Uses of Class
org.anchoranalysis.io.output.error.OutputWriteFailedException
Packages that use OutputWriteFailedException
Package
Description
Generates output images to illustrate a
Assignment
between annotations.Metadata for writing feature calculation-results in CSV format.
Writing the results from feature-calculation to a CSV file.
A
Generator
for writing a table of feature values as a
CSV.Writes feature-calculation results in different formats, also grouped results.
Various different outputs that can be written for the a grouped version of the results in
LabelledResultsCollector
.Non-bean classes for writing a
Channel
to the
filesystem.Non-bean classes for writing a
Histogram
to the
filesystem.Writing an
ObjectCollection
to the filesystem as a
single-channeled stack.Writing an
ObjectCollection
to the filesystem as
multiple binary singled-channeled images.Writing an
ObjectCollection
to the filesystem as
RGB raster-images.Non-bean classes for writing a
Stack
to the
filesystem.Base classes for generators that ultimately write only a bounding-box portion of a
Stack
to the filesystem.Base classes for generators that ultimately write a
Stack
to the filesystem.Base-classes and utilities for generators, which write different types of objects to the file
system.
Outputting more than one element collectively using a generator.
Combining multiple generators into one.
Writing a sequence of elements using a generator.
Generators for writing serialized objects.
Generators for writing tabular data, including CSV.
Generators for writing textual data, including strings.
Allows a generators to write element(s) to the filesystem.
Non-beans for writing data structures related to marked point processes from the file system.
Beans to combine two or more annotations.
Non-bean classes pertaining to
Feature
s as used in tasks.Non-bean classes for image-segmentation.
Rules for preserving or changing the naming of files when copying on the file-system.
Implementations of
CopyFilesNaming
that perform clustering of files.Testing utilities and fixtures with no greater downstream dependency than anchor-image-io
or anchor-io-bioformats or anchor-imagej.
-
Uses of OutputWriteFailedException in org.anchoranalysis.annotation.io.assignment.generator
Methods in org.anchoranalysis.annotation.io.assignment.generator that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionDrawColoredObjects.createObjectsImage
(Assignment<ObjectMask> assignment, boolean left, AssignmentColorPool colorPool) Creates an image with the objects colored, as indicated in the class description.AssignmentGenerator.transform
(Assignment<ObjectMask> element) -
Uses of OutputWriteFailedException in org.anchoranalysis.feature.io.csv
Methods in org.anchoranalysis.feature.io.csv that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionstatic Optional
<FeatureCSVWriter> FeatureCSVWriter.create
(FeatureCSVMetadata metadata, Outputter outputter, boolean visuallyShortenedDecimals) Maybe creates aFeatureCSVWriter
depending if the output is allowed. -
Uses of OutputWriteFailedException in org.anchoranalysis.feature.io.csv.results
Methods in org.anchoranalysis.feature.io.csv.results that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionFeatureCSVWriterFactory.create
(FeatureCSVMetadata metadata) Maybe creates aFeatureCSVWriter
corresponding to particular metadata.static LabelledResultsCSVWriter
LabelledResultsCSVWriterFactory.create
(FeatureCSVMetadataForOutput outputMetadata, FeatureCSVWriterFactory writerCreator, Optional<Consumer<LabelledResultsVector>> consumeAfterAdding, boolean removeNaNColumns) Creates with appropriate support classes for outputting.protected Optional
<FeatureCSVWriter> LabelledResultsCSVWriter.createWriter
(FeatureCSVMetadata csvMetadata) Creates aCSVWriter
.abstract void
LabelledResultsCSVWriter.end()
Stops writing the CSV file.abstract void
LabelledResultsCSVWriter.start()
Starts writing the CSV file. -
Uses of OutputWriteFailedException in org.anchoranalysis.feature.io.csv.table
Methods in org.anchoranalysis.feature.io.csv.table that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionprotected 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) -
Uses of OutputWriteFailedException in org.anchoranalysis.feature.io.results
Methods in org.anchoranalysis.feature.io.results that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
LabelledResultsCollector.flushAndClose
(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, 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. -
Uses of OutputWriteFailedException in org.anchoranalysis.feature.io.results.group
Methods in org.anchoranalysis.feature.io.results.group that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
GroupedResults.writeGroupResults
(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, FeatureOutputMetadata outputMetadata, FeatureCSVWriterFactory createAggregatedCSVWriter, InputOutputContextSubdirectoryCache contextGroups) Writes outputs for groups that have been previously added withGroupedResults.addResultsFor(org.anchoranalysis.feature.io.results.LabelledResultsVector)
. -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.channel.output
Methods in org.anchoranalysis.image.io.channel.output that throw OutputWriteFailedException -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.histogram.output
Methods in org.anchoranalysis.image.io.histogram.output that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
HistogramCSVGenerator.writeToFile
(Histogram element, OutputWriteSettings settings, Path filePath) -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.object.output.grayscale
Methods in org.anchoranalysis.image.io.object.output.grayscale that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionObjectsAsUniqueValueGenerator.transform
