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
Channel s. |
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
Channel s 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
Channel s. |
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.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.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.marks |
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
|
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.feature.mark |
Non-bean classes for calculating feature-values related to
Mark s. |
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.mark |
Non-bean classes related to
Mark s. |
org.anchoranalysis.mpp.segment.bean.optimization.feedback |
Providing feedback on the progress of a
OptimizationScheme . |
org.anchoranalysis.mpp.segment.bean.optimization.kernel |
Base classes for kernels that transition a configuration of marks (a
MarkCollection ) into an altered version. |
org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
org.anchoranalysis.mpp.segment.transformer |
Mapping one type of optimization state to another.
|
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.object.merge |
Merging
ObjectMask s. |
org.anchoranalysis.plugin.image.object.merge.condition |
Conditions for merging
ObjectMask s. |
org.anchoranalysis.plugin.image.object.merge.priority |
Assigning priority when merging
ObjectMask s. |
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
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.channel.map |
Implementations of
ChannelMapCreator . |
org.anchoranalysis.plugin.io.bean.input.stack |
Implementations of
InputManager that process Stack s. |
org.anchoranalysis.plugin.io.multifile |
Non-bean classes to help use multiple files to represent a single
Stack . |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.mpp.experiment.objects |
Non-bean classes used in
org.anchoranalysis.plugin.mpp.experiment.bean.objects . |
org.anchoranalysis.plugin.mpp.segment.optimization |
Non-bean classes to help with optimization in
org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages. |
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.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.
|
Modifier and Type | Method and Description |
---|---|
NamedStacksSupplier |
AnnotationWithStrategy.stacks(Logger logger)
All stacks associated with the input, lazily evaluated.
|
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
void |
NullParametersBean.initializeRecursive(Logger logger)
Initialize this bean and any suitable child beans.
|
Modifier and Type | Method and Description |
---|---|
protected Logger |
InitializableBean.getLogger()
The logger.
|
Modifier and Type | Method and 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)
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Logger |
CommonContext.getLogger()
The logger.
|
Constructor and Description |
---|
CommonContext(Logger logger,
Path modelDirectory) |
Modifier and Type | Method and Description |
---|---|
Logger |
OperationContext.getLogger()
Where to write informative messages to, and and any non-fatal errors (fatal errors are throw
as exceptions).
|
Constructor and Description |
---|
OperationContext(ExecutionTimeRecorder executionTimeRecorder,
Logger logger) |
OperationContext(Logger logger)
Creates with a
Logger ignoring execution-times. |
Modifier and Type | Method and Description |
---|---|
Logger |
InitializationContext.getLogger()
The associated logger.
|
Modifier and Type | Method and Description |
---|---|
Logger |
InputBound.getLogger()
The
Logger associated with this input, as it is being processed as a job. |
Logger |
InputOutputContextStateful.getLogger() |
Modifier and Type | Method and Description |
---|---|
void |
FeatureList.initializeRecursive(FeatureInitialization initialization,
Logger logger)
Initializes all features in the list, and recursively any features they contain.
|
Modifier and Type | Method and Description |
---|---|
void |
FeatureCalculationCache.initialize(FeatureInitialization initialization,
Logger logger)
Initializes the cache.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
static <T extends FeatureInput> |
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> |
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> |
FeatureSession.with(Feature<T> feature,
Logger logger)
Starts a feature-session for a single feature.
|
static <T extends FeatureInput> |
FeatureSession.with(Feature<T> feature,
SharedFeatures sharedFeatures,
Logger logger)
Starts a feature-session for a single feature, with default initialization.
|
static <T extends FeatureInput> |
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> |
FeatureSession.with(FeatureList<T> features,
FeatureInitialization initialization,
SharedFeatures sharedFeatures,
Logger logger)
Starts a feature-session for a list of features, with particular initialization.
|
static <T extends FeatureInput> |
FeatureSession.with(FeatureList<T> features,
Logger logger)
Starts a feature-session for a list of features, with default initialization.
