Package | Description |
---|---|
org.anchoranalysis.annotation.io |
Reading and writing annotations to the filesystem.
|
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.bean.task |
Defines a task,
which is a set of operations run on an input, that may or may not generate an output.
|
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.experiment.task.processor |
Non-bean classes related to
JobProcessor . |
org.anchoranalysis.image.io.bean.stack.reader |
Bean classes for reading raster-files from the filesystem.
|
org.anchoranalysis.image.io.channel.input |
Non-bean classes for reading a
Channel from the
filesystem. |
org.anchoranalysis.image.io.stack.input |
Non-bean classes for reading a
Stack from the
filesystem. |
org.anchoranalysis.io.input |
Classes relating to creating inputs for an experiment / task.
|
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.launcher.run.tasks |
Loading and displaying pre-defined tasks.
|
org.anchoranalysis.mpp.io.input |
Non-beans for reading data structures related to marked point processes from the file system.
|
org.anchoranalysis.plugin.annotation.bean.comparison |
Task to compare a set of annotations to a segmentation or another set of annotations.
|
org.anchoranalysis.plugin.annotation.comparison |
Non-bean classes for comparing two sets of annotations.
|
org.anchoranalysis.plugin.image.task.bean.feature |
Tasks pertaining to
Feature s. |
org.anchoranalysis.plugin.image.task.bean.feature.source |
Source of rows in feature-tables with
FeatureSource and derived classes. |
org.anchoranalysis.plugin.io.bean.input |
Implementations of
InputManager . |
org.anchoranalysis.plugin.io.bean.input.files |
InputManager s that accept a set of named-files. |
org.anchoranalysis.plugin.io.bean.input.filter |
Implementations of
InputManager that filter inputs. |
org.anchoranalysis.plugin.io.bean.input.stack |
Implementations of
InputManager that process Stack s. |
org.anchoranalysis.plugin.io.bean.summarizer.input |
Implementations of
Summarizer that summarize
generically InputFromManager s. |
org.anchoranalysis.plugin.io.bean.task |
Implementations of
Task related to file-system
I/O. |
org.anchoranalysis.plugin.io.input.filter |
Non-bean classes to help tasks in
org.anchoranalysis.plugin.io.bean.input.filter . |
org.anchoranalysis.plugin.mpp.experiment.bean.convert |
Converting from
NamedChannelsInput to the
input-type expected by a Task . |
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.experiment.shared |
Shared-state use across tasks in this JAR.
|
org.anchoranalysis.plugin.quick.bean.experiment |
Quickly defining experiments via several assumptions, including particular file-paths.
|
org.anchoranalysis.plugin.quick.bean.input |
Specifying inputs when quickly defining an experiment.
|
org.anchoranalysis.plugin.quick.bean.structure |
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
|
org.anchoranalysis.test.experiment.task |
Helper classes to execute
Task s in tests. |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationWithStrategy<T extends AnnotatorStrategy>
One particular annotation, associated with its strategy.
|
Modifier and Type | Class and Description |
---|---|
class |
InputOutputExperiment<T extends InputFromManager,S>
An experiment that uses both an
InputManager to specify inputs and a OutputManager to specify outputting. |
Modifier and Type | Class and Description |
---|---|
class |
DebugDependentProcessor<T extends InputFromManager,S>
Executes different processors depending on whether we are in debug mode or not.
|
class |
JobProcessor<T extends InputFromManager,S>
Base class for a method to apply a task on inputs.
|
class |
ParallelProcessor<T extends InputFromManager,S>
Executes jobs in parallel across cores on the system.
|
class |
SequentialProcessor<T extends InputFromManager,S>
Executes jobs sequentially, without any parallelism.
|
Modifier and Type | Method and Description |
---|---|
boolean |
JobProcessor.isInputCompatibleWith(Class<? extends InputFromManager> inputClass)
Is an input-type compatible with this particular task?
|
Modifier and Type | Class and Description |
---|---|
class |
Task<T extends InputFromManager,S>
Encapsulates some kind of processing to be performed on a set of inputs.
|
class |
TaskWithoutSharedState<T extends InputFromManager>
A particular type of task that doesn't share-state between running jobs
|
Modifier and Type | Method and Description |
---|---|
boolean |
Task.isInputCompatibleWith(Class<? extends InputFromManager> inputClass)
Is an input-object type compatible with this particular task?
