Package | Description |
---|---|
org.anchoranalysis.annotation.io.assignment.generator |
Generates output images to illustrate a
Assignment between annotations. |
org.anchoranalysis.feature.io.csv |
Metadata for writing feature calculation-results in CSV format.
|
org.anchoranalysis.feature.io.csv.results |
Writing the results from feature-calculation to a CSV file.
|
org.anchoranalysis.feature.io.csv.table |
A
Generator for writing a table of feature values as a
CSV. |
org.anchoranalysis.feature.io.results |
Writes feature-calculation results in different formats, also grouped results.
|
org.anchoranalysis.feature.io.results.group |
Various different outputs that can be written for the a grouped version of the results in
LabelledResultsCollector . |
org.anchoranalysis.image.io.channel.output |
Non-bean classes for writing a
Channel to the
filesystem. |
org.anchoranalysis.image.io.histogram.output |
Non-bean classes for writing a
Histogram to the
filesystem. |
org.anchoranalysis.image.io.object.output.grayscale |
Writing an
ObjectCollection to the filesystem as a
single-channeled stack. |
org.anchoranalysis.image.io.object.output.mask |
Writing an
ObjectCollection to the filesystem as
multiple binary singled-channeled images. |
org.anchoranalysis.image.io.object.output.rgb |
Writing an
ObjectCollection to the filesystem as
RGB raster-images. |
org.anchoranalysis.image.io.stack.output |
Non-bean classes for writing a
Stack to the
filesystem. |
org.anchoranalysis.image.io.stack.output.box |
Base classes for generators that ultimately write only a bounding-box portion of a
Stack to the filesystem. |
org.anchoranalysis.image.io.stack.output.generator |
Base classes for generators that ultimately write a
Stack to the filesystem. |
org.anchoranalysis.io.generator |
Base-classes and utilities for generators, which write different types of objects to the file
system.
|
org.anchoranalysis.io.generator.collection |
Outputting more than one element collectively using a generator.
|
org.anchoranalysis.io.generator.combined |
Combining multiple generators into one.
|
org.anchoranalysis.io.generator.sequence |
Writing a sequence of elements using a generator.
|
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.output.writer |
Allows a generators to write element(s) to the filesystem.
|
org.anchoranalysis.mpp.io.marks.generator | |
org.anchoranalysis.mpp.io.output |
Non-beans for writing data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.segment.bean.define |
DefineOutputter and its sub-classes. |
org.anchoranalysis.mpp.segment.bean.optimization.feedback |
Providing feedback on the progress of a
OptimizationScheme . |
org.anchoranalysis.plugin.annotation.bean.aggregate |
Beans to combine two or more annotations.
|
org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.segment |
Non-bean classes for image-segmentation.
|
org.anchoranalysis.plugin.io.bean.file.copy.naming |
Rules for preserving or changing the naming of files when copying on the file-system.
|
org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster |
Implementations of
CopyFilesNaming
that perform clustering of files. |
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 |
---|---|
Stack |
DrawColoredObjects.createObjectsImage(Assignment<ObjectMask> assignment,
boolean left,
AssignmentColorPool colorPool)
Creates an image with the objects colored, as indicated in the class description.
|
Stack |
AssignmentGenerator.transform(Assignment<ObjectMask> element) |
Modifier and Type | Method and Description |
---|---|
static Optional<FeatureCSVWriter> |
FeatureCSVWriter.create(FeatureCSVMetadata metadata,
Outputter outputter,
boolean visuallyShortenedDecimals)
Maybe creates a
FeatureCSVWriter depending if the output is allowed. |
Modifier and Type | Method and Description |
---|---|
Optional<FeatureCSVWriter> |
FeatureCSVWriterFactory.create(FeatureCSVMetadata metadata)
Maybe creates a
FeatureCSVWriter corresponding to particular metadata. |
static LabelledResultsCSVWriter |
LabelledResultsCSVWriterFactory.create(FeatureCSVMetadataForOutput outputMetadata,
FeatureCSVWriterFactory writerCreator,
Optional<java.util.function.Consumer<LabelledResultsVector>> consumeAfterAdding,
boolean removeNaNColumns)
Creates with appropriate support classes for outputting.
|
protected Optional<FeatureCSVWriter> |
LabelledResultsCSVWriter.createWriter(FeatureCSVMetadata csvMetadata)
Creates a
CSVWriter . |
abstract void |
LabelledResultsCSVWriter.end()
Stops writing the CSV file.
|
abstract void |
LabelledResultsCSVWriter.start()
Starts writing the CSV file.