|
Constructor and Description |
---|
HorizontalCacheCreator(FeatureList<? extends FeatureInput> namedFeatures,
SharedFeatures sharedFeatures,
FeatureInitialization initialization,
Logger logger) |
Modifier and Type | Method and 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. |
Modifier and Type | Method and Description |
---|---|
void |
SharedFeaturesSubset.initializeRecursive(FeatureInitialization initialization,
Logger logger)
Initialize all features in this instance, recursively also initializating any child-features.
|
Modifier and Type | Method and Description |
---|---|
void |
ChannelAggregator.addChannel(Channel channel,
Logger logger)
Adds a
Channel to the aggregation. |
Modifier and Type | Method and Description |
---|---|
void |
ImageInitialization.populate(BeanInitializer<?> propertyInitializer,
Define define,
Logger logger)
Adds diverse entities from a
Define into the corresponding name-collections. |
Constructor and Description |
---|
PopulateStoreFromDefine(Define define,
BeanInitializer<?> propertyInitializer,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
SingleTableCalculator.start(ImageInitialization initialization,
Optional<EnergyStack> energyStack,
Logger logger) |
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
|
Modifier and Type | Method and Description |
---|---|
void |
PairsTableCalculator.start(ImageInitialization initializtion,
Optional<EnergyStack> energyStack,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
Logger |
ImageInferenceContext.getLogger()
Where to log information messages during inference.
|
Constructor and Description |
---|
ImageInferenceContext(DualScale<Dimensions> dimensions,
ScaleFactor scaleFactor,
Optional<List<String>> classLabels,
VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder,
Logger logger) |
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
abstract ChannelMap |
ChannelMapCreator.create(OpenedImageFile openedFile,
Logger logger)
Creates the
ChannelMap . |
Modifier and Type | Method and 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.
|
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) |
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.
|
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)
|
StoreSupplier<Stack> |
OpenedNamedChannels.allChannelsAsStack(int t,
Logger logger) |
StoreSupplier<Stack> |
NamedChannelsConcatenate.allChannelsAsStack(int t,
Logger logger) |
StoreSupplier<Stack> |
NamedChannelsMap.allChannelsAsStack(int timeIndex,
Logger logger)
Combines all channels as a single
Stack at a particular time-frame. |
Dimensions |
OpenedNamedChannels.dimensions(Logger logger) |
Dimensions |
NamedChannelsConcatenate.dimensions(Logger logger) |
Dimensions |
NamedChannelsMap.dimensions(Logger logger)
The dimensions of each
Channel . |
Channel |
OpenedNamedChannels.getChannel(String channelName,
int timeIndex,
Logger logger) |
Channel |
NamedChannelsConcatenate.getChannel(String channelName,
int timeIndex,
Logger logger) |
Optional<Channel> |
OpenedNamedChannels.getChannelOptional(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.
|
boolean |
OpenedNamedChannels.isRGB(Logger logger) |
boolean |
NamedChannelsConcatenate.isRGB(Logger logger) |
boolean |
NamedChannelsMap.isRGB(Logger logger)
Whether the channels describe an RGB image.
|
int |
OpenedNamedChannels.sizeT(Logger logger) |
int |
NamedChannelsConcatenate.sizeT(Logger logger) |
int |
NamedChannelsMap.sizeT(Logger logger)
The number of frames along the time-axis.
|
Modifier and Type | Method and Description |
---|---|
String |
HDF5ObjectsGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
Modifier and Type | Method and Description |
---|---|
OrientationChange |
CalculateOrientationChange.calculateOrientationChange(Logger logger)
Calculates any needed orientation change.
|
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
Stack s. |
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.
|
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.
|
int |
OpenedImageFile.numberFrames(Logger logger)
The number of frames in the image-file i.e.
|
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.
|
Modifier and Type | Method and 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 . |
Constructor and Description |
---|
ConcurrentModelPool(ConcurrencyPlan plan,
CreateModelForPool<T> createModel,
Logger logger)
Creates with a particular plan and function to create models.