|
Modifier and Type | Interface and Description |
---|---|
interface |
ReplaceInputManager<T extends InputFromManager>
Indicates and provides a mechanism that the
InputManager can be replaced. |
interface |
ReplaceTask<T extends InputFromManager,S>
Indicates and provides a mechanism that the
Task can be replaced. |
Modifier and Type | Method and Description |
---|---|
void |
InputTypesExpected.add(Class<? extends InputFromManager> inputTypeClass)
Appends an input-type class to the existing list.
|
boolean |
InputTypesExpected.doesClassInheritFromAny(Class<? extends InputFromManager> childClass)
Does the child-class inherit from any one of expected input-types?
|
Constructor and Description |
---|
InputTypesExpected(Class<? extends InputFromManager> inputTypeClass)
Creates with the class of the input-type.
|
Modifier and Type | Class and Description |
---|---|
class |
CallableJob<T extends InputFromManager,S>
A job derived from a
Task that can be placed on different threads |
Modifier and Type | Class and Description |
---|---|
class |
InputManagerWithStackReader<T extends InputFromManager>
Extends an
InputManager to add a StackReader bean property. |
Modifier and Type | Class and Description |
---|---|
class |
NamedChannelsInput
Provides a set of channels as an input, with each channel having a name.
|
class |
NamedChannelsInputPart
One part of a
NamedChannelsInput that can be combined with others. |
Modifier and Type | Interface and Description |
---|---|
interface |
ProvidesStackInput
Base class for inputs which somehow eventually send up providing stacks, with or without names.
|
interface |
StackSequenceInput
Provides a single stack (or a time series of such stacks) as an input
|
Modifier and Type | Class and Description |
---|---|
class |
ImageMetadataInput
An input that provides a
ImageMetadata but only lazily when first called. |
Modifier and Type | Class and Description |
---|---|
class |
InputFromManagerDelegate<T extends InputFromManager>
A base class for
InputFromManager -implementing classes that delegate to another. |
class |
InputsWithDirectory<T extends InputFromManager>
All inputs for an experiment, together with any parent directory which is specified as a parent
for these inputs.
|
Modifier and Type | Class and Description |
---|---|
class |
InputFromManagerDelegate<T extends InputFromManager>
A base class for
InputFromManager -implementing classes that delegate to another. |
Modifier and Type | Method and Description |
---|---|
<S extends InputFromManager,E extends Exception> |
InputsWithDirectory.map(CheckedFunction<T,S,E> mapFunction,
Class<? extends E> throwableClass)
Creates a new
InputsWithDirectory which is the result of mapping the existing inputs. |
<S extends InputFromManager> |
InputsWithDirectory.map(java.util.function.Function<T,S> mapFunction)
Creates a new
InputsWithDirectory which is the result of mapping the existing inputs. |
<S extends InputFromManager> |
InputsWithDirectory.withInputs(List<S> inputsToAssign)
Changes the inputs, but preserves the directory.
|
Modifier and Type | Class and Description |
---|---|
class |
InputManager<T extends InputFromManager>
Base class for describing the inputs.
|
class |
InputManagerUnary<T extends InputFromManager>
Base class for an
InputManager that delegates to another InputManager with the
same input-type. |
Modifier and Type | Class and Description |
---|---|
class |
FileInput
An input pertaining to a single file on the file-system.
|
class |
FileWithDirectoryInput
An input pertaining to a single file on the file-system - and a directory in which it resides.
|
class |
SingleFileInputBase
A base class for inputs that refer to a single file.
|
Modifier and Type | Class and Description |
---|---|
class |
HelloWorld<S extends InputFromManager>
A dummy task that simply writes a message to all log files, specifically: 1.
|
Modifier and Type | Class and Description |
---|---|
class |
MultiInput
An input to an experiment that combines a particular
Stack with other types of entities. |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonInputManager<T extends InputFromManager> |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonInput<T extends InputFromManager> |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonInput<T extends InputFromManager> |
Modifier and Type | Class and Description |
---|---|
class |
ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>
Calculates features and exports them as a CSV file.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureSource<T extends InputFromManager,S,U extends FeatureInput>
Extracts features from some kind of inputs to produce one or more rows in a feature-table.
