anchoranalysis.io.input.file that return Logger

Modifier and Type	Method	Description
Logger	FileNamerContext.getLogger()	Logs information messages.

Constructors in org.anchoranalysis.io.input.file with parameters of type Logger

Modifier	Constructor	Description
	FileNamerContext(String elseName, Logger logger)	Creates with a fallback-name and a logger, but otherwise using sensible defaults.
	FileNamerContext(Optional<Path> inputDirectory, boolean relativeToDirectory, String elseName, Optional<IndexRangeNegative> nameSubrange, Logger logger)	Creates a new FileNamerContext instance.
	FileNamerContext(Optional<Path> inputDirectory, boolean relativeToDirectory, Optional<IndexRangeNegative> nameSubrange, Logger logger)	Creates with specific parameters.
	FileNamerContext(Logger logger)	Creates with a logger, and otherwise uses sensible defaults.

Uses of Logger in org.anchoranalysis.io.output.outputter

Methods in org.anchoranalysis.io.output.outputter that return Logger

Modifier and Type	Method	Description
Logger	InputOutputContext.getLogger()	The associated logger.

Methods in org.anchoranalysis.io.output.outputter with parameters of type Logger

Modifier and Type	Method	Description
void	OutputterChecked.assignLogger(Logger logger)	Assigns a logger to the outputter, which is used to output warnings or messages when outputting.

Method parameters in org.anchoranalysis.io.output.outputter with type arguments of type Logger

Modifier and Type	Method	Description
static OutputterChecked	OutputterChecked.createForDirectoryPermissive(Path pathDirectory, DirectoryCreationParameters directoryCreation, Optional<Logger> logger)	Creates, defaulting to a permissive output-manager in a particular directory.

Uses of Logger in org.anchoranalysis.io.output.writer

Methods in org.anchoranalysis.io.output.writer that return types with arguments of type Logger

Modifier and Type	Method	Description
Optional<Logger>	ElementOutputter.logger()	The associated logger.

Constructor parameters in org.anchoranalysis.io.output.writer with type arguments of type Logger

Modifier	Constructor	Description
	ElementOutputter(OutputterChecked outputter, ExecutionTimeRecorder executionTimeRecorder, Supplier<Optional<Logger>> logger)	Creates a new ElementOutputter instance.

Uses of Logger in org.anchoranalysis.launcher

Methods in org.anchoranalysis.launcher with parameters of type Logger

Modifier and Type	Method	Description
static void	Launch.runCommandLineApplication(String[] args, LauncherConfig config, Logger logger)	Runs a command-line application, by parsing arguments, and then executing an experiment.

Uses of Logger in org.anchoranalysis.launcher.executor

Methods in org.anchoranalysis.launcher.executor with parameters of type Logger

Modifier and Type	Method	Description
void	ExperimentExecutor.executeExperiment(ExecutionArguments executionArguments, boolean alwaysShowExperimentArguments, Logger logger)	Executes an experiment after finding a single experiment XML file, and reading the experiment from this file.

Uses of Logger in org.anchoranalysis.launcher.run

Constructors in org.anchoranalysis.launcher.run with parameters of type Logger

Modifier	Constructor	Description
	ParseArgumentsAndRunExperiment(Logger logger)	Creates a new ParseArgumentsAndRunExperiment instance.

Uses of Logger in org.anchoranalysis.mpp.feature.addcriteria

Methods in org.anchoranalysis.mpp.feature.addcriteria with parameters of type Logger

Modifier and Type	Method	Description
void	RandomCollectionWithAddCriteria.initUpdatableMarks(MemoForIndex marks, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)

Uses of Logger in org.anchoranalysis.mpp.feature.energy.saved

Methods in org.anchoranalysis.mpp.feature.energy.saved with parameters of type Logger

Modifier and Type	Method	Description
void	EnergySavedPairs.initUpdatableMarks(MemoForIndex pxlMarkMemoList, EnergyStack stack, Logger logger, SharedFeatures sharedFeatures)

Uses of Logger in org.anchoranalysis.mpp.feature.energy.scheme

Constructors in org.anchoranalysis.mpp.feature.energy.scheme with parameters of type Logger

Modifier	Constructor	Description
	DictionaryForImageCreator(EnergyScheme energyScheme, SharedFeatures sharedFeatures, Logger logger)	Creates a new DictionaryForImageCreator instance.
	EnergySchemeWithSharedFeatures(EnergyScheme energyScheme, SharedFeatures sharedFeatures, Logger logger)	Creates a new EnergySchemeWithSharedFeatures.

