All Classes

Class	Description
AlwaysReject	A special ImageMetadataReader that will always throw an exception and reject a file.
Anonymize	Copies files to a number 001, 002 etc.
AnonymizeSharedState
AtLeastZSlices
Autoname	Names of the channels from the metadata if it exists, or after RGB, or by index.
BitDepth
BMP	The headers found in a BMP file.
BranchChannels	Uses different raster-writers depending on the number/type of channels.
BranchExtension	If the extension(s) of a path matches a particular value, then use a particular reader, otherwise a fallback.
BranchIfDebug<T extends org.anchoranalysis.io.input.InputFromManager>	Uses one input-manager normally, but a different one if in debug mode.
BranchStack	Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
BranchSuggestedFormat	Selects particular writers based on if particular suggested image formats are present.
Bytewise	Makes a simple bytewise copy of a file, where no byte is changed.
CheckParsedFilePathBag
ClusterByTimestamp	Associates particular timestamp with each file, and clusters.
ClusterIdentifier	Uniquely identifies a cluster.
ClusterMembership	A mapping of files to membership of particular clusters.
CollapseFileName	Removes the file-name from a path, but keeps the directories and preserves the file-extension.
Combine
CombineCSV	Combines multiple CSV files into a single CSV file.
CompressAnyTIFF	Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a Bytewise copy.
Concatenate<T extends org.anchoranalysis.io.input.InputFromManager>	Concatenates the inputs from multiple InputManagers that all provide the same input-type.
Constant	Always generates a constant path irrespective of the the input
ConvertNamedChannelsInputToStack	An input object that converts NamedChannelsInput to StackSequenceInput.
ConvertNamedChannelsToStack	Manager that converts (one channel) NamedChannelsInput to StackSequenceInput.
CopyContext<T>	Context parameters when copying many files from a source directory to a destination directory.
CopyFiles<T>	Copy files to the output-directory, possibly changing the name or performing other operations like compression in the process.
CopyFilesMethod	A method used for copying files (e.g.
CopyFilesNaming<T>	How an output name (and path) is selected for an input file when copying.
CopyFilesNamingOne
CopyFilesNamingWithoutSharedState	Base class for implementations of CopyFilesNaming where each file is copied independently of the others.
DateStyle	How to style a date in a file-name.
DirectoryDepth	Lists all directories to a certain depth
DirectoryStructure	Reuses the directories between a path and its root to form the output - and also the filename.
Exclude<T extends org.anchoranalysis.io.input.InputFromManager>	Excludes all inputs whose identifiers match a regular expression.
ExtensionCount	Remembers each unique extension, and associated count
ExtractIdentifier<T extends org.anchoranalysis.io.input.InputFromManager>	Extracts the identifier from an InputFromManager to summarize further.
ExtractIdentifierAndPath<T extends org.anchoranalysis.io.input.InputFromManager>	Extracts the identifier and path from an InputFromManager to summarize further.
ExtractPath<T extends org.anchoranalysis.io.input.InputFromManager>	Extracts a Path from an input to summarize further.
FileDetails
FilePath
FilePathParser
FilePathPattern	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.
FileSetFromStringSet
FileSizeStatistics	Tracks the range of file-size.
FilterCSVColumn<T extends org.anchoranalysis.io.input.InputFromManager>	Finds a CSV file with the names of an input as the first-column.
FilterDescriptiveName<T extends org.anchoranalysis.io.input.InputFromManager>	Filters all the input objects for only those with certain types of descriptive-names.
FilterDescriptiveNameEqualsContains	Filters a list of input-objects by the descriptive name
FilterForExistingFiles
FilterIfDebug<T extends org.anchoranalysis.io.input.InputFromManager>	Filters a list of inputs when in debug-mode
FilterWithRegularExpression	Rejects files that fail to match a particular regular-expression
FlattenAsChannel	Combines all series and frames returned by a reader by converting them into multiple channels in the same image.
FrequencyMap<T>	Counts the frequency of certain strings, and describes the contents in human language.
FromDescriptiveName	The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix.
FromEntries
FromMetadata
FromOutputName
GroupFiles	An InputManagerWithStackReader that can unify separate images in separate files to form a single Stack.
HeaderFormat	Populates ImageMetadata from the header of an image-file.
HomeSubdirectory
IfGroupIndexRange	When a IndexRangeNegative is passed as an argument, an InputGrouper is constructed that extracts elements from a Path.
IfIncrementingNumberRequested	Multiplexes between two PathPrefixers depending on whether an incrementing number sequence was output was requested.
IfRelativeToDirectory	Multiplexes between two namers depending on if the relative-to-directory option is selected.
ImageIOWriter
ImageSize	Summarizes the size of images.
ImposeResolution	Adds an explicit Resolution to an image after it has been read.
InferFromHeader	Tries to construct the ImageMetadata from EXIF and other metadata, if available, or otherwise falls back to another reader.
InsertRegExGroups	Generates an out string where $digit$ is replaced with the #digit group from a regex
IntegerRange
JoinRegExGroups	Generates an outstring of the form
JPEG	The headers found in a JPEG file.
