Package | Description |
---|---|
org.anchoranalysis.annotation.io.bean.comparer |
What to compare an annotation (ground truth) against?
|
org.anchoranalysis.bean |
Defining, loading, initializing Anchor Beans.
|
org.anchoranalysis.bean.define |
Define and related-classes. |
org.anchoranalysis.feature.bean.list |
A feature-list (custom list type for features) and associated providers.
|
org.anchoranalysis.feature.initialization |
Initialization parameters used for beans in
org.anchoranalysis.feature.bean . |
org.anchoranalysis.feature.store |
A collection of named-
Feature s. |
org.anchoranalysis.io.output.bean |
Beans for the framework around writing files to the file-system.
|
org.anchoranalysis.io.output.bean.rules |
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
|
org.anchoranalysis.mpp.feature.bean.energy.scheme |
Creating
EnergyScheme s. |
org.anchoranalysis.mpp.feature.energy.scheme |
Factorized form of storing the energy during an energy-minimization optimization scheme.
|
org.anchoranalysis.mpp.io.bean.input |
Beans for reading data structures related to marked point processes from the file system.
|
org.anchoranalysis.plugin.annotation.bean.strategy |
Strategies for how to annotate an image, such label per image etc.
|
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.task.bean.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.image.task.bean.grouped.selectchannels |
Selecting a subset of a set of channels.
|
org.anchoranalysis.plugin.image.task.bean.labeller |
Associating labels with images.
|
org.anchoranalysis.plugin.image.task.bean.segment |
Tasks to segment an image.
|
org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.io.bean.input.channel |
InputManager s that accept a set of
named-channels. |
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source |
Implementations of
FeatureSource . |
org.anchoranalysis.plugin.mpp.experiment.bean.objects |
Tasks involving
ObjectMask s. |
org.anchoranalysis.plugin.quick.bean.input.filepathappend |
Appending other entities to inputs when quickly defining experiments.
|
org.anchoranalysis.test.feature.plugins |
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<ComparableSource>> |
MultipleComparer.getSources()
The other entities to compare with the annotation.
|
Modifier and Type | Method and Description |
---|---|
void |
MultipleComparer.setSources(List<NamedBean<ComparableSource>> sources)
The other entities to compare with the annotation.
|
Modifier and Type | Method and Description |
---|---|
void |
BeanInstanceMap.addFrom(List<NamedBean<?>> listNamedInstances)
Populates from a list of
NamedBean . |
Modifier and Type | Method and Description |
---|---|
<T extends AnchorBean<?>> |
Define.listFor(Class<?> groupingRoot)
Retrieves the list of elements associated with a grouping-root.
|
Modifier and Type | Method and Description |
---|---|
void |
Define.add(NamedBean<?> bean)
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine
a group where definitions are stored.
|
Modifier and Type | Method and Description |
---|---|
<T extends AnchorBean<?>> |
Define.addAll(List<NamedBean<T>> list)
Adds all the named-beans from source to the current map.
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<T>>> |
DefinedNamed.getList()
A list of
FeatureListProvider s with an associated name. |
Modifier and Type | Method and Description |
---|---|
void |
DefinedNamed.setList(List<NamedBean<FeatureListProvider<T>>> list)
A list of
FeatureListProvider s with an associated name. |
Modifier and Type | Method and Description |
---|---|
void |
FeatureRelatedInitialization.populate(List<NamedBean<FeatureListProvider<FeatureInput>>> namedProviders,
Logger logger)
Adds features into the shared-feature storage from a list of named-beans.
|
Modifier and Type | Method and Description |
---|---|
NamedBean<Feature<T>> |
NamedFeatureStore.get(int index)
Gets a feature at a particular position.
|
NamedBean<Feature<T>> |
NamedFeatureStore.get(String name)
Gets a feature corresponding to a particular name.