|
class |
SingleRowPerInput<T extends InputFromManager,S extends FeatureInput>
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore . |
Modifier and Type | Class and Description |
---|---|
class |
BranchIfDebug<T extends InputFromManager>
Uses one input-manager normally, but a different one if in debug mode.
|
class |
Concatenate<T extends InputFromManager>
Concatenates the inputs from multiple
InputManager s that all provide the same input-type. |
class |
Exclude<T extends InputFromManager>
Excludes all inputs whose identifiers match a regular expression.
|
class |
Limit<T extends InputFromManager>
Limits the number of input-objects to a certain hard-maximum
|
class |
LimitIfRequested<T extends InputFromManager>
Like
Limit if it is requested in the InputContextParameters , makes no change to
the inputs. |
class |
Shuffle<T extends InputFromManager>
Randomly shuffles the order of the inputs.
|
class |
ShuffleIfRequested<T extends InputFromManager>
Like
Shuffle if requested in the InputContextParameters otherwise makes no change
to the inputs. |
class |
SortAlphabetically<T extends InputFromManager>
Sorts the input-items in alphabetical order of their input-name.
|
Modifier and Type | Class and Description |
---|---|
class |
NamedFilesBase<T extends InputFromManager>
Base class for an
InputManager that produces inputs that are created from a NamedFile . |
Modifier and Type | Class and Description |
---|---|
class |
FilterCSVColumn<T extends InputFromManager>
Finds a CSV file with the names of an input as the first-column.
|
class |
FilterDescriptiveName<T extends InputFromManager>
Filters all the input objects for only those with certain types of descriptive-names.
|
class |
FilterIfDebug<T extends InputFromManager>
Filters a list of inputs when in debug-mode
|
Modifier and Type | Class and Description |
---|---|
class |
ConvertNamedChannelsInputToStack
An input object that converts
NamedChannelsInput to StackSequenceInput . |
Modifier and Type | Class and Description |
---|---|
class |
ExtractIdentifier<T extends InputFromManager>
Extracts the identifier from an
InputFromManager to summarize further. |
class |
ExtractIdentifierAndPath<T extends InputFromManager>
Extracts the identifier and path from an
InputFromManager to summarize further. |
class |
ExtractPath<T extends InputFromManager>
Extracts a
Path from an input to summarize further. |
class |
SummarizerInputFromManager<T extends InputFromManager,S>
Extracts a particular item from an
InputFromManager for further summarization downstream. |
Modifier and Type | Class and Description |
---|---|
class |
SummarizeBase<T extends InputFromManager,S> |
class |
SummarizeInputs<T extends InputFromManager> |
Modifier and Type | Method and Description |
---|---|
<T extends InputFromManager> |
FilterDescriptiveNameEqualsContains.removeNonMatching(List<T> in) |
Modifier and Type | Class and Description |
---|---|
class |
ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>
Converts
NamedChannelsInput to a variety of others to match a delegate task. |
Modifier and Type | Class and Description |
---|---|
class |
ExportObjectsBase<T extends InputFromManager,S> |
Modifier and Type | Class and Description |
---|---|
class |
FromCSVInput |
Modifier and Type | Class and Description |
---|---|
class |
ConvertedInput<U extends InputFromManager>
A converted-input, together with any logged messages associated with it.
|
class |
SharedStateRememberConverted<U extends InputFromManager,S>
Shared-state that remembers converted inputs for corresponding unconverted inputs.
|
Modifier and Type | Class and Description |
---|---|
class |
QuickMultiDatasetExperiment<T extends InputFromManager,S>
Makes a lot of assumptions, that allows us to reduce the number of inputs to an
InputOutputExperiment . |
Modifier and Type | Class and Description |
---|---|
class |
QuickBase<T extends InputFromManager>
A base for quick managers that make various assumptions about file-structure.
|
Modifier and Type | Class and Description |
---|---|
class |
QuickMultiDatasetStructuredExperiment<T extends InputFromManager,S>
Similar to
QuickMultiDatasetStructuredExperiment put sets properties according to an
expected directory structure. |
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.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.