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
Features 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 aFeatureCSVWriterdepending 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 aFeatureCSVWritercorresponding to particular metadata.static LabelledResultsCSVWriterLabelledResultsCSVWriterFactory.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 voidLabelledResultsCSVWriter.end()Stops writing the CSV file.abstract voidLabelledResultsCSVWriter.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 voidFeatureTableCSVGenerator.writeFeaturesToCSV(CSVWriter writer, T allFeatureResults, List<String> headerNames) Writes the features to the CSV-file.voidFeatureTableCSVGenerator.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 TypeMethodDescriptionvoidLabelledResultsCollector.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 TypeMethodDescriptionvoidGroupedResults.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 TypeMethodDescriptionvoidHistogramCSVGenerator.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 voidNamedStacksOutputter.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.voidOutputSequenceStackFactory.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 TypeMethodDescriptionvoidRasterGenerator.write(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) protected abstract voidRasterGenerator.writeToFile(T untransformedElement, Stack transformedElement, StackWriteOptions options, OutputWriteSettings settings, Path filePath) Writes a stack to the file-system.protected voidRasterGeneratorSelectFormat.writeToFile(T element, Stack transformedElement, StackWriteOptions options, OutputWriteSettings settings, Path filePath) voidRasterGenerator.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.voidGeneratorBridge.write(S element, OutputNameStyle outputNameStyle, ElementOutputter outputter) voidSingleFileTypeGenerator.write(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) voidTransformingGeneratorBridge.write(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) abstract voidSingleFileTypeGenerator.writeToFile(T element, OutputWriteSettings settings, Path filePath) Write generated content for {code element} to the filefilePath.voidSingleFileTypeGeneratorBridge.writeToFile(T element, OutputWriteSettings settings, Path filePath) voidGeneratorBridge.writeWithIndex(S element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) voidSingleFileTypeGenerator.writeWithIndex(T element, String index, IndexableOutputNameStyle outputNameStyle, ElementOutputter outputter) voidTransformingGeneratorBridge.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 TypeMethodDescriptionvoidOutputs the entities using a particular output-name.voidCollectionGenerator.write(Collection<T> element, OutputNameStyle outputNameStyle, ElementOutputter outputter) voidCollectionGenerator.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 TypeMethodDescriptionvoidCombinedListGenerator.write(T element, OutputNameStyle outputNameStyle, ElementOutputter outputter) voidCombinedListGenerator.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 TypeMethodDescriptionvoidOutputs an additional element in the sequence.voidOutputs an additional element in the sequence.voidOutputs 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.voidOutputSequenceFactory.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 TypeMethodDescriptionvoidDictionaryGenerator.writeToFile(Dictionary element, OutputWriteSettings settings, Path filePath) voidObjectOutputStreamGenerator.writeToFile(T element, OutputWriteSettings settings, Path filePath) voidXStreamGenerator.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 CSVWriterCreates 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 TypeMethodDescriptionvoidTextFileOutput.start()This should be called once before subsequently writing content withTextFileOutput.getWriter()voidStringGenerator.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 theElementWriterto be used for an output.<T> booleanAlwaysAllowed.write(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) <T> booleanCheckIfAllowed.write(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) voidElementWriter.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> booleanWriter.write(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) Writes an element using anElementWriterto the current directory.<T> booleanAlwaysAllowed.writeWithIndex(IndexableOutputNameStyle outputNameStyle, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element, String index) <T> booleanCheckIfAllowed.writeWithIndex(IndexableOutputNameStyle outputNameStyle, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element, String index) voidElementWriter.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> booleanWriter.writeWithIndex(IndexableOutputNameStyle outputNameStyle, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element, String index) Writes an indexed-element using anElementWriterin the current directory.<T> booleanAlwaysAllowed.writeWithoutName(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) <T> booleanCheckIfAllowed.writeWithoutName(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) <T> booleanWriter.writeWithoutName(String outputName, ElementWriterSupplier<T> elementWriter, ElementSupplier<T> element) Writes an element using anElementWriterto 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 TypeMethodDescriptionvoidEnergyStackWriter.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 voidAnnotationAggregateCSVGenerator.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 TypeMethodDescriptionvoidFeatureExporter.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 aFeatureCSVWriterfor the non-aggregated results.voidFeatureResultsAndThumbnails.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 TypeMethodDescriptionvoidSharedStateSegmentInstance.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 voidDefineOutputter.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 TypeMethodDescriptionvoidWriteIntoDirectory.writeList(String outputName, List<DisplayStack> stacks, boolean always2D) Writes a list of display-stacks.