|
Modifier and Type | Method and Description |
---|---|
Iterator<NamedBean<Feature<T>>> |
NamedFeatureStore.iterator() |
Modifier and Type | Method and Description |
---|---|
<T extends FeatureInput> |
NamedFeatureStoreFactory.createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>> namedFeatures)
Create a
NamedFeatureStore from a list of beans. |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<?>> |
OutputWriteSettings.getWriters()
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
|
Modifier and Type | Method and Description |
---|---|
void |
OutputWriteSettings.setWriters(List<NamedBean<?>> writers)
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<StringSet>> |
OutputEnableRulesSpecify.getSecond()
Output-names in the second-level (for all first level output-names).
|
Modifier and Type | Method and Description |
---|---|
void |
OutputEnableRulesSpecify.setSecond(List<NamedBean<StringSet>> second)
Output-names in the second-level (for all first level output-names).
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<FeatureInputStack>>> |
EnergySchemeCreatorByElement.getListImageFeatures() |
Modifier and Type | Method and Description |
---|---|
void |
EnergySchemeCreatorByElement.setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>> listImageFeatures) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<Feature<FeatureInputStack>>> |
EnergyScheme.getListImageFeatures() |
Constructor and Description |
---|
EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd,
FeatureList<FeatureInputPairMemo> elemPair,
FeatureList<FeatureInputAllMemo> elemAll,
RegionMap regionMap,
AddCriteriaPair pairAddCriteria,
Optional<DictionaryProvider> dictionary,
List<NamedBean<Feature<FeatureInputStack>>> listImageFeatures) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendDictionary() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendFilePath() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendHistogram() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendMarks() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendMarksFromAnnotation() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendMarksFromAnnotationAcceptedOnly() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendMarksFromAnnotationRejectedOnly() |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendObjects()
Appends object-collections to the
MultiInput . |
List<NamedBean<DerivePath>> |
MultiInputManager.getAppendStack() |
Modifier and Type | Method and Description |
---|---|
void |
MultiInputManager.setAppendDictionary(List<NamedBean<DerivePath>> appendDictionary) |
void |
MultiInputManager.setAppendFilePath(List<NamedBean<DerivePath>> appendFilePath) |
void |
MultiInputManager.setAppendHistogram(List<NamedBean<DerivePath>> appendHistogram) |
void |
MultiInputManager.setAppendMarks(List<NamedBean<DerivePath>> appendMarks) |
void |
MultiInputManager.setAppendMarksFromAnnotation(List<NamedBean<DerivePath>> appendMarksFromAnnotation) |
void |
MultiInputManager.setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>> appendMarksFromAnnotationAcceptedOnly) |
void |
MultiInputManager.setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>> appendMarksFromAnnotationRejectedOnly) |
void |
MultiInputManager.setAppendObjects(List<NamedBean<DerivePath>> appendObjects)
Appends object-collections to the
MultiInput . |
void |
MultiInputManager.setAppendStack(List<NamedBean<DerivePath>> appendStack) |
Modifier and Type | Method and Description |
---|---|
NamedBean<MarkEvaluator> |
MarkProposerStrategy.getMarkEvaluator()
A mark-evaluator that is added to the GUI to support this annotation
|
Modifier and Type | Method and Description |
---|---|
void |
MarkProposerStrategy.setMarkEvaluator(NamedBean<MarkEvaluator> markEvaluator)
A mark-evaluator that is added to the GUI to support this annotation
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<FeatureInputStack>>> |
PairNeighbors.getFeaturesImage()
Additional features that only depend on the image, so do not need to be replicated for every
object.
|
List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> |
PairNeighbors.getFeaturesPair()
Additional features that are processed on the pair of images (i.e.
|
Modifier and Type | Method and Description |
---|---|
FeatureTableCalculator<FeatureInputPairObjects> |
PairNeighbors.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list,
NamedFeatureStoreFactory storeFactory,
boolean suppressErrors) |
FeatureTableCalculator<FeatureInputSingleObject> |
EachObjectIndependently.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> list,
NamedFeatureStoreFactory storeFactory,
boolean suppressErrors) |
abstract FeatureTableCalculator<T> |
CombineObjectsForFeatures.createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> featuresSingleObject,
NamedFeatureStoreFactory storeFactory,
boolean suppressErrors)
Creates features that will be applied on the objects.