Uses of Logger in org.anchoranalysis.mpp.init

Methods in org.anchoranalysis.mpp.init with parameters of type Logger

Modifier and Type	Method	Description
void	MarksInitialization.populate(BeanInitializer<?> initializer, Define define, Logger logger)	Populates the stores with beans from the given Define.
void	PointsInitialization.populate(BeanInitializer<?> initializer, Define define, Logger logger)	Populates the stores with beans from the given Define.

Uses of Logger in org.anchoranalysis.mpp.io.input

Methods in org.anchoranalysis.mpp.io.input with parameters of type Logger

Modifier and Type	Method	Description
void	MultiInputSubMap.addToStore(NamedProviderStore<T> namedStore, Logger logger)	Copies all the existing entries into a NamedProviderStore.
void	OperationMap.addToStore(NamedProviderStore<T> namedStore, Logger logger)
void	StackWithMap.addToStore(NamedProviderStore<TimeSeries> stackCollection, int seriesNum, Logger logger)	Adds the main stack and other stacks to the store.
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	ExportSharedObjects.copyTo(SharedObjects target, Logger logger)	Adds any exported shared objects to the target container.
void	MultiInput.copyTo(SharedObjects target, Logger logger)

Uses of Logger in org.anchoranalysis.mpp.mark

Methods in org.anchoranalysis.mpp.mark with parameters of type Logger

Modifier and Type	Method	Description
void	UpdatableMarks.initUpdatableMarks(MemoForIndex memo, EnergyStack energyStack, Logger logger, SharedFeatures sharedFeatures)	Initializes the updatable marks with necessary context.

Uses of Logger in org.anchoranalysis.plugin.image.feature.bean.object.combine

Methods in org.anchoranalysis.plugin.image.feature.bean.object.combine with parameters of type Logger

Modifier and Type	Method	Description
protected abstract List<T>	CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)	Derives a list of inputs from an object-collection.
List<FeatureInputSingleObject>	EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)
List<FeatureInputPairObjects>	PairNeighbors.startBatchDeriveInputs(ObjectCollection objects, EnergyStack energyStack, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.image.object.merge

Constructors in org.anchoranalysis.plugin.image.object.merge with parameters of type Logger

Modifier	Constructor	Description
	GraphLogger(DescribeGraph describeGraph, Logger logger)	Creates a new GraphLogger instance.
	MergeGraph(PayloadCalculator payloadCalculator, UpdatableBeforeCondition beforeCondition, Optional<UnitConverter> unitConverter, AssignPriority prioritizer, Logger logger, boolean logPayload)	Constructor.

Uses of Logger in org.anchoranalysis.plugin.image.object.merge.condition

Methods in org.anchoranalysis.plugin.image.object.merge.condition with parameters of type Logger

Modifier and Type	Method	Description
void	AfterCondition.initialize(Logger logger)	Initializes the condition with a logger.
void	IncreaseFeatureCondition.initialize(Logger logger)

Uses of Logger in org.anchoranalysis.plugin.image.object.merge.priority

Methods in org.anchoranalysis.plugin.image.object.merge.priority with parameters of type Logger

Modifier and Type	Method	Description
PrioritisedVertex	Prioritizer.createPriority(ObjectVertex source, ObjectVertex destination, Logger logger)	Creates a prioritized vertex based on the source and destination vertices.

Uses of Logger in org.anchoranalysis.plugin.image.task.bean.format.convertstyle

Methods in org.anchoranalysis.plugin.image.task.bean.format.convertstyle with parameters of type Logger

Modifier and Type	Method	Description
abstract NamedStacks	ChannelConvertStyle.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)	Converts a particular set of channels.
NamedStacks	ExtractToRGB.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)
NamedStacks	IndependentChannels.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)
NamedStacks	RGBIfNamesMatch.convert(Set<String> channelNames, ChannelGetterForTimepoint channelGetter, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.image.task.feature

Methods in org.anchoranalysis.plugin.image.task.feature that return Logger

Modifier and Type	Method	Description
Logger	FeatureCalculationContext.getLogger()	Gets the logger for the context.