(ObjectCollection element) ObjectsMergedAsMaskGenerator.transform
(ObjectCollection element) -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.object.output.mask
Methods in org.anchoranalysis.image.io.object.output.mask that throw OutputWriteFailedException -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.object.output.rgb
Methods in org.anchoranalysis.image.io.object.output.rgb that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionObjectsAsRGBGenerator.transform
(ObjectCollectionWithProperties element) -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.stack.output
Methods in org.anchoranalysis.image.io.stack.output that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionOutputSequenceStackFactory.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.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. -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.stack.output.box
Methods in org.anchoranalysis.image.io.stack.output.box that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionDrawObjectOnStackGenerator.transform
(BoundedList<ObjectMask> element) ExtractBoundingBoxAreaFromStackGenerator.transform
(BoundingBox element) -
Uses of OutputWriteFailedException in org.anchoranalysis.image.io.stack.output.generator
Methods in org.anchoranalysis.image.io.stack.output.generator that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
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. -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator
Methods in org.anchoranalysis.io.generator that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionApplies any necessary preprocessing to create an element suitable for writing to the filesystem.void
GeneratorBridge.write
(S element, OutputNameStyle outputNameStyle, ElementOutputter outputter) void
SingleFileTypeGenerator.write
(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) void
TransformingGeneratorBridge.write
(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) abstract void
SingleFileTypeGenerator.writeToFile
(T element, OutputWriteSettings settings, Path filePath) Write generated content for {code element} to the filefilePath
.void
SingleFileTypeGeneratorBridge.writeToFile
(T element, OutputWriteSettings settings, Path filePath) void
GeneratorBridge.writeWithIndex
(S element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) void
SingleFileTypeGenerator.writeWithIndex
(T element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) void
TransformingGeneratorBridge.writeWithIndex
(T element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.collection
Methods in org.anchoranalysis.io.generator.collection that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
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) -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.combined
Methods in org.anchoranalysis.io.generator.combined that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
CombinedListGenerator.write
(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) void
CombinedListGenerator.writeWithIndex
(T element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.sequence
Methods in org.anchoranalysis.io.generator.sequence that return types with arguments of type OutputWriteFailedExceptionModifier and TypeMethodDescriptionOutputSequenceIncrementing.addAsynchronously
(T element) LikeOutputSequenceIncrementing.add(Object)
but does not immediately execute the underlying add operation, instead returning an operation that can be called later.Methods in org.anchoranalysis.io.generator.sequence that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
Outputs an additional element in the sequence.void
Outputs an additional element in the sequence.void
Outputs an additional element in the sequence.OutputSequenceIncrementing.addAsynchronously
(T element) LikeOutputSequenceIncrementing.add(Object)
but does not immediately execute the underlying add operation, instead returning an operation that can be called later.OutputSequenceFactory.incrementingByOne
(OutputPatternIntegerSuffix pattern) Writes elements todirectory
, with an incrementing integer in the filename.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, Stream<T> stream) Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.OutputSequenceFactory.indexedWithInteger
(OutputPatternIntegerSuffix pattern) Writes elements (indexed by integers) todirectory
, without any order in the sequence.OutputSequenceFactory.withoutOrder
(OutputPatternStringSuffix pattern) Writes elements (indexed by strings) todirectory
, without any order in the sequence.OutputSequenceFactory.withoutOrderCurrentDirectory
(String outputName) Writes elements (indexed by strings) to the current directory, without any order in the sequence.Constructors in org.anchoranalysis.io.generator.sequence that throw OutputWriteFailedExceptionModifierConstructorDescriptionOutputSequenceIncrementing
(BoundOutputter<T> outputter) Create with an outputter. -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.serialized
Methods in org.anchoranalysis.io.generator.serialized that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
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) -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.tabular
Methods in org.anchoranalysis.io.generator.tabular that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionstatic CSVWriter
Creates and starts a CSVWriter (it's always allowed, so will never return null)CSVWriter.createFromOutputter
(String outputName, OutputterChecked outputter) Creates and starts a CSVWriter if it's allowed, otherwise returnsOptional.empty()
. -
Uses of OutputWriteFailedException in org.anchoranalysis.io.generator.text
Methods in org.anchoranalysis.io.generator.text that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