|
Modifier and Type | Method and Description |
---|---|
protected abstract void |
FeatureTableCSVGenerator.writeFeaturesToCSV(CSVWriter writer,
T allFeatureResults,
List<String> headerNames)
Writes the features to the CSV-file.
|
void |
FeatureTableCSVGenerator.writeToFile(T element,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
void |
LabelledResultsCollector.flushAndClose(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
FeatureOutputMetadata outputMetadata,
InputOutputContext context)
Writes any queued (but not yet written elements to the file-system), and closes open
file-handles.
|
Modifier and Type | Method and Description |
---|---|
void |
GroupedResults.writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
FeatureOutputMetadata outputMetadata,
FeatureCSVWriterFactory createAggregatedCSVWriter,
InputOutputContextSubdirectoryCache contextGroups)
Writes outputs for groups that have been previously added with
GroupedResults.addResultsFor(org.anchoranalysis.feature.io.results.LabelledResultsVector) . |
Modifier and Type | Method and Description |
---|---|
Stack |
ChannelGenerator.transform(Channel element) |
Modifier and Type | Method and Description |
---|---|
void |
HistogramCSVGenerator.writeToFile(Histogram element,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectsMergedAsMaskGenerator.transform(ObjectCollection element) |
Stack |
ObjectsAsUniqueValueGenerator.transform(ObjectCollection element) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectAsMaskGenerator.transform(ObjectMask element) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectsAsRGBGenerator.transform(ObjectCollectionWithProperties element) |
Modifier and Type | Method and Description |
---|---|
OutputSequenceIncrementing<Stack> |
OutputSequenceStackFactory.incrementingByOne(String subdirectoryName,
OutputterChecked outputter)
Creates an sequence of stacks in a subdirectory with a number in the outputted file name that
increments each time by one.
|
static void |
NamedStacksOutputter.output(NamedProvider<Stack> stacks,
String outputName,
boolean suppressSubdirectory,
OutputterChecked outputter)
Writes all or a subset from a set of named-stacks to a directory as a raster.
|
OutputSequenceIndexed<Stack,String> |
OutputSequenceStackFactory.withoutOrderCurrentDirectory(String outputName,
OutputterChecked outputter)
Creates a sequence of stacks in the current context's directory that has no pattern.
|
void |
OutputSequenceStackFactory.withoutOrderSubset(NamedProvider<Stack> stacks,
String outputName,
boolean suppressSubdirectory,
OutputterChecked outputter)
Writes all or a subset from a set of named-stacks to a directory.
|
Modifier and Type | Method and Description |
---|---|
Stack |
DrawObjectOnStackGenerator.transform(BoundedList<ObjectMask> element) |
Stack |
ExtractBoundingBoxAreaFromStackGenerator.transform(BoundingBox element) |
Modifier and Type | Method and Description |
---|---|
Stack |
StackGenerator.transform(Stack element) |
Stack |
RasterGeneratorDelegateToRaster.transform(T element) |
Stack |
RasterGeneratorBridge.transform(T element) |
Stack |
RasterGeneratorDelegateToDisplayStack.transform(T element) |
void |
RasterGenerator.write(T element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
protected abstract void |
RasterGenerator.writeToFile(T untransformedElement,
Stack transformedElement,
StackWriteOptions options,
OutputWriteSettings settings,
Path filePath)
Writes a stack to the file-system.
|
protected void |
RasterGeneratorSelectFormat.writeToFile(T element,
Stack transformedElement,
StackWriteOptions options,
OutputWriteSettings settings,
Path filePath) |
void |
RasterGenerator.writeWithIndex(T element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter)
As only a single-file is involved, this methods delegates to a simpler virtual method.
|
Modifier and Type | Method and Description |
---|---|
S |
TransformingGenerator.transform(T element)
Applies any necessary preprocessing to create an element suitable for writing to the
filesystem.
|
S |
SingleFileTypeGeneratorBridge.transform(T element) |
S |
TransformingGeneratorBridge.transform(T element) |
T |
OneStageGenerator.transform(T element) |
void |
GeneratorBridge.write(S element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
TransformingGeneratorBridge.write(T element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
SingleFileTypeGenerator.write(T element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
SingleFileTypeGeneratorBridge.writeToFile(T element,
OutputWriteSettings settings,
Path filePath) |
abstract void |
SingleFileTypeGenerator.writeToFile(T element,
OutputWriteSettings settings,
Path filePath) |
void |
GeneratorBridge.writeWithIndex(S element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
TransformingGeneratorBridge.writeWithIndex(T element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
SingleFileTypeGenerator.writeWithIndex(T element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter) |
Modifier and Type | Method and Description |
---|---|
void |
NamedProviderOutputter.output(String outputName,
boolean suppressSubdirectory)
Outputs the entities using a particular output-name.