LastDirectories	Derives a name by taking the filename together with optionally several subdirectories names.
LastDirectoryAsPrefix	Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
Limit
Limit<T extends org.anchoranalysis.io.input.InputFromManager>	Limits the number of input-objects to a certain hard-maximum
LimitIfRequested<T extends org.anchoranalysis.io.input.InputFromManager>	Like Limit if it is requested in the InputContextParameters, makes no change to the inputs.
LimitWithDirectory
MultiBufferSized
MultiFileReader
NamedChannels	An image viewed as a set of channels, each with a unique name.
NamedChannelsAppend
NamedChannelsBase	Parent for all the NamedChannels classes
NamedFiles	Implementation of NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name.
NamedFilesBase<T extends org.anchoranalysis.io.input.InputFromManager>	Base class for an InputManager that produces inputs that are created from a NamedFile.
NamedFilesWithDirectory	Like NamedFiles but rather accepts a FileWithDirectoryInput rather than a FileInput.
NormalizedPath	Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
NumberChannels
NumberToStringConverter	Converts a number to a strings of constant width by padding with leading zeros.
OpenedMultiFile	A OpenedImageFile where the image is formed from more than one file on the file-system.
OutputPrefixWithExtension	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.
ParsedFilePathBag
PathOperations	Helper routines for performing operations on Paths.
PathRegEx	Matches a regex against incoming file-paths to form a prefix for output
PatternSpan	Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the name.
PNG	The headers found in a PNG file.
PreserveName	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.
RandomOrder
ReadVoxelExtentXml	Reads Resolution from an XML file associated an image.
RecordingCounter<T>	A counter that also records outputs in a message-log and CSV file.
RegExMatcher
RegularExpression
RegularExpressionBase	A base class for CopyFilesNaming classes that use a regular-expression.
RejectIfConditionXYResolution	If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
RelativeToDirectory	Constructs a name by finding the relative-path between the file and the input-directory.
RemoveExtension	Removes extensions from the identifier (but not from the file) and only if the extension hasn't already been removed upstream.
RemoveLastElement	Splits an identifier into elements by the directory separator, and removes the final element.
RemoveMatching
RemoveTrailingDirectory
RemoveWhitespace	Removes any whitespace characters from the path
Replace	Generates a file-path by replacing all occurrences of a string-pattern with another
ResolutionAsXML	Reads and writes a metadata XML file specifying the image-resolution.
Rooted	Prepend a 'root' before the file-path-prefix obtained from a delegate
Rooted	Represents a set of files, with a different path-root depending on context.
Rooted
RootedFilePath
RootedFilePathUtilities
RootPathMap	A collection of root-paths indexed by their name.
RotateImageToMatchEXIFOrientation	Rotates an image to match any EXIF orientation information, if it exists.
SampleWithDirectory
Shuffle<T extends org.anchoranalysis.io.input.InputFromManager>	Randomly shuffles the order of the inputs.
ShuffleIfRequested<T extends org.anchoranalysis.io.input.InputFromManager>	Like Shuffle if requested in the InputContextParameters otherwise makes no change to the inputs.
SingleChannel	For an image with a single channel
SizeExtents	Remembers the different sizes among the files
SortAlphabetically
SortAlphabetically<T extends org.anchoranalysis.io.input.InputFromManager>	Sorts the input-items in alphabetical order of their input-name.
SortAlphabeticallyWithDirectory
SortedSetChannel
SortedSetSlice
Stacks	An InputManager where each file provides one or more Stacks.
StackWriterDelegateBase	A base class for a StackWriter delegates to another StackWriter based on values of a StackWriteAttributes.
StaticFilePath
SubsetRangeIfRequested	If specified in the context, the existing name if subsetted according to an index range.
SubstituteRegularExpression	A regular expression substitution (replaceAll) is applied to the relative-path
SummarizeBase<T extends org.anchoranalysis.io.input.InputFromManager,S>
SummarizeInputs<T extends org.anchoranalysis.io.input.InputFromManager>
Summarizer<T>	Summarizes a set of elements by outputting a descriptive string.
SummarizerAggregate<T>	Collects summary data about a set of input files that will eventually be outputted to the user
SummarizerCount<T>	A count of the number of inputs.
SummarizerImageMetadata<T>	Summarizes ImageMetadataInput in different ways.
SummarizerImageMetadataSimple<T>	A simple summarizer, where there's one summary-item per image.
SummarizerInputFromManager<T extends org.anchoranalysis.io.input.InputFromManager,S>	Extracts a particular item from an InputFromManager for further summarization downstream.
SummarizerListMultiline<T>	Creates a string where each line is an element.
SummarizerPath	Base class for Summarizers that operate on the Path associated with inputs.
SummarizerSplitMoreThan<T>	Multiplexes between two summarizers depending on the total number of count.
TimeIntervalNamer	Derives a human-friendly name for a time-interval.
TimestampPattern	Extracts a timestamp from a file-name if it exists.
TimeStyle	How to style a time in a file-name.
WriteResolutionXml	When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.