Uses of Logger in org.anchoranalysis.plugin.image.task.stack

Methods in org.anchoranalysis.plugin.image.task.stack with parameters of type Logger

Modifier and Type	Method	Description
Channel	ChannelGetterForTimepoint.getChannel(String channelName, Logger logger)	Retrieves a channel with the given name for the specified timepoint.

Uses of Logger in org.anchoranalysis.plugin.io.bean.channel.map

Methods in org.anchoranalysis.plugin.io.bean.channel.map with parameters of type Logger

Modifier and Type	Method	Description
ChannelMap	Autoname.create(OpenedImageFile openedFile, Logger logger)
ChannelMap	FromEntries.create(OpenedImageFile openedFile, Logger logger)
ChannelMap	FromMetadata.create(OpenedImageFile openedFile, Logger logger)
ChannelMap	SingleChannel.create(OpenedImageFile openedFile, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.io.bean.input.stack

Methods in org.anchoranalysis.plugin.io.bean.input.stack with parameters of type Logger

Modifier and Type	Method	Description
void	ConvertNamedChannelsInputToStack.addToStoreInferNames(NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
void	ConvertNamedChannelsInputToStack.addToStoreWithName(String name, NamedProviderStore<TimeSeries> stacks, int seriesIndex, Logger logger)
TimeSeries	ConvertNamedChannelsInputToStack.createStackSequenceForSeries(int seriesIndex, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.io.multifile

Methods in org.anchoranalysis.plugin.io.multifile with parameters of type Logger

Modifier and Type	Method	Description
int	OpenedMultiFile.bitDepth(Logger logger)
Optional<List<String>>	OpenedMultiFile.channelNames(Logger logger)
Dimensions	OpenedMultiFile.dimensionsForSeries(int seriesIndex, Logger logger)
boolean	OpenedMultiFile.isRGB(Logger logger)
int	OpenedMultiFile.numberChannels(Logger logger)
int	OpenedMultiFile.numberFrames(Logger logger)
TimeSeries	OpenedMultiFile.open(int seriesIndex, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.onnx.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.onnx.bean.object.segment.stack with parameters of type Logger

Modifier and Type	Method	Description
ConcurrentModelPool<OnnxModel>	SegmentObjectsFromONNXModel.createModelPool(ConcurrencyPlan plan, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.opencv.bean.object.segment.stack

Methods in org.anchoranalysis.plugin.opencv.bean.object.segment.stack with parameters of type Logger

Modifier and Type	Method	Description
ConcurrentModelPool<OpenCVModel>	SegmentObjectsFromTensorFlowModel.createModelPool(ConcurrencyPlan plan, Logger logger)

Uses of Logger in org.anchoranalysis.plugin.points.bean

Methods in org.anchoranalysis.plugin.points.bean that return Logger

Modifier and Type	Method	Description
Logger	FitPoints.getLogger()	The logger for recording errors.

Uses of Logger in org.anchoranalysis.test

Methods in org.anchoranalysis.test that return Logger

Modifier and Type	Method	Description
static Logger	LoggerFixture.suppressedLogger()	A Logger that doesn't output anything.

Uses of Logger in org.anchoranalysis.test.experiment

Methods in org.anchoranalysis.test.experiment with parameters of type Logger

Modifier and Type	Method	Description
static <T extends InitializableBean<?, P>, P extends BeanInitialization> T	BeanTestChecker.checkAndInit(T bean, P initialization, Logger logger)	Checks if a bean has all necessary items as with BeanTestChecker.check(T) and also initializes the bean.

Uses of Logger in org.anchoranalysis.test.image

Methods in org.anchoranalysis.test.image with parameters of type Logger

Modifier and Type	Method	Description
static InputOutputContext	InputOutputContextFixture.withLogger(Logger logger)	Creates an InputOutputContext with a specified logger.