|
void |
PairNeighbors.setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>> featuresImage)
Additional features that only depend on the image, so do not need to be replicated for every
object.
|
void |
PairNeighbors.setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>> featuresPair)
Additional features that are processed on the pair of images (i.e.
|
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<U>>> |
ExportFeatures.getFeatures()
The features to be exported (after possibly some manipulation or augmentation).
|
List<NamedBean<FeatureListProvider<FeatureInputResults>>> |
ExportFeatures.getFeaturesAggregate()
Features applied to each group to aggregate values (accepting
FeatureInputResults ). |
Modifier and Type | Method and Description |
---|---|
void |
ExportFeatures.setFeatures(List<NamedBean<FeatureListProvider<U>>> features)
The features to be exported (after possibly some manipulation or augmentation).
|
void |
ExportFeatures.setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>> featuresAggregate)
Features applied to each group to aggregate values (accepting
FeatureInputResults ). |
Modifier and Type | Method and Description |
---|---|
FeatureExporter<FeatureList<S>> |
SingleRowPerInput.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<S>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context) |
abstract FeatureExporter<S> |
FeatureSource.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<U>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Creates the
FeatureExporter to be used for calculating and exporting feature-results. |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FromStack>> |
SpecificAndRename.getList() |
Modifier and Type | Method and Description |
---|---|
void |
SpecificAndRename.setList(List<NamedBean<FromStack>> list) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<FeatureInputStack>>> |
BinaryClassifierImageLabeller.getListFeatures() |
Modifier and Type | Method and Description |
---|---|
void |
BinaryClassifierImageLabeller.setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>> listFeatures) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> |
SegmentInstanceWithModel.getFeatures()
Features to calculate for objects in the features output.
|
Modifier and Type | Method and Description |
---|---|
void |
SegmentInstanceWithModel.setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> features)
Features to calculate for objects in the features output.
|
Modifier and Type | Method and Description |
---|---|
static <T extends FeatureInput> |
FeatureExporter.create(List<NamedBean<FeatureListProvider<T>>> features,
LabelHeaders metadataHeaders,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Alternative static constructor that creates a shared-state from a list of named
FeatureListProvider s. |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<DerivePath>> |
NamedChannelsAppend.getListAppend() |
Modifier and Type | Method and Description |
---|---|
void |
NamedChannelsAppend.setListAppend(List<NamedBean<DerivePath>> listAppend) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<ObjectCollectionProvider>> |
FromObjects.getObjects() |
Modifier and Type | Method and Description |
---|---|
FeatureExporter<FeatureTableCalculator<T>> |
FromObjects.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context) |
void |
FromObjects.setObjects(List<NamedBean<ObjectCollectionProvider>> objects) |
Modifier and Type | Method and Description |
---|---|
List<NamedBean<StackProvider>> |
ExportObjectsAsCroppedImages.getListStackProvider()
The channels we extract the object-masks from - all assumed to be of same dimension
|
List<NamedBean<StackProvider>> |
ExportObjectsAsCroppedImages.getListStackProviderMIP()
The channels we extract the object-masks from - all assumed to be of same dimension
|
Modifier and Type | Method and Description |
---|---|
void |
ExportObjectsAsCroppedImages.setListStackProvider(List<NamedBean<StackProvider>> listStackProvider)
The channels we extract the object-masks from - all assumed to be of same dimension
|
void |
ExportObjectsAsCroppedImages.setListStackProviderMIP(List<NamedBean<StackProvider>> listStackProviderMIP)
The channels we extract the object-masks from - all assumed to be of same dimension
|
Modifier and Type | Method and Description |
---|---|
NamedBean<DerivePath> |
FilePathAppendBase.createPathDeriver(String rootName,
String regEx)
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups
The first group should correspond to top-level folder for the project The second group should
correspond to the unique name of the dataset.
|
Modifier and Type | Method and Description |
---|---|
static <T extends FeatureInput> |
FeaturesFromXmlFixture.createNamedFeatureProviders(String xmlPath,
TestLoader loader) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.