|
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 |
---|---|
String |
SerializedGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
String |
DictionaryGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
Modifier and Type | Method and Description |
---|---|
String |
CSVGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
Modifier and Type | Method and Description |
---|---|
String |
StringGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
Modifier and Type | Method and Description |
---|---|
String |
XMLGenerator.selectFileExtension(OutputWriteSettings settings,
Optional<Logger> logger) |
Modifier and Type | Method and Description |
---|---|
Logger |
InputManagerParameters.getLogger()
Where to write informative messages to, and and any non-fatal errors (fatal errors are throw
as exceptions).
|
Constructor and Description |
---|
InputManagerParameters(Logger logger)
Create with only a logger, and using sensible default values for the other fields.
|
Modifier and Type | Method and Description |
---|---|
Logger |
FileNamerContext.getLogger()
Logs information messages.
|
Constructor and Description |
---|
FileNamerContext(Logger logger)
Creates with a logger, and otherwise uses sensible defaults.
|
FileNamerContext(Optional<Path> inputDirectory,
boolean relativeToDirectory,
Optional<IndexRangeNegative> nameSubrange,
Logger logger)
Creates with specific parameters.
|
FileNamerContext(Optional<Path> inputDirectory,
boolean relativeToDirectory,
String elseName,
Optional<IndexRangeNegative> nameSubrange,
Logger logger) |
FileNamerContext(String elseName,
Logger logger)
Creates with a fallback-name and a logger, but otherwise using sensible defaults.
|
Modifier and Type | Method and Description |
---|---|
OutputterChecked |
OutputManager.createExperimentOutputter(Optional<String> experimentIdentifier,
MultiLevelOutputEnabled outputsEnabled,
Optional<MultiLevelRecordedOutputs> recordedOutputs,
OutputWriteContext writeContext,
PathPrefixerContext prefixerContext,
Optional<java.util.function.Consumer<Path>> callUponDirectoryCreation,
Optional<Logger> logger)
Creates an outputter for the experiment in general.
|
Modifier and Type | Method and Description |
---|---|
Logger |
InputOutputContext.getLogger()
The associated logger.
|
Modifier and Type | Method and Description |
---|---|
void |
OutputterChecked.assignLogger(Logger logger)
Assigns a logger to the outputter, which is used to output warnings or messages when
outputting.
|
Modifier and Type | Method and Description |
---|---|
static OutputterChecked |
OutputterChecked.createForDirectoryPermissive(Path pathDirectory,
DirectoryCreationParameters directoryCreation,
Optional<Logger> logger)
Creates, defaulting to a permissive output-manager in a particular directory.
|
static OutputterChecked |
OutputterChecked.createWithPrefix(DirectoryWithPrefix prefix,
MultiLevelOutputEnabled outputEnabled,
OutputWriteContext context,
Optional<MultiLevelRecordedOutputs> recordedOutputs,
DirectoryCreationParameters directoryCreation,
Optional<Logger> logger)
Creates a bound output-manager from an existing
OutputManager with a prefix. |
Modifier and Type | Method and Description |
---|---|
Optional<Logger> |
ElementOutputter.logger() |
Constructor and Description |
---|
ElementOutputter(OutputterChecked outputter,
ExecutionTimeRecorder executionTimeRecorder,
java.util.function.Supplier<Optional<Logger>> logger) |
Modifier and Type | Method and Description |
---|---|
static void |
Launch.runCommandLineApplication(String[] args,
LauncherConfig config,
Logger logger)
Runs a command-line application, by parsing arguments, and then executing an experiment.
