Index (anchor-plugin-io 0.1.0 API)

A B C D E F G H I J L M N O P R S T V W
All Classes All Packages

A

accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.CheckParsedFilePathBag
add(int, String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
add(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
add(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
add(FileDetails) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Adds a element to the summary.
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
addAll(Collection<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Adds the elements to the summary.
addFromXmlFile(Path) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Adds root-paths contained in a list of XML Beans in an xml file
addTimestamp(long) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Adds a timestamp to the cluster.
addToStoreInferNames(NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
addToStoreWithName(String, NamedProviderStore<TimeSeries>, int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
AlwaysReject - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: A special ImageMetadataReader that will always throw an exception and reject a file.
AlwaysReject() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.AlwaysReject
Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to a number 001, 002 etc.
Anonymize() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
assignName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Assigns a name for the cluster.
associateFileWithCluster(File, long, ClusterIdentifier) - Method in class org.anchoranalysis.plugin.io.file.copy.ClusterMembership: Indicates a particular file is a member of a particular cluster.
AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
AtLeastZSlices() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map: Names of the channels from the metadata if it exists, or after RGB, or by index.
Autoname() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.Autoname

B

beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<FileWithDirectoryInput>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: To be called once before any calls to CopyFilesNaming.destinationPath(File, DirectoryWithPrefix, int, CopyContext).
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingWithoutSharedState
beforeCopying(Path, List<FileWithDirectoryInput>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
bitDepth(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
BitDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
BMP - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a BMP file.
BMP() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on the number/type of channels.
BranchChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
BranchExtension - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.
BranchExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension
BranchIfDebug<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Uses one input-manager normally, but a different one if in debug mode.
BranchIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchStack() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
BranchSuggestedFormat - Class in org.anchoranalysis.plugin.io.bean.stack.writer: Selects particular writers based on if particular suggested image formats are present.
BranchSuggestedFormat() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat
Bytewise - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Makes a simple bytewise copy of a file, where no byte is changed.
Bytewise() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.Bytewise

C

canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
channelNames(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
CheckParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.check.CheckParsedFilePathBag
close() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
closeLogger() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Closes the logger.
ClusterByTimestamp - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Associates particular timestamp with each file, and clusters.
ClusterByTimestamp() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
clusterFor(File) - Method in class org.anchoranalysis.plugin.io.file.copy.ClusterMembership: Finds the corresponding cluster for a particular file.
ClusterIdentifier - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Uniquely identifies a cluster.
ClusterIdentifier(String, ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Creates with a constant-name.
ClusterIdentifier(ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Creates with no name.
ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy: A mapping of files to membership of particular clusters.
ClusterMembership(ClusterIdentifier) - Constructor for class org.anchoranalysis.plugin.io.file.copy.ClusterMembership
CollapseFileName - Class in org.anchoranalysis.plugin.io.bean.path.derive: Removes the file-name from a path, but keeps the directories and preserves the file-extension.
CollapseFileName() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName
Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
Combine() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Combine
CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task: Combines multiple CSV files into a single CSV file.
CombineCSV() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CombineCSV
compareTo(SortedSetChannel) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
compareTo(SortedSetSlice) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a Bytewise copy.
CompressAnyTIFF() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.CompressAnyTIFF
Concatenate<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Concatenates the inputs from multiple InputManagers that all provide the same input-type.
Concatenate() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Concatenate
Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive: Always generates a constant path irrespective of the the input
Constant() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
Constant(String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
convert(int) - Method in class org.anchoranalysis.plugin.io.shared.NumberToStringConverter: Converts number to a string, padding with leading zeros if necessary to ensure the desired width.
ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: An input object that converts NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsInputToStack(NamedChannelsInput, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack: Create with an input.
ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack: Manager that converts (one channel) NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsToStack() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
convertToString(Path) - Static method in class org.anchoranalysis.plugin.io.file.copy.PathOperations: Converts a path to a string, making sure it uses UNIX-style separators.
CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path: Context parameters when copying many files from a source directory to a destination directory.
CopyContext(Path, Path, T) - Constructor for class org.anchoranalysis.plugin.io.input.path.CopyContext
CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task: Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.
CopyFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CopyFiles
CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method: A method used for copying files (e.g.
CopyFilesMethod() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod
CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: How an output name (and path) is selected for an input file when copying.
CopyFilesNaming() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming
CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
CopyFilesNamingOne() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Base class for implementations of CopyFilesNaming where each file is copied independently of the others.
CopyFilesNamingWithoutSharedState() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingWithoutSharedState
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
create(OpenedImageFile, Logger) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
create(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
createInputGrouper(Optional<IndexRangeNegative>) - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange
createInputsFromFiles(FilesProvider, InputManagerParameters, Function<NamedFile, T>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase: Creates a list of inputs from a FilesProvider which together with the namer can create the inputs.
createSequence(VoxelDataType) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
createStackSequenceForSeries(int, Logger) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack

D

DateStyle - Enum in org.anchoranalysis.plugin.io.naming.interval: How to style a date in a file-name.
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.NormalizedPath
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
deriveName(File, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RelativeToDirectory
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
deriveName(List<File>, FileNamerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested
deriveRootedPath(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.plugin.io.input.path.RootedFilePathUtilities
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: A string summarizing this item.
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
describe(String) - Method in class org.anchoranalysis.plugin.io.shared.FrequencyMap
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
destinationPath(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: Returns the output path (destination to to be copied to) for a given single file.
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.OutputPrefixWithExtension
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<ClusterMembership>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<AnonymizeSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.Anonymize
destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNaming: Calculates the relative-output path (to be appended to destDir)
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RemoveWhitespace
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
dimensionsForSeries(int, Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider: Lists all directories to a certain depth
DirectoryDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Reuses the directories between a path and its root to form the output - and also the filename.
DirectoryStructure() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
doJobOnInput(InputBound<FileWithDirectoryInput, RecordingCounter<T>>) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase

E

equals(Object) - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
equals(Object) - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
Exclude<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Excludes all inputs whose identifiers match a regular expression.
Exclude() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Exclude
ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Remembers each unique extension, and associated count
ExtensionCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
ExtractIdentifier<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier from an InputFromManager to summarize further.
ExtractIdentifier() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
ExtractIdentifierAndPath<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts the identifier and path from an InputFromManager to summarize further.
ExtractIdentifierAndPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
extractKey(ImageMetadataInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase: Extract object for summary.
extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
ExtractPath<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a Path from an input to summarize further.
ExtractPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath

F

FileDetails - Class in org.anchoranalysis.plugin.io.multifile
FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class org.anchoranalysis.plugin.io.multifile.FileDetails
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
fileFormat(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
FilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
FilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.FilePath
filePathDifference(Path, Path) - Static method in class org.anchoranalysis.plugin.io.file.copy.PathOperations: Finds the difference between a path and a base.
FilePathParser - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
FilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library.
FilePathPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
FilePathPattern(String...) - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Create with one or more paths.
FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.file.provider
FileSetFromStringSet() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Tracks the range of file-size.
FileSizeStatistics() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
FilterCSVColumn<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Finds a CSV file with the names of an input as the first-column.
FilterCSVColumn() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
FilterDescriptiveName<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter: Filters a list of input-objects by the descriptive name
FilterDescriptiveNameEqualsContains(String, String) - Constructor for class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
FilterForExistingFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
FilterIfDebug<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter: Filters a list of inputs when in debug-mode
FilterIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
FilterWithRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Rejects files that fail to match a particular regular-expression
FilterWithRegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression
findRoot(String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Finds a root to match a name and debug/status
FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Combines all series and frames returned by a reader by converting them into multiple channels in the same image.
FlattenAsChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: The associated ImageFileFormat with this header.
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG
format() - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
formatter() - Method in enum org.anchoranalysis.plugin.io.naming.interval.DateStyle: Derives a formatter for the particular date-style.
FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.shared: Counts the frequency of certain strings, and describes the contents in human language.
FrequencyMap() - Constructor for class org.anchoranalysis.plugin.io.shared.FrequencyMap
FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix.
FromDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName
FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromEntries() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
FromMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
FromOutputName - Class in org.anchoranalysis.plugin.io.bean.file.namer
FromOutputName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName

G

getChannelGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getChannelIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getChannelMap() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
getCheckParsedFilePathBag() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
getContains() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
getCountThreshold() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
getCsvFilePath() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: Character used to split the name into groups.
getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
getDepth() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in z-dimension.
getDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: Called as a delegate to provide a source Path.
getDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getDestinationDirectory() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: Destination directory for copying.
getDirectory() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
getEquals() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
getExactDepth() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
getExpression() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getExtensions() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: Any extensions to match (case insensitive) excluding any leading period.
getFallback() - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: Fallback to use if EXIF information is non-existing or absent.
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
getFiles() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory: The files to use as inputs.
getFormats() - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.
getGroup() - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange: Fallback to use when no group-index-range is specified.
getHeight() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in y-dimension.
getImgChannelMapCreator() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getIndexDay() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the day, starting from 0 for the first group.
getIndexHours() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.
getIndexMinutes() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.
getIndexMonth() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the month, starting from 0 for the first group.
getIndexSeconds() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.
getIndexYear() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the year, starting from 0 for the first group.
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getInputDebug() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug: If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.
getItem() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getKey() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
getKey() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getKeyGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getList() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
getList() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
getList() - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate: The list of InputManagers that will be concatenated.
getList() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
getListAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
getMapping() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
getMatch() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
getMaxInstant() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Maximum timestamp in cluster.
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
getMaxPathWidth() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath: The maximum width permitted for an identifier, so that it is printed as one line.
getMaxTime() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Gets the latest date-time in the cluster.
getMethod() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How the copying occurs from source to destination file.
getMin(Function<FileDetails, Optional<Integer>>) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
getMinimumPerCluster() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The minimum number of files that must exist for a cluster.
getMinInstant() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Minimum timestamp in cluster.
getMinNumZSlices() - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
getMinTime() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Gets the earliest date-time in the cluster.
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
getNamer() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
getNaming() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How an output name (and path) is selected for an input file.
getNamingSharedState() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter
getNavigateHigherDirectories() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file.
getNumberConverter() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
getNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: How many directories to include in the name.
getOffset() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: The offset to assume the time-stamp belongs in.
getOtherwise() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
getOutPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
getOutputNameStyle() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
getPath() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
getPath() - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
getPath() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getPathParser() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
getPaths() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
getPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
getPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
getPrefixerElse() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is not true.
getPrefixerIf() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is true.
getPrefixToRemove() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
getRangeC() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeT() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getRangeZ() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
getReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation: Reads the image that is subsequently flattened.
getReaderMatching() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension matches.
getReaderNotMatching() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension does not match.
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
getRegex() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching: If a path matches a regular expression it is removed.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude: A regular-expression to be matched against the identifiers of inputs.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
getRegExDirectory() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories.
getRegExFile() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files.
getRegularExpression() - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The regular-expression that checks a match and specifies groups for the encoded date-time.
getRelation() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted: The name of the root-path to associate with this fileset.
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
getRootName() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
getSampleEvery() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
getSeperator() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
getSharedState() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: State shared across all inputs when copying.
getSize() - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getSkipNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Initially skip this number of directories before including them in the description.
getSliceIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getSourceDirectory() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext: Source directory of copying.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel: Reads the image that is subsequently flattened.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Reads an image before a resolution is imposed.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Reads an image before a resolution is imposed.
getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
getSummarizerElse() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
getSummarizerGreaterThan() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
getThresholdHours() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: Files whose creation-time differs <= this parameter are joined into the same cluster.
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
getTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
getTimeIndexGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getTimestampPatterns() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The patterns which can be used to extract a date-time from a filename.
getTimeZoneOffset() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If >= 0, sets a specific time-offset in hours.
getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
getValue() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
getWhenBinaryChannel() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled binary image.
getWhenNotEightBit() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack contains channels that are not 8-bit.
getWhenRelative() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
getWhenRGB() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image.
getWhenRGBAlpha() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a four-channeled RGBA image.
getWhenSingleChannel() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
getWhenThreeChannels() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
getWidth() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in x-dimension.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
getWriterAlways2D() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
getWriterElse() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
getWriterIfNoSuggestion() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: The writer to use if there is no suggested file-format.
getWritersIfSuggested() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: A list of writers to select if a given format is used
getZSliceGroupID() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
getZSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group: An InputManagerWithStackReader that can unify separate images in separate files to form a single Stack.
GroupFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles

H

hashCode() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
hashCode() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
hasNecessaryExtents() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
HeaderFormat - Class in org.anchoranalysis.plugin.io.bean.metadata.header: Populates ImageMetadata from the header of an image-file.
HeaderFormat() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat
HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
HomeSubdirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory

I

IfGroupIndexRange - Class in org.anchoranalysis.plugin.io.bean.grouper: When a IndexRangeNegative is passed as an argument, an InputGrouper is constructed that extracts elements from a Path.
IfGroupIndexRange() - Constructor for class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange
IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Multiplexes between two PathPrefixers depending on whether an incrementing number sequence was output was requested.
IfIncrementingNumberRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested
IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer: Multiplexes between two namers depending on if the relative-to-directory option is selected.
IfRelativeToDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory
IGNORE_SECONDS - org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The time is included in the name, but without seconds: hh.mm
IGNORE_YEAR - org.anchoranalysis.plugin.io.naming.interval.DateStyle: The date is included in the name, but without the year: mmm-dd
ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
ImageIOWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes the size of images.
ImageSize() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Adds an explicit Resolution to an image after it has been read.
ImposeResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
INCLUDE_ENTIRELY - org.anchoranalysis.plugin.io.naming.interval.DateStyle: The entire date is included in the name: yyyy-mm-dd
INCLUDE_ENTIRELY - org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The entire time is included in the name: hh.mm.ss
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
incrementCount(T) - Method in class org.anchoranalysis.plugin.io.shared.FrequencyMap
incrementCounter() - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Increments the counter.
index(int) - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange: Maps an original integer to it's index from (0..size]
InferFromHeader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader: Tries to construct the ImageMetadata from EXIF and other metadata, if available, or otherwise falls back to another reader.
InferFromHeader() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader
InferFromHeader(ImageMetadataReader, List<HeaderFormat>) - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
inputs(InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.LimitIfRequested
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested
inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles
inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an out string where $digit$ is replaced with the #digit group from a regex
InsertRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
InsertRegExGroups(RegEx, String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
instance() - Static method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
IntegerRange(int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
IntegerRange(int, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
isAcceptNoResolution() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: If false, an exception is thrown if the resolution file is missing for a particular image.
isAddName() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isAvoidBulletOnFirst() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
isCaseSensitive() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan: Iff true, a case sensitive search is used to match patterns.
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
isFirstLineHeaders() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isForceEagerEvaluation() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isIgnoreCase() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, case is ignored in the pattern matching.
isIgnoreFileNotFoundAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isIgnoreHidden() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Iff true, any hidden-path is not considered, and simply ignored
isIncludeDirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
isInvert() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression: Iff true, then a file is rejected if the regular-expression matches and vice-versa.
isKeepExtension() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: When true, the extension is appended to the directory.
isKeepZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
isKeyRequired() - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
isLogPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
isPreserveExtensionIfDuplicate() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension: Keeps the extension if the file-name (without the extension) becomes duplicated with another.
isPreserveSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If true, the entire relative-path is used when copying files into the cluster directory.
isRecurseSubfolders() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
isRemoveExtension() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, the extension is removed from paths before finding the pattern.
isRemoveExtensionInDescription() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Whether to remove the file-extension from the filename.
isRequireAllFilesMatch() - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
isRGB(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
isSkipFileName() - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Iff true the filename is not considered, only the subdirectories.
isSkipMissingChannels() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
isSortIfNotRequested() - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested: When true, the inputs are sorted alphabetically, if a shuffle is not requested.
isSuppressDirectories() - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName: If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.
isSuppressRootOut() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
isTransposed() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
iterator() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel

J

JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates an outstring of the form
JoinRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
JPEG - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a JPEG file.
JPEG() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG

L

LastDirectories - Class in org.anchoranalysis.plugin.io.bean.file.namer: Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectories() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories
LastDirectories(int) - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Creates for a particular number of subdirectories.
LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
LastDirectoryAsPrefix() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
Limit - Class in org.anchoranalysis.plugin.io.bean.file.provider
Limit<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Limits the number of input-objects to a certain hard-maximum
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Limit
Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Limit
LimitIfRequested<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Like Limit if it is requested in the InputContextParameters, makes no change to the inputs.
LimitIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.input.LimitIfRequested
LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
LimitWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory

M

makeCopy(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod: Makes a copy of the file at source at destination.
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.Bytewise
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CompressAnyTIFF
makeCopyWithDirectory(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.method.CopyFilesMethod: Like CopyFilesMethod.makeCopy(Path,Path) but after any necessary directories are created so destination can be written.
match(String, ZoneOffset) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: Matches certain times.
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
matchingFilesForDirectory(Path, InputManagerParameters) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
MultiBufferSized(Stack, SizeExtents) - Constructor for class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
MultiFileReader() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader

N

name() - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterIdentifier: Derives a name for the cluster, based upon its contents.
NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel: An image viewed as a set of channels, each with a unique name.
NamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
NamedChannelsAppend() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel: Parent for all the NamedChannels classes
NamedChannelsBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsBase
NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files: Implementation of NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name.
NamedFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFiles(FilesProvider) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFiles(FilesProvider, FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
NamedFilesBase<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.files: Base class for an InputManager that produces inputs that are created from a NamedFile.
NamedFilesBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
NamedFilesBase(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
NamedFilesWithDirectory - Class in org.anchoranalysis.plugin.io.bean.input.files: Like NamedFiles but rather accepts a FileWithDirectoryInput rather than a FileInput.
NamedFilesWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory
nameFor(LocalDateTime, LocalDateTime, DateStyle, TimeStyle) - Method in class org.anchoranalysis.plugin.io.naming.interval.TimeIntervalNamer: Derives a name from the time-range in the cluster and some parameters.
NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.file.namer: Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NormalizedPath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.NormalizedPath
numberChannels(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
NumberChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
numberFrames() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsInputToStack
numberFrames(Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
numberSeries() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
NumberToStringConverter - Class in org.anchoranalysis.plugin.io.shared: Converts a number to a strings of constant width by padding with leading zeros.
NumberToStringConverter(int) - Constructor for class org.anchoranalysis.plugin.io.shared.NumberToStringConverter: Creates with a constant width just enough to be able to represent maxNumberToRepresent.
numSlices() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel

O

OMIT - org.anchoranalysis.plugin.io.naming.interval.DateStyle: The date is omitted from the name.
OMIT - org.anchoranalysis.plugin.io.naming.interval.TimeStyle: The time is omitted from the name.
open(int, Logger) - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
OpenedMultiFile - Class in org.anchoranalysis.plugin.io.multifile: A OpenedImageFile where the image is formed from more than one file on the file-system.
OpenedMultiFile(StackReader, ParsedFilePathBag, ExecutionTimeRecorder) - Constructor for class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
openFile(Path, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.AlwaysReject
openFile(Path, StackReader, OperationContext) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader
openFile(Path, CalculateOrientationChange, ExecutionTimeRecorder) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map: Implementations of ChannelMapCreator.
org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method: Methods for copying files on the file-system.
org.anchoranalysis.plugin.io.bean.file.copy.naming - package 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 - package org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster: Implementations of CopyFilesNaming that perform clustering of files.
org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group: Grouping files together so that they collectively represent a single entity.
org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check: Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser: Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer: Implementations of FileNamer.
org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan: Implementations of FileNamer that look for a pattern across many files.
org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path: Beans to specify a file-path.
org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer: Implementations of PathPrefixer.
org.anchoranalysis.plugin.io.bean.file.pattern - package org.anchoranalysis.plugin.io.bean.file.pattern: Extracting a pattern from a file-path.
org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.grouper - package org.anchoranalysis.plugin.io.bean.grouper: Implementations of Grouper.
org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input: Implementations of InputManager.
org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel: InputManagers that accept a set of named-channels.
org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files: InputManagers that accept a set of named-files.
org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider: Implementations of FilesProvider.
org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter: Implementations of InputManager that filter inputs.
org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack: Implementations of InputManager that process Stacks.
org.anchoranalysis.plugin.io.bean.metadata.header - package org.anchoranalysis.plugin.io.bean.metadata.header: Different types of image-file-formats whose headers can provide ImageMetadata.
org.anchoranalysis.plugin.io.bean.metadata.reader - package org.anchoranalysis.plugin.io.bean.metadata.reader: Implementations of ImageMetadataReader.
org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive: Implementations of DerivePath.
org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader: Implementations of StackReader.
org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer: Implementations of StackWriter.
org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer: Summarizing a set of elements into a descriptive-string.
org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image: Implementations of Summarizer that summarize images.
org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input: Implementations of Summarizer that summarize generically InputFromManagers.
org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path: Implementations of Summarizer that summarize generically Paths.
org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task: Implementations of Task related to file-system I/O.
org.anchoranalysis.plugin.io.file.copy - package org.anchoranalysis.plugin.io.file.copy: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter: Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path: Non-bean classes to help in processing paths.
org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile: Non-bean classes to help use multiple files to represent a single Stack.
org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer: Buffers used in org.anchoranalysis.plugin.io.multifile.
org.anchoranalysis.plugin.io.naming.interval - package org.anchoranalysis.plugin.io.naming.interval: How to write parts of a time-interval in a file-name.
org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared: Objects used in shared-state in Tasks in this plugin.
org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml: Reading and writing metadata XML.
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory
outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx
OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files using whatever prefix is assigned to an input by the OutputManager as the file-name, adding the same extension as the source file.
OutputPrefixWithExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.OutputPrefixWithExtension

P

ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile
ParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
parsePath(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.FilePathParser
parsePath(Path) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.FilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
PathOperations - Class in org.anchoranalysis.plugin.io.file.copy: Helper routines for performing operations on Paths.
PathRegEx - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Matches a regex against incoming file-paths to form a prefix for output
PathRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx
pattern() - Method in enum org.anchoranalysis.plugin.io.naming.interval.DateStyle: Derives a pattern for the formatter for the particular date-style.
PatternSpan - Class in org.anchoranalysis.plugin.io.bean.file.namer.patternspan: Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the name.
PatternSpan() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan
patternWithDate(DateStyle) - Method in enum org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Derives a formatter for the particular date AND time-style.
PNG - Class in org.anchoranalysis.plugin.io.bean.metadata.header: The headers found in a PNG file.
PNG() - Constructor for class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
populateFrom(Path) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: Creates a ImageMetadata, if possible, from the metadata at path.
populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.BMP
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.HeaderFormat: Creates a ImageMetadata, if possible, from metadata.
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.JPEG
populateFromMetadata(Metadata, ImageFileAttributes) - Method in class org.anchoranalysis.plugin.io.bean.metadata.header.PNG
populateMissingFromArbitrarySlice(Stack) - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
PreserveName - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Copies files to maintain the same relative-path from the destination file to the destination-directory, as existed from the source file to the source-directory.
PreserveName() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.PreserveName
pyramid() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile

R

RandomOrder - Class in org.anchoranalysis.plugin.io.bean.file.provider
RandomOrder() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.RandomOrder
rangeChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
rangeCPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
rangeSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
rangeTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
rangeTPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
readMetadata(Path, boolean) - Static method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Looks for a metadata file describing the resolution
readResolutionXml(File) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXML: Retrieves resolution from a XML file previously written by writeResolutionXML(Resolution, Path).
ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Reads Resolution from an XML file associated an image.
ReadVoxelExtentXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
recordCopiedOutput(Path, Optional<Path>, int) - Method in class org.anchoranalysis.plugin.io.shared.RecordingCounter: Records an copy operation in the log / CSV path mapping.
RecordingCounter<T> - Class in org.anchoranalysis.plugin.io.shared: A counter that also records outputs in a message-log and CSV file.
RecordingCounter(Counter, Outputter, T) - Constructor for class org.anchoranalysis.plugin.io.shared.RecordingCounter
RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.file.namer
RegExMatcher() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
RegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
RegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
RegularExpressionBase - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: A base class for CopyFilesNaming classes that use a regular-expression.
RegularExpressionBase() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader: If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
RejectIfConditionXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
RelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer: Constructs a name by finding the relative-path between the file and the input-directory.
RelativeToDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RelativeToDirectory
RemoveExtension - Class in org.anchoranalysis.plugin.io.bean.file.namer: Removes extensions from the identifier (but not from the file) and only if the extension hasn't already been removed upstream.
RemoveExtension() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
RemoveExtension(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
RemoveLastElement - Class in org.anchoranalysis.plugin.io.bean.grouper: Splits an identifier into elements by the directory separator, and removes the final element.
RemoveLastElement() - Constructor for class org.anchoranalysis.plugin.io.bean.grouper.RemoveLastElement
RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.file.provider
RemoveMatching() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching
removeNonMatching(List<T>) - Method in class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.io.bean.path.derive
RemoveTrailingDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: Removes any whitespace characters from the path
RemoveWhitespace() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.RemoveWhitespace
Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive: Generates a file-path by replacing all occurrences of a string-pattern with another
Replace() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Replace
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifier
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.SummarizerPath
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer: Whether a ImageMetadataInput is required as an input.
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
requiresImageMetadata() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
ResolutionAsXML - Class in org.anchoranalysis.plugin.io.xml: Reads and writes a metadata XML file specifying the image-resolution.
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory
rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
Rooted - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer: Prepend a 'root' before the file-path-prefix obtained from a delegate
Rooted - Class in org.anchoranalysis.plugin.io.bean.file.provider: Represents a set of files, with a different path-root depending on context.
Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
Rooted(PathPrefixerAvoidResolve, String) - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
RootedFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
RootPathMap - Class in org.anchoranalysis.plugin.io.input.path: A collection of root-paths indexed by their name.
RotateImageToMatchEXIFOrientation - Class in org.anchoranalysis.plugin.io.bean.stack.reader: Rotates an image to match any EXIF orientation information, if it exists.
RotateImageToMatchEXIFOrientation() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation
RotateImageToMatchEXIFOrientation(StackReaderOrientationCorrection) - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation

S

SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
SampleWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat
selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase: Selects a StackWriter to use as a delegate.
selectDerivePath() - Method in class org.anchoranalysis.plugin.io.bean.grouper.RemoveLastElement
setAcceptNoResolution(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: If false, an exception is thrown if the resolution file is missing for a particular image.
setAddName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setAvoidBulletOnFirst(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate: Iff true no bullet is added for the very first-item in the list
setCaseSensitive(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.patternspan.PatternSpan: Iff true, a case sensitive search is used to match patterns.
setChannelGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setChannelMap(ChannelMapCreator) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack: By default all channels are converted into a stack.
setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles: Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be included.
setContains(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must contain (case-sensitive) this string.
setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.CopyFilesNamingOne
setCountThreshold(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: If there are more than countThreshold elements, use summarizerGreaterThan, else summarizerElse.
setCsvFilePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: Character used to split the name into groups.
setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
setDepth(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in z-dimension.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: Called as a delegate to provide a source Path.
setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.HomeSubdirectory: A relative-path (to the user home directory) which is used as an output directory
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setEquals(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName: A descriptive-name must be exactly equal to (case-sensitive) this string.
setExactDepth(int) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
setExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setExtensions(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: Any extensions to match (case insensitive) excluding any leading period.
setFallback(ImageMetadataReader) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: Fallback to use if EXIF information is non-existing or absent.
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setFileInput(NamedFiles) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setFilePath(String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setFiles(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles: The files to use as inputs.
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setFiles(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesWithDirectory: The files to use as inputs.
setFirstLineHeaders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setForceEagerEvaluation(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setFormats(List<HeaderFormat>) - Method in class org.anchoranalysis.plugin.io.bean.metadata.reader.InferFromHeader: The formats whose headers will be searched, to find sufficient metadata to populate ImageMetadata.
setGroup(Grouper) - Method in class org.anchoranalysis.plugin.io.bean.grouper.IfGroupIndexRange: Fallback to use when no group-index-range is specified.
setHeight(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in y-dimension.
setIgnoreCase(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, case is ignored in the pattern matching.
setIgnoreFileNotFoundAppend(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setIgnoreHidden(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: Iff true, any hidden-path is not considered, and simply ignored
setImgChannelMapCreator(ChannelMapCreator) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setIncludeDirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure: If false, the folders are ignored, and only the file-name is used in the output
setIndexDay(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the day, starting from 0 for the first group.
setIndexHours(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the hours, starting from 0 for the first group.
setIndexMinutes(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the minutes, starting from 0 for the first group.
setIndexMonth(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the month, starting from 0 for the first group.
setIndexSeconds(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the seconds, starting from 0 for the first group.
setIndexYear(int) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The index of the group in regularExpression that encodes the year, starting from 0 for the first group.
setInput(InputManager<NamedChannelsInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setInput(InputManager<NamedChannelsInputPart>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setInputDebug(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug: If defined, this provides an input to the manager when in debug-mode, rather than than otherwise inputs.
setInvert(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.FilterWithRegularExpression: Iff true, then a file is rejected if the regular-expression matches and vice-versa.
setItem(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setKeepExtension(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.CollapseFileName: When true, the extension is appended to the directory.
setKeepZ(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Keep the z-resolution if it is already defined
setKeyGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setKeyRequired(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setList(List<IndexedChannel>) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
setList(List<FilesProvider>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Combine
setList(List<InputManager<T>>) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate: The list of InputManagers that will be concatenated.
setList(List<Summarizer<T>>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
setListAppend(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setLogPath(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the pathIn and pathOut are logged.
setMatch(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCSVColumn
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
setMaxPathWidth(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractIdentifierAndPath: The maximum width permitted for an identifier, so that it is printed as one line.
setMethod(CopyFilesMethod) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How the copying occurs from source to destination file.
setMinimumPerCluster(int) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The minimum number of files that must exist for a cluster.
setMinNumZSlices(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.check.AtLeastZSlices
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested: The namer that is called to provide names that are subsetted.
setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFilesBase
setNaming(CopyFilesNaming<T>) - Method in class org.anchoranalysis.plugin.io.bean.task.CopyFiles: How an output name (and path) is selected for an input file.
setNavigateHigherDirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: Search x number directories higher than file.
setNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: How many directories to include in the name.
setOtherwise(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is not selected.
setOutPath(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: Constructs a path as an output, replacing $1, $2 etc.
setOutputNameStyle(IndexableOutputNameStyle) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.FromOutputName
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
setPathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setPaths(List<DerivePath>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles: All files need to be present
setPaths(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.FileSetFromStringSet
setPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.LastDirectoryAsPrefix
setPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted
setPrefixerElse(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is not true.
setPrefixerIf(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.IfIncrementingNumberRequested: Called if the requested condition is true.
setPrefixToRemove(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.DirectoryStructure
setPreserveExtensionIfDuplicate(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RemoveExtension: Keeps the extension if the file-name (without the extension) becomes duplicated with another.
setPreserveSubdirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If true, the entire relative-path is used when copying files into the cluster directory.
setReader(StackReaderOrientationCorrection) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RotateImageToMatchEXIFOrientation: Reads the image that is subsequently flattened.
setReaderMatching(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension matches.
setReaderNotMatching(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.BranchExtension: The reader to use if the extension does not match.
setRecurseSubfolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.RegularExpressionBase
setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: Regular expression to match against string
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.RegExMatcher
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.PathRegEx: Regular expression to use to match path with at least one group in it.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching: If a path matches a regular expression it is removed.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude: A regular-expression to be matched against the identifiers of inputs.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups.
setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
setRegExDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to directories.
setRegExFile(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader: If non-empty a regular-expression is applied to files.
setRegExString(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups: The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.
setRegularExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern: The regular-expression that checks a match and specifies groups for the encoded date-time.
setRelation(RelationToThreshold) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: A predicate defined by the relationship of the XY-resolution to a constant threshold.
setRemoveExtension(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern: if true, the extension is removed from paths before finding the pattern.
setRemoveExtensionInDescription(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Whether to remove the file-extension from the filename.
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace: What to replace in the path
setRequireAllFilesMatch(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.group.GroupFiles
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.Rooted: The name of the root-path to associate with this fileset.
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.path.RootedFilePath
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Rooted
setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
setSampleEvery(int) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
setSeperator(String) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Iff true the filename is not considered, only the subdirectories.
setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setSkipMissingChannels(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
setSkipNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.LastDirectories: Initially skip this number of directories before including them in the description.
setSortIfNotRequested(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested: When true, the inputs are sorted alphabetically, if a shuffle is not requested.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel: Reads the image that is subsequently flattened.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Reads an image before a resolution is imposed.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml: Reads an image before a resolution is imposed.
setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution: Reads an image before a resolution is imposed.
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
setSummarizerElse(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) <= countThreshold
setSummarizerGreaterThan(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan: Used for summary if count(elements) > countThreshold
setSuppressDirectories(boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.path.prefixer.FromDescriptiveName: If true, any directory separators in the identifier in a descriptive-name are replaced by underscores.
setSuppressRootOut(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted: if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
setThresholdHours(double) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: Files whose creation-time differs <= this parameter are joined into the same cluster.
setTimeIndex(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
setTimeIndexGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setTimestampPatterns(List<TimestampPattern>) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: The patterns which can be used to extract a date-time from a filename.
setTimeZoneOffset(int) - Method in class org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster.ClusterByTimestamp: If >= 0, sets a specific time-offset in hours.
setTransposed(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.RemoveTrailingDirectory
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
setValue(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
setWhenBinaryChannel(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled binary image.
setWhenNotEightBit(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack contains channels that are not 8-bit.
setWhenRelative(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.file.namer.IfRelativeToDirectory: The namer to use if the relative-to-directory option is selected.
setWhenRGB(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled RGB image.
setWhenRGBAlpha(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a four-channeled RGBA image.
setWhenSingleChannel(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
setWhenThreeChannels(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Writer employed if a stack is a three-channeled non-RGB image.
setWidth(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution: Physical pixel size of a voxel in x-dimension.
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels: Default writer, if a more specific writer is not specified for a condition.
setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
setWriterAlways2D(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Writer to use if it is guaranteed that the image will always be 2D.
setWriterElse(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack: Otherwise the writer to use.
setWriterIfNoSuggestion(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: The writer to use if there is no suggested file-format.
setWritersIfSuggested(List<StackWriter>) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchSuggestedFormat: A list of writers to select if a given format is used
setZSliceGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.file.group.parser.RegularExpression
setZSliceNum(int) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
Shuffle<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Randomly shuffles the order of the inputs.
Shuffle() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Shuffle
ShuffleIfRequested<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Like Shuffle if requested in the InputContextParameters otherwise makes no change to the inputs.
ShuffleIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.input.ShuffleIfRequested
SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map: For an image with a single channel
SingleChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
SingleChannel(String) - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
size() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
SizeExtents - Class in org.anchoranalysis.plugin.io.multifile: Remembers the different sizes among the files
SizeExtents(ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.SizeExtents
SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider
SortAlphabetically<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input: Sorts the input-items in alphabetical order of their input-name.
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabetically
SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
SortAlphabeticallyWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabeticallyWithDirectory
SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
SortedSetChannel() - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
SortedSetSlice(String, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
split(Path, String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap: Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)
Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack: An InputManager where each file provides one or more Stacks.
Stacks() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
Stacks(InputManager<FileInput>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer: A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteAttributes.
StackWriterDelegateBase() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
StaticFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.file.path.StaticFilePath
SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer: If specified in the context, the existing name if subsetted according to an index range.
SubsetRangeIfRequested() - Constructor for class org.anchoranalysis.plugin.io.bean.file.namer.SubsetRangeIfRequested
SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming: A regular expression substitution (replaceAll) is applied to the relative-path
SubstituteRegularExpression() - Constructor for class org.anchoranalysis.plugin.io.bean.file.copy.naming.SubstituteRegularExpression
SummarizeBase<T extends org.anchoranalysis.io.input.InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeBase() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
SummarizeInputs<T extends org.anchoranalysis.io.input.InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
SummarizeInputs() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Summarizes a set of elements by outputting a descriptive string.
Summarizer() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Collects summary data about a set of input files that will eventually be outputted to the user
SummarizerAggregate() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: A count of the number of inputs.
SummarizerCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
SummarizerImageMetadata<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: Summarizes ImageMetadataInput in different ways.
SummarizerImageMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadata
SummarizerImageMetadataSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image: A simple summarizer, where there's one summary-item per image.
SummarizerImageMetadataSimple() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerImageMetadataSimple
SummarizerInputFromManager<T extends org.anchoranalysis.io.input.InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input: Extracts a particular item from an InputFromManager for further summarization downstream.
SummarizerInputFromManager() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Creates a string where each line is an element.
SummarizerListMultiline() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
SummarizerPath - Class in org.anchoranalysis.plugin.io.bean.summarizer.path: Base class for Summarizers that operate on the Path associated with inputs.
SummarizerPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.SummarizerPath
SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer: Multiplexes between two summarizers depending on the total number of count.
SummarizerSplitMoreThan() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan

T

TimeIntervalNamer - Class in org.anchoranalysis.plugin.io.naming.interval: Derives a human-friendly name for a time-interval.
TimeIntervalNamer(ZoneOffset) - Constructor for class org.anchoranalysis.plugin.io.naming.interval.TimeIntervalNamer
TimestampPattern - Class in org.anchoranalysis.plugin.io.bean.file.pattern: Extracts a timestamp from a file-name if it exists.
TimestampPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern
TimestampPattern(String) - Constructor for class org.anchoranalysis.plugin.io.bean.file.pattern.TimestampPattern
timestamps() - Method in class org.anchoranalysis.plugin.io.multifile.OpenedMultiFile
TimeStyle - Enum in org.anchoranalysis.plugin.io.naming.interval: How to style a time in a file-name.
toExtent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
toString() - Method in class org.anchoranalysis.plugin.io.input.path.CopyContext
toString() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
toString() - Method in class org.anchoranalysis.plugin.io.shared.AnonymizeSharedState
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.LimitWithDirectory
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SampleWithDirectory
transform(List<File>) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabeticallyWithDirectory
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.Limit
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RandomOrder
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.RemoveMatching
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.file.provider.SortAlphabetically
transform(List<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles

V

valueOf(String) - Static method in enum org.anchoranalysis.plugin.io.naming.interval.DateStyle: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.anchoranalysis.plugin.io.naming.interval.DateStyle: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.anchoranalysis.plugin.io.naming.interval.TimeStyle: Returns an array containing the constants of this enum type, in the order they are declared.

W

writeResolutionXML(Resolution, Path) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXML: Writes a XML metadata file describing the image-resolution.
WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer: When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.
WriteResolutionXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.StackWriterDelegateBase
writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter

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