|
void |
CollectionGenerator.write(Collection<T> element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
CollectionGenerator.writeWithIndex(Collection<T> element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter) |
Modifier and Type | Method and Description |
---|---|
void |
CombinedListGenerator.write(T element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter) |
void |
CombinedListGenerator.writeWithIndex(T element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter) |
Modifier and Type | Method and Description |
---|---|
CheckedRunnable<OutputWriteFailedException> |
OutputSequenceIncrementing.addAsynchronously(T element)
Like
OutputSequenceIncrementing.add(Object) but does not immediately execute the underlying add operation,
instead returning an operation that can be called later. |
Modifier and Type | Method and Description |
---|---|
void |
OutputSequenceIncrementing.add(T element)
Outputs an additional element in the sequence.
|
void |
OutputSequenceIndexed.add(T element,
Optional<S> index)
Outputs an additional element in the sequence.
|
void |
OutputSequenceIndexed.add(T element,
S index)
Outputs an additional element in the sequence.
|
CheckedRunnable<OutputWriteFailedException> |
OutputSequenceIncrementing.addAsynchronously(T element)
Like
OutputSequenceIncrementing.add(Object) but does not immediately execute the underlying add operation,
instead returning an operation that can be called later. |
OutputSequenceIncrementing<T> |
OutputSequenceFactory.incrementingByOne(OutputPatternIntegerSuffix pattern)
Writes elements to
directory , with an incrementing integer in the filename. |
OutputSequenceIncrementing<T> |
OutputSequenceFactory.incrementingByOneCurrentDirectory(String outputName,
String prefix,
int numberDigits)
Writes elements to the current directory, with an incrementing integer in the filename.
|
void |
OutputSequenceFactory.incrementingByOneStream(OutputPatternIntegerSuffix pattern,
java.util.stream.Stream<T> stream)
Writes file for each element in a stream with an incrementing integer sequence in the
outputted file-name.
|
OutputSequenceIndexed<T,Integer> |
OutputSequenceFactory.indexedWithInteger(OutputPatternIntegerSuffix pattern) |
OutputSequenceIndexed<T,String> |
OutputSequenceFactory.withoutOrder(OutputPatternStringSuffix pattern)
Writes elements (indexed by strings) to
directory , without any order in the sequence. |
OutputSequenceIndexed<T,String> |
OutputSequenceFactory.withoutOrderCurrentDirectory(String outputName)
Writes elements (indexed by strings) to the current directory, without any order in the
sequence.
|
Constructor and Description |
---|
OutputSequenceIncrementing(BoundOutputter<T> parameters) |
Modifier and Type | Method and Description |
---|---|
void |
DictionaryGenerator.writeToFile(Dictionary element,
OutputWriteSettings settings,
Path filePath) |
void |
ObjectOutputStreamGenerator.writeToFile(T element,
OutputWriteSettings settings,
Path filePath) |
void |
XStreamGenerator.writeToFile(T element,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
static CSVWriter |
CSVWriter.create(Path path)
Creates and starts a CSVWriter (it's always allowed, so will never return null)
|
static Optional<CSVWriter> |
CSVWriter.createFromOutputter(String outputName,
OutputterChecked outputter)
Creates and starts a CSVWriter if it's allowed, otherwise returns
Optional.empty() . |
Modifier and Type | Method and Description |
---|---|
void |
TextFileOutput.start() |
void |
StringGenerator.writeToFile(String element,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
Optional<OutputterChecked> |
AlwaysAllowed.createSubdirectory(String outputName,
boolean inheritOutputRulesAndRecording) |
Optional<OutputterChecked> |
Writer.createSubdirectory(String outputName,
boolean inheritOutputRulesAndRecording)
Maybe creates a subdirectory for writing to.
|
Optional<OutputterChecked> |
CheckIfAllowed.createSubdirectory(String outputName,
boolean inheritOutputRulesAndRecording) |
ElementWriter<T> |
ElementWriterSupplier.get()
Gets/creates the
ElementWriter to be used for an output. |
T |
ElementSupplier.get()
Gets/creates the element to be written.