TextFileOutput.start()
This should be called once before subsequently writing content withTextFileOutput.getWriter()
void
StringGenerator.writeToFile
(String element, OutputWriteSettings settings, Path filePath) -
Uses of OutputWriteFailedException in org.anchoranalysis.io.output.writer
Methods in org.anchoranalysis.io.output.writer that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionAlwaysAllowed.createSubdirectory
(String outputName, boolean inheritOutputRulesAndRecording) CheckIfAllowed.createSubdirectory
(String outputName, boolean inheritOutputRulesAndRecording) Writer.createSubdirectory
(String outputName, boolean inheritOutputRulesAndRecording) Maybe creates a subdirectory for writing to.ElementSupplier.get()
Gets/creates the element to be written.ElementWriterSupplier.get()
Gets/creates theElementWriter
to be used for an output.<T> boolean
AlwaysAllowed.write
(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) <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
Writer.write
(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) Writes an element using anElementWriter
to the current directory.<T> boolean
AlwaysAllowed.writeWithIndex
(IndexableOutputNameStyle outputNameStyle, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element, String index) <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
Writer.writeWithIndex
(IndexableOutputNameStyle outputNameStyle, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element, String index) Writes an indexed-element using anElementWriter
in the current directory.<T> boolean
AlwaysAllowed.writeWithoutName
(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) <T> boolean
CheckIfAllowed.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 anElementWriter
to the current directory, without including an output name in the path. -
Uses of OutputWriteFailedException in org.anchoranalysis.mpp.io.output
Methods in org.anchoranalysis.mpp.io.output that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
EnergyStackWriter.writeEnergyStack()
Writes the energy stack to output. -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.annotation.bean.aggregate
Methods in org.anchoranalysis.plugin.annotation.bean.aggregate that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionprotected void
AnnotationAggregateCSVGenerator.writeFeaturesToCSV
(CSVWriter writer, List<ImageAnnotation> allFeatureResults, List<String> headerNames) -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.image.task.feature
Methods in org.anchoranalysis.plugin.image.task.feature that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
FeatureExporter.closeAndWriteOutputs
(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, 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.FeatureExporterContext.csvWriter
(FeatureCSVMetadata metadata) Creates aFeatureCSVWriter
for the non-aggregated results.void
FeatureResultsAndThumbnails.writeGroupedResults
(Optional<NamedFeatureStore<FeatureInputResults>> featuresAggregate, boolean includeGroups, Function<InputOutputContext, FeatureCSVWriterFactory> csvWriterCreator, InputOutputContext context) Writes all the results that have been collected as a CSV file.Constructors in org.anchoranalysis.plugin.image.task.feature that throw OutputWriteFailedExceptionModifierConstructorDescriptionFeatureExporter
(FeatureOutputMetadata outputMetadata, Supplier<S> featureSource, Optional<InputGrouper> grouper, FeatureExporterContext context) Creates the shared state.FeatureResultsAndThumbnails
(FeatureOutputMetadata outputMetadata, FeatureExporterContext context) Creates a newFeatureResultsAndThumbnails
. -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.image.task.segment
Methods in org.anchoranalysis.plugin.image.task.segment that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
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. -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.io.bean.file.copy.naming
Methods in org.anchoranalysis.plugin.io.bean.file.copy.naming that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionCopyFilesNaming.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.Anonymize.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int iter, CopyContext<AnonymizeSharedState> context) CopyFilesNaming.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int index, CopyContext<T> context) Calculates the relative-output path (to be appended to destDir)CopyFilesNamingOne.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int iter, CopyContext<NoSharedState> context) OutputPrefixWithExtension.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int index, CopyContext<NoSharedState> context) PreserveName.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int iter, CopyContext<NoSharedState> context) -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
Methods in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionClusterByTimestamp.destinationPathRelative
(File file, DirectoryWithPrefix outputTarget, int index, CopyContext<ClusterMembership> context) -
Uses of OutputWriteFailedException in org.anchoranalysis.plugin.mpp.bean.define
Methods in org.anchoranalysis.plugin.mpp.bean.define that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionprotected void
DefineOutputter.outputSharedObjects
(SharedObjects sharedObjects, Optional<EnergyStack> energyStack, Outputter outputter) Outputs shared objects and optionally an energy stack. -
Uses of OutputWriteFailedException in org.anchoranalysis.test.image
Methods in org.anchoranalysis.test.image that throw OutputWriteFailedExceptionModifier and TypeMethodDescriptionvoid
WriteIntoDirectory.writeList
(String outputName, List<DisplayStack> stacks, boolean always2D) Writes a list of display-stacks.