|
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
ParseArgumentsAndRunExperiment(Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
RandomCollectionWithAddCriteria.initUpdatableMarks(MemoForIndex marks,
EnergyStack stack,
Logger logger,
SharedFeatures sharedFeatures) |
Constructor and Description |
---|
VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown marks,
EnergyStack energyStack,
SharedFeatures sharedFeatures,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
EnergySavedPairs.initUpdatableMarks(MemoForIndex pxlMarkMemoList,
EnergyStack stack,
Logger logger,
SharedFeatures sharedFeatures) |
Constructor and Description |
---|
DictionaryForImageCreator(EnergyScheme energyScheme,
SharedFeatures sharedFeatures,
Logger logger) |
EnergySchemeWithSharedFeatures(EnergyScheme energyScheme,
SharedFeatures sharedFeatures,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
UpdatableMarksList.initUpdatableMarks(MemoForIndex marks,
EnergyStack stack,
Logger logger,
SharedFeatures sharedFeatures) |
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 void |
ReportFeatureEvaluator.initialize(MarksInitialization so,
Logger logger) |
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 . |
Modifier and Type | Method and Description |
---|---|
void |
UpdatableMarks.initUpdatableMarks(MemoForIndex memo,
EnergyStack energyStack,
Logger logger,
SharedFeatures sharedFeatures) |
Modifier and Type | Method and Description |
---|---|
protected Logger |
ReporterAggregate.getLogger() |
Modifier and Type | Method and Description |
---|---|
void |
KernelProposer.initWithProposerSharedObjects(MarksInitialization initialization,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
Logger |
OptimizationContext.getLogger() |
Modifier and Type | Method and Description |
---|---|
Logger |
TransformationContext.getLogger() |
Constructor and Description |
---|
TransformationContext(Dimensions dimensions,
KernelCalculationContext kernelCalcContext,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
List<FeatureInputPairObjects> |
PairNeighbors.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger) |
List<FeatureInputSingleObject> |
EachObjectIndependently.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger) |
protected abstract List<T> |
CombineObjectsForFeatures.startBatchDeriveInputs(ObjectCollection objects,
EnergyStack energyStack,
Logger logger)
Derives a list of inputs from an object-collection.
|
Constructor and Description |
---|
GraphLogger(DescribeGraph describeGraph,
Logger logger) |
MergeGraph(PayloadCalculator payloadCalculator,
UpdatableBeforeCondition beforeCondition,
Optional<UnitConverter> unitConverter,
AssignPriority prioritizer,
Logger logger,
boolean logPayload)
Constructor
|
Modifier and Type | Method and Description |
---|---|
void |
AfterCondition.initialize(Logger logger) |
void |
IncreaseFeatureCondition.initialize(Logger logger) |
Modifier and Type | Method and Description |
---|---|
PrioritisedVertex |
Prioritizer.createPriority(ObjectVertex source,
ObjectVertex destination,
Logger logger) |
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 |
---|---|
Logger |
FeatureCalculationContext.getLogger() |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelGetterForTimepoint.getChannel(String channelName,
Logger logger) |
Modifier and Type | Method and 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) |
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) |
TimeSeries |
ConvertNamedChannelsInputToStack.createStackSequenceForSeries(int seriesIndex,
Logger logger) |
Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
protected ObjectCollection |
ExportObjectsBase.inputs(ImageInitialization initialization,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
FromCSVInput.copyTo(SharedObjects target,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
static VoxelizedMarksWithEnergy |
VoxelizedMarksWithEnergyFactory.createFromMarks(MarkCollection marks,
KernelCalculationContext context,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
ConcurrentModelPool<OnnxModel> |
SegmentObjectsFromONNXModel.createModelPool(ConcurrencyPlan plan,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
ConcurrentModelPool<OpenCVModel> |
SegmentObjectsFromTensorFlowModel.createModelPool(ConcurrencyPlan plan,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
static Logger |
LoggerFixture.suppressedLogger()
A
Logger that doesn't output anything. |
Modifier and Type | Method and Description |
---|---|
static <T extends InitializableBean<?,P>,P extends BeanInitialization> |
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. |
Modifier and Type | Method and Description |
---|---|
static InputOutputContext |
InputOutputContextFixture.withLogger(Logger logger) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.