|
<T> boolean |
AlwaysAllowed.write(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element) |
<T> boolean |
Writer.write(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element)
Writes an element using an
ElementWriter to the current directory. |
<T> boolean |
CheckIfAllowed.write(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element) |
void |
ElementWriter.write(T element,
OutputNameStyle outputNameStyle,
ElementOutputter outputter)
Writes a non-indexable output (an output that isn't part of a collection of other similar
items).
|
<T> boolean |
AlwaysAllowed.writeWithIndex(IndexableOutputNameStyle outputNameStyle,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element,
String index) |
<T> boolean |
Writer.writeWithIndex(IndexableOutputNameStyle outputNameStyle,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element,
String index)
Writes an indexed-element using an
ElementWriter in the current directory. |
<T> boolean |
CheckIfAllowed.writeWithIndex(IndexableOutputNameStyle outputNameStyle,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element,
String index) |
void |
ElementWriter.writeWithIndex(T element,
String index,
IndexableOutputNameStyle outputNameStyle,
ElementOutputter outputter)
Writes an indexable output (many outputs of the same type, uniquely identified by an index).
|
<T> boolean |
AlwaysAllowed.writeWithoutName(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element) |
<T> boolean |
Writer.writeWithoutName(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element)
Writes an element using an
ElementWriter to the current directory, without
including an output name in the path. |
<T> boolean |
CheckIfAllowed.writeWithoutName(String outputName,
ElementWriterSupplier<T> elementWriter,
ElementSupplier<T> element) |
Modifier and Type | Method and Description |
---|---|
Stack |
MarksGeneratorBase.transform(ColoredMarksWithDisplayStack element) |
Stack |
MarksAsUniqueValueGenerator.transform(MarkCollection element) |
Modifier and Type | Method and Description |
---|---|
void |
EnergyStackWriter.writeEnergyStack() |
Modifier and Type | Method and Description |
---|---|
protected void |
DefineOutputter.outputSharedObjects(SharedObjects sharedObjects,
Optional<EnergyStack> energyStack,
Outputter outputter) |
Modifier and Type | Method and Description |
---|---|
protected void |
PeriodicSubdirectoryReporter.initialize(Generator<T> generator)
We setup the sequence-writer.
|
Modifier and Type | Method and Description |
---|---|
protected void |
AnnotationAggregateCSVGenerator.writeFeaturesToCSV(CSVWriter writer,
List<ImageAnnotation> allFeatureResults,
List<String> headerNames) |
Modifier and Type | Method and Description |
---|---|
void |
FeatureExporter.closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
|
Optional<FeatureCSVWriter> |
FeatureExporterContext.csvWriter(FeatureCSVMetadata metadata)
Creates a
FeatureCSVWriter for the non-aggregated results. |
void |
FeatureResultsAndThumbnails.writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate,
boolean includeGroups,
java.util.function.Function<InputOutputContext,FeatureCSVWriterFactory> csvWriterCreator,
InputOutputContext context)
Writes all the results that have been collected as a CSV file.
|
Constructor and Description |
---|
FeatureExporter(FeatureOutputMetadata outputMetadata,
java.util.function.Supplier<S> featureSource,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Creates the shared state.
|
FeatureResultsAndThumbnails(FeatureOutputMetadata outputMetadata,
FeatureExporterContext context) |
Modifier and Type | Method and Description |
---|---|
void |
SharedStateSegmentInstance.closeAndWriteOutputs(ExportFeaturesStyle style)
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
|
Modifier and Type | Method and Description |
---|---|
Optional<Path> |
CopyFilesNaming.destinationPath(File file,
DirectoryWithPrefix outputTarget,
int index,
CopyContext<T> context)
Returns the output path (destination to to be copied to) for a given single file.
|
Optional<Path> |
Anonymize.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int iter,
CopyContext<AnonymizeSharedState> context) |
Optional<Path> |
PreserveName.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int iter,
CopyContext<NoSharedState> context) |
Optional<Path> |
CopyFilesNamingOne.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int iter,
CopyContext<NoSharedState> context) |
Optional<Path> |
OutputPrefixWithExtension.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int index,
CopyContext<NoSharedState> context) |
abstract Optional<Path> |
CopyFilesNaming.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int index,
CopyContext<T> context)
Calculates the relative-output path (to be appended to destDir)
|
Modifier and Type | Method and Description |
---|---|
Optional<Path> |
ClusterByTimestamp.destinationPathRelative(File file,
DirectoryWithPrefix outputTarget,
int index,
CopyContext<ClusterMembership> context) |
Modifier and Type | Method and Description |
---|---|
void |
WriteIntoDirectory.writeList(String outputName,
List<DisplayStack> stacks,
boolean always2D)
Writes a list of display